RECOMBINANT HIV-1 ENVELOPE PROTEINS AND THEIR USE

Abstract
HIV-1 Env ectodomain trimers stabilized in a prefusion mature closed conformation and methods of their use and production are disclosed. In several embodiments, the HIV-1 Env ectodomain trimers and/or nucleic acid molecules can be used to generate an immune response to HIV-1 in a subject. In additional embodiments, the therapeutically effective amount of the HIV-1 Env ectodomain trimers can be administered to a subject in a method of treating or preventing HIV-1 infection.
Description
FIELD

This disclosure relates to recombinant human immunodeficiency virus type 1 (HIV-1) envelope (Env) polypeptides and immunogenic fragments thereof for treatment and prevention of Human Immunodeficiency Virus (HIV) infection and disease.


BACKGROUND

Over the last 50 years, millions of people have been infected or killed by HIV-1. A dominant contributing factor has been the immunoevasion of the HIV-1-Env ectodomain trimer, a type 1 fusion machine that facilitates virus entry into cells by interacting with host cellular receptors and fusing virus and host-cell membranes. Despite its exposed position on the viral membrane and high titers of Env-reactive antibodies in infected individuals, the HIV-1-Env ectodomain trimer successfully evades most antibody-mediated neutralization. This evasion is to a large degree responsible for the difficulty in developing an effective HIV-1 vaccine.


The HIV-1-Env ectodomain trimer includes three gp120-gp41 protomers, and displays unusual posttranslation processing including the addition of 25-30 N-linked glycans per gp120-gp41 protomer, tyrosine sulfation, and slow signal peptide cleavage. As an entry machine, HIV-1 Env undergoes several structural rearrangements from a prefusion mature (cleaved) closed conformation that evades antibody recognition, through intermediate conformations triggered by CD4 and co-receptor (either CCR5 or CXCR4) binding, to a postfusion conformation. Over the last 20 years substantial atomic-level detail has been obtained on these conformations, including structures of CD4-bound gp120, postfusion gp41, and the trimeric arrangement of prefusion gp120. The prefusion mature closed conformation of HIV-1 Env has, however, resisted atomic-level analysis.


It is believed that immunization with an HIV-1 Env ectodomain trimer stabilized in its prefusion mature closed conformation can elicit a neutralizing immune response that is protective against HIV infection. However, the lack of an atomic-level structure of the HIV-1 Env ectodomain trimer in this conformation stymied attempts to design HIV-1 Env proteins that are stabilized in a prefusion mature closed conformation for use as immunogens.


SUMMARY

Disclosed herein for the first time is the atomic-level three dimensional structure of the HIV-1 Env ectodomain (including gp120 and the extracellular portion of gp41) in its prefusion mature closed conformation, the conformation of Env recognized by most broadly neutralizing antibodies. When viewed in the context of previously determined structures of HIV-1 Env in a CD4-bound conformation, the new structure provided herein affords a mechanistic understanding of the conformational transitions that HIV-1 Env undergoes from the mature closed to CD4-bound open prefusion conformations. Analysis of these conformational rearrangements, combined with an understanding of the evasion from and vulnerabilities to the immune system, provided an information matrix that was used to generate recombinant HIV-1 Env ectodomain trimers stabilized in the prefusion mature closed conformation.


The disclosed recombinant HIV-1 Env ectodomain trimers resist transition to the CD4-bound open conformation of HIV-1 Env when incubated with CD4, and thus will retain the prefusion mature closed conformation when used as an immunogen to generate an HIV-1 Env immune response in a subject expressing CD4, such as a human. Retention of the prefusion mature closed conformation in the presence of CD4 avoids exposure of highly antigenic sites on the open conformation of the HIV-1 Env ectodomain that are targeted by poorly neutralizing antibodies (such as 447-52D), and maximizes exposure of antigenic sites on the V1V2 “cap” of the HIV-1 ectodomain that are targeted by broadly neutralizing antibodies.


In several embodiments, an isolated immunogen is provided that comprises a recombinant HIV-1 Env ectodomain trimer or immunogenic fragment thereof stabilized in a prefusion mature closed conformation by one or more amino acid substitutions compared to a native HIV-1 Env sequence. The recombinant HIV-1 Env ectodomain comprises three gp120-gp41 protomers comprising a gp120 polypeptide and a gp41 ectodomain, and remains in the prefusion mature closed conformation when incubated with a molar excess of soluble CD4 (sCD4). In several embodiments, the recombinant HIV-1 Env ectodomain trimer comprises an α7 helix that forms after position 570 of the gp41 ectodomain, and comprises V1V2 domains wherein the distance between positions 200 and 313 of adjacent V1V2 domains in the ectodomain trimer is less than five angstroms. In additional embodiments, the recombinant HIV-1 Env ectodomain trimer or immunogenic fragment specifically binds to VRC26 mAb and/or PGT145 mAb, and does not specifically bind to 17b mAb when incubated with a molar excess of sCD4.


In some embodiments, the recombinant HIV-1 Env ectodomain can be stabilized in the prefusion mature closed conformation by a non-natural disulfide bond between cysteine substitutions at positions 201 and 433. In additional embodiments, the recombinant HIV-1 Env ectodomain can be stabilized in the prefusion mature closed conformation by a non-natural disulfide bond between cysteine substitutions at positions 201 and 433, a non-natural disulfide bond between cysteine substitutions at positions 501 and 605, and a proline substitution at position 559. The HIV-Env positions correspond to a HXB2 reference sequence set forth as SEQ ID NO: 1. The recombinant HIV-1 Env ectodomain can comprises the sequence from a native HIV-1 Env ectodomain, such as from any one of a BG505 (SEQ ID NO: 2), CAP256.SU (SEQ ID NO: 51), a BB201.B42 (SEQ ID NO: 81), a KER2018.11 (SEQ ID NO: 107), a CH070.1 (SEQ ID NO: 174), a ZM233.6 (SEQ ID NO: 745), a Q23.17 (SEQ ID NO: 746), a A244 (SEQ ID NO: 747), a T250-4 (SEQ ID NO: 2114), 426c (SEQ ID NO: 2144), 45_01dG5 (SEQ ID NO: 2145), JRFL (SEQ ID NO: 2115), or a WITO.33 (SEQ ID NO: 748) strain of HIV-1, that has been modified to include the amino acid substitutions that stabilize the recombination HIV-1 Env ectodomain in the prefusion mature closed conformation.


In some embodiments, the recombinant HIV-1 Env ectodomain trimer can be a chimeric HIV-1 Env ectodomain trimer that comprises amino acid sequences from two or more HIV-1 strains. The use of immunogens based on diverse HIV-1 strains can overcome the intrinsic sequence diversity of HIV-1 Env. For example, the recombinant HIV-1 Env ectodomain trimer can comprise a V1V2 domain (such as HIV-1 positions 126-196) from a first strain of HIV-1, with the remainder of the recombinant HIV-1 Env ectodomain trimer from a heterologous strain of HIV-1. In one example, the recombinant HIV-1 Env ectodomain trimer can comprise a V1V2 domain sequence from any one of a CAP256.SU (SEQ ID NO: 51), a BB201.B42 (SEQ ID NO: 81), a KER2018.11 (SEQ ID NO: 107), a CH070.1 (SEQ ID NO: 174), a ZM233.6 (SEQ ID NO: 745), a Q23.17 (SEQ ID NO: 746), a A244 (SEQ ID NO: 747), a T250-4 (SEQ ID NO: 2114), or a WITO.33 (SEQ ID NO: 748) strain of HIV-1, with the remainder of the recombinant HIV-1 Env ectodomain sequence from the BG505 (SEQ ID NO: 2) strain of HIV-1. The chimeric HIV-1 Env ectodomain trimer further includes the one or more amino acid substitutions compared to a native HIV-1 Env sequence for stabilization in the prefusion mature closed conformation. In some embodiments, the chimeric HIV-1 Env ectodomain trimer can comprise a non-natural disulfide bond between cysteine substitutions at positions 201 and 433, a non-natural disulfide bond between cysteine substitutions at positions 501 and 605, and a proline substitution at position 559, to stabilize the HIV-1 Env trimer in the prefusion mature closed conformation.


As described in the Examples, prefusion mature gp41 wraps its hydrophobic core around extended N- and C-termini-strands of gp120. Accordingly, in some embodiments, the recombinant HIV-1 Env ectodomain trimer can include a membrane proximal “platform” including the N- and C-terminal regions of gp120, and the gp41 ectodomain, from a first HIV-1 strain (such as BG505), and the remainder of gp120 from one or more heterologous HIV-1 strains. This chimeric design allows for production of heterogeneous HIV-1 Env proteins that comprise membrane distal features of interest (such as the V1V2 domain, V3 domain, and CD4 binding site) from diverse strains. In some embodiments, the recombinant Env ectodomain can include gp120 residues 31-45 and 478-507, and the gp41 ectodomain (e.g., positions 512-664) from the first HIV-1 strain (such as BG505), and the remainder of the gp120 residues in the Env protein can be from a heterologous HIV-1 strain. In some embodiments, the heterologous HIV-1 strain can be selected from one of a CAP256.SU (SEQ ID NO: 51), a BB201.B42 (SEQ ID NO: 81), a KER2018.11 (SEQ ID NO: 107), a CH070.1 (SEQ ID NO: 174), a ZM233.6 (SEQ ID NO: 745), a Q23.17 (SEQ ID NO: 746), a A244 (SEQ ID NO: 747), a T250-4 (SEQ ID NO: 2114), 426c (SEQ ID NO: 2144), 45_01dG5 (SEQ ID NO: 2145), a JRFL (SEQ ID NO: 2115) or a WITO.33 (SEQ ID NO: 748) strain of HIV-1. The chimeric HIV-1 Env ectodomain trimer further includes the one or more amino acid substitutions compared to a native HIV-1 Env sequence for stabilization in the prefusion mature closed conformation. In some embodiments, the chimeric HIV-1 Env ectodomain trimer can comprise a non-natural disulfide bond between cysteine substitutions at positions 201 and 433, a non-natural disulfide bond between cysteine substitutions at positions 501 and 605, and a proline substitution at position 559, to stabilize the HIV-1 Env trimer in the prefusion mature closed conformation.


In some embodiments, the gp120-gp41 protomers in the recombinant HIV-1 Env ectodomain trimer can be single chain HIV-1 Env ectodomains, wherein the C-terminal residue of the gp120 polypeptide is linked to the N-terminal residues of the gp41 ectodomain (for example, by a peptide linker, such as a 10 amino acid or 15 amino acid glycine-serine peptide linker). In some embodiments, the recombinant HIV-1 Env ectodomain trimer can be linked to a transmembrane domain. For example, the C-terminal residue of gp41 (such as position 664) can be lined to a transmembrane domain by a peptide linker, such as a 10 amino acid glycine-serine peptide linker. The transmembrane domain can be, for example, an influenza HA transmembrane domain.


In additional embodiments, the recombinant HIV-1 Env ectodomain trimer stabilized in the prefusion mature closed conformation can be included on a protein nanoparticle, such as a ferritin or lumazine synthase protein nanoparticle. Nucleic acid molecules encoding the recombinant HIV-1 Env ectodomain trimer stabilized in the prefusion mature closed conformation and vectors including the nucleic acid molecules are also provided. Compositions including the recombinant HIV-1 Env ectodomain trimer or immunogenic fragments thereof, protein nanoparticles, nucleic acid molecules or vectors are also provided. The composition may be a pharmaceutical composition suitable for administration to a subject, and may also be contained in a unit dosage form. The compositions can further include an adjuvant. The recombinant HIV-1 Env ectodomain trimers may also be conjugated to a carrier to facilitate presentation to the immune system.


Methods of generating an immune response in a subject are disclosed, as are methods of treating, inhibiting or preventing a HIV-1 infection in a subject. In such methods a subject, such as a human subject, is administered an effective amount of a disclosed recombinant HIV-1 Env ectodomain trimer or fragment thereof, protein nanoparticle, nucleic acid molecule or viral vector.


The foregoing and other features and advantages of this disclosure will become more apparent from the following detailed description of several embodiments which proceeds with reference to the accompanying figures.





BRIEF DESCRIPTION OF THE FIGURES


FIGS. 1A and 1B illustrate the structure of a prefusion HIV-1-Env trimer bound by PGT122 and 35O22 antibodies. FIG. 1A, smFRET of functional viral ectodomains, unliganded or in the presence of antibodies PGT122 and 35O22. Fluorophores were introduced into the V1 and V4 regions of JR-FL gp120, and smFRET signals measured with HIV-1 Env in the membrane-bound virion context (see FIG. 7). The concordance between conformational ensembles indicates unliganded and PGT122+35O22-bound conformation to be similar (Spearman correlation coefficient of 0.988). FIG. 1B, Ternary complex structure of HIV-1-Env trimer BG505 SOSIP.664 with PGT122 Fab and 35O22 Fab. The gp120 subunit is shown in dark grey, the gp41 subunit in lighter grey. One protomer and associated Fabs is shown in ribbon and stick representation, a second protomer in surface representation, and the third protomer in grey.



FIGS. 2A-2C illustrate the prefusion structure of gp41. FIG. 2A, gp41 forms a 4-helix collar which wraps around extended N and C termini of gp120. Both gp120 (darker grey) and gp41 (lighter grey) are depicted in ribbon representation, with select residues and secondary structure labeled. The orientation shown here is similar to that of FIG. 1C, with perpendicular orientations provided in FIGS. 2B and 2C. (insert). The gp41 collar is clasped by the insertion of Met530gp41 into a tryptophan sandwich and by the complementary dipoles of helices α6 and α8. 2Fo-Fe electron density for clasp residues is depicted at is. FIG. 2B, gp41 holds the N and C termini of gp120 in its hydrophobic core. Representation are the same as in a, excepted that hydrophobic side chains are shown in stick representation and the orientation is rotated 90°, to depict the view from the viral membrane. FIG. 2C, gp41-trimer interfaces as viewed from side in ribbon and surface representation.



FIGS. 3A-3D illustrate entry rearrangements of HIV-1 Env. FIG. 3A, BG505 sequence of gp41 subunit (positions 512-664 of SEQ ID NO: 2), with prefusion and postfusion secondary structure. Fusion peptide (FP) is underlined. FIG. 3B, Difference distance analysis of prefusion BG505 and postfusion HIV-1/SIV chimeric gp41. Missing residues of BG505 (548-569) and of SIV (611-614) are indicated, along with secondary structure. FIG. 3C, Superposition of postfusion gp41 onto prefusion gp41 for α7 (left) and α9 (right) prefusion helices. FIG. 3D, HIV-1-Env entry rearrangements. EM reconstructions (top row) with gp120 (middle) and gp41 (bottom) rearrangements between each conformational state highlighted with lines to depict moving Ca between each conformation. Subunit models are shown in gray with modeling parameters provided in FIG. 15. Antigenic recognition of each of these state is shown in FIG. 26.



FIGS. 4A-4C illustrate that the prefusion HIV-1 gp120-gp41 structure shares conserved structural and topological features with other type 1 fusion machines. FIG. 4A, Prefusion (left) and postfusion (right) structures. The prefusion structures are shown for a single protomer in ribbon-representation. FIG. 4 B, the preformed C-terminal helix of postfusion coiled coil from a is shown, with fusion peptides (FP) and N and C terminal residues of postfusion coiled coils labeled, and the distance the inner coiled coil extends between prefusion and postfusion conformations indicated. FIG. 4C, The gp41-equivalents encircle extended β-strands of their gp120-equivalent partners. Ribbon representation are shown looking towards the viral membrane.



FIGS. 5A-5C illustrate the fully assembled shield revealed by prefusion HIV-1 gp120-gp41 trimer. FIG. 5A, Glycan shield. Env N-linked glycans are depicted in light grey (conserved; greater than 90% conservation) or dark grey (variable; less than 90% conservation) on the mature near-native Env structures for BG505 strain of HIV-1 (left), influenza virus H3 hemagglutinin (PDB: 2YP7) (middle), and RSV fusion glycoprotein subtype A (PDB: 4JHW) (right). Two conserved glycans, at residues 241gp120 and 616gp41 are not in the BG505 sequence. FIG. 5B, Env sequence variability. FIG. 5C, HIV-1-Env N-linked glycans and sequence variability for near-native and CD4-bound conformations.



FIGS. 6A-6E illustrate the location and prevalence on the HIV-1-Env ectodomain trimer of neutralizing responses identified serologically from cohorts from 2-3 and 5+ years post-infection. FIG. 6A, The location of the neutralization epitopes for the different antibody specificities on the prefusion mature closed Env ectodomain trimer is depicted (top), with CD4-binding-site-directed antibody specificities (VRC01-, b12-, CD4-, and HJ16-like), 8ANC195-like, PG9-like (V1V2-directed), glycan V3 specificities (PGT128- and 2G12-like), 35O22-like specificities, and PGT151-like specificities indicated. FIG. 6B, (top) Broadly neutralizing epitopes on influenza virus hemagglutinin (left) and RSV fusion glycoprotein (right). (bottom) Glycan surface area and residue entropy in antibody epitopes for HIV-1, influenza, and RSV. FIG. 6C, Neutralization fingerprint. For each serum, the predicted neutralization prevalence for each of the 12 antibody specificities is shown based on neutralization of 21 diverse HIV-1 strains. FIG. 6D, Prevalence of antibody specificities onto the HIV-1-Env. FIG. 6E, Antibody specificities with high serum prevalence in the 5+ years cohort are depicted with antigen-binding fragments of representative antibodies (surface transparency proportional to prevalence) on the BG505 Env trimer, which is shown in cartoon representation, with glycans as sticks.



FIGS. 7A-7D show smFRET of HIV-1 Env in the context of infectious JR-FL virions. HIV-1JR-FL gp160 was labelled with fluorescent dyes in variable regions V1 and V4 at positions that did not interfere with Env function, and virus was surface immobilized for imaging via total internal reflection fluorescence microscopy (Munro, et al. Biophysical Journal 104, 415A (2013)). smFRET trajectories were compiled into histograms for the HIV-1JR-FL Env trimer, either unliganded or after pre-incubated for 30 min with 0.1 mg/ml PGT122, 35O22, or both PGT122 and 35O22 prior to imaging. Resultant Env conformational landscapes could be deconvoluted into three gaussian distributions: a low-FRET population that predominated for the prefusion mature unliganded state, and intermediate- and high-FRET populations, which predominated in the presence of CD4 receptor and CD4-induced antibody (Munro, et al. Biophysical Journal 104, 415A (2013)). FIG. 7A, smFRET trajectories of the unliganded HIV-1JR-FL Env trimer. Similar histograms were obtained in the presence of PGT122 (FIG. 7B), 35O22 (FIG. 7C), and both PGT122 and 35O22 (FIG. 7D).



FIGS. 8A-8C show antibody 35O22 and interface details. Despite the substantial immune evasion protecting the mature unliganded state from humoral recognition, after several years of infection, the human immune system does generate broadly neutralizing antibodies. One of these is the 35O22 antibody, which neutralizes 62% of HIV-1 isolates at a median IC50 of 0.033 μg/ml. 35O22 binds parallel to the viral membrane, at a gp120-gp41 epitope (FIG. 1B). FIG. 8A, 35O22 Fab, gp120 subunit, gp41 subunit, and glycans are green. Complementary determining regions (CDRs) are labeled, and interactive HIV-1-Env residues highlighted in surface representation. At the membrane-distal surface of 35O22, an extended framework 3 region (FW3) of the heavy chain (resulting from an insertion of 8 residues) interacts with strand 31 of the 7-stranded inner domain sandwich of gp120. The heavy chain-CDRs from extensive contacts with the N-linked glycan extending from residue 88gp120. In addition to glycan contacts, the CDR H3 of 35O22 interacts with the α9 helix of gp41. Helix α9 interactions are also made by the FW3 of the light chain (a complete list of contacts is provided in FIG. 28). Overall, 35O22 buries 1,105 Å2 solvent surface on gp120 (including 793 Å2 with the Asn88gp120 glycan) and 594 Å2 solvent surface on gp41 (including 127 Å2 with the Asn618gp41 glycan). Despite residue 625gp41 being part of the glycan sequon “NMT”, no glycan is observed; indeed, the side-chain amide of residue 625gp41 hydrogen bonds with the side-chain oxygen of Tyβ2 in the 35O22 heavy chain, and the presence of an N-linked glycan at residue 625gp41 is difficult to reconcile with 35O22 recognition. FIG. 8B, 35O22 Fab shown in surface representation. FIG. 8C, 2Fo-Fc at 16 contour shown around glycan 88 of gp120. Antibody 35O22 employs a novel mechanism of glycan-protein recognition, combining a protruding FW3 with CDR H1, H2 and H3 to form a “bowl” that holds glycan. FW3 and CDR H3 provide the top edges of the bowl and interact with the protein surface of gp120, whereas CDR H1 and H2 are recessed and hold/recognize glycan. This structural mechanism of recognition contrasts with the extended CDR H3-draping glycan observed with other antibodies that penetrate the glycan shield such as PG9 and PGT128.



FIG. 9 shows a comparison of bound and unbound Fab conformations. Unbound and HIV-1-Env bound Fabs were superimposed, and ribbon representations and rmsds are displayed here. (left), Regions which showed conformational changes are highlighted with black dotted lines. A complete list of contacts between PGT122 and BG505 SOSIP.664 is provided in FIG. 29).



FIGS. 10A and 10B show the principal component analysis of HIV-1 Env. Principle component analysis indicated each gp120-gp41 blade to form a rectangle, with height of ˜100 Å, width of ˜65 Å, and thickness of ˜35 Å. FIG. 10A, Minimum bounding box, generated by principle component analysis, in shown encasing the HIV-1-Env gp120-gp41 protomer; subunits displayed in ribbon representation. As previously visualized (Walker, et al. Nature 477, 466-470 (2011)) the membrane-distal portion of the rectangle is made up of the gp120-outer and -inner domains, with the central 7-stranded 3-sandwich of the inner domain occupying the trimer-distal, membrane-proximal portion of gp120. The rest of the ectodomain trimer is now resolved: the membrane-proximal portion of the rectangle is made up of gp41, with the membrane-distal portion of gp41 closest to the molecular 3-fold axis occupied by a helix (which corresponds in register to the C-terminal portion of the postfusion HR1 helix of gp41), and the rest of gp41 folding around N- and C-termini-strands of gp120, which extend over 20 Å toward the viral membrane. FIG. 10B, Different views of trimeric protomer association.



FIGS. 11A and 11B show the conformational changes between gp120 prefusion and CD4-bound state. FIG. 11A, gp120 from BG505 (positions 31-511 of SEQ ID NO: 2) is shown in cartoon representation in prefusion (dark grey) and CD4-bound (light grey, PDB ID 3JWD) conformation. V1V2 (PDB ID 3U2S) has been modeled onto the CD4-bound conformation. Secondary structure changes from prefusion to CD4-bound conformation are shown with cylinders representing α-helix and arrows β-strands. Disordered residues are indicated by “X”. Residues that move more than 3 Å between the prefusion and the CD4-bound conformations are shown with grey shadows. FIG. 11B, Details of conformational changes between the prefusion and the CD4-bound conformation of gp120 (shown in cartoon): regions highlighted cover layer 1 with α0 changes, layer 2 with α1 changes and β20-21 rearrangements. All atoms rmsd for the following region are: for residues 54-74 in gp120, rmsd=4.759; for residues 98-117 in gp120, rmsd=0.497; for residues 424-436 gp120, rmsd=3.196. FIG. 11A is produced in color as extended data FIG. 4a in Pancera et al., Nature, 514(7523, 455-461, 2014, extended data FIG. 4a of Pancera et al. is incorporated by reference herein.



FIGS. 12A-12C show the relative protein surface occlusion by glycans. The solvent-accessible protein surface is shown in red and N-linked glycans are shown in green. Calculations of the percentage coverage of the protein surface were determined for the four trimer models based on two probe sizes of 1.4 Å (solvent radius) and 10.0 Å (the estimated steric footprint of an antibody combining region). FIG. 12A, Estimated Man-9 glycan coverage. FIG. 12B, Estimated Man-5 glycan coverage. FIG. 12C, Visualization of Man-9 N-linked glycan coverage for two probe radii. Surface area calculations were carried out according to Kong et al. (Kong, et al. Journal of molecular biology 403, 131-147 (2010)) and images were generated using Grasp v1.3 (Nicholls, et al. Proteins 11, 281-296 (1991)). The PDB IDs associated with the glycosylated models are: 4TVP (HIV-1), 2YP7 (Flu) and 4JHW (RSV).



FIGS. 13A and 13B show the prevalence of neutralizing responses identified serologically from cohorts from (FIG. 13A) years 2-3 and (FIG. 13B) years 5+ post infection. For each serum, the predicted neutralization prevalence for each of 12 antibody specificities is shown based on neutralization of 21 diverse HIV-1 strains. Serum neutralization on 21-strain virus panel is shown in FIG. 30.



FIG. 14 is a table providing data collection and refinement statistics for the BG505.SOSIP.664-PGT122-35O22 protein complex structure.



FIG. 15 is a table listing the modeling parameters for gp120 and gp41 rearrangements. To provide reference frames for the various prefusion conformational states, we extracted Env component of SOSIP bound by VRC-PG04 (Lyumkis, et al. Science 342, 1484-1490 (2013)) and by VRC03 (Bartesaghi, et al. Nature structural & molecular biology 20, 1352-1357 (2013)) and the resultant maps with the CD4-bound conformation trimeric BAL (Tran, et al. PLoS pathogens 8, e1002797 (2012)). Once maps were aligned, gp120 and gp41 models were fit to each of the maps as defined in the table in black text after “gp120” and “gp41”. In addition to rigid-body fits of crystal structures, specific regions of gp120 and gp41 were modeled and are defined in the table in red text after different portions of gp120 and gp41 relative to the prefusion mature closed conformation.


The prefusion mature closed conformation of gp120 and gp41 was established from the crystal structure presented in Example 1 and was fit without modification to EMDB-5779 with density from PGV04 fabs computationally removed. The prefusion partially open intermediate conformation was modeled by a rigid body fitting of gp120 to EMDB-2484 with density from VRC03 Fabs computationally removed. α7 of gp41 was extended into the unoccupied density at the N-terminus of the helix using the mature closed structure as a starting model. The prefusion receptor-bound intermediate was modeled by fitting the CD4-bound gp120 core crystal structure (PDB ID 3JWD) to the CD4-bound EMDB-5455 map. V3 of the crystal structure (PDB ID 3HI1) was aligned to the core and the V1V2 crystal structure (PDB ID 3U4E) was fit to the remaining density. α7 of gp41 was extended through an alignment with crystal structures of postfusion gp41 (PDB IDs 2X7R, 2EZO). Postfusion gp120 is in the same conformation as the prefusion receptor-bound intermediate and the postfusion gp41 structure was derived from an alignment of SIV and HIV postfusion crystal structures (PDB IDs 2X7R, 2EZO).



FIGS. 16A and 16B are tables showing binding parameters of the 35O22, PGT151, and PGT145 antibodies to trimeric BG505 SOSIP.664. *NBD: No binding detected, (double dagger) SE: Standard error calculated from global fit of 6 independent injections. FIG. 16A: # Levels of captured trimer varied between 400-500 RU for the CD4 Ig and 2G12 captures, whereas ˜1500 RUs of trimer (+sCD4) was captures in the 17b capture format. FIG. 16B: SE: Standard error calculated from global fit of 6 independent injections; SD: Standard deviation of trimer capture from 6 independent injection; Normalized: (Rmax/Level of trimer capture)*100.



FIG. 17 is a table showing the atomic-level structures for HIV-1-Env regions determined in complex with HIV-1-neutralizing antibodies. Neutralizing antibodies generally recognize the prefusion conformation of HIV-1 Env. Thus structures highlighted here display a cumulative sum total of prefusion HIV-1-Env structural information. Env residues are numbered according to standard HXB2 numbering (from PDBs). One structure, for antibody D5, is in the postfusion gp41 conformation, and is thus not included in the sum total. Other structures for PDB 4CC8, 4NCO, and 3J5M, do not define sequence register, and are also not included in the sum total.



FIGS. 18A-18C show biolayer interferometry binding profiles of monoclonal antibodies to BG505 SOSIP.664. Octet Biosensorgrams of BG505 SOSIP.664 (FIG. 18A) or BG505 gp120 (FIG. 18B) binding to human monoclonal IgGs. Human monoclonal antibodies were loaded onto AMC probes and association with gp140 or gp120 proteins (at 50 μM concentration) were allowed to proceed for 300s, followed by dissociation for 300s with the responses measured in nm using an Octet Red 384 machine. All experiments were carried out at 30° C. in PBS buffer (pH 7.4) supplemented with 1% BSA to minimize non-specific binding. The dotted line indicates the beginning of the dissociation phase and the maximal specific binding after 300s reported in the table shown in FIG. 18C (− no binding, + from background to 0.175 RU, ++ 0.175 RU to 0.35 RU and +++ from 0.35 RU to 0.8 RU). BG505gp120 did not contain the T332N mutation (no glycan at that position). The antigenicity of the BG505 SOSIP.664 protein varied depending on the assay done. Thus, using surface plasmon resonance, no CD4i antibodies binding was detected while some binding could be observed using biolayer interferometry.



FIG. 19 is a set of ribbon diagrams showing modeling of gp41 residues 548-568. At low contour, suggestive density is observed that might correspond to the connection between α6 and α7 helices. To investigate the degree to which a model for this region might be defined, two different models for this region were built and refined, as shown in FIG. 19A, with electron density shown for 2F0-Fc density at 1σ contour. The location of the I/P mutation at 559 is indicated. FIG. 19B, Superimposed models shown in perpendicular orientations.



FIGS. 20A-20C illustrate the gp120-gp41 and gp41-gp41 interfaces. FIG. 20A, Cartoon representation of gp120 and gp41. Region of gp120 that interacts with gp41 is shown in surface representation and region of gp41 that interacts with gp120 is shown in semitransparent surface. FIG. 20B, gp41-trimer interfaces as viewed from the viral membrane in ribbon and surface representation (90° rotation from FIG. 2C). FIG. 20C, Residues that have been shown by mutagenesis (Helseth et al., J Virol, 65, 2119-2123 (1991); Thali et al., J Virol, 66, 5516-5524 (1992); Cao, J. et al. J Virol, 67, 2747-2755 (1993); Leavitt et al., J Virol, 77, 560-570 (2003); Yang et al., Virology 313, 117-125 (2003); Sen et al., Biochemistry 47, 7788-7795 (2008); Wang et al., J Biol Chem 283, 32644-32649 (2008)) to be important for gp120/gp41 association are underlined on sequence and residues that are shown to interact between gp120 and gp41 from the crystal structure are indicated in red from the same protomer and in orange if between two protomers. The sequence of HIV-1 Env ectodomdina from BG505 (positions 31-664 of SEQ ID NO: 2 is shown). Sites of N-linked glycosylation are shown in green.



FIG. 21 illustrates HIV-SIV postfusion chimera. Sequences of HIV-1 gp41 prefusion, postfusion (HIVpost, PDB ID: 2X7R) and SIV postfusion (SIVpost, PDB ID: 2EZO) are aligned with secondary structure indicated. Residues that were used to make the postfusion HIV-1/SIV chimera used in FIG. 3 are shown in red.



FIGS. 22A and 22B illustrate the fusion-intermediate entry inhibitors of HIV-1 envelope. FIG. 22A, The binding residues of representative fusion-intermediate targeting entry inhibitors or antibodies were mapped onto the structure of pre-fusion envelope (Lawless et al., Biochemistry 35, 13697-13708 (1996); Chen et al., J Virol, 69, 3771-3777 (1995); Root et al., Science 291, 884-888 (2001)). Upper panels, ribbon representation of pre-fusion envelope protomer A, at two orientations, with the binding residues of the fusion-intermediate inhibitors 5-helix, T20, and monoclonal antibody D5 indicated. Lower panels, surface representation of the pre-fusion envelope trimer, with the fusion-intermediate binding residues mapped onto the surfaces of all protomers. gp120 is colored lighter gray and gp41 is colored darker grey. Binding residues of fusion-intermediate inhibitors 5-helix, T20, and monoclonal antibody D5 (Luftig et al., Nature structural & molecular biology 13, 740-747 (2006)) are indicated. FIG. 22B, Fusion-intermediate entry inhibitors T20, 5-helix, and D5 Fab docked onto a model of fusion-intermediate gp41.



FIG. 23 shows a set of graphs showing the effect of CD4 and CD4/17b on binding of antibodies 35O22 and PGT151 to BG505 SOSIP.664. The structure of a near-native prefusion state of HIV-1 provides a critical addition to the pantheon of HIV-1 Env structures with atomic-level detail. Moreover, antibodies 35O22 and PGT151, which bind specifically to the trimeric prefusion conformation of gp41, provide new tools by which to assess the conformational state of gp41 (Blattner et al., Immunity 40, 669-680 (2014); Falkowska et al., Immunity 40, 657-668 (2014). The binding of antibodies 35O22 and PGT151 to BG505 SOSIP.664 trimer was tested in the presence of the CD4 receptor and the 17b antibody (Thali et al., J Virol, 67, 3978-3988 (1993) (a co-receptor surrogate which recognizes a bridging sheet epitope that overlaps the site of co-receptor recognition). In the case of antibody 35O22, CD4 binding to the BG505 SOSIP.664 trimer impacted the kinetics, affinity and stoichiometry of binding. 35O22 bound to BG505 SOSIP.664 with an 8.4-fold reduced affinity, primarily contributed by an increased rate of dissociation. The overall binding level (Rmax) normalized to the average level of trimer captured (see also FIG. 16) was lower suggesting substoichiometric binding. Capturing the trimer on a CD4-Ig surface reduced normalized Rmax for PGT151 compared to the 2G12 capture format, suggesting reduced stoichiometry for PGT151 binding to trimer pre-bound with CD4, although kinetics and affinity of interaction were similar. A BG505 SOSIP.664 trimer+sCD4 complex captured onto a 17b surface bound 35O22 but showed no detectable binding to PGT151.



FIGS. 24A and 24B illustrate the postfusion binding pocket of gp41 clasp residues Trp628 and Trp631 is targeted by neutralizing antibodies. FIG. 24A, Shown are ribbon representations of gp41 5-helix protein (Root, et al 2001) (left) docked with an additional C-heptad repeat (CHR) helix (middle panel) or with a representative neutralizing antibody, D5, that targets this site (Luftig et al., Nature structural & molecular biology 13, 740-747 (2006); Gustchina et al., PLoS pathogens 6, e1001182 (2010); Sabin et al., PLoS pathogens 6, e1001195 (2010)) (right panel). Residues of the prefusion clasp, W628 and W631, that are part of CHR are indicated. N-heptad repeat (NHR) helices and CHR helices are indicated. FIG. 24B, Surface representation of 5-helix protein (same orientation and coloring as in FIG. 24A) is shown with the footprints of gp41 clasp residues W628 and W631 (middle panel) and antibody D5 (right panel).



FIGS. 25A-25E are a set of tables showing binding and contact parameters for the gp120-gp41 interface in the HIV-1 viral spike. D: Disulfide bond, H: Hydrogen bond, S: Salt bridge. ASA: Accessible Surface Area, Å2, BSA: Buried Surface Area, Å2, ΔiG: Solvation energy effect, kcal/mol, III: Buried area percentage, one bar per 10%.



FIG. 26 is a table and a set of ribbon diagrams illustrating structures that are related to the gp120/gp41 structure in the prefusion mature closed conformation of the HIV-1 Env ectodomain trimer.



FIGS. 27A and 27B illustrate qualitative recognition of HIV-1 envelope by diverse antibodies is shown for five conformational states. Light grey bars indicate anticipated recognition, dark grey bars no recognition, and absence of a bar indicates that recognition is undefined. HIV-1 recognition is from cited references (Luftig et al., Nature structural & molecular biology 13, 740-747 (2006); Blattner et al., Immunity 40, 669-680 (2014); Gustchina et al., PLoS pathogens 6, e1001182 (2010); Sabin et al., PLoS pathogens 6, e1001195 (2010); Liao et al., Nature 496, 469-476 (2013); Zhou et al., Science 329, 811-817 (2010); Scheid et al., Science 333, 1633-1637 (2011); Sanders et al., PLoS pathogens 9, e1003618 (2013); Yasmeen et al., Retrovirology 11, 41 (2014); Lyumkis et al., Science 342, 1484-1490 (2013); Ringe et al., PNAS USA 110, 18256-18261 (2013); Julien et al., Science 342, 1477-1483 (2013); Walker et al., Nature 477, 466-470 (2011); Stanfield et al., Human antibodies 14, 73-80 (2005); Pancera et al., PNAS USA 107, 1166-1171 (2010); Huang et al., Science 310, 1025-1028 (2005); Huang et al., Science 317, 1930-1934 (2007); Rizzuto et al., Science 280, 1949-1953. (1998); Guan et al., PNAS USA 110, E69-78 (2013); Gorny et al., Virology 267, 220-228 (2000); Yuan et al., AIDS research and human retroviruses 25, 319-328 (2009); Moore et al., J Virol, 80, 2515-2528 (2006); Miller et al., PNAS USA 102, 14759-14764 (2005); Chen et al., J Virol, 88, 1249-1258 (2014); Chakrabarti et al., AIDS research and human retroviruses 27, 877-887 (2011); Frey et al., PNAS USA 105, 3739-3744 (2008); Nicely et al., Nature structural & molecular biology 17, 1492-1494 (2010); Huang et al., Nature 491, 406-412 (2012)) or from antibodies 35O22 and PGT151 recognition of HIV-1 Env as shown herein (see FIG. 16).



FIGS. 28A-28D and 29A-29D show a set of tables listing binding and contact parameters for the interaction of the 35O22 heavy and light chains variable regions with the trimeric HIV-1 Env ectodomain. D: Disulfide bond, H: Hydrogen bond, S: Salt bridge. ASA: Accessible Surface Area, Å2, BSA: Buried Surface Area, Å2, ΔiG: Solvation energy effect, kcal/mol, III: Buried area percentage, one bar per 10%.



FIGS. 30A and 30B are a set of tables listing serum neutralization results from a 21-strain virus panel.



FIG. 31 is a schematic diagram illustrating structural implementation of HIV-1 evasion.



FIGS. 32A-32D are a set of ribbon diagrams and graphs illustrating that the unliganded HIV-1 Env trimer is structurally compatible with epitopes of broadly neutralizing but not ineffective antibodies. FIG. 32A, Superposition of unliganded and antibody bound HIV-1 Env structures. (Left) The unliganded gp120 core monomer is shown in ribbons representation, with regions of less (or greater) than 2 Å RMSD upon antibody binding indicated, and representative antibody-bound structures in black. (Middle and right) Unliganded and antibody-bound HIV-1 Env trimers. (In the right panel, antibodies PGT122 and 35O22 are shown in gray semitransparent surfaces, and the rear protomer has been removed for clarity). FIG. 32B, Breadth-potency of broadly neutralizing and ineffective antibodies on a diverse 170 HIV-1 isolate panel. FIG. 32C, Unliganded Env structure is displayed as a Ca-ribbon, with antibody epitope residues light grey (structurally compatible) or dark grey (incompatible). RMSD (solid fill) and volume overlap (striped fill) with the respective antibody-Env complexes are shown as a bar graph, with two linear scales split at the RMSD and antibody-antigen volume overlap cutoffs of 2 Å and 500 Å3, respectively; bars below the respective cutoffs. Antibody labels are dark grey if incompatible, and gray if not present in the structure. FIG. 32D, Structural compatibility versus breadth. Volume overlap (left), RMSD (middle) and Antigenic Structural Compatibility score (ASC) (right) are graphed versus antibody breadth on a diverse 170 HIV-1 isolate panel. P-values for Spearman correlations provided.



FIGS. 33A-33F are a set of diagrams and graphs illustrating the antigenicity and conformational fixation of unliganded HIV-1 Env. FIG. 33A, BG505 SOSIP.664 structural compatibility versus binding antigenicity, in the absence (left) and presence (right) of CD4; average binding of each antibody is provided, and ineffective antibodies labeled (CD4bs:CD4-binding site, CD4i: CD4-induced, non: non-neutralizing, V3: V3-loop directed). FIG. 33B, Conformationally stabilized BG505 SOSIP.664 variants. The central image depicts the unliganded BG505 SOSIP.664 HIV-1 Env trimer, with two protomers shown in cartoon representation. Insets: atomic-level details. *Residue 559 is disordered in the unliganded structure. FIG. 33C, Binding antigenicity of BG505 SOSIP.664 and alterations to BG505 SOSIP.664 that stabilize the unliganded closed state. Heat map shows binding of BG505 SOSIP.664 and variants to a panel of antibodies. A433P was temporally less stable than 201C-433C (Extended Data FIG. 6b) FIG. 33D, Structure of BG505 SOSIP.664 201C-433C is compatible with binding antigenicity, in both the absence (left) and presence (right) of CD4, with antibodies and average binding of broadly neutralizing and ineffective antibodies as in FIG. 33A. FIG. 33E, Atomic-level models of residues 201 and 433 in unliganded prefusion closed and CD4-bound conformations. Ribbon representation of the two structures are shown with bridging sheet shown in dark grey, residues 201 and 433 highlighted and Cα distance between the two indicated. Positions of the variable loops are shown. (Monomeric CD4-bound conformation from PDB ID 3JWD, 3U4E and 2B4C.) FIG. 33F, Differential scanning calorimetry.



FIGS. 34A-34F are a set of diagrams and graphs illustrating that unliganded HIV-1 Env binds a single CD4 without the typical antigenic hallmarks of CD4 triggering. FIG. 34A, Binding of soluble CD4 to SOSIP.664 and mutants that stabilize the prefusion mature closed state measured by SPR (CD4 on chip). FIG. 34B, Kinetics of CD4 activation by SPR measured by binding to 17b, which recognizes a bridging sheet epitope (17b on chip; left) and to 3074, which recognizes a V3 epitope (3074 on chip; right). FIG. 34C, Sedimentation equilibrium analytical ultracentrifugation measurements of BG505 SOSIP.664 and 201C-433C variant in presence of excess soluble CD4. FIG. 34D, Butterfly plots display the HDX profiles of BG505 SOSIP.664 DS variant (left) and DS variant with CD4 (right). The percent exchange is plotted for each peptide; raw difference plots are shown below. Qualitative changes by HDX are displayed on one lobe of the unliganded trimer with regions becoming more ordered and disordered. FIG. 34E, smFRET of JR-FL virions with and without 201C-433C substitution. Population FRET histograms are each paired with transition density plots, which display the relative density of observed transitions. FIG. 34F, HIV-1 entry mechanism with conformation-blocking mutations, antigenicity, and interactions with functional ligands. The results reveal a new mechanistic state, which is characterized by the binding of a single molecule of CD4, no bridging sheet formation and reduced V3 loop exposure.



FIGS. 35A and 35B are a set of graphs illustrating properties of conformationally fixed HIV-1 Env trimeric immunogens. FIG. 35A, Physical stability of trimeric BG505 SOSIP.664 201C-433C as determined by the quaternary specific antibody VRC26.09 after 60 minutes of incubation at extremes of temperature, pH, or ten freeze-thaw cycles. FIG. 35B, Virus-like particle (VLP) antigenicity. Strain JR-FL was modified with E168K to allow binding of V1V2-directed broadly neutralizing antibodies; strain BG505 was modified with T332N to allow binding of 2G12 antibody. While broadly neutralizing antibody binding is maintained between parent and 201C-433C VLPs, the 201C-433C variant shows reduced ineffective antibody binding, especially in the presence of CD4. Ineffective antibodies labeled (CD4bs: CD4-binding site, CD4i: CD4-induced, V3: V3-loop directed) FIGS. 36A-36D are a set of graphs and tables illustrating the characterization of purified BG505 SOSIP.664 and selected variants. FIG. 36A, Properties of purified gp140 proteins. *the percentage of trimers was obtained by measuring area under the curve of the gel filtration profile of the various peaks representing aggregates, gp140 trimer, dimer and monomer. FIG. 36B, gel filtration profiles on Superdex 200 with indicated line showing a second round of purification when performed. Dotted lines show the fractions selected for analyses. FIG. 36C, 2D class averages from a reference-free classification of negative stained EM data for each protein. Box size=28 nm. FIG. 36D, 447-52D negative selection. Trimeric peak of BG505 SOSIP.664 purified over gel filtration is used as starting point. Protein is passed over a 447-52D affinity column and flow through collected as well as eluate from the 447-52D column (with 3 M MgCl2). SDS-page under reducing (R) and non-reducing conditions (NR) is shown with protein before 447-52 negative selection, protein after 447-52D negative selection and eluate from the 447-52D affinity column. A higher molecular weight band can be removed by 447-52D negative selection. SPR measurement of the same three fractions, before, after and eluate binding to 2G12, 447-52D and CD4. The portion of the protein that binds to 447-52D can be removed by negative selection while maintaining CD4 and 2G12 binding. 80% of the protein is recovered after 447-52D negative selection.



FIGS. 37A-37E are a set of graphs illustrating the antigenicity of purified BG505 SOSIP.664 and selected variants by MSD and ELISA. FIG. 37A, Antigenicity of BG505 SOSIP.664 and mutants by MSD-ECLIA. Plots show binding of neutralizing, non- or weakly neutralizing antibodies (dark grey) and antibodies in presence of CD4 to BG505 SOSIP.664 and mutants. FIG. 37B, Temporal stability of BG505 SOSIP.664, A433P and 201C-433C. FIG. 37C, Comparison of antigenicity of BG505 SOSIP.664 and 201C-433C in absence and presence of soluble, 2-domain CD4. FIG. 37D, Antigenicity of BG505 SOSIP.664 and 201C-433C assessed by ELISA. FIG. 37E, Pair wise comparison of antigenicity data obtained by MSD-ECLIA and ELISA.



FIGS. 38A-38 are a set of graphs and tables illustrating the antigenicity of purified BG505 SOSIP.664 and 201C-433C by SPR and BLI. Binding of BG505 SOSIP.664 and 201C-433C measured by FIG. 38A, Surface Plasmon Resonance and FIG. 38B, Biolayer Interferometry. FIG. 38C, Affinities of BG505 SOSIP.664 and 201C-433C to neutralizing and non-neutralizing antibodies by SPR and Biolayer interferometry. FIG. 38D, Pairwise comparison of antigenicity data by 4 methods—MSD, ELISA, BLI and SPR. The P values were corrected for false discovery rate for multiple comparisons.



FIGS. 39A-39D are a set of graphs illustrating the characterization of BG505 SOSIP.664 and 201C-433C binding to CD4-induced epitopes in absence and presence of CD4 by FIG. 39A, MSD-ECLIA FIG. 39B, SPR with antibodies captured on an anti-Fc surface and trimer as analyte, SOSIP is shown in solid line and 201C-433C in dashed line, trimer without CD4 is dark grey and trimer with CD4 light grey. FIG. 39C and FIG. 39D, ELISA at 0.5 μg/ml and 2 μg/ml trimer captured on D7324-coated plates, respectively.



FIGS. 40A-40E are a set of graphs illustrating the CD4-induced activation of HIV-1 Env. FIG. 40A, SPR analysis of (top panel) co-receptor site exposure and (bottom panel) HR2-site exposure upon CD4 activation. FIG. 40B, CD4-induced binding of SOSIP and P313W mutant to 17b. Trimer samples at concentrations from 40 nM to 2.5 nM in 2-fold dilutions were combined with 200 nM sCD4 and injected on a 200RU 17b IgG surface. FIG. 40C, SPR single-cycle kinetics analysis of 17b Fab binding to soluble trimers activated with sCD4. Under conditions of constant 50 nM sCD4 flow, 17b Fab at was injected incrementally in 2-fold dilutions from 25 nM to 1.5 nM on trimer captured on a 2G12 chip. A433P and 201C-433C were further subjected to 17b Fab concentrations ranging from 500 nM to 31.25 nM (insets). FIG. 40D, Time-dependent increase in exposure of V3 epitope (3074 detection) and bridging sheet (17b detection) in SOSIP trimers on incubation with sCD4. FIG. 40E, Ability of HIV-1 BG505 and mutants to enter CD4+CCR5+ cells.



FIG. 41 is a set of graphs illustrating the analysis of stoichiometry of CD4-binding to BG505SOSIP.664.332N or the DS variant, BG505SOSIP 201C-433C. Masses were determined for each molecule by MALDI-TOF mass spectrometry, as follows: BG505.SOSIP.664 ((109,994±11 Da)×3=329,982±33 Da), BG505.SOSIP.664 201C-433C ((109,006±10 Da)×3=327,018±30 Da), and CD4 d1d2 (20,329±2 Da). For the BG505 SOSIP molecules, monomer masses were determined, but trimeric masses were used in the analytical ultracentrifugation fitting. Four fittings are shown for each experiment, with fits calculated for 0, 1, 2, or 3 bound CD4 molecules, respectively. For BG505SOSIP.664.N332, the residual errors switch direction between 1:2 and 1:3 stoichiometries, suggesting 2-3 CD4 molecules bound. For the DS mutant, BG505SOSIP 201C-433C, the residual errors fit best at 1:1 stoichiometry and fail to fit higher numbers of bound CD4 molecules, indicating 1 CD4 molecule bound per DS trimer.



FIGS. 42A-42G, 43 and 44 are a set of tables showing antigenic characteristics of recombinant HIV-1 Env ectodomain trimers (FIGS. 42A-42G, and 44), protein nanoparticles including recombinant HIV-1 Env ectodomain trimers (FIG. 43). The binding activity of the recombinant HIV-1 Env trimers or protein nanoparticles including recombinant HIV-1 Env ectodomain trimers was compared to that of the HIV-1 Env BG505 SOSIP.664 construct by ELISA assay. “+++” indicates binding within 75% of HIV-1 Env BG505 SOSIP.664, “++” indicates binding between 50-75% of HIV-1 Env BG505 SOSIP.664, “+” indicates binding within 25-50% of HIV-1 Env BG505 SOSIP.664, and “−” indicates binding within 0-25% of HIV-1 Env BG505 SOSIP.664.



FIGS. 45 and 46 are schematic diagrams illustrating the construction of chimeric HIV-1 Env ectodomain trimers including gp120 N- and C-terminal sequences from a first HIV-1 strain (shown in lighter grey) with the remainder of gp120 from a second HIV-1 strain (shown in darker grey).



FIG. 47 is a ribbon diagram showing a single protomer of the HIV-1 Env ectodomain in a mature prefusion closed conformation, with certain structural elements and residues indicated. The β-4 and β-3 strands at the N-terminal region of gp120 and the β26 and β25 strands and α5 helix at the C-terminal region of gp120 indicated. Many of the residues of gp120 that interface with gp41 (residues 46-54, 70-75, 84-89, 99, 102, 106, 107, 114, 215, 220-224, 226, 244, 471-473, 476-477) are present.



FIG. 48 shows a set of coommassie stained SDS-PAGE gels and elution profile graphs illustrating purification chimeric HIV-1 Env ectodomain trimers including sequences of the BG505 HIV-1 strain and one of the 3301, ZM53, CAP256-SU, and 25925 HIV-1 strains.



FIG. 49 is a set of graphs illustrating the antigenicity of chimeric HIV-1 Env trimers including the ZM53_BG505-NCgp120_gp41.SOSIP (SEQ ID NO: 386), 25925-2.22_BG505-NCgp120_gp41.SOSIP (SEQ ID NO: 383), and 3301_V1_C24_BG505-NCgp120+gp41.SOSIP (SEQ ID NO: 384) constructs.



FIG. 50 shows a coommassie blue stained polyacrylamide gel and a graph illustrating expression, purification, and antigenicity of a chimeric HIV-1 Env trimers including a gp120 sequence from the BG505 strain, a gp41 sequence from the CAP45 strain, and the SOSIP mutations (SEQ ID NO: 772).



FIG. 51 is a set of graphs illustrating that the neutralization profile of the indicated antibodies for the native DU156 virus correlates with the antigenic profile of a recombinant HIV-1 Env ectodomain trimer stabilized in the prefusion mature closed conformation as disclosed herein.



FIG. 52 shows a set of electron micrograph images indicating that purified CNE58-strandC, CAP256-SU, and 3301_V1_C24_bg505 chimeric HIV-1 Env ectodomains attain trimeric closed configuration.



FIGS. 53A-53D are a set of tables illustrating the antigenic characteristics of the indicated recombinant HIV-1 Env ectodomain trimers. A “1” following the name of recombinant Env ectodomain indicates that the assayed HIV-1 Env ectodomain is a chimeric HIV-1 Env ectodomain including gp120 residues 31-45 and 478-507, and gp41 residues 512-664 from the BG505 strain with SOSIP substitutions, and a disulfide between residues 201-433, with the remainder of the gp120 sequence from a second HIV-1 strain. A “2” following the name of recombinant Env ectodomain indicates that the assayed HIV-1 Env ectodomain is a chimeric HIV-1 Env ectodomain including gp120 residues 31-45, 478-507, and Interface Residue Set A (see Example 5), and gp41 residues 512-664 from the BG505 strain with SOSIP substitutions, and a disulfide between residues 201-433, with the remainder of the gp120 sequence from a second HIV-1 strain. A “3” following the name of recombinant Env ectodomain indicates that assayed HIV-1 Env ectodomain is a chimeric single chain HIV-1 Env ectodomain including gp120 residues 31-45 and 478-507, and gp41 residues 512-664 from the BG505 strain with SOSIP substitutions, and a disulfide between residues 201-433, with the remainder of the gp120 sequence from a second HIV-1 strain, and peptide linker in place of the protease cleavage site between gp120 and gp41. A “4” following the name of recombinant Env ectodomain indicates that the assayed HIV-1 Env ectodomain includes the SOSIP substitutions is a chimeric protein including gp120 residues 31-34 from the BG505 strain with SOSIP substitutions, and a disulfide between residues 201-433, with the remainder of the gp120 and gp41 sequences from a second HIV-1 strain.



FIGS. 54A and 54B are a set of graphs illustrating results from ELISA assays showing that the BG505.SOSIP.664.201C-433C HIV-1 Env ectodomain trimer induces production of HIV-1 Env trimer specific and V3-peptide specific antibodies in rabbits (FIG. 54A) and guinea pigs (FIG. 54B).



FIGS. 55A-55C are a table and a set of graphs showing results from HIV-1 neutralization assays using sera collected from rabbits or guinea pigs immunized with the BG505.SOSIP.664 HIV-1 Env ectodomain trimer or the BG505.SOSIP.664.201C-433C “DS” HIV-1 Env ectodomain trimer. Each immunogen elicited comparable autologous virus (BG505.W6M.C2.T332N) and V3 directed tier 1 virus (MW965.26) neutralizing activity as measured by IC50. A summary of the results for autologous virus and V3 directed tier 1 virus is provided for guinea pig week 18 sera (FIG. 55B) and rabbit week 18 sera (FIG. 55C).



FIG. 56 is a table listing antigenic characteristics of chimeric HIV-1 Env ectodomains linked to a transmembrane domain as expressed on surface of cells.



FIG. 57 is a graph and a sequence alignment showing that the inferred ancestor and intermediates of V1V2-directed bNAbs neutralize a common set of HIV-1 isolates. “Neutralized” represents the number of HIV-1 strains with IC50 of less than 50 μg/ml, and “Total” indicates the number of HIV-1 strains tested; IC50 for select strains is indicated by a colored dot. Nomenclature of the revertants is as follows: unmutated common ancestor (UCA), reverted V-gene, mature CDR3 (gHgL), early intermediate from next-generation sequencing (I1). The sequence of the V1V2 domain (positions 129-196) of the BG505 (SEQ ID NO: 2), CAP256.SU (SEQ ID NO: 51), BB201.B42 (SEQ ID NO: 81), KER2018.11 (SEQ ID NO: 107), CH070.1 (SEQ ID NO: 174), ZM233.6 (SEQ ID NO: 745), Q23.17 (SEQ ID NO: 746), A244 (SEQ ID NO: 747), T250-4 (SEQ ID NO: 2114), and WITO.33 (SEQ ID NO: 748) strains of HIV-1 is shown.



FIGS. 58A-58C illustrate the design and antigenicity of HIV-1 Env ectodomain trimer immunogens stabilized in the prefusion mature closed conformation that include a chimeric V1V2 domain sequence. (FIG. 58A) Design of chimeric V1V2 DS-SOSIP.664 trimers. Residues 126-196 of strains found to preferentially interact with germline-reverted V1V2-directed antibodies were transferred to the corresponding region of BG505 DS-SOSIP.664, with D368R mutation. (FIG. 58B) Gel filtration and negative stain EM (2D class averages) of BG505 SOSIP.664.DS.368R.CAP256-SU, a representative chimera. (FIG. 58C) Binding of chimeric DS-SOSIP.664s and neutralization of corresponding pseudoviruses by ancestors, intermediates, and mature V1V2-directed bNAbs. Antibodies are listed in the left column, and HIV-1 strains are listed across the top; results are tabulated in double cells, with the left cell showing binding and the right cell showing neutralization. Immunogens contain the 201C-433C disulfide mutation for stabilization and also contain a D368R CD4 binding site knock out mutation to prevent the trimer from opening in vivo.



FIG. 59 is a table illustrating the antigenic characteristics of the indicated recombinant HIV-1 Env ectodomain trimers, which are chimeric HIV-1 Env ectodomain stabilized in the prefusion mature closed conformation and include BG505 and JRFL sequences.



FIG. 60 is a set of graphs showing binding to VRC20gHgL and VRC01 gHgL unmutated common ancestor (UCA) antibodies, as well as the indicated neutralizing antibodies by a chimeric HIV-1 Env ectodomain trimer including a BG505 “platform” and 426c gp120 residues with mutation of the glycan sequons at positions 276, 460 and 463 and the “DS” substitutions (201C/433C).





SEQUENCES

The nucleic and amino acid sequences are shown using standard letter abbreviations for nucleotide bases, and amino acids, as defined in 37 C.F.R. 1.822. Only one strand of each nucleic acid sequence is shown, but the complementary strand is understood as included by any reference to the displayed strand. The Sequence Listing is submitted as an ASCII text file in the form of the file named “Sequence.txt” (˜11 MB), which was created on Sep. 3, 2015, which is incorporated by reference herein.


Table 13 in Example 15 provides a list of sequences and additional information concerning the sequences.


Structural Coordinates

The atomic coordinates of an asymmetric unit of the crystal structure of a trimeric HIV-1 Env ectodomain (BG505.SOSIP.664) bound to PGT122 and 35O22 Fabs in the prefusion mature closed conformation (as described in Example 1) are recited in Table 1 submitted as an ASCII text named “Table_1.txt” (˜2 MB, created on Aug. 7, 2014) in U.S. Provisional Application No. 62/046,059, filed Sep. 4, 2014, and have been deposited with the Protein Data Bank as Acc. No. 4TVP. Table 1 submitted in U.S. Provisional Application No. 62/046,059, and Protein Data Bank Acc. No. 4TVP, are incorporated by reference herein.


The atomic coordinates of the crystal structure of an HIV-1 Env ectodomain trimer provided in Table 1, without the PGT122 and 35O22 Fabs, are recited in Table 2 submitted as an ASCII text named “Table_2.txt” (˜2 MB, created on Aug. 7, 2014) in U.S. Provisional Application No. 62/046,059, filed Sep. 4, 2014. Table 2 provided in U.S. Provisional Application No. 62/046,059 is incorporated by reference herein.


The atomic coordinates of an asymmetric unit of the crystal structure of an unliganded trimeric HIV-1 Env ectodomain in the prefusion mature closed conformation (as described in Example 2) are recited in Table 3 submitted as an ASCII text named “Table_3.txt” (˜0.7 MB, created on Aug. 7, 2014) in U.S. Provisional Application No. 62/046,059, filed Sep. 4, 2014, and have been deposited with the Protein Data Bank as Acc. No. 47MJ. Table 3 submitted in U.S. Provisional Application No. 62/046,059, and Protein Data Bank Acc. No. 47MJ, are incorporated by reference herein.


The atomic coordinates of the crystal structure of an unliganded trimeric HIV-1 Env ectodomain in the prefusion mature closed conformation (as described in Example 2) are recited in Table 4 submitted as an ASCII text named “Table_4.txt” (˜2 MB, created on Aug. 7, 2014) in U.S. Provisional Application No. 62/046,059, filed Sep. 4, 2014. Table 4 provided in U.S. Provisional Application No. 62/046,059 is incorporated by reference herein.


DETAILED DESCRIPTION

The HIV-1 Env trimer undergoes a dramatic structural rearrangement between its prefusion mature closed conformation and the CD4-bound open conformation (see Example 1, below). As shown in FIGS. 1-3, in the prefusion mature closed conformation, the HIV-1 Env trimer includes a V1V2 domain “cap” at its membrane distal apex, with the V1V2 domain of each gp120-gp41 protomer in the trimer coming together at the membrane distal apex. At the membrane proximal aspect, the HIV-1 Env ectodomain trimer includes distinct α6 and α7 helices. CD4 binding causes changes in the conformation of the HIV-1 Env ectodomain trimer, including disruption of the V1V1 domain cap, which “opens” as each V1V2 domain moves outward from the longitudinal axis of the Env trimer following CD4 binding, and formation of the HR1 helix, which includes both the α6 and α7 helices (which are no longer distinct, see FIG. 3D). These conformational changes bring the N-terminus of the fusion peptide within close proximity of the target cell membrane, and expose “CD4-induced” epitopes (such as the 17b epitope) that are present in the CD4-bound open conformation, but not the mature closed conformation, of the HIV-1 Env ectodomain trimer.


Thus, the membrane distal and membrane proximal aspects of the HIV-1 Env ectodomain trimer in its prefusion mature closed conformation include several distinct structural elements that are absent from the corresponding regions of the HIV-1 Env ectodomain trimer in its CD4-bound open conformation. Amino acid positions (and sequences) corresponding to these regions are indicated in FIGS. 3 and 11.


Notably, in a previously identified HIV-1 Env ectodomain triner (BG505.SOSIP, described in more detail in Example 1), CD4 triggered recognition by ineffective antibodies so that their average binding was tighter than that of broadly neutralizing antibodies (see Example 2, FIG. 33A). Such CD4 triggering makes HIV-1 Env ectodomain trimers that cannot resist conformational changes to the CD-bound open conformation less desirable as an immunogen: in primates, such immunogens would bind CD4 in vivo and would thus be expected to elicit production of primarily ineffective antibodies against highly immunogenic CD4-induced epitopes.


Accordingly, recombinant HIV-1 Env proteins are provided that are stabilized or “locked” in the prefusion mature closed conformation. Using structure-guided design, positions of the HIV-1 Env protein were targeted for modification (e.g., amino acid substitution) to hinder or prevent the HIV-1 Env ectodomain trimer from transitioning from the prefusion mature closed conformation to CD4-bound open conformations. These recombinant HIV-1 Env ectodomain trimers resist transition to the CD4-bound open state of HIV-1 Env, and thus will retain the prefusion mature closed conformation when used as an immunogen to generate an immune response to HIV-1 Env in a subject expressing CD4, such as a human.


I. Summary of Terms

Unless otherwise noted, technical terms are used according to conventional usage. Definitions of common terms in molecular biology may be found in Benjamin Lewin, Genes X, published by Jones & Bartlett Publishers, 2009; and Meyers et al. (eds.), The Encyclopedia of Cell Biology and Molecular Medicine, published by Wiley-VCH in 16 volumes, 2008; and other similar references.


As used herein, the singular forms “a,” “an,” and “the,” refer to both the singular as well as plural, unless the context clearly indicates otherwise. For example, the term “an antigen” includes single or plural antigens and can be considered equivalent to the phrase “at least one antigen.” As used herein, the term “comprises” means “includes.” It is further to be understood that any and all base sizes or amino acid sizes, and all molecular weight or molecular mass values, given for nucleic acids or polypeptides are approximate, and are provided for descriptive purposes, unless otherwise indicated. Although many methods and materials similar or equivalent to those described herein can be used, particular suitable methods and materials are described herein. In case of conflict, the present specification, including explanations of terms, will control. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting. To facilitate review of the various embodiments, the following explanations of terms are provided:


17b: A monoclonal antibody that specifically binds to a CD4-induced epitope on the HIV-1 Env ectodomain trimer, that is, CD4 binding causes a conformation change in the HIV-1 Env ectodomain trimer that exposes the 17b epitope. Thus, 17b mAb is a “CD4-induced” antibody. The 17b antibody does not specifically bind to the HIV-1 Env ectodomain trimer in its prefusion mature closed conformation. The person of ordinary skill in the art is familiar with monoclonal antibody 17b and with methods of producing this antibody (see, for example, Kwong et al., J. Biol. Chem., 274, 4115-4123, 1999, which is incorporated by reference herein). The amino acid sequences of the heavy and light variable regions of the 17b antibody are known and have been deposited in GenBank as Nos. 1G9N_H (17b VH) and 1G9N_L (17b VL), each of which is incorporated by reference herein as present in the database on Jun. 20, 2014).


35O22: A neutralizing monoclonal antibody that specifically binds to an epitope on the membrane-proximal region of HIV-1 Env including residues of both gp120 and gp41. The amino acid sequences of the heavy and light variable regions of the 35O22 antibody are set forth as SEQ ID NOs: 2099 and 2100, respectively, and can be used to generate an antibody with the 35O22 antigen binding domain.


447-52D: A monoclonal antibody that specifically binds to the V3 loop of HIV-1 Env. The person of ordinary skill in the art is familiar with monoclonal antibody 447-52D and with methods of producing this antibody (see, for example, Stanfield et al., Structure, 12, 193-204, which is incorporated by reference herein). The amino acid sequences of the heavy and light variable regions of the 447-52D antibody are known and have been deposited in the Protein Data Bank as Nos. 1Q1J_H (447-52D VH) and 1Q1J_L (447-52D VL), each of which is incorporated by reference herein as present in the database on Jun. 20, 2014).


Adjuvant: A vehicle used to enhance antigenicity. In some embodiments, an adjuvant can include a suspension of minerals (alum, aluminum hydroxide, or phosphate) on which antigen is adsorbed; or water-in-oil emulsion, for example, in which antigen solution is emulsified in mineral oil (Freund incomplete adjuvant), sometimes with the inclusion of killed mycobacteria (Freund's complete adjuvant) to further enhance antigenicity (inhibits degradation of antigen and/or causes influx of macrophages). Immunostimulatory oligonucleotides (such as those including a CpG motif) can also be used as adjuvants. Adjuvants include biological molecules (a “biological adjuvant”), such as costimulatory molecules. Exemplary adjuvants include IL-2, RANTES, GM-CSF, TNF-α, IFN-γ, G-CSF, LFA-3, CD72, B7-1, B7-2, OX-40L, 4-1BBL and toll-like receptor (TLR) agonists, such as TLR-9 agonists. In some embodiments, the Adjuplex™ (Advanced BioAdjuvants) can be used with any of the recombinant HIV-1 Env ectodomain trimers to elicit an immune response to HIV-1 Env. The person of ordinary skill in the art is familiar with adjuvants (see, e.g., Singh (ed.) Vaccine Adjuvants and Delivery Systems. Wiley-Interscience, 2007). Adjuvants can be used in combination with the disclosed immunogens.


Administration: The introduction of a composition into a subject by a chosen route. Administration can be local or systemic. For example, if the chosen route is intravenous, the composition (such as a composition including a disclosed immunogen) is administered by introducing the composition into a vein of the subject. Exemplary routes of administration include, but are not limited to, oral, injection (such as subcutaneous, intramuscular, intradermal, intraperitoneal, and intravenous), sublingual, rectal, transdermal (for example, topical), intranasal, vaginal, and inhalation routes.


Agent: Any substance or any combination of substances that is useful for achieving an end or result; for example, a substance or combination of substances useful for inhibiting HIV infection in a subject. Agents include proteins, nucleic acid molecules, compounds, small molecules, organic compounds, inorganic compounds, or other molecules of interest. An agent can include a therapeutic agent (such as an anti-retroviral agent), a diagnostic agent or a pharmaceutical agent. In some embodiments, the agent is a protein agent (such as a recombinant HIV-1 Env polypeptide or immunogenic fragment thereof), or an anti-viral agent. The skilled artisan will understand that particular agents may be useful to achieve more than one result.


Amino acid substitutions: The replacement of one amino acid in a polypeptide with a different amino acid or with no amino acid (i.e., a deletion). In some examples, an amino acid in a polypeptide is substituted with an amino acid from a homologous polypeptide, for example, and amino acid in a recombinant Clade A HIV-1 Env polypeptide can be substituted with the corresponding amino acid from a Clade B HIV-1 Env polypeptide.


Antibody: An immunoglobulin, antigen-binding fragment, or derivative thereof, that specifically binds and recognizes an analyte (antigen) such as HIV-1 gp120, an antigenic fragment thereof, or a dimer or multimer of the antigen. The term “antibody” is used herein in the broadest sense and encompasses various antibody structures, including but not limited to monoclonal antibodies, polyclonal antibodies, multispecific antibodies (e.g., bispecific antibodies), and antibody fragments, so long as they exhibit the desired antigen-binding activity.


Non-limiting examples of antibodies include, for example, intact immunoglobulins and variants and fragments thereof known in the art that retain binding affinity for the antigen. Examples of antibody fragments include but are not limited to Fv, Fab, Fab′, Fab′-SH, F(ab′)2; diabodies; linear antibodies; single-chain antibody molecules (e.g. scFv); and multispecific antibodies formed from antibody fragments. Antibody fragments include antigen binding fragments either produced by the modification of whole antibodies or those synthesized de novo using recombinant DNA methodologies (see, e.g., Kontermann and Dubel (Ed), Antibody Engineering, Vols. 1-2, 2nd Ed., Springer Press, 2010).


Typically, a naturally occurring immunoglobulin has heavy (H) chains and light (L) chains interconnected by disulfide bonds. Immunoglobulin genes include the kappa, lambda, alpha, gamma, delta, epsilon and mu constant region genes, as well as the myriad immunoglobulin variable domain genes. There are two types of light chain, lambda (λ) and kappa (κ). There are five main heavy chain classes (or isotypes) which determine the functional activity of an antibody molecule: IgM, IgD, IgG, IgA and IgE.


Light and heavy chain variable regions contain a “framework” region interrupted by three hypervariable regions, also called “complementarity-determining regions” or “CDRs” (see, e.g., Kabat et al., Sequences of Proteins of Immunological Interest, U.S. Department of Health and Human Services, 1991). The sequences of the framework regions of different light or heavy chains are relatively conserved within a species. The framework region of an antibody, that is the combined framework regions of the constituent light and heavy chains, serves to position and align the CDRs in three-dimensional space. The CDRs are primarily responsible for binding to an epitope of an antigen.


A “monoclonal antibody” is an antibody produced by a single clone of B-lymphocytes or by a cell into which nucleic acid encoding the light and heavy chains of a single antibody have been transfected, or a progeny thereof. Monoclonal antibodies are produced by methods known to those of skill in the art, for instance by making hybrid antibody-forming cells from a fusion of myeloma cells with immune spleen cells. These fused cells and their progeny are termed “hybridomas.” In some examples monoclonal antibodies are isolated from a subject. Monoclonal antibodies can have conservative amino acid substitutions which have substantially no effect on antigen binding or other immunoglobulin functions. (See, for example, Harlow & Lane, Antibodies, A Laboratory Manual, 2nd ed. Cold Spring Harbor Publications, New York (2013).)


Antigen: A compound, composition, or substance that can stimulate the production of antibodies or a T cell response in an animal, including compositions that are injected or absorbed into an animal. An antigen reacts with the products of specific humoral or cellular immunity, including those induced by heterologous antigens, such as the disclosed HIV antigens. Examples of antigens include, but are not limited to, polypeptides, peptides, lipids, polysaccharides, combinations thereof (such as glycopeptides) and nucleic acids containing antigenic determinants, such as those recognized by an immune cell. In some examples, antigens include peptides derived from a pathogen of interest, such as HIV. An antigen can include one or more epitopes.


Anti-retroviral agent: An agent that specifically inhibits a retrovirus from replicating or infecting cells. Non-limiting examples of antiretroviral drugs include entry inhibitors (e.g., enfuvirtide), CCR5 receptor antagonists (e.g., aplaviroc, vicriviroc, maraviroc), reverse transcriptase inhibitors (e.g., lamivudine, zidovudine, abacavir, tenofovir, emtricitabine, efavirenz), protease inhibitors (e.g., lopivar, ritonavir, raltegravir, darunavir, atazanavir), maturation inhibitors (e.g., alpha interferon, bevirimat and vivecon).


Anti-retroviral therapy (ART): A therapeutic treatment for HIV infection involving administration of at least one anti-retroviral agents (e.g., one, two, three or four anti-retroviral agents) to an HIV infected individual during a course of treatment. Non-limiting examples of antiretroviral agents include entry inhibitors (e.g., enfuvirtide), CCR5 receptor antagonists (e.g., aplaviroc, vicriviroc, maraviroc), reverse transcriptase inhibitors (e.g., lamivudine, zidovudine, abacavir, tenofovir, emtricitabine, efavirenz), protease inhibitors (e.g., lopivar, ritonavir, raltegravir, darunavir, atazanavir), maturation inhibitors (e.g., alpha interferon, bevirimat and vivecon). One example of an ART regimen includes treatment with a combination of tenofovir, emtricitabine and efavirenz. In some examples, ART include Highly Active Anti-Retroviral Therapy (HAART).


Atomic coordinates or structure coordinates: Mathematical coordinates derived from mathematical equations related to the patterns obtained on diffraction of a monochromatic beam of X-rays by the atoms (scattering centers) such as an antigen, or an antigen in complex with an antibody. In some examples that antigen can be HIV-1 Env polypeptide (for example stabilized in a prefusion conformation by binding to a prefusion-specific antibody, or by introduction of stabilizing modifications) in a crystal. The diffraction data are used to calculate an electron density map of the repeating unit of the crystal. The electron density maps are used to establish the positions of the individual atoms within the unit cell of the crystal. In one example, the term “structure coordinates” refers to Cartesian coordinates derived from mathematical equations related to the patterns obtained on diffraction of a monochromatic beam of X-rays, such as by the atoms of a HIV-1 Env polypeptide in crystal form.


Those of ordinary skill in the art understand that a set of structure coordinates determined by X-ray crystallography is not without standard error. For the purpose of this disclosure, any set of structure coordinates that have a root mean square deviation of protein backbone atoms (N, Cα, C and O) of less than about 1.0 Angstroms when superimposed, such as about 0.75, or about 0.5, or about 0.25 Angstroms, using backbone atoms, shall (in the absence of an explicit statement to the contrary) be considered identical.


Cavity-filling amino acid substitution: An amino acid substitution that fills a cavity within the protein core of the HIV-1 Env ectodomain trimer. Cavities are essentially voids within a folded protein where amino acids or amino acid side chains are not present. In several embodiments, a cavity filling amino acid substitution is introduced to fill a cavity in the HIV-1 Env ectodomain trimer core present in the prefusion mature closed conformation of HIV-1 Env ectodomain trimer that collapses (e.g., has reduced volume) upon transition to the CD4-bound open conformation.


CD4: Cluster of differentiation factor 4 polypeptide; a T-cell surface protein that mediates interaction with the MHC class II molecule. CD4 also serves as the primary receptor site for HIV on T-cells during HIV infection. CD4 is known to bind to gp120 from HIV-1 Env. The sequence of the CD4 precursor has a hydrophobic signal peptide, an extracellular region of approximately 370 amino acids, a highly hydrophobic stretch with significant identity to the membrane-spanning domain of the class II MHC beta chain, and a highly charged intracellular sequence of 40 resides (Maddon, Cell 42:93, 1985). The amino acid sequence of human CD4 is deposited in GenBank as No. P01730.1. Several embodiments utilize soluble CD4 (sCD4), which includes the extracellular domain of CD4 (without the signal peptide), approximately CD4 amino acids 26-390 (e.g., SEQ ID NO: 2118). Soluble CD4 can be obtained commercially (e.g., from Mybiosource); methods of its production are well known in the art.


CD4-induced antibody: An antibody that binds to an epitope present on the CD4-bound open conformation of the HIV-1 Env ectodomain trimer, but not present on the mature closed conformation of the HIV-1 Env ectodomain trimer. An example of a CD4-induced antibody is 17b mAb.


Conditions sufficient to form an immune complex: Conditions which allow an antibody or antigen binding fragment thereof to bind to its cognate epitope to a detectably greater degree than, and/or to the substantial exclusion of, binding to substantially all other epitopes. Conditions sufficient to form an immune complex are dependent upon the format of the binding reaction and typically are those utilized in immunoassay protocols or those conditions encountered in vivo. See Harlow & Lane, Antibodies, A Laboratory Manual, 2nd ed. Cold Spring Harbor Publications, New York (2013) for a description of immunoassay formats and conditions. The conditions employed in the methods are “physiological conditions” which include reference to conditions (e.g., temperature, osmolarity, pH) that are typical inside a living mammal or a mammalian cell. While it is recognized that some organs are subject to extreme conditions, the intra-organismal and intracellular environment normally lies around pH 7 (e.g., from pH 6.0 to pH 8.0, more typically pH 6.5 to 7.5), contains water as the predominant solvent, and exists at a temperature above 0° C. and below 50° C. Osmolarity is within the range that is supportive of cell viability and proliferation.


Conservative variants: “Conservative” amino acid substitutions are those substitutions that do not substantially affect or decrease a function of a protein, such as the ability of the protein to induce an immune response when administered to a subject. The term conservative variation also includes the use of a substituted amino acid in place of an unsubstituted parent amino acid. Furthermore, one of ordinary skill will recognize that individual substitutions, deletions or additions which alter, add or delete a single amino acid or a small percentage of amino acids (for instance less than 5%, in some embodiments less than 1%) in an encoded sequence are conservative variations where the alterations result in the substitution of an amino acid with a chemically similar amino acid.


Conservative amino acid substitution tables providing functionally similar amino acids are well known to one of ordinary skill in the art. The following six groups are examples of amino acids that are considered to be conservative substitutions for one another:


1) Alanine (A), Serine (S), Threonine (T);


2) Aspartic acid (D), Glutamic acid (E);


3) Asparagine (N), Glutamine (Q);


4) Arginine (R), Lysine (K);


5) Isoleucine (I), Leucine (L), Methionine (M), Valine (V); and


6) Phenylalanine (F), Tyrosine (Y), Tryptophan (W).


Non-conservative substitutions are those that reduce an activity or function of the recombinant Env protein, such as the ability to induce an immune response when administered to a subject. For instance, if an amino acid residue is essential for a function of the protein, even an otherwise conservative substitution may disrupt that activity. Thus, a conservative substitution does not alter the basic function of a protein of interest.


Circular permutant: A modified recombinant protein in which the connections between different regions of a protein tertiary structure is modified, so that the relative order of different regions in the primary sequence is altered, but the placement of the regions in the tertiary structure is preserved. For example, with a 4-stranded antiparallel sheet, with strand A, B, C and D, which has the following N and C termini and connectivity:


Nterm-strand A-linker-strand B-linker-strand C-linker-strand D-Cterm,


circular permutants of the 4 strands, A, B, C and D by altering linker connection between strands can include:

    • Permutation with N- and C-termini altered:


Nterm-strand C-linker-strand D-linker-strand A-linker-strand B-Cterm

    • Permutation with N terminus preserved:


Nterm-strand A-linker-strand D-linker-strand C-linker-strand B-C term

    • Permutation with C terminus preserved:


Nterm-strand C-linker-strand B-linker-strand A-linker-strand D-C term.


Contacting: Placement in direct physical association; includes both in solid and liquid form, which can take place either in vivo or in vitro. Contacting includes contact between one molecule and another molecule, for example the amino acid on the surface of one polypeptide, such as a peptide, that contacts another polypeptide. Contacting can also include contacting a cell for example by placing a polypeptide in direct physical association with a cell.


Control: A reference standard. In some embodiments, the control is a negative control sample obtained from a healthy patient. In other embodiments, the control is a positive control sample obtained from a patient diagnosed with HIV infection. In still other embodiments, the control is a historical control or standard reference value or range of values (such as a previously tested control sample, such as a group of HIV patients with known prognosis or outcome, or group of samples that represent baseline or normal values).


A difference between a test sample and a control can be an increase or conversely a decrease. The difference can be a qualitative difference or a quantitative difference, for example a statistically significant difference. In some examples, a difference is an increase or decrease, relative to a control, of at least about 5%, such as at least about 10%, at least about 20%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 100%, at least about 150%, at least about 200%, at least about 250%, at least about 300%, at least about 350%, at least about 400%, at least about 500%, or greater than 500%.


Degenerate variant: In the context of the present disclosure, a “degenerate variant” refers to a polynucleotide encoding a polypeptide (such as a recombinant HIV-1 Env ectodomain or immunogenic fragment thereof) that includes a sequence that is degenerate as a result of the genetic code. There are 20 natural amino acids, most of which are specified by more than one codon. Therefore, all degenerate nucleotide sequences encoding a peptide are included as long as the amino acid sequence of the peptide encoded by the nucleotide sequence is unchanged.


Detecting: To identify the existence, presence, or fact of something. General methods of detecting are known to the skilled artisan and may be supplemented with the protocols and reagents disclosed herein. For example, included herein are methods of detecting the level of a protein in a sample or a subject.


Epitope: An antigenic determinant. These are particular chemical groups or peptide sequences on a molecule that are antigenic, such that they elicit a specific immune response, for example, an epitope is the region of an antigen to which B and/or T cells respond. An antibody can bind to a particular antigenic epitope, such as an epitope on HIV-1 Env.


Expression: Transcription or translation of a nucleic acid sequence. For example, a gene is expressed when its DNA is transcribed into an RNA or RNA fragment, which in some examples is processed to become mRNA. A gene may also be expressed when its mRNA is translated into an amino acid sequence, such as a protein or a protein fragment. In a particular example, a heterologous gene is expressed when it is transcribed into an RNA. In another example, a heterologous gene is expressed when its RNA is translated into an amino acid sequence. The term “expression” is used herein to denote either transcription or translation. Regulation of expression can include controls on transcription, translation, RNA transport and processing, degradation of intermediary molecules such as mRNA, or through activation, inactivation, compartmentalization or degradation of specific protein molecules after they are produced.


Expression control sequences: Nucleic acid sequences that regulate the expression of a heterologous nucleic acid sequence to which it is operatively linked. Expression control sequences are operatively linked to a nucleic acid sequence when the expression control sequences control and regulate the transcription and, as appropriate, translation of the nucleic acid sequence. Thus expression control sequences can include appropriate promoters, enhancers, transcription terminators, a start codon (ATG) in front of a protein-encoding gene, splicing signal for introns, maintenance of the correct reading frame of that gene to permit proper translation of mRNA, and stop codons. The term “control sequences” is intended to include, at a minimum, components whose presence can influence expression, and can also include additional components whose presence is advantageous, for example, leader sequences and fusion partner sequences. Expression control sequences can include a promoter.


A promoter is a minimal sequence sufficient to direct transcription. Also included are those promoter elements which are sufficient to render promoter-dependent gene expression controllable for cell-type specific, tissue-specific, or inducible by external signals or agents; such elements may be located in the 5′ or 3′ regions of the gene. Both constitutive and inducible promoters are included (see for example, Bitter et al., Methods in Enzymology 153:516-544, 1987). For example, when cloning in bacterial systems, inducible promoters such as pL of bacteriophage lambda, plac, ptrp, ptac (ptrp-lac hybrid promoter) and the like may be used. In one embodiment, when cloning in mammalian cell systems, promoters derived from the genome of mammalian cells (such as metallothionein promoter) or from mammalian viruses (such as the retrovirus long terminal repeat; the adenovirus late promoter; the vaccinia virus 7.5K promoter) can be used. Promoters produced by recombinant DNA or synthetic techniques may also be used to provide for transcription of the nucleic acid sequences.


A polynucleotide can be inserted into an expression vector that contains a promoter sequence which facilitates the efficient transcription of the inserted genetic sequence of the host. The expression vector typically contains an origin of replication, a promoter, as well as specific nucleic acid sequences that allow phenotypic selection of the transformed cells.


Expression vector: A vector comprising a recombinant polynucleotide comprising expression control sequences operatively linked to a nucleotide sequence to be expressed. An expression vector comprises sufficient cis-acting elements for expression; other elements for expression can be supplied by the host cell or in an in vitro expression system. Expression vectors include all those known in the art, such as cosmids, plasmids (e.g., naked or contained in liposomes) and viruses (e.g., lentiviruses, retroviruses, adenoviruses, and adeno-associated viruses) that incorporate the recombinant polynucleotide.


Heterologous: Originating from a different genetic source. A nucleic acid molecule that is heterologous to a cell originated from a genetic source other than the cell in which it is expressed. In one specific, non-limiting example, a heterologous nucleic acid molecule encoding a recombinant HIV-1 Env polypeptide is expressed in a cell, such as a mammalian cell. Methods for introducing a heterologous nucleic acid molecule in a cell or organism are well known in the art, for example transformation with a nucleic acid, including electroporation, lipofection, particle gun acceleration, and homologous recombination.


F105: A monoclonal antibody that specifically binds to a conformational epitope on HIV-1 Env that is not present on the prefusion mature closed conformation. The F105 antibody does not specifically bind to HIV-1 Env in its prefusion mature closed conformation. The person of ordinary skill in the art is familiar with monoclonal antibody F105 and with methods of producing this antibody (see, for example, Posner et al. J Acquired Immune Defic Syndr 6:7-14, 1993; which is incorporated by reference herein). The amino acid sequences of the heavy and light variable regions of the F105 antibody are known and have been deposited in the Protein Data Bank (PDB) as No. 1U6A_H (F105 VH) and 1U6A-L (F105 VL), each of which is incorporated by reference herein as present in the database on Jun. 20, 2014).


Ferritin: A protein that stores iron and releases it in a controlled fashion. The protein is produced by almost all living organisms. Ferritin polypeptides assemble into a globular protein complex of 24 protein subunits, each of the 24 subunits includes a single ferritin polypeptide. In some examples, ferritin is used to form a nanoparticle presenting antigens on its surface, for example, an HIV antigen.


Foldon domain: An amino acid sequence that naturally forms a trimeric structure. In some examples, a Foldon domain can be included in the amino acid sequence of a disclosed recombinant protein so that the antigen will form a trimer. In one example, a Foldon domain is the T4 Foldon domain including the amino acid sequence set forth as (GYIPEAPRDGQAYVRKDGEWVLLSTF (SEQ ID NO: 578). Several embodiments include a Foldon domain that can be cleaved from a purified protein, for example by incorporation of a thrombin cleave site adjacent to the Foldon domain that can be used for cleavage purposes.


Glycosylation site: An amino acid sequence on the surface of a polypeptide, such as a protein, which accommodates the attachment of a glycan. An N-linked glycosylation site is triplet sequence of NX(S/T) in which N is asparagine, X is any residues except proline, and (S/T) is a serine or threonine residue. A glycan is a polysaccharide or oligosaccharide. Glycan may also be used to refer to the carbohydrate portion of a glycoconjugate, such as a glycoprotein, glycolipid, or a proteoglycan.


Homologous proteins: Proteins that have a similar structure and function, for example, proteins from two or more species or viral strains that have similar structure and function in the two or more species or viral strains. For example a HIV-1 Env protein from a Clade A virus is a homologous protein to a HIV-1 Env protein from Clade B virus. Homologous proteins share similar protein folding characteristics and can be considered structural homologs.


Homologous proteins typically share a high degree of sequence conservation, such as at least 80%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, or at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence conservation, and a high degree of sequence identity, such as at least 80%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, or at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity.


Host cells: Cells in which a vector can be propagated and its DNA expressed. The cell may be prokaryotic or eukaryotic. The term also includes any progeny of the subject host cell. It is understood that all progeny may not be identical to the parental cell since there may be mutations that occur during replication. However, such progeny are included when the term “host cell” is used.


Human Immunodeficiency Virus (HIV): A retrovirus that causes immunosuppression in humans (HIV disease), and leads to a disease complex known as the acquired immunodeficiency syndrome (AIDS). “HIV disease” refers to a well-recognized constellation of signs and symptoms (including the development of opportunistic infections) in persons who are infected by an HIV virus, as determined by antibody or western blot studies. Laboratory findings associated with this disease include a progressive decline in T cells. HIV includes HIV type 1 (HIV-1) and HIV type 2 (HIV-2). Related viruses that are used as animal models include simian immunodeficiency virus (SIV), and feline immunodeficiency virus (FIV). Treatment of HIV-1 with HAART has been effective in reducing the viral burden and ameliorating the effects of HIV-1 infection in infected individuals.


HIV-1 broadly neutralizing antibody: An antibody that reduces the infectious titer of HIV-1 by binding to and inhibiting the function of related HIV-1 antigens, such as antigens that share at least 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity with antigenic surface of the antigen. In some embodiments, broadly neutralizing antibodies to HIV are distinct from other antibodies to HIV in that they neutralize a high percentage (such as at least 50% or at least 80%) of the many types of HIV in circulation. Non-limiting examples of HIV-1 broadly neutralizing antibodies include PGT122, VRC01, and 35O22.


HIV envelope protein (Env): The HIV envelope protein is initially synthesized as a precursor protein of 845-870 amino acids in size, designated gp160. Individual gp160 polypeptides form a homotrimer and undergo glycosylation within the Golgi apparatus as well as processing to remove the signal peptide, and cleavage by a cellular protease between approximately positions 511/512 to generate separate gp120 and gp41 polypeptide chains, which remain associated as gp120-gp41 protomers within the homotrimer. The ectodomain (that is, the extracellular portion) of the HIV-1 Env trimer undergoes several structural rearrangements from a prefusion mature (cleaved) closed conformation that evades antibody recognition, through intermediate conformations that bind to receptors CD4 and co-receptor (either CCR5 or CXCR4), to a postfusion conformation. The HIV-1 Env ectodomain includes the gp120 protein (approximately HIV-1 Env positions 31-511) and the gp41 ectodomain (approximately HIV-1 Env positions 512-644). An HIV-1 Env ectodomain trimer includes a protein complex of three HIV-1 Env ectodomains.


Mature gp120 includes approximated HIV-1 Env residues 31-511, contains most of the external, surface-exposed, domains of the HIV-1 Env trimer, and it is gp120 which binds both to cellular CD4 receptors and to cellular chemokine receptors (such as CCR5). A mature gp120 polypeptide is an extracellular polypeptide that interacts with the gp41 ectodomain to form an HIV-1 Env protomer that trimerizes to form the HIV-1 Env trimer.


The mature gp120 wild-type polypeptide is heavily N-glycosylated, giving rise to an apparent molecular weight of 120 kD. Native gp120 includes five conserved regions (C1-C5) and five regions of high variability (V1-V5). See FIG. 11 for an illustration of gp120 primary and secondary structures.


Variable region 1 and Variable Region 2 (V1/V2 domain) of gp120 are comprised of ˜50-90 residues which contain two of the most variable portions of HIV-1 (the V1 domain and the V2 loop), and one in ten residues of the V1/V2 domain are N-glycosylated. Despite the diversity and glycosylation of the V1/V2 domain, a number of broadly neutralizing human antibodies have been identified that target this region, including PG9 and PGT122. In some examples the V1/V2 domain includes gp120 positions 126-196. Variable region 3 (V3) of gp120 includes approximately 35-45 amino acids. In some examples the V1/V2 domain includes gp120 positions 296-331. Mature gp41 includes approximately HIV-1 Env residues 512-860, and includes cytosolic-, transmembrane- and ecto-domains. The gp41 ectodomain (including approximately HIV-1 Env residues 512-644) can interact with gp120 to form an HIV-1 Env protomer that trimerizes to form the HIV-1 Env trimer. See FIG. 3 for an illustration of the primary and secondary structure of a gp41 ectodomain.


The numbering used in the disclosed HIV-1 Env proteins and fragments thereof is relative to the HXB2 numbering scheme as set forth in Numbering Positions in HIVRelative to HXB2CG Bette Korber et al., Human Retroviruses and AIDS 1998: A Compilation and Analysis of Nucleic Acid and Amino Acid Sequences. Korber et al., Eds. Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, N. Mex., which is incorporated by reference herein in its entirety.


In one example, an HIV-1 Env protein is from the BG505 strain of HIV, which is a Clade A HIV-1 virus isolated from a six-week old HIV-1 infected infant. The amino acid sequence of BG505 Env protein is known (see, e.g., GenBank accession no. ABA61516, incorporated by reference herein as present in the database on Jun. 20, 2014), and set forth as SEQ ID NO: 2.


HIV-1 Env ectodomain trimer prefusion mature closed conformation: A structural conformation adopted by the ectodomain of the HIV-1 Env ectodomain trimer after cellular processing to a mature prefusion state with distinct gp120 and gp41 polypeptide chains, and before specific binding to the CD4 receptor. In the prefusion mature closed conformation, the HIV-1 Env ectodomain trimer includes a V1V2 domain “cap” at its membrane distal apex, with the V1V2 domain of each Env protomer in the trimer coming together at the membrane distal apex. At the membrane proximal aspect, the HIV-1 Env ectodomain trimer includes distinct α6 and α7 helices. CD4 binding to the Env trimer causes changes in the conformation of the HIV-1 Env ectodomain trimer, including disruption of the V1V1 domain cap, which “opens” as each V1V2 domain moves outward from the longitudinal axis of the Env trimer, and formation of the HR1 helix, which includes both the α6 and α7 helices (which are no longer distinct, see FIG. 3D). These conformational changes bring the N-terminus of the fusion peptide within close proximity of the target cell membrane, and expose “CD4-induced” epitopes (such as the 17b epitope) that are present in the CD4-bound open conformation, but not the mature closed conformation, of the HIV-1 Env ectodomain trimer. The three-dimensional structure of an exemplary HIV-1 Env ectodomain trimer in the prefusion mature closed conformation is disclosed herein (see Example 1).


HIV-1 Env ectodomain trimer stabilized in a prefusion mature closed conformation: A HIV-1 Env ectodomain trimer having a prefusion mature closed conformation and including one or more amino acid substitutions, deletions, or insertions compared to a native HIV-1 Env sequence that provide for increased retention of the prefusion mature closed conformation upon CD4 binding compared to a corresponding native HIV-1 Env sequence. In some embodiments, the HIV-1 Env ectodomain trimer can include one or more cysteine substitutions that allow formation of a non-natural disulfide bond that stabilizes the HIV-1 Env ectodomain trimer in its prefusion mature closed conformation.


A HIV-1 Env ectodomain trimer stabilized in the prefusion mature closed conformation has at least 90% (such as at least 95% or at least 99%) reduced transition to the CD4-bound open conformation upon CD4 binding compared to a corresponding native HIV-1 Env sequence. The “stabilization” of the prefusion mature closed conformation by the one or more amino acid substitutions, deletions, or insertions can be, for example, energetic stabilization (for example, reducing the energy of the prefusion mature closed conformation relative to the CD4-bound open conformation) and/or kinetic stabilization (for example, reducing the rate of transition from the prefusion mature closed conformation to the prefusion mature closed conformation). Additionally, stabilization of the HIV-1 Env ectodomain trimer in the prefusion mature closed conformation can include an increase in resistance to denaturation compared to a corresponding native HIV-1 Env sequence.


Methods of determining if a HIV-1 Env ectodomain trimer is in the prefusion mature closed conformation are provided herein, and include (but are not limited to) negative stain electron microscopy and antibody binding assays using a prefusion mature closed conformation specific antibody, such as VRC26 or PGT145. Methods of determining if a HIV-1 Env ectodomain trimer is in the CD4-bound open conformation are also provided herein, and include (but are not limited to) negative stain electron microscopy and antibody binding assays using a CD4-bound open conformation specific antibody, such as 17b, which binds to a CD4-induced epitope. Transition from the prefusion mature closed conformation upon CD4 binding can be assayed, for example, by incubating a HIV-1 Env ectodomain trimer of interest that is in the prefusion mature closed conformation with a molar excess of CD4, and determining if the HIV-1 Env ectodomain trimer retains the prefusion mature closed conformation (or transitions to the CD4-bound open conformation) by negative stain electron microscopy analysis, or antigenic analysis. HIV-1 gp140: A recombinant HIV Env polypeptide including gp120 and the gp41 ectodomain, but not the gp41 transmembrane or cytosolic domains. HIV-1 gp140 polypeptides can trimerize to form a soluble HIV-1 Env ectodomain trimer.


HIV-1 gp145: A recombinant HIV Env polypeptide including gp120, the gp41 ectodomain, and the gp41 transmembrane domain. HIV-1 gp145 polypeptides can trimerize to form membrane bound HIV-1 Env ectodomain trimers.


HXB2 numbering system: A reference numbering system for HIV protein and nucleic acid sequences, using the HIV-1 HXB2 strain sequences as a reference for all other HIV-1 strain sequences. The person of ordinary skill in the art is familiar with the HXB2 numbering system, and this system is set forth in “Numbering Positions in HIV Relative to HXB2CG,” Bette Korber et al., Human Retroviruses and AIDS 1998: A Compilation and Analysis of Nucleic Acid and Amino Acid Sequences. Korber B, Kuiken C L, Foley B, Hahn B, McCutchan F, Mellors J W, and Sodroski J, Eds. Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, N. Mex., which is incorporated by reference herein in its entirety. Unless context indicates otherwise, the numbering used in HIV-1 polypeptides disclosed herein is relative to the HXB2 numbering scheme. For reference, the amino acid sequence of HIV-1 Env of HXB2 is set forth as SEQ ID NO: 1 (GENBANK® Accession No. K03455, incorporated by reference herein as present in the database on Jun. 20, 2014).


Immune response: A response of a cell of the immune system, such as a B cell, T cell, or monocyte, to a stimulus. In one embodiment, the response is specific for a particular antigen (an “antigen-specific response”). In one embodiment, an immune response is a T cell response, such as a CD4+ response or a CD8+ response. In another embodiment, the response is a B cell response, and results in the production of specific antibodies. “Priming an immune response” refers to pre-treatment of a subject with an adjuvant to increase the desired immune response to a later administered immunogenic agent. “Enhancing an immune response” refers to co-administration of an adjuvant and an immunogenic agent, wherein the adjuvant increases the desired immune response to the immunogenic agent compared to administration of the immunogenic agent to the subject in the absence of the adjuvant.


Immunogen: A protein or a portion thereof that is capable of inducing an immune response in a mammal, such as a mammal infected or at risk of infection with a pathogen. Administration of an immunogen can lead to protective immunity and/or proactive immunity against a pathogen of interest. In some examples, an immunogen comprises a recombinant HIV-1 Env ectodomain trimer as disclosed herein.


Immunogenic composition: A composition comprising an immunogenic polypeptide, or a nucleic acid molecule or vector encoding an immunogenic polypeptide that induces a measurable CTL response against the immunogenic polypeptide, or induces a measurable B cell response (such as production of antibodies) against the immunogenic polypeptide. In one example, an “immunogenic composition” is a composition that includes a disclosed recombinant HIV-1 Env ectodomain trimer or immunogenic fragment thereof, that induces a measurable CTL response against an HIV-1 virus, or induces a measurable B cell response (such as production of antibodies) against a HIV-1. It further refers to isolated nucleic acids encoding an antigen, such as a nucleic acid that can be used to express the antigen (and thus be used to elicit an immune response against this peptide).


For in vitro use, an immunogenic composition may comprise or consist of the isolated protein or nucleic acid molecule encoding the protein. For in vivo use, the immunogenic composition will typically include the protein or nucleic acid molecule in a pharmaceutically acceptable carrier and may also include other agents, such as an adjuvant. Any particular protein, such as a disclosed recombinant HIV-1 Env ectodomain trimer or a nucleic acid encoding the protein, can be readily tested for its ability to induce a CTL or B cell response by art-recognized assays. Immunogenic compositions can include adjuvants, which are well known to one of skill in the art.


Immunogenic polypeptide: A polypeptide which comprises an allele-specific motif, an epitope or other sequence such that the polypeptide will bind an MHC molecule and induce an immune response, such as a cytotoxic T lymphocyte (“CTL”) response, and/or a B cell response (for example, antibody production), and/or a T-helper lymphocyte response against the antigen from which the immunogenic polypeptide is derived.


Isolated: An “isolated” biological component (such as a protein, for example a disclosed immunogen or nucleic acid encoding such an antigen) has been substantially separated or purified away from other biological components, such as other biological components in which the component naturally occurs, such as other chromosomal and extrachromosomal DNA, RNA, and proteins. Proteins, peptides and nucleic acids that have been “isolated” include proteins purified by standard purification methods. The term also embraces proteins or peptides prepared by recombinant expression in a host cell as well as chemically synthesized proteins, peptides and nucleic acid molecules. Isolated does not require absolute purity, and can include protein, peptide, or nucleic acid molecules that are at least 50% isolated, such as at least 75%, 80%, 90%, 95%, 98%, 99%, or even 99.9% isolated. The HIV-1 Env proteins herein that are stabilized in a prefusion mature closed conformation can be isolated from HIV-1 Env proteins in a prefusion CD4 bound conformation, for example, can be at least 80% isolated, at least 90%, 95%, 98%, 99%, or even 99.9% isolated from HIV-1 Env proteins in a prefusion CD4 bound conformation.


KD: The dissociation constant for a given interaction, such as a polypeptide ligand interaction or an antibody antigen interaction. For example, for the bimolecular interaction of an antibody or antigen binding fragment and an immunogen (such as HIV-1 Env polypeptide) it is the concentration of the individual components of the bimolecular interaction divided by the concentration of the complex.


Linker: A bi-functional molecule that can be used to link two molecules into one contiguous molecule, for example, to link a carrier molecule to a immunogenic polypeptide. Non-limiting examples of peptide linkers include glycine-serine linkers, such as a (GGGGS)x linker or a 10 amino acid glycine-serine linker. Unless context indicates otherwise, reference to “linking” a first polypeptide and a second polypeptide (or to two polypeptides “linked” together) refers to covalent linkage by peptide bond, or (if a peptide linker is involved) covalent linkage of the first and second polypeptides to the N and C termini of a peptide linker. Thus, reference to a gp120 polypeptide “linked” to a gp41 ectodomain by a peptide linker indicates that the gp120 polypeptide and the gp41 ectodomain are linked to opposite ends of the peptide linker by peptide bonds. Typically, such linkage is accomplished using molecular biology techniques to genetically manipulate DNA encoding the first polypeptide linked to the second polypeptide by the peptide linker.


The terms “conjugating,” “joining,” “bonding,” can refer to making two molecules into one contiguous molecule; for example, joining two polypeptides into one contiguous polypeptide, or covalently attaching a carrier molecule or other molecule to an immunogenic polypeptide, such as an recombinant HIV-1 Env ectodomain as disclosed herein. The conjugate can be either by chemical or recombinant means. “Chemical means” refers to a reaction, for example, between the immunogenic polypeptide moiety and the carrier molecule such that there is a covalent bond formed between the two molecules to form one molecule.


Neutralizing antibody: An antibody which reduces the infectious titer of an infectious agent by binding to a specific antigen on the infectious agent. In some examples the infectious agent is a virus. In some examples, an antibody that is specific for HIV-1 Env neutralizes the infectious titer of HIV. A “broadly neutralizing antibody” is an antibody that binds to and inhibits the function of related antigens, such as antigens that share at least 85%, 90%, 95%, 96%, 97%, 98% or 99% identity antigenic surface of antigen. With regard to an antigen from a pathogen, such as a virus, the antibody can bind to and inhibit the function of an antigen from more than one class and/or subclass of the pathogen. For example, with regard to a human immunodeficiency virus, the antibody can bind to and inhibit the function of an antigen, such as HIV-1 Env from more than one clade. In one embodiment, broadly neutralizing antibodies to HIV are distinct from other antibodies to HIV in that they neutralize a high percentage of the many types of HIV in circulation.


Native protein, sequence, or di-sulfide bond: An polypeptide, sequence or di-sulfide bond that has not been modified, for example by selective mutation. For example, selective mutation to focus the antigenicity of the antigen to a target epitope, or to introduce a di-sulfide bond into a protein that does not occur in the native protein. Native protein or native sequence are also referred to as wild-type protein or wild-type sequence. A non-native di-sulfide bond is a disulfide bond that is not present in a native protein, for example a di-sulfide bond that forms in a protein due to introduction of one or more cysteine residues into the protein by genetic engineering.


Nucleic acid: A polymer composed of nucleotide units (ribonucleotides, deoxyribonucleotides, related naturally occurring structural variants, and synthetic non-naturally occurring analogs thereof) linked via phosphodiester bonds, related naturally occurring structural variants, and synthetic non-naturally occurring analogs thereof. It will be understood that when a nucleotide sequence is represented by a DNA sequence (i.e., A, T, G, C), this also includes an RNA sequence (i.e., A, U, G, C) in which “U” replaces “T.”


“Nucleotide” includes, but is not limited to, a monomer that includes a base linked to a sugar, such as a pyrimidine, purine or synthetic analogs thereof, or a base linked to an amino acid, as in a peptide nucleic acid (PNA). A nucleotide is one monomer in a polynucleotide. A nucleotide sequence refers to the sequence of bases in a polynucleotide.


Conventional notation is used herein to describe nucleotide sequences: the left-hand end of a single-stranded nucleotide sequence is the 5′-end; the left-hand direction of a double-stranded nucleotide sequence is referred to as the 5′-direction. The direction of 5′ to 3′ addition of nucleotides to nascent RNA transcripts is referred to as the transcription direction. The DNA strand having the same sequence as an mRNA is referred to as the “coding strand;” sequences on the DNA strand having the same sequence as an mRNA transcribed from that DNA and which are located 5′ to the 5′-end of the RNA transcript are referred to as “upstream sequences;” sequences on the DNA strand having the same sequence as the RNA and which are 3′ to the 3′ end of the coding RNA transcript are referred to as “downstream sequences.”


“cDNA” refers to a DNA that is complementary or identical to an mRNA, in either single stranded or double stranded form.


“Encoding” refers to the inherent property of specific sequences of nucleotides in a polynucleotide, such as a gene, a cDNA, or an mRNA, to serve as templates for synthesis of other polymers and macromolecules in biological processes having either a defined sequence of nucleotides (i.e., rRNA, tRNA and mRNA) or a defined sequence of amino acids and the biological properties resulting therefrom. Thus, a gene encodes a protein if transcription and translation of mRNA produced by that gene produces the protein in a cell or other biological system. Both the coding strand, the nucleotide sequence of which is identical to the mRNA sequence and is usually provided in sequence listings, and non-coding strand, used as the template for transcription, of a gene or cDNA can be referred to as encoding the protein or other product of that gene or cDNA. Unless otherwise specified, a “nucleotide sequence encoding an amino acid sequence” includes all nucleotide sequences that are degenerate versions of each other and that encode the same amino acid sequence. Nucleotide sequences that encode proteins and RNA may include introns.


Operably linked: A first nucleic acid sequence is operably linked with a second nucleic acid sequence when the first nucleic acid sequence is placed in a functional relationship with the second nucleic acid sequence. For instance, a promoter, such as the CMV promoter, is operably linked to a coding sequence if the promoter affects the transcription or expression of the coding sequence. Generally, operably linked DNA sequences are contiguous and, where necessary to join two protein-coding regions, in the same reading frame.


PGT121, PGT122, and PGT123: A family of neutralizing monoclonal antibodies that specifically bind to the V1/V2 and V3 regions of HIV-1 Env and can inhibit HIV-1 infection of target cells. The person of ordinary skill in the art is familiar with the PGT121, PGT122, and PGT123 mAbs and with methods of producing them (see, for example, Walker et al., Nature, 477:466-470, 2011, and Int. Pub. No. WO 2012/030904, each of which is incorporated by reference herein). The amino acid sequences of the heavy and light variable regions of the PGT121, PGT122, and PGT123 antibodies are known and have been deposited in GenBank as Nos. AEN14390.1 (PGT121 VH), AEN14407.1 (PGT121 VL), JN201895.1 (PGT122 VH), JN201912.1 (PGT122 VL), JN201896.1 (PGT123 VH), and JN201913.1 (PGT123 VL), each of which is incorporated by reference herein as present in the database on Jun. 20, 2014)


PGT141, PGT142, PGT143, and PGT145: A family of broadly neutralizing monoclonal antibodies that specifically bind to the V1/V2 domain of the HIV-1 Env ectodomain trimer in its prefusion mature closed conformation, and which can inhibit HIV-1 infection of target cells. The person of ordinary skill in the art is familiar with the PGT141, PGT142, PGT143, and PGT145 mAbs and with methods of producing them (see, for example, Walker et al., Nature, 477:466-470, 2011, and Int. Pub. No. WO2012/030904, each of which is incorporated by reference herein). The amino acid sequences of the heavy and light variable regions of the PGT141, PGT142, PGT143, PGT144, and PGT145 mAbs are known and have been deposited in GenBank as Nos. JN201906.1 (PGT141 VH), JN201923.1 (PGT141 VL), JN201907.1 (PGT142 VH), JN201924.1 (PGT142 VL), JN201908.1 (PGT143 VH), JN201925.1 (PGT143 VL), JN201909.1 (PGT144 VH), JN201926.1 (PGT144 VL), JN201910.1 (PGT145 VH), and JN201927.1 (PGT145 VL), each of which is incorporated by reference herein as present in the database on Jun. 20, 2014).


PGT151: A broadly neutralizing monoclonal antibody that specifically bind to the gp120/gp41 interface of HIV-1 Env in its prefusion mature (cleaved) conformation, and which can inhibit HIV-1 infection of target cells. The person of ordinary skill in the art is familiar with the PGT151 antibody and with methods of producing this antibody (see, for example, Blattner et al., Immunity, 40, 669-680, 2014, and Falkowska et al., Immunity, 40, 657-668, 2014, each of which is incorporated by reference herein). The amino acid sequences of the heavy and light variable regions of the PGT151 mAb are known and have been deposited in GenBank as Nos. KJ700282.1 (PGT151 VH) and KJ700290.1 (PGT151 VL), each of which is incorporated by reference herein as present in the database on Jun. 20, 2014).


Pharmaceutically acceptable carriers: The pharmaceutically acceptable carriers of use are conventional. Remington's Pharmaceutical Sciences, by E. W. Martin, Mack Publishing Co., Easton, Pa., 19th Edition, 1995, describes compositions and formulations suitable for pharmaceutical delivery of the disclosed immunogens.


In general, the nature of the carrier will depend on the particular mode of administration being employed. For instance, parenteral formulations usually comprise injectable fluids that include pharmaceutically and physiologically acceptable fluids such as water, physiological saline, balanced salt solutions, aqueous dextrose, glycerol or the like as a vehicle. For solid compositions (e.g., powder, pill, tablet, or capsule forms), conventional non-toxic solid carriers can include, for example, pharmaceutical grades of mannitol, lactose, starch, or magnesium stearate. In addition to biologically neutral carriers, pharmaceutical compositions to be administered can contain minor amounts of non-toxic auxiliary substances, such as wetting or emulsifying agents, preservatives, and pH buffering agents and the like, for example sodium acetate or sorbitan monolaurate. In particular embodiments, suitable for administration to a subject the carrier may be sterile, and/or suspended or otherwise contained in a unit dosage form containing one or more measured doses of the composition suitable to induce the desired anti-HIV-1 immune response. It may also be accompanied by medications for its use for treatment purposes. The unit dosage form may be, for example, in a sealed vial that contains sterile contents or a syringe for injection into a subject, or lyophilized for subsequent solubilization and administration or in a solid or controlled release dosage.


Polypeptide: Any chain of amino acids, regardless of length or post-translational modification (e.g., glycosylation or phosphorylation). “Polypeptide” applies to amino acid polymers including naturally occurring amino acid polymers and non-naturally occurring amino acid polymer as well as in which one or more amino acid residue is a non-natural amino acid, for example an artificial chemical mimetic of a corresponding naturally occurring amino acid. A “residue” refers to an amino acid or amino acid mimetic incorporated in a polypeptide by an amide bond or amide bond mimetic. A polypeptide has an amino terminal (N-terminal) end and a carboxy terminal (C-terminal) end. “Polypeptide” is used interchangeably with peptide or protein, and is used herein to refer to a polymer of amino acid residues. A protein can include multiple polypeptide chains; for example, mature HIV-1 Env includes gp120 and gp41 polypeptide chains. Additionally, a single contiguous polypeptide chain of amino acid residues can include multiple polypeptides. For example, a single chain HIV-1 Env can include a gp120 polypeptide linked to a gp41 polypeptide by a peptide linker.


In many instances, one or more polypeptides can fold into a specific three-dimensional structure including surface-exposed amino acid residues and non-surface-exposed amino acid residues. In some instances a protein can include multiple polypeptides that fold together into a functional unit. For example, the HIV-1 Env protein is composed of three gp120-gp41 protomers that trimerize in to a multimeric protein. “Surface-exposed amino acid residues” are those amino acids that have some degree of exposure on the surface of the protein, for example such that they can contact the solvent when the protein is in solution. In contrast, non-surface-exposed amino acids are those amino acid residues that are not exposed on the surface of the protein, such that they do not contact solution when the protein is in solution. In some examples, the non-surface-exposed amino acid residues are part of the protein core.


A “protein core” is the interior of a folded protein, which is substantially free of solvent exposure, such as solvent in the form of water molecules in solution. Typically, the protein core is predominately composed of hydrophobic or apolar amino acids. In some examples, a protein core may contain charged amino acids, for example aspartic acid, glutamic acid, arginine, and/or lysine. The inclusion of uncompensated charged amino acids (a compensated charged amino can be in the form of a salt bridge) in the protein core can lead to a destabilized protein. That is, a protein with a lower Tm then a similar protein without an uncompensated charged amino acid in the protein core. In other examples, a protein core may have a cavity within the protein core. Cavities are essentially voids within a folded protein where amino acids or amino acid side chains are not present. Such cavities can also destabilize a protein relative to a similar protein without a cavity. Thus, when creating a stabilized form of a protein, it may be advantageous to substitute amino acid residues within the core in order to fill cavities present in the wild-type protein.


Polypeptide modifications: Polypeptides and peptides, such as the recombinant HIV-1 Env proteins disclosed herein can be modified by a variety of chemical techniques to produce derivatives having essentially the same activity as the unmodified peptides, and optionally having other desirable properties. For example, carboxylic acid groups of the protein, whether carboxyl-terminal or side chain, may be provided in the form of a salt of a pharmaceutically-acceptable cation or esterified to form a C1-C16 ester, or converted to an amide of formula NR1R2 wherein R1 and R2 are each independently H or C1-C16 alkyl, or combined to form a heterocyclic ring, such as a 5- or 6-membered ring. Amino groups of the peptide, whether amino-terminal or side chain, may be in the form of a pharmaceutically-acceptable acid addition salt, such as the HCl, HBr, acetic, benzoic, toluene sulfonic, maleic, tartaric and other organic salts, or may be modified to C1-C16 alkyl or dialkyl amino or further converted to an amide. Hydroxyl groups of the peptide side chains can be converted to C1-C16 alkoxy or to a C1-C16 ester using well-recognized techniques. Phenyl and phenolic rings of the peptide side chains can be substituted with one or more halogen atoms, such as F, Cl, Br or I, or with C1-C16 alkyl, C1-C16 alkoxy, carboxylic acids and esters thereof, or amides of such carboxylic acids. Methylene groups of the peptide side chains can be extended to homologous C2-C4 alkylenes. Thiols can be protected with any one of a number of well-recognized protecting groups, such as acetamide groups. Those skilled in the art will also recognize methods for introducing cyclic structures into the peptides of this disclosure to select and provide conformational constraints to the structure that result in enhanced stability. For example, a C- or N-terminal cysteine can be added to the peptide, so that when oxidized the peptide will contain a disulfide bond, generating a cyclic peptide. Other peptide cyclizing methods include the formation of thioethers and carboxyl- and amino-terminal amides and esters.


Prime-boost vaccination: An immunotherapy including administration of a first immunogenic composition (the primer vaccine) followed by administration of a second immunogenic composition (the booster vaccine) to a subject to induce an immune response. The primer vaccine and/or the booster vaccine include a vector (such as a viral vector, RNA, or DNA vector) expressing the antigen to which the immune response is directed. The booster vaccine is administered to the subject after the primer vaccine; the skilled artisan will understand a suitable time interval between administration of the primer vaccine and the booster vaccine, and examples of such timeframes are disclosed herein. In some embodiments, the primer vaccine, the booster vaccine, or both primer vaccine and the booster vaccine additionally include an adjuvant. In one non-limiting example, the primer vaccine is a DNA-based vaccine (or other vaccine based on gene delivery), and the booster vaccine is a protein subunit or protein nanoparticle based vaccine.


Protein nanoparticle: A multi-subunit, protein-based polyhedron shaped structure. The subunits are each composed of proteins or polypeptides (for example a glycosylated polypeptide), and, optionally of single or multiple features of the following: nucleic acids, prosthetic groups, organic and inorganic compounds. Non-limiting examples of protein nanoparticles include ferritin nanoparticles (see, e.g., Zhang, Y. Int. J. Mol. Sci., 12:5406-5421, 2011, incorporated by reference herein), encapsulin nanoparticles (see, e.g., Sutter et al., Nature Struct. and Mol. Biol., 15:939-947, 2008, incorporated by reference herein), Sulfur Oxygenase Reductase (SOR) nanoparticles (see, e.g., Urich et al., Science, 311:996-1000, 2006, incorporated by reference herein), lumazine synthase nanoparticles (see, e.g., Zhang et al., J. Mol. Biol., 306: 1099-1114, 2001) or pyruvate dehydrogenase nanoparticles (see, e.g., Izard et al., PNAS 96: 1240-1245, 1999, incorporated by reference herein). Ferritin, encapsulin, SOR, lumazine synthase, and pyruvate dehydrogenase are monomeric proteins that self-assemble into a globular protein complexes that in some cases consists of 24, 60, 24, 60, and 60 protein subunits, respectively. In some examples, ferritin, encapsulin, SOR, lumazine synthase, or pyruvate dehydrogenase monomers are linked to a recombinant HIV-1 Env ectodomain and self-assemble into a protein nanoparticle presenting the recombinant HIV-1 Env ectodomain on its surface, which can be administered to a subject to stimulate an immune response to the antigen.


Recombinant: A recombinant nucleic acid is one that has a sequence that is not naturally occurring or has a sequence that is made by an artificial combination of two otherwise separated segments of sequence. This artificial combination can be accomplished, for example, the artificial manipulation of isolated segments of nucleic acids, for example using genetic engineering techniques. A recombinant protein is one that has a sequence that is not naturally occurring or has a sequence that is made by an artificial combination of two otherwise separated segments of sequence. In several embodiments, a recombinant protein is encoded by a heterologous (for example, recombinant) nucleic acid that has been introduced into a host cell, such as a bacterial or eukaryotic cell. The nucleic acid can be introduced, for example, on an expression vector having signals capable of expressing the protein encoded by the introduced nucleic acid or the nucleic acid can be integrated into the host cell chromosome.


Root mean square deviation (RMSD): The square root of the arithmetic mean of the squares of the deviations from the mean. In several embodiments, RMSD is used as a way of expressing deviation or variation from the structural coordinates of a reference three dimensional structure. This number is typically calculated after optimal superposition of two structures, as the square root of the mean square distances between equivalent C atoms.


Sample (or biological sample): A biological specimen containing genomic DNA, RNA (including mRNA), protein, or combinations thereof, obtained from a subject. Examples include, but are not limited to, peripheral blood, tissue, cells, urine, saliva, tissue biopsy, fine needle aspirate, surgical specimen, and autopsy material.


Sequence identity: The similarity between amino acid sequences is expressed in terms of the similarity between the sequences, otherwise referred to as sequence identity. Sequence identity is frequently measured in terms of percentage identity (or similarity or homology); the higher the percentage, the more similar the two sequences are. Homologs, orthologs, or variants of a polypeptide will possess a relatively high degree of sequence identity when aligned using standard methods.


Methods of alignment of sequences for comparison are well known in the art. Various programs and alignment algorithms are described in: Smith & Waterman, Adv. Appl. Math. 2:482, 1981; Needleman & Wunsch, J. Mol. Biol. 48:443, 1970; Pearson & Lipman, Proc. Natl. Acad. Sci. USA 85:2444, 1988; Higgins & Sharp, Gene, 73:237-44, 1988; Higgins & Sharp, CABIOS 5:151-3, 1989; Corpet et al., Nuc. Acids Res. 16:10881-90, 1988; Huang et al. Computer Appls. in the Biosciences 8, 155-65, 1992; and Pearson et al., Meth. Mol. Bio. 24:307-31, 1994. Altschul et al., J. Mol. Biol. 215:403-10, 1990, presents a detailed consideration of sequence alignment methods and homology calculations.


Once aligned, the number of matches is determined by counting the number of positions where an identical nucleotide or amino acid residue is present in both sequences. The percent sequence identity is determined by dividing the number of matches either by the length of the sequence set forth in the identified sequence, or by an articulated length (such as 100 consecutive nucleotides or amino acid residues from a sequence set forth in an identified sequence), followed by multiplying the resulting value by 100. For example, a peptide sequence that has 1166 matches when aligned with a test sequence having 1554 amino acids is 75.0 percent identical to the test sequence (1166÷1554*100=75.0). The percent sequence identity value is rounded to the nearest tenth. For example, 75.11, 75.12, 75.13, and 75.14 are rounded down to 75.1, while 75.15, 75.16, 75.17, 75.18, and 75.19 are rounded up to 75.2. The length value will always be an integer.


Homologs and variants of a polypeptide are typically characterized by possession of at least about 75%, for example at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% sequence identity counted over the full length alignment with the amino acid sequence of interest. Proteins with even greater similarity to the reference sequences will show increasing percentage identities when assessed by this method, such as at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% sequence identity. When less than the entire sequence is being compared for sequence identity, homologs and variants will typically possess at least 80% sequence identity over short windows of 10-20 amino acids, and may possess sequence identities of at least 85% or at least 90% or 95% depending on their similarity to the reference sequence. Methods for determining sequence identity over such short windows are available at the NCBI website on the internet. One of skill in the art will appreciate that these sequence identity ranges are provided for guidance only; it is entirely possible that strongly significant homologs could be obtained that fall outside of the ranges provided.


For sequence comparison of nucleic acid sequences, typically one sequence acts as a reference sequence, to which test sequences are compared. When using a sequence comparison algorithm, test and reference sequences are entered into a computer, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated. Default program parameters are used. Methods of alignment of sequences for comparison are well known in the art. Optimal alignment of sequences for comparison can be conducted, e.g., by the local homology algorithm of Smith & Waterman, Adv. Appl. Math. 2:482, 1981, by the homology alignment algorithm of Needleman & Wunsch, J. Mol. Biol. 48:443, 1970, by the search for similarity method of Pearson & Lipman, Proc. Natl. Acad. Sci. USA 85:2444, 1988, by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, Wis.), or by manual alignment and visual inspection (see, e.g., Sambrook et al. (Molecular Cloning: A Laboratory Manual, 4th ed, Cold Spring Harbor, N.Y., 2012) and Ausubel et al. (In Current Protocols in Molecular Biology, John Wiley & Sons, New York, through supplement 104, 2013). One example of a useful algorithm is PILEUP. PILEUP uses a simplification of the progressive alignment method of Feng & Doolittle, J. Mol. Evol. 35:351-360, 1987. The method used is similar to the method described by Higgins & Sharp, CABIOS 5:151-153, 1989. Using PILEUP, a reference sequence is compared to other test sequences to determine the percent sequence identity relationship using the following parameters: default gap weight (3.00), default gap length weight (0.10), and weighted end gaps. PILEUP can be obtained from the GCG sequence analysis software package, e.g., version 7.0 (Devereaux et al., Nuc. Acids Res. 12:387-395, 1984.


Another example of algorithms that are suitable for determining percent sequence identity and sequence similarity are the BLAST and the BLAST 2.0 algorithm, which are described in Altschul et al., J. Mol. Biol. 215:403-410, 1990 and Altschul et al., Nucleic Acids Res. 25:3389-3402, 1977. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information (ncbi.nlm.nih.gov). The BLASTN program (for nucleotide sequences) uses as defaults a word length (W) of 11, alignments (B) of 50, expectation (E) of 10, M=5, N=−4, and a comparison of both strands. The BLASTP program (for amino acid sequences) uses as defaults a word length (W) of 3, and expectation (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff & Henikoff, Proc. Natl. Acad. Sci. USA 89:10915, 1989). An oligonucleotide is a linear polynucleotide sequence of up to about 100 nucleotide bases in length.


As used herein, reference to “at least 80% identity” (or similar language) refers to “at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or even 100% identity” to a specified reference sequence. As used herein, reference to “at least 90% identity” (or similar language) refers to “at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or even 100% identity” to a specified reference sequence.


Single chain HIV-1 Env ectodomain: A recombinant polypeptide including gp120 and the gp41 ectodomain in a single polypeptide chain. Single chain HIV-1 Env ectodomains can trimerize to form a trimeric HIV-1 Env ectodomain. A single chain HIV-1 Env ectodomain does not include the furin cleavage site separating gp120 and gp41; therefore, when produced in cells, the Env ectodomain is not cleaved into separate gp120 and gp41 ectodomain polypeptides. For example, the gp120 and gp41 proteins can be linked by a peptide linker, or directly linked. In some embodiments, a single chain HIV-1 Env ectodomain includes a circular permuted HIV-1 Env ectodomain. Single chain HIV-1 Env ectodomains are of particular interest for DNA or vector encoded immunogens, as it can be beneficial in these immunogen format to not need to rely on the presence of furin (or furin-like) protease in a host cell for maturation of separate gp120/gp41 polypeptides.


Signal Peptide: A short amino acid sequence (e.g., approximately 18-25 amino acids in length) that directs newly synthesized secretory or membrane proteins to and through membranes (for example, the endoplasmic reticulum membrane). Signal peptides are typically located at the N-terminus of a polypeptide and are removed by signal peptidases after the polypeptide has crossed the membrane. Signal peptide sequences typically contain three common structural features: an N-terminal polar basic region (n-region), a hydrophobic core, and a hydrophilic c-region). Exemplary signal peptide sequences are set forth as residues 1-30 of SEQ ID NO: 1 (HXB2 Env signal peptide) and SEQ ID NO: 2 (BG505 Env signal peptide).


Specifically bind: When referring to the formation of an antibody:antigen protein complex, or a protein:protein complex, refers to a binding reaction which determines the presence of a target protein, peptide, or polysaccharide (for example a glycoprotein), in the presence of a heterogeneous population of proteins and other biologics. Thus, under designated conditions, an particular antibody or protein binds preferentially to a particular target protein, peptide or polysaccharide (such as an antigen present on the surface of a pathogen, for example gp120) and does not bind in a significant amount to other proteins or polysaccharides present in the sample or subject. Specific binding can be determined by methods known in the art. A first protein or antibody specifically binds to a target protein when the interaction has a KD of less than 10−6 Molar, such as less than 10−8 Molar, less than 10−8 Molar, less than 10−9, or even less than 10−10 Molar. In some embodiments, an antibody does not specifically bind to a disclosed recombinant HIV-1 Env ectodomain trimer if the binding interaction of the antibody to trimer has a KD of more than 10−6 when assayed at stoichiometry of at least one antibody Fab per protomer in the trimer. Subject: Living multi-cellular vertebrate organisms, a category that includes human and non-human mammals. In an example, a subject is a human. In a particular example, the subject is a newborn infant. In an additional example, a subject is selected that is in need of inhibiting of an HIV infection. For example, the subject is either uninfected and at risk of HIV infection or is infected in need of treatment.


T Cell: A white blood cell critical to the immune response. T cells include, but are not limited to, CD4+ T cells and CD8+ T cells. A CD4+ T lymphocyte is an immune cell that expresses CD4 on its surface. These cells, also known as helper T cells, help orchestrate the immune response, including antibody responses as well as killer T cell responses. Th1 and Th2 cells are functional subsets of helper T cells. Th1 cells secrete a set of cytokines, including interferon-gamma, and whose principal function is to stimulate phagocyte-mediated defense against infections, especially related to intracellular microbes. Th2 cells secrete a set of cytokines, including interleukin (IL)-4 and IL-5, and whose principal functions are to stimulate IgE and eosinophil/mast cell-mediated immune reactions and to downregulate Th1 responses.


Therapeutically effective amount: The amount of agent, such as a disclosed immunogen or immunogenic composition that is sufficient to prevent, treat (including prophylaxis), reduce and/or ameliorate the symptoms and/or underlying causes of a disorder or disease, for example to prevent, inhibit, and/or treat HIV-1 infection. In some embodiments, a therapeutically effective amount is sufficient to reduce or eliminate a symptom of a disease, such as HIV-1 infection. For instance, this can be the amount necessary to inhibit or prevent viral replication or to measurably alter outward symptoms of the viral infection. In general, this amount will be sufficient to measurably inhibit virus replication or infectivity.


In one example, a desired response is to inhibit or reduce or prevent HIV infection. The HIV infected cells do not need to be completely eliminated or reduced or prevented for the composition to be effective. For example, administration of a therapeutically effective amount of the agent can decrease the number of HIV infected cells (or prevent the infection of cells) by a desired amount, for example by at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98%, or even at least 100% (elimination or prevention of detectable HIV infected cells), as compared to the number of HIV infected cells in the absence of the composition.


It is understood that to obtain a protective immune response against a pathogen can require multiple administrations of the immunogenic composition. Thus, a therapeutically effective amount encompasses a fractional dose that contributes in combination with previous or subsequent administrations to attaining a protective immune response. For example, a therapeutically effective amount of an agent can be administered in a single dose, or in several doses, for example daily, during a course of treatment (such as a prime-boost vaccination treatment). However, the therapeutically effective amount can depend on the subject being treated, the severity and type of the condition being treated, and the manner of administration. A unit dosage form of the agent can be packaged in a therapeutic amount, or in multiples of the therapeutic amount, for example, in a vial (e.g., with a pierceable lid) or syringe having sterile components.


Transmembrane domain: An amino acid sequence that inserts into a lipid bilayer, such as the lipid bilayer of a cell or virus or virus-like particle. A transmembrane domain can be used to anchor an antigen to a membrane. In some examples a transmembrane domain is a HIV-1 Env transmembrane domain. Exemplary HIV-1 Env transmembrane domains are familiar to the person of ordinary skill in the art, and provided herein, for example as SEQ ID NOs: 758, 760, and 762.


Treating or preventing a disease: Inhibiting the full development of a disease or condition, for example, in a subject who is at risk for a disease such as HIV-1 infection or acquired immunodeficiency syndrome (AIDS). “Treatment” refers to a therapeutic intervention that ameliorates a sign or symptom of a disease or pathological condition after it has begun to develop. The term “ameliorating,” with reference to a disease or pathological condition, refers to any observable beneficial effect of the treatment. The beneficial effect can be evidenced, for example, by a delayed onset of clinical symptoms of the disease in a susceptible subject, a reduction in severity of some or all clinical symptoms of the disease, a slower progression of the disease, a reduction in the viral load, an improvement in the overall health or well-being of the subject, or by other parameters well known in the art that are specific to the particular disease. A “prophylactic” treatment is a treatment administered to a subject who does not exhibit signs of a disease or exhibits only early signs for the purpose of decreasing the risk of developing pathology.


The term “reduces” is a relative term, such that an agent reduces a response or condition if the response or condition is quantitatively diminished following administration of the agent, or if it is diminished following administration of the agent, as compared to a reference agent. Similarly, the term “prevents” does not necessarily mean that an agent completely eliminates the response or condition, so long as at least one characteristic of the response or condition is eliminated. Thus, an immunogenic composition that reduces or prevents an infection or a response, can, but does not necessarily completely, eliminate such an infection or response, so long as the infection or response is measurably diminished, for example, by at least about 50%, such as by at least about 70%, or about 80%, or even by about 90% of (that is to 10% or less than) the infection or response in the absence of the agent, or in comparison to a reference agent.


Tyrosine Sulfation: Addition of a sulfate group to a tyrosine residue in a protein. In cells, tyrosine sulfation is a post translational modification where a sulfate group is added to a tyrosine residue of a protein molecule in the Golgi or endoplasmic reticulum. Tyrosine sulfation can be catalyzed by a tyrosyl-protein sulfotransferase (TPST), such as TPST1 or TPST2. The reaction catalyzed by TPST is a transfer of sulfate from the universal sulfate donor 3′-phosphoadenosine-5′-phosphosulfate (PAPS) to the side-chain hydroxyl group of a tyrosine residue. Tyrosine sulfation can also be accomplished in vitro, for example by incubating a peptide containing one or more tyrosine residues with a TBST enzyme (such as TBST1 or TBST2) under appropriate conditions. Methods of sulfating a tyrosine residue on a protein are known (see, e.g., U.S. Pat. No. 5,541,095, 2009/0042738, 2006/0009631, 2003/0170849, 2006/0115859, Liu et al., Mol. Biosyst., 7:38-47, 2011, and Choe and Farzan, Methods in Enzymology, 461: 147-170, 2009) each of which is incorporated by reference herein).


Under conditions sufficient for: A phrase that is used to describe any environment that permits a desired activity.


Vaccine: A pharmaceutical composition that elicits a prophylactic or therapeutic immune response in a subject. In some cases, the immune response is a protective immune response. Typically, a vaccine elicits an antigen-specific immune response to an antigen of a pathogen, for example a viral pathogen, or to a cellular constituent correlated with a pathological condition. A vaccine may include a polynucleotide (such as a nucleic acid encoding a disclosed antigen), a peptide or polypeptide (such as a disclosed antigen), a virus, a cell or one or more cellular constituents. In one specific, non-limiting example, a vaccine reduces the severity of the symptoms associated with HIV infection and/or decreases the viral load compared to a control. In another non-limiting example, a vaccine reduces HIV-1 infection compared to a control.


Vector: A nucleic acid molecule as introduced into a host cell, thereby producing a transformed host cell. Recombinant DNA vectors are vectors having recombinant DNA. A vector can include nucleic acid sequences that permit it to replicate in a host cell, such as an origin of replication. A vector can also include one or more selectable marker genes and other genetic elements known in the art. Viral vectors are recombinant nucleic acid vectors having at least some nucleic acid sequences derived from one or more viruses. A replication deficient viral vector is a vector that requires complementation of one or more regions of the viral genome required for replication due to a deficiency in at least one replication-essential gene function. For example, such that the viral vector does not replicate in typical host cells, especially those in a human patient that could be infected by the viral vector in the course of a therapeutic method.


Virus-like particle (VLP): A non-replicating, viral shell, derived from any of several viruses. VLPs are generally composed of one or more viral proteins, such as, but not limited to, those proteins referred to as capsid, coat, shell, surface and/or envelope proteins, or particle-forming polypeptides derived from these proteins. VLPs can form spontaneously upon recombinant expression of the protein in an appropriate expression system. Methods for producing particular VLPs are known in the art. The presence of VLPs following recombinant expression of viral proteins can be detected using conventional techniques known in the art, such as by electron microscopy, biophysical characterization, and the like. Further, VLPs can be isolated by known techniques, e.g., density gradient centrifugation and identified by characteristic density banding. See, for example, Baker et al. (1991) Biophys. J. 60:1445-1456; and Hagensee et al. (1994) J. Virol. 68:4503-4505; Vincente, J Invertebr Pathol., 2011; Schneider-Ohrum and Ross, Curr. Top. Microbiol. Immunol., 354: 53073, 2012).


VRC01: A neutralizing monoclonal antibody that specifically binds to the CD4 binding site on HIV-1 Env and can inhibit HIV-1 infection of target cells. The person of ordinary skill in the art is familiar with the VRC01 mAb and with methods of its use and production (see, for example, Wu et al., Science, 329(5993):856-861, 2010, and PCT publication WO2012/154312, each of which is incorporated by reference herein). The amino acid sequences of the heavy and light variable regions of the VRC01 mAb are known and have been deposited in GenBank as Nos. ADF47181.1 (VRC01 VH) and ADF47184.1 (VRC01 VL), each of which is incorporated by reference herein as present in the database on Jun. 20, 2014)


VRC26: A neutralizing monoclonal antibody that specifically binds to the V1/V2 domain of HIV-1 Env trimer in its prefusion mature closed conformation, and which can inhibit HIV-1 infection of target cells. As used herein, “VRC26” refers to the VRC26.09 antibody, which is one of several clonal variants isolated from donor CAP256. The person of ordinary skill in the art is familiar with the VRC26.09 mAb and with methods of its use and production (see, for example, Doria-Rose et al., Nature, 509, 55-62, 2014, which is incorporated by reference herein). The amino acid sequences of the heavy and light variable regions of the VRC26 mAb are known and have been deposited in GenBank as Nos. KJ134874 (VRC26.09 VH) and KJ134886 (VRC26.09 VL), each of which is incorporated by reference herein as present in the database on Jun. 20, 2014).


II. Description of Several Embodiments
A. Native HIV-1 Sequences

HIV can be classified into four groups: the “major” group M, the “outlier” group O, group N, and group P. Within group M, there are several genetically distinct clades (or subtypes) of HIV-1. The disclosed recombinant HIV-1 Env proteins can be derived from any type of HIV, such as groups M, N, O, or P, or clade, such as clade A, B, C, D, F, G, H, J, or K, and the like. HIV-1 Env proteins from the different HIV clades, as well as nucleic acid sequences encoding such proteins and methods for the manipulation and insertion of such nucleic acid sequences into vectors, are known (see, e.g., HIV Sequence Compendium, Division of AIDS, National Institute of Allergy and Infectious Diseases (2013); HIV Sequence Database (hiv-web.lanl.gov/content/hiv-db/mainpage.html); see, e.g., Sambrook et al. (Molecular Cloning: A Laboratory Manual, 4th ed, Cold Spring Harbor, N.Y., 2012) and Ausubel et al. (In Current Protocols in Molecular Biology, John Wiley & Sons, New York, through supplement 104, 2013). Exemplary native HIV-1 Env protein sequences are available in the HIV Sequence Database (hiv-web.lanl.gov/content/hiv-db/mainpage.html), further, Table 5 provides sequences for Exemplary native HIV-1 Env proteins.









TABLE 5







Exemplary Native HIV-1 Env sequences











Strain
Clade
Env sequence







HXB2
B
SEQ ID NO: 1



BG505
A
SEQ ID NO: 2



CAP256.SU
C
SEQ ID NO: 51



BB201.B42
A
SEQ ID NO: 81



KER2018.11
A
SEQ ID NO: 107



CH070.1
BC
SEQ ID NO: 174



ZM233.6
C
SEQ ID NO: 745



Q23.17
A
SEQ ID NO: 746



A244
AE
SEQ ID NO: 747



WITO.33
B
SEQ ID NO: 748



ZM53.12
C
SEQ ID NO: 749



CNE58
C
SEQ ID NO: 750



3301_V1_C24
AC
SEQ ID NO: 751



T250-4
AE
SEQ ID NO: 2114



JRFL
B
SEQ ID NO: 2115










In several embodiments, a disclosed immunogen can include a modification (e.g., cysteine substitutions that can form a disulfide bond to stabilize the HIV1 Env protein in a prefusion closed mature conformation) from a native HIV-1 Env protein sequence that has been determined to produce broadly neutralizing antibodies in a human subject, for example broadly neutralizing antibodies that specifically bind the V1V2 domain of HIV-1 Env. For example, in some embodiments, an HIV-1 Env (or fragment thereof) sequence from a CAP256.SU, BB201.B42, KER2018.11, CH070.1, ZM233.6, Q23.17, A244, T250-4, or WITO.33 strain of HIV-1 is mutated to include one or more of the disclosed amino acid substitutions to generate a recombinant HIV Env protein (or fragment thereof, such as a gp140 or gp145 protein) that is stabilized in a prefusion mature closed conformation. For example, in some non-limiting embodiments, cysteine substitutions at positions 201 and 433, and the SOSIP mutations, are made to a gp140 sequence from a CAP256.SU, BB201.B42, KER2018.11, CH070.1, ZM233.6, Q23.17, A244, T250-4, or WITO.33 strain of HIV-1 to generate the recombinant HIV-1 Env ectodomain that can form a trimer stabilized in the prefusion mature closed conformation.


In view of the conservation and breadth of knowledge of HIV-1 Env sequences, the person of ordinary skill in the art can easily identify corresponding HIV-1 Env amino acid positions between different HIV-1 Env strains and subtypes. The HXB2 numbering system has been developed to assist comparison between different HIV amino acid and nucleic acid sequences. The person of ordinary skill in the art is familiar with the HXB2 numbering system (see, e.g., Korber et al., Human Retroviruses and AIDS 1998: A Compilation and Analysis of Nucleic Acid and Amino Acid Sequences. Korber B, Kuiken C L, Foley B, Hahn B, McCutchan F, Mellors J W, and Sodroski J, Eds. Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, N. Mex., which is incorporated by reference herein in its entirety). The numbering of amino acid substitutions disclosed herein is made according to the HXB2 numbering system, unless context indicates otherwise.


B. Recombinant HIV-1 Env Ectodomains Stabilized in a Prefusion Mature Closed Conformation

Isolated immunogens are disclosed herein that include a recombinant HIV-1 Env ectodomain trimer or immunogenic fragment thereof that is modified from a native form (e.g., by introduction of one or more amino acid substitutions) to be stabilized in the prefusion mature closed conformation.


The HIV-1 Env ectodomain trimer can include a prefusion mature closed conformation wherein the V1V2 domain of each Env ectodomain protomer in the trimer comes together at the membrane distal apex. At the membrane proximal aspect, the HIV-1 Env ectodomain trimer in the prefusion mature closed conformation includes distinct α6 and α7 helices; the α7 helix does not start until after residue 570. For example, in the prefusion mature closed conformation, the interprotomer distance between residues 200 and 313 can be less than 5 Angstroms.


In several embodiments, the immunogen includes a recombinant HIV-1 Env ectodomain trimer, which can include, for example, a trimeric complex of recombinant HIV-1 Env ectodomains that are stabilized in the prefusion mature closed conformation by one or more amino acid substitutions. The recombinant HIV-1 Env ectodomain trimer typically includes a protein complex of gp120-gp41 ectodomain protomers. The gp120-gp41 protomer can include separate gp120 and gp41 polypeptide chains, or can include gp120 and gp41 polypeptide chains that are linked (e.g., by a peptide linker) to form a single polypeptide chain (e.g., as described in the “single chain” section below). In several embodiments, the recombinant HIV-1 Env ectodomain trimer is membrane anchored and can include a trimeric complex of recombinant HIV-1 Env ectodomains that are linked to a transmembrane domain (e.g., a gp145 protein including a gp120 protein and a gp41 ectodomain and transmembrane domain).


The recombinant HIV-1 Env ectodomain includes a gp120 protein and a gp41 ectodomain. The gp120 protein typically does not include a signal peptide (for example, the gp120 protein typically does not include gp120 residues 1-30), as the signal peptide is proteolytically cleaved during cellular processing. Additionally, the gp41 ectodomain includes the extracellular portion of gp41 (e.g., positions 512-664). In embodiments including a soluble recombinant HIV-1 Env ectodomain, the gp41 ectodomain is not linked to a transmembrane domain or other membrane anchor. However, in embodiments including a membrane anchored recombinant HIV-1 Env ectodomain the gp41 ectodomain can be linked to a transmembrane domain (such as, but not limited to, an HIV-1 Env transmembrane domain).


In several embodiments, the recombinant HIV-1 Env ectodomain includes a gp120 polypeptide and a gp41 ectodomain, wherein


the n-terminal residue of the gp120 polypeptide is one of HIV-1 Env positions 1-35;


the c-terminal residue of the gp120 polypeptide is one of HIV-1 Env positions 503-511;


the n-terminal residue of the gp41 ectodomain is one of HIV-1 Env positions 512-522; and/or


the c-terminal residue of the gp41 ectodomain is one of HIV-1 Env positions 624-705.


In one non-limiting example, the recombinant HIV-1 Env ectodomain includes a gp120 polypeptide and a gp41 ectodomain, wherein the n-terminal residue of the gp120 polypeptide is HIV-1 Env position 31; the c-terminal residue of the gp120 polypeptide is HIV-1 Env position 511; the n-terminal residue of the gp41 polypeptide is HIV-1 Env position 512; and/or the c-terminal residue of the gp41 polypeptide is HIV-1 Env position 664. In some embodiments, the C-terminal residue of the recombinant HIV-1 Env ectodomain is position 683 (the entire ectodomain, terminating just before the transmembrane domain). In additional embodiments, the C-terminal residue of the recombinant HIV-1 Env ectodomain is position 707 (the entire ectodomain, terminating just after the transmembrane domain).


Native HIV-1 Env sequences include a furin cleavage site (e.g., REKR, SEQ ID NO: 572) between positions 508 and 512 (HXB2 numbering), that separates gp120 and gp41. Any of the disclosed recombinant HIV-1 Env ectodomains can further include an enhanced cleavage site between gp120 and gp41 proteins. The enhanced cleavage cite can include, for example, substitution of six arginine resides for the four residues of the native cleavage site (e.g., REKR (SEQ ID NO: 572) to RRRRRR (SEQ ID NO: 573). As used herein, reference to “R6” indicates that a HIV Env protein includes the RRRRRR (SEQ ID NO: 573) substitution for the native furin cleavage site. It will be understood that protease cleavage of the furin or enhanced cleavage site separating gp120 and gp41 can remove a few amino acids from either end of the cleavage site.


Stabilization of the recombinant HIV-1 Env ectodomain trimer or immunogenic fragment in the prefusion mature closed conformation prevents transition of the HIV-1 Env ectodomain to the CD-bound open conformation. Thus, the disclosed recombinant HIV-1 Env ectodomain trimers can be specifically bound by an antibody that is specific for the mature closed conformation of HIV-1 Env (e.g., VRC26, PGT151, PGT122, or PGT145), but are not specifically bound by an antibody specific for the CD4-bound open conformation, of HIV-1 Env (e.g., 17b mAb in the presence of sCD4). In one example, the recombinant HIV-1 Env ectodomain trimer is not specifically bound by an antibody specific for a CD4-induced epitope on the recombinant HIV-1 Env ectodomain trimer, such as the 17b antibody. Methods of determining if a recombinant HIV-1 Env ectodomain trimer includes a CD4-induced epitope are known in the art and disclosed herein (See Examples 1 and 2). For example, the antibody binding assay can be conducted in the presence of a molar excess of soluble CD4 as described in Sanders et al. (Plos Pathogens, 9, e1003618, 2013).


In several embodiments, the recombinant HIV-1 Env ectodomain trimers can be specifically bound by an antibody that specifically binds to the V1V2 domain on a HIV-1 Env trimer, but not an Env monomer. Exemplary antibodies with such antigen binding characteristics include the PGT141, PGT142, PGT143, PGT144, PGT145, and VRC26 antibodies. Additional examples include the PG9, PG16, and CH01-CH04 antibodies. Accordingly, in some embodiments the recombinant HIV-1 Env ectodomain trimer specifically binds to an antibody (such as a PGT141, PGT142, PGT143, PGT144, PGT145, and VRC26 antibody) that specifically binds to the V1V2 domain of a HIV-1 Env in its trimeric, but not monomeric, form with a dissociation constant of less than 10−6 Molar, such as less than 10−7 Molar, less than 10−8 Molar, or less than 10−9 Molar. Specific binding can be determined by methods known in the art. The determination of specific binding may readily be made by using or adapting routine procedures, such as ELISA, immunocompetition, surface plasmon resonance, or other immunosorbant assays (described in many standard texts, including Harlow and Lane, Using Antibodies: A Laboratory Manual, CSHL, New York, 1999).


The recombinant HIV-1 Env ectodomain trimers or immunogenic fragments are stabilized in the prefusion mature closed conformation by one or more amino acid substitutions. Thus, the recombinant HIV-1 Env ectodomain trimers or immunogenic fragments are not stabilized by non-specific crosslinking, for example glutaraldehyde crosslinking of membrane bound HIV-1 Env trimers.


In several embodiments, the recombinant HIV-1 Env ectodomain trimer is soluble in aqueous solution. In some embodiments, the recombinant HIV-1 Env ectodomain trimer dissolves to a concentration of at least 0.5 mg/ml (such as at least 1.0 mg/ml, 1.5 mg/ml, 2.0 mg/ml, 3.0 mg/ml, 4.0 mg/ml or at least 5.0 mg/ml) in phosphate buffered saline (pH 7.4) at room temperature (e.g., 20-22 degrees Celsius) and remains dissolved for at least for at least 12 hours (such as at least 24 hours, at least 48 hours, at least one week, at least two weeks, or more time). In one embodiment, the phosphate buffered saline includes NaCl (137 mM), KCl (2.7 mM), Na2HPO4 (10 mM), KH2PO4 (1.8 mM) at pH 7.4. In some embodiments, the phosphate buffered saline further includes CaCl2 (1 mM) and MgCl2 (0.5 mM). The person of skill in the art is familiar with methods of determining if a protein remains in solution over time. For example, the concentration of the protein dissolved in an aqueous solution can be tested over time using standard methods.


In some embodiments, the recombinant HIV-1 Env ectodomain trimer, when incubated in an aqueous solution, forms a population of recombinant HIV-1 Env ectodomain trimers stabilized in a prefusion mature closed conformation, wherein at least 70% (such as at least 80%, or at least 90% or at least 95% or at least 98%) of the recombinant HIV-1 Env ectodomain trimers in the population specifically bind to an antibody that specifically binds to the V1V2 domain of a trimer, but not monomeric HIV-1 Env (such as a PGT141, PGT142, PGT143, PGT144, PGT145, and VRC26 antibody) after


(a) incubation for one hour in 350 mM NaCl pH 7.0, at 50° C.;


(b) incubation for one hour in 350 mM NaCl pH 3.5, at 25° C.;


(c) incubation for one hour in 350 mM NaCl pH 10, at 25° C.;


(d) incubation for one hour in 10 mM osmolarity, pH 7.0, at 25° C.;


(e) incubation for one hour in 3000 mM osmolarity, pH 7.0, at 25° C.;


(g) a combination of two or more of (a)-(e); or


a combination of (a) and (b); (a) and (c); (a) and (d); (a) and (e); (b) and (d); (b) and (e); (c) and (d); (c) and (e); (a), (b), and (d); (a), (c), and (d); (a), (b), and (e); or (a), (c), and (e).


In some embodiments, the recombinant HIV-1 Env ectodomain trimer, when incubated in an aqueous solution, forms a population of recombinant HIV-1 Env ectodomain trimers stabilized in a prefusion mature closed conformation, wherein at least 70% (such as at least 80%, or at least 90% or at least 95% or at least 98%) of the recombinant HIV-1 Env ectodomain trimers in the population specifically bind to an antibody that specifically binds to the V1V2 domain of a trimer, but not monomeric HIV-1 Env (such as a PGT141, PGT142, PGT143, PGT144, PGT145, and VRC26 antibody) ten freeze-thaw cycles in 350 mM NaCl pH 7.0.


Several embodiments include a multimer of the recombinant HIV-1 Env ectodomain trimer or immunogenic fragment thereof, for example, a multimer including 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more of the recombinant HIV-1 Env ectodomain trimers or immunogenic fragment thereof.


It is understood in the art that some variations can be made in the amino acid sequence of a protein without affecting the activity of the protein. Such variations include insertion of amino acid residues, deletions of amino acid residues, and substitutions of amino acid residues. These variations in sequence can be naturally occurring variations or they can be engineered through the use of genetic engineering technique known to those skilled in the art. Examples of such techniques are found in see, e.g., Sambrook et al. (Molecular Cloning: A Laboratory Manual, 4th ed, Cold Spring Harbor, N.Y., 2012) and Ausubel et al. (In Current Protocols in Molecular Biology, John Wiley & Sons, New York, through supplement 104, 2013, both of which are incorporated herein by reference in their entirety.


The recombinant HIV-1 Env ectodomain can include modifications of the native HIV-1 sequence, such as amino acid substitutions, deletions or insertions, glycosylation and/or covalent linkage to unrelated proteins (e.g., a protein tag), as long as the recombinant HIV-1 Env ectodomain can form a trimer that is stabilized in the prefusion mature closed conformation. HIV-1 Env proteins from the different Clades, as well as nucleic acid sequences encoding such proteins and methods for the manipulation and insertion of such nucleic acid sequences into vectors, are disclosed herein and known in the art.


In some embodiments a recombinant HIV-1 Env ectodomain included in the disclosed trimers includes a gp120 polypeptide and a gp41 ectodomain including amino acid sequences at least 75% (for example at least 85%, 90%, 95%, 96%, 97%, 98% or 99%) sequence identity to a corresponding native HIV-1 gp120 or gp41 ectodomain polypeptide sequence (e.g., a native gp120 or gp41 ectodomain protein sequence from a clade A, B, C, D, F, G, H, J or K HIV-1 Env protein), such a native HIV-1 sequence available in the HIV Sequence Database (hiv-web.lanl.gov/content/hiv-db/mainpage.html) or a native HIV-1 Env polypeptide sequence set forth in Table 5, and include the one or more amino acid substitutions that stabilize the protein in the prefusion mature closed conformation.


In additional embodiments, a recombinant HIV-1 Env ectodomain included in the disclosed trimers includes a gp120 polypeptide and/or a gp41 ectodomain including one or more amino acid substitutions compared to a corresponding native HIV-1 Env sequence. For example, in some embodiments, the gp120 polypeptide, gp41 ectodomain, or both, can include up to 20 (such as up to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, or 19) amino acid substitutions compared to a native HIV-1 gp140 polypeptide sequence (e.g., a native gp120 or gp41 ectodomain protein sequence from a clade A, B, C, D, F, G, H, J or K HIV-1 Env protein), such a native HIV-1 sequence available in the HIV Sequence Database (hiv-web.lanl.gov/content/hiv-db/mainpage.html) or a native HIV-1 Env polypeptide sequence set forth in Table 5, and include the one or more amino acid substitutions that stabilize the protein in the prefusion mature closed conformation. The simplest modifications involve the substitution of one or more amino acids for amino acids having similar biochemical properties. These so-called conservative substitutions are likely to have minimal impact on the activity of the resultant protein.


The recombinant HIV-1 Env ectodomain included in the disclosed trimers can be derivatized or linked to another molecule (such as another peptide or protein). In general, the recombinant HIV-1 Env ectodomain is derivatized such that the binding to broadly neutralizing antibodies to a trimer of the recombinant HIV-1 ectodomain, such as PGT122, is not affected adversely by the derivatization or labeling. For example, the recombinant HIV-1 Env ectodomain can be functionally linked (by chemical coupling, genetic fusion, noncovalent association or otherwise) to one or more other molecular entities, such as an antibody or protein or detection tag.


The stabilizing modifications provided herein are targeted modifications that stabilize the recombinant HIV-1 Env ectodomain trimer in the prefusion mature closed conformation. Guided by the structural features identified in the prefusion mature closed conformation, several modes of stabilizing the HIV-1 Env ectodomain trimer in this conformation are available, including (but not limited to) amino acid substitutions that introduce one or more non-natural disulfide bonds, fill cavities within the HIV-1 ectodomain trimer, prevent structural rearrangements, introduce N-linked glycosylation sites, and combinations thereof. Corresponding mutations are discussed in more detail below:


Reference to Table 13

Several stabilizing mutations are provided that can be included on a HIV-1 ectodomain to generate a trimeric HIV-1 ectodomain stabilized in the prefusion mature closed conformation. These mutations include, but are not limited to, those provided in Table 13. In several embodiments, the recombinant HIV-1 Env ectodomain trimer includes a HIV-1 Env ectodomain including the amino acid substitutions set forth in any one row of column 5, column 6, or columns 5 and 6, of Table 13. In additional embodiments, the recombinant HIV-1 Env ectodomain trimer includes a HIV-1 Env ectodomain including an amino acid sequence at least 80% identical to any one of the modified HIV-1 Env Ectodomain sequences listed in Table 13. In further embodiments, the recombinant HIV-1 Env ectodomain trimer includes a HIV-1 Env ectodomain including the amino acid sequence of any one of the modified HIV-1 Env Ectodomain sequences listed in of Table 13


Some of the sequences of recombinant HIV-1 ectodomains provided herein include the sequence of protease cleavage sites (such as thrombin sites), protein tags (such as a His tag, a Strep Tag II, a Avi tag, etc.), signal peptides, that the person of ordinary skill in the art will understand would not be included in an isolated immunogen including a recombinant HIV-1 Env ectodomain immunogen. The person of ordinary skill in the art will recognize such sequences, and when appropriate, understand that these tags or protease cleavage sites are not included in a disclosed recombinant HIV-1 Env protein.


In some embodiments, the recombinant HIV-1 Env ectodomain trimer includes the SOSIP, R6, 664 and 201C/433C modifications, an asparagine at position 332, and the substitutions listed in column 6 of any one of the rows for SEQ ID NO: 1245-1367 or 1580-1610 of Table 13. In some embodiments, the recombinant HIV-1 Env ectodomain trimer includes the SOSIP, R6, and 664 substitutions, an asparagine at position 332, and the substitutions listed in column 6 of any one of the rows for SEQ ID NO: 1368-1399 or 1580-1610 of Table 13. In several such embodiments, the recombinant HIV-1 Env ectodomain trimer can be based on a JRFL or a BG505 strain of HIV-1. In some embodiments, the gp120/gp41 ectodomains in the recombinant HIV-1 Env ectodomain trimer can comprise an amino acid sequence set forth as any one of SEQ ID NO: 1245-1399 or 1580-1610, or a sequence at least 90% identical thereto.


In some embodiments, the recombinant HIV-1 Env ectodomain trimer includes the SOSIP, R6, 664, and 201C/433C substitutions, an asparagine at position 332, and is based on a strain of HIV-1 as listed in column 4 of any one of the rows for SEQ ID NO: 26, 1057-1077, 1400-1579 of Table 13. In some embodiments, the gp120/gp41 ectodomains in the recombinant HIV-1 Env ectodomain trimer can comprise an amino acid sequence set forth as any one of SEQ ID NO: 26, 1057-1077, 1400-1579, or a sequence at least 90% identical thereto.


Non-Natural Disulfide Bonds

In several embodiments, the recombinant HIV-1 Env ectodomain trimer includes one or more non-natural disulfide bonds that stabilize the HIV-1 Env ectodomain trimer in the prefusion mature closed conformation. A non-natural disulfide bond is one that does not occur in a native HIV-1 Env protein, and is introduced by protein engineering (e.g., by including one or more substituted cysteine residues that form the non-natural disulfide bond). For example, in some embodiments, any of the disclosed recombinant HIV-1 Env ectodomain trimers can be stabilized in a prefusion mature closed conformation by any one of 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 non-natural disulfide bonds.


The cysteine residues that form the disulfide bond can be introduced into a native HIV-1 sequence by one or more amino acid substitutions. For example, in some embodiments, a single amino acid substitution introduces a cysteine that forms a disulfide bond with a cysteine residue present in the native HIV-1 sequence. Alternately, two cysteine residues can be introduced into a native HIV-1 Env ectodomain sequence to form the disulfide bond. The location of the cysteine (or cysteines) of the non-natural disulfide bond can be determined by the person of ordinary skill in the art using the disclosed structure of the HIV-1 ectodomain trimer in a prefusion mature closed conformation.


For example, the amino acid positions of the cysteines are typically within a sufficiently close distance for formation of a disulfide bond in the prefusion mature closed conformation of the HIV-1 Env protein trimer. Methods of using three-dimensional structure data to determine if two residues are within a sufficiently close distance to one another for disulfide bond formation are known (see, e.g., Peterson et al., Protein engineering, 12:535-548, 1999 and Dombkowski, Bioinformatics, 19:1852-1853, 3002 (disclosing DISULFIDE BY DESIGN™), each of which is incorporated by reference herein). Residues can be selected manually, based on the three dimensional structure of the HIV-1 Env trimer in a prefusion mature closed conformation provided herein, or a software, such as DISULFIDEBYDESIGN™, can be used. Without being bound by theory, ideal distances for formation of a disulfide bond are generally considered to be about ˜5.6 Å for Cα-Cα distance, ˜2.02 Å for Sγ-Sγ distance, and 3.5-4.25 Å for Cβ-Cβ distance (using the optimal rotomer). The person of ordinary skill in the art will appreciate that variations from these distances are included when selecting residues in a three dimensional structure that can be substituted for cysteines for introduction of a disulfide bond. For example, in some embodiments the selected residues have a Cα-Cα distance of less than 7.0 Å and/or a Cβ-Cβ distance of less than 4.7 Å. In some embodiments the selected residues have a Cα-Cα distance of from 2.0-8.0 Å and/or a Cβ-Cβ distance of from 2.0-5.5 Å. In several embodiments, the amino acid positions of the cysteines are within a sufficiently close distance for formation of a disulfide bond in the prefusion mature closed conformation, but not the CD4-bound open conformation of the HIV-1 Env protein.


For example, the person of ordinary skill in the art can determine the relative position of a particular amino acid between the prefusion mature closed and CD4-bound conformations of the HIV-1 Env ectodomain by comparing the prefusion mature closed structures disclosed in the Examples and the structural coordinates provided in Tables 1-4, with the previously identified CD4-bound conformation described in Example 1. Methods of determining relative position of a particular amino acid between the two protein structures (e.g., between the three dimensional structures prefusion mature closed- and CD4-bound-HIV-1 Env protein) are known. For example the person of ordinary skill in the art can use known superimposition methods to compare the two structures (e.g., methods using the LSQKAB program (Kabsch W. Acta. Cryst. A32 922-923 (1976)).


In several embodiments, the recombinant HIV-1 Env protein is stabilized in a prefusion mature closed conformation by a disulfide bond between a cysteine introduced at an amino acid position that changes conformation, and a cysteine introduced into an amino acid position that does not change conformation, between the prefusion mature closed conformation and the CD4-bound conformation of HIV-1 Env. For example, in some embodiments, the recombinant HIV-1 Env protein is stabilized in a prefusion mature closed conformation by a disulfide bond between a pair of cysteines, wherein the first cysteine is in an amino acid position of the HIV-1 Env protein that has a root mean square deviation of at least 5 (such as at least 6, at least 7, at least 8, at least 9 or at least 10) angstroms between the three-dimensional structure of the HIV-1 Env protein prefusion mature closed and CD4-bound conformations, and the second cysteine is in an amino acid position of the HIV-1 Env protein that has a root mean square deviation of less than 4 (such as less than 3, 2, or 1) angstroms between the three-dimensional structure of the HIV-1 Env protein prefusion mature closed and CD4-bound conformations.


In additional embodiments, the recombinant HIV-1 Env protein is stabilized in a prefusion mature closed conformation by a disulfide bond between cysteines that are introduced at amino acid positions that both change conformation between the prefusion mature closed and CD4-bound conformations. For example, in some embodiments, the recombinant HIV-1 Env protein includes amino acid substitutions introducing a pair of cysteines, wherein the first cysteine and the second cysteine are at amino acid positions of the HIV-1 Env protein that both have a root mean square deviation of at least 5 (such as at least 6, at least 7, at least 8, at least 9 or at least 10) angstroms between the three-dimensional structure of the prefusion mature closed and CD4-bound conformations of the HIV-1 Env protein.


In several embodiments the recombinant HIV-1 Env ectodomain included in the trimer includes one or more amino acid substitutions that stabilize the V1V2 domain “cap” and/or V3 domain in the prefusion mature closed conformation.


For example, in some embodiments, the recombinant HIV-1 Env ectodomain included in the trimer includes a non-natural disulfide bond between a first cysteine in a position of the β2 sheet and a second cysteine in a gp120 positions of the β21 sheet of the HIV-1 ectodomain in the mature closed conformation as disclosed herein (see FIG. 11).


In some embodiments, the gp120 polypeptide in the recombinant HIV-1 Env ectodomain can include a non-natural disulfide bond between a pair of cysteine substitutions at one of gp120 positions 179-180 and one of gp120 positions 420-423; one of gp120 positions 190-210 and one of gp120 positions 425-437; one of gp120 positions 198-202 and one of gp120 positions 428-437; one of gp120 positions 179-180 and one of gp120 positions 421-423; or one of gp120 positions 195-201 to one of gp120 positions 423-433, wherein the non-natural disulfide bond stabilizes the HIV-1 Env ectodomain in the prefusion mature closed conformation.


In some embodiments, the gp120 polypeptide in the recombinant HIV-1 Env ectodomain can include a pair of cysteine substitutions that can form a disulfide bond to stabilize a trimer of the recombinant HIV-1 Env ectodomain in the mature closed conformation. Exemplary gp120 positions that can be mutated to cysteine, as well as exemplary mutations (in the context of the BG505 strain), and an exemplary sequence including the indicated mutations are provided in Table 6.









TABLE 6







Non-natural gp120-gp120 disulfide bonds.











Exemplary Env
Exemplary





positions
Substitutions
Intra- or


(HXB2
(HXB2
Inter-

Exemplary


numbering)
numbering)
protomer?
Comment
SEQ ID NO














 36 and 496
V36C/V496C
Intra
Stabilize gp120 N and C termini
649


 36 and 498
V36C/P498C
Intra
Stabilize gp120 N and C termini
650


 37 and 497
T37C/A497C
Intra
Stabilize gp120 N and C termini
651


 38 and 496
V38C/V496C
Intra
Stabilize gp120 N and C termini
652


 36 and 608
V36C/V608C
Intra
stabilize V1V2 mature closed conformation
82


55 and 77
A55C/T77C
Intra
Inhibit α0 formation
683


57 and 77
D57C/T77C
Intra
Inhibit α0 formation
98


58 and 77
A58C/T77C
Intra
Inhibit α0 formation
97


 66 and 209
V66C/S209C
Intra
Inhibit α0 formation
101


 68 and 208
V68C/V208C
Intra
Inhibit α0 formation
100


 68 and 209
V68C/S209C
Intra
Inhibit α0 formation
99


120 and 315
V120C/Q315C
Intra
stabilize V1V2 mature closed conformation
70


122 and 125
L122C/L125C
Intra
stabilize V1V2 mature closed conformation
64


122 and 203
L122C/Q203C
Intra
stabilize V1V2 mature closed conformation
77, 785


122 and 317
L122C/F317C
Intra
Locking the V3 to gp120 to prevent exposure/opening
789


122 and 433
L122C/A433C
Intra
stabilize V1V2 mature closed conformation
162


124 and 164
P124C/T164C
Inter
stabilize V1V2 mature closed conformation
71


124 and 166
P124C/R166C
Inter
stabilize V1V2 mature closed conformation
20


128 and 165
T128C/L165C
Inter
stabilize V1V2 mature closed conformation


128 and 167
T128C/T167C
Inter
stabilize V1V2 mature closed conformation
72


163 and 170
T163C/Q170C
Intra
Stabilize V1V2
662


164 and 197
E164C/N197C
Inter
stabilize V1V2 mature closed conformation
19


164 and 308
S164C/H308C
Intra
Locking the V3 to V1V2 to prevent exposure/opening
794


172 and 307
E172C/I307C
Intra
Locking the V3 to V1V2 to prevent exposure/opening
791


174 and 318
S174C/A319C
Intra
stabilize V1V2 mature closed conformation
8


174 and 319
S174C/T319C
Intra
Locking the V3 to V1V2 to prevent exposure/opening
793


175 and 320
L175C/T320C
Intra
stabilize V1V2 mature closed conformation
 9, 795


176 and 180
F176C/D180C
Intra
stabilize V1V2 mature closed conformation
57


180 and 421
D180C/K421C
Intra
stabilize V1V2 mature closed conformation
28


180 and 423
D180C/I423C
Intra
stabilize V1V2 mature closed conformation
21


195 and 423
N195C/I423C
Intra
stabilize V1V2 mature closed conformation
22


195 and 433
N195C/A433C
Intra
stabilize V1V2 mature closed conformation
23, 777


199 and 431
S199C/G431C
Intra
stabilize V1V2 mature closed conformation
25


199 and 433
S199C/A433C
Intra
stabilize V1V2 mature closed conformation
24, 778


200 and 313
A200C/P313C
Inter
stabilize V1V2 mature closed conformation
12


200 and 432
A200C/Q432C
Intra
Stabilize β21 to V1V2
653


201 and 433
I201C/A433C
Intra
stabilize V1V2 mature closed conformation
26, 773


202 and 434
T202C/M434C
Intra
Stabilize β21 to V1V2
654


202 and 433
T202C/A433C
Intra
Stabilize β21 to V1V2
656


203 and 317
Q203C/F317C
Intra
Locking the V3 to gp120 to prevent exposure/opening
788


204 and 434
A204C/M434C
Intra
stabilize V1V2 mature closed conformation
63


204 and 436
A204C/A436C
Intra
stabilize V1V2 mature closed conformation
58


206 and 318
P206C/Y318C
Intra
Locking the V3 to gp120 to prevent exposure/opening
792


212 and 252
P212C/K252C
intra
stabilize V1V2 mature closed conformation
60


225 and 245
I225C/V245C
Intra
Stabilizes V1V1
646


225 and 488
I225C/V488C
Intra
Stabilize V1V2 mature closed conformation
659


257 and 375
T257C/S375C
Intra
Stabilize V1V2 mature closed conformation
682


294 and 333
I294C/V333C
Intra
Stabilize core
664


298 and 329
R298C/A329C
Intra
stabilize V1V2 mature closed conformation
74


304 and 440
R304C/Q440C
Intra
Stabilize prefusion close conformation (through V3)
743, 779,






787


318 and 437
Y318C/P437C
Intra
stabilize V1V2 mature closed conformation
53, 790


320 and 438
T320C/P438C
Intra
stabilize V1V2 mature closed conformation
27, 796


364 and 372
S364C/T372C
Intra
stabilize V1V2 mature closed conformation
80


370 and 426
E370C/M426C
Intra
stabilize strand β20 to core gp120
170


380 and 426
G380C/M426C
Intra
stabilize strand β20 to core gp120
171


382 and 424
F382C/I424C
Intra
stabilize V1V2 mature closed conformation
73


425 and 433
N425C/A433C
Intra
stabilize V1V2 mature closed conformation (stabilize
69, 783





β20 to β21)


425 and 430
N425C/I430C
Intra
Stabilizes CD4 binding loop (stabilize β20 to β21)
52









In one non-limiting embodiment, the recombinant HIV-1 Env ectodomain can include cysteine substitutions at positions 201 and 433 (e.g., I201C and A433C substitutions). In additional embodiments, the recombinant HIV-1 Env ectodomain can include cysteine substitutions at positions 201 and 433 (e.g., I201C and A433C substitutions) and further include one or more additional mutations as disclosed herein. Exemplary additional mutations include those disclosed herein that stabilize the V1V2 domain, the V3 domain, or the CD4 binding site in the prefusion mature closed conformation, or a mutation that stabilizes gp41 in the prefusion mature closed conformation, such as a mutation that inhibits HR1 or HR2 formation or fusion peptide extension. Non-limiting examples of mutations that can be combined with the cysteine substitutions at positions 201 and 433 include the SOS, IP, SOSIP mutations, as well as any of the mutations listed in Table 9, below.


Cavity Filling Amino Acid Substitutions

Comparison of the structure of the mature closed conformation of the HIV-1 Env ectodomain trimer (e.g., in complex with PGT122 and 35O22 Fabs as disclosed herein) to the structure of the CD4-bound conformation of HIV-1 Env identifies several internal cavities or pockets in the mature closed conformation that collapse when the HIV-1 Env ectodomain trimer transitions from the prefusion closed conformation to the CD4-bound open conformation. These cavities include those listed in Table 8, below.


Accordingly, in several embodiments, the recombinant HIV-1 Env ectodomain trimer can be stabilized in the mature closed conformation by one or more amino acid substitutions that reduce the volume of an internal cavity that collapses in the CD4-bound conformation of the HIV-1 Env ectodomain trimer. For example, cavities can be filled by substituting amino acids with large side chains for those with small side chains. The cavities can be intra-protomer cavities, or inter-protomer cavities. The person of ordinary skill in the art can use methods provided herein to compare the structures of the mature closed and CD4-bound conformations of HIV-1 Env to identify suitable cavities, and amino acid substitutions for filling the identified cavities. Exemplary cavities, amino acid substitutions for reducing the volume of these cavities are provided in Table 8.


Exemplary HIV-1 Env positions for introducing cavity filling amino acid substitutions that stabilize the prefusion mature closed conformation of the HIV-1 Env ectodomain trimer are provided in Table 8, as are corresponding amino acid substitutions with reference to the BG505 strain, and an exemplary sequence including the indicated substitution.









TABLE 8







Exemplarity cavity-filling amino acid substitutions












Exemplary






substitution
Exemplary
Exemplary


Position
residues
substitution(s)
SEQ ID NO
Cavity Location (CL) and stabilizing mechanism (SM)














39
W, M, I, F
Y39F, Y39W
47-48
CL: gp120/gp41 interface






SM: fill cavity and add hydrophobic interactions at the gp120-






gp41 interactive surface


50
F, Y, L, I, M, V, W
T50W
181
CL: gp120/gp41 interface






SM: stabilize gp120/gp41 interface


53
W
F53W
197
CL: gp120-gp41 interface, near N-term of β-2






SM: Fill cavity between gp120 and gp41 to stabilize gp41






disordered region and gp120/gp41 interaction


55
F
A55F
678
CL: gp120 C1 with F substitution to stabilize gp120 N terminus


61
W
Y61W
195
CL: Middle of α1






SM: Fill cavity between gp120 and gp41; prevent CD4-induced






α0 formation/α1 disruption


68
F, W, Y, L, I, M
V68L
196
CL: Loop between α-1 and β0






SM: Fill cavities that are otherwise filled by CD4 induced α0






formation


70
F, Y, W
A70F, A70Y
143, 144
CL: Close to A70, α0/α7






SM: Extension of hydrophobic/aromatic patch-gp41/gp120






stabilization


75
W, F, M
V75W, V75F,
90, 91,
CL: gp120/gp41 interface




V75M
92
SM: stabilize gp120/gp41 interface


77
F
T77F
676
CL: gp120 C1 with F substitution to stabilize gp120 N terminus


110
F, Y, L, I, M, V, W
S110W
178
CL: trimer axis/gp41 interface boundary






SM: stabilize prefusion axis interactions/gp41 interface/prevent






helix movement


111
F, Y, W
L111Y, L111F,
145, 146,
CL: gp120 C1, Close to A70, α0/α7




L111W
697
SM: Extension of hydrophobic/aromatic patch-gp41/gp120






stabilization (α7/α0, cavity close to A70), Substitute W to






stabilize gp120 terminus


114
F, Y, L, I, M, V, W
Q114W
179
CL: trimer axis/gp41 interface boundary






SM: stabilize prefusion axis interactions/gp41 interface/prevent






helix movement


115
F, W, Y, L, I, M, V
S115W
139
CL: C-term of α1






SM: Reduces cavity at top of α1, which shifts conformation in






CD4-bound state


117
F, Y, L, I, H, R,
K117E, K117W
175, 176
CL: trimer axis



E, D, M, V, W


SM: stabilize prefusion axis interactions


118
F, W, Y, L, I, M, V
P118W
140
CL:






SM: Reduces cavity near top (c-term) of α1, which shifts






conformation in CD4-bound state


120
F, Y, L, I, H, R, E,
V120W
128
CL: Under V1V2 cap at N-term of β2



D, M, V, W


SM: stabilize V1V2 mature closed conformation/prevent






bridging sheet formation, β2 extends in CD4-bound state, this






stabilizes small hydrophobic pocket in ground state


121
F, Y, L, I, H, R, E,
K121E
177
CL: trimer axis



D, M, V


SM: stabilize prefusion axis interactions


123
F, Y, L, M, V, W
T123W
172
CL: trimer axis






SM: stabilize prefusion axis interactions


125
F, W, Y, L, I, M, V
L125W, L125F
131, 685
CL: Cavity near N-term of V1V2 domain and V3 near residue






127 and 126-196 disulfide of V1V2






SM: Removal of ground state destabilization/flexibility cavity






filling, stabilize V1/V2/V3


136
W
N136W
686
CL: gp120 V1. Substitute W to stabilize V1/V2/V3


139
F, M, I, Y, T;
T139W
 45
CL: interface of V1V2 and V3 loops






SM: Stabilize interactions between V1V2 and V3 loops in the






mature closed state


151
F, W, Y, L, I, M, V
R151E,
132
CL: near V1 loop at position 153






SM: Adding hydrophobic patch at V1 loop to V3 loop


153
F, W
E153F, E153W
707, 708
CL: V1V2-V3/gp120core interface,


154
F, W
L154F, L154W
709, 710
CL: gp120 V1/V2. Substitute F, Y or W, stabilize V1/V2/V3


159
W, Y
F159W, F159Y
133, 30 
CL: Primary hydrophobic pocket between V1V2 and V3 near






residue 159






SM: Stabilize hydrophobic core of V1V2-V3 interactions


161
F, W, Y, L, I
M161W
135
CL: Hydrophobic patch at Cterm of V1V2 strand B






SM: Stabilize V1V2 strand B to V3 near trimeric interface


164
F, W
E164F, E164W
711, 712
CL: inter-protomer, Substitute F or W,


173

Y173W
703
CL: gp120 V1/V2/V3. 173: Substitute W or F


175
F, W
L175F, L175W
705, 706
CL: V1V2-V3 interface, Substitute F or W,


176
W
F176W
733
CL: gp120 V1/V2. Substitute Y or W, stabilize V1/V2/V3


177
W
Y177W
198
CL: C-term of beta C






SM: Fills cavity between V3 and gp120 core to stabilize closed






V1V2 cap


179
F, Y, M, I, W
L179W
 46
CL: V1V2 loop gp120 core interface






SM: Stabilize V1V2 loop-gp120 core interaction in mature






closed state


180
180: L, V, I, M
D180L
123
CL: V1V2 interaction near residue 180 with V3 and base of






β21






SM: stabilize v1v2 to v3 along with destabilizing β21 from






adopting CD4-bound-conformation


191
W, F
Y191W, Y191F
4, 5
CL:






SM: Stabilize V1V2 cap


198
F
T198F
713
CL: V1V2-gp120 core interface


201
F, Y, L, M, V
I201W
173
CL: parallel β #






SM: prevent bridging sheet formation


202
F, W
T202F, T202W
714
CL: V1V2-gp120 core interface, Substitute F or W,


203
F, W, Y, L, I, M, V
Q203V
129
CL: Under V1V2 cap at N-term of β2






SM: stabilize prefusion cap/prevent bridging sheet formation,






β2 extends in CD4-bound state, this stabilizes small






hydrophobic pocket in ground state


204
F, W
A204F, A204W
716, 724
CL: V1V2-gp120 core interface, Substitute F or W,


208
W, Y, F, M
V208W,
93-96
CL: between α1 and strand leading to bridging sheet in the




V208Y, V208F,

CD4-bound conformation




V208

SM: Destabilize CD4-bound conformation


209
R
S209R,
196
CL: Loop between β3 and β4






SM: Fill cavity otherwise filled by CD4 induced α0 formation


220
F, Y, L, I, M, V, W
P220W
180
CL:






SM: stabilize gp41 interface


223
Y, W
F223W
 31, 780
CL: near β5






SM: stabilize gp120/gp41 interface


245
F
V245F
700
CL: gp120 C2. Substitute F to stabilize gp120 V1/V2/V3,






interprotomer


246
F, W, Y, L, I, M, V
Q246W
197
CL: gp120-gp41 interface, near middle of β8






SM: Fill a cavity between gp120 and gp41 to stabilize gp41






disordered region and gp120/gp41 interaction


254
F
V254F
670
CL: gp120 C2 with F substitution to stabilize gp120


260
F
L260F
671
CL: gp120 C2 with F substitution to stabilize gp120


261
F
L261F
672
CL: gp120 C2 with F substitution to stabilize gp120,






interprotomer


263
W
G263W
673
CL: gp120 C2 with W substitution to stabilize gp120,






interprotomer


302
F, W
N302F, N302W
725, 726
CL: V3-V1V2/gp120 core interface


309
F, W, Y, L, M
I309W
136
CL: Hydrophobic patch at C-term of V1V2 strand B






SM: Stabilize V1V2 strand B to V3 near trimeric interface


317
W, Y
F317W
134
CL: Primary hydrophobic pocket between V1V2 and V3 near






position 159






SM: Stabilize hydrophobic core of V1V2-V3 interactions


323
W
I323W
690
CL: gp120 V3. Substitute F to stabilize V1/V2/V3


326
M, W, F, Y, R
I326R, I326F
 45, 691
CL: at the interface of V1V2 and V3 loops






SM: Stabilize interactions between V1V2 and V3 loops in the






mature closed state


328
328: F, W, Y, L, I,
Q328W
132
CL: near V3 loop



M, V


SM: Adding hydrophobic patch at V1 loop to V3 loop


332
F, Y, W
I332F
198
CL: C-term of beta V3B,






SM: Fills cavity between V3 and gp120 core to stabilize closed






V1V2 cap


380
F
G380F
667
CL: gp120 C4 with F substitution to stabilize gp120


421
421: F, W, Y
K421W,
123
CL: V1V2 interaction near residue 180 with V3 and base of






β21






SM: This will stabilize v1v2 to v3 along with destabilizing β21






from adopting CD4-bound-conformation


423
F, Y, L, M, V, W
I423F, I423W
173, 717,
CL: gp120core-V1V2 interface, parallel β #





718
SM: prevent bridging sheet formation


426
G, V, I, L, F, Y, W,
M426W,
54, 75,
CL: CD4 binding site



R, K, P
M426A,
78, 83
SM: Constrains CD4 binding loop, Blocks transition to CD4




M426F,

bound conformation




M426P


429
F, Y, L, I, M, V, W
R429W
182
CL: under parallel β#






SM: prevent bridging sheet formation


431
Any
G431P
 68, 782
CL: CD4 binding site






SM: sterically interferes with CD4 binding specifically without






affecting antibody binding


432
F, W
Q432F, Q432W
719, 720
CL: stabilize unliganded conformation of bridging sheet region


436
M, F, W
A436M, A436F,
721, 722,
CL: stabilize unliganded conformation of bridging sheet region




A436W
723


437
F
P437F
668
CL: gp120 C terminus with F substitution and stabilize gp120






C terminus


473
Any
G473A, G473S,
65-67,
CL: CD4 binding site




G473Y
781
SM: sterically interferes with CD4 binding specifically without






affecting antibody binding


478
F
N478F
660
CL: gp120 C terminus substituted with F and stabilize gp120 C






terminus


522
Y
F522Y
 34
CL: near N-tern of fusion peptide






SM: Fusion Peptide Cavity Fill


523
F
L523F
 33
CL: near N-tern of fusion peptide






SM: Fusion Peptide Cavity Fill


530
W
M530W
 29
CL: gp41-tryptophan clasp






SM: stabilize interactions within gp41-tryptophan clasp


534
I, W, F, A, M, V
S534V, S534A
47-48
CL: gp120/gp41 interface






SM: fill cavity and add hydrophobic interactions at the gp120-






gp41 interactive surface


544
F, Y, W
L544Y
 32
CL: gp41 tip of α6






SM: stabilize gp120/gp41 interface









The recombinant HIV-1 Env ectodomain included in the trimer can include any one of the cavity filling substitution at one of the HIV-1 Env positions listed in Table 8. The recombinant HIV-1 Env ectodomain can also include a combination of two or more (e.g., 3, 4, 5, 6, 7, or 8) of the cavity filling substitutions provided in Table 8 to stabilize the HIV-1 Env ectodomain trimer in the prefusion mature closed conformation.


Additional Substitutions

In some embodiments, the recombinant HIV-1 Env ectodomain can include one or more amino acid substitutions that destabilize the CD4-bound open conformation of the HIV-1 Env ectodomain trimer (and thereby prevent transition of the trimer from the prefusion closed conformation to the CD4-bound open conformation).


For example, in some embodiments the recombinant HIV-1 Env ectodomain can include an amino acid substitution that introduces a proline residue in the β21 sheet (e.g., positions 430-435), such as a proline substitution at position 432 or 433.


Exemplary HIV-1 Env positions for introducing an amino acid substitutions that destabilizes the CD4-bound open conformation of the HIV-1 Env ectodomain trimer are provided in Table 7, as are corresponding amino acid substitutions with reference to the BG505 strain, and an exemplary sequence including the indicated substitution.









TABLE 7







Destabilization of CD4-induced- and stabilization


of prefusion mature conformations










Exem-
Substi-

Exem-


plary
tution

plary


substi-
compared

SEQ


tution
to BG505

ID NO













112I
W112I
Stabilize V1V2
116


112M
W112M
Stabilize V1V2
117


120T
V120T
Stabilize V1V2
149


122K
L122K
Stabilize V1V2
150


120P
V120P
Stabilize V1V2
148


202P
T202P
Stabilize V1V2
147


427I
W427I
Stabilize prefusion closed conformation
118


427M
W427M
Stabilize prefusion closed conformation
119


429N
R429N
Stabilize prefusion closed conformation
120


429L
R429L
Stabilize prefusion closed conformation
116


432P
Q432P
Destabilizes CD4-bound conformation
7, 775


432E
Q432E
Destabilizes CD4-bound conformation
42


432D
Q432D
Destabilizes CD4-bound conformation
43


433P
A433P
Destabilizes CD4-bound conformation
6, 774


434P
434P
Destabilizes CD4-bound conformation
44


435P
435P
Destabilizes CD4-bound conformation
45


436P
436P
Destabilizes CD4-bound conformation
46


437A
P437A
Destabilizes CD4-bound conformation
47


438A
P438A
Destabilizes CD4-bound conformation
48


474A
D474A
Stabilize prefusion closed conformation
118


476A
R476A
Stabilize prefusion closed conformation
124









In several embodiments, the recombinant HIV-1 Env ectodomain can include one or more (e.g., 2, 3, 4, 5, 6, 7, or 8) of the amino acid substitutions as listed in Table 7 to destabilize the CD4-induced conformation of the HIV-1 ectodomain trimer (and thereby stabilize the HIV-1 Env ectodomain trimer in the prefusion mature closed conformation). Additionally, any of the substitutions shown in Table 7 can be combined with the other stabilizing substitutions described herein to stabilize the HIV-1 Env ectodomain trimer in the prefusion mature closed conformation.


In some embodiments, the recombinant HIV-1 Env ectodomain includes one or more amino acid substitutions that destabilize the formation of the α0 helix. As described in Example 1, the α0 helix (˜residues 64-74) is present in the CD4-bound open conformation, but not the prefusion mature closed conformation, of trimeric HIV-1 Env. In some embodiments, the recombinant HIV-1 Env ectodomain includes a proline amino acid substitution at position 66 or 67, or both positions 66 and 67 (such as a H66P and/or N67P substitution) that disrupts formation of the α0 helix in the recombinant HIV-1 Env ectodomain trimer. Exemplary sequences including these mutations are set forth as SEQ ID NOs: 102-104.


In some embodiments, the recombinant HIV-1 Env ectodomain includes a non-natural disulfide bond between a pair of cysteine substitutions at one of positions 57-58 and position 77, or between position 66 or 68 and one of positions 207-209, wherein the non-natural disulfide bond destabilizes or disrupts formation of the α0 helix in the recombinant HIV-1 ectodomain. In some embodiments, the recombinant HIV-1 Env ectodomain can include a non-natural disulfide bond between a pair of cysteine substitutions at one or more of the following sets positions: 55 and 77, 57 and 77, 58 and 77, 66 and 207, 66 and 208, 66 and 209, 68 and 209, and 68 and 208, wherein the non-natural disulfide bond disrupts formation of the α0 helix in the recombinant HIV-1 ectodomain. In some embodiments, the recombinant HIV-1 Env ectodomain can include one or more of the following sets of amino acid substitutions: A55C and T77C, D57C and T77C, A58C and T77C, V66C and K207C, V66C and S209C, V68C and S209C, and V68C and V208C. Exemplary sequences including these mutations are set forth as SEQ ID NOs: 87, 98-101, and 683.


In more embodiments, the recombinant HIV-1 Env ectodomain can include a proline amino acid substitution at position 66 or 67, or both positions 66 and 67 (such as a H66P and/or N66P substitutions), and further include a pair of cysteine substitutions at positions 57 and 77, 58 and 77, 68 and 208, or 68 and 209, the combination of which disrupts formation of the α0 helix in the recombinant HIV-1 ectodomain. For example, in some embodiments, the recombinant HIV-1 Env ectodomain can include one of the following sets of amino acid substitutions: D57C/T77C, H66P, N67P; A58C/T77C, H66P, N67P; V68C/S209C, H66P, N67P; V68C/V208C, H66P, N67P; or V68C/S209C, H66P, N67P. Exemplary HIV-1 Env ectodomain sequences including these mutations are set forth as SEQ ID NOs: 105-108 and 109.


Stabilizing Gp41

In additional embodiments, the recombinant HIV-1 Env ectodomain can include one or more disulfide bonds that stabilize gp41 in the mature closed prefusion conformation. Exemplary mutations include those that can form a non-natural gp120-gp41 disulfide bond or a non-natural gp41-gp41 disulfide bond. Exemplary HIV-1 Env positions that can be mutated to cysteine to form such stabilizing disulfide bonds, as well as exemplary mutations (in the context of the BG505 strain), and sequences including the indicated mutations are provided in Table 9, below.









TABLE 9







Non-natural gp120-gp41 and gp41 disulfide bonds













Intra- or




Exemplary Env
Exemplary
Inter-

Exemplary


positions
Substitutions
protomer?
Comment
SEQ ID NO










gp120-gp41 disulfide bonds











41 and 540
G41C/Q540C
Intra
Stabilize α6/Prevent HR1 formation
14


41 and 541
G41C/A541C
Intra
Stabilize α6/Prevent HR1 formation
199, 200,






201


43 and 526
P43C/A526C
Intra
Stabilize α6/Prevent HR1 formation
15


51 and 574
T51C/K574C
Intra
Stabilize α7/Prevent HR1 formation
151


53 and 574
F53C/K574C
Intra
Stabilize α7/Prevent HR1 formation
152


51 and 578
T51C/A578C
Intra
Stabilize α7/Prevent HR1 formation
153


 43and 540
P43C/Q540C
Intra
Stabilize α6/Prevent HR1 formation
18


88 and 527
N88C/G527C
Intra
Stabilize fusion peptide
17


107 and 574 
D107C/K574C
Intra
Stabilize α7/Prevent HR1 formation
166


220 and 578 
P220C/A578C
Intra
Stabilize α7/Prevent HR1 formation
10


221 and 582 
A221C/A582C
Intra
Stabilize α7/Prevent HR1 formation
11, 16


428 and 560 
Q428C/E560C
Inter
Stabilize α6/α7 linker/Prevent HR1
163





formation


428 and 561 
Q428C/A561C
Inter
Stabilize α6/α7 linker/Prevent HR1
164





formation


428 and 562 
Q428C/Q562C
Inter
Stabilize α6/α7 linker/Prevent HR1
165





formation


498 and 610 
498C/W610C
Intra
Prevent HR1/2 formation
13


36 and 606
V36C/T606C
Intra
Prevent HR1 formation
647


37 and 606
T37C/T606C
Intra]
Prevent HR1 formation
648


41 and 537
G41C/L537C
Intra
Prevent HR1 formation
734


41 and 541
G41C/A541C
Intra
Prevent HR1 formation
736


43 and 526
P43C/A526C
Intra
Prevent HR1 formation
737


73 and 572
A73C/G572C
Intra
Prevent HR1 formation
738


84 and 521
I84C/G521C
Intra
Prevent HR1 formation
739


89 and 527
V89C/G527C
Intra
Prevent HR1 formation
740


73 and 572
A73C/G572C
Intra
Prevent HR1 formation
741


84 and 521
I84C/G521C
Intra
Prevent HR1 formation
742


89 and 527
V89C/G527C
Intra
Prevent HR1 formation
743







gp41 disulfide bonds











550 and 575 
Q550C/Q579C
Intra
Prevent HR1 formation
167, 169


551 and 575 
Q551C/Q575C
Intra
Prevent HR1 formation
168









Any one or more of the pairs of cysteine substitutions listed in Table 9 can be included on a recombinant HIV-1 Env ectodomain to generate a recombinant HIV-1 Env ectodomain trimer stabilized in the prefusion mature closed conformation. Further, the recombinant HIV-1 Env ectodomain can include any one or more of the pairs of cysteine substitutions listed in Table 9 in combination with any of the other stabilizing mutations disclosed herein to generate a recombinant HIV-1 Env ectodomain that can form a trimer stabilized in the prefusion mature closed conformation.


Additionally, the recombinant HIV-1 Env ectodomain can include the SOS (501C and 605C), IP (559P), and/or SOSIP (501C, 605C, 559P) substitutions in combination with any of the stabilizing mutations disclosed herein to generate a recombinant HIV-1 Env ectodomain that can form a trimer stabilized in the prefusion mature closed conformation.


Exemplary Combinations

In several embodiments, any two or more of the HIV-1 Env mutations disclosed herein can combined to generate the recombinant HIV-1 Env ectodomain that can form a trimer stabilized in the prefusion mature closed conformation.


For example, in some embodiments, the recombinant HIV-1 Env ectodomain can include a non-natural disulfide bond that stabilizes the protein in a PGT122-bound conformation (e.g., with a V1V2 domain in a mature closed conformation; such as a non-natural disulfide bond between one or more of positions 201 and 433) and further include one or more amino acid substitutions that stabilize gp41 in a mature closed conformation (e.g., with distinct α6 and α7 helices; such as substitutions listed in Table 9, such as 41C/540C substitutions or a SOS, IP, SOSIP substitution). In further embodiments, the recombinant HIV-1 Env ectodomain can include a non-natural disulfide bond that stabilizes the protein in a PGT122-bound conformation (e.g., with a V1V2 domain in a mature closed conformation; such as a non-natural disulfide bond between one or more of positions 201 and 433) and includes one or more mutations that destabilize the CD4 binding domain, such as a substitution at position 473, and/or includes a cavity filling substitution, and further includes one or more amino acid substitutions that stabilize gp41 in a mature closed conformation (e.g., with distinct α6 and α7 helices; such as substitutions listed in Table 9, such as 41C/540C substitutions or a SOS, IP, SOSIP substitution).


In some embodiments, the recombinant HIV-1 Env ectodomain includes a pair of cysteine substitutions at one of positions 198-202 and one of positions 428-437 that form a non-natural disulfide bond, and further includes one or more amino acid substitutions that stabilize gp41 as described above (e.g., as listed in Table 9, such as 41C/540C substitutions), and/or can further include the SOS, IP, SOSIP mutations. In a non-limiting embodiment, the recombinant HIV-1 Env ectodomain includes 201C, 433C, 501C, 605C, and 559P substitutions (such as I201C, A433C, A501C, T605C, and I559P substitutions).


In some embodiments, the recombinant HIV-1 Env ectodomain includes a pair of cysteine substitutions at one of positions 174 and 319, 195 and 433, 199 and 433, 199 and 431, 201 and 433, 221 and 582, or 304 and 440, that form a non-natural disulfide bond, and further includes one or more amino acid substitutions that stabilize gp41 as described above (e.g., as listed in Table 9, such as 41C/540C substitutions), and/or can further include the SOS, IP, SOSIP mutations. In a non-limiting embodiment, the recombinant HIV-1 Env ectodomain includes 201C, 433C, 501C, 605C, and 559P substitutions (such as I201C, A433C, A501C, T605C, and I559P substitutions). In some such embodiments, the recombinant HIV-1 Env ectodomain can further includes a tryptophan substitution at position 223, or a proline substitution at position 432 or 433.


In more embodiments, the recombinant HIV-1 Env ectodomain includes two pairs of cysteine substitutions at one of positions (i) 195 and 433, and 304 and 440; (ii) 195 and 433, and 174 and 319; (iii) 199 and 433, and 304 and 440; (iv) 199 and 433, and 174 and 319; (v) 201 and 433, and 304 and 440; (vi) 201 and 433, and 174 and 319; that form two non-natural disulfide bonds, and can further includes one or more amino acid substitutions that stabilize gp41 as described above (e.g., as listed in Table 9, such as 41C/540C substitutions), and/or can further include the SOS, IP, SOSIP mutations. In a non-limiting embodiment, the recombinant HIV-1 Env ectodomain includes 201C, 433C, 501C, 605C, and 559P substitutions (such as I201C, A433C, A501C, T605C, and I559P substitutions). In some such embodiments, the recombinant HIV-1 Env ectodomain can further includes a tryptophan substitution at position 223, or a proline substitution at position 432 or 433. Exemplary immunogens include those with a BG505gp140.6R.SOSIP.664 background sequence further including I201C/A433C and R304C/Q440C substitutions; S199C/A433C and R304C/Q440C substitutions; I201C/A433C and V120C/Q315C substitutions; G473P and V120C/Q315C substitutions; G473Y and V120C/Q315C substitutions; G473P and R304C/Q440C substitutions; G473Y and R304C/Q440C substitutions; N425C/A433C and V120C/Q315C substitutions; and I201C/A433C and V120C/Q315C substitutions.


In additional embodiments, the recombinant HIV-1 Env ectodomain can include a combination of two or more non-natural disulfide bonds between pairs of cysteine substitutions as described above that (e.g., as listed in Table 6). Non-limiting examples of combinations of two or more non-natural disulfide bonds between pairs of cysteine substitutions are provided in Table 10. In some embodiments, the recombinant HIV-1 Env ectodomain can include one or more pairs of cysteine substitutions as described above that form a non-natural disulfide bond (e.g., as listed in Table 6), or a combination of pairs of cysteine substitutions as listed in Table 10, and further includes one or more amino acid substitutions that stabilize gp41 as described above (e.g., as listed in Table 9, such as 41C/540C substitutions), and/or can further include the SOS, IP, SOSIP mutations.









TABLE 10







Exemplary combinations of cysteine substitutions


to generate non-natural disulfide bonds











Exemplary


Positions
Exemplary substitutions
SEQ ID NO












200C/313C, 51C/574C
A200C/P313C, T51C/K574C
151


200C/313C, 53C/574C
A200C/P313C, F53C/K574C
152


200C/313C, 51C/578C
A200C/P313C, T51C/A578C
153


128C/165C, 200C/313C,
T128C/L165C, A200C/P313C,
154


51C/574C
T51C/K574C


128C/165C, 200C/313C,
T128C/L165C, A200C/P313C,
155


53C/574C
F53C/K574C


128C/165C, 200C/313C,
T128C/L165C, A200C/P313C,
156


51C/578C
T51C/A578C









In some embodiments, the recombinant HIV-1 Env ectodomain can include a non-natural disulfide bond that stabilizes the protein in a PGT122-bound conformation (e.g., with a V1V2 domain in a mature closed conformation; such as a non-natural disulfide bond between one or more of positions 128 and 167, 174 and 318, 175 and 319, 204 and 434, 204 and 436, or 318 and 437) and further includes one or more mutations that destabilize the CD4 binding domain, such as a substitution at position 473 (such as a G473A substitution). For example, in some embodiments, the recombinant HIV-1 Env ectodomain can include one of the following sets of amino acid substitutions: T128C/T167C and G473A, S174C/A318C and G473A, L175C/A319C and G473A, A204C/M434C and G473A, A204C/A436C and G473A, or Y318C/P437C and G473A. In additional such embodiments, the recombinant HIV-1 Env ectodomain can further include one or more amino acid substitutions that stabilize gp41 as described above (e.g., as listed in Table 9, such as 41C/540C substitutions), and/or can further include the SOS, IP, SOSIP mutations. Exemplary gp140 sequences including such substitutions are set forth as SEQ ID NOs: 53, 55, 56, 58, 59, 72.


In additional embodiments, the recombinant HIV-1 Env ectodomain can include a cavity filling substitution as described above, and further includes an amino acid substitution that destabilizes the CD4-induced conformation of HIV-1 Env, such as a A433P substitution. In additional such embodiments, the recombinant HIV-1 Env ectodomain can further include one or more amino acid substitutions that stabilize gp41 as described above (e.g., as listed in Table 9, such as 41C/540C substitutions), and/or can further include the SOS, IP, SOSIP mutations. In a non-limiting embodiment, the recombinant HIV-1 Env ectodomain includes 433P, 501C, 605C, and 559P substitutions (such as A433P, A501C, T605C, and I559P substitutions).


In additional embodiments, the recombinant HIV-1 Env ectodomain includes a combination of two or more of the stabilizing substitutions described herein. For example, the recombinant HIV-1 Env ectodomain can include 429L and 427M (e.g., R429L and W427M substitutions), 437A and 438A (e.g., P437A and P438A substitutions), or 474A and 476A (e.g., D474A and R476A substitutions). In additional such embodiments, the recombinant HIV-1 Env ectodomain can further include one or more amino acid substitutions that stabilize gp41 as described above (e.g., as listed in Table 9, such as 41C/540C substitutions), and/or can further include the SOS, IP, SOSIP mutations. Exemplary sequences including these substitutions include those provided as SEQ ID NOs: 49, 115, and 122.


Additionally, any of the above cavity filling substitutions can be combined with the other stabilizing substitutions described herein to stabilize the HIV-1 Env ectodomain trimer in the prefusion mature closed conformation. For example, in some embodiments, the recombinant HIV-1 Env ectodomain includes a cavity filling substitution as described above, such as at one or more of gp120 positions 50, 110, 114, 117, 117, 120, 121, 121, 123, 159, 220, 426, 220, 429, and further includes substitutions to introduce a non-natural disulfide bond, such as I201C/A433C substitutions. In some non-limiting embodiments, the recombinant HIV-1 Env ectodomain includes a non-natural disulfide bond between I201C and A433C substitutions and further includes one of a T50W, S110W, Q114W, K117W, K117E, V120W, K121W, K121E, T123W, F159Y, M426W, P220W, or R429W cavity filling amino acid substitution. In some embodiments, the recombinant HIV-1 Env ectodomain includes a cavity filling substitution at position 193 (e.g., L193F), and further includes substitutions to introduce a non-natural disulfide bond between positions 195 and 423, such as N195C/I423C substitutions; an exemplary sequence is set forth as SEQ ID NO: 688. In some embodiments, the recombinant HIV-1 Env ectodomain includes a cavity filling substitution at position 431 (e.g., G431F), and further includes substitutions to introduce a non-natural disulfide bond between positions 202 and 434, such as T202C/M434C substitutions; an exemplary sequence is set forth as SEQ ID NO: 655. In some non-limiting embodiments, the recombinant HIV-1 Env ectodomain includes a non-natural disulfide bond between I201C and A433C substitutions and further includes one of a T50W, S110W, Q114W, K117W, K117E, V120W, K121W, K121E, T123W, F159Y, M426W, P220W, or R429W cavity filling amino acid substitution. In additional such embodiments, the recombinant HIV-1 Env ectodomain can further include one or more amino acid substitutions that stabilize gp41 as described above (e.g., as listed in Table 9, such as 41C/540C substitutions), and/or can further include the SOS, IP, SOSIP mutations. Exemplary recombinant HIV-1 Env ectodomain sequences including such substitutions are set forth as SEQ ID NOs: 120, 183-194.


In several embodiments, the recombinant HIV-1 Env ectodomain can include a combination of substitutions as set forth in Table 11, that include at least one cavity filling substitution.









TABLE 11







Exemplarity cavity-filling amino acid substitutions












Exemplary
Exemplary
Exemplary



Position
substitutions
Substitutions
SEQ ID NO
Cavity Location (CL) and stabilizing mechanism (SM)














120, 203
201:
V120W, Q203V
129
CL: Under V1V2 cap at N-term of β2



F, W, Y, L, I, M;


SM: stabilize prefusion cap/prevent bridging sheet formation,



203:


β2 extends in CD4-bound state, this stabilizes small



F, W, Y, L, I, M, V


hydrophobic pocket in ground state


 39, 534
39: W, M, I, F
Y39F, S534V;
47-48
CL: gp120/gp41 interface



534: I, W, F, A, M,
Y39W, S534A

SM: fill cavity and add hydrophobic interactions at the gp120-



V


gp41 interactive surface


39, 534 +
39: W, M, I, F;
Y39F, S534V,
49
CL: gp120/gp41 interface


T37V,
534: I, W, F, A, M,
T37V, T499V

SM: fill cavity and add hydrophobic interactions at the gp120-


T499V
V


gp41 interactive surface


39, 534 +
39: W, M, I, F;
Y39F, Y40F,
50
CL: gp120/gp41 interface


Y40F,
534: I, W, F, A, M,
S534V, T37V,

SM: fill cavity and add hydrophobic interactions at the gp120-


T37V,
V
T499V

gp41 interactive surface


T499V


 53, 246
246: F, W, Y, L, I,
F53W, Q246W
197
CL: gp120-gp41 interface, N-term of β2, middle of β8



M, V


SM: Fill a cavity between gp120 and gp41 to stabilize gp41






disordered region and gp120/gp41 interaction


  68, 209,
68: F, W, Y, L, I, M
V68L, S209R
196
CL: Loop between α1 and β0 and loop between β3 and β4






SM: Fill cavities that are otherwise filled by CD4 induced α0






formation


125,
F, W, Y, L, I, M, V
L125W_deltaP124
131
CL: Cavity between N-term of V1V2 domain and V3 near


delP124



residue 127 and 126-196 disulfide of V1V2






SM: Removal of ground state destabilization/flexibility cavity






filling/proline removal


139, 326
139: F. M, I, Y,
T139W, I326R
45
CL: at the interface of V1V2 and V3 loops



T;


SM: Stabilize interactions between V1V2 and V3 loops in the



326: M, W, F,


mature closed state



Y, R


151, 153,
153: F, W, Y, L, I,
R151E, E153W,
132
CL: V1 loop at position 153


328
M, V;
Q328W

SM: Adding hydrophobic patch at V1 loop to V3 loop



328: F, W, Y, L, I,



M, V


177, 323
323: F, Y, W
Y177W, I332F
198
CL: C-term of beta C, C-term of beta V3B,






SM: Fills cavity between V3 and gp120 core to stabilize closed






V1V2 cap


180, 421,
421: F, W, Y; 180:
D180L, K421W
123
CL: V1V2 interaction near residue 180 with V3 and base of



L, V, I, M


β21






SM: This will stabilize v1v2 to v3 along with destabilizing β21






from adopting CD4-bound-conformation


201, 423
F, Y, L, M, V
I201W, I423W
173
CL: parallel β #






SM: prevent bridging sheet formation


223, 544
223: Y, W
F223W, L544Y
32
CL: gp41 tip of α6



544: F, Y, W


SM: stabilize gp120/gp41 interface


L125, 195 
W
L125W, I195W
701
CL: V1V2-V3 interface near 126-196 disulfide bond


176, 323
176: Y, W; 323:
F176W/I323Y
730
CL: gp120 V1/V2/V3, stabilize V1/V2/V3



F, Y, W


176, 154
176: Y, W; 154:
F176W/L154W
731
CL: gp120 V1/V2, stabilize V1/V2/V3



F, Y, W


159, 154
159: Y, W; 154:
F159Y/L154W
732
CL: gp120 V1/V2, stabilize V1/V2/V3



F, Y, W


I251, 260 
F
I251F/L260F
658
CL: Engineering hydrophobic core between gp120 V2/V3 with






double F substitution to stabilize V1/V2/V3









In some embodiments, the recombinant HIV-1 Env ectodomain comprises gp120-gp41 protomers comprising the SOSIP and 201C/433C substitutions and further comprising a cavity filling substitution (such as a Y, F, or M substitution) at any one of positions: 70; 75; 110; 111; 112; 115; 117; 118; 120; 153; 154; 159; 164; 172; 175; 176; 179; 191; 193; 194; 198; 202; 204; 208; 223; 304; 307; 309; 315; 316; 323; 423; 427; 430; 432; 432; 436; 544; 580; 583; 159 and 323; 44 and 537; 544 and 223; 544, 537, and 223; 580 and 583; 125 and 194; 134, 175, 322, and 326; 134, 322, and 326; 134, 136, 150, and 326; 154, 300, 302, and 320; 120, 203, and 318; 120 and 315; 177 and 420; 177, 328, and 420; 116, 426, and 432; 426 and 432; 134, 175, 322, 326, 136, and 150; 120, 203, 318, and 315; 154, 300, 302, 320, 177, and 420; or 139, 140, 324, and 325.


In some embodiments, the recombinant HIV-1 Env ectodomain comprises gp120-gp41 protomers comprising the SOSIP and 201C/433C substitutions and further comprising a substitution to destabilize the CD4-induced conformation, such as a F210A; F210S; Q432P; R429N; R429L; R429L and W427M; T202P; or V120T substitution


In some embodiments, the recombinant HIV-1 Env ectodomain comprises gp120-gp41 protomers comprising the SOSIP and 201C/433C substitutions and further comprising cysteine substitutions to introduce a non-natural disulfide bond, such as T538C and Q652C; R304C and Q440C; G431GC and S199C; A58C and T77C; D57C and T77C


In some embodiments, the recombinant HIV-1 Env ectodomain comprises gp120-gp41 protomers comprising the SOSIP and 201C/433C substitutions and further comprising substitutions to disrupt formation of helix 0, such as W69P; V68P; T71P; N67P; H66P; or N67P and H66P


In some embodiments, the recombinant HIV-1 Env ectodomain comprises gp120-gp41 protomers comprising the SOSIP and 201C/433C substitutions and further comprising substitutions to destabilize the gp41 helix bundle, such as I573T; G594N; I573T and G594N; I573T and G594N and K574E; I573T, G594N, and K574T.


N-Linked Glycosylation Sites

In several embodiments, the recombinant HIV-1 Env ectodomain trimer can includes one or more N-linked glycosylation sites introduced onto the membrane proximal portion of the trimer to mask non-neutralizing epitopes present on this portion of the trimer. Such mutations are typically utilized in soluble embodiments of the recombinant HIV-1 Env ectodomain trimer. To create an N-linked glycosylation site, the sequence Asn-X-Ser/Thr (where X is any amino acid except Pro) can to be introduced. This can be accomplished by substitution of a Ser/Thr amino acid two residues C-terminal to a native Asn residue, or by substitution of an Asn amino acid two residues N-terminal to a native Ser/Thr residue, or by substitution of both an Asn and Ser/Thr residue separated by one non-proline amino acid. In some embodiments, the recombinant HIV-1 Env ectodomain comprises one or more amino acid substitutions that introduce an N-linked glycosylation site at the N-terminus of the gp120 polypeptide, the C-terminus of the gp120 polypeptide, and/or the C-terminus of the gp41 polypeptide. Exemplary amino acid substitutions for introducing one or more such N-linked glycosylation sites are provided under code D of the Table in Table 13, and are provided in Table 12, below:









TABLE 12







Exemplary N-linked glycan mutants


to mask non-neutralizing epitopes.









Glycan
Exemplary
Exemplary


position
substitutions
SEQ ID NO












504
504N/506T
453


661
661N/663T
454


504 and 661
504N/506T, 661N/663T
455


502
K502N/R504T
456


658
Q658N/L660T
457


 33
W35T
458


 35
W35N
459


 35 and 504
W35N, R504N/V506T
460


 33 and 661
W35T, L661N/L663T
461


502 and 661
K502N/R504T, L661N/L663T
462









Antibody Stabilization

In additional embodiments, the disclosed immunogens can include a recombinant HIV-1 Env ectodomain trimer covalently linked (e.g., by a non-natural disulfide bond) to one or more neutralizing antibodies, such as the VRC01, PGT122, or 35O22 antibodies. Linkage to the neutralizing antibody can increase the stability of the immunogen in the prefusion mature closed conformation.


35O22

In some embodiments, the recombinant HIV-1 Env ectodomain trimer includes a recombinant HIV-1 Env ectodomain including a cysteine substitution that can form a non-natural disulfide bond with a cysteine residue in the heavy or light chain variable region of the 35O22 monoclonal antibody. For example, in some embodiments, the HIV-1 ectodomain includes a cysteine substitution at position 90, which can form a non-natural disulfide bond with a cysteine at position 80 (kabat numbering) of the 35O22 heavy chain variable region. In some embodiments, the HIV-1 ectodomain includes a cysteine substitution at position 238, which can form a non-natural disulfide bond with a cysteine at position 77 (kabat numbering) of the 35O22 heavy chain variable region. In some embodiments, the HIV-1 ectodomain includes a cysteine substitution at position 529, which can form a non-natural disulfide bond with a cysteine at position 111 (kabat numbering) of the 35O22 heavy chain variable region. In some embodiments, the HIV-1 ectodomain includes a cysteine substitution at position 624, which can form a non-natural disulfide bond with a cysteine at position 109 or 112 (kabat numbering) of the 35O22 heavy chain variable region. In some embodiments, the HIV-1 ectodomain includes a cysteine substitution at position 625, which can form a non-natural disulfide bond with a cysteine at position 109 (kabat numbering) of the 35O22 heavy chain variable region. Exemplary sequences for use in such embodiments are provided under code C of the Table in Table 13. For example, exemplary recombinant HIV-1 Env ectodomain sequences including such cysteine substitutions are set forth as SEQ ID NOs: 401-405, and 411. Additionally, exemplary 35O22 heavy chain variable region sequences for use in such embodiments are set forth as SEQ ID NOs: 406-410.


VRC01

In some embodiments, the recombinant HIV-1 Env ectodomain trimer includes a recombinant HIV-1 Env ectodomain including a cysteine substitution that can form a non-natural disulfide bond with a cysteine residue in the heavy or light chain variable region of the VRC01 monoclonal antibody. In some embodiments, the recombinant HIV-1 Env ectodomain trimer includes a recombinant HIV-1 Env ectodomain including a cysteine substitution at position 449 (e.g., a G459C substitution, HXB2 numbering) that can form a non-natural disulfide bond with a heavy chain variable region of a VRC01 monoclonal antibody comprising a cysteine substitution at heavy chain position 60 or 61 (kabat numbering). Exemplary sequences for use in such embodiments are provided under code C of the Table in Table 13. For example, exemplary recombinant HIV-1 Env ectodomain sequences including a position 459 cysteine substitution are set forth as SEQ ID NOs: 412-436. Exemplary VRC01 heavy and light chain sequences for use in such embodiments (e.g., including heavy chain variable region with a cysteine substitution at position 60 or 61) are set forth as SEQ ID NOs: 437-448.


PGT122

In some embodiments, the recombinant HIV-1 Env ectodomain trimer includes a recombinant HIV-1 Env ectodomain including a cysteine substitution that can form a non-natural disulfide bond with a cysteine residue in the heavy or light chain variable region of the PGT122 monoclonal antibody. In some embodiments, the recombinant HIV-1 Env ectodomain trimer includes a recombinant HIV-1 Env ectodomain including a cysteine substitution at position β23 (e.g., a 1323C substitution, HXB2 numbering) that can form a non-natural disulfide bond with a heavy chain variable region of a PGT122 monoclonal antibody comprising a cysteine substitution at heavy chain position 29 or 67 (kabat numbering). Exemplary sequences for use in such embodiments are provided under code C of the Table in Table 13. For example, exemplary recombinant HIV-1 Env ectodomain sequences including a position β23 cysteine substitution are set forth as SEQ ID NOs: 449-450. Exemplary VRC01 heavy and light chain sequences for use in such embodiments (e.g., including heavy chain variable region with a cysteine substitution at position 29 or 67) are set forth as SEQ ID NOs: 451-452.


Chimeric Env Ectodomains

In some embodiments, the recombinant HIV-1 Env ectodomain stabilized in the prefusion mature closed conformation can include sequences from multiple strains of HIV-1. For example, the recombinant HIV-1 Env ectodomain can include a gp120 sequence from a first HIV-1 strain and a gp41 sequence from a heterologous HIV-1 strain, or a particular structural domain (such as the V1V2 domain) from a HIV-1 strain of interest (such as CAP256.SU, a BB201.B42, a KER2018.11, a CH070.1, a ZM233.6, a Q23.17, a A244, a T250-4, or a WITO.33) with the remainder of the HIV-1 Env ectodomain from a heterologous HIV-1 strain (such as BG505). The chimeric HIV-1 Env ectodomain can further include any of the amino acid substitutions described herein, for example the 201C/433C, SOSIP, and DS substitutions for stabilization in the prefusion mature closed conformation. In the context of inducing an immune response in a subject that can control infection across multiple HIV-1 strains, the use of immunogens based on diverse HIV-1 strains can overcome the intrinsic sequence diversity of HIV-1 Env. Exemplary sequences of recombinant HIV-1 Env ectodomains linked to a nanoparticle subunit are provided under code H in Table 13 included in Example 15.


Exemplary sequences of chimeric HIV-1 Env ectodomain trimers that include the V1V2 domain sequence (positions 126-196) of the CAP256.SU, BB201.B42, KER2018.11, CH070.1, ZM233.6, Q23.17, A244, T250-4, or WITO.33 strains of HIV-1, with the remainder including BG505.SOSIP.DS.368R sequence, are provided as follows: Q23.17 V1V2 chimera (SEQ ID NO: 2126), ZM233.6 V1V2 chimera (SEQ ID NO: 2125), WITO.33 V1V2 chimera (SEQ ID NO: 2128), A244 V1V2 chimera (SEQ ID NO: 2127), BB201.B42 V1V2 chimera (SEQ ID NO: 2122), KER2018.11 V1V2 chimera (SEQ ID NO: 2123), CH070.1 V1V2 chimera (SEQ ID NO: 2124), CAP256.SU V1V2 chimera (SEQ ID NO: 2121), and T-250-4 V1V2 chimera (SEQ ID NO: 2129).


Platform

As described in the Examples, prefusion mature gp41 wraps its hydrophobic core around extended N- and C-termini-strands of gp120 (see FIGS. 11 and 38). Accordingly, in some embodiments, the recombinant HIV-1 Env ectodomain trimer can include a membrane proximal “platform” including the N- and C-terminal regions of gp120, and the gp41 ectodomain, from a first HIV-1 strain (such as BG505), and the remainder of gp120 from one or more heterologous HIV-1 strains. This chimeric design allows for production of heterogeneous HIV-1 Env proteins that comprise membrane distal features of interest (such as the V1V2 domain, V3 domain, and CD4 binding site).


In some embodiments, the recombinant Env ectodomain includes N- and C-terminal regions of gp120 as well as the gp41 ectodomain from a first HIV-1 strain (such as BG505, for example, with SOSIP substitutions), and the remainder of gp120 from a heterologous HIV-1 strain. In some embodiments, the heterologous HIV-1 strain can be a subtype A (such as BI369.9A, MB201.A1, QH209.14M.A2), subtype B (such as AC10.29), subtype C (such as 0921.V2.C14, 16055-2.3, 25925-2.22, 286.36, CAP45.G3, CNE58, DU156.12, DU422.01, MW965.26, ZM53.12, ZM55.28a, ZM106.9), subtype CRF AC (such as 3301.V1.C24, 6545.V4.C1), subtype CFR AE (such as 620345.c1, C1080.c3, C4118.09, CNE55, TH966.8) and subtype CRF BC (such as CH038.12, CH117.4) strain of HIV-1.


In some embodiments, the recombinant HIV-1 Env ectodomain can include a gp41 ectodomain, an N-terminal region of the gp120 polypeptide comprising a β-4 strand and a C-terminal region of the gp120 polypeptide comprising a β26 strand from a first strain of HIV-1 (such as BG505), and all or a portion of the remaining residues of the gp120 polypeptide are from one or more heterologous HIV-1 strains. The heterologous strain can be, for example, one of CAP256.SU (SEQ ID NO: 51), a BB201.B42 (SEQ ID NO: 81), a KER2018.11 (SEQ ID NO: 107), a CH070.1 (SEQ ID NO: 174), a ZM233.6 (SEQ ID NO: 745), a Q23.17 (SEQ ID NO: 746), a A244 (SEQ ID NO: 747), a T250-4 (SEQ ID NO: 2114), a WITO.33 (SEQ ID NO: 748), a 426c (with N276D, N460D, N463D, SEQ ID NO: 2144, a d45-01dG5 (2145), or a JRFL (SEQ ID NO: 2115) strain of HIV-1. In additional embodiments, the N-terminal region of the gp120 polypeptide can further include the β-3 strand from the first HIV-1 strain (such as BG505). In more embodiments the C-terminal region of the gp120 polypeptide can further include the β25 strand or the β25 strand and all or a portion of the α5 helix from the first HIV-1 strain (such as BG505). In more embodiments, the N-terminal region of the gp120 polypeptide can include from 5 to 30 (such as 10, 30, 5-20, 5-25, 5-15, 5-10, 10-20, 20-30, 15-25, or 5, 10, 15, 20, 25) amino acids and/or the C-terminal region of the gp120 polypeptide can include from 5-40 (such as 10-40, 5-30, 5-25, 5-20, 10-20, 20-30, 30-40, 10-30, 20-40, or 5, 10, 15, 20, 25, 30, or 35) amino acids, from the N- or C-terminus of the gp120 polypeptide, respectively, from the first strain of HIV-1 (such as BG505). Any of the stabilizing amino acid substitutions (such as the SOSIP substitutions, and/or the 201C/433C substitutions) can be included in the chimeric HIV-1 Env ectodomain.


In some embodiments, the recombinant Env ectodomain can include gp120 residues 31-45 and 478-507, and gp41 residues (e.g., 512-664) from the first HIV-1 strain (such as BG505), and the remainder of the gp120 residues in the Env protein can be from a heterologous HIV-1 strain. For example, the recombinant Env ectodomain can include gp120 positions 31-45 and 478-507, and gp41 residues (e.g., 512-664) from the BG505 strain with SOSIP substitution (e.g., as set forth as SEQ ID NO: 3), and the remaining gp120 residues in the Env ectodomain can be from any one of the CAP256.SU, BB201.B42, KER2018.11, CH070.1, ZM233.6, Q23.17, A244, WITO.33, JRFL, 426c (with N276D, N460D, N463D), d45-01dG5, BI369.9A, MB201.A1, QH209.14M.A2, 0921.V2.C14, 16055-2.3, 25925-2.22, 286.36, CAP45.G3, DU156.12, DU422.01, MW965.26, ZM53.12, ZM55.28a, ZM106.9, 3301.V1.C24, 6545.V4.C1, 620345.c1, C1080.c3, C4118.09, CNE55, TH966.8, AC10.29, CH038.12, CNE58, or CH117.4 strains of HIV-1. Any of the stabilizing amino acid substitutions (such as the SOSIP substitutions, and/or the 201C/433C substitutions) can be included in the chimeric HIV-1 Env ectodomain. Non-limiting examples of sequences of such chimeric HIV-1 Env ectodomains (that may also include one or more amino acid substitutions, such as 201C/433C and SOSIP substitutions to stabilize the HIV-1 ectodomain in the prefusion mature closed conformation) are provided herein as SEQ ID NOs: 379-386, 387, 764-772, and 856-1036. Thus, in some embodiments, the recombinant HIV-1 Env protein includes an amino acid sequence set forth as any one of SEQ ID NOs: 379-386, 387, 764-772, and 856-1036, or an amino acid sequence at least 80% (such as at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to any one of SEQ ID NOs: 379-386, 387, 764-772, and 856-1036. In a preferred embodiment, the recombinant HIV-1 Env protein includes an amino acid sequence set forth as any one of SEQ ID NOs: 856, 872, 881, 888, 902, 908, 917, 924, 930, 933, 937, 938, 940, 953, 956, 962, 964, 978, 871, 973, 990, 1010, 1025, 1034, or 1098, or an amino acid sequence at least 80% (such as at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to any one of SEQ ID NOs: 856, 872, 881, 888, 902, 908, 917, 924, 930, 933, 937, 938, 940, 953, 956, 962, 964, 978, 871, 973, 990, 1010, 1025, 1034, or 1098.


Interface Residues

In more embodiments, the gp120 portion of the recombinant HIV-1 Env ectodomain (from the heterologous HIV-1 strain) can further include one or more substitutions at the gp120-gp41 interface that introduce residues from the first HIV-1 strain. In some embodiments, such substitutions can enhance the stabilization of the HIV-1 ectodomain in the prefusion mature conformation by maintaining native BG505 interaction between the membrane proximal “platform” and the core gp120. In some embodiments, the substitutions at the gp120-gp41 interface that introduce residues from the first HIV-1 strain can include substitutions at gp120 positions 46-54, 70-75, 84-89, 99, 102, 106, 107, 114, 215, 220-224, 226, 244, 471-473, and 476-477 (referred to herein as “Interface Residue Set A”). In some embodiments, the recombinant HIV-1 Env ectodomain includes gp120 residues 31-45 and 478-507, and gp41 residues (e.g., 512-664), from a first HIV-1 strain (such as the BG505 strain), and includes gp120 residues 46-477 from a heterologous strain of HIV-1 (such as the CAP256.SU, BB201.B42, KER2018.11, CH070.1, ZM233.6, Q23.17, A244, WITO.33, JRFL, 426c (with N276D, N460D, N463D), d45-01dG5, BI369.9A, MB201.A1, QH209.14M.A2, 0921.V2.C14, 16055-2.3, 25925-2.22, 286.36, CAP45.G3, DU156.12, DU422.01, MW965.26, ZM53.12, ZM55.28a, ZM106.9, 3301.V1.C24, 6545.V4.C1, 620345.c1, C1080.c3, C4118.09, CNE55, TH966.8, AC10.29, CH038.12, CNE58, or CH117.4 strain of HIV-1), and further includes substitutions in the gp120 residues from the heterologous strain that introduce residues from the first HIV-1 strain at the Interface Residue Set A positions of gp120. Non-limiting examples of sequences of such chimeric HIV-1 Env ectodomains (that may also include one or more amino acid substitutions, such as 201C/433C and SOSIP substitutions to stabilize the HIV-1 ectodomain in the prefusion mature closed conformation) are provided herein as SEQ ID NOs: 579-586, 588-595, and 1036-1056. Thus, in some embodiments, the recombinant HIV-1 Env protein includes an amino acid sequence set forth as any one of SEQ ID NOs: 579-586, 588-595, and 1036-1056, or an amino acid sequence at least 80% (such as at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to any one of SEQ ID NOs: 579-586, 588-595, and 1036-1056.


Additional Description of Chimeric Domains

In some embodiments, the chimeric HIV-1 Env ectodomain can further include additional structural domains or elements from the first HIV-1 strain (such as BG505) in place of those of the heterologous strain, for example, strand C of the V1V2 domain (such as gp120 positions 166-173), a V3 domain (such as gp120 positions 296-331), a V2 loop (such as gp120 positions 154-205), a V1 loop (such as gp120 positions 119-153), positions 191-205. In some embodiments, the chimeric HIV-1 Env ectodomain can include from the first HIV-1 strain (such as BG505): a V2 loop and a V3 loop; a Strand C of the V1V2 domain and a V3 domain; positions 191-205 and a Strand C of the V1V2 domain; a V1 loop and a V3 domain; a V1 loop, a Strand C of the V1V2 domain, and a V3 domain; a V1 loop, a V2 loop, and a V3 domain; or a V1V2 domain. Exemplary sequences concerning such chimeric HIV-1 Env ectodomains are provided as SEQ ID NOs: 1727-1764.


Chimeras of Three Strains

In additional embodiments, the recombinant HIV-1 Env ectodomain trimer can be a chimera having unique antigenic characteristics that provide for binding to mature and unmutated common ancestor (UCA) forms of multiple classes of broadly neutralizing antibodies (e.g., targeting the CD4 binding site and the V1V2 domain). Such recombinant HIV-1 Env ectodomain trimers are of particular interest for use as a “prime” immunogen in a prime-boost immunization protocol for eliciting an immune response to HIV-1 Env.


For example, in some embodiments, the recombinant HIV-1 Env ectodomain trimer can be a chimera comprising amino acid sequences from three HIV-1 strains, including a membrane proximal “platform” from a first strain, a V1V2 domain from a second strain, and the remainder from a heterologous strain. In a non-limiting example, the V1V2 domain can be from an Env protein (such as one of CAP256.SU, BB201.B42, KER2018.11, CH070.1, ZM233.6, Q23.17, A244, T250-4, or WITO.33) that binds to a UCA form of a broadly neutralizing antibody (e.g., VRC26 or PGT145), such as described in Example 13. The remainder sequences of the chimera can also be from an Env protein that binds to a UCA form of a broadly neutralizing antibody (such as 45_01dG5 or 426c with amino acid substitutions to remove N-linked glycan sequons at positions 276, 460, 463), such as a UCA form or a VRC01-class antibody, for example VRC01 gHgL as described in Example 13. The sequences of the first, second, and heterologous strains are further modified to include the one or more amino acid substitutions that stabilize the recombinant HIV-1 Env ectodomain trimer in the prefusion mature closed conformation (such as SOS, IP, and DS substitutions), and can also include additional substitutions as needed, for example, substitutions to increase protease cleavage (such as the R6 substitution), or to increase or decrease the desired number of glycans (such as addition of glycan sequons at positions 504 and 661, and/or at position 332).


In some embodiments, the recombinant HIV-1 Env ectodomain trimer can be a chimera comprising amino acid sequences from three HIV-1 strains, wherein the recombinant HIV-1 Env ectodomain includes (1) a gp41 ectodomain (such as positions 512-664), an N-terminal region of the gp120 polypeptide comprising a 3-4 strand, and a C-terminal region of the gp120 polypeptide comprising a β26 strand, from a first strain of HIV-1 (such as BG505), (2) a V1V2 domain (such as gp120 positions 126-196) of the gp120 polypeptide from a second strain of HIV-1 (such as one of CAP256.SU, BB201.B42, KER2018.11, CH070.1, ZM233.6, Q23.17, A244, T250-4, or WITO.33; and (3) the remaining sequence of the gp120 polypeptide from a heterologous strain of HIV-1 (such as 45_01dG5 or 426c with amino acid substitutions to remove N-linked glycan sequons at positions 276, 460, 463). In some such embodiments, the N-terminal region of the gp120 polypeptide can further comprises a β-3 strand from the first HIV-1 strain; and the C-terminal region of the gp120 polypeptide further comprises a β25 strand or a β25 strand and a α5 helix from the first HIV-1 strain. In additional embodiments, the N- and C-terminal regions of the gp120 polypeptide comprise gp120 positions 31-45 and 478-508, respectively. the gp120 polypeptide can further comprises positions 46-54, 70-75, 84-89, 99, 102, 106, 107, 114, 215, 220-224, 226, 244, 471-473, and 476-477 from the first HIV-1 strain. The sequences of the first, second, and heterologous strains are further modified to comprise the one or more amino acid substitutions that stabilize the recombinant HIV-1 Env ectodomain trimer in the prefusion mature closed conformation.


In some embodiments, the second and heterologous strains are respectively one of: CAP256.SU and 426c; BB201.B42 and 426c; KER2018.11 and 426c; CH070.1 and 426c; ZM233.6 and 426c; Q23.17 and 426c; A244 and 426c; T250-4 and 426c; WITO.33 and 426c; CAP256.SU and 45_01dG5; BB201.B42 and 45_01dG5; KER2018.11 and 45_01dG5; CH070.1 and 45_01dG5; ZM233.6 and 45_01dG5; Q23.17 and 45_01dG5; A244 and 45_01dG5; T250-4 and 45_01dG5; or WITO.33 and 45_01dG5; and wherein the 426c strain further comprises amino acid substitutions to remove the N-linked glycan sequons at positions 276, 460, 463. The sequences of the first, second, and heterologous strains are further modified to include the one or more amino acid substitutions that stabilize the recombinant HIV-1 Env ectodomain trimer in the prefusion mature closed conformation (such as SOS, IP, and DS substitutions), and can also include additional substitutions as needed,


In some embodiments, the second HIV-1 strain (providing the V1V2 domain) can be one of BI369.9A, MB201.A1, QH209.14M.A2, 0921.V2.C14, 16055-2.3, 25925-2.22, 286.36, CAP45.G3, DU156.12, DU422.01, MW965.26, ZM53.12, ZM55.28a, ZM106.9, 3301.V1.C24, 6545.V4.C1, 620345.c1, C1080.c3, C4118.09, CNE55, TH966.8, AC10.29, CH038.12, CNE58, CH117.4, CAP256.SU, BB201.B42, KER2018.11, CH070.1, ZM233.6, Q23.17, A244, T250-4, WITO.33, or JRFL. For example, the second HIV-1 strain can be one of CAP256.SU, BB201.B42, KER2018.11, CH070.1, ZM233.6, Q23.17, A244, T250-4, WITO.33, and JRFL.


Non-limiting examples of sequences of such chimeric HIV-1 Env ectodomains (that may also include one or more amino acid substitutions, such as 201C/433C and SOSIP substitutions to stabilize the HIV-1 ectodomain in the prefusion mature closed conformation) are provided herein as SEQ ID NOs: 2146-2159. Thus, in some embodiments, the recombinant HIV-1 Env protein includes an amino acid sequence set forth as any one of SEQ ID NOs: 2146, 2147, 2148, 2149, 2150, 2151, 2152, 2153, 2154, 2155, 2156, 2157, 2158, or 2159, or an amino acid sequence at least 80% (such as at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to any one of SEQ ID NOs: 2146, 2147, 2148, 2149, 2150, 2151, 2152, 2153, 2154, 2155, 2156, 2157, 2158, or 2159.


Residue Set B

In more embodiments, the gp120 portion of the recombinant HIV-1 Env ectodomain (from the heterologous HIV-1 strain) can include additional substitutions to alter the antigenicity of the ectodomain. In some embodiments, the substitutions at the gp120-gp41 interface that introduce residues from the first HIV-1 strain can include substitutions at gp120 positions 133-134, 164, 169, 308, and 316 (referred to herein as “Residue Set B”). In some embodiments, the recombinant HIV-1 Env ectodomain includes gp120 residues 31-45 and 478-507, and gp41 residues (e.g., 512-664), from a first HIV-1 strain (such as the BG505 strain with SOSIP substitutions set forth as SEQ ID NO: 3), and includes gp120 residues 46-477 from a heterologous strain of HIV-1 (such as the CAP256.SU, BB201.B42, KER2018.11, CH070.1, ZM233.6, Q23.17, A244, WITO.33, BI369.9A, MB201.A1, QH209.14M.A2, 0921.V2.C14, 16055-2.3, 25925-2.22, 286.36, CAP45.G3, CNE58, DU156.12, DU422.01, MW965.26, ZM53.12, ZM55.28a, ZM106.9, 3301.V1.C24, 6545.V4.C1, 620345.c1, C1080.c3, C4118.09, CNE55, TH966.8, AC10.29, CH038.12, or CH117.4 strain of HIV-1), and further includes substitutions in the gp120 residues from the heterologous strain that introduce residues from the first HIV-1 strain at the Residue Set B positions of gp120. Non-limiting examples of sequences of such chimeric HIV-1 Env ectodomains (that may also include one or more amino acid substitutions, such as 201C/433C and SOSIP substitutions to stabilize the HIV-1 ectodomain in the prefusion mature closed conformation) are provided herein as SEQ ID NOs: 1114-1142. Thus, in some embodiments, the recombinant HIV-1 Env protein includes an amino acid sequence set forth as any one of SEQ ID NOs: 1114-1142, or an amino acid sequence at least 80% (such as at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to any one of SEQ ID NOs: 1114-1142.


Residue Set C

In more embodiments, the gp120 portion of the recombinant HIV-1 Env ectodomain (from the heterologous HIV-1 strain) can include additional substitutions to alter the antigenicity of the ectodomain. In some embodiments, the substitutions at the gp120-gp41 interface that introduce residues from the first HIV-1 strain can include substitutions at gp120 positions 49, 133-134, 149-152, 164, 169, 188, 190, 211, 223, 252, 281, 293, 308, 316, 336, 340, 352, 360, 362-363, 369, 372, 393, 410, 432, 442, 444, 446, 474, and 476 (referred to herein as “Residue Set C”). In some embodiments, the recombinant HIV-1 Env ectodomain includes gp120 residues 31-45 and 478-507, and gp41 residues (e.g., 512-664), from a first HIV-1 strain (such as the BG505 strain with SOSIP substitutions set forth as SEQ ID NO: 3), and includes gp120 residues 46-477 from a heterologous strain of HIV-1 (such as the CAP256.SU, BB201.B42, KER2018.11, CH070.1, ZM233.6, Q23.17, A244, WITO.33, BI369.9A, MB201.A1, QH209.14M.A2, 0921.V2.C14, 16055-2.3, 25925-2.22, 286.36, CAP45.G3, CNE58, DU156.12, DU422.01, MW965.26, ZM53.12, ZM55.28a, ZM106.9, 3301.V1.C24, 6545.V4.C1, 620345.c1, C1080.c3, C4118.09, CNE55, TH966.8, AC10.29, CH038.12, or CH117.4 strain of HIV-1), and further includes substitutions in the gp120 residues from the heterologous strain that introduce residues from the first HIV-1 strain at the Residue Set C positions of gp120. Non-limiting examples of sequences of such chimeric HIV-1 Env ectodomains (that may also include one or more amino acid substitutions, such as 201C/433C and SOSIP substitutions to stabilize the HIV-1 ectodomain in the prefusion mature closed conformation) are provided herein as SEQ ID NOs: 1143-1171. Thus, in some embodiments, the recombinant HIV-1 Env protein includes an amino acid sequence set forth as any one of SEQ ID NOs: 1143-1171, or an amino acid sequence at least 80% (such as at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to any one of SEQ ID NOs: 1143-1171.


Residue Set D

In more embodiments, the gp120 portion of the recombinant HIV-1 Env ectodomain (from the heterologous HIV-1 strain) can include additional substitutions to alter the antigenicity of the ectodomain. In some embodiments, the substitutions at the gp120-gp41 interface that introduce residues from the first HIV-1 strain can include substitutions at gp120 positions of Residue Set C and also gp120 positions 46, 60, 62-63, 84-85, 87, 99, 102, 130, 132, 135, 153, 158, 160-161, 165-167, 171-173, 175, 177-178, 181, 184-185, 189, 202, 232, 234, 236, 240, 268-271, 275, 277, 287, 289, 292, 295, 297, 305, 315, 317, 319, 322, 328, 330, 332-335, 337, 339, 343-347, 350-351,357, 371, 375, 379, 387, 389, 394, 411, 412-413, 415, 424, 426, 429, 440, 460-461, 465, 475, and 477 (referred to herein as “Residue Set D”). In some embodiments, the recombinant HIV-1 Env ectodomain includes gp120 residues 31-45 and 478-507, and gp41 residues (e.g., 512-664), from a first HIV-1 strain (such as the BG505 strain with SOSIP substitutions set forth as SEQ ID NO: 3), and includes gp120 residues 46-477 from a heterologous strain of HIV-1 (such as the CAP256.SU, BB201.B42, KER2018.11, CH070.1, ZM233.6, Q23.17, A244, WITO.33, BI369.9A, MB201.A1, QH209.14M.A2, 0921.V2.C14, 16055-2.3, 25925-2.22, 286.36, CAP45.G3, CNE58, DU156.12, DU422.01, MW965.26, ZM53.12, ZM55.28a, ZM106.9, 3301.V1.C24, 6545.V4.C1, 620345.c1, C1080.c3, C4118.09, CNE55, TH966.8, AC10.29, CH038.12, or CH117.4 strain of HIV-1), and further includes substitutions in the gp120 residues from the heterologous strain that introduce residues from the first HIV-1 strain at the Residue Set C and Residue Set D positions of gp120. Non-limiting examples of sequences of such chimeric HIV-1 Env ectodomains (that may also include one or more amino acid substitutions, such as 201C/433C and SOSIP substitutions to stabilize the HIV-1 ectodomain in the prefusion mature closed conformation) are provided herein as SEQ ID NOs: 1172-1200. Thus, in some embodiments, the recombinant HIV-1 Env protein includes an amino acid sequence set forth as any one of SEQ ID NOs: 1172-1200, or an amino acid sequence at least 80% (such as at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to any one of SEQ ID NOs: 1172-1200.


Additional Substitutions

The chimeric recombinant HIV-1 Env ectodomain can be mutated to include one or more of the disclosed amino acid substitutions to generate a chimeric recombinant HIV Env protein (or fragment thereof, such as a gp140 or gp145 protein) that is stabilized in a prefusion mature closed conformation. For example, in some non-limiting embodiments, cysteine substitutions at positions 201 and 433, and the SOSIP mutations, are made to a recombinant HIV-1 Env ectodomain including a V1V2 domain from a CAP256.SU, BB201.B42, KER2018.11, CH070.1, ZM233.6, Q23.17, A244, T250-4, or WITO.33 strain of HIV-1 to generate the recombinant HIV-1 Env ectodomain that can form a trimer stabilized in the prefusion mature closed conformation. In some embodiments, the N-terminal residue of the transplanted V1V2 domain can include one of Env positions 120-130 and the C-terminal residue of the transplanted V1V2 domain can include one of Env positions 195-205. In one non-limiting example, the transplanted V1V2 domain includes HIV-1 Env positions 126-196. Exemplary sequences of HIV-1 ectodomains including a transplanted V1V2 domain are provided under code H of the Table in Table 13 and as SEQ ID NOs: 379-386, or 511-518.


Sequences from additional HIV-1 strains (such as a third, fourth or fifth strain) can be incorporated into the chimeric HIV-1 Env ectodomain. For example, any of the chimeric HIV-1 Env ectodomains disclosed herein can be further modified to include all or portions of the V1V2 domain (such as strand C of the V1V2 domain, for example, HIV-1 Env positions 166-173) from a heterologous HIV-1 strain (such as CAP256 SU). In a non-limiting embodiment, SEQ ID NO: 382 (CNE58_SU-strandC_bg505-NCgp120+gp41.SOSIP) provided herein includes gp41 and gp120 N- and C-terminal regions (31-45 and 478-507, respectively) from BG505.SOSIP.664, with residues 166-173 (V1V2 strand C) from CAP256 SU, and the rest of gp120 from CNE58.


Any of the chimeric HIV-1 Env ectodomain trimers provided herein can comprise gp120-gp41 protomers that are single chain Env ectodomains, including a single polypeptide chain including the gp120 polypeptide linked to the gp41 ectodomain by a heterologous peptide linker.


In some embodiments, the gp120/gp41 protomers in the chimeric HIV-1 Env ectodomain can comprise an amino acid sequence set forth as any one of SEQ ID NOs: 1580-1610, 1648-1650, 1657-1659, 1663-1673, 1676-2098, or an amino acid sequence at least 90% identical thereto.


In any of the disclosed embodiments that include a chimeric V1V2 domain, the V1V2 domain can comprise or consist of gp120 positions 126-196 (HXB2 numbering).


Single Chain HIV-1 Env Proteins

In some embodiments, the recombinant HIV-1 Env ectodomain is a single chain HIV-1 Env protein, which includes a single polypeptide chain including the gp120 polypeptide and the gp41 ectodomain. Native HIV-1 Env sequences include a furin cleavage site at position 511 (e.g., REKR511), which is cleaved by a cellular protease to generate the gp120 and gp41 polypeptides. The disclosed single chain proteins do not include the furin cleavage site separating the gp120 and gp41 polypeptides; therefore, when produced in cells, the Env polypeptide is not cleaved into separate gp120 and gp41 polypeptides.


Single chain HIV-1 proteins can be generated by mutating the furin cleavage site to prevent cleave and formation of separate gp120 and gp41 polypeptide chains. In several embodiments, the gp120 and gp41 polypeptides in the single chain HIV-1 Env protein are joined by a linker, such as a peptide linker. Examples of peptide linkers that can be used include glycine, serine, and glycine-serine linkers, such as a G, S, GG, GS, SG, GGG, or GSG linker or any of the linkers set forth as SEQ ID NOs: 519-542. In some embodiments, the peptide linker can comprise a 10 amino acid glycine-serine peptide linker, such as a peptide linker comprising the amino acid sequence set forth as SEQ ID NOs: 528 (GGSGGGGSGG). In some embodiments, the single chain HIV-1 protein can include a heterologous peptide linker between one of HIV-1 Env residues 507 and 512, 503 and 519, 504 and 519, 503 and 522, or 504 and 522. In some embodiments, the single chain HIV-1 protein can include a heterologous peptide linker between HIV-1 Env residues 507 and 512.


Any amino acid substitution or insertion can be used that effectively prevents furin (or other protease) cleavage of HIV-1 Env into separate gp120 and gp41 polypeptide chains, and also allows folding of the HIV-1 Env ectodomain into its prefusion mature closed conformation.


Any of the stabilizing mutations (or combinations thereof) disclosed herein can be included in the single chain HIV-1 Env protein as long as the single chain HIV-1 Env protein retains the HIV-1 Env prefusion mature closed conformation. For example, in some embodiments, the single chain HIV-1 Env protein can include cysteine substitutions at positions 201 and 433 that form a disulfide bond and one or more of the pairs of cysteine substitutions listed in Table 9, or the single chain HIV-1 Env protein can include cysteine substitutions at positions 201 and 433 that form a disulfide bond and further include the SOSIP mutations.


It will be appreciated that the single chain HIV-1 Env proteins can be incorporated into any embodiment disclosed herein in which the cleaved HIV-1 Env proteins can be used. For example, the single chain HIV-1 Env proteins can be linked to a protein nanoparticle subunit to generate a protein nanoparticle including the single chain Env protein, and can also be used in the context of a chimeric HIV-1 Env ectodomain including sequences from two or more different strains of HIV-1.


Exemplary single chain HIV-1 Env sequences are provided under code B of the Table in Table 13 and set forth as SEQ ID NOs: 210-408. Additional exemplary single chain chimeric HIV-1 Env ectodomain sequences are indicated as such in column 7 of the tables in Table 13, and also provides as SEQ ID NOs: 1078-1098, and 1643-1650.


Membrane Anchored Embodiments

In some embodiments, the recombinant HIV-1 Env ectodomain is a membrane anchored protein, for example, the recombinant Env ectodomain can be linked to a transmembrane domain. The transmembrane domain can be linked to any portion of the recombinant HIV-1 Env ectodomain, as long as the presence of the transmembrane domain does not disrupt the structure of the HIV-1 Env ectodomain, or its ability to induce an immune response to HIV-1. In non-limiting examples, the transmembrane domain can be linked to the N- or C-terminal reside of a gp120 polypeptide, or the C-terminal residue of a gp41 ectodomain included in the recombinant HIV-1 Env protein. In some embodiments, the C-terminal residue of the gp41 ectodomain included in the recombinant HIV-1 Env ectodomain can be linked to the transmembrane domain. One or more peptide linkers (such as a gly-ser linker, for example a 10 amino acid glycine-serine peptide linker, such as a peptide linker comprising the amino acid sequence set forth as SEQ ID NOs: 528 (GGSGGGGSGG)) can be used to link the transmembrane domain and the gp120 or gp41 protein. In some embodiments a native HIV-1 Env MPER sequence can be used to link the transmembrane domain and the gp120 or gp41 protein.


Non-limiting examples of transmembrane domains for use with the disclosed embodiments include the BG505 TM domain (KIFIMIVGGLIGLRIVFAVLSVIHRVR, SEQ ID NO: 758), the Influenza A Hemagglutinin™ domain (ILAIYSTVASSLVLLVSLGAISF, SEQ ID NO: 760, and the Influenza A Neuraminidase™ domain (IITIGSICMVVGIISLILQIGNIISIWVS, SEQ ID NO: 762). Nucleic acid sequences encoding these™ domains are provided as SEQ ID NOs: 759, 761, and 763, respectively.


The recombinant HIV-1 Env ectodomain linked to the transmembrane domain can include any of the stabilizing mutations provided herein. For example, the transmembrane domain can be linked to the C-terminal residue of a gp41 ectodomain included in a recombinant HIV-1 Env ectodomain including the DS substitutions (I201C/A433C), and/or can be linked to any of the disclosed chimeric recombinant HIV-1 Env ectodomains.


Exemplary sequences of recombinant HIV-1 Env ectodomain (or a fragment thereof) linked to a transmembrane domain and including amino acid substitutions to stabilize the ectodomain in the prefusion mature closed conformation are provided under code T of the Table in Table 13, and as SEQ ID NOs: 544-571, and 1765-2098.


Linkage to a Trimerization Domain

In several embodiments, the recombinant HIV-1 Env ectodomain can be linked to a trimerization domain, for example the C-terminus of the gp41 protein included in the recombinant HIV-1 Env ectodomain can be linked to the trimerization domain. The trimerization domain can promotes trimerization of the three protomers of the recombinant HIV-1 Env protein. Non-limiting examples of exogenous multimerization domains that promote stable trimers of soluble recombinant proteins include: the GCN4 leucine zipper (Harbury et al. 1993 Science 262:1401-1407), the trimerization motif from the lung surfactant protein (Hoppe et al. 1994 FEBS Lett 344:191-195), collagen (McAlinden et al. 2003 J Biol Chem 278:42200-42207), and the phage T4 fibritin Foldon (Miroshnikov et al. 1998 Protein Eng 11:329-414), any of which can be linked to the recombinant HIV-1 Env ectodomain (e.g., by linkage to the C-terminus of the gp41 polypeptide to promote trimerization of the recombinant HIV-1 protein, as long as the recombinant HIV-1 Env ectodomain retains specific binding activity for a mature closed conformation specific antibody, prefusion-specific antibody (e.g., PGT122), and/or includes a HIV-1 Env mature closed conformation.


In some examples, the recombinant HIV-1 Env ectodomain can be linked to a Foldon domain, for example, the recombinant HIV-1 Env ectodomain can include a gp41 polypeptide with a Foldon domain linked to its C-terminus. In specific examples, the Foldon domain is a T4 fibritin Foldon domain such as the amino acid sequence GYIPEAPRDGQAYVRKDGEWVLLSTF (SEQ ID NO: 578), which adopts a β-propeller conformation, and can fold and trimerize in an autonomous way (Tao et al. 1997 Structure 5:789-798). Modified Foldon domains can also be used, such as a Foldon domain including an amino acid sequence set forth as GYIPEAPRDGQCYVRCDGEWVLLSTF (SEQ ID NO: 752), GYIPECPRDGQAYVCKDGEWVLLSTF (SEQ ID NO: 753), GYIPEAPRDGQCYCRKDGEWVLLSTF (SEQ ID NO: 754), or GYIPEAPRDGQACVRKDGECVLLSTF (SEQ ID NO: 755). These modified Foldon domains include amino acid substitutions that add two cysteine residues for formation of stabilizing disulfide bonds. In some embodiments, any of the disclosed recombinant HIV-1 Env ectodomains can be linked to a modified Foldon domain as described herein.


Exemplary sequences of recombinant HIV-1 Env ectodomain linked to a trimerization domain are provided under code G of the Table in Table 13, and as SEQ ID NOs: 508-510.


Typically, the heterologous trimerization domain is positioned C-terminal to the gp41 polypeptide. Optionally, the multimerization domain is connected to the recombinant HIV-1 Env ectodomain via a linker, such as an amino acid linker. Exemplary linkers are provided herein and are known in the art; non-limiting examples include Gly or Gly-Ser linkers, such as the amino acid sequence: GGSGGSGGS; SEQ ID NO: 574). Numerous conformationally neutral linkers are known in the art that can be used in this context without disrupting the conformation of the recombinant HIV-1 Env protein. Some embodiments include a protease cleavage site for removing the trimerization domain from the HIV polypeptide, such as, but not limited to, a thrombin site between the recombinant HIV-1 Env ectodomain and the trimerization domain.


Additional Descriptions of Recombinant HIV-1 Env Ectodomains

Any of the recombinant HIV-1 Env ectodomains disclosed herein can further include an N-linked glycosylation site at gp120 position 332 (if not already present on the ectodomain). For example, by T332N substitution in the case of BG505 based immunogens. The presence of the glycosylation site at N332 allows for binding by 2G12 antibody.


Any of the recombinant HIV-1 Env ectodomains disclosed herein can include a lysine residue at gp120 position 168 (if not already present on the ectodomain). For example, the lysine residue can be added by amino acid substitution (such as an E168K substitution in the case of the JR-FL based immunogens). The presence of the lysine residue at position 168 allows for binding of particular broadly neutralizing antibodies to the V1V2 loop of gp120.


Any of the recombinant HIV-1 Env ectodomains disclosed herein can include an arginine residue at gp120 position 368 (if not already present on the ectodomain). For example, the arginine residue can be added by amino acid substitution (such as a D368R substitution). The presence of the arginine residue at position 368 reduces binding of CD4 to the HIV-1 Env ectodomain to inhibit the trimer from adopting the CD4-bound conformation.


Any of the recombinant HIV-1 Env ectodomains disclosed herein can further include a non-natural disulfide bond between gp120 positions 201 and 433 (if not already present on the ectodomain). For example, the non-natural disulfide bond can be introduced by including cysteine substitutions at positions 201 and 433. The presence of the non-natural disulfide bond between residues 201 and 433 contributes to the stabilization of the HIV-1 Env ectodomain in the prefusion mature closed conformation.


Any of the recombinant HIV-1 Env ectodomains disclosed herein can further include a non-natural disulfide bond between HIV-1 Env positions 501 and 605 (if not already present on the ectodomain). For example, the non-natural disulfide bond can be introduced by including cysteine substitutions at positions 501 and 605. The presence of the non-natural disulfide bond between positions 501 and 605 contributes to the stabilization of the HIV-1 Env ectodomain in the prefusion mature closed conformation.


Any of the recombinant HIV-1 Env ectodomains disclosed herein can further include a proline residue at HIV-1 Env positions 559 (if not already present on the ectodomain). For example, the proline residue can be introduced at position 559 by amino acid substitution (such as an I559P substitution). The presence of the proline residue at position 559 contributes to the stabilization of the HIV-1 Env ectodomain in the prefusion mature closed conformation.


Any of the recombinant HIV-1 Env ectodomains disclosed herein can further include a non-natural disulfide bond between HIV-1 Env positions 501 and 605 and a proline residue at HIV-1 Env positions 559 (if not already present on the ectodomain). For example, the non-natural disulfide bond can be introduced by including cysteine substitutions at positions 501 and 605, and the proline residue can be introduced at position 559 by amino acid substitution (such as an I559P substitution). The presence of the non-natural disulfide bond between positions 501 and 605 and the proline residue at position 559 contributes to the stabilization of the HIV-1 Env ectodomain in the prefusion mature closed conformation.


Any of the recombinant HIV-1 Env ectodomains disclosed herein can be further modified to be a singly chain HIV-1 Env ectodomain including a 10 amino acid glycine serine linker between HIV-1 Env residues 507 and 512 (if the recombinant HIV-1 Env ectodomains is not already a single chain ectodomain).


Any of the recombinant HIV-1 Env ectodomains disclosed herein can be further modified to include the “R6” mutation, which provides six Arginine residues in place of the naïve furin cleavage site between gp120 and gp41.


Any of the soluble recombinant HIV-1 Env ectodomain trimers disclosed herein can include mutations to add a N-linked glycan sequon at position 504, position 661, or positions 504 and 661, to increase glycosylation of the membrane proximal region of the ectodomain.


Any of the recombinant HIV-1 Env ectodomain trimers disclosed herein that include a protease cleavage site between the gp120 and gp41 polypeptides can be modified to be a single chain HIV-1 Env ectodomain by mutation of the protease cleavage site for example by introducing a 10 amino acid linker connecting gp120 and gp41 or a 15 amino acid linker connecting g120 and gp41, for example as shown in SEQ ID NOs: 2158 (15 AA linker) and 2159 (10 AA linker).


In some embodiments, the recombinant HIV-1 Env ectodomain can comprise a circular permutant of the Env ectodomain. For example, the circular permutant can comprise, from N-terminus to C-terminus,


(A) the gp41 polypeptide and the gp120 polypeptide linked by a peptide linker or directly linked; or


(B) a first segment of the gp41 polypeptide comprising a α6 helix, a α7 helix, and/or a 127 strand of the prefusion mature closed conformation of the HIV-1 Env protein;


the gp120 polypeptide; and


a second segment of the gp41 polypeptide comprising the α8 helix and/or the α9 helix of the prefusion mature closed conformation, wherein


the first and second segments of the gp41 polypeptide are linked to the gp120 polypeptide by a peptide linker, or are directly linked to the gp120 polypeptide.


The recombinant HIV-1 Env ectodomain comprising the circular permutant of the Env ectodomain can further comprise any of the amino acid substitutions disclosed herein for stabilizing the HIV-1 Env ectodomain in the prefusion mature closed conformation, such as the DS-SOSIP substitutions.


C. V1V2V3 Immunogens

The V1, V2, and V3 domains of HIV-1 Env are located on the apex of the trimer in the prefusion mature closed conformation and include regions recognized by several neutralizing antibodies. Provided herein are immunogens that include these minimal domains of the HIV-1 Env protein in a format that maintains their structure in the prefusion mature closed conformation, and which are useful, for example, for inducing an immune response to HIV-1 Env. These immunogens are also useful for specific binding to antibodies that target the V1, V2, or V3 domains of HIV-1 Env, for example as probes to identify or detect such antibodies.


In several embodiments, the V1, V2, and V3 domains are included on a protein scaffold, such as a scaffold protein based on the 1VH8 protein (SEQ ID NO: 855), which is deposited in the Protein Data Bank as No. 1VH8, and incorporated by reference herein in its entirety. In another example, the “scaffold” can be any of the recombinant HIV-1 ectodomain trimers described herein, and the V1V2V3 immunogen can be included on the recombinant HIV-1 ectodomain trimer in place of the corresponding sequence of thHIV-1 ectodomain (e.g., the V1V2V3 immunogen can be “transplanted” on the recombinant HIV-1 ectodomain trimer). In some embodiments, the V1V2V3 scaffold protein comprises a circular permutant of the V1, V2, and V3 domains of HIV-1 linked to the 1VH8 protein. In some embodiments, the V1V2V3 scaffold protein comprises from N- to C-terminus:


(1VH8 residues 36-159)-L1-(1VH8 residues 2-15)-L2-(V1V2 domain)-L3-(V3 domain)


In some embodiments, the V1V2 domain portion of the V1V2V3 scaffold protein can include HIV-1 Env residues 120-203. In some embodiments, the V3 domain portion of the V1V2V3 scaffold protein can be a circular permutant of the V3 domain including, from N- to C-terminus,


(HIV-1 Env residues 317-330)-L4-(HIV-1 Env residues 297-314)


The linkers in the V1V2V3 scaffold protein are peptide linkers, for example glycine-serine linkers. In some embodiments, the L1 linker can include a GSG sequence, the L2 linker can include SEQ ID NO: 528 or SEQ ID NO: 854, the L3 linker can include SEQ ID NO: 319, and/or the L4 linker can include AA-GSG-A.


Exemplary V1V2V3 scaffold proteins are provided as SEQ ID NOs: 836-843. In some embodiments, the immunogen includes an amino acid sequence at least 80% (such as at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to any one of SEQ ID NOs: 836-843.


The V1V2V3 scaffold protein can include any of the stabilizing mutations described herein that include mutations to the V1, V2, and/or V3 domain to stabilize the V1, V2, and/or V3 domains in the prefusion mature closed conformation of the HIV-1 Env protein, for example the V1V2V3 scaffold protein can include cysteine substitutions at positions 174 and 319, or 175 and 320, which stabilize the V1, V2 and/or V3 domains in the prefusion mature closed conformation.


D. Protein Nanoparticles

In some embodiments a protein nanoparticle is provided that includes one or more of the disclosed recombinant HIV-1 Env ectodomains stabilized in a prefusion mature closed conformation, or an immunogenic fragment thereof. Such a protein nanoparticle can be specifically bound by one or more antibodies that specifically bind to the HIV-1 Env prefusion mature closed conformation, such as VRC26, PGT122, PGT145, and 35O22. Additionally, in several embodiments, the disclosed nanoparticles do not specifically bind to an antibody that specifically binds to HIV-1 Env in its CD4 bound conformation, but not to HIV-1 Env in its prefusion mature closed conformation. For example, the disclosed protein nanoparticles do not specifically bind to 17b antibody in the presence of a molar excess of CD4. Non-limiting example of nanoparticles include ferritin nanoparticles, an encapsulin nanoparticles, Sulfur Oxygenase Reductase (SOR) nanoparticles, and lumazine synthase nanoparticles, which are comprised of an assembly of monomeric subunits including ferritin proteins, encapsulin proteins, SOR proteins, and lumazine synthase respectively. Exemplary sequences of recombinant HIV-1 Env ectodomains linked to a nanoparticle subunit are provided under code F in the Table included in Table 13. To construct protein nanoparticles including a HIV-1 Env proteins stabilized in a prefusion mature closed conformation or immunogenic fragment thereof, the HIV-1 Env protein or fragment can be linked to a subunit of the protein nanoparticle (such as a ferritin protein, an encapsulin protein, a SOR protein, or a lumazine synthase protein). The fusion protein self-assembles into a nanoparticle under appropriate conditions.


In several embodiments, the protein nanoparticle comprises two or more of the recombinant HIV-1 Env proteins, wherein the two or more recombinant HIV-1 Env proteins are from at least two different strains of HIV-1.


In some embodiments, the immunogen comprises a recombinant HIV-1 Env protein linked to a protein nanoparticle subunit, and comprises an amino acid sequence at least 80% (such as at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to the sequence set forth as one of 471-507, or 596-645, wherein the recombinant HIV-1 Env protein linked to the nanoparticle subunit can oligomerizes to form a functional protein nanoparticle including a recombinant HIV-1 Env ectodomain trimer (or immunogenic fragment thereof) in a prefusion mature closed conformation.


In some embodiments, a disclosed recombinant HIV-1 Env ectodomain stabilized in a prefusion mature closed conformation or immunogenic fragment thereof can be linked to a ferritin subunit to construct a ferritin nanoparticle. Ferritin nanoparticles and their use for immunization purposes (e.g., for immunization against influenza antigens) have been disclosed in the art (see, e.g., Kanekiyo et al., Nature, 499:102-106, 2013, incorporated by reference herein in its entirety). Ferritin is a globular protein that is found in all animals, bacteria, and plants, and which acts primarily to control the rate and location of polynuclear Fe(III)2O3 formation through the transportation of hydrated iron ions and protons to and from a mineralized core. The globular form of the ferritin nanoparticle is made up of monomeric subunits, which are polypeptides having a molecule weight of approximately 17-20 kDa. An example of the amino acid sequence of one such monomeric subunit is represented by SEQ ID NO: 575.


Each monomeric subunit has the topology of a helix bundle which includes a four antiparallel helix motif, with a fifth shorter helix (the c-terminal helix) lying roughly perpendicular to the long axis of the 4 helix bundle. According to convention, the helices are labeled ‘A, B, C, D & E’ from the N-terminus respectively. The N-terminal sequence lies adjacent to the capsid three-fold axis and extends to the surface, while the E helices pack together at the four-fold axis with the C-terminus extending into the capsid core. The consequence of this packing creates two pores on the capsid surface. It is expected that one or both of these pores represent the point by which the hydrated iron diffuses into and out of the capsid. Following production, these monomeric subunit proteins self-assemble into the globular ferritin protein. Thus, the globular form of ferritin comprises 24 monomeric, subunit proteins, and has a capsid-like structure having 432 symmetry. Methods of constructing ferritin nanoparticles are known to the person of ordinary skill in the art and are further described herein (see, e.g., Zhang, Int. J. Mol. Sci., 12:5406-5421, 2011, which is incorporated herein by reference in its entirety).


In specific examples, the ferritin polypeptide is E. coli ferritin, Helicobacter pylori ferritin, human light chain ferritin, bullfrog ferritin or a hybrid thereof, such as E. coli-human hybrid ferritin, E. coli-bullfrog hybrid ferritin, or human-bullfrog hybrid ferritin. Exemplary amino acid sequences of ferritin polypeptides and nucleic acid sequences encoding ferritin polypeptides for use to make a ferritin nanoparticle including a recombinant HIV-1 Env ectodomain or immunogenic fragment thereof can be found in GENBANK®, for example at accession numbers ZP_03085328, ZP_06990637, EJB64322.1, AAA35832, NP_000137 AAA49532, AAA49525, AAA49524 and AAA49523, which are specifically incorporated by reference herein in their entirety as available Jun. 20, 2014. In some embodiments, a disclosed recombinant HIV-1 Env ectodomain stabilized in a prefusion mature closed conformation or immunogenic fragment thereof can be linked to a ferritin subunit including an amino acid sequence at least 80% (such as at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to amino acid sequence set forth as SEQ ID NO: 575.


Non-limiting examples of a recombinant HIV-1 Env ectodomains stabilized in a prefusion mature closed conformation or immunogenic fragments thereof linked to a ferritin subunit include the amino acid sequence set forth as any one of SEQ ID NO: 471, 473-475, 626-637, 797-802, 809-814, 821-835, 1099-1113, and 1201-1218.


In additional embodiments, any of the disclosed recombinant HIV-1 Env proteins stabilized in a prefusion mature closed conformation or immunogenic fragments thereof can be linked to a lumazine synthase subunit to construct a lumazine synthase nanoparticle. The globular form of lumazine synthase nanoparticle is made up of monomeric subunits; an example of the sequence of one such monomeric subunit is provides as the amino acid sequence set forth as SEQ ID NO: 576.


In some embodiments, a disclosed recombinant HIV-1 Env ectodomain stabilized in a prefusion mature closed conformation or immunogenic fragment thereof can be linked to a lumazine synthase subunit including an amino acid sequence at least 80% (such as at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to amino acid sequence set forth as SEQ ID NO: 576. Specific examples of a recombinant HIV-1 Env ectodomain stabilized in a prefusion mature closed conformation or immunogenic fragments thereof linked to a lumazine synthase subunit is provided as the amino acid sequence set forth as SEQ ID NO: 472, 476-477, 638-645, 803-808, and 815-820.


In additional embodiments, a disclosed recombinant HIV-1 Env ectodomain stabilized in a prefusion mature closed conformation or immunogenic fragment thereof can be linked to an encapsulin subunit to construct an encapsulin nanoparticle. The globular form of the encapsulin nanoparticle is made up of monomeric subunits; an example of the sequence of one such monomeric subunit is provides as the amino acid sequence set forth as SEQ ID NO: 756.


In some embodiments, a disclosed recombinant HIV-1 Env ectodomain stabilized in a prefusion mature closed conformation or immunogenic fragment thereof can be linked to an encapsulin subunit including an amino acid sequence at least 80% (such as at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to amino acid sequence set forth as SEQ ID NO: 756.


Encapsulin proteins are a conserved family of bacterial proteins also known as linocin-like proteins that form large protein assemblies that function as a minimal compartment to package enzymes. The encapsulin assembly is made up of monomeric subunits, which are polypeptides having a molecule weight of approximately 30 kDa. Following production, the monomeric subunits self-assemble into the globular encapsulin assembly including 60 monomeric subunits. Methods of constructing encapsulin nanoparticles are known to the person of ordinary skill in the art, and further described herein (see, for example, Sutter et al., Nature Struct. and Mol. Biol., 15:939-947, 2008, which is incorporated by reference herein in its entirety). In specific examples, the encapsulin polypeptide is bacterial encapsulin, such as E. coli or Thermotoga maritime encapsulin.


In additional embodiments, a disclosed recombinant HIV-1 Env ectodomain stabilized in a prefusion mature closed conformation or immunogenic fragment thereof can be linked to a Sulfer Oxygenase Reductase (SOR) subunit to construct a recombinant SOR nanoparticle. In some embodiments, the SOR subunit can include the amino acid sequence set forth as SEQ ID NO: 577.


In some embodiments, a disclosed recombinant HIV-1 Env ectodomain stabilized in a prefusion mature closed conformation or immunogenic fragment thereof can be linked to a SOR subunit including an amino acid sequence at least 80% (such as at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to amino acid sequence set forth as SEQ ID NO: 577.


SOR proteins are microbial proteins (for example from the thermoacidophilic archaeon Acidianus ambivalens that form 24 subunit protein assemblies. Methods of constructing SOR nanoparticles are known to the person of ordinary skill in the art (see, e.g., Urich et al., Science, 311:996-1000, 2006, which is incorporated by reference herein in its entirety). An example of an amino acid sequence of a SOR protein for use to make SOR nanoparticles is set forth in Urich et al., Science, 311:996-1000, 2006, which is incorporated by reference herein in its entirety.


In some examples, the disclosed recombinant HIV-1 Env ectodomain stabilized in a prefusion mature closed conformation or immunogenic fragment thereof can be linked to the N- or C-terminus, or placed within an internal loop of a ferritin, encapsulin, SOR, or lumazine synthase subunit, for example with a linker, such as a Ser-Gly linker. When the constructs have been made in HEK 293 Freestyle cells, the fusion proteins are secreted from the cells and self-assembled into nanoparticles. The nanoparticles can be purified using known techniques, for example by a few different chromatography procedures, e.g. Mono Q (anion exchange) followed by size exclusion (SUPEROSE® 6) chromatography.


Several embodiments include a monomeric subunit of a ferritin, encapsulin, SOR, or lumazine synthase protein, or any portion thereof which is capable of directing self-assembly of monomeric subunits into the globular form of the protein. Amino acid sequences from monomeric subunits of any known ferritin, encapsulin, SOR, or lumazine synthase protein can be used to produce fusion proteins with the disclosed recombinant HIV-1 Env ectodomain or immunogenic fragment thereof, so long as the monomeric subunit is capable of self-assembling into a nanoparticle displaying recombinant HIV-1 Env ectodomain or immunogenic fragment thereof on its surface.


The fusion proteins need not comprise the full-length sequence of a monomeric subunit polypeptide of a ferritin, encapsulin, SOR, or lumazine synthase protein. Portions, or regions, of the monomeric subunit polypeptide can be utilized so long as the portion comprises amino acid sequences that direct self-assembly of monomeric subunits into the globular form of the protein.


In some embodiments, it may be useful to engineer mutations into the amino acid sequence of the monomeric ferritin, encapsulin, SOR, or lumazine synthase subunits. For example, it may be useful to alter sites such as enzyme recognition sites or glycosylation sites in order to give the fusion protein beneficial properties (e.g., half-life).


It will be understood by those skilled in the art that fusion of any of the disclosed recombinant HIV-1 Env proteins stabilized in a prefusion mature closed conformation or immunogenic fragments thereof to the ferritin, encapsulin, SOR, or lumazine synthase protein should be done such that the disclosed recombinant HIV-1 Env proteins stabilized in a prefusion mature closed conformation or immunogenic fragments thereof does not interfere with self-assembly of the monomeric ferritin, encapsulin, SOR, or lumazine synthase subunits into the globular protein, and that the ferritin, encapsulin, SOR, or lumazine synthase subunits do not interfere with the ability of the disclosed recombinant HIV-1 Env proteins stabilized in a prefusion mature closed conformation or immunogenic fragments thereof to elicit an immune response to HIV. In some embodiments, the ferritin, encapsulin, SOR, or lumazine synthase protein and disclosed recombinant HIV-1 Env proteins stabilized in a prefusion mature closed conformation or immunogenic fragments thereof can be joined together directly without affecting the activity of either portion. In other embodiments, the ferritin, encapsulin, SOR, or lumazine synthase protein and the disclosed recombinant HIV-1 Env proteins stabilized in a prefusion mature closed conformation or immunogenic fragments thereof can be joined using a linker (also referred to as a spacer) sequence. The linker sequence is designed to position the ferritin, encapsulin, SOR, or lumazine synthase portion of the fusion protein and the recombinant HIV-1 Env ectodomain stabilized in a prefusion mature closed conformation or immunogenic fragments thereof can be linked to an portion of the fusion protein, with regard to one another, such that the fusion protein maintains the ability to assemble into nanoparticles, and also elicit an immune response to HIV. In several embodiments, the linker sequences comprise amino acids. Preferable amino acids to use are those having small side chains and/or those which are not charged. Such amino acids are less likely to interfere with proper folding and activity of the fusion protein. Accordingly, preferred amino acids to use in linker sequences, either alone or in combination are serine, glycine and alanine. One example of such a linker sequence is SGG. Amino acids can be added or subtracted as needed. Those skilled in the art are capable of determining appropriate linker sequences for construction of protein nanoparticles.


The disclosed recombinant HIV-1 Env proteins stabilized in a prefusion mature closed conformation or immunogenic fragments thereof can be linked to ferritin, encapsulin, SOR, or lumazine synthase subunits can self-assemble into multi-subunit protein nanoparticles, termed ferritin nanoparticles, encapsulin nanoparticles, SOR nanoparticles, and lumazine synthase nanoparticles, respectively. The nanoparticles including a disclosed recombinant HIV-1 Env ectodomain stabilized in a prefusion mature closed conformation or immunogenic fragment thereof have substantially the same structural characteristics as the native ferritin, encapsulin, SOR, or lumazine synthase nanoparticles that do not include the disclosed recombinant HIV-1 Env ectodomain or immunogenic fragment thereof. That is, they contain 24, 60, 24, or 60 subunits (respectively) and have similar corresponding symmetry.


Additional sequences of recombinant HIV-1 Env proteins as disclosed herein linked to a protein nanoparticle subunit are provided as SEQ ID NOs: 478-507.


In some embodiments, the recombinant HIV-1 Env ectodomain stabilized in a prefusion mature closed conformation or immunogenic fragment thereof can be linked to Escherichia coli enzyme 2-hydroxypentadienoic acid hydratase subunit (see Montgomery et al., J. Mol. Biol. 396: 1379-1391, 2010), which can include, for example, the amino acid sequence set forth as SEQ ID NO: 2101 or a fragment thereof. In some embodiments, a disclosed recombinant HIV-1 Env ectodomain stabilized in a prefusion mature closed conformation or immunogenic fragment thereof can be linked to a cocksfoot mottle virus coat protein subunit (see Tars et al., Virology 310: 287-297, 2003), which can include, for example, the amino acid sequence set forth as SEQ ID NO: 2102 or a fragment thereof. In some embodiments, a disclosed recombinant HIV-1 Env ectodomain stabilized in a prefusion mature closed conformation or immunogenic fragment thereof can be linked to a Rice yellow mottle virus capsid protein subunit (see Qu et al., Structure Fold. Des. 8: 1095-1103, 2000), which can include, for example, the amino acid sequence set forth as SEQ ID NO: 2103 or a fragment thereof. In some embodiments, a disclosed recombinant HIV-1 Env ectodomain stabilized in a prefusion mature closed conformation or immunogenic fragment thereof can be linked to a sesbania mosaic virus coat protein subunit (see Bhuvaneshwari et al., Structure 3: 1021-1030, 1995), which can include, for example, the amino acid sequence set forth as SEQ ID NO: 2104 or a fragment thereof. In some embodiments, a disclosed recombinant HIV-1 Env ectodomain stabilized in a prefusion mature closed conformation or immunogenic fragment thereof can be linked to a tomato bushy stunt virus coat protein subunit (see Hopper et al., J. Mol. Biol. 177: 701-713, 1984), which can include, for example, the amino acid sequence set forth as SEQ ID NO: 2105 or a fragment thereof. In some embodiments, a disclosed recombinant HIV-1 Env ectodomain stabilized in a prefusion mature closed conformation or immunogenic fragment thereof can be linked to a phage MS2 protein capsid subunit (see van den Worm et al., Nucleic Acids Res. 26: 1345-1351, 1998), which can include, for example, the amino acid sequence set forth as SEQ ID NO: 2106 or a fragment thereof. In some embodiments, a disclosed recombinant HIV-1 Env ectodomain stabilized in a prefusion mature closed conformation or immunogenic fragment thereof can be linked to bacteriophage fr capsid subunit (see Liljas et al., J. Mol. Biol. 244: 279-290, 1994), which can include, for example, the amino acid sequence set forth as SEQ ID NO: 2107 or a fragment thereof. In some embodiments, a disclosed recombinant HIV-1 Env ectodomain stabilized in a prefusion mature closed conformation or immunogenic fragment thereof can be linked to a bacteriophage phiCb5 coat protein subunit (see Plevka et al. J. Mol. Biol. 391: 635-647, 2009), which can include, for example, the amino acid sequence set forth as SEQ ID NO: 2108 or a fragment thereof. In some embodiments, a disclosed recombinant HIV-1 Env ectodomain stabilized in a prefusion mature closed conformation or immunogenic fragment thereof can be linked to a HK97 bacteriophage capsid subunit (see Helgstrand et al., J. Mol. Biol. 334: 885, 2003), which can include, for example, the amino acid sequence set forth as SEQ ID NO: 2109 or a fragment thereof. In some embodiments, a disclosed recombinant HIV-1 Env ectodomain stabilized in a prefusion mature closed conformation or immunogenic fragment thereof can be linked to a bacteriophage GA protein capsid subunit (see Tars et al., J. Mol. Biol. 271: 759-773, 1997), which can include, for example, the amino acid sequence set forth as SEQ ID NO: 2110 or a fragment thereof. In some embodiments, a disclosed recombinant HIV-1 Env ectodomain stabilized in a prefusion mature closed conformation or immunogenic fragment thereof can be linked to a bacteriophage PRR1 coat protein subunit (see Persson et al., J. Mol. Biol. 383: 914, 2008), which can include, for example, the amino acid sequence set forth as SEQ ID NO: 2111 or a fragment thereof. In some embodiments, a disclosed recombinant HIV-1 Env ectodomain stabilized in a prefusion mature closed conformation or immunogenic fragment thereof can be linked to a bacteriophage PP7 coat protein subunit (see Tars et al., Acta Crystallogr., Sect. D 56: 398, 2000), which can include, for example, the amino acid sequence set forth as SEQ ID NO: 2112 or a fragment thereof. In some embodiments, a disclosed recombinant HIV-1 Env ectodomain stabilized in a prefusion mature closed conformation or immunogenic fragment thereof can be linked to a bacteriophage Q beta capsid subunit (see Golmohammadi et al., Structure 4: 543-554, 1996), which can include, for example, the amino acid sequence set forth as SEQ ID NO: 2113 or a fragment thereof.


E. Polynucleotides and Expression

Polynucleotides encoding a disclosed immunogen (e.g., a HIV-1 Env ectodomain stabilized in a prefusion mature closed conformation, or an immunogenic fragment thereof), or protein nanoparticles (or a subunit thereof) or vectors, disclosed herein are also provided. These polynucleotides include DNA, cDNA and RNA sequences which encode the antigen. One of skill in the art can readily use the genetic code to construct a variety of functionally equivalent nucleic acids, such as nucleic acids which differ in sequence but which encode the same antibody sequence, or encode a conjugate or fusion protein including the nucleic acid sequence.


In a non-limiting example, a polynucleotide sequence set forth as SEQ ID NO: 757, which encodes the single chain HIV-1 Env set forth as SEQ ID NO: 352. In another example, a polynucleotide sequence set forth as SEQ ID NO: 2119, which encodes the BG505.SOSIP.R6.664.T332N_I201C/A433C HIV-1 Env set forth as SEQ ID NO: 26. For reference, native BG505 DNA sequence is provided as SEQ ID NO: 2120.


In several embodiments, the nucleic acid molecule encodes a precursor of a disclosed recombinant HIV-1 Env ectodomain or immunogenic fragment thereof, that, when expressed in an appropriate cell, is processed into a disclosed recombinant HIV-1 Env ectodomain or immunogenic fragment thereof. For example, the nucleic acid molecule can encode a recombinant HIV-1 Env ectodomain including a N-terminal signal sequence for entry into the cellular secretory system that is proteolytically cleaved in the during processing of the HIV-1 Env protein in the cell. In some embodiments, the signal peptide includes the amino acid sequence set forth as residues 1-30 of SEQ ID NO: 2.


Exemplary nucleic acids can be prepared by cloning techniques. Examples of appropriate cloning and sequencing techniques, and instructions sufficient to direct persons of skill through many cloning exercises are known (see, e.g., Sambrook et al. (Molecular Cloning: A Laboratory Manual, 4th ed, Cold Spring Harbor, N.Y., 2012) and Ausubel et al. (In Current Protocols in Molecular Biology, John Wiley & Sons, New York, through supplement 104, 2013). Product information from manufacturers of biological reagents and experimental equipment also provide useful information. Such manufacturers include the SIGMA Chemical Company (Saint Louis, Mo.), R&D Systems (Minneapolis, Minn.), Pharmacia Amersham (Piscataway, N.J.), CLONTECH Laboratories, Inc. (Palo Alto, Calif.), Chem Genes Corp., Aldrich Chemical Company (Milwaukee, Wis.), Glen Research, Inc., GIBCO BRL Life Technologies, Inc. (Gaithersburg, Md.), Fluka Chemica-Biochemika Analytika (Fluka Chemie AG, Buchs, Switzerland), Invitrogen (Carlsbad, Calif.), and Applied Biosystems (Foster City, Calif.), as well as many other commercial sources known to one of skill.


Nucleic acids can also be prepared by amplification methods. Amplification methods include polymerase chain reaction (PCR), the ligase chain reaction (LCR), the transcription-based amplification system (TAS), the self-sustained sequence replication system (3SR). A wide variety of cloning methods, host cells, and in vitro amplification methodologies are well known to persons of skill.


The polynucleotides encoding a recombinant HIV-1 Env proteins stabilized in a prefusion mature closed conformation, fragments thereof, and protein nanoparticles (or a subunit thereof) can include a recombinant DNA which is incorporated into a vector into an autonomously replicating plasmid or virus or into the genomic DNA of a prokaryote or eukaryote, or which exists as a separate molecule (such as a cDNA) independent of other sequences. The nucleotides can be ribonucleotides, deoxyribonucleotides, or modified forms of either nucleotide. The term includes single and double forms of DNA.


Polynucleotide sequences encoding recombinant HIV-1 Env proteins stabilized in a prefusion mature closed conformation, fragments thereof, and protein nanoparticles (or a subunit thereof) can be operatively linked to expression control sequences. An expression control sequence operatively linked to a coding sequence is ligated such that expression of the coding sequence is achieved under conditions compatible with the expression control sequences. The expression control sequences include, but are not limited to, appropriate promoters, enhancers, transcription terminators, a start codon (i.e., ATG) in front of a protein-encoding gene, splicing signal for introns, maintenance of the correct reading frame of that gene to permit proper translation of mRNA, and stop codons.


DNA sequences encoding the recombinant HIV-1 Env proteins stabilized in a prefusion mature closed conformation, fragments thereof, and protein nanoparticles (or a subunit thereof) can be expressed in vitro by DNA transfer into a suitable host cell. The cell may be prokaryotic or eukaryotic. The term also includes any progeny of the subject host cell. It is understood that all progeny may not be identical to the parental cell since there may be mutations that occur during replication. Methods of stable transfer, meaning that the foreign DNA is continuously maintained in the host, are known in the art.


Hosts can include microbial, yeast, insect and mammalian organisms. Methods of expressing DNA sequences having eukaryotic or viral sequences in prokaryotes are well known in the art. Non-limiting examples of suitable host cells include bacteria, archea, insect, fungi (for example, yeast), plant, and animal cells (for example, mammalian cells, such as human). Exemplary cells of use include Escherichia coli, Bacillus subtilis, Saccharomyces cerevisiae, Salmonella typhimurium, SF9 cells, C129 cells, 293 cells, Neurospora, and immortalized mammalian myeloid and lymphoid cell lines. Techniques for the propagation of mammalian cells in culture are well-known (see, e.g., Helgason and Miller (Eds.), 2012, Basic Cell Culture Protocols (Methods in Molecular Biology), 4th Ed., Humana Press). Examples of commonly used mammalian host cell lines are VERO and HeLa cells, CHO cells, and WI38, BHK, and COS cell lines, although cell lines may be used, such as cells designed to provide higher expression, desirable glycosylation patterns, or other features. In some embodiments, the host cells include HEK293 cells or derivatives thereof, such as GnTI−/− cells (ATCC® No. CRL-3022), or HEK-293F cells.


Transformation of a host cell with recombinant DNA can be carried out by conventional techniques as are well known to those skilled in the art. Where the host is prokaryotic, such as, but not limited to, E. coli, competent cells which are capable of DNA uptake can be prepared from cells harvested after exponential growth phase and subsequently treated by the CaCl2 method using procedures well known in the art. Alternatively, MgCl2 or RbCl can be used. Transformation can also be performed after forming a protoplast of the host cell if desired, or by electroporation.


When the host is a eukaryote, such methods of transfection of DNA as calcium phosphate coprecipitates, conventional mechanical procedures such as microinjection, electroporation, insertion of a plasmid encased in liposomes, or viral vectors can be used. Eukaryotic cells can also be co-transformed with polynucleotide sequences encoding a disclosed antigen, and a second foreign DNA molecule encoding a selectable phenotype, such as the herpes simplex thymidine kinase gene. Another method is to use a eukaryotic viral vector, such as simian virus 40 (SV40) or bovine papilloma virus, to transiently infect or transform eukaryotic cells and express the protein (see for example, Viral Expression Vectors, Springer press, Muzyczka ed., 2011). One of skill in the art can readily use an expression systems such as plasmids and vectors of use in producing proteins in cells including higher eukaryotic cells such as the COS, CHO, HeLa and myeloma cell lines.


In one non-limiting example, a disclosed immunogen is expressed using the pVRC8400 vector (described in Barouch et al., J. Virol, 79, 8828-8834, 2005, which is incorporated by reference herein).


Modifications can be made to a nucleic acid encoding a recombinant HIV-1 Env ectodomain stabilized in a prefusion mature closed conformation, fragment thereof, and protein nanoparticle (or a subunit thereof) described herein without diminishing its biological activity. Some modifications can be made to facilitate the cloning, expression, or incorporation of the targeting molecule into a fusion protein. Such modifications are well known to those of skill in the art and include, for example, termination codons, a methionine added at the amino terminus to provide an initiation, site, additional amino acids placed on either terminus to create conveniently located restriction sites, or additional amino acids (such as poly His) to aid in purification steps.


In addition to recombinant methods, the recombinant HIV-1 Env proteins stabilized in a prefusion mature closed conformation, fragments thereof, and protein nanoparticles (or a subunit thereof) can also be constructed in whole or in part using protein synthesis methods known in the art.


F. Virus-Like Particles

In some embodiments, a virus-like particle (VLP) is provided that includes a disclosed immunogen (e.g., a recombinant HIV-1 Env ectodomain or immunogenic fragment thereof). VLPs lack the viral components that are required for virus replication and thus represent a highly attenuated form of a virus. The VLP can display a polypeptide (e.g., a recombinant HIV-1 Env protein) that is capable of eliciting an immune response to HIV when administered to a subject. Virus like particles and methods of their production are known and familiar to the person of ordinary skill in the art, and viral proteins from several viruses are known to form VLPs, including human papillomavirus, HIV (Kang et al., Biol. Chem. 380: 353-64 (1999)), Semliki-Forest virus (Notka et al., Biol. Chem. 380: 341-52 (1999)), human polyomavirus (Goldmann et al., J. Virol. 73: 4465-9 (1999)), rotavirus (Jiang et al., Vaccine 17: 1005-13 (1999)), parvovirus (Casal, Biotechnology and Applied Biochemistry, Vol 29, Part 2, pp 141-150 (1999)), canine parvovirus (Hurtado et al., J. Virol. 70: 5422-9 (1996)), hepatitis E virus (Li et al., J. Virol. 71: 7207-13 (1997)), and Newcastle disease virus. The formation of such VLPs can be detected by any suitable technique. Examples of suitable techniques known in the art for detection of VLPs in a medium include, e.g., electron microscopy techniques, dynamic light scattering (DLS), selective chromatographic separation (e.g., ion exchange, hydrophobic interaction, and/or size exclusion chromatographic separation of the VLPs) and density gradient centrifugation.


The virus like particle can include any of the recombinant HIV-1 Env ectodomain trimers or immunogenic fragments thereof, that are disclosed herein. For example, the virus like particle can include the recombinant HIV-1 Env ectodomain trimer or immunogenic fragments thereof, of any of claims X-Y included in the claim set below. Embodiments concerning the virus-like particles are further described in Clauses 1-16, below.


Clause 1. A virus like particle comprising the recombinant HIV-1 Env ectodomain trimer or immunogenic fragment thereof of any one of claims 1-67;


particularly wherein the recombinant HIV-1 Env ectodomain trimer or immunogenic fragment thereof is linked to a transmembrane domain;


particularly wherein the recombinant HIV-1 Env ectodomain trimer comprises DS and SOS substitutions as described herein;


particularly wherein the recombinant HIV-1 Env ectodomain trimer is a chimeric HIV-1 Env trimer comprising a BG505 “platform” as described herein, a V1V2 domain from a CAP256.SU (SEQ ID NO: 51), a BB201.B42 (SEQ ID NO: 81), a KER2018.11 (SEQ ID NO: 107), a CH070.1 (SEQ ID NO: 174), a ZM233.6 (SEQ ID NO: 745), a Q23.17 (SEQ ID NO: 746), a A244 (SEQ ID NO: 747), a T250-4 (SEQ ID NO: 2114), or a WITO.33 (SEQ ID NO: 748) strain of HIV-1, with the remainder of the HIV-1 Env ectodomain based on Env from a 45_01dG5 Env or a 426c Env that further comprises amino acid substitutions to remove the N-linked glycan sequons at positions 276, 460, 463.


Clause 2. An isolated nucleic acid molecule encoding the virus like particle of clause 1.


Clause 3. The nucleic acid molecule of clause 2, wherein the nucleic acid molecule encodes a precursor protein of the gp120/gp41 protomers in the recombinant HIV-1 Env ectodomain trimer.


Clause 4. The nucleic acid molecule of clause 2 or clause 3, operably linked to a promoter.


Clause 5. A vector comprising the nucleic acid molecule of clause 4.


Clause 6. An isolated host cell comprising the vector of clause 5.


Clause 7. The virus-like particle of any one of the prior clauses, wherein administration of an effective amount of the virus like particle induces a neutralizing immune response to HIV-1 Env in the subject.


Clause 8. An immunogenic composition comprising an effective amount of the virus like particle of any one of the prior clauses, and a pharmaceutically acceptable carrier.


Clause 9. The immunogenic composition of clause 8, further comprising an adjuvant.


Clause 10. A method for generating an immune response to Human Immunodeficiency Virus type 1 (HIV-1) gp120 in a subject, comprising administering to the subject an effective amount of the immunogenic composition of clause 9 or clause 10, thereby generating the immune response.


Clause 11. A method for treating or preventing a Human Immunodeficiency Virus type 1 (HIV-1) infection in a subject, comprising administering to the subject a therapeutically effective amount of the immunogenic composition of clause 9 or clause 10, thereby treating the subject or preventing HIV-1 infection of the subject.


Clause 12. The method of clause 10 clause 11, comprising a prime-boost administration of the immunogenic composition.


Clause 13. The method of any of clauses 10-12, wherein the subject is at risk of or has an HIV-1 infection.


Clause 14. A kit comprising the virus like particle, nucleic acid molecule, vector, or composition, of any of clauses 1-9, and instructions for using the kit.


Clause 15. Use of the virus like particle, nucleic acid molecule, vector, or composition of any of clauses 1-9, to inhibit or prevent HIV-1 infection in a subject.


Clause 16. Use of the virus like particle, nucleic acid molecule, vector, or composition of any of clauses 1-9, to induce an immune response to HIV-1 Env in a subject.


G. Viral Vectors

The nucleic acid molecules encoding the disclosed immunogens (e.g., a recombinant HIV-1 Env ectodomain stabilized in a prefusion mature closed conformation or an immunogenic fragment thereof) can be included in a viral vector, for example for expression of the antigen in a host cell, or for immunization of a subject as disclosed herein. In some embodiments, the viral vectors are administered to a subject as part of a prime-boost vaccination. In several embodiments, the viral vectors are included in a vaccine, such as a primer vaccine or a booster vaccine for use in a prime-boost vaccination.


In several examples, the viral vector can be replication-competent. For example, the viral vector can have a mutation in the viral genome that does not inhibit viral replication in host cells. The viral vector also can be conditionally replication-competent. In other examples, the viral vector is replication-deficient in host cells.


A number of viral vectors have been constructed, that can be used to express the disclosed antigens, including polyoma, i.e., SV40 (Madzak et al., 1992, J. Gen. Virol., 73:15331536), adenovirus (Berkner, 1992, Cur. Top. Microbiol. Immunol., 158:39-6; Berliner et al., 1988, Bio Techniques, 6:616-629; Gorziglia et al., 1992, J. Virol., 66:4407-4412; Quantin et al., 1992, Proc. Natl. Acad. Sci. USA, 89:2581-2584; Rosenfeld et al., 1992, Cell, 68:143-155; Wilkinson et al., 1992, Nucl. Acids Res., 20:2233-2239; Stratford-Perricaudet et al., 1990, Hum. Gene Ther., 1:241-256), vaccinia virus (Mackett et al., 1992, Biotechnology, 24:495-499), adeno-associated virus (Muzyczka, 1992, Curr. Top. Microbiol. Immunol., 158:91-123; On et al., 1990, Gene, 89:279-282), herpes viruses including HSV and EBV (Margolskee, 1992, Curr. Top. Microbiol. Immunol., 158:67-90; Johnson et al., 1992, J. Virol., 66:29522965; Fink et al., 1992, Hum. Gene Ther. 3:11-19; Breakfield et al., 1987, Mol. Neurobiol., 1:337-371; Fresse et al., 1990, Biochem. Pharmacol., 40:2189-2199), Sindbis viruses (H. Herweijer et al., 1995, Human Gene Therapy 6:1161-1167; U.S. Pat. Nos. 5,091,309 and 5,2217,879), alphaviruses (S. Schlesinger, 1993, Trends Biotechnol. 11:18-22; I. Frolov et al., 1996, Proc. Natl. Acad. Sci. USA 93:11371-11377) and retroviruses of avian (Brandyopadhyay et al., 1984, Mol. Cell Biol., 4:749-754; Petropouplos et al., 1992, J. Virol., 66:3391-3397), murine (Miller, 1992, Curr. Top. Microbiol. Immunol., 158:1-24; Miller et al., 1985, Mol. Cell Biol., 5:431-437; Sorge et al., 1984, Mol. Cell Biol., 4:1730-1737; Mann et al., 1985, J. Virol., 54:401-407), and human origin (Page et al., 1990, J. Virol., 64:5370-5276; Buchschalcher et al., 1992, J. Virol., 66:2731-2739). Baculovirus (Autographa californica multinuclear polyhedrosis virus; AcMNPV) vectors are also known in the art, and may be obtained from commercial sources (such as PharMingen, San Diego, Calif.; Protein Sciences Corp., Meriden, Conn.; Stratagene, La Jolla, Calif.).


In several embodiments, the viral vector can include an adenoviral vector that expresses a disclosed recombinant HIV-1 Env ectodomain or immunogenic fragment thereof. Adenovirus from various origins, subtypes, or mixture of subtypes can be used as the source of the viral genome for the adenoviral vector. Non-human adenovirus (e.g., simian, chimpanzee, gorilla, avian, canine, ovine, or bovine adenoviruses) can be used to generate the adenoviral vector. For example, a simian adenovirus can be used as the source of the viral genome of the adenoviral vector. A simian adenovirus can be of serotype 1, 3, 7, 11, 16, 18, 19, 20, 27, 33, 38, 39, 48, 49, 50, or any other simian adenoviral serotype. A simian adenovirus can be referred to by using any suitable abbreviation known in the art, such as, for example, SV, SAdV, SAV or sAV. In some examples, a simian adenoviral vector is a simian adenoviral vector of serotype 3, 7, 11, 16, 18, 19, 20, 27, 33, 38, or 39. In one example, a chimpanzee serotype C Ad3 vector is used (see, e.g., Peruzzi et al., Vaccine, 27:1293-1300, 2009). Human adenovirus can be used as the source of the viral genome for the adenoviral vector. Human adenovirus can be of various subgroups or serotypes. For instance, an adenovirus can be of subgroup A (e.g., serotypes 12, 18, and 31), subgroup B (e.g., serotypes 3, 7, 11, 14, 16, 21, 34, 35, and 50), subgroup C (e.g., serotypes 1, 2, 5, and 6), subgroup D (e.g., serotypes 8, 9, 10, 13, 15, 17, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 36-39, and 42-48), subgroup E (e.g., serotype 4), subgroup F (e.g., serotypes 40 and 41), an unclassified serogroup (e.g., serotypes 49 and 51), or any other adenoviral serotype. The person of ordinary skill in the art is familiar with replication competent and deficient adenoviral vectors (including singly and multiply replication deficient adenoviral vectors). Examples of replication-deficient adenoviral vectors, including multiply replication-deficient adenoviral vectors, are disclosed in U.S. Pat. Nos. 5,837,511; 5,851,806; 5,994,106; 6,127,175; 6,482,616; and 7,195,896, and International Patent Application Nos. WO 94/28152, WO 95/02697, WO 95/16772, WO 95/34671, WO 96/22378, WO 97/12986, WO 97/21826, and WO 03/02231 1.


H. Neutralizing Immune Response

A disclosed recombinant HIV-1 Env ectodomain stabilized in a prefusion mature closed conformation, or immunogenic fragment thereof, can be used to elicit a neutralizing immune response to HIV-1 in a subject. In several such embodiments, induction of the immune response includes production of neutralizing antibodies to HIV-1.


In several embodiments, following immunization of a subject with a disclosed immunogen (e.g., as described herein) serum can be collected from the subject at appropriate time points, frozen, and stored for neutralization testing. Methods to assay for neutralization activity are known to the person of ordinary skill in the art and are further described herein, and include, but are not limited to, plaque reduction neutralization (PRNT) assays, microneutralization assays, flow cytometry based assays, single-cycle infection assays (e.g., as described in Martin et al. (2003) Nature Biotechnology 21:71-76), and pseudovirus neutralization assays (e.g., as described in Georgiev et al. (Science, 340, 751-756, 2013), Seaman et al. (J. Virol., 84, 1439-1452, 2005), and Mascola et al. (J. Virol., 79, 10103-10107, 2005), each of which is incorporated by reference herein in its entirety.


In some embodiments, the serum neutralization activity can be assayed using a panel of HIV-1 pseudoviruses as described in Georgiev et al., Science, 340, 751-756, 2013 or Seaman et al. J. Virol., 84, 1439-1452, 2005. Briefly, pseudovirus stocks are prepared by co-transfection of 293T cells with an HIV-1 Env-deficient backbone and an expression plasmid encoding the Env gene of interest. The serum to be assayed is diluted in Dulbecco's modified Eagle medium-10% FCS (Gibco) and mixed with pseudovirus. After 30 min, 10,000 TZM-bl cells are added, and the plates are incubated for 48 hours. Assays are developed with a luciferase assay system (Promega, Madison, Wis.), and the relative light units (RLU) are read on a luminometer (Perkin-Elmer, Waltham, Mass.). To account for background, a cutoff of ID50≧40 can be used as a criterion for the presence of serum neutralization activity against a given pseudovirus.


In some embodiments, administration of a therapeutically effective amount of one or more of the disclosed immunogens to a subject (e.g., by a prime-boost administration of a DNA vector encoding a disclosed immunogen (prime) followed by a protein nanoparticle including a disclosed immunogen (boost)) induces a neutralizing immune response in the subject. In several embodiments, the neutralizing immune response can be detected using a pseudovirus neutralization assay against a panel of HIV-1 pseudoviruses including HIV-1 Env proteins from different HIV-1 strains. In one example, the panel can include pseudoviruses including Env proteins from HIV-1 strains from Clade A (KER2018.11, Q23.17, Q168.a2, Q769.h5, and RW020.2), Clade B (BaL.01, 6101.10, BG1168.01, CAAN.A2, JR-FL, JR-CSF.JB, PVO.4, THRO4156.18, TRJO4551.58, TRO.11, and YU2), and Clade C (DU156.12, DU422.01, ZA012.29, ZM55.28a, and ZM106.9). In other examples, the panel can include pseudoviruses including Env proteins from the HIV-1 strains listed in Table S5 or Table S6 of Georgiev et al. (Science, 340, 751-756, 2013, which is incorporated by reference herein in its entirety), or Table 1 of Seaman et al. (J. Virol., 84, 1439-1452, 2005, which is incorporated by reference herein in its entirety).


In some embodiments, administration of a therapeutically effective amount of one or more of the disclosed immunogen to a subject (e.g., by a prime-boost administration of a DNA vector encoding a disclosed immunogen (prime) followed by a protein nanoparticle including a disclosed immunogen (boost)) induces a neutralizing immune response in the subject, wherein serum from the subject neutralizes, with an ID50≧40, at least 30% (such as at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, or at least 90%) of pseudoviruses is a panel of pseudoviruses including the HIV-1 Env proteins listed in Table S5 or Table S6 of Georgiev et al. (Science, 340, 751-756, 2013), or Table 1 of Seaman et al. (J. Virol., 84, 1439-1452, 2005) or including Env proteins from HIV-1 strains from Clade A (KER2018.11, Q23.17, Q168.a2, Q769.h5, and RW020.2), Clade B (BaL.01, 6101.10, BG1168.01, CAAN.A2, JR-FL, JR-CSF.JB, PVO.4, THRO4156.18, TRJO4551.58, TRO.11, and YU2), and Clade C (DU156.12, DU422.01, ZA012.29, ZM55.28a, and ZM106.9).


In additional embodiments, administration of a therapeutically effective amount of one or more of the disclosed immunogen to a subject (e.g., by a prime-boost administration of a DNA vector encoding a disclosed immunogen (prime) followed by a protein nanoparticle including a disclosed immunogen (boost)) induces a neutralizing immune response in the subject, wherein serum from the subject neutralizes, with an ID50≧40, at least 30% (such as at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, or at least 90%) of pseudoviruses is a panel of pseudoviruses including the Clade A, Clade B, or Clade C HIV-1 Env proteins listed in Table S5 or Table S6 of Georgiev et al. (Science, 340, 751-756, 2013), or Table 1 of Seaman et al. (J. Virol., 84, 1439-1452, 2005) or including Env proteins from HIV-1 strains from Clade A (KER2018.11, Q23.17, Q168.a2, Q769.h5, and RW020.2), Clade B (BaL.01, 6101.10, BG1168.01, CAAN.A2, JR-FL, JR-CSF.JB, PVO.4, THR04156.18, TRJ04551.58, TRO.11, and YU2), and Clade C (DU156.12, DU422.01, ZA012.29, ZM55.28a, and ZM106.9).


I. Compositions

The disclosed immunogens (for example, a recombinant HIV-1 Env ectodomain or immunogenic fragment thereof, or a protein nanoparticle including such proteins), or nucleic acid molecule encoding an immunogen, can be included in a pharmaceutical composition (including therapeutic and prophylactic formulations), often combined together with one or more pharmaceutically acceptable vehicles and, optionally, other therapeutic ingredients (for example, antibiotics or antiviral drugs). In several embodiments, pharmaceutical compositions including one or more of the disclosed immunogens are immunogenic compositions.


Such pharmaceutical compositions can be administered to subjects by a variety of administration modes known to the person of ordinary skill in the art, for example, intramuscular, subcutaneous, intravenous, intra-arterial, intra-articular, intraperitoneal, or parenteral routes.


To formulate the pharmaceutical compositions, the disclosed immunogens (for example, a recombinant HIV-1 Env ectodomain or immunogenic fragment thereof, or a protein nanoparticle including such proteins), or nucleic acid molecule encoding an immunogen, can be combined with various pharmaceutically acceptable additives, as well as a base or vehicle for dispersion of the conjugate. Desired additives include, but are not limited to, pH control agents, such as arginine, sodium hydroxide, glycine, hydrochloric acid, citric acid, and the like. In addition, local anesthetics (for example, benzyl alcohol), isotonizing agents (for example, sodium chloride, mannitol, sorbitol), adsorption inhibitors (for example, TWEEN® 80), solubility enhancing agents (for example, cyclodextrins and derivatives thereof), stabilizers (for example, serum albumin), and reducing agents (for example, glutathione) can be included. Adjuvants, such as aluminum hydroxide (ALHYDROGEL®, available from Brenntag Biosector, Copenhagen, Denmark and AMPHOGEL®, Wyeth Laboratories, Madison, N.J.), Freund's adjuvant, MPL™ (3-O-deacylated monophosphoryl lipid A; Corixa, Hamilton, Ind.) and IL-12 (Genetics Institute, Cambridge, Mass.), among many other suitable adjuvants well known in the art, can be included in the compositions.


When the composition is a liquid, the tonicity of the formulation, as measured with reference to the tonicity of 0.9% (w/v) physiological saline solution taken as unity, is typically adjusted to a value at which no substantial, irreversible tissue damage will be induced at the site of administration. Generally, the tonicity of the solution is adjusted to a value of about 0.3 to about 3.0, such as about 0.5 to about 2.0, or about 0.8 to about 1.7.


The disclosed immunogens (for example, a recombinant HIV-1 Env ectodomain or immunogenic fragment thereof, or a protein nanoparticle including such proteins), or nucleic acid molecule encoding an immunogen can be dispersed in a base or vehicle, which can include a hydrophilic compound having a capacity to disperse the antigens, and any desired additives. The base can be selected from a wide range of suitable compounds, including but not limited to, copolymers of polycarboxylic acids or salts thereof, carboxylic anhydrides (for example, maleic anhydride) with other monomers (for example, methyl (meth)acrylate, acrylic acid and the like), hydrophilic vinyl polymers, such as polyvinyl acetate, polyvinyl alcohol, polyvinylpyrrolidone, cellulose derivatives, such as hydroxymethylcellulose, hydroxypropylcellulose and the like, and natural polymers, such as chitosan, collagen, sodium alginate, gelatin, hyaluronic acid, and nontoxic metal salts thereof. Often, a biodegradable polymer is selected as a base or vehicle, for example, polylactic acid, poly(lactic acid-glycolic acid) copolymer, polyhydroxybutyric acid, poly(hydroxybutyric acid-glycolic acid) copolymer and mixtures thereof. Alternatively or additionally, synthetic fatty acid esters such as polyglycerin fatty acid esters, sucrose fatty acid esters and the like can be employed as vehicles. Hydrophilic polymers and other vehicles can be used alone or in combination, and enhanced structural integrity can be imparted to the vehicle by partial crystallization, ionic bonding, cross-linking and the like. The vehicle can be provided in a variety of forms, including fluid or viscous solutions, gels, pastes, powders, microspheres and films, for examples for direct application to a mucosal surface.


The disclosed immunogens (for example, a recombinant HIV-1 Env ectodomain or immunogenic fragment thereof, or a protein nanoparticle including such proteins), or nucleic acid molecule encoding an immunogen can be combined with the base or vehicle according to a variety of methods, and release of the antigens can be by diffusion, disintegration of the vehicle, or associated formation of water channels. In some circumstances, the disclosed immunogens (for example, a recombinant HIV-1 Env ectodomain or immunogenic fragment thereof, or a protein nanoparticle including such proteins), or nucleic acid molecule encoding an immunogen is dispersed in microcapsules (microspheres) or nanocapsules (nanospheres) prepared from a suitable polymer, for example, isobutyl 2-cyanoacrylate (see, for example, Michael et al., J. Pharmacy Pharmacol. 43:1-5, 1991), and dispersed in a biocompatible dispersing medium, which yields sustained delivery and biological activity over a protracted time.


The pharmaceutical compositions of the disclosure can alternatively contain as pharmaceutically acceptable vehicles substances as required to approximate physiological conditions, such as pH adjusting and buffering agents, tonicity adjusting agents, wetting agents and the like, for example, sodium acetate, sodium lactate, sodium chloride, potassium chloride, calcium chloride, sorbitan monolaurate, and triethanolamine oleate. For solid compositions, conventional nontoxic pharmaceutically acceptable vehicles can be used which include, for example, pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharin, talcum, cellulose, glucose, sucrose, magnesium carbonate, and the like.


Pharmaceutical compositions for administering the immunogenic compositions can also be formulated as a solution, microemulsion, or other ordered structure suitable for high concentration of active ingredients. The vehicle can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, liquid polyethylene glycol, and the like), and suitable mixtures thereof. Proper fluidity for solutions can be maintained, for example, by the use of a coating such as lecithin, by the maintenance of a desired particle size in the case of dispersible formulations, and by the use of surfactants. In many cases, it will be desirable to include isotonic agents, for example, sugars, polyalcohols, such as mannitol and sorbitol, or sodium chloride in the composition. Prolonged absorption of the disclosed antigens can be brought about by including in the composition an agent which delays absorption, for example, monostearate salts and gelatin.


In certain embodiments, the disclosed immunogens (for example, a recombinant HIV-1 Env ectodomain or immunogenic fragment thereof, or a protein nanoparticle including such proteins), or nucleic acid molecule encoding an immunogen can be administered in a time-release formulation, for example in a composition that includes a slow release polymer. These compositions can be prepared with vehicles that will protect against rapid release, for example a controlled release vehicle such as a polymer, microencapsulated delivery system or bioadhesive gel. Prolonged delivery in various compositions of the disclosure can be brought about by including in the composition agents that delay absorption, for example, aluminum monostearate hydrogels and gelatin. When controlled release formulations are desired, controlled release binders suitable for use in accordance with the disclosure include any biocompatible controlled release material which is inert to the active agent and which is capable of incorporating the disclosed antigen and/or other biologically active agent. Numerous such materials are known in the art. Useful controlled-release binders are materials that are metabolized slowly under physiological conditions following their delivery (for example, at a mucosal surface, or in the presence of bodily fluids). Appropriate binders include, but are not limited to, biocompatible polymers and copolymers well known in the art for use in sustained release formulations. Such biocompatible compounds are non-toxic and inert to surrounding tissues, and do not trigger significant adverse side effects, such as nasal irritation, immune response, inflammation, or the like. They are metabolized into metabolic products that are also biocompatible and easily eliminated from the body. Numerous systems for controlled delivery of therapeutic proteins are known (e.g., U.S. Pat. No. 5,055,303; U.S. Pat. No. 5,188,837; U.S. Pat. No. 4,235,871; U.S. Pat. No. 4,501,728; U.S. Pat. No. 4,837,028; U.S. Pat. No. 4,957,735; and U.S. Pat. No. 5,019,369; U.S. Pat. No. 5,055,303; U.S. Pat. No. 5,514,670; U.S. Pat. No. 5,413,797; U.S. Pat. No. 5,268,164; U.S. Pat. No. 5,004,697; U.S. Pat. No. 4,902,505; U.S. Pat. No. 5,506,206; U.S. Pat. No. 5,271,961; U.S. Pat. No. 5,254,342; and U.S. Pat. No. 5,534,496).


Exemplary polymeric materials for use in the present disclosure include, but are not limited to, polymeric matrices derived from copolymeric and homopolymeric polyesters having hydrolyzable ester linkages. A number of these are known in the art to be biodegradable and to lead to degradation products having no or low toxicity. Exemplary polymers include polyglycolic acids and polylactic acids, poly(DL-lactic acid-co-glycolic acid), poly(D-lactic acid-co-glycolic acid), and poly(L-lactic acid-co-glycolic acid). Other useful biodegradable or bioerodable polymers include, but are not limited to, such polymers as poly(epsilon-caprolactone), poly(epsilon-aprolactone-CO-lactic acid), poly(epsilon.-aprolactone-CO-glycolic acid), poly(beta-hydroxy butyric acid), poly(alkyl-2-cyanoacrilate), hydrogels, such as poly(hydroxyethyl methacrylate), polyamides, poly(amino acids) (for example, L-leucine, glutamic acid, L-aspartic acid and the like), poly(ester urea), poly(2-hydroxyethyl DL-aspartamide), polyacetal polymers, polyorthoesters, polycarbonate, polymaleamides, polysaccharides, and copolymers thereof. Many methods for preparing such formulations are well known to those skilled in the art (see, for example, Sustained and Controlled Release Drug Delivery Systems, J. R. Robinson, ed., Marcel Dekker, Inc., New York, 1978). Other useful formulations include controlled-release microcapsules (U.S. Pat. Nos. 4,652,441 and 4,917,893), lactic acid-glycolic acid copolymers useful in making microcapsules and other formulations (U.S. Pat. Nos. 4,677,191 and 4,728,721) and sustained-release compositions for water-soluble peptides (U.S. Pat. No. 4,675,189).


The pharmaceutical compositions of the disclosure typically are sterile and stable under conditions of manufacture, storage and use. Sterile solutions can be prepared by incorporating the conjugate in the required amount in an appropriate solvent with one or a combination of ingredients enumerated herein, as required, followed by filtered sterilization. Generally, dispersions are prepared by incorporating the disclosed antigen and/or other biologically active agent into a sterile vehicle that contains a basic dispersion medium and the required other ingredients from those enumerated herein. In the case of sterile powders, methods of preparation include vacuum drying and freeze-drying which yields a powder of the disclosed antigen plus any additional desired ingredient from a previously sterile-filtered solution thereof. The prevention of the action of microorganisms can be accomplished by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, sorbic acid, thimerosal, and the like.


Actual methods for preparing administrable compositions will be known or apparent to those skilled in the art and are described in more detail in such publications as Remingtons Pharmaceutical Sciences, 19th Ed., Mack Publishing Company, Easton, Pa., 1995.


In several embodiments, the compositions include an adjuvant. The person of ordinary skill in the art is familiar with adjuvants, for example, those that can be included in an immunogenic composition. It will be appreciated that the choice of adjuvant can be different in these different applications, and the optimal adjuvant and concentration for each situation can be determined empirically by those of skill in the art.


The pharmaceutical composition typically contains a therapeutically effective amount of a disclosed immunogen (for example, a recombinant HIV-1 Env ectodomain or immunogenic fragment thereof, or a protein nanoparticle including such proteins), or nucleic acid molecule encoding an immunogen, or viral vector can be prepared by conventional techniques. Preparation of immunogenic compositions, including those for administration to human subjects, is generally described in Pharmaceutical Biotechnology, Vol. 61 Vaccine Design—the subunit and adjuvant approach, edited by Powell and Newman, Plenum Press, 1995. New Trends and Developments in Vaccines, edited by Voller et al., University Park Press, Baltimore, Md., U.S.A. 1978. Encapsulation within liposomes is described, for example, by Fullerton, U.S. Pat. No. 4,235,877. Conjugation of proteins to macromolecules is disclosed, for example, by Likhite, U.S. Pat. No. 4,372,945 and by Armor et al., U.S. Pat. No. 4,474,757. Typically, the amount of antigen in each dose of the immunogenic composition is selected as an amount which induces an immune response without significant, adverse side effects.


The amount of the disclosed immunogen (for example, a recombinant HIV-1 Env ectodomain or immunogenic fragment thereof, or a protein nanoparticle including such proteins), or nucleic acid molecule encoding an immunogen, or viral vector can vary depending upon the specific antigen employed, the route and protocol of administration, and the target population, for example. For protein therapeutics, typically, each human dose will comprise 1-1000 μg of protein, such as from about 1 μg to about 100 μg, for example, from about 1 μg to about 50 μg, such as about 1 μg, about 2 μg, about 5 μg, about 10 μg, about 15 μg, about 20 μg, about 25 μg, about 30 μg, about 40 μg, or about 50 μg. The amount utilized in an immunogenic composition is selected based on the subject population (e.g., infant or elderly). An optimal amount for a particular composition can be ascertained by standard studies involving observation of antibody titers and other responses in subjects. It is understood that a therapeutically effective amount of a disclosed immunogen, such as a recombinant HIV-1 Env ectodomain or fragment thereof, protein nanoparticle, viral vector, or nucleic acid molecule in a immunogenic composition, can include an amount that is ineffective at eliciting an immune response by administration of a single dose, but that is effective upon administration of multiple dosages, for example in a prime-boost administration protocol.


In some embodiments, the composition can be provided as a sterile composition. In more embodiments, the composition can be provided in unit dosage form for use to induce an immune response in a subject, for example, to prevent HIV-1 infection in the subject. A unit dosage form contains a suitable single preselected dosage for administration to a subject, or suitable marked or measured multiples of two or more preselected unit dosages, and/or a metering mechanism for administering the unit dose or multiples thereof. In other embodiments, the composition further includes an adjuvant.


J. Therapeutic Methods

The recombinant HIV-1 Env proteins, immunogenic fragments thereof, protein nanoparticles, polynucleotides encoding the recombinant HIV-1 Env proteins or immunogenic fragments, vectors and compositions, can be used in methods of preventing, inhibiting and treating an HIV-1 infection, as well as methods of inducing an immune response to HIV-1, as described below. In several embodiments, a therapeutically effective amount of an immunogenic composition including one or more of the disclosed recombinant HIV-1 Env proteins or immunogenic fragments thereof, or protein nanoparticles of VLPs, or nucleic acid molecule or viral vector encoding a recombinant HIV-1 Env proteins or immunogenic fragments thereof, can be administered to a subject in order to generate an immune response to HIV-1.


In some embodiments, a subject is selected for treatment that has, or is at risk for developing, an HIV infection, for example because of exposure or the possibility of exposure to HIV. Following administration of a therapeutically effective amount of a recombinant HIV-1 Env proteins, immunogenic fragments thereof, protein nanoparticles, polynucleotides encoding the recombinant HIV-1 Env proteins or immunogenic fragments, vectors and compositions, the subject can be monitored for HIV-1 infection, symptoms associated with HIV-1 infection, or both.


Typical subjects intended for treatment with the therapeutics and methods of the present disclosure include humans, as well as non-human primates and other animals. To identify subjects for prophylaxis or treatment according to the methods of the disclosure, accepted screening methods are employed to determine risk factors associated with a targeted or suspected disease or condition, or to determine the status of an existing disease or condition in a subject. These screening methods include, for example, conventional work-ups to determine environmental, familial, occupational, and other such risk factors that may be associated with the targeted or suspected disease or condition, as well as diagnostic methods, such as various ELISA and other immunoassay methods, which are available and well known in the art to detect and/or characterize HIV infection. These and other routine methods allow the clinician to select patients in need of therapy using the methods and pharmaceutical compositions of the disclosure. In accordance with these methods and principles, a composition can be administered according to the teachings herein, or other conventional methods known to the person of ordinary skill in the art, as an independent prophylaxis or treatment program, or as a follow-up, adjunct or coordinate treatment regimen to other treatments.


The methods can be used to inhibit, treat or prevent HIV infection in vivo. When inhibiting, treating, or preventing infection in vivo, the methods can be used either to avoid infection in an HIV-seronegative subject (e.g., by inducing an immune response that protects against HIV-1 infection), or to treat existing infection in an HIV-seropositive subject. The HIV-seropositive subject may or may not carry a diagnosis of AIDS. Hence in some embodiments the methods involves selecting a subject at risk for contracting HIV infection, or a subject at risk of developing AIDS (such as a subject with HIV infection), and administering a recombinant HIV-1 Env proteins, immunogenic fragments thereof, protein nanoparticles, polynucleotides encoding the recombinant HIV-1 Env proteins or immunogenic fragments, vectors and compositions, to the subject.


Treatment of HIV by inhibiting HIV replication or infection can include delaying the development of AIDS in a subject. Treatment of HIV can also include reducing signs or symptoms associated with the presence of HIV (for example by reducing or inhibiting HIV replication). In some examples, treatment using the methods disclosed herein prolongs the time of survival of the subject.


The administration of a disclosed recombinant HIV-1 Env protein, immunogenic fragment thereof, protein nanoparticle, polynucleotide encoding a recombinant HIV-1 Env ectodomain or immunogenic fragment, vector or composition can be for prophylactic or therapeutic purpose. When provided prophylactically, the disclosed therapeutic agents are provided in advance of any symptom, for example in advance of infection. The prophylactic administration of the disclosed therapeutic agents serves to prevent or ameliorate any subsequent infection. When provided therapeutically, the disclosed therapeutic agents are provided at or after the onset of a symptom of disease or infection, for example after development of a symptom of HIV-1 infection, or after diagnosis of HIV-1 infection. The therapeutic agents can thus be provided prior to the anticipated exposure to HIV virus so as to attenuate the anticipated severity, duration or extent of an infection and/or associated disease symptoms, after exposure or suspected exposure to the virus, or after the actual initiation of an infection.


The immunogenic composition including one or more of the disclosed agents (for example, a recombinant HIV-1 Env protein, immunogenic fragments thereof, protein nanoparticles, or VLP), or nucleic acid molecule or viral vector encoding a recombinant HIV-1 Env ectodomain or immunogenic fragment thereof, can be used in coordinate vaccination protocols or combinatorial formulations. In certain embodiments, novel combinatorial immunogenic compositions and coordinate immunization protocols employ separate immunogens or formulations, each directed toward eliciting an anti-HIV immune response, such as an immune response to HIV-1 Env protein. Separate immunogenic compositions that elicit the anti-HIV immune response can be combined in a polyvalent immunogenic composition administered to a subject in a single immunization step, or they can be administered separately (in monovalent immunogenic compositions) in a coordinate immunization protocol.


HIV infection does not need to be completely eliminated or reduced or prevented for the methods to be effective. For example, treatment with one or more of the disclosed therapeutic agents can reduce or inhibit HIV infection by a desired amount, for example by at least 10%, at least 20%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98%, or even at least 100% (elimination or prevention of detectable HIV infected cells), as compared to HIV infection in the absence of the therapeutic agent. In additional examples, HIV replication can be reduced or inhibited by the disclosed methods. HIV replication does not need to be completely eliminated for the method to be effective. For example, treatment with one or more of the disclosed recombinant HIV-1 Env proteins, immunogenic fragment thereof, protein nanoparticles, polynucleotides encoding a recombinant HIV-1 Env ectodomain or immunogenic fragment, vectors or compositions can HIV replication by a desired amount, for example by at least 10%, at least 20%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98%, or even at least 100% (elimination or prevention of detectable HIV replication), as compared to HIV replication in the absence of the therapeutic agent.


To successfully reproduce itself, HIV must convert its RNA genome to DNA, which is then imported into the host cell's nucleus and inserted into the host genome through the action of HIV integrase. Because HIV's primary cellular target, CD4+ T-Cells, can function as the memory cells of the immune system, integrated HIV can remain dormant for the duration of these cells' lifetime. Memory T-Cells may survive for many years and possibly for decades. This latent HIV reservoir can be measured by co-culturing CD4+ T-Cells from infected patients with CD4+ T-Cells from uninfected donors and measuring HIV protein or RNA (See, e.g., Archin et al., AIDS, 22:1131-1135, 2008). In some embodiments, the provided methods of treating or inhibiting HIV infection include reduction or elimination of the latent reservoir of HIV infected cells in a subject. For example, a reduction of at least 10%, at least 20%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98%, or even at least 100% (elimination of detectable HIV) of the latent reservoir of HIV infected cells in a subject, as compared to the latent reservoir of HIV infected cells in a subject in the absence of the treatment with one or more of the provided recombinant HIV-1 Env proteins, immunogenic fragments thereof, protein nanoparticles, polynucleotides encoding a recombinant HIV-1 Env ectodomain or immunogenic fragment, vectors or compositions.


Studies have shown that the rate of HIV transmission from mother to infant is reduced significantly when zidovudine is administered to HIV-infected women during pregnancy and delivery and to the offspring after birth (Connor et al., 1994 Pediatr Infect Dis J 14: 536-541). Several studies of mother-to-infant transmission of HIV have demonstrated a correlation between the maternal virus load at delivery and risk of HIV transmission to the child. The disclosed recombinant HIV-1 Env proteins, immunogenic fragments thereof, protein nanoparticles, polynucleotides encoding a recombinant HIV-1 Env ectodomain or immunogenic fragment, vectors and compositions are of use in decreasing HIV-transmission from mother to infant. Thus, in some embodiments a therapeutically effective amount of one or more of the provided therapeutic agents is administered in order to prevent transmission of HIV, or decrease the risk of transmission of HIV, from a mother to an infant. In some embodiments, a therapeutically effective amount of the agent can be administered to a pregnant subject to induce an immune response that generates neutralizing antibodies that are passes to the fetus via the umbilical cord to protect the fetus from infection during birth. In some embodiments, both a therapeutically effective amount of a disclosed recombinant HIV-1 Env protein, immunogenic fragment thereof, protein nanoparticle, polynucleotide encoding a recombinant HIV-1 Env ectodomain or immunogenic fragment, vector or composition and a therapeutically effective amount of another anti-HIV agent, such as zidovudine, is administered to the mother and/or infant.


Administration of a therapeutically effective amount of a disclosed recombinant HIV-1 Env protein, immunogenic fragment thereof, protein nanoparticle, polynucleotide encoding a recombinant HIV-1 Env ectodomain or immunogenic fragment, vector or composition induces a sufficient immune response to treat or inhibit or prevent the pathogenic infection, for example, to inhibit the infection and/or reduce the signs and/or symptoms of the infection. Amounts effective for this use will depend upon the severity of the disease, the general state of the subject's health, and the robustness of the subject's immune system.


For prophylactic and therapeutic purposes, a therapeutically effective amount of a disclosed recombinant HIV-1 Env protein, immunogenic fragment thereof, protein nanoparticle, polynucleotide encoding a recombinant HIV-1 Env ectodomain or immunogenic fragment, vector or composition can be administered to the subject in a single bolus delivery, via continuous delivery (for example, continuous transdermal, mucosal or intravenous delivery) over an extended time period, or in a repeated administration protocol (for example, by an hourly, daily or weekly, repeated administration protocol). The therapeutically effective dosage of the therapeutic agents can be provided as repeated doses within a prolonged prophylaxis or treatment regimen that will yield clinically significant results to alleviate one or more symptoms or detectable conditions associated with a targeted disease or condition as set forth herein.


In several embodiments, a prime-boost immunization protocol is used, and a recombinant HIV-1 Env ectodomain trimer including that binds to mature and unmutated common ancestor (UCA) forms of multiple classes of broadly neutralizing antibodies (e.g., targeting the CD4 binding site and the V1V2 domain) is used for the prime, and (in some embodiments, also for the boost. Exemplary recombinant HIV-1 Env ectodomain fur use as a prime in such embodiments are provided herein and include those set forth as SEQ ID NOs: SEQ ID NOs: 2146, 2147, 2148, 2149, 2150, 2151, 2152, 2153, 2154, 2155, 2156, 2157, 2158, and 2159.


Determination of effective dosages in this context is typically based on animal model studies followed up by human clinical trials and is guided by administration protocols that significantly reduce the occurrence or severity of targeted disease symptoms or conditions in the subject, or that induce a desired response in the subject (such as a neutralizing immune response). Suitable models in this regard include, for example, murine, rat, porcine, feline, ferret, non-human primate, and other accepted animal model subjects known in the art. Alternatively, effective dosages can be determined using in vitro models (for example, immunologic and histopathologic assays). Using such models, only ordinary calculations and adjustments are required to determine an appropriate concentration and dose to administer a therapeutically effective amount of the composition (for example, amounts that are effective to elicit a desired immune response or alleviate one or more symptoms of a targeted disease). In alternative embodiments, an effective amount or effective dose of the composition may simply inhibit or enhance one or more selected biological activities correlated with a disease or condition, as set forth herein, for either therapeutic or diagnostic purposes.


Dosage can be varied by the attending clinician to maintain a desired concentration at a target site (for example, systemic circulation). Higher or lower concentrations can be selected based on the mode of delivery, for example, trans-epidermal, rectal, oral, pulmonary, or intranasal delivery versus intravenous or subcutaneous delivery. The actual dosage of disclosed recombinant HIV-1 Env ectodomain, immunogenic fragment thereof, protein nanoparticle, polynucleotide encoding a recombinant HIV-1 Env ectodomain or immunogenic fragment, vector or composition will vary according to factors such as the disease indication and particular status of the subject (for example, the subject's age, size, fitness, extent of symptoms, susceptibility factors, and the like), time and route of administration, other drugs or treatments being administered concurrently, as well as the specific pharmacology of the composition for eliciting the desired activity or biological response in the subject. Dosage regimens can be adjusted to provide an optimum prophylactic or therapeutic response. As described above in the forgoing listing of terms, a therapeutically effective amount is also one in which any toxic or detrimental side effects of the disclosed immunogen and/or other biologically active agent is outweighed in clinical terms by therapeutically beneficial effects.


A non-limiting range for a therapeutically effective amount of the disclosed immunogen (e.g., a recombinant HIV-1 Env protein, or nucleic acid encoding such protein, or nanoparticle including such protein) within the methods and immunogenic compositions of the disclosure is about 0.0001 mg/kg body weight to about 10 mg/kg body weight, such as about 0.01 mg/kg, about 0.02 mg/kg, about 0.03 mg/kg, about 0.04 mg/kg, about 0.05 mg/kg, about 0.06 mg/kg, about 0.07 mg/kg, about 0.08 mg/kg, about 0.09 mg/kg, about 0.1 mg/kg, about 0.2 mg/kg, about 0.3 mg/kg, about 0.4 mg/kg, about 0.5 mg/kg, about 0.6 mg/kg, about 0.7 mg/kg, about 0.8 mg/kg, about 0.9 mg/kg, about 1 mg/kg, about 1.5 mg/kg, about 2 mg/kg, about 2.5 mg/kg, about 3 mg/kg, about 4 mg/kg, about 5 mg/kg, or about 10 mg/kg, for example 0.01 mg/kg to about 1 mg/kg body weight, about 0.05 mg/kg to about 5 mg/kg body weight, about 0.2 mg/kg to about 2 mg/kg body weight, or about 1.0 mg/kg to about 10 mg/kg body weight.


In some embodiments, the dosage includes a set amount of a disclosed immunogen (e.g., a recombinant HIV-1 Env protein, or nucleic acid encoding such protein, or nanoparticle including such protein) such as from about 1-300 μg, for example, a dosage of about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250, or about 300 μg. The dosage and number of doses will depend on the setting, for example, in an adult or anyone primed by prior HIV infection or immunization, a single dose may be a sufficient booster. In naïve subjects, in some examples, at least two doses would be given, for example, at least three doses. In some embodiments, an annual boost is given, for example, along with an annual influenza vaccination.


Actual methods for preparing administrable compositions will be known or apparent to those skilled in the art and are described in more detail in such publications as Remingtons Pharmaceutical Sciences, 19th Ed., Mack Publishing Company, Easton, Pa., 1995.


In several embodiments, it may be advantageous to administer the therapeutic agents disclosed herein with other agents such as proteins, peptides, antibodies, and other antiviral agents, such as anti-HIV agents. Examples of such anti-HIV therapeutic agents include nucleoside reverse transcriptase inhibitors, such as abacavir, AZT, didanosine, emtricitabine, lamivudine, stavudine, tenofovir, zalcitabine, zidovudine, and the like, non-nucleoside reverse transcriptase inhibitors, such as delavirdine, efavirenz, nevirapine, protease inhibitors such as amprenavir, atazanavir, indinavir, lopinavir, nelfinavir, osamprenavir, ritonavir, saquinavir, tipranavir, and the like, and fusion protein inhibitors such as enfuvirtide and the like. In some examples, the disclosed therapeutic agents are administered with T-helper cells, such as exogenous T-helper cells. Exemplary methods for producing and administering T-helper cells can be found in International Patent Publication WO 03/020904, which is incorporated herein by reference.


For any application, treatment with a disclosed recombinant HIV-1 Env protein, immunogenic fragment thereof, protein nanoparticle, polynucleotide encoding a recombinant HIV-1 Env ectodomain or immunogenic fragment, vector or composition can be combined with anti-retroviral therapy, such as HAART. Antiretroviral drugs are broadly classified by the phase of the retrovirus life-cycle that the drug inhibits. The therapeutic agents can be administered before, during, concurrent to and/or after retroviral therapy. In some embodiments, the therapeutic agents are administered following a course of retroviral therapy. The disclosed therapeutic agents can be administered in conjunction with nucleoside and nucleotide reverse transcriptase inhibitors (nRTI), non-nucleoside reverse transcriptase inhibitors (NNRTI), protease inhibitors, Entry inhibitors (or fusion inhibitors), Maturation inhibitors, or a broad spectrum inhibitors, such as natural antivirals. Exemplary agents include lopinavir, ritonavir, zidovudine, lamivudine, tenofovir, emtricitabine and efavirenz.


In some embodiments, a disclosed recombinant HIV-1 Env protein, immunogenic fragment thereof, protein nanoparticle, polynucleotide encoding a recombinant HIV-1 Env ectodomain or immunogenic fragment, vector or composition can be used as an immunogen to prime or induce an immune response (such as a T or B cell response) to HIV-1 in a subject. In some such embodiments, the T cell response is a CD4+ T helper cell response, such as a Th1 cell response.


In some embodiments, the disclosed recombinant HIV-1 Env protein, immunogenic fragment thereof, protein nanoparticle, polynucleotide encoding a recombinant HIV-1 Env ectodomain or immunogenic fragment, vector or composition is administered to the subject simultaneously with the administration of the adjuvant. In other embodiments, the recombinant HIV-1 Env protein, immunogenic fragment thereof, protein nanoparticle, polynucleotide encoding a recombinant HIV-1 Env ectodomain or immunogenic fragment, vector or composition is administered to the subject after the administration of the adjuvant and within a sufficient amount of time to induce the immune response.


The recombinant HIV-1 Env protein, immunogenic fragment thereof, protein nanoparticle, polynucleotide encoding a recombinant HIV-1 Env ectodomain or immunogenic fragment, vector or composition can be used in coordinate vaccination protocols or combinatorial formulations. In certain embodiments, combinatorial and coordinate immunization protocols employ separate immunogens or formulations, each directed toward eliciting an anti-HIV immune response, such as an immune response to HIV-1 Env. Separate immunogenic compositions that elicit the anti-HIV immune response can be combined in a polyvalent immunogenic composition administered to a subject in a single immunization step, or they can be administered separately (in monovalent immunogenic compositions) in a coordinate immunization protocol.


In one embodiment, a suitable immunization regimen includes at least two separate inoculations with one or more immunogenic compositions, with a second inoculation being administered more than about two, about three to eight, or about four, weeks following the first inoculation. A third inoculation can be administered several months after the second inoculation, and in specific embodiments, more than about five months after the first inoculation, more than about six months to about two years after the first inoculation, or about eight months to about one year after the first inoculation. Periodic inoculations beyond the third are also desirable to enhance the subject's “immune memory.” The adequacy of the vaccination parameters chosen, e.g., formulation, dose, regimen and the like, can be determined by taking aliquots of serum from the subject and assaying antibody titers during the course of the immunization program. Alternatively, the T cell populations can be monitored by conventional methods. In addition, the clinical condition of the subject can be monitored for the desired effect, e.g., prevention of HIV-1 infection or progression to AIDS, improvement in disease state (e.g., reduction in viral load), or reduction in transmission frequency to an uninfected partner. If such monitoring indicates that vaccination is sub-optimal, the subject can be boosted with an additional dose of immunogenic composition, and the vaccination parameters can be modified in a fashion expected to potentiate the immune response. Thus, for example, the dose of the disclosed recombinant HIV-1 Env protein, immunogenic fragment thereof, protein nanoparticle, polynucleotide encoding a recombinant HIV-1 Env ectodomain or immunogenic fragment, vector or composition and/or adjuvant can be increased or the route of administration can be changed.


It is contemplated that there can be several boosts, and that each boost can be a different disclosed recombinant HIV-1 Env protein, immunogenic fragment thereof, protein nanoparticle, polynucleotide encoding a recombinant HIV-1 Env ectodomain or immunogenic fragment, vector or composition. It is also contemplated in some examples that the boost may be the same recombinant HIV-1 Env protein, immunogenic fragment thereof, protein nanoparticle, polynucleotide encoding a recombinant HIV-1 Env ectodomain or immunogenic fragment, vector or composition as another boost, or the prime.


The prime can be administered as a single dose or multiple doses, for example two doses, three doses, four doses, five doses, six doses or more can be administered to a subject over days, weeks or months. The boost can be administered as a single dose or multiple doses, for example two to six doses, or more can be administered to a subject over a day, a week or months. Multiple boosts can also be given, such one to five, or more. Different dosages can be used in a series of sequential inoculations. For example a relatively large dose in a primary inoculation and then a boost with relatively smaller doses. The immune response against the selected antigenic surface can be generated by one or more inoculations of a subject.


Upon administration of a disclosed recombinant HIV-1 Env protein, immunogenic fragment thereof, protein nanoparticle, polynucleotide encoding a recombinant HIV-1 Env ectodomain or immunogenic fragment, vector or composition of this disclosure, the immune system of the subject typically responds to the immunogenic composition by producing antibodies specific for HIV-1 Env protein. Such a response signifies that an immunologically effective dose was delivered to the subject.


An immunologically effective dosage can be achieved by single or multiple administrations (including, for example, multiple administrations per day), daily, or weekly administrations. For each particular subject, specific dosage regimens can be evaluated and adjusted over time according to the individual need and professional judgment of the person administering or supervising the administration of the immunogenic composition. In some embodiments, the antibody response of a subject will be determined in the context of evaluating effective dosages/immunization protocols. In most instances it will be sufficient to assess the antibody titer in serum or plasma obtained from the subject. Decisions as to whether to administer booster inoculations and/or to change the amount of the therapeutic agent administered to the individual can be at least partially based on the antibody titer level. The antibody titer level can be based on, for example, an immunobinding assay which measures the concentration of antibodies in the serum which bind to an antigen including, for example, a disclosed recombinant HIV-1 Env protein. The methods of using immunogenic composition, and the related compositions and methods of the disclosure are useful in increasing resistance to, preventing, ameliorating, and/or treating infection and disease caused by HIV (such as HIV-1) in animal hosts, and other, in vitro applications.


In certain embodiments, the recombinant HIV-1 Env protein, immunogenic fragment thereof, protein nanoparticle, polynucleotide encoding a recombinant HIV-1 Env ectodomain or immunogenic fragment, vector or composition is administered sequentially with other anti-HIV therapeutic agents, such as before or after the other agent. One of ordinary skill in the art would know that sequential administration can mean immediately following or after an appropriate period of time, such as hours, days, weeks, months, or even years later.


In additional embodiments, a therapeutically effective amount of a pharmaceutical composition including a nucleic acid encoding a disclosed recombinant HIV-1 Env ectodomain or immunogenic fragment thereof is administered to a subject, for example to generate an immune response. In one specific, non-limiting example, a therapeutically effective amount of a nucleic acid encoding a disclosed recombinant HIV-1 Env ectodomain or immunogenic fragment thereof, is administered to a subject to treat or prevent or inhibit HIV infection, or to induce an immune response to HIV-1 (such as to gp120) in the subject.


One approach to administration of nucleic acids is direct immunization with plasmid DNA, such as with a mammalian expression plasmid. As described above, the nucleotide sequence encoding a disclosed recombinant HIV-1 Env ectodomain or immunogenic fragment thereof can be placed under the control of a promoter to increase expression of the molecule.


Immunization by nucleic acid constructs is well known in the art and taught, for example, in U.S. Pat. No. 5,643,578 (which describes methods of immunizing vertebrates by introducing DNA encoding a desired antigen to elicit a cell-mediated or a humoral response), and U.S. Pat. No. 5,593,972 and U.S. Pat. No. 5,817,637 (which describe operably linking a nucleic acid sequence encoding an antigen to regulatory sequences enabling expression). U.S. Pat. No. 5,880,103 describes several methods of delivery of nucleic acids encoding immunogenic peptides or other antigens to an organism. The methods include liposomal delivery of the nucleic acids (or of the synthetic peptides themselves), and immune-stimulating constructs, or ISCOMS™, negatively charged cage-like structures of 30-40 nm in size formed spontaneously on mixing cholesterol and Quil A™ (saponin). Protective immunity has been generated in a variety of experimental models of infection, including toxoplasmosis and Epstein-Barr virus-induced tumors, using ISCOMS™ as the delivery vehicle for antigens (Mowat and Donachie, Immunol. Today 12:383, 1991). Doses of antigen as low as 1 μg encapsulated in ISCOMS™ have been found to produce Class I mediated CTL responses (Takahashi et al., Nature 344:873, 1990).


In another approach to using nucleic acids for immunization, a disclosed recombinant HIV-1 Env ectodomain or immunogenic fragment thereof, can also be expressed by attenuated viral hosts or vectors or bacterial vectors. Recombinant vaccinia virus, adeno-associated virus (AAV), herpes virus, retrovirus, cytogmeglo virus or other viral vectors can be used to express the peptide or protein, thereby eliciting a CTL response. For example, vaccinia vectors and methods useful in immunization protocols are described in U.S. Pat. No. 4,722,848. BCG (Bacillus Calmette Guerin) provides another vector for expression of the peptides (see Stover, Nature 351:456-460, 1991).


In one embodiment, a nucleic acid encoding a disclosed recombinant HIV-1 Env ectodomain or immunogenic fragment thereof, is introduced directly into cells. For example, the nucleic acid can be loaded onto gold microspheres by standard methods and introduced into the skin by a device such as Bio-Rad's HELIOS™ Gene Gun. The nucleic acids can be “naked,” consisting of plasmids under control of a strong promoter. Typically, the DNA is injected into muscle, although it can also be injected directly into other sites, including tissues in proximity to metastases. Dosages for injection are usually around 0.5 μg/kg to about 50 mg/kg, and typically are about 0.005 mg/kg to about 5 mg/kg (see, e.g., U.S. Pat. No. 5,589,466).


K. Immunodiagnostic Methods

In addition to the therapeutic methods provided above, any of the disclosed immunogens (for example, disclosed recombinant HIV-1 Env ectodomain or immunogenic fragment thereof) can be utilized to produce antigen specific immunodiagnostic reagents, for example, for serosurveillance. Immunodiagnostic reagents can be designed from any of the antigenic polypeptide described herein. For example, in the case of the disclosed immunogens, the presence of serum antibodies to HIV is monitored using the isolated immunogens disclosed herein, such as to detect an HIV infection and/or the presence of antibodies that specifically bind to HIV-1 Env in a unliganded conformation.


Methods are further provided for a diagnostic assay to monitor HIV-1 induced disease in a subject and/or to monitor the response of the subject to immunization with one or more of the disclosed antigens. By “HIV-1 induced disease” is intended any disease caused, directly or indirectly, by HIV. An example of an HIV-1 induced disease is acquired immunodeficiency syndrome (AIDS). The method includes contacting a disclosed immunogen with a sample of bodily fluid from the subject, and detecting binding of antibodies in the sample to the disclosed immunogens. In addition, the detection of the HIV-1 binding antibody also allows the response of the subject to immunization with the disclosed antigen to be monitored. In still other embodiments, the titer of the HIV-1 binding antibodies is determined. The binding can be detected by any means known to one of skill in the art, including the use of labeled secondary antibodies that specifically bind the antibodies from the sample. Labels include radiolabels, enzymatic labels, and fluorescent labels. In other embodiments, a disclosed immunogen is used to isolate antibodies present in a subject or biological sample obtained from a subject.


Generally, the method includes contacting a sample from a subject, such as, but not limited to a blood, serum, plasma, urine or sputum sample from the subject with one or more of the disclosed recombinant HIV-1 Env proteins or immunogenic fragments thereof (including a polymeric form thereof) and detecting binding of antibodies in the sample to the disclosed immunogens. The binding can be detected by any means known to one of skill in the art, including the use of labeled secondary antibodies that specifically bind the antibodies from the sample. Labels include radiolabels, enzymatic labels, and fluorescent labels.


L. Kits

Any immunodiagnostic or therapeutic reagents can be provided as components of a kit. Optionally, such a kit includes additional components including packaging, instructions and various other reagents, such as buffers, substrates, antibodies or ligands, such as control antibodies or ligands, and detection reagents. The kit can include a container and a label or package insert on or associated with the container. Suitable containers include, for example, bottles, vials, syringes, etc. The containers may be formed from a variety of materials such as glass or plastic. The container typically holds a composition including one or more of the disclosed recombinant HIV-1 Env proteins, immunogenic fragments thereof, protein nanoparticles, polynucleotides encoding a recombinant HIV-1 Env ectodomain or immunogenic fragment, vectors or compositions, which is effective for treating, preventing, diagnosing, monitoring HIV infection or immune response. In several embodiments the container may have a sterile access port (for example the container may be an intravenous solution bag or a vial having a stopper pierceable by a hypodermic injection needle). The label or package insert indicates that the composition is used for treating the particular condition.


The label or package insert typically will further include instructions for use of an antigen, or a nucleic acid or a viral vector encoding, expressing or including the antigen, for example, in a method of treating or preventing a HIV infection. The package insert typically includes instructions customarily included in commercial packages of therapeutic products that contain information about the indications, usage, dosage, administration, contraindications and/or warnings concerning the use of such therapeutic products. The instructional materials may be written, in an electronic form (such as a computer diskette or compact disk) or may be visual (such as video files). The kits may also include additional components to facilitate the particular application for which the kit is designed. The kits may additionally include buffers and other reagents routinely used for the practice of a particular method. Such kits and appropriate contents are well known to those of skill in the art.


EXAMPLES

The following examples are provided to illustrate particular features of certain embodiments, but the scope of the claims should not be limited to those features exemplified.


Example 1
Structure, Activation, and Immune Recognition of Prefusion HIV-1 Env

This example illustrates the structure, activation, and immune recognition of prefusion HIV-1 Env. The HIV-1-Env ectodomain trimer, comprising three gp120 and three gp41 subunits, is a conformational machine that facilitates HIV-1 entry by rearranging from a mature unliganded state, through receptor-bound intermediates, to a postfusion state. This example shows the structure at 3.5-Å resolution for an HIV-1-Env trimer bound by antibodies PGT122 and 35O22. This structure reveals the prefusion conformation of gp41, indicates rearrangements needed for fusion activation, and defines parameters of immune evasion for the antigenic target of most neutralizing antibodies. Prefusion gp41 encircles extended N- and C-terminal strands of gp120 with a 4-helix collar, which is fastened by insertion of a fusion peptide-proximal methionine into a gp41-tryptophan clasp. Spike rearrangements required for entry likely involve opening the clasp and expelling the termini. N-linked glycosylation and sequence-variable regions cover the mature ectodomain trimer: the prevalence and location of effective neutralizing responses from seroconverter and chronic cohorts are mapped, and alterations that stabilize its conformation are identified.


Initially synthesized as a gp160 precursor, which is cleaved into gp120 and gp41 subunits, the trimeric HIV-1-Env ectodomain trimer displays unusual posttranslational processing including the addition of 25-30 N-linked glycans per gp120-gp41 protomer, tyrosine sulfation, and slow signal peptide cleavage. It rearranges from a mature unliganded state that evades antibody recognition, through intermediate states that bind to receptors CD4 and co-receptor (either CCR5 or CXCR4), to a postfusion state (reviewed in Wyatt, R. & Sodroski, Science 280, 1884-1888, 1998). Over the last 20 years substantial atomic-level detail has been obtained on these states, including structures of receptor-bound gp120 (Kwong et al. Nature 393, 648-659, 1998), postfusion gp41 (Chan at al., Cell 89, 263-273, 1997; Weissenhorn et al., Nature 387, 426-430, 1997), and the trimeric arrangement of prefusion gp120 along with two gp41 helices, one of which was aligned in sequence (Chan at al., Cell 89, 263-273, 1997; Weissenhom et al., Nature 387, 426-430, 1997). The prefusion structure of gp41 has, however, resisted atomic-level analysis. Because the primary structural rearrangement driving membrane fusion is the gp41 transition from prefusion to postfusion conformations, the lack of a prefusion gp41 structure has stymied attempts to provide a coherent picture of the conformational rearrangements the spike undergoes to facilitate entry.


Here, neutralizing antibodies PGT122 (Walker et al., Nature 477, 466-470, 2011) and 35O22 were used to capture the HIV-1 ectodomain trimer in a mature near-native state. Crystals of the antigen-binding fragments (Fabs) of these two antibodies were obtained in complex with a soluble, cleaved, Env trimer construct (BG505 SOSIP.664; Sanders et al., Journal of virology 76, 8875-8889, 2002; Julien et al., PNAS 110, 4351-4356, 2013; Sanders, PLoS pathogens 9, e1003618, 2013) and the structure of this elusive immunological target was determined at atomic-level detail. Analysis of this structure in the context of previously determined gp120 and gp41 structures affords a mechanistic understanding of the conformational transitions the ectodomain trimer undergoes to facilitate virus entry. Delineate aggregate parameters of glycan shielding and genetic variation were determined and a cohort serum was used to determine where the immune system succeeds in recognizing the HIV-1 ectodomain trimer. Analysis of the mature HIV-1-Env structure and its conformational rearrangements, combined with an understanding of its evasion from and vulnerabilities to the immune system, provide an information matrix which can be exploited to manipulate this critical vaccine target.


Structure Determination and Overall Structure.


Atomic-level information for virtually all of the HIV-1 Env ectodomain has been obtained as antibody-bound Env complexes (FIG. 17). FIG. 17 illustrates structure determination as deposited as PDB Accession Nos. 1GGI (Stanfield et al., PNAS, 90, 6325-6329, 1993), 1GC1 (Kwong et al., Nature, 393, 648-659, 1998), 1F58 (Stanfield et al., Structure, 7, 131-142, 1999), 1B03 (Tugarinov et al., Nat. Struct. Biol., 6, 331-335, 1999), 2F5B (Pai et al., Patent No. CA2371929), 1TJI (Ofek et al., J. Virol., 78, 10724-10737, 2004), 1TZG (Cardoso et al., Immunity, 22, 163-173, 2005), 2B4C (Huang et al., Science, 310, 1025-1028, 2005), 2CMR (Luftig et al., Nat. Struct. Mol. Biol., 13, 740-747, 2006), 2FX7 (Cardoso et al., J. Mol. Biol., 365, 1533-1544, 2007), 3JWD (Pancera et al., PNAS, 107, 1166-1171, 2010), 3U2S (McLellan et al., Nature, 480, 336-343, 2011), 4G6F (Huang et al., Nature, 491, 406-412, 2012), 4CC8 (Bartesaghi et al., Nat. Struct. Mol. Biol., 20, 1352-1357, 2013), 4NCO (Julien et al. Science 342, 1477-1483, 2013), and 3J5M (Lymunkis et al., Science, 342, 1484-1490, 2013).


The recently determined electron microscopy (EM) reconstruction (Lyumkis et al., Science 342, 1484-1490, 2013) and crystal structure (Julien et al., Science 342, 1477-1483, 2013) of a soluble cleaved HIV-1 Env based on the BG505 SOSIP.664 construct were no exceptions, in particular—while an artificial disulfide and other modification of the SOSIP.664 construct were critical for production of homogeneous, soluble, cleaved trimers (Ringe et al., PNAS 110, 18256-18261, 2013)—antibody PGT122 appeared to facilitate crystallization of a near-native mature state (Julien et al., Science 342, 1477-1483, 2013). Diffraction from crystals of the PGT122 complex, however, extended to only 4.7-Å resolution hampering the trace of non-helical regions of gp41 as well as the placement and registry of side chains (Julien et al., Science 342, 1477-1483, 2013). Addition of antibody 35O22 to PGT122-bound viral spike in the membrane-bound virion context showed single-molecule fluorescent resonance energy transfer (smFRET) responses that closely resembled that of the mature native unliganded ectodomain trimer (FIG. 1a, FIG. 7; Munro et al. Biophysical Journal 104, 415A, 2013). In the context of crystallization, addition of 35O22 to the PGT122-BG505 SOSIP.664 complex led to ternary complex crystals in space group P63. While diffraction was anisotropic, we succeeded in collecting ˜3.5-Å data from a single crystal (57.2% complete with 2.2 I/σ in the 3.49-3.68 Å shell with 3 I/σ measurements extending to 2.9 Å along the 6-fold axis) (FIG. 14; FIG. 18). Structure solution by molecular replacement with free structures of Fab PGT122 (Julien et al., PLoS pathogens 9, e1003342, 201) and Fab 35O22 and antibody-bound gp120 (Georgiev et al., Science 340, 751-756, 2013) followed by model building and refinement revealed a double antibody-bound protomer to occupy the asymmetric unit and led to an Rwork/Rfree of 21.35%/24.80%. The final model, comprising PGT122 and 35O22 Fabs, residues 31-505 of gp120 (except 185a-186 and 399-410 in variable regions V2 and V4, respectively) and residues 518-664 of gp41 (except 548-568) along with 22-N-linked glycans and 10-sulfate ions is shown in FIG. 1B (for clarity, from this point forwards in this Example, residue numbers are cited with a subscript defining the molecule). 35O22 interactions with the HIV-1-Env trimer are shown in FIG. 8, and comparison of bound vs. unbound Fab structures is shown in FIG. 9.


Overall, the HIV-1 ectodomain trimer forms a 3-blade propeller, capped at the membrane-distal apex by trimer association domains with antibodies PGT122 and 35O22 binding to membrane-distal and membrane-proximal ends, respectively, of the ectodomain trimer (FIG. 10). Protomer interactions occur through the trimer association domains at the membrane-distal portion of the ectodomain trimer and also through gp41, primarily between helical interactions around the trimer axis. No trimeric interactions are contributed by the gp120 core: indeed, a cleft or opening is found under the trimer association domains along the 3-fold axis where such associations might occur. The trimeric gp41 forms a platform, through which the gp120 termini extend towards the viral membrane (FIG. 1b). Unusually slow signal peptide cleavage, which keeps the N terminus of gp120 proximal to the membrane during the folding, may facilitate gp41 folding.


Prefusion Structure of Gp41.


Prefusion gp41 wraps its hydrophobic core around extended N- and C-termini-strands of gp120 (FIG. 2a). It forms a 4-helix collar comprising helices α6 (Met530gp41-Asn543gp41), α7 (Gly572gp41-Ile595gp41—which aligns in sequence with the C-terminal portion of the postfusion HR1 helix), α8 (Leu619gp41-Trp623gp41), and α9 (Trp628gp41-Asp664gp41—which aligns in sequence with the postfusion HR2 helix) (the numbering of prefusion gp41-helices and -strands continues the nomenclature established for the gp120 subunit, which ends with helix α5 and strand β26). The first residue of gp41 visible in the electron density corresponds to Val518gp41, in the fusion peptide. An extended stretch connects to Leu523gp41, which interacts hydrophobically with Trp45gp120 and Ile84gp120, both of which are part of the 7-stranded β-sandwich around which the gp120-inner domain is organized (Pancera PNAS 107, 1166-1171, 2010; Finzi et al., Molecular cell 37, 656-667, 2010). The main chain of gp41 follows gp120-strand β0 away from the trimer axis towards the viral membrane, until residue Met530gp41, where the fold reverses itself and extends through the α6 helix towards the trimer axis and away from the viral membrane. Density between residues 547gp41 and 569gp41 is sparse (FIG. 19), and ultimately connects to α7, which forms a coiled-coil with itself around the trimer axis, extending from the middle of the HIV-1 ectodomain trimer towards the viral membrane. At the end of α7 is the gp41-cysteine loop (spanned by the Cys598gp41-Cys604gp41 disulfide), whose C-terminal residues initiate strand β27 (Leu602gp41-Thr606gp41), which hydrogen bonds in anti-parallel fashion with strand 3-4 from the N terminus of gp120. The intersubunit disulfide (‘SOS’) between residues 501gp120 and 605gp41 welds the C terminus of gp120 to the membrane-proximal end of strand 3-4 (FIG. 2a). These membrane-proximal interactions are further stabilized by hydrophobic interactions, which gp41 makes with the N and C termini of gp120—such as between Trp35gp120 and Pro609gp41 and between Trp610gp41 and Pro498gp120. Upon passing the gp120 termini, gp41 reaches α8, whose C terminus aligns spatially with the N terminus of α6. After α8, the α9 helix reverses direction, again wraps past the N- and C-termini of gp120, before extending horizontally along the rim of the ectodomain trimer to reach the gp120 termini from a neighboring protomer.


Topologically, the gp41 subunit completes a single circle around the gp120 termini with the insertion of a hydrophobic prong comprising the side chain of Met530gp41 (which is located at the start of α6, proximal to the fusion peptide), into a triple tryptophan-clasp formed by Trp623gp41 (from the end of α8), Trp628gp41 (from the start of α9) and Trp631gp41 (one turn into α9) (FIG. 2a insert). The alignment of dipoles from helices α6 and α8 likely provides electrostatic complementarity that help to stabilize the neighboring methionine-tryptophan clasp.


Within a single protomer, the buried surface between gp41 and gp120 totals 5,268 Å2, including 216 Å2 from glycan-protein interactions (FIG. 25). A substantial portion of this is hydrophobic: gp41 essentially wraps its hydrophobic core around the N- and C-termini of gp120 (FIG. 2b). Trimer interfaces also bury a large surface area (3,138 Å2 contributed by each protomer, comprising 1,917 Å2 from the gp41-gp41 interface, 861 Å2 from the gp120-gp120 interface and 360 Å2 from the gp120-gp41 interface) (FIGS. 20 and 25). Close to the trimer axis, these involve helix α7, as well as the N-terminal portion of the gp41-cysteine loop. Further from the trimer axis, interactions involve α9. Other than interactions of α7, most of the interprotomer interactions are hydrophilic (FIG. 2c, FIG. 20B). Overall, the prefusion structure of gp41 as well as its trimeric arrangement appears to have no close structural relatives in the PDB (FIG. 26).


Prefusion to Postfusion Gp41 Transition.


To understand the conformational transition from prefusion to postfusion gp41, the gp41-prefusion structure in the near-native HIV-1 Env trimer was compared with previously determined postfusion structures (FIG. 3). Several postfusion gp41 structures have been determined ranging from a minimal, protease-treated, crystal structure (residues 556gp41-581gp41; 628gp41-661gp41; PDB 1AIK; Chan at al., Cell 89, 263-273, 1997) with 80% sequence identity to BG505 (Wu et al. Journal of virology 80, 835-844, 2006) to a more complete gp41 structure (residues 531gp41-581gp41; 624-681gp41; PDB 2X7R; Buzon et al. PLoS pathogens 6, e1000880, 2010) and an NMR structure that includes the cysteine loop (residues 539gp41-665gp41; PDB 2EZO; Caffrey, M. et al. EMBO 17, 4572-4584 (1998) of the simian immunodeficiency virus (SIV), which shares 48% sequence identity with BG505 (Wu et al. Journal of virology 80, 835-844, 2006) and is substantially similar to the HIV-1 structures (less than 1-Å Cα root-mean-square deviation (rmsd) between overlapping residues of 1AIK and 2EZO). To provide comparison with a “complete” postfusion structure, a chimera of HIV-1/SIV structures was prepared (FIG. 21). Distance difference analysis (FIG. 3B) of prefusion and postfusion structures indicated two regions of substantial similarity, corresponding to (i) the prefusion α7 helix aligned with the C-terminal half of the postfusion HR1 helix and (ii) the prefusion α9 helix aligned with much of the postfusion HR2 helix. Superposition of prefusion α7 and postfusion HR1 placed residues 569gp41-593gp41 within 5 Å, with a rmsd of 1.35 Å. For this superposition to occur, Ca-movements of over 80 Å are required for the gp41-fusion peptide and a6 helix as well as for the C-terminal portion of the α9 helix. Notably, this superposition preserves the coiled coil trimeric interaction of both prefusion and postfusion molecules and thus likely mimics the natural conformational transition that occurs during membrane fusion. Meanwhile, superposition of prefusion α9 and postfusion HR2 placed residues 634gp41-664gp41 within 5 Å, with a rmsd of 3.58 Å; the substantial alignment of the α9 and HR2 helices indicate that the HR2 helix is mostly preformed in the prefusion structure.


Entry Rearrangements of HIV-1 Env.


Biosynthesis of HIV-1 Env starts with an uncleaved gp160 trimer. Binding by antibodies PG9 and PGT145 to both uncleaved and mature Env indicate the trimer association domains at the spike apex likely assume conformations similar to that observed for the mature ectodomain trimer (Walker et al., Nature 477, 466-470, 2011; Walker et al. Science 326, 285-289, 2009) (FIG. 27). The structure of gp41 in the uncleaved state remains unknown, but antigenic differences with the mature cleaved state (Blattner et al. Immunity 40, 669-680, 2014; Falkowska et al. Immunity 40, 657-668, 2014) suggest a distinct gp41 conformation; in the prefusion HIV-1-Env structure, the observed C terminus of gp120 at residue 505gp120 and N terminus of gp41 at residue 518gp41 are 37 Å apart, a distance which cleavage may help the prefusion structure to accommodate. After cleavage, the ectodomain trimer condenses into the closed near-native mature structure described here. In the gp120-inner domain, helix α-1 is formed, and a parallel strand exists between β3 and β21; in gp41, helix α7 was observed to begin around residue 571gp41. A partially open ectodomain trimer conformation has been reported at 6 Å by EM reconstruction (Bartesaghi, Nature structural & molecular biology 20, 1352-1357, 2013). The trimer association domains appear to be displaced from the trimeric axis, and helical density suggests helix α7 to start several turns earlier, extending ˜20 Å towards the target cell membrane; we modeled these rearrangements with a rigid body motion of 6 degrees of the gp120 protomer and by the conversion of ˜15 residues of helix α6 and connecting stretch into helix α7 (FIG. 3D, middle panel; 15).


The CD4-bound state has been visualized by a number of EM reconstructions (Liu, Nature 455, 109-113, 2008; White et al. PLoS pathogens 6, e1001249, 2010) and atomic-level structures (Kwong et al. Nature 393, 648-659, 1998; Pancera PNAS 107, 1166-1171, 2010). In this state, V1V2 separates from V3: V3 points towards the target cell (Huang et al. Science 310, 1025-1028, 2005), and the bridging sheet (Kwong et al. Nature 393, 648-659, 1998) assembles with β2 forming antiparallel hydrogen bonds with β21 (as opposed to the parallel β3-β21 interaction of the near-native mature state; notably, the only parallel β-strand in the RSV F glycoprotein prefusion structure also changes conformation in RSV F pre- to postfusion transition; McLellan et al. Science 340, 1113-1117, 2013). With layer 1 of the inner domain (Finzi et al., Molecular cell 37, 656-667, 2010), helix α0 forms and Gln428gp120 and strand β21 invert; and in layer 2, inner domain rearrangements include the swapping of distinct perpendicular interactions of Trp112gp120 and Trp427gp120 (FIG. 11). CD4 binding allows HR2 peptide analogues (such as T20 or C34) to bind (Yuan et al., Journal of virology 78, 5448-5457, 2004; and helix α7 can be modeled starting as early as 554gp41 with Met530gp41 still in its membrane-proximal tryptophan clasp (FIG. 22), as expected because 35O22 binds the CD4-bound SOSIP (FIGS. 16 and 23). It is expected that Env-CCR5 interactions (Huang et al., Science 317, 1930-1934, 2007) bring the CD4-bound state close to the target cell membrane, where the “de-assembling α6/assembling α7 helices” coupled to release of the Met530gp41 prong from its tryptophan clasp ultimately amasses the gp41-fusion peptide(s) (FIG. 3d, 2nd panel from right).


At this receptor-bound stage, it is easy to imagine the fusion peptide penetrating the target cell membrane, while β27 gp41-cysteine loop remains hydrogen bonded to the gp120 termini (and with the C terminus of the gp41 ectodomain is in the viral membrane). Rearrangement of gp41 to its postfusion conformation may be triggered by gp120 shedding (Moore et al., Science 250, 1139-1142, 1990), with expulsion of its termini tugging on the gp41-cysteine loop and destabilizing the prefusion gp41 core. We note that the three tryptophans that make up the gp41-tryptophan clasp are essential to the folding of the post-fusion coiled coil, so they appear to be critical in both conformations (FIG. 24). The MPER region likely associates with a number of lipids assisting the fusion of viral and target cell membrane.


HIV-1 Rearrangements and Other Type 1 Fusion Machines.


To determine whether the distinct elements observed in prefusion gp41 were preserved elsewhere, prefusion and postfusion states of other type I fusion machines from influenza virus (a member of the Orthomyxoviridae family of viruses; Wilson et al., Nature 289, 366-373, 1981, Bullough et al., Nature 371, 37-43, 1994), respiratory syncytial virus (RSV; Paramyxoviridae, McLellan et al. Science 340, 1113-1117, 2013, McLellan et al., Journal of virology 85, 7788-7796, 2011), and Ebola virus (Filoviridae, Weissenhorn et al., Molecular cell 2, 605-616, 1998, Lee et al., Nature 454, 177-182, 2008) were examined (FIG. 4a). In all cases, a helix was observed in the gp41-prefusion equivalents, which corresponds in sequence to the C-terminal portion of the helix, which in the postfusion conformation, comprises the internal coiled coil characteristic of type I fusion machines (FIG. 4b). With prefusion machines from HIV-1, influenza, and Ebola, the nascent prefusion helix adopts a coiled coil; with RSV, a coiled coil assembles immediately N terminal to the nascent postfusion helix. Despite dramatic differences in gp120-equivalents, similarity is also observed in the overall topology of subunit interactions. Notably, all of the gp41-equivalents wrap hydrophobic residues around extended termini (or terminus) of their gp120-equivalents (FIG. 4c). With influenza, it is only the N terminus of the gp120-equivalent (HA1) that is wrapped by the gp41-equivalent (HA2), with the N terminus of HA2 completing about 20% more than a single encirclement. With RSV, it is also only the N terminus of the gp120 equivalent (F2) that is wrapped by the gp41-equivalent (F1), and the termini do not have to be expelled to transition to the postfusion form. With Ebola, the gp41-equivalent (gp2) wraps around both N and C termini-strands of the gp120-equivalent (gp1), completing about 70% of a single encirclement. Overall, the similarity in prefusion folding topology and in prefusion and post-fusion inner helices observed here, along with the previously observed similarity in postfusion coiled coils (reviewed in Colman et al., Nature reviews. Molecular cell biology 4, 309-319, 2003), provide a more general and integrated view of the conformational rearrangements that type 1 fusion machines undergo to facilitate virus-cell membrane fusion.


Glycan Shield and Genetic Variation of Mature Unliganded Env.


The mature unliganded conformation of HIV-1 Env is the target of most neutralizing antibodies. Substantial detail has already been reported regarding antibody recognition of gp120 in this conformation (Julien et al., Science 342, 1477-1483, 2013; Lyumkis et al., Science 342, 1484-1490, 2013). The newly revealed structure of a near-complete gp120-gp41 Env trimer provides an opportunity to understand aggregate properties of glycosylation and variation. Glycan shielding and genetic variation have long been recognized as mechanisms to avoid recognition by antibody (Wyatt et al., Nature 393, 705-711., 1998). The BG505 SOSIP.664 sequence contains 28 sequons specifying N-linked glycosylation (including a T332N mutation). We modeled high mannose glycans (either Man9 or Man5) on each sequon and calculated accessible surface for radii ranging from 1.4 Å (the radius of a water molecule) to 10 Å (the approximate radius of a single immunoglobulin domain) (FIG. 12). In the Man9-glycosylated structure, 29% of the protein surface was solvent accessible, whereas only 3% of the surface was immunoglobulin-domain accessible. By contrast, with the fusion glycoproteins from influenza and RSV, 14% and 48%, respectively, of these surfaces were immunoglobulin-domain accessible (FIG. 5a).


In terms of genetic variation, the per-residue Shannon entropy of 3,943 sequences of HIV-1 was calculated (FIG. 5b). Approximately 50% of the surface was shown to have a variability of greater than 10%, a degree of surface variation shared by influenza, but not by RSV. When glycan shielding and genetic variation were combined, only ˜2% of the surface was immunoglobulin accessible with a variability of less than 10% (FIG. 5c, upper panels); much of this conserved surface occurred at the membrane-proximal “base” of the ectodomain trimer, which is expected to be sterically occluded by the viral membrane. To determine how this fully assembled shield compared to other conformations, the immunoglobulin accessibility of the CD4-bound conformation was also assessed (FIG. 5c). Notably the CD4-bound conformation showed substantially higher percentage of glycan-free, conserved surface, providing insight into the greater ease by which antibodies reactive with the CD4-bound conformation are elicited—and by contrast, the difficulty in eliciting broadly neutralizing antibodies against the variable, glycan-covered mature state.


Serologic Recognition of Mature Env.


Despite the multiple mechanisms of evasion shielding mature HIV-1 Env, potent broadly neutralizing antibodies do develop (Hraber et al. AIDS 28, 163-169, 2014). Many of these, including the PGT122 and 35O22 co-crystallized here, require N-linked glycosylation to bind; indeed, 35O22 utilizes a new mode of glycan recognition, involving a framework 3 insertion to create a “bowl” that cups glycan N88gp120 (FIG. 8). The near-native mature prefusion structure of HIV-1 Env allows us to map known epitopes (FIG. 6a) and to compare the recognition of broadly neutralizing HIV-1 antibodies, with those capable of neutralizing influenza virus and RSV. Notably, the epitopes for broadly neutralizing HIV-1 antibodies were significantly more glycosylated and variable (FIG. 6b).


To determine the location and prevalence of effective humoral responses, a serological analysis was used that determined sites of HIV-1 vulnerability to antibody based on serum neutralization of a panel of diverse HIV-1 isolates (Georgiev et al., Science 340, 751-756, 2013). Sera from a cohort that had been infected for 2-3 years as well as sera from a cohort of donors that had been infected for more than 5 years were assessed on a panel of 21 diverse HIV-1 isolates, and the neutralization phenotypes assigned to 12 prototypic antibody-neutralization fingerprints (FIG. 6c, FIG. 13). We then mapped the responses to the surface of the near-native mature HIV-1-Env ectodomain trimer (FIG. 6d). The most prevalent response corresponded to the glycan V3 epitope epitomized by antibody PGT128. CD4-binding site-directed responses and also V1V2-directed responses were prevalent. Overall, responses to both cohorts were highly correlated indicating little evolution in the location or prevalence of effective neutralizing responses between 2-3 years and 5+ years. Notably, when mapping Env sites of vulnerability to neutralizing antibody, the majority of prevalent sites corresponded to Env surfaces covered by N-linked glycosylation and/or of high sequence variability. Overall, mapping of the location of cohort humoral responses directly visualized prevalent targets of vaccine relevance (FIG. 6e).


Viral Evasion and Immune Recognition.


In addition to merging virus and host cell membranes as an essential step in entry, viral fusion machines must contend with antibody-mediated neutralization. With RSV, peak infection occurs at 6-12 months of life, when maternal antibodies wane; with influenza virus, natural infection elicits strain-specific antibodies, and evasion occurs seasonally on a global scale. HIV-1, however, confronts the immune system in each individual directly, often presenting high titers of Env antigens over years of chronic infection. These differences in evasion are reflected in structural difference in the fusion machines. The structure of the HIV-1-Env ectodomain trimer revealed here allows the molecular trickery behind single spike entry (Yang et al., Journal of virology 79, 12132-12147, 2005), glycan shielding (Wei, X. et al. Antibody neutralization and escape by HIV-1. Nature 422, 307-312, 2003), and conformational masking (Kwong et al. Nature 420, 678-682, 2002) to be visualized at the atomic level (FIG. 31). Thus, avoidance of antibody avidity through the ability of a single HIV-1 spike to fuse viral and target cell membranes (Yang et al., Journal of virology 79, 12132-12147, 2005) is likely assisted by the membrane-proximity of the co-receptor and the membrane-associating MPER regions (FIG. 3); despite these differences, the HIV-1-Env ectodomain trimer appears to share mechanism and topology with other type 1 fusion machines (FIG. 4). In terms of glycan shielding (Wei, X. et al. Antibody neutralization and escape by HIV-1. Nature 422, 307-312, 2003), we have modeled the structure of a fully assembled glycan shield for a tier II transmitted founder virus (Wu et al. Journal of virology 80, 835-844, 2006) (FIG. 5). While glycan masking appears complete at the HIV-1-spike apex, closer to the membrane substantial “holes” are observed. And with conformational masking (Kwong et al. Nature 420, 678-682, 2002), evasion is optimal for the prefusion mature closed state, with CD4-binding unmasking conserved glycan-free surfaces (FIG. 5c). Despite extraordinary glycosylation and sequence variation, the human immune system appears up to the challenge of generating broadly neutralizing antibodies (FIG. 6). It is noted that recognition of glycosylation appears to be a trait common only to broadly neutralizing HIV-1 antibodies, although broad influenza virus-neutralizing antibodies do appear to tolerate epitope-sequence variation (FIG. 6b). The structure of the HIV-1-Env ectodomain trimer described here thus reveals not only commonalities in entry and evasion with other type 1 fusion machines, but also commonalities in recognition by the human immune system.


Methods

BG505 SOSIP.664 Expression and Purification.


The crystallized HIV-1-Env construct from strain BG505 was synthesized as described in (Julien et al., Science, 342, 1477-1483, 2013; Julien et al., Proc. Nat'l. Acad. Sci. U.S.A., 110, 4351-4356, 2013; Sanders et al., PLoS pathogens, 9, e1003618, 2013), using BG505 GenBank® Acc. Nos., using BG505 GenBank accession numbers ABA61516 and DQ208458 (Wu et al. Journal of virology 80, 835-844, 2006), including the “SOS” mutations (A501C, T605C), the isoleucine to proline mutation at residue 559 (I559P), and the glycan site at residue 332 (T332N); mutating the cleavage site to 6R (REKR to RRRRR); and truncating the C terminus to residue 664 (all HIV-1 Env numbering according to the HX nomenclature). This construct is referred to as BG505 SOSIP.664 herein.


The construct was cotransfected with furin in HEK 293 S GnTI−/− cells using 600 μgs plasmid DNA and 150 μgs of furin as described previously (Sanders, PLoS pathogens 9, e1003618, 2013). Transfection supernatants were harvested after 7 days, and passed over either a 2G12 antibody- or VRC01 antibody-affinity column. After washing with PBS, bound proteins were eluted with 3M MgCl2, 10 mM Tris pH 8.0. The eluate was concentrated to less than 5 ml with Centricon-70 and applied to a Superdex 200 column, equilibrated in 5 mM HEPES, pH 7.5, 150 mM NaCl, 0.02% azide. The peak corresponding to trimeric HIV-1 Env was identified, pooled, and concentrated or flash-frozen in liquid nitrogen and stored at −80° C.


Fab Expression and Purification.


PGT122 and 35O22 IgGs were expressed as previously described (McLellan et al., Nature 480, 336-343, 2011). Heavy chain plasmids containing an HRV3C cleavage site after Lys 218 in the hinge region were co-transfected with light chain plasmids in 293F (35O22) or GnTI−/− (PGT122, which is glycosylated) using TrueFect-Max transfection reagent (United Biosystems) according to manufacturer's protocol. Cultures were fed with fresh 293FreeStyle media (Life Technologies) 4 h post-transfection and with HyClone SFM4HEK293 enriched medium (HyClone) containing valproic acid (4 mM final concentration) 24 h after transfection. Cultures were then incubated at 33° C. for 6 days, and supernatants harvested and passed over a protein A affinity column. After PBS wash and low pH elution, pH of eluate was neutralized with 1M Tris pH 8.5. Fabs were obtained using HRV3C digestion and collecting flow-thru from protein A column to remove Fc fraction. Fabs were further purified over Superdex 200 in 5 mM HEPES, pH 7.5, 150 mM NaCl, 0.02% azide.


Ternary Complex Preparation.


PGT122 and 35O22 Fabs were added to a solution of purified trimeric BG505 SOSIP.664 in 5 fold molar excess for 30 min at room temperature (RT). The complex was then partially deglycosylated by adding Endo H (50 μl) for 1 hour at RT in the gel filtration buffer. The complex was then purified over gel filtration equilibrated in 5 mM HEPES, pH 7.5, 150 mM NaCl, 0.02% azide. Fractions were pooled, concentrated down to 5-10 OD280/mL and used immediately for crystal screening or flash frozen in liquid nitrogen and kept at −80° C. until further use.


Crystallization screening. The ternary complex was screened for crystallization using 572 conditions from Hampton, Wizard and Precipitant Synergy (Majeed, S. et al. Structure 11, 1061-1070 (2003) screens using a Cartesian Honeybee crystallization robot as described previously (McLellan et al., Nature 480, 336-343, 2011) and a mosquito robot using 0.1 μl of reservoir solution and 0.1 μl of protein solution. Crystals suitable for structural determination grew in 0.2M Li2SO4, 6.65% PEG 1500, 20% isopropanol and 0.1M sodium acetate pH 5.5. Crystals were reproduced in hanging droplets containing 0.5 μl of reservoir solution and 0.5 μl of protein solution. The final crystals were obtained in 16% isopropanol, 5.32% PEG 1500, 0.2M Li2SO4, 0.1M Na acetate pH 5.5. The crystals were cryoprotected in a solution of 15% 2R3R-butanediol, 5% isopropanol in paratone N and data were collected at a wavelength of 1.00 Å at the SER-CAT beamline ID-22 (Advanced Photon Source, Argonne National Laboratory).


X-Ray Data Collection, Structure Solution and Model Building.


Diffraction data were processed with the HKL2000 suite (Otwinowski and Minor, Meth. Enzymol., 276, 307-326, 1997). The data were corrected for anisotropy by services.mbi.ucla.edu/anisoscale/with truncations to 3.5 Å, 3.5 Å, 3.1 Å along a, b, and c axes, respectively. Structure solution was obtained with Phaser using gp120 (PDB ID: 4J6R; Georgiev et al., Science 340, 751-756, 2013), PGT122 (PDB ID: 4JY5; Julien et al., PLoS pathogens 9, e1003342, 2013) and 35O22Fv as search models. Refinement was carried out with Phenix (Adams et al. J Synchrotron Radiat, 11, 53-55, 2004) imposing PGT122, 35O22 and gp120 model-based refinement restraint during initial round of refinement. Model building was carried out with Coot (Emsley and Cowtan, Acta crystallographica. Section D, Biological crystallography, 60, 2126-2132, 2004). The Ramachandran plot as determined by MOLPROBITY (Davis et al., Nucleic Acids Res, 32, W615-619, 2004) showed 92.66% of all residues in favored regions and 99.03% of all residues in allowed regions. Data collection and refinement statistics are shown in FIG. 14.


Smfret.


Peptides for site-specific fluorescent labeling were inserted into HIV-1JR-FL gp160 at positions that did not interfere with Env function by overlap extension PCR. Tagged virus was purified and labelled with Cy3B and Cy5(4S)COT fluorophores, and surface immobilized for imaging via total internal reflection fluorescence (TIRF) microscopy as described (Munro et al. Biophysical Journal 104, 415A, 2013). Labelled virus was pre-incubated for 30 min with 0.1 mg/ml PGT122 or 35O22, or with both PGT122 and 35O22 prior to imaging. Fluorescence trajectories were acquired at 25 frames/s. Traces that presented anticorrelated fluctuations in fluorescence intensity, indicative of FRET, were identified and compiled into histograms. Histograms were fit to the sum of three Gaussian distributions in Matlab. smFRET revealed that HIV-1 Env is conformationally dynamic, transitioning between three distinct conformations. Response to various ligands identified the low-FRET conformation as the predominant population of mature prefusion unliganded HIV-1 Env; intermediate- and high-FRET conformations predominant in the presence of CD4 and CD4-induced antibodies (Munro et al. Biophysical Journal 104, 415A, 2013).


Binding Studies Using Biolayer Interferometry.


A forteBio Octet Red384 instrument was used to measure binding of BG505 SOSIP. 664 and BG505 gp120 molecules to neutralizing antibodies (VRC01, VRC03, b6, b12, F105, PGT122, PGT128, PGT135, 2G12, 8ANC195, 17b, 2.2C, 412d, PG9, PGT145, VRC26.09, 35O22, PGT151) and CD4 Ig. All the assays were performed with agitation set to 1,000 rpm in phosphate-buffered saline (PBS) buffer supplemented with 1% bovine serum albumin (BSA) in order to minimize nonspecific interactions. The final volume for all the solutions was 40-50 μl/well. Assays were performed at 30° C. in solid black tilted-bottom 384-well plates (Geiger Bio-One). Human antibodies (40-50 μg/ml) in PBS buffer was used to load anti-human IgG Fc capture (AHC) probes for 300 s. Typical capture levels were between 1 and 1.5 nm, and variability within a row of eight tips did not exceed 0.1 nm. Biosensor tips were then equilibrated for 180 s in PBS/1% BSA buffer prior to binding assessment of the BG505 SOSIP.664 and BG505 gp120 molecules in solution for 300 s; binding was then allowed to dissociate for 300 s. Parallel correction to subtract systematic baseline drift was carried out by subtracting the measurements recorded for a sensor without monoclonal antibody incubated in PBS/1% BSA. Data analysis were carried out using Octet software, version 8.0.


Difference Distance Analysis.


Difference distance matrices were produced by distance sorting atom positions and plotting with the program DDMP (Nishikawa et al., J. Physical Society of Japan 32, 1331-1337 (1972).


Surface Plasmon Resonance Analysis.


Affinities and kinetics of binding of antibodies 35O22 and PGT151 to BG505 SOSIP.664 soluble trimer were assessed by surface plasmon resonance on a Biacore T-200 (GE Healthcare) at 20° C. with buffer HBS-EP+ (10 mM HEPES, pH 7.4, 150 mM NaCl, 3 mM EDTA, and 0.05% surfactant P-20). In general, mouse anti-human Fc antibody was first immobilized onto two flow cells on a CM5 chip at ˜10000 response units (RU) with standard amine coupling protocol (GE Healthcare). Either CD4-Ig, 2G12 IgG or 17b IgG was then captured on both flow cells by flowing over a 200 nM solution at 5 l/min flow rate for two minutes. This was followed by a 1-minute injection of 1 μM human Fc on both flow cells to block unliganded mouse anti-human Fc antibody. The captured 2G12, CD4 or 17b were used to immobilize BG505 SOSIP.664 trimer on only one flow cell, with no trimer captured on the other flow cell (reference cell). For capturing with 2G12 or CD4-Ig, 500 nM of unliganded trimer was used, whereas, a complex of 500 nM trimer+1500 nM sCD4 was used for capturing with 17b. Antibody Fab fragments at 2-fold dilutions starting from 885 nM, 600 nM and 460 nM for 35O22, PGT151 and PGT145, respectively, were injected over the captured trimer channel and the reference channel at a flow rate of 50 μl/min for 2 minutes and allowed to dissociate for 3-30 minutes depending on the rate of dissociation of each interaction. The cells were regenerated with two 10 μl injections of 3.0 M MgCl2 at a flow rate of 100 μl/min. Blank sensorgrams were obtained by injection of same volume of HBS-EP+ buffer in place of antibody Fab fragments. Sensorgrams of the concentration series were corrected with corresponding blank curves and fitted globally with Biacore T200 evaluation software using a 1:1 Langmuir model of binding. The stoichiometry of binding of antibodies to the trimer were estimated by normalizing the Rmax values to the amount of trimer captured and performing linear regression analysis using the Rmax values for the antibodies with known stoichiometries.


Modeling of Missing Loops, Side Chains, and the N-Linked Glycan Shield.


Missing loops not defined in the HIV-1-Env trimer crystal structure were modeled using Loopy (Xiang et al., Proc. Nat'l. Acad. Sci. U.S.A., 99, 7432-7437, 2002). The Missing side chains were modeled with Scap (Xiang and Honig, J Mol. Biol., 311, 421-430, 2001).


To model the N-linked glycan shield, we first determined all possible N-linked sequons in the HIV-1 Env trimer structure. A single asparagine residue in each sequon was targeted for computational N-linked glycan addition using a series of oligmannose 9 rotamer libraries at different resolutions. In constructing the rotamer libraries, the asparagine side chain rotamers were also considered. To avoid a combinatorial explosion in the search space, select torsion angles in the oligomannose 9 rotamer libraries were allowed to vary in increments between 30-60 degrees. An overlap factor (ofac) was used to screen for clashes between the sugar moieties and the trimer structure. The ofac between two nonbonded atoms is defined as the distance between two atoms divided by the sum of their van der Waal's radii. For the modeling carried out here, the ofac was set to a value of 0.60. For sterically occluded positions, the ofac was set to 0.55. To remove steric bumps between sugar moieties, all models were subjected to 100 cycles of conjugate gradient energy minimization using the GLYCAM (Kirschner et al. Journal of computational chemistry 29, 622-655 (2008)) force field in Amber12 (Cornell J. Am. Chem. Soc. 117, 5179-5197, 1995). with a distance-dependent dielectric.


Mapping Sequence Variability onto Trimer Structure.


For each of HIV-1 Env, influenza HA, and RSV F, residue sequence variability was computed as the Shannon entropy for each residue position, based on representative sets of 3943 HIV-1 strains, 4467 influenza strains, and 212 RSV strains, respectively. Residues were colored based on the computed entropy values, on a scale of white (conserved) to purple (variable).


Serum Neutralization Fingerprinting Analysis.


The prevalence of effective neutralizing responses against HIV-1 Env in cohorts from 2-3 and 5+ years post-infection was estimated using a neutralization fingerprinting approach, as described previously (Georgiev et al., Science, 340, 751-756, 2013). Briefly, serum neutralization over a set of 21 diverse viral strains was compared to neutralization of the same viruses by a set of broadly neutralizing antibodies grouped into 12 epitope-specific antibody clusters. For each serum, the relative prevalence of each of the 12 antibody specificities was estimated by representing serum neutralization as a linear combination of the monoclonal specificities, with prevalence values of 0.2 deemed as positive. Sera with less than 30% breadth on the 21-virus panel as well as sera with high residual values from the computation (data not shown) were not included in the analysis. For mapping prevalence values onto the BG505 structure, residues part of multiple antibody epitopes were colored according to the respective antibody specificity with the highest prevalence in the 5+ years cohort. Antibody neutralization was measured using single-round-of-infection HIV-1 Env-pseudoviruses and TZM-bl target cells, as described previously (Li et al., J. Virol., 79, 10108-10125, 2005). Neutralization curves were fit by nonlinear regression using a 5-parameter hill slope equation as previously described (Li et al., J. Virol., 79, 10108-10125, 2005).


Patient Information.


In the CHAVI 001 cohort, high-risk subjects were screened for HIV-1 infection by ELISA, Western blotting, and plasma RNA to recruit individuals with acute HIV infection, who were then followed for ˜2 years until plasma neutralization breadth developed (Tomaras et al., J. Virol., 82, 12449-12463, 2008). In addition, a group of individuals were enrolled in the CHAVI 001 or CHAVI 008 cohorts who were chronically infected with HIV-1 strains clade A, B or C, and were screened for plasma neutralization breadth. The trial participants were enrolled at sites in Tanzania, South Africa, Malawi, the United States, and the United Kingdom (Tomaras et al., J. Virol., 85, 11502-11519, 2011). Both CHAVI001 and CHAVI008 protocols were approved by the institutional review boards of each of the participating institutions where blood samples were received or processed for analysis.


Epitope Analysis for HIV-1 Env, Influenza HA, and RSV F Antibodies.


Glycan usage and average residue entropy were calculated for eight representative HIV-1 Env (VRC01, b12, CD4, HJ16, 8ANC195, PG9, PGT122, 2G12, and 35O22), four representative influenza HA (2D1, C05, F10, and CR8043), and three representative RSV F (D25, Motavizumab, and 101F) epitopes based on their respective crystal structures. The selection of the flu antibodies was done as follows: F10 (stem targeting) and C05 (head targeting) were selected based on their cross-neutralizing ability for group 1 and group 2 of influenza A. CR8043 (group 2 specific) and 2D1 (H1 specific), which targets distinct regions from F10 and C05 at the stem and head of the HA respectively, were also selected for epitope analysis. An antigen residue was defined as an epitope residue if it had a non-zero BSA in the crystal structure. The fraction of glycan surface area in an epitope was calculated as the buried surface area of epitope glycans divided by the buried surface area of the full epitope. Mann-Whitney test was used to quantify the statistical difference between glycan fraction or average residue entropy for HIV-1 vs. influenza or RSV antibody epitopes.


Figures.


Structure figures were prepared using PYMOL (The PyMOL Molecular Graphics System, DeLano Scientific, San Carlos, Calif., 2002).


Interfaces.


Interactive surfaces were obtained from PISA (ebi.ac.uk/pdbe/pisa/).


Example 2
Crystal Structure of Unliganded HIV-1 Env Trimer in the Prefusion Mature Closed Conformation and Stabilization of the HIV-1 Env Ectodomain in a Prefusion Mature Closed Conformation

This example illustrates the three dimensional structure of the BG505 SOSIP.664 trimer in the prefusion mature closed conformation when not bound by neutralizing antibody. Additionally, this example illustrates exemplary HIV-1 Env ectodomains stabilized in a prefusion mature closed conformation. The crystal structure of the HIV-1 Env ectodomain in complex with the PGT122 and 35O22 Fabs (i.e., in a prefusion mature closed conformation) or in unliganded (without bound antibody) compared to the structure of HIV-1 Env in the CD4 bound conformation shows dramatic structural rearrangements in both the membrane-proximal and membrane-distal regions, providing guidance for the stabilization of the mature closed conformation of HIV-1 Env.


The structure of the unliganded HIV-1 Env ectodomain trimer is substantially identical to HIV-1 Env in the PGT122/35O22-bound BG505 SOSIP structure (discussed in Example 1) with rmsd of Cα ˜1.1 Å. This finding confirms that the HIV-1 Env ectodomain is not significantly distorted by binding to PGT122 and 35O22 antibodies, and therefore, that the structure disclosed in Example 1 provides an accurate view of the HIV-1 Env ectodomain in the prefusion mature closed conformation.


As the sole viral antigen on the HIV-1-virion surface, trimeric Env—and its gp120 and gp41 subunits—have been the focus of extensive vaccine efforts (Rerks-Ngarm et al., N Engl J Med, 361, 2209-2220, 2009; Flynn et al., J Infect Dis, 191, 654-665, 2005). These have been stymied, however, by unfavorable Env properties including substantial conformational diversity (Kwong et al., Nature, 420, 678-682, 2002). While a near-native soluble Env trimer (BG505 SOSIP.664) has been developed, which is preferentially recognized by broadly neutralizing antibodies (Binley et al., J Virol., 74, 627-643, 2000; Sanders et al., PLoS pathogens 9, e1003618, 2013; Sanders et al., J Virol., 76, 8875-8889, 2002), this trimer can be triggered by the CD4 receptor to expose epitopes recognized by ineffective antibodies, and a conformationally fixed trimer remains a key goal for vaccine designers. Here the crystal structure at 3.7 Å resolution of the unliganded SOSIP.664 trimer is presented, its structural compatibility with Env-reactive antibodies is characterized, and structure-based design is used to fix its conformation. The unliganded SOSIP.664 trimer assumed a closed structure, highly similar to antibody-bound structures (Example 1; Julien et al., Science, 342, 1477-1483, 2013; Lyumkis et al., Science 342, 1484-1490, 2013), which epitope analysis revealed to be structurally compatible with broadly neutralizing antibodies, but not ineffective ones. Structural compatibility correlated with binding antigenicity, except for ineffective antibodies directed to CD4-induced epitopes. Structure-based design yielded conformationally fixed variants, including a 201-433 double cysteine (DS) mutant, with improved specificity for broadly neutralizing antibodies. The DS-SOSIP.664 mutant retained nanomolar affinity for CD4, with which it formed a new structural state: a closed trimer bound by a single CD4 without the typical antigenic hallmarks of CD4 induction. This new structural state appeared to be an obligatory intermediate between the unliganded closed state and an activated state recognized by multiple CD4s and co-receptor. Conformational fixation—enabled by antigenicity-guided structural design—can thus be used to delineate mechanistic states and to improve Env-antigenic specificity, with DS-Env trimers fixed in the unliganded closed state defining a new generation of vaccine immunogens.


HIV-1 uses multiple mechanisms to evade the immune system, and these have stymied the development of an effective vaccine. One mechanism—conformational masking (Kwong et al., Nature, 420, 678-682, 2002)—hides the vulnerable shape of trimeric Env recognized by broadly neutralizing antibodies via structural rearrangements that expose immunodominant Env epitopes recognized by non- or poorly neutralizing antibodies. A potential solution is to determine the structure of the vulnerable conformation of Env and to use this structural information and protein design to stabilize or fix the vulnerable shape. Definition of the structure of trimeric HIV-1 Env in its vulnerable shape has been accomplished at increasing resolution by crystallography and cryo-electron microscopy (Example 1; Julien et al., Science, 342, 1477-1483, 2013; Lyumkis et al., Science 342, 1484-1490, 2013; Liu et al., Nature 455, 109-113, 2008). These studies have culminated in atomic-level structures of antibody-bound forms of a soluble, near-native trimer mimic, named BG505 SOSIP.664 for HIV-1 strain (BG505, Wu et al., J Virol., 80, 835-844, 2006) and stabilizing mutations (SOSIP.664, Binley et al., J Virol., 74, 627-643, 2000; Sanders et al., PLoS pathogens 9, e1003618, 2013; Sanders et al., J Virol., 76, 8875-8889, 2002). Antibodies, however, can influence conformation, and structures of the Env gp120 subunit can differ substantially when unliganded or antibody-bound (FIG. 32A). It was thus sought to determine and to fix the structure of the unliganded HIV-1 Env trimer. A sparse-matrix approach was used to crystallize an endoglycosidase H-treated BG505 SOSIP.664 trimer from a PEG 400-PEG 3,350 precipitant mixture (Majeed et al., Structure, 11, 1061-1070, 2003). Diffraction data extended to 3.7-Å resolution, and structure solution and refinement yielded Rwork/Rfree of 26.1%/28.3%.


Overall, despite differences in glycosylation and lattice packing, the structure of the unliganded trimer assumed a closed conformation, which was remarkably similar to antibody-bound trimers (Example 1; Julien et al., Science, 342, 1477-1483, 2013; Lyumkis et al., Science 342, 1484-1490, 2013), with an overall root-mean-square deviation (RMSD) in Cα positions of less than 1 Å—substantially lower than observed with monomeric gp120 (FIG. 32A). To determine whether the unliganded closed structure was an appropriate vaccine template, structurally specific for effective HIV-1-neutralizing antibodies and incompatible with non- or poorly neutralizing antibodies, it was first sought to categorize antibodies by their functional efficacy (FIG. 32B). Broadly neutralizing antibodies were defined as those of greater than 35% breadth on a diverse panel of 170 isolates, with ineffective antibodies of less than 15% breadth. Antibodies b12, 35O22 and PGT135 were close to the cutoff for the broadly neutralizing category; and while some antibodies such as the V3-directed 447-52D showed clade-specific breadth (447-52D neutralizes over 20% of clade B isolates), 447-52D was nonetheless categorized as ineffective because its overall breadth was only 12%. The unliganded closed structure was analyzed for its structural compatibility with antibody epitopes—most determined structurally in the context of monomeric gp120 or peptide epitope—based on two measures: antibody-volume overlap and epitope RMSD (FIG. 32C). Antibody-volume overlap correlated strongly with neutralization breadth (p=0.0020). Epitope RMSD trended with breadth, but did not achieve statistical significance (FIG. 32D). An antibody structural compatibility score (ASC), which combined both overlap and RMSD, did achieve significance (p=0.0069) (FIG. 32D).


The unliganded closed structure was compatible with the epitopes for all broadly neutralizing epitopes, except those of the membrane-proximal external region, which recognize epitopes downstream of residue 664, and of antibodies b1214 and CH10315, with CH103 exceeding a 2 Å threshold of epitope similarity and with b12 exceeding a volume threshold of 500 Å3 (FIG. 32D, left). In light of the poor RMSD correlation with trimer structure (FIG. 32D), the RMSD threshold was somewhat arbitrary. Nonetheless, the specific incompatibility of these moderately effective CD4-binding site antibodies suggest that movement of residues of the CD4-binding site could occur relative to the unliganded closed trimer and still achieve moderate neutralization breadth; indeed, induced trimer movements have been observed for b12 (which binds poorly to the BG505 SOSIP.664 trimer, Sanders et al., PLoS pathogens 9, e1003618, 2013) by electron microscopy (Liu et al., Nature 455, 109-113, 2008) and hydrogendeuterium exchange. By contrast, none of the epitopes for non- or poorly-neutralizing antibodies were structurally compatible with the unliganded closed structure (FIG. 32D, right).


These results indicate the unliganded closed trimer to be structurally specific for neutralizing antibodies. Structural specificity as measured by epitope compatibility, however, is only one of the requirements of an appropriate vaccine template: antigenic specificity as measured by binding to broadly neutralizing and not ineffective antibodies is also crucial. The BG505 SOSIP.664 had previously been shown by Moore, Sanders, and colleagues to be antigenically specific for broadly neutralizing antibodies, though binding to poorly neutralizing antibodies directed at the V3 loop was reported (Sanders et al., PLoS pathogens 9, e1003618, 2013). Negative selection by ineffective antibodies such as the V3-directed antibody 447-52D17 to remove aberrantly folded molecules was used (FIG. 36). However, even after V3-antibody negative selection, CD4 triggering efficiently exposed V3 epitopes (Mbah et al., J Virol., 75, 7785-7788, 2001) as well as bridging sheet epitopes (Kwong et al., Nature 393, 648-659, 1998) recognized by antibodies like 17b (Thali et al., J Virol., 67, 3978-3988, 1993) (FIG. 33A; FIGS. 37-40). Overall, while structural compatibility (and neutralization breadth) generally correlated with antibody binding, in the presence of CD4, this correlation was lost (FIG. 33A; FIG. 37). Notably, CD4 triggered ineffective antibodies so that their average binding was higher than for broadly neutralizing ones (FIG. 33A, right). CD4 triggering makes BG505 SOSIP.664 less desirable as an immunogen: in primates, it would bind CD4 in vivo and would thus be predicted to elicit ineffective antibodies against the highly immunogenic CD4-induced epitopes.


To fix the unliganded closed state and to prevent CD4 triggering, regions of the unliganded closed structure that moved upon CD4 binding were analyzed to identify cavity-filling hydrophobic substitutions, side-chain pairs capable of forming disulfide bonds, and positions where the introduction of a proline would be compatible with only the unliganded closed structure of Env, but not its receptor-bound conformation (FIG. 33B, insets). These substitutions were engineered into BG505 SOSIP.664, co-expressed with furin in a 96-well transfection format (McLellan et al., Science 342, 592-598, 2013) and assessed supernatants on an antigenic panel, comprising broadly neutralizing antibodies PGT122 (Walker et al., Nature 477, 466-470, 2011) and VRC01 (Wu et al., Science 329, 856-861, 2010), quaternary-specific broadly neutralizing antibodies PGT145 (Walker et al., Nature 477, 466-470, 2011) and CAP256-VRC26 (Doria-Rose et al., Nature, 509, 55-62, 2014), and poorly neutralizing antibodies F105 and 17b, with the latter tested alone and in the presence of CD4. Several different constructs were tested (FIG. 42). Several promising constructs were purified and analyzed for gp120-gp41 cleavage and oligomeric heterogeneity (FIG. 36) and by meso-scale discovery-electrochemiluminescence immunoassay (MSD-ECLIA) for recognition on a more comprehensive panel of HIV-1-reactive antibodies (FIG. 33C and FIG. 37). One cavity-filling alteration, Y191W, retained recognition of broadly neutralizing antibodies, but only moderately reduced the binding of antibody 17b, while two proline substitutions, Q432P and A433P, showed improved antigenic specificity. A 201C-433C double cysteine (DS) mutant showed virtually no antibody 17b recognition, even in the presence of CD4, while retaining strong recognition of antibody PGT145 and increasing the recognition of antibody CAP256-VRC26 (FIG. 33C). While A433P showed better recognition for broadly neutralizing antibodies compared to 201C-433C, the temporal stability of A433P was found to be lower than that of both BG505 SOSIP.664 and 201C-433C, with 201C-433C exhibiting highest temporal stability (FIG. 37). Notably, with the 201C-433C DS variant, structural compatibility (and neutralization breadth) correlated with antibody binding, even in the presence of CD4 (FIG. 33D; FIG. 37). Modeling of the DS substitution indicated a 201C-433C disulfide to be incompatible with the CD4-bound state, where α-carbons (Ca) of residues 201 and 433 are 9.4 Å apart, separated by a strand of the bridging sheet (Kwong et al., Nature 393, 648-659, 1998), and the V3 loop is fully exposed (Huang et al. Science 310, 1025-1028, 2005) (FIG. 33E). By contrast, the 201C-433C substitutions are expected to form a disulfide in the unliganded closed trimer, and indeed the unliganded BG505 SOSIP.664 201C-433C exhibited a 6.1° C. increase in thermostability (to 73.10° C.) relative to the parent SOSIP.664 (FIG. 33F).


These results indicate the 201C-433C ‘DS’ variant of BG505 SOSIP.664 (termed “DS-SOSIP.664”) is not triggered by CD4. To define the interaction of the DS-SOSIP.664 variant with CD4, surface plasmon resonance (SPR) was used (FIG. 34A). The DS-SOSIP.664 recognized CD4 with a similar on-rate as the parent SOSIP.664, but with ˜10-fold faster off-rate, resulting in a ˜10-fold reduction in KD relative to SOSIP.664 (FIG. 34A). To test for CD4 triggering over a longer time scale, both DS-SOSIP.664 and parent SOSIP.664 were incubated for 100 h in the presence of CD4, and SPR readout of 17b and 3074 epitopes was used to assess triggering. With the parent SOSIP.664, CD4 induced a slow transition to a state with bridging sheet formed (t1/2 of 3.3±0.7 h for antibody 17b) and V3 loop exposed (t1/2 of 4.2±1.0 h for antibody 307426) (FIG. 34B and FIG. 40). With DS-SOSIP.664, triggering by CD4 of bridging sheet or V3 was not observed over the entire 100 h time course (FIG. 34B). To define the stoichiometry of CD4 interaction, sedimentation equilibrium analytical ultracentrifugation of parent and DS-SOSIP.664 variants in the presence of excess CD4 was used. Molecular weights consistent with the parent SOSIP.664 binding two to three CD4s and the DS-SOSIP.664 variant binding only one CD4 were observed (FIG. 34C and FIG. 41).


DS-SOSIP.664 can thus capture Env in a single CD4-bound state. To obtain structural information on this single CD4 bound state, the hydrogen-deuterium exchange (HDX) of DS-SOSIP.664 with and without CD4 was characterized. Without CD4, the hydrogen-deuterium exchange of DS-SOSIP.664 appeared similar to the exchange of the parent SOSIP.664 (FIG. 34D); with CD4, the gp120 inner domain, the bridging sheet, and gp41 showed little change upon the addition of soluble CD4 (FIG. 34D). The V2, V3 and the stem of V1 showed a response to CD4, consistent with the slightly increase exposure of V3 epitope observed by MSD-ECLIA (FIG. 33D), but this was substantially less than observed for the parent SOSIP.664. The single CD4-bound DS-SOSIP.664 thus differs from previously observed CD4-bound states in that the typical hallmarks of CD4-induction—such as bridging sheet formation and V3 loop exposure—are absent or substantially reduced.


As the single-CD4-bound state could be SOSIP.664 specific, and indeed both SOSIP.664 and DS-SOSIP.664 variant appear to be extraordinarily rigid, DS-stabilized Envs were assessed in other contexts. When DS mutations were placed into functional virus, they ablated entry (FIG. 40). Single molecule fluorescence energy transfer (smFRET) measurements, utilizing donor-acceptors placed in the first and fourth variable Env loops of functional JR-FL viral spikes, revealed DS mutations to reduce transitions from the ground state. DS-viral spikes remained primarily in the closed ground state, even in the presence of dodecameric CD428 (FIG. 34E). Overall, the asymmetric single CD4-bound state—with fast off-rate for CD4—appeared to be an obligatory intermediate between the unliganded state and a more fully CD4-triggered state capable of binding multiple CD4s and co-receptor (FIG. 34F). In this context, it is noted that the high off-rate of CD4 in the single CD4-bound state, coupled with the slow transition to a 3:1 CD4:trimer stoichiometry, provides a kinetic-based molecular mechanism for the ability of primary HIV-1 isolates to resist neutralization by monomeric CD429.


Additional HIV-1 Env ectodomain variants including one or more amino acid substitutions to stabilize the ectodomain in the prefusion mature closed conformation are set forth in Table 13 and described herein, the antigenicity of some of which is presented in FIGS. 42-53. The antigenicity of exemplary protein nanoparticles including a recombinant HIV-1 Env protein is provided in FIG. 43. The antigenicity of exemplary chimeric HIV-1 Env proteins is provided in FIG. 42.


The unliganded Env trimer—fixed in the pre-fusion closed conformation—may be an ideal HIV-1 immunogen. We assessed DS-SOSIP.664 for physical stability to conditions typically encountered during manufacturing and observed increased stability relative to the parent SOSIP.664 to denaturation by temperature, pH or freeze-thaw (FIG. 35A). To see if the 201C-433C substitutions might serve as a general means of reducing CD4-induced transition in other Env antigens, the 201C-433C and SOS mutations were placed into HIV-1 Env expressed on the surface of enzyme-treated pseudovirions (Crooks et al., J Virol., 85, 5825-5839, 2011). These viral spikes were observed to resist CD4 triggering and to retain the antigenic profile of the soluble trimer for broadly neutralizing antibodies in both BG505 and JR-FL Env backgrounds (FIG. 35B). Overall, the results indicate the disulfide-shackled 201C-433C variants of soluble SOSIP.664 and VLP SOS to be highly desirable antigens: conformationally fixed trimers in which neutralizing epitopes are almost exclusively exposed even in the presence of CD4. It is noted that the path to identify the 201C-433C DS substitution involved an information flow from broadly neutralizing antibodies, through structural compatibility and binding antigenicity, to obtain a conformationally fixed immunogen of appropriate antigenicity (FIG. 35C). What was unexpected was the separation of CD4 binding by the 201C-433C DS alteration into two mechanistic steps: the recognition of one CD4 without any of the antigenic hallmarks of CD4 binding such as bridging sheet formation, and the binding of more than one CD4 along with exposure or formation of characteristic CD4-induced epitopes. In addition to improving the antigenic specificity of unliganded HIV-1 Env immunogens, antigenic-guided conformational fixation can thus reveal additional mechanistic steps of the HIV-1 entry pathway.


Methods

BG505 SOSIP.664 Expression, Purification, and Deglycosylation.


BG505 SSOIP.664 trimer was produced in HEK 293 GnTI −/− cells via transient transfection of the BG505 SOSIP expressing plasmid with furin and purified as described previously (Sanders et al., PLoS pathogens 9, e1003618, 2013; Julien et al., Science, 342, 1477-1483, 2013) and in Example 1. Briefly, the BG505 SOSIP.664 expressed supernatant was passed over the 2G12 IgG-conjugated protein A column, washed with phosphate-buffered saline (PBS), and eluted with the elution buffer containing 3M MgCl2, pH 8.5. The eluted protein was then dialyzed against PBS and set for deglycosylation reaction at 37° C. in the reaction buffer containing 1 mM EDTA, 150 mM NaCl, protease inhibitor cocktail (Roche), 17,000 units of Endo H/ml, and 50 mM sodium acetate, pH 5.8. The deglycosylated BG505 SOSIP was further purified with Superdex 200 16/60 (GE Healthcare) column in the buffer containing 5 mM HEPES 7.5, 150 mM NaCl, and 0.02% NaN3. The peak corresponding to trimeric HIV-1 Env was identified, pooled and concentrated to ˜10 mg/ml using an Amicon Ultra-15 centrifugal filter (MWCO 50,000, Millipore) and screened for crystallization. For antigenicity and stability analyses, trimers were purified by affinity chromatography over a VRC01 column, purified by gel filtration over a Superdex 200 16/60 (GE Healthcare) column in buffer containing 5 mM HEPES 7.5, 150 mM NaCl, and 0.02% NaN3, and finally, passed through a 447-52D column to remove aberrant trimer species (FIG. 36).


Crystallization Screening.


Deglycosylated BG505 SOSIP.664 was screened for crystallization using 572 conditions from Hampton, Wizard and Precipitant Synergy (Majeed et al., Structure, 11, 1061-1070, 2003) screens using a Cartesian Honeybee crystallization robot as described previously (McLellan et al., Nature, 480, 336-343, 2011) and a mosquito robot using 0.1 μl of reservoir solution and 0.1 μl of protein solution. Crystals suitable for structural determination were obtained robotically in 26% PEG 400, 3.2% PEG 3350, and 0.1M sodium acetate pH 5.5. Crystals were cryoprotected in a solution containing 30% glycerol, 30% PEG 400, 4% PEG 3350, and 0.1M sodium acetate pH 5.5, and flash-frozen in liquid nitrogen. Data were collected at a wavelength of 1.00 Å at the SER-CAT beamline ID-22 (Advanced Photon Source, Argonne National Laboratory).


X-Ray Data Collection, Structure Solution and Model Building.


Diffraction data were processed with the HKL2000 suite (Otwinowski & Minor, Methods Enzymol., 276, 307-326, 1997). The data were corrected for anisotropy using the anisotropy server services.mbi.ucla.edu/anisoscale/with truncations to 3.7 Å, 3.7 Å, 3.3 Å along a, b, and c axes, respectively. Structure solution was obtained with Phaser using 35O22- and PGT122-bound BG505 SOSIP.664 (PDB ID: 4TVP10) as search models. Refinement was carried out with Phenix (Adams et al., J Synchrotron Radiat., 11, 53-55, 2004). Model building was carried out with Coot (Emsley & Cowtan, Acta crystal. Section D, Biol. Crystal., 60, 2126-2132, 2004).


Structural Analyses Involving Residue-Specific Properties.


To estimate the degree of structural flexibility in the unliganded HIV-1 trimer, we determined the average Cα RMSD distance for each residue position in the unliganded trimer structure (FIG. 32A). The average Cα RMSD distance served as a proxy for structural plasticity and was computed between corresponding residues after optimal superimposition onto a set of 91 X-ray structures from the Protein Data Bank (PDB) (Bernstein et al. J mol. Biol., 112, 535-542, 1977). Each domain of the unliganded trimer was considered separately and superimposed onto the set of structures using the program TM-align (Zhang & Skolnick, Nucleic Acids Res., 33, 2302-2309, 2005). To obtain the best possible registry between corresponding residues, structural superimpositions were guided by amino acid sequence alignments when necessary. A total of 54 monomeric structures were used for superimpositions involving the gp120 domain. To generate FIG. 32A (left), five representative gp120 structures were used; unliganded clade A/E HIV-1 gp120 coree(3TGT) (Kwon et al. PNAS, 109, 5663-5668, 2012), b12-bound gp120 (2NY7) (Zhou et al., Nature 445, 732-737, 2007), b13-bound gp120 (3IDX) (Chen et al., Science, 326, 1123-1127, 2009), F105-bound gp120 (3HI1)38, and CD4- and 48d-bound gp120 (3JWD) (Pancera et al. PNAS, 107, 1166-1171, 2010) structures. For the gp41 domain a total of 37 structures from the PDB that included hexameric bundles as well as disordered peptides were used.


Hydrogen/deuterium exchange (HDX) mass spectrometry (MS) is indicative of intrinsic amide exchange of peptide segments and is a useful technique to monitor dynamic characteristics of proteins in solution. Qualitative exchange profiles for observable peptides of SOSIP.664 after 3s were extracted from individual HDX-MS exchange plots (Guttman et al., Structure, 22, 974-984, 2014). The average exchange values (0-75%) were substituted in the B-factor field for the observed peptides of SOSIP.664 coordinates and displayed within PyMol. Non-observable peptides in the deuterium exchange experiment as well as peptides with missing electron density were excluded from the analysis.


Residue sequence variability was computed as the Shannon entropy for each residue position based on a representative set of 3,943 HIV-1 strains. The electrostatic potential surfaces were generated using GRASP41.


Assessment of Antibody Functionality on a Panel of 170 Diverse HIV-1.


Neutralization was measured using single-round-of-infection HIV-1 Env-pseudoviruses and TZM-bl target cells, as described previously (Sarzotti-Kelsoe et al., J. Immunol. Meth., 409, 131-146, 2014). Neutralization curves were fit by nonlinear regression using a 5-parameter hill slope equation. The 50% and 80% inhibitory concentrations (IC50 and IC80) were reported as the antibody concentrations required to inhibit infection by 50% and 80% respectively.


Computation of Antibody Epitope RMSD, Volume Overlap, and Epitope Presence.


HIV-1-specific antibody-antigen complex structures were compiled from the PDB, and antibodies were defined as broadly or poorly/non-neutralizing based on published or in-house neutralization data of diverse viral strains (Georgiev et al., Science, 340, 751-756, 2013). Antibodies that were deemed to have insufficient evidence for being classified as broadly or poorly/non-neutralizing were excluded from the analysis. A single antibody representative was included in the analysis in cases where multiple antibody clonal relatives were found. The epitope residues for each antibody were defined based on the respective antibody-antigen complex crystal structures, with an antigen residue being defined as an epitope residue if any of its heavy atoms were within 5.5 Å of any antibody heavy atom. To compute the RMSD between the epitope residues in the antibody-antigen complex structure and the same residues in the unliganded trimer structure: (1) the epitope residues from the complex structure were aligned to the unliganded trimer structure using the align function in PyMOL, then (2) the Cα RMSD of the epitope residues was calculated. To remove outlier residues, the top and bottom 10% of the Cα deviations were removed from the RMSD calculation. To calculate the volume overlap between a given antibody and the unliganded trimer structure, the alignment from above was used to compute the overlap volume between the antibody from the complex structure and the unliganded trimer structure by using the phase_volCalc utility from Schrödinger. An antibody epitope was considered as present in the unliganded trimer structure if at least 70% of the epitope residues as defined by the antibody antigen complex structure were also present in the unliganded trimer structure. For mapping the per-residue RMSD computation onto the unliganded trimer structure, residues part of any antibody epitope (including epitopes with less than 70% total residues present) were included in the analysis; if a given residue was part of more than one antibody epitope, the highest RMSD value for that residue among all epitopes was used. Antibody volume overlap values were mapped onto the unliganded trimer structure for all residues part of the epitope for the given antibody; if a residue was part of more than one antibody epitope, then the lowest volume overlap for that residue among all epitopes was used. Correlations of structural properties with neutralization and/or binding data were computed using the Spearman correlation coefficient.


Structural Compatibility Analysis.


For a given antibody, the Antigenic Structural Compatibility (ASC) score with the HIV-1 Env unliganded pre-fusion trimer structure was computed based on a comparison to a structure of the antibody bound to an Env-derived antigen (e.g., gp120 core or V3 peptide). ASC scores were computed on a 0-1 scale using the following variables: (i) The fraction f of epitope residues (as defined by the structure of the antibody complex) exposed to solvent in the unliganded trimer structure was computed, with a residue considered accessible to solvent if its solvent-accessible surface area (SASA) was at least half its SASA in the respective antibody complex structure; f was set to 0 if less than 70% of epitope residues were present in the antigen. (ii) A resolution estimate r was used such that Cα RMSDs d below r=2 were not penalized in the scores. (iii) The volume overlap values were used to define a volume overlap factor v that is equal to 1 for overlap below 200 Å3, is equal to 0 for overlap over 1000 Å3, and decays linearly in between. Intuitively, the unliganded trimer structure is expected to be structurally compatible with an antibody if f and v are high and if the RMSD d is low, since such conditions would indicate similarity between the unliganded trimer structure and the Env conformation in the antibody complex. Thus, the ASC score for each antibody with the unliganded trimer was defined by the formula: fv exp(−0.5 max(0, d−r)).


Transient Transfection Expression of Immunogens in 96-Well Microplates.


A 96-well microplate-formatted transient transfection expression approach was used to achieve high-throughput expression of various immunogen proteins as follows. HEK GnTi-cells were thawed and incubated with growth medium (293 FreeStyle Expression Medium supplemented with 10% Fetal Bovine Serum and 1% streptomycin-penicillin) (Invitrogen, CA) at 37° C., 5% CO2, until the cells reached logarithmic physiological growth. 24 hours prior to DNA-transient transfection, 100 μl of physiologically growing cells was seeded in each well of a 96-well microplate at a density of 2.5×105 cells/ml in expression medium (293 FreeStyle Expression Medium supplemented with 10% Ultra-Low IgG Fetal Bovine Serum and 1×-Non-Essential Amino Acids) (Invitrogen, CA), and incubated at 37° C., 5% CO2 for 20 h. Two hours prior to transfection, 100 μl of spent medium from each well was replaced with 60 μl of fresh expression medium. DNA-TrueFect-Max complexes were used for transfection, and these were prepared by mixing 0.2 μg plasmid DNA in 10 μl of Opti-MEM transfection medium (Invitrogen, CA) with 0.4 μl of TrueFect-Max (United BioSystems, MD) in 10 μl of Opti-MEM, and incubating for 15 min prior to transfection. 20 μl of the complex was added into each well and mixed with growing cells, and the 96-well plate was incubated at 37° C., 5% CO2. One day post transfection, 20 μl of enriched medium (293 FreeStyle Expression Medium supplemented 25% Ultra-Low IgG Fetal Bovine Serum, 2× Non-Essential Amino Acids and 2× glutamine) was added to each well, and returned to incubator for continuous culture. On days three to five post transfection, the culture was exposed to oxygen in the sterilized air once per day. After day five post transfection, the biological function of the expressed protein in the supernatant in 96-well microplate was analyzed using an ELISA assay.


Antigenic analysis of stabilized HIV-1 Env trimeric immunogens in 96-well microplate by antibody binding ELISA assay. The D7324 antibody-coated 96-well ELISA plate was prepared by incubating 2 μg/ml of D7324 Antibody (Aalto, Ireland) in 100 μl PBS in 96 Well Flat-Bottom Immuno Plate (nunc, Thermo, IL) overnight at 4° C., followed by removal of coating solution and incubation of 200 μl/well, 2% (W/V) dry milk in PBS overnight at 4° C., and then the wells were washed 5 times with PBS+0.05% Tween 20. 30 μl of supernatant expressed in each well of the 96-well microplate was incubated with 70 μl of PBS in each well of a D7324 antibody-coated 96-well ELISA plate for two hours at room temperature (RT), and then the wells were washed 5 times with PBS+0.05% Tween 20. 100 μl of anti-specific epitope primary antibody (prepared in our lab) at a concentration of 10 μg/ml in PBS with 0.2% (W/V) dry milk and 0.2% Tween 20 was incubated into each well for 1 hour at RT, and then the wells were washed 5 times with PBS+0.05% Tween 20. 100 μl of Horseradish peroxidase (HRP)-conjugated goat anti-human IgG antibody (Jackson ImmunoResearch Laboratories Inc., PA) at 1:10,000 in PBS with 1.0% (W/V) dry milk and 0.2% Tween 20 was incubated into each well for 30 min at RT, and then the wells were washed 5 times in PBS+0.05% Tween 20. The wells were developed using TMB at RT for 10 min, and the reaction was stopped with 180 mM HCl. The readout was measured at a wavelength of 450 nm. All samples were performed in duplicate.


Antigenic Analysis of BG505 SOSIP.664 and Mutants by MSD-ECLIA Assay Using D7324 Detection.


Standard 96-well bare MULTI-ARRAY Meso Scale Discovery (MSD) Plates (MSD, cat #L15XA-3) were coated with a panel of HIV neutralizing and non-neutralizing monoclonal antibodies in duplicates (30 μL/well) at a concentration of 10 μg/mL, diluted in 1×PBS and the plates were incubated overnight at 4° C. The following day, plates were washed (wash buffer: 0.05% Tween-20+1×PBS) and blocked with 150 μL of blocking buffer [5% [W/V] MSD Blocker A (MSD, Cat # R93BA-4)] and incubated for 1 hr on a vibrational shaker (Heidolph TITRAMAX 100; CAT # P/N: 544-11200-00) at 650 rpm. All the incubations were performed at room temperature, except the coating step. During the incubation, BG505 SOSIP trimer was titrated down in a serial 2 fold dilutions starting at 4 μg/mL concentration of the trimer in assay diluent (1% [W/V] MSD blocker A+0.05% Tween-20). After the incubation with blocking buffer was complete, the plates were washed and the diluted trimer was transferred (25 l/well) to the MSD plates and incubated for 2 hrs on the vibrational shaker at 650 rpm. For soluble CD4 (sCD4) induction, trimer was pre-incubated with sCD4 at a constant molar concentration of 1 μM for 1 hour before adding to the MSD plate. After the 2 hr incubation with trimer, the plates were washed again and secondary detection MSD Sulfotag labeled D7324 antibody (Prior to running the assay D7324 antibody was labeled with MSD Sulfotag (MSD; Cat #R91AN-1) at a conjugation ratio of 1:15 [D7324: Sulfotag]), which was diluted in assay diluent at 5 μg/mL and was added to the plates (25 μL/well) and incubated for 1 hr on the vibrational shaker at 650 rpm. The plates were washed and read using the 1× read buffer (MSD Read Buffer T (4×); Cat# R92TC-2) on MSD Sector Imager 2400.


Antigenic Analysis of Stabilized HIV-1 Env Trimeric Immunogens by Antibody Binding ELISA Assay.


Similar to what was done for the 96 well plate ELISA, the D7324 (Aalto, Ireland) antibody was coated overnight at 2 μg/ml in 100 μl PBS at 4° C. Wells were washed once in PBS/Tween 20 (0.2%) and blocked with 200 μl/well of 2% (W/V) dry milk in PBS for one hour at room temperature (RT). The wells were then washed 5 times in PBS+0.05% Tween 20 (PBST) and purified proteins (BG505 SOSIP.664 and mutants) were then coated at either 0.5 or 2 μg/ml in PBS, 10% FBS for 2 hours at RT. The wells were washed 5 times in PBS-T. 100 μl of primary antibody at a concentration of 10 μg/ml in PBS/Tween 20 (0.2%) was incubated into each well for 1 hour at RT, and then the wells were washed 5 times in PBS-T. 100 μl of Horseradish peroxidase (HRP)-conjugated goat anti-human IgG antibody (Santa Cruz Biotechnology) at 1:5,000 in PBS with 0.2% Tween 20 was added to each well for 1 hour at RT. The wells were washed 5 times in PBS-T. The wells were developed using Sureblue (KPL) at RT for 10 min, and the reaction was stopped with 180 mM HCl. The readout was measured at a wavelength of 450 nm. All samples were performed in duplicate.


Surface Plasmon Resonance Analysis.


Affinities and kinetics of binding to BG505 SOSIP.664 soluble trimer and its mutants were assessed by surface plasmon resonance on a Biacore T-200 (GE Healthcare) at 20° C. with buffer HBS-EP+(10 mM HEPES, pH 7.4, 150 mM NaCl, 3 mM EDTA, and 0.05% surfactant P-20).


For assessing binding of trimer to CD4i antibody 17b and HR2-reactive peptide C34, mouse anti-human Fc antibody was first immobilized onto two flow cells on a CM5 chip at ˜10,000 response units (RU) with standard amine coupling protocol (GE Healthcare). Either 17b IgG or C34-Ig was then captured on one flow cell by flowing over a 200 nM solution at 5 μl/min flow rate for two minutes. The other flow cell was used as reference. To block unliganded mouse anti-human Fc antibody, this was followed by a 1-minute injection of 1 μM human Fc on both flow cells. 500 nM unliganded trimer (−CD4) or a complex of 500 nM trimer+1500 nM sCD4 (+CD4) was flowed over the sample flow at a flow rate of 50 μl/min for 2 minutes and allowed to dissociate for 5 minutes. The cells were regenerated with two 10 μl injections of 3.0 M MgCl2, pH 7.5 at a flow rate of 100 μl/min. Blank sensorgrams were obtained by injection of the same volume of HBS-EP+ buffer. Sensorgrams were corrected with corresponding blank curves.


For assessing binding of trimer to sCD4, single-cycle kinetics analyses were carried out. First, ˜2000RU of antibody 2G12 were immobilized on two flow cells. Next, 200 nM of trimer was injected on the sample flow cell. Finally, 5 concentrations of sCD4 (100 nM, 50 nM, 25 nM, 12.5 nM, 6.25 nM) were injected incrementally in a single cycle, starting from the lowest concentration, followed by a dissociation phase of 30 min. Blank sensorgrams were obtained by injection of same volume of HBS-EP+ buffer in place of sCD4. Sensorgrams of the concentration series were corrected with corresponding blank curves and fitted globally with Biacore T200 evaluation software using a 1:1 Langmuir model of binding.


For assessing affinity and kinetics of antibody 17b binding, trimer was captured onto a 2G12 surface that was obtained by capturing 2G12 IgG on a flow cell immobilized with ˜10,000 response units (RU) of mouse anti-human Fc antibody. To block unliganded mouse anti-human Fc antibody, this was followed by a 1-minute injection of 1 μM human Fc on both flow cells. Binding to 17b Fab was carried out in the single-cycle kinetics format with successive injections of 5 concentrations of 17b Fab. Blank sensorgrams were obtained by injection of the same volume of HBS-EP+ buffer in place of antibody Fab fragments. Sensorgrams of the concentration series were corrected with corresponding blank curves and fitted globally with Biacore T200 evaluation software using a 1:1 Langmuir model of binding.


For determining the time-course of CD4 activation of the soluble trimers, 17b IgG, 3074 IgG and 2G12 IgG were captured on three separate flow cells of a CM5 chip immobilized with ˜10,000 RU of mouse anti-human Fc antibody. Trimers were incubated in 4-fold molar excess of sCD4 and samples were injected at different time-points. Blank sensorgrams were obtained by injection of same volume of HBS-EP+ buffer in place of trimer. To measure any change in the trimer samples on incubation, unliganded trimers were injected before and 72 hours after start of the experiment.


Biolayer Interferometry Analysis.


A fortéBio HTX instrument was used to measure affinities of BG505 SOSIP.664 and the 201C-430C variant to a panel of HIV-1 Env reactive antibodies at 30° C. All assays were carried out with agitation set to 1,000 rpm in PBS supplemented with 1% BSA (PBS/1% BSA) using solid black 96-well plates (Geiger Bio-One). For the quaternary-specific antibodies CAP256-VRC26.09 and PGT145, the IgG (40 μg/ml) was directly immobilized onto an anti-human capture sensor for 300 s. Typical capture levels were between 1.2 and 1.4 nm, and variability within a row of eight tips did not exceed 0.1 nm. Biosensor tips were then equilibrated for 300 s in PBS/1% BSA buffer prior to assessment of binding to the HIV-1 trimer molecules in solution (0.015 to 0.5 μM). Association was allowed to proceed for 300 s followed by dissociation for 300 s. Dissociation wells were used only once to prevent contamination. Parallel correction to subtract systematic baseline drift was carried out by subtracting the measurements recorded for a sensor loaded with the respiratory syncytial virus (RSV)-specific antibody D25 incubated in PBS/1% BSA.


For all other binding studies, 2G12 (60 μg/ml) was immobilized onto an anti-human capture sensor for 300 s (typical loading levels 1.0 nm) followed by incubation with either the BG505.SOSIP or the 201C-433C variant for 600 s (resulting in loading levels of ˜0.8 nm). The 2G12: HIV-1 Env complex was then allowed to associate with Fab molecules (2.5 μM-0.2 μM) in PBS/1% BSA for 300s followed by dissociation for 300-1800 s. A D25:RSV fusion glycoprotein complex was used to control for non-specific binding of the Fab molecules. Data analysis and curve fitting were carried out using Octet software, version 8.1. Experimental data were fitted with the binding equations describing a 1:1 interaction. Global analyses of the complete data sets assuming binding was reversible (full dissociation) were carried out using nonlinear least-squares fitting allowing a single set of binding parameters to be obtained simultaneously for all concentrations used in each experiment.


Negative-Stain Electron Microscopy.


Negative-stain electron microscopy samples were diluted to about 0.03 mg/ml, adsorbed to a freshly glow-discharged carbon-film grid for 15s, and stained with 0.7% uranyl formate. Images were collected semi-automatically using SerialEM44 on a FEI Tecnai T20 with a 2k×2k Eagle CCD camera at a pixel size of 0.22 nm/px. Particles were picked automatically and reference-free 2D classification was performed in EMAN245.


Differential Scanning Calorimetry.


The heat capacity of BG505 SOSIP.664 and BG505 SOSIP.664.201C-433C was measured as a function of temperature using a high-precision differential scanning VP-DSC microcalorimeter (GE Healthcare/Microcal, Northampton, Mass.). The samples were extensively dialyzed against PBS, pH 7.4, and then degassed to avoid the formation of bubbles in the calorimetric cells. Thermal denaturation scans were conducted from 10 to 100° C. at a rate of 1° C./min. The protein concentration was about 0.3 mg/mL.


Analytical Ultracentrifugation Equilibrium Measurements.


Analytical ultracentrifugation (AUC) equilibrium experiments were performed at 15° C., using a Beckman XL-A/I ultracentrifuge equipped with a Ti60An rotor. Data was collected using UV absorbance at 230 nm. Samples were dialyzed in Na2HPO4 10 mM, NaCl 140 mM, pH 7.4 overnight at 4° C. and loaded into six-channel equilibrium cells with parallel sides and quartz windows. 120 μL aliquots of sample diluted to 0.25 (78), 0.16 (51) and 0.087 (27) μM (μg/mL) were loaded, respectively, into three channels A, B and C of the cell, with three of the channels used for buffer reference. Samples were spun at 5000 rpm (9810*g) for 20 hours, after which four scans were collected at a rate of 1 per hour. The rotor speed was then increased to 6500 rpm (12750*g) for 10 hours, after which four additional scans were collected at the same rate. The speed was further increased to 8000 rpm (15690*g) for another 10 hours and four more scans were recorded under the same conditions. During the last step, the rotor speed was increased to 10000 rpm (19620*g) for four more scans, resulting in a total of 16 scans for each concentration and a total of 48 scans per protein. The data was processed and analyzed using HeteroAnalysis 1.1.44 software (biotech.uconn.edu/auf) and SEDPHAT46. Buffer density and protein v-bars were calculated using the SednTerp (Alliance Protein Laboratories) software. The data for all concentrations and speeds were globally fit using nonlinear regression to an ideal monomer model.


Hydrogen Deuterium Exchange (HDX).


The hydrogen-deuterium exchange rates for BG505 SOSIP.664 and the DS-SOSIP.664 both alone and in the presence of CD4 were assessed. Complexes with soluble CD4 (D1D2) were formed by overnight incubation with a nine-fold molar excess of ligand (relative to trimer). Proteins (10 μg) were diluted 10-fold into deuterated PBS buffer and incubated at room temperature. Aliquots removed after 3 s, 1 min, 30 min and 20 h were quenched by mixing with an equal volume of cold 200 mM Tris-2-carboxyethyl phosphine (TCEP), 0.2% formic acid (final pH 2.5). The samples were subsequently digested with pepsin (at 0.15 mg/mL) for 5 min on ice, flash frozen in liquid nitrogen, and stored at −80° C. For LC-MS analysis, samples were thawed on ice for 5 minutes and manually injected onto a Waters BEH 1.7 gm 1.2×5 mm trap column (Waters) flowing 0.1% TFA at 200 μL/min. After 3 minutes of washing the peptides were resolved over a Hypersil 1×50 mm 2.1 gm C18 column (Thermo Scientific) using a gradient of 15 to 40% B in 8 minutes (A: 0.05% TFA 5% ACN; B: 0.05% TFA 80% ACN). Eluted peptides were analyzed with a Waters Synapt Q-TOF mass spectrometer. Peptide identification and exchange analysis were as described previously (Guttman et al., Structure, 22, 974-984, 2014).


Neutralization of Viral Entry.


The point mutations were introduced into full-length Env clone BG505.W6M.C212 in expression vector pcDNA3.1/V5-His-TOPO (Invitrogen). Pseudotyped, single round of entry virus was produced as described in Shu et al. (Shu et al., Vaccine, 25, 1398-1408, 2007). Briefly, plasmid DNA was used to transfect 293T cells along with an envelope-deficient HIV-1 subtype A proviral plasmid, SG3dEnv48 to generate pseudotyped viral particles. Serial dilutions of the pseudovirus stocks were added to TZMbl reporter cells, and two days later the activity of the luciferase reporter gene in infected cells was assessed with a Luciferase Assay kit (Promega) and measured in a luminometer; activity was reported as Relative Light Units (RLU).


smFRET on JR-FL Viral Spikes.


Briefly, HEK293 cells were transfected at a 40:1 ratio of wild-type HIV-1JR-FL or HIV-1JR-FL 201C-433C Env to dually V1-Q3/V4-A1 tagged Env and the additional presence of pNL4-3 Δenv ART. Virus was concentrated from supernatants 40 h post-transfection and dually labelled overnight in a reaction with 0.5 μM Cy3B(3S)-cadaverine, 0.5 μM Cy5(4S)COT-CoA, 0.65 μM transglutaminase (Sigma), and 5 μM AcpS at room temperature. After addition of DSPE-PEG2,000-biotin (Avanti) at 0.02 mg/ml (30 min), the viruses were purified on a 6-18% Optiprep gradient in 50 mM Tris pH 7.4, 100 mM NaCl and stored at −80° C. For smFRET imaging, viruses were immobilized on streptavidincoated quartz microfluidic devices and imaged at room temperature on a wide-field prism-based TIRF instrument equipped with an Opus 532 nm laser (Laser Quantum). Donor and acceptor fluorescence were collected through a 1.27-NA 60× water-immersion objective (Nikon), and recorded using an ORCA-Flash4.0 sCMOS camera (Hamamatsu) at 25 frames/s for 80 s. All smFRET imaging experiments were performed in buffer containing 50 mM Tris pH7.5, 100 mM NaCl, and a cocktail of triplet-state quenchers and oxygen scavengers. The conformational effects of dodecameric sCD4D1D2 (sCD4D1D2-Igαtp) on wild-type and HIV-1JR-FL 201C-433C mutant Env were tested after incubation with the ligand for 30 min at 0.01 mg/ml. Histograms were fitted into three-state Gaussian curves; and occupancies of each FRET state were calculated from histogram fitting. Following Hidden Markov Modeling, all transitions were displayed in transition density plots (TDP).


Assessment of Physical Stability.


To assess the physical stability of the closed, prefusion conformation of trimeric BG505 SOSIP and 201C-433C proteins, the proteins were subjected to a variety of pharmaceutically relevant stresses such as extreme pH, high temperature, low and high osmolarity, as well as repeated freeze/thaw cycles. The physical stability of treated BG505 SOSIP and 201C-433C proteins was evaluated by measuring the retention of binding to the quaternary-specific V1V2-directed antibodies CAP256-VRC26.09 and PGT145 and induction of binding to the V3-loop antibody 447.52D and the CD4i antibody 17b which is not observed in the closed prefusion conformation of the SOSIP trimer. The retention of binding to CD4-Ig and VRC01 was also measured. In the pH treatment experiments, HIV-1 proteins were prepared at an initial concentration of 125 μg/ml, and pH was adjusted using either pH 3.5 or pH 10 with 0.5 M citrate, pH 2.8 or 1 M CAPS, pH 10.5 buffer respectively and incubated at room temperature for 60 minutes before returning the pH to pH 7.5 using 1 M Tris, pH 8.5 or 1 M Tris, pH 7.0, respectively. In the temperature treatment experiments, HIV-1 proteins at 125 μg/ml concentration were incubated at 50° C., 70° C. and 90° C. for 60 minutes in PCR cyclers with heated lids to prevent evaporation and ramp rates of 2.5° C./s. To assess antigenic characteristics following extremes of low and high osmolarity, spin desalting columns (Thermo Scientific) were used to buffer exchange the proteins into either 5 mM Tris, pH 7.5, 10 mM NaCl or 3 M MgCl2, pH 7.5. Proteins were incubated at room temperature for 60 minutes before buffer exchange into 1×PBS, pH 7.4 and concentrating the sample to 125 μg/ml concentration. The freeze/thaw treatment was carried out by repeatedly flash freezing protein in liquid nitrogen and thawing at 37° C. ten times. All protein solutions were supplemented with 0.2% BSA for a final HIV-1 protein concentration of 100 μg/ml and antibody binding measurements were carried out using a fortéBio Octet HTX instrument. Assays were performed at 30° C. with agitation set to 1000 rpm in tilted black 384-well plates (Geiger Bio-One) and a volume of 50 μl/well. Anti-human Fc probes were loaded with full-length IgG of the antibodies mentioned above at 50 μg/ml in PBS buffer for 180 seconds, which were then equilibrated for 240 seconds in PBS+0.2% BSA before being used to immobilize treated or untreated BG505 SOSIP and 201C-433C proteins for 300 seconds. Parallel measurements of antibody binding to PBS+0.2% BSA and soluble recombinant Influenza hemagglutinin in PBS+0.2% BSA were used to assess systematic baseline drift and non-specific binding. The fractional degree of retention of quaternary structure integrity is reported as the ratio of steady state binding level before and after stress treatment. To assess the physical stability of the closed, prefusion conformation of trimeric BG505 SOSIP, A433P and 201C-433C proteins over time, we incubated a 40 nM solution of each trimer in HBS-EP+ buffer at 4 different temperatures—4° C., 20° C., 37° C. and 42° C. Aliquots were taken at different time points over the course of 10 days, and retention of quaternary structure in the trimers was assessed by SPR by flowing over antibody VRC26.09 captured on an Fc surface. A parallel lane with 2G12 captured on it served as control for equal protein loading. Blank subtractions were carried out as described in the SPR section above. The fractional degree of retention of quaternary structure integrity is reported as the ratio of steady state binding level before and after incubation.


Virus-Like Particles ELISAs.


ELISAs were performed as described previously49. Briefly, Immulon II plates were coated overnight at 4° C. with VLPs at 20 times their concentration in transfection supernatants. Wells were washed with PBS and then blocked with 4% bovine serum albumin/10% fetal bovine serum in PBS. Various biotinylated monoclonal antibodies (biotinylated using sulfo-NHSXbiotin, Thermo), and CD4-IgG2 were then titrated in the presence or absence of a fixed concentration of 2 μg/ml soluble CD4. Alkaline phosphatase conjugated to streptavidin (Vector Laboratories, Burlingame, Calif.; to detect biotinylated mAbs) or anti-Fc (Accurate, Westbury, N.Y.; to detect CD4-IgG2) and SigmaFAST p-nitrophenyl phosphate tablets (Sigma) were then used to detect binding. Plates were read at 405 nm.


Figures.


Structure figures were prepared using PYMOL50.


Coordinates.


The atomic coordinates of an asymmetric unit of the crystal structure of the unliganded trimeric HIV-1 Env ectodomain in the prefusion mature closed conformation are recited in Table 3 submitted as an ASCII text named “Table_3.txt” (˜0.7 MB, created on Aug. 7, 2014) in U.S. Provisional Application No. 62/046,059, filed Sep. 4, 2014, and have been deposited with the Protein Data Bank as Acc. No. 47MJ. The atomic coordinates of the crystal structure of an unliganded trimeric HIV-1 Env ectodomain in the prefusion mature closed conformation are recited in Table 4 submitted as an ASCII text named “Table_4.txt” (˜2 MB, created on Aug. 7, 2014) in U.S. Provisional Application No. 62/046,059, filed Sep. 4, 2014.


Example 3
Production of HIV-1 Env Protein Covalently Linked to Antibody

This example provides an exemplary protocol for producing a recombinant HIV-1 Env protein covalently linked to a broadly neutralizing antibody.


HIV-1 Env expression construct were designed to contain a cysteine mutation at a key complementary site at the antibody complex interface and a protease cleavable Streptactin II tag C-terminal of the HIV-1 Env residue 664. The respective antibodies were mutated to contain a cysteine at a key complementary site at the antibody complex interface and the antibody heavy chain had a C-terminal cleavable His6 tag after the Fab region. In the case of covalently linking VRC01 to HIV-1 gp140 trimer, mutations 459C in HIV-1 Env and 60C in VRC01 heavy chain enabled covalent assembly of the complex within the producer cells.


DNA for the HIV-1 Env, antibody heavy, antibody light and furin were mixed together in a molar ratio of approximately 1:0.25:0.25:0.5 and transfected into suspension HEK 293F cells. 7 days post transfection the supernatants were harvested, clarified and filtered. The media was passed through NiNTA resin and after washing with PBS eluted in 250 mM imidazole. The eluate was passed over a 2 ml streptactin column, washed with 5 ml wash buffer and eluted in 3 ml elution buffer using the manufacturer's buffer formulations. The resulting eluate was concentrated to 1.5 ml and passed through a Superdex S200 gel filtration column equilibrated in phosphate buffered saline and the main peak containing the covalently linked complex was verified to contain the intermolecular disulfide bond by reducing and non-reducing SDS-PAGE. Fractions corresponding to the covalently linked antibody-Env complex were pooled and flash frozen in liquid nitrogen and stored at −80C.


Example 4
Single Chain HIV-1 Env Proteins

HIV-1-Env constructs from various strains were synthesized and include the “SOS” mutations (A501C, T605C), the isoleucine to proline mutation at residue 559 (I559P), and the glycan site at residue 332 (T332N); mutating the gp120/gp41 cleavage site to a ten-amino-acid linker; and truncating the C terminus to residue 664 (all HIV-1 Env numbering according to the HXB2 nomenclature). This construct in the case of the BG505 strain is referred to as bC10ln.


The bC10ln construct was transfected in HEK 293 F cells using 1 mg plasmid DNA and transfection supernatants were harvested after 7 days, and passed over either a 2G12 antibody- or VRC01 antibody-affinity column. After washing with PBS, bound proteins were eluted with 3M MgCl2, 10 mM Tris pH 8.0. The eluate was concentrated to less than 5 ml using a Centricon-70 and applied to a Superdex 200 column, equilibrated in phosphate buffered saline. The peak corresponding to trimeric HIV-1 Env was identified, pooled, and concentrated or flash-frozen in liquid nitrogen and stored at −80° C.


Constructs such as bC10ln were also designed with a C-terminal Thrombin cleavage site, His6-tag, Streptactin II tag to enable purification as described in McLellan et al. Science 340, 1113-1117, 2013. Briefly, supernatants were harvested after 7 days, and passed over NiNTA affinity column. After washing with PBS, bound proteins were eluted with 250 mM imidazole. The eluate was concentrated to less than 3 ml using a Centricon-70 and applied to a 2 ml Streptactin column, equilibrated in phosphate buffered saline. The sample was eluted in 8 ml of elution buffer. The eluate was concentrated to less than 5 ml using a Centricon-70 and applied to a Superdex 200 column, equilibrated in phosphate buffered saline. The peak corresponding to trimeric HIV-1 Env was identified, pooled, and concentrated or flash-frozen in liquid nitrogen and stored at −80° C.


Example 5
Chimeric HIV-1 Env Proteins

This example describes the design and production of chimeric HIV-1 Env immunogens based on diverse HIV-1 strains. In the context of inducing an immune response in a subject that can control infection across multiple HIV-1 strains, the use of immunogens based on diverse HIV-1 strains can overcome the intrinsic sequence diversity of HIV-1 Env.


The structural data provided in the prior Examples illustrates that the HIV-1 Env ectodomain in the prefusion mature closed conformation includes a “base” or “platform” including three gp41 molecules, each of which wrap their hydrophobic core around the extended N- and C-termini-strands of gp120 (see, e.g., FIGS. 45-46). Accordingly, chimeric HIV-1 Env ectodomains were designed with N- and C-terminal regions of gp120 and the gp41 ectodomain from a first HIV-1 strain, and the remainder of gp120 from a second HIV-1 strain. As illustrated in FIGS. 45-46, these chimeric HIV-1 Env proteins allow for a gp41 “platform” on which a chimeric gp120 sequence can be presented to the immune system. The variable gp120 molecule sits on top of a gp41 from the BG505 strain (with SOSIP substitutions), with the N- and C-terminal regions of gp120 also from the BG505 strain. As shown in red in FIG. 47, the N- and C-terminal regions of gp120 can include all or part of the β-4 strand, the β-3 strand, the β26 strand, the β25 strand and/or the α5 helix.


The interface between the gp41 and gp120 proteins in the HIV-1 Env trimer includes gp120 residues 46-54, 70-75, 84-89, 99, 102, 106, 107, 114, 215, 220-224, 226, 244, 471-473, and 476-477 (“Interface Residue set A”). In FIG. 47, these residues are shaded light blue. Accordingly, additional chimeric HIV-1 Env ectodomains were designed with N- and C-terminal regions of gp120, Interface Residue Set A, and the gp41 ectodomain from a first HIV-1 strain, and the remainder of gp120 from a second HIV-1 strain (these chimeras include reference to “Interface Residue Set A” in columns 6 or 7 of the tables in Table 13). These chimeric HIV-1 Env ectodomains include an expanded “platform” on which a chimeric gp120 sequence can be presented to the immune system.


A chimeric HIV-1-Env construct was synthesized that includes gp120 residues 31-45 and 478-507, and gp41 residues 512-664 from the BG505 strain with SOSIP and 332N substitutions (e.g., as set forth as SEQ ID NO: 3), and the remainder of the gp120 residues (46-477) from the 3301_V1_C24 HIV-1 strain (SEQ ID NO: 751), which is a clade C virus. The protease cleavage site separating gp120/gp41 was mutated to include six arginine residues, and the C-terminus of gp41 was set at position 664 (all HIV-1 Env numbering according to the HXB2 nomenclature). The amino acid sequence of the resulting chimeric Env protein is provided as SEQ ID NO: 384 (3301_V1_C24_bg505-NCgp120+gp41.SOSIP). Additional variants were designed and produced, including a chimeric HIV-1 Env ectodomain trimer having gp41, and gp120 N- and C-terminal region sequences from the BG505 strain (with SOSIP substitutions), with the remaining gp120 sequence from the ZM53, or 25925-2.22 strains. The corresponding chimeric proteins were termed ZM53_BG505-NCgp120_gp41.SOSIP (SEQ ID NO: 386), 25925-2.22_BG505-NCgp120_gp41.SOSIP (SEQ ID NO: 383), and 3301_V1_C24_BG505-NCgp120+gp41.SOSIP (SEQ ID NO: 384). Expression and purification was performed as described in Examples 1 and 2 above.


A further variant was produced, SEQ ID NO: 382 (CNE58_SU-strandC_bg505-NCgp120+gp41.SOSIP) that includes gp41 and gp120 N- and C-terminal regions (31-45 and 478-507, respectively) from BG505.SOSIP.664, with residues 166-173 (V1V2 strand C) from CAP256 SU, and the rest of gp120 from the CNE58 strain. DNA constructs encoding the chimeric Env proteins were transfected in HEK 293 F cells using 1 mg plasmid DNA and 250 μg plasmid encoding Furin as described previously (Sanders, PLoS pathogens 9, e1003618, 2013, incorporated by reference herein). Transfection supernatants were harvested after 7 days, and constructs that ended at residue 664 were purified using a GNA-Lectin affinity column as described in Pejchal et al., Science, 334: 1097-1103, 2011, incorporated by reference herein. Briefly, supernatants were passed over the GNA-lectin-affinity column and after washing with PBS, bound proteins were eluted with 1 M methyl α-D-mannoside. The eluate was concentrated to less than 5 ml using a Centricon-70 and applied to a Superdex 200 column, equilibrated in phosphate buffered saline. The peak corresponding to trimeric HIV-1 Env was identified, pooled, and concentrated or flash-frozen in liquid nitrogen and stored at −80° C.


Constructs were also designed with a C-terminal Thrombin cleavage site, His6-tag, Streptactin II tag to enable purification as described in McLellan et al. Science 340, 1113-1117, 2013. Briefly, supernatants were harvested after 7 days, and passed over NiNTA affinity column. After washing with PBS, bound proteins were eluted with 250 mM imidazole. The eluate was concentrated to less than 3 ml using a Centricon-70 and applied to a 2 ml Streptactin column, equilibrated in phosphate buffered saline. The sample was eluted in 8 ml of elution buffer. The eluate was concentrated to less than 5 ml using a Centricon-70 and applied to a Superdex 200 column, equilibrated in phosphate buffered saline. The peak corresponding to trimeric HIV-1 Env was identified, pooled, and concentrated or flash-frozen in liquid nitrogen and stored at −80° C.


The 3301_V1_C24_bg505-NCgp120+gp41.SOSIP and ZM53_BG505-NCgp120_gp41.SOSIP chimeras had nearly full gp120/gp41 cleavage, as shown by SDS-page (FIG. 48, left). Further, these chimeras eluted from the purification column in trimeric form under a single peak (FIG. 48, right). The antigenicity of the 3301_V1_C24_bg505-NCgp120+gp41.SOSIP, ZM53_BG505-NCgp120_gp41.SOSIP, 25925-2.22_BG505-NCgp120_gp41.SOSIP, and 3301_V1_C24_BG505-NCgp120+gp41.SOSIP chimeric HIV-1 Env trimers was interrogated using Meso Scale Discovery multi-array electro-chemiluminescence (FIG. 49). As illustrated in FIG. 49, the chimeras specifically bound to quaternary specific antibodies, but not to non- or poorly-neutralizing antibodies.


Additional variants were designed and produced, including a chimeric HIV-1 Env including a BG505 gp120 sequence with SOSIP substitutions, and a CAP45 gp41 sequence. The sequence of this chimera is provided as SEQ ID NO: 772. Structural analysis of the gp120 and gp41 contacts confirm that there is minimal disruption between the gp120-gp41 interface when substituting this strain. The BG505.SOSIP/CAP45 chimera had nearly full gp120/gp41 cleavage, as shown by SDS-page (FIG. 50, left). Further, antigenic analysis by ELISA confirmed that this chimera specifically bound to quaternary specific antibodies, but not to non- or poorly-neutralizing antibodies (FIG. 50, right).


The neutralization profile of several neutralizing and non-neutralizing antibodies was compared with the antigenic profile of a chimeric HIV-1 Env ectodomain based on the native DU156 virus. As shown in FIG. 51, the neutralization profile correlates with the antigenic profile, particularly for the chimeric HIV-1 Env ectodomain including the 201C/433C substitutions.


Many additional chimeric HIV-1 Env ectodomain proteins were designed and produced, including those provided as SEQ ID NOs: 379-386, 579-595, 764-772, 856-1056, 1077-1098, and 1114-1200. The details of the design of each of these chimeric Env proteins are provided in Table 13. Additional recombinant HIV-1 Env ectodomains including stabilizing substitutions and based on more HIV-1 strains were also produced, including those provided as SEQ ID NOs: 1057-1077. The recombinant HIV-1 Env ectodomains were expressed in cells and the corresponding antigenic characteristics of each ectodomain was evaluated by bind antibody binding assay.


Binding to several different antibodies was assayed to evaluate the antigenic profile of each the recombinant HIV-1 Env proteins (FIGS. 44 and 53). The antibodies tested included VRC26 and PGT145 (which bind V1V2 specific epitopes present on the prefusion mature closed conformation of HIV-1 Env), F105 (which binds an epitope that is not present on the prefusion mature closed conformation of HIV-1 Env), 17b (which binds a CD4-induced epitope) in the presence or absence of sCD4, PGT151 and 35O22 (which bind conformational epitopes including gp120 and gp41 residues of HIV-1 Env in its prefusion mature conformation), PGT122 (which binds a conformation epitope including V1V2 and V3-glycan residues), 447-52D (which binds a V3-loop epitope), and VRC01 (which binds the CD4 binding site).



FIG. 53 shows the antigenic readout of many chimeric HIV-1 Env ectodomains, each of which was stabilized in a prefusion mature conformation using the SOSIP substitutions and a 201C-433C disulfide bond. The antigenicity assays show that all of the recombinant HIV-1 Env proteins tested exhibited little to no binding to the 17b antibody, even in the presence of a molar excess of soluble CD4. This finding illustrates the effectiveness of this mutation (201C-433C) for stabilizing the HIV-1 Env ectodomain in a conformation that is resistant to CD4-induced change.


Additionally, bioinformatics algorithms were used to identify chimeric HIV-1 Env ectodomains that exhibited relatively strong binding to quaternary-specific antibodies (e.g., VRC26) and relatively weak binding to weakly neutralizing antibodies (e.g., F105). Based on these algorithms, several chimeras of particular interest were identified, including the following:


DU422.01-chim_d7324.201C-433C (SEQ ID NO: 964)


ZM106.9-chim_d7324.201C-433C (SEQ ID NO: 1025)


CH038.12-chim_d7324.201C-433C (SEQ ID NO: 938)


16055-2.3-chim_d7324.201C-433C (SEQ ID NO: 872)


ZM55.28a-chim_d7324.201C-433C (SEQ ID NO: 1098)


CH117.4-chim_d7324.201C-433C (SEQ ID NO: 940)


ZM53.12-chim_d7324.201C-433C (SEQ ID NO: 1034)


25925-2.22-chim_d7324.201C-433C (SEQ ID NO: 881)


BI369.9A-chim_d7324.201C-433C (SEQ ID NO: 924)


3301.V1.C24-chim_d7324.201C-433C (SEQ ID NO: 888)


CAP45.G3-chim_d7324.201C-433C (SEQ ID NO: 937)


C1080.c3-chim_d7324.201C-433C (SEQ ID NO: 930)


286.36-chim_d7324.201C-433C (SEQ ID NO: 856)


MW965.26-chim_d7324.201C-433C (SEQ ID NO: 978)


CNE55-chim_d7324.201C-433C (SEQ ID NO: 953)


C4118.09-chim_d7324.201C-433C (SEQ ID NO: 933)


DU156.12-chim_d7324.201C-433C (SEQ ID NO: 962)


TH966.8-chim_d7324.201C-433C (SEQ ID NO: 1010)


6545.V4.C1-chim_d7324.201C-433C (SEQ ID NO: 908)


620345.c1-chim_d7324.201C-433C (SEQ ID NO: 902)


0921.V2.C14-chim_d7324.201C-433C (SEQ ID NO: 871)


AC10.29-chim_d7324.201C-433C (SEQ ID NO: 917)


QH209.14M.A2-chim_d7324.201C-433C (SEQ ID NO: 990)


MB201.A1-chim_d7324.201C-433C (SEQ ID NO: 973)


These chimeras include gp120 sequences from several different HIV-1 subtypes, including subtype A (BI369.9A, MB201.A1, QH209.14M.A2), subtype B (AC10.29), subtype C (0921.V2.C14, 16055-2.3, 25925-2.22, 286.36, CAP45.G3, DU156.12, DU422.01, MW965.26, ZM53.12, ZM55.28a, ZM106.9), subtype CRF AC (3301.V1.C24, 6545.V4.C1), subtype CFR AE (620345.c1, C1080.c3, C4118.09, CNE55, TH966.8) and subtype CRF BC (CH038.12, CH117.4). Thus, these results demonstrate that the strategies for stabilizing chimeric HIV-1 Env ectodomains in the prefusion mature closed conformation disclosed herein can be applied across a diverse array of HIV-1 strains.


Based on the antigenic characteristics of the assayed chimeras, additional chimeric HIV-1 Env ectodomains were constructed. By comparing the sequences for assayed chimeras with good antigenic characteristics (e.g., strong binding to VRC26 and low binding to F105) to chimeras with poor antigenic characteristics (e.g., low binding to VRC26 and strong binding to F105), residue positions within gp120 that had different amino acid composition in the former vs. the latter set of chimeras were identified using bioinformatics algorithms. In a non-limiting embodiment, such residue positions included Residue Set B (SEQ 1114-1142): 133-134, 164, 169, 308, and 316 from BG505. In another non-limiting embodiment, such residue positions included the expanded set Residue Set C (SEQ 1143-1171: 49, 133-134, 149-152, 164, 169, 188, 190, 211, 223, 252, 281, 293, 308, 316, 336, 340, 352, 360, 362-363, 369, 372, 393, 410, 432, 442, 444, 446, 474, and 476 from BG505. In another non-limiting embodiment, such residue positions included the expanded set Residue Set C+Residue Set D (SEQ 1172-1200): 46, 60, 62-63, 84-85, 87, 99, 102, 130, 132, 135, 153, 158, 160-161, 165-167, 171-173, 175, 177-178, 181, 184-185, 189, 202, 232, 234, 236, 240, 268-271,275, 277, 287, 289, 292, 295, 297, 305, 315, 317, 319, 322, 328, 330, 332-335, 337, 339, 343-347, 350-351, 357, 371, 375, 379, 387, 389, 394, 411, 412-413, 415, 424, 426, 429, 440, 460-461, 465, 475, and 477 from BG505.


Example 6
Protein Nanoparticles Including Recombinant HIV-1 Env Proteins

This example provides an exemplary protocol for producing a protein nanoparticle including a recombinant HIV-1 Env protein that is stabilized in a prefusion mature conformation.


BG505 SOSIP.664 linked to nanoparticles (e.g. Ferritin) was cotransfected with furin in HEK 293 S GnTI−/− cells using 500 μgs plasmid DNA and 125 μgs of furin. Transfection supernatants were harvested after 7 days, and passed over either a 2G12 antibody- or VRC01 antibody-affinity column. After washing with PBS, bound proteins were eluted with 3M MgCl2, 10 mM Tris pH 8.0. The eluate was concentrated to less than 5 ml with Centricon-70 and applied to a Superdex 200 column, equilibrated in 5 mM HEPES, pH 7.5, 150 mM NaCl, 0.02% azide. The peak corresponding to the nanoparticle size was identified, pooled, and concentrated or flash-frozen in liquid nitrogen and stored at −80° C.


Alternatively, other methods as described in Kanekiyo et al., Nature, 499, 102-106, 2013, incorporated by reference herein, can be used to purify nanoparticles including recombinant HIV-1 Env proteins.


Example 7
Immunization of Animals

This example describes exemplary procedures for the immunization of animals with the disclosed immunogens, and measurement of the corresponding immune response.


In some examples nucleic acid molecules encoding the disclosed immunogens are cloned into expression vector CMV/R. Expression vectors are then transfected into 293F cells using 293Fectin (Invitrogen, Carlsbad, Calif.). Seven days after transfection, cell culture supernatant is harvested and passed over either a 2G12 antibody- or VRC01 antibody-affinity column. After washing with PBS, bound proteins were eluted with 3M MgCl2, 10 mM Tris pH 8.0. The eluate was concentrated to less than 5 ml with Centricon-70 and applied to a Superdex 200 column, equilibrated in 5 mM HEPES, pH 7.5, 150 mM NaCl, 0.02% azide. The peak corresponding to trimeric HIV-1 Env was identified, pooled, and concentrated or flash-frozen in liquid nitrogen and stored at −80° C. Some proteins are purified using HiTrap IMAC HP Column (GE, Piscataway, N.J.), and subsequent gel-filtration using SUPERDEX™ 200 (GE). In some examples the 6×His tag is cleaved off using 3C protease (Novagen, Madison, Wis.).


For vaccinations with the disclosed immunogens 4-6 months old guinea pigs (Strain Hartley)(Charles River Laboratories, MA) are immunized using polyIC (High molecular weight, InvivoGen Inc, CA) as the adjuvant. Specifically, four guinea pigs in each group are vaccinated with 25 μg of protein and 100 μg of polyIC in 400 μl intramuscularly (both legs, 200 μl each leg) for example at week 0, 4, 8, 12, 22. Sera are collected for example at week 2 (Post-1), 6 (Post-2), 10 (Post-3), 14 (Post-4) and 24 (Post-5), and subsequently analyzed for their neutralization activities against a panel of HIV-1 strains, and the profile of antibodies that mediate the neutralization.


The immunogens are also used to probe for guinea pig anti-sera for existence of HIV-1 neutralizing antibodies in the anti-sera, such as antibodies that compete for binding to the recombinant HIV-1 Env ectodomain trimer with PGT122, PGT145, PGT151, and/or VRC26.


Example 8
Immunization of Non-Human Primates

This example describes exemplary procedures for the immunization of non-human primates with the disclosed immunogens, and measurement of the corresponding immune response.


In some examples nucleic acid molecules encoding the disclosed immunogens are cloned into expression vector CMV/R. Expression vectors are then transfected into 293F cells using 293Fectin (Invitrogen, Carlsbad, Calif.). Seven days after transfection, cell culture supernatant is harvested and passed over either a 2G12 antibody- or VRC01 antibody-affinity column. After washing with PBS, bound proteins were eluted with 3M MgCl2, 10 mM Tris pH 8.0. The eluate was concentrated to less than 5 ml with Centricon-70 and applied to a Superdex 200 column, equilibrated in 5 mM HEPES, pH 7.5, 150 mM NaCl, 0.02% azide. The peak corresponding to trimeric HIV-1 Env was identified, pooled, and concentrated or flash-frozen in liquid nitrogen and stored at −80° C. Some proteins are purified using HiTrap IMAC HP Column (GE, Piscataway, N.J.), and subsequent gel-filtration using SUPERDEX™ 200 (GE). In some examples the 6×His tag is cleaved off using 3C protease (Novagen, Madison, Wis.).


For vaccinations with the disclosed immunogens, Indian origin Rhesus Macaque (bodyweights more than 2 kg) are immunized with polyIC-LC as the adjuvant. Specifically, five monkeys in each group are vaccinated with 100 μg of protein and 500 μg polyIC-LC in 1 ml intramuscularly in the Quadriceps muscle for example at week 0, 4, 20. Sera are collected for example at week 2 (Post-1), 6 (Post-2), 24 (Post-3), and subsequently analyzed for their neutralization activities against a panel of HIV-1 strains, and the profile of antibodies that mediate the neutralization.


The immunogens are also used to probe for Rhesus Macaque anti-sera for existence of HIV-1 neutralizing antibodies in the anti-sera, such as antibodies that compete for binding to the recombinant HIV-1 Env ectodomain trimer with PGT122, PGT145, PGT151, and/or VRC26.


Example 9
Assaying Serum Neutralization Activity

Following immunization with a disclosed immunogen (e.g., as described above) serum can be collected at appropriate time points, frozen, and stored for neutralization testing. The serum neutralization activity can be assayed using various assays, such as a pseudoviruses neutralization assay.


In some embodiments, the serum neutralization activity can be assayed essentially as previously described (see, e.g., Georgiev et al., Science, 340, 751-756, 2013, which is incorporated by reference herein in its entirety). Briefly, frozen serum from the immunized subject is heat-inactivated at 56° C. for 30 min prior to the assay. Pseudovirus stocks are prepared by co-transfection of 293T cells with an HIV-1 Env-deficient backbone and an expression plasmid for the Env gene of interest. The serum to be assayed is diluted in Dulbecco's modified Eagle medium-10% FCS (Gibco) and mixed with pseudovirus. After 30 min, 10,000 TZM-bl cells are added, and the plates are incubated for 48 hours. Assays are developed with a luciferase assay system (Promega, Madison, Wis.), and the relative light units (RLU) are read on a luminometer (Perkin-Elmer, Waltham, Mass.). The percent neutralization is calculated as follows: % neutralization=100×(V0−Vn)/Vo, where Vn is the RLU in the virus and antibody wells and V0 is the RLU in the virus-only wells. The reciprocal dilution at which 50% of the virus is neutralized (ID50) is computed for each virus-serum pair. To account for background, a cutoff of ID50>=40 is used as a criterion for the presence of serum neutralization activity against a given virus.


Standard panels of Env proteins from selected HIV-1 strains have been developed for co-expression with the Env-deficient backbone in the neutralization assay (see, e.g., Georgiev et al., Science, 340, 751-756, 2013, incorporated by reference herein). For example, the standard panel can include Env proteins from HIV-1 strains from Clade A (KER2018.11, Q23.17, Q168.a2, Q769.h5, and RW020.2), Clade B (BaL.01, 6101.10, BG1168.01, CAAN.A2, JR-FL, JR-CSF.JB, PVO.4, THRO4156.18, TRJO4551.58, TRO.11, and YU2), and Clade C (DU156.12, DU422.01, ZA012.29, ZM55.28a, and ZM106.9). An additional standard panel is provided in Table S5 of Georgiev et al. (Science, 340, 751-756, 2013, which is incorporated by reference herein in its entirety) and Table 1 of Seaman et al., J. Virol., 84, 1439-1452, 2005, which is incorporated by reference herein in its entirety).


Example 10
Treatment of Subjects

This example describes methods that can be used to treat a subject that has or is at risk of having an infection from HIV-1 that can be treated by eliciting an immune response, such as a neutralizing antibody response to HIV-1. In particular examples, the method includes screening a subject having, thought to have or at risk of having a HIV-1 infection. Subjects of an unknown infection status can be examined to determine if they have an infection, for example using serological tests, physical examination, enzyme-linked immunosorbent assay (ELISA), radiological screening or other diagnostic technique known to those of skill in the art. In some examples, subjects are screened to identify a HIV-1 infection, with a serological test, or with a nucleic acid probe specific for a HIV-1. Subjects found to (or known to) have a HIV-1 infection can be administered a disclosed immunogen (such as a recombinant HIV-1 Env stabilized in a prefusion mature closed conformation) that can elicit an antibody response to HIV. Subjects may also be selected who are at risk of developing HIV, such as subjects exposed to HIV.


Subjects selected for treatment can be administered a therapeutic amount of a disclosed immunogen as disclosed herein. For example, a disclosed HIV-1 Env protein stabilized in a prefusion mature closed conformation can be administered at doses of 0.5 μg/kg body weight to about 1 mg/kg body weight per dose, such as 1 μg/kg body weight-100 μg/kg body weight per dose, 100 μg/kg body weight-500 μg/kg body weight per dose, or 500 μg/kg body weight-1000 μg/kg body weight per dose. However, the particular dose can be determined by a skilled clinician. The immunogen can be administered in one or several doses, for example in a prime-boost vaccination. The mode of administration can be any used in the art. The amount of agent administered to the subject can be determined by a clinician, and may depend on the particular subject treated. Specific exemplary amounts are provided herein (but the disclosure is not limited to such doses).


Example 11
Inducing a Neutralizing Immune Response in an Animal Model

This example provides data showing that a HIV-1 Env ectodomain trimer stabilized in the prefusion mature conformation can induce a neutralizing immune response in multiple animal models.


Two months old Hartley guinea pigs (four animals per study group) or New Zealand white rabbits (five animals per study group) were immunized at weeks 0, 4, and 16, as follows: Guinea pigs


1) BG505 SOSIP (25 μg) and polyIC (100 μg) as adjuvant


2) BG505 SOSIP DS (25 μg) and polyIC (100 μg) as adjuvant


3) BG505 SOSIP (25 μg) and Matrix M (25 μg) as adjuvant


4) BG505 SOSIP DS (25 μg) and Matrix M (25 μg) as adjuvant Rabbits


1) BG505 SOSIP (30 μg) and Matrix M (30 μg) as adjuvant


2) BG505 SOSIP DS (30 μg) and Matrix M (30 μg) as adjuvant


Serum collected from immunized rabbits (FIG. 54A) or guinea pigs (FIG. 54B) was assayed for binding to BG505.SOSIP trimer and a V3 peptide. The immunization groups elicited comparable anti-BG505 trimer or anti-V3 peptide antibodies in rabbits (p<0.05, week 18, Mann Whitney t-test).


Serum collected at weeks 6 and 18 was also tested for neutralization activity against a panel of HIV-1 strains (FIG. 55). Sera from immunized animals were assessed for virus neutralization using a single round infection assay of TZM-bl cells to determine IC50 values. As shown in FIG. 55, the BG505 SOSIP DS immunogen elicited an immune response that neutralized both autologous virus (BG505.W6M.C2.T332N) and V3 directed tier 1 virus (MW965.26) infection, as measured by IC value. As expected because rabbits and guinea pigs do not express CD4, the neutralization activity of sera from BG505 SOSIP DS and BG505 SOSIP immunized animals was similar.


Methods

Immunogen Preparation.


HIV-1 Env trimer preparation was performed substantially as described in Example 2. The BG505.SOSIP.664 HIV-1 Env ectodomain trimer (SEQ ID NO: 3) or the BG505.SOSIP.664.201C-433C HIV-1 Env ectodomain trimer (SEQ ID NO: 26) were used. Trimers were purified by affinity chromatography over a VRC01 column, purified by gel filtration over a Superdex 200 16/60 (GE Healthcare) column in buffer containing 5 mM HEPES 7.5, 150 mM NaCl, and 0.02% NaN3, and finally, passed through a 447-52D column to remove aberrant trimer species (as described in Example 2 and illustrated in FIG. 36). The materials used for immunization were tested using Meso-Scale Discovery-Electrochemiluminescence Immunoassay (MSD-ECLIA) Analysis as described in Example 2 to confirm antigenic properties (binding to broadly neutralizing antibodies).


Immunizations.


Guinea pig injections consisted of 25 μg of Env trimer formulated in a 400 ul volume in PBS, with 100 μg of PolylC adjuvant (HMW, Invivogen) or 25 μg Matrix M (Novavax; see Reimer et al., PLoS One, 7(7):e41451, 2012). For rabbit studies, 30 μg of Env trimer was formulated with 30 μg Matrix M in a 1 ml volume in PBS. The immunization was administered intramuscularly as two separate injections into each quadriceps. PolylC adjuvant was prepared by making a 2 mg/ml stock solution in saline, heating the necessary amount for 10 min at 70° C., and cooling at room temperature for 1 hour prior to injection. Immunizations were performed on weeks 0, 4, and 16. Blood draws for immune assessment included a prebleed −1 week sample, followed by blood draws 2 weeks after each immunization. Collected sera were heat inactivated for 1 hour at 56° C. before being analyzed.


Enzyme-Linked Immunosorbent Assays (ELISAs) for Anti-V3 Peptide Responses.


96 well plates (Reacti-Bind®, Pierce) were coated with 100 μl/well of 2 μg/ml peptide in PBS overnight at 4° C. (MW965.26 V3 peptide: TRPNNNTRKSIRIGPGQTFYATG (residues 265-287 of SEQ ID NO: 2); BG505 V3 peptide: TRPNNNTRKSIRIGPGQAFYATG (residues 296-318 of SEQ ID NO: 2), amino acid difference underlined). For each consecutive step following coating, plates were washed 5 times with PBS-T (PBS+0.05% tween) and incubated at 37° C. for 1 hour. After coating, plates were blocked with 200 μl/well of blocking buffer (B3T: 150 mM NaCl, 50 mM Tris-HCl, 1 mM EDTA, 3.3% fetal bovine serum, 2% bovine albumin, 0.07% Tween 20, 0.02% thimerosal). Next, guinea pig sera was diluted in B3T and added in 5-fold serial dilutions to the plates. Then goat anti-guinea pig antibody conjugated with horseradish peroxidase (KPL, Gaithersburg, Md.,) at a 1:10,000 dilution in B3T was added to each well. TMB substrate (SureBlue™, KPL, Gaithersburg, Md., cat #52-00-03) was used to develop plates for 10 minutes before 1N sulfuric acid was added to stop the reaction without washing beforehand. Plates were read at 450 nm (Molecular Devices, SpectraMax using SoftMax Pro 5 software) and the final optical density was determined after the horseradish peroxidase nonspecific background binding was subtracted.


D7324—Capture Enzyme Linked Immunosorbent Assays (ELISAs) for Anti-BG505 Envelope Trimer Responses.


96 well plates (Reacti-Bind®, Pierce) were coated with 100 μl/well of 2 μg/ml of anti-D7324 antibody (Aalto Bioreagents, Dublin, Ireland) in PBS overnight at 4 degrees Celsius. After coating, plates were blocked for 1 hour at room temperature with PBS+5% skim milk (Difco, Bectin, Dickinson and Company). Plates were then washed five times with PBS-T (PBS+0.2% tween-20) before adding 0.5 μg/ml of BG505 SOSIP.664-D7324 trimer diluted in PBS+10% FBS for two hours at room temperature. After the addition of the trimer, subsequent procedures mimic the anti-V3 ELISAs except dilutions were made in PBS-T instead of B3T.


HIV-1 Neutralization Assays.


Sera from immunized animals were assessed for virus neutralization using previously described methods (Li et al., J. Virol., 79, 10108-10125, 2005). In the single round infection assay, a reduction in a luciferase luminescence indicates neutralization activity. Target cells were TZM-bl cells, which are a clonal HeLa cell line expressing CD4, CXCR4 and CCR5. Upon infection, the HIV-1 viral protein Tat induces a luciferase reporter gene, whose expression is measured as relative light units. Data are represented as the inhibitory reciprocal dilutions of sera required to inhibit either 50% of infection (IC50), calculated using a regression fit as previously described.


Example 12
Membrane Anchored HIV-1 Env Ectodomain Trimers

This example illustrates production and antigenicity of exemplary HIV-1 Env ectodomain trimers stabilized in a prefusion mature closed conformation that include a transmembrane domain for anchoring to the cell surface.


Numerous HIV-1 Env ectodomain trimers stabilized in a prefusion mature closed conformation were linked to a transmembrane domain and expressed in cells for anchoring to the cell membrane, as listed below. Variation within the membrane anchored sequences includes strain (including chimeras), single chain or not (e.g., sc15ln (15 A.A. linker between gp120/gp41), sc10ln (10 A.A. linker between gp120/gp41)), stabilizing mutations (e.g., SOS, DS, IP, or combinations thereof), linker between position 664 and the TM domain (e.g., MPER sequence, or 10ln (10 A.A. linker)), TM domain (e.g, HA or HIV-1 TM), and presence or absence of a cytoplasmic tail. Exemplary constructs are listed below


TH966.8-chim_sc10ln-IP-10ln-HA™ (SEQ ID NO: 1765)


6545.V4.C1-chim_sc10ln-IP-10ln-HA™ (SEQ ID NO: 1766)


R2184.c4-chim_sc10ln-IP-10ln-HA™ (SEQ ID NO: 1767)


ZM197.7-chim_sc10ln-IP-10ln-HA™ (SEQ ID NO: 1768)


ZM106.9-chim_sc10ln-IP-10ln-HA™ (SEQ ID NO: 1769)


ZM53.12-chim_sc101ln-IP-10ln-HA™ (SEQ ID NO: 1770)


R2184.c4-chim_sc10ln-IP-MPER-TM (SEQ ID NO: 1771)


CNE55-chim_sc10ln-IP-10ln-HA™ (SEQ ID NO: 1772)


6545.V4.C1-chim_sc10ln-IP-MPER-TM (SEQ ID NO: 1773)


DU422.01-chim_sc10ln-IP-10ln-HA™ (SEQ ID NO: 1774)


25925-2.22-chim_sc10ln-IP-10ln-HA™ (SEQ ID NO: 1775)


CNE58-chim_sc101ln-IP-10ln-HA™ (SEQ ID NO: 1776)


16055-2.3-chim_sc10ln-IP-10ln-HA™ (SEQ ID NO: 1777)


TH966.8-chim_sc10ln-IP-MPER-TM (SEQ ID NO: 1778)


ZM55.28a-chim_sc10ln-IP-MPER-TM (SEQ ID NO: 1779)


ZM53.12-chim_sc10ln-IP-MPER-TM (SEQ ID NO: 1780)


BI369.9A-chim_sc10ln-IP-10ln-HA™ (SEQ ID NO: 1781)


ZM197.7-chim_sc10ln-IP-MPER-TM (SEQ ID NO: 1782)


16055-2.3-chim_sc10ln-IP-MPER-TM (SEQ ID NO: 1783)


ZM55.28a-chim_sc15ln-SOS-DS-10ln-HA™ (SEQ ID NO: 1784)


A FACS-based assay was used to interrogate the antigenicity of the membrane anchored HIV-1 Env ectodomain trimers. Briefly, expression vectors encoding an immunogen of interest were transfected into cells in a 96-well format. The cells were harvested 2 or 3 days following transfection, and stained with antibodies specific for trimeric HIV-1 Env (such as VRC26, PGT145, or PGT151), non-trimer specific but broadly neutralizing antibodies (such as VRC01 or PGT128) and non-trimer specific poorly neutralizing antibodies (such as 447-52D). The cells were then stained with appropriate secondary antibody, and analyzed by FACS to assay for antigenicity and expression.



FIG. 56 lists the antigenic characteristics of the constructs listed above. The designed with the most desirable antigenic characteristics were those with a single chain HIV-1 Env ectodomain including a 10 amino acid peptide linker between gp120 and gp41, the “IP” substitution, and a 10 amino acid peptide linker or the native MPER sequence between residue 664 of gp41 and a TM domain, such as the HA™ domain or the HIV-1 Env™ domain.


Example 13
HIV-1 Env Ectodomain Trimer Immunogens Based on Ontogeny of Broadly Neutralizing Antibodies

This example illustrates chimeric HIV-1 Env ectodomain trimer immunogens stabilized in the prefusion mature closed conformation that include a V1V2 domain sequence that (1) bind to mature broadly neutralizing antibodies that target the V1V2 domain, as well as immature somatic precursors thereof, and that (2) are from a strain of HIV-1 that can be neutralized by V1V2-directed broadly neutralizing antibodies produced by multiple donors.


Antibodies capable of neutralizing a majority of circulating HIV-1 isolates develop in approximately half of those infected with HIV-1 for over five years (Hraber, P. et al. AIDS 28, 163-9 (2014). Intense interest has focused on these antibodies, as they provide clues to how an effective vaccine might be developed (Burton, D. R. et al. Nat Immunol 5, 233-6 (2004); Haynes, B. F., Kelsoe, G., Harrison, S.C. & Kepler, T.B. Nature biotechnology 30, 423-33 (2012). In specific, broadly neutralizing antibodies (bNAbs)—that arise in multiple donors and share common features of Env recognition and B-cell ontogeny—may have utility as vaccine templates, due to the potential for similar antibodies to be elicited by a common immunogen (or common set of immunogens) in the general population (Kwong, P. D. & Mascola, J. R. Immunity 37, 412-25 (2012), Jardine, J. et al. Science 340, 711-6 (2013).


An increasing number of such “multidonor” bNAbs have been identified, such as those of the VRC01 class (named for the first antibody of the class), which share ‘class’ features of molecular recognition and B-cell ontogeny (Scheid, J. F. et al. Science 333, 1633-7 (2011); Wu, X. et al. Science 333, 1593-602 (2011); Zhou, T. et al. Immunity 39, 245-58 (2013); Zhou, T. et al. Cell 161, 1280-92 (2015)). This commonality has motivated the development of immunogens, designed to target class-specific features of recognition and to overcome class-specific roadblocks in developmental ontogeny, and success with this strategy has been achieved with immunogens capable of priming the initial stage of VRC01-class development in mouse models (Dosenovic, P. et al. Cell 161, 1505-15 (2015); Jardine, J. G. et al. Science 349, 156-61 (2015), each of which is incorporated by reference herein).


Structures of the ligand-free forms of these antibodies reveal a protruding third heavy chain complementarity determining region (CDR H3), which is anionic, often tyrosine sulfated, and critical for Env interaction. The epitope appears to be quaternary in nature and to include an N-linked glycan at residue 160 along with strand C of V1V2. In terms of B-cell ontogeny, approximations of the unmutated common ancestor (UCA) have been inferred for V1V2-directed bNAb lineages from donors CH0219 and CAP256 (Bonsignori, M. et al. J Virol 85, 9998-10009 (2011); Doria-Rose, N. A. et al. Nature 509, 55-62 (2014), each of which his incorporated by reference herein), which indicate the long anionic CDR H3 to be a product of recombination. Initial recognition of UCA (or of V-gene reverted approximations) appears to be restricted to select strains of HIV-1 (e.g. CAP256-SU or ZM233), to use similar D genes and in some cases related V genes, and to contain similar motifs (e.g. YYD) in the CDR H3.


While antibodies against the same supersite of HIV-1 vulnerability often show diverse modes of recognition, bNAbs against the membrane-distal V1V2 apex of pre-fusion closed conformation of HIV-1 Env appear to share a number of characteristics. Thus far, V1V2-directed bNAbs have been identified in four donors: the CH0219 donor, with bNAbs CH01-CH04 (Bonsignori, M. et al. J Virol 85, 9998-10009 (2011)); the CAP256 donor, with bNAbs CAP256-VRC26.01-12 (Doria-Rose, N. A. et al. Nature 509, 55-62 (2014); the IAVI 24 donor, with bNAbs PG9 and PG16 (Walker, L. M. et al. Science 326, 285-9 (2009); and the IAVI 84 donor with bNAbs PGT141-145 (Walker, L. M. et al. Nature 477, 466-70 (2011) and PGDM1400-1412 (Sok, D. et al. Recombinant HIV envelope trimer selects for quaternary-dependent antibodies targeting the trimer apex. Proc Natl Acad Sci USA 111, 17624-9 (2014).


Neutralization screening with UCA and intermediates of V1V2-directed bNAbs was used to engineer antigens capable of interacting with developmental intermediates. Altogether the structural similarities in antibody recognition along with ontogeny similarities (and differences) in development indicate the V1V2-directed bNAbs to form an ‘extended class’, which do not necessarily share genetic commonalities, but nonetheless display a characteristic mode of antigen interaction. Extended-class immunogens—such as the soluble chimeric trimers disclosed herein through an ontogeny-based chimera strategy—provide a general means for eliciting bNAbs against specific sites of Env vulnerability.


V1V2 Chimeras

Several HIV-1 Env molecules that specifically bind to mature broadly neutralizing antibodies that target the V1V2 domain, as well as immature somatic precursors thereof, were identified (FIG. 57). These include Env proteins from the CAP256.SU, BB201.B42, KER2018.11, CH070.1, ZM233.6, Q23.17, A244, T250-4, and WITO.33 strains of HIV-1. To identify the HIV-1 strains shown in FIG. 57, mature and reverted V1V2-directed bNAbs were tested for neutralization across ˜200 exemplary HIV-1 isolates. The V1V2 sequence of each of the HIV-1 strains (positions 126-196, HXB2 numbering) is shown, with the A, B, C, C′ and D secondary structures indicated.


With regard to FIG. 57, inferred ancestor and intermediates of V1V2-directed bNAbs neutralize a common set of HIV-1 isolates. Mature and reverted V1V2-directed bNAbs were tested for neutralization across ˜200 HIV-1 isolates. “Neutralized” represents the number of HIV-1 strains with IC50 of less than 50 mg/ml, and “Total” indicates the number of HIV-1 strains tested; IC50 for select strains is indicated by an enlarged colored dot. The reverted antibodies were previously identified, see, e.g., Bonsignori et al., J. Virol., 85(19):9998-10009, 2011, which is incorporated by reference herein.


HIV-1 strains neutralized by the broadly neutralizing antibody revertants shown in FIG. 57 were ranked according to probabilities obtained by frequentist analysis, for which enhancement in likelihood of interaction with the earliest neutralizers is provided. The fold enhancement of interaction probability for the selected strains relative to a random strain from the ˜200-virus panel using a frequentist approach is shown in the following table, as evaluated based on (i) all 13 antibodies in FIG. 57, (ii) mature antibodies (CH04, PG9, CAP256-CAP256.08, and PGT145), (iii) non-mature antibodies, (iv) germline or UCA antibodies (CH0219-UCA, PG9-gHgL, PGT145-gHgL, CAP256-VRC26.UCA), (v) intermediate antibodies (non-mature or non-germline/UCA), and (vi) earliest neutralizers (CH0219-UCA, PG9-gHgL, PGT145-gHL, CAP256-VRC26.I1). The enhancement of interaction probability for using nine selected strains compared to a random strain is also shown.




















Mature
Non-Mature
Intermediate
Germline and
Earliest


Strain
All Abs
Abs
Abs
Abs
UCA Abs
neutralizers















Fold enhancement of interaction probability for each selected strain













WITO.33
2.07
1.23
4.28
3.45
14.98
23.02


ZM233.6
2.24
1.63
4.28
2.3
29.96
23.02


T250-4
2.36
1.63
4.28
4.6
0
11.51


CH070.1
1.77
1.23
3.21
2.3
14.98
11.51


BB201.B42
2.07
1.63
3.21
2.3
14.98
11.51


KER2018.11
2.07
1.63
3.21
2.3
14.98
11.51


Q23.17
2.07
1.63
3.21
2.3
14.98
11.51


A244
2.36
1.63
4.28
3.45
14.98
11.51


CAP256.SU
2.07
1.63
3.21
3.45
0
11.51







Fold enhancement of interaction probability for using the nine selected strains














3.25
1.63
7.48
5.76
29.96
46.04










Chimeric HIV-1 Env ectodomain trimer immunogens were produced that include the V1V2 domain sequence (positions 126-196) of the CAP256.SU, BB201.B42, KER2018.11, CH070.1, ZM233.6, Q23.17, A244, T250-4, or WITO.33 strains of HIV-1, with the remainder including BG505.SOSIP.DS.368R sequence (including gp120 positions 31-125 and 197-511 and gp41 positions 512-644), as follows: Q23.17 chimera (SEQ ID NO: 2126), ZM233.6 chimera (SEQ ID NO: 2125), WITO.33 chimera (SEQ ID NO: 2128), A244 chimera (SEQ ID NO: 2127), BB201.B42 chimera (SEQ ID NO: 2122), KER2018.11 chimera (SEQ ID NO: 2123), CH070.1 chimera (SEQ ID NO: 2124), CAP256.SU chimera (SEQ ID NO: 2121), and T-250-4 chimera (SEQ ID NO: 2129).


The transplanted V1V2 region is illustrated in FIG. 58A. FIG. 58B shows an exemplary gel filtration and negative stain EM (2D class averages) of a representative chimera, BG505 SOSIP.664.DS.368R.CAP256-SU. The binding of the soluble chimeric HIV-1 Env ectodomains to the ancestors, intermediates, and mature V1V2-directed bNAbs listed in FIG. 57 was assayed by ELISA (FIG. 58C). Additionally, these chimeric HIV-1 Env ectodomain trimers were incubated with a molar excess of soluble CD4 and tested for binding to 17b mAb—none of the chimeric HIV-1 Env ectodomain trimers specifically bound to 17b in the presence of sCD4. Further, each of the chimeric HIV-1 Env ectodomain trimers did not specifically bind to the poorly neutralizing antibody 447-52D, but did specifically bind to V1V2 targeted broadly neutralizing antibodies such as PGT145, VRC26, PGT121, and/or 2G12.


426c and d45-01dG5 Chimeras


Additional chimeras were generated that combine the BG505 “platform” described in Example 5, with a V1V2 domain from a CAP256.SU, BB201.B42, KER2018.11, CH070.1, ZM233.6, Q23.17, A244, T250-4, or WITO.33 strain as described in this example, with the remainder of the gp120 portion of the HIV-1 Env ectodomain from a HIV-1 Env molecule known to interact with mature and UCA forms of VRC01-class antibodies (such as Env from the clade C 426c strain with N276D, N460D, N463D substitutions (see Wu et al., Cell, 161, 470-485, 2015, which is incorporated by reference herein), or Env from the clade B d45-01dG5 strain (see McGuire et al., J Exp. Med., 210, 655-663, 2013, incorporated by reference herein).


The amino acid sequence of 426c Env with N276D, N460D, N463D substitutions is provided as SEQ ID NO: 2144. The amino acid sequence of d45-01dG5 Env is provided as SEQ ID NO: 2145. These ectodomain trimers have unique antigenic characteristics that provide for binding to mature and UCA forms of multiple classes or broadly neutralizing antibodies (targeting the CD4 binding site and the V1V2 domain) and can be used to induce an immune response to HIV-1 Env in a subject. These immunogens are of particular interest for use as a “prime” immunogen in a prime-boost immunization protocol for eliciting an immune response to HIV-1 Env.


The chimeric Env ectodomains included the sequences from the following (HXB2 numbering):


For the 426c chimera:


BG505 “platform”: 31-45 and 478-507, 512-664;


V1V2 domain: positions 126-196 from CAP256.SU, BB201.B42, KER2018.11, CH070.1, ZM233.6, Q23.17, A244, T250-4, or WITO.33


426c: 46-125, 197-478


This chimeric Env ectodomain further included SOSIP substitutions, DS substitutions (201C/433C), and N276D, N460D, N463D substitutions to eliminate the glycosylation sites at positions 276, 460, 463.


For the d45-01dG5 chimera:


BG505: 31-45 and 478-507, 512-664 with SOSIP substitutions;


V1V2 domain: 126-196 positions 126-196 from CAP256.SU, BB201.B42, KER2018.11, CH070.1, ZM233.6, Q23.17, A244, T250-4, or WITO.33


This chimeric Env ectodomain further included SOSIP substitutions and DS substitutions (201C/433C). The donor 45_01dG5 Env naturally lacks a glycan at 276 and 460 and this is sufficient to allow UCA forms of VRC-01 class antibodies to bind. Specific examples of sequences of such chimeric HIV-1 Env ectodomains are provided as SEQ ID NOs: 2146-2159.


As proof-of-principle, a chimera was generated that includes the BG505 “platform” (positions 31-45 and 478-507, 512-664), with the remainder of gp120 from the 426c strain with mutations of the glycan sequon at positions 276, 460 and 463, and the “DS” substitutions (201C/433C) and tested antigenically (FIG. 60). This construct bound to VRC20 gHgL and VRC01 gHgL UCA antibodies, as well as the indicated neutralizing antibodies.


UCA and intermediate matured antibodies related to known broadly neutralizing antibodies that can be used to interrogate the antigenicity of the disclosed chimeras are known. Non-limiting examples include UCA and intermediate matured antibodies related to VRC26, PGT145, CH01, PG9 (see, e.g., Alam et al., PNAS, 110, 18214-9, 2013; Bonsignori et al, J Virol, 85, 9998-10009, 2011; Bonsignori et al, J Virol, 86, 4688-4692, 2012; doria-rose et al, Nature, 509, 55-62, 2014; Pancera et al., J Virol, 84, 8098-8110, 2010; Walker et al., Nature, 477, 466-470, 2011; each of which is incorporated by reference herein) and VRC01 (see, e.g., Jardine, J. et al. Science 340, 711-6, 2013, which is incorporated by reference herein).


Example 14
Recombinant HIV-1 Env Ectodomain Trimers Including BG505 and JRFL Sequences

This example describes chimeric HIV-1 Env ectodomain trimers that include chimeric sequences having a BG505 “platform,” as well as other BG505 structural elements (such as a V1, V2, and/or V3 domain), with the remaining sequence of the HIV-1 ectodomain based on the JRFL strain of HIV-1.


Chimeric HIV-1 Env ectodomains were expressed that include HIV-1 Env positions 31-507 joined by a 6R cleavable linker to gp41 positions 512-664. The BG505 sequence was used for gp120 positions 31-45 and 478-507 and gp41 residues 512-664. Some constructs also included BG505 residues for “Interface Residue Set A” or “Int. Res. Set A:” gp120 positions 46-54, 70-75, 84-89, 99, 102, 106, 107, 114, 215, 220-224, 226, 244, 471-473, and 476-477. Some constructs also included BG505 sequence for particular structural elements, such as the:


V1 loop (gp120 positions 119-153)


V2 loop (gp120 positions 154-205)


Strand C of the V1V2 domain (gp120 positions 166-173)


V3 domain (gp120 positions 296-331)


Positions 191-205


V2 loop and V3 domain


Strand C and V3 domain


Positions 191-205 and Strand C


V1 and V3


V1, Strand C, and V3


V1, V2, and V3


HIV1 Env positions 191-205 are a set of residues in strand D of the V1V2 which forms extensive contacts with the B20-B21 sheets and may help to stabilize the chimeric JRFL molecule. The recombinant HIV-1 Env proteins also included the SOSIP and 201C/433C substitutions (for stabilization) and an E168K substitution to maximize binding to V1V2-directed broadly neutralizing antibodies.


The JRFL sequence was used for the remaining HIV-1 Env sequence. The following recombinant HIV-1 Env ectodomain trimers were expressed according to methods described in Examples 1 and 2, and their antigenicity was assayed using a panel of antibodies (FIG. 59).
















SEQ


Name
Chimeric positions
ID NO







JRFLgp140.6R.SOSIP.664.E168K, BG505 gp41
BG505: gp120 positions 31-45 and 478-507, V2, V3, gp41
1732


chim, I201C, A433C,_v2_v3
512-664; JRFL: remainder


JRFLgp140.6R.SOSIP.664.E168K, BG505 gp41
BG505: gp120 positions 31-45 and 478-507, V3; gp41 512-
1735


chim, I201C, A433C,_v3
664; JRFL: remainder


JRFLgp140.6R.SOSIP.664.E168K, BG505 gp41
BG505: gp120 positions 31-45 and 478-507, Int. Res. Set A,
1736


chim, +int I201C, A433C,_strC_v3
Strand C, V3; gp41 512-664; JRFL: remainder


JRFLgp140.6R.SOSIP.664.E168K, BG505 gp41
BG505: gp120 positions 31-45 and 478-507, Int. Res. Set A,
1738


chim, +int I201C, A433C,_191-205_v3
positions 191-205, V3; gp41 512-664; JRFL: remainder


JRFLgp140.6R.SOSIP.664.E168K, BG505 gp41
BG505: gp120 positions 31-45 and 478-507, Int. Res. Set A,
1739


chim, +int I201C, A433C,_v1_v3
positions 191-205, V1, V3; gp41 512-664; JRFL: remainder


JRFLgp140.6R.SOSIP.664.E168K, BG505 gp41
BG505: gp120 positions 31-45 and 478-507, Int. Res. Set A,
1741


chim, +int I201C, A433C,_v3
V3; gp41 512-664; JRFL: remainder


JRFLgp140.6R.SOSIP.664.E168K, BG505 gp41
BG505: gp120 positions 31-45 and 478-507, Int. Res. Set A,
1742


chim, +int I201C, A433C,_v2_v3
V2, V3; gp41 512-664; JRFL: remainder


JRFLgp140.6R.SOSIP.664.E168K, BG505 gp41
BG505: gp120 positions 31-45 and 478-507, Int. Res. Set A,
1744


chim, +int I201C, A433C,_v1_strC_v3
V1, Strand C, V3; gp41 512-664; JRFL: remainder


JRFLgp140.6R.SOSIP.664.E168K, BG505 gp41
BG505: gp120 positions 31-45 and 478-507, V1, V3; gp41
1758


chim, I201C, A433C,_v1_v3
512-664; JRFL: remainder


JRFLgp140.6R.SOSIP.664.E168K, BG505 gp41
BG505: gp120 positions 31-45 and 478-507, Int. Res. Set A,
1759


chim, +int I201C, A433C,_v1_191-205_v3
V1, positions 191-205, V3; gp41 512-664; JRFL: remainder


JRFLgp140.6R.SOSIP.664.E168K, BG505 gp41
BG505: gp120 positions 31-45 and 478-507, positions 191-
1760


chim, I201C, A433C,_191-205_v3
205, V3; gp41 512-664; JRFL: remainder


JRFLgp140.6R.SOSIP.664.E168K, BG505 gp41
BG505: gp120 positions 31-45 and 478-507, Int. Res. Set A,
1761


chim, +int I201C, A433C,_strC_191-205_v3
Strand C, positions 191-205, V3; gp41 512-664; JRFL:



remainder


JRFLgp140.6R.SOSIP.664.E168K, BG505 gp41
BG505: gp120 positions 31-45 and 478-507, Int. Res. Set A,
1762


chim, +int I201C, A433C,_v1_v2_v3
V1, V2, V3; gp41 512-664; JRFL: remainder


JRFLgp140.6R.SOSIP.664.E168K, BG505 gp41
BG505: gp120 positions 31-45 and 478-507, V1, Strand C, V3;
1763


chim, I201C, A433C,_v1_strC_v3
gp41 512-664; JRFL: remainder










Each of the recombinant HIV-1 Env ectodomain trimers listed in the above table also included the SOSIP, R6, 664, E168K, I201C, and A433C substitutions.


As illustrated in FIG. 59, each of these recombinant HIV-1 Env ectodomain trimers has substantially reduced binding to 17b antibody in the presence of sCD4 compared to control BG505.SOSIP, and bound to prefusion mature closed conformation targeted antibodies, such as PGT145. The binding assays were performed as described in Examples 1 and 2. The reduced binding to VRC26 of JRFL based constructs is due to the fact that this antibody interacts poorly with JRFL Env.


Example 15

The following table (Table 13) provides a description of sequences provided herein. Sequence of particular interest for use as immunogens to induce an immune response to HIV-1 Env are marked with a “*”


















1


4
5




SEQ
2
3
Native
Mutations Compared to
6
7


ID NO
Code
Name
Background
Native Background
Additional mutations
Comment







0001
0
HXB2













MRVKEKYQHLWRWGWRWGTMLLGMLMICSATEKLWVTVYYGVPVWKEATTTLFCASDAKAYDTEVHNVWATHACVPTDPNPQEVVLVNVTENFNMWKNDMVEQMHEDIISLWDQSLKPCVKLTPLCVSLK



CTDLKNDTNTNSSSGRMIMEKGEIKNCSFNISTSIRGKVQKEYAFFYKLDIIPIDNDTTSYKLTSCNTSVITQACPKVSFEPIPIHYCAPAGFAILKCNNKTFNGTGPCTNVSTVQCTHGIRPVVSTQLL



LNGSLAEEEVVIRSVNFTDNAKTIIVQLNTSVEINCTRPNNNTRKRIRIQRGPGRAFVTIGKIGNMRQAHCNISRAKWNNTLKQIASKLREQFGNNKTIIFKQSSGGDPEIVTHSFNCGGEFFYCNSTQL



FNSTWFNSTWSTEGSNNTEGSDTITLPCRIKQIINMWQKVGKAMYAPPISGQIRCSSNITGLLLTRDGGNSNNESEIFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTKAKRRVVQREKRAVGIGALFL



GFLGAAGSTMGAASMTLTVQARQLLSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARILAVERYLKDQQLLGIWGCSGKLICTTAVPWNASWSNKSLEQIWNHTTWMEWDREINNYTSLIHSLIEESQ



NQQEKNEQELLELDKWASLWNWFNITNWLWYIKLFIMIVGGLVGLRIVFAVLSIVNRVRQGYSPLSFQTHLPTPRGPDRPEGIEEEGGERDRDRSIRLVNGSLALIWDDLRSLCLFSYHRLRDLLLIVTR



IVELLGRRGWEALKYWWNLLQYWSQELKNSAVSLLNATAIAVAEGTDRVIEVVQGACRAIRHIPRRIRQGLERILL
















0002
0
BG505
BG505












MRVMGIQRNCQHLFRWGTMILGMIIICSAAENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQC



TNVTNNITDDMRGELKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLL



NGSLAEEEVMIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCTVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFN



STWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRAKRRVVGREKRAVGIGAVFLGFL



GAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAIEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICTTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQ



EKNEQDLLALDKWASLWNWFDISNWLWYIKIFIMIVGGLIGLRIVFAVLSVIHRVRQGYSPLSFQTHTPNPRGLDRPERIEEEDGEQDRGRSTRLVSGFLALAWDDLRSLCLFCYHRLRDFILIAARIVE



LLGHSSLKGLRLGWEGLKYLWNLLAYWGRELKISAINLFDTIAIAVAEWTDRVIEIGQRLCRAFLHIPRRIRQGLERALL
















0003
A001
BG505 SOSIP
BG505
SOSIP







0004
A002
BG505.SOSIP.R6.664.T332N_Y191F
BG505
SOSIP, R6, 664, T332N
Y191F
Stabilized V1V2 cap





0005
A003
BG505, SOSIP, R6, 664, T332N_Y191W
BG505
SOSIP, R6, 664, T332N
Y191W
Stabilized V1V2 cap





0006
A004
BG505.SOSIP.R6.664.T332N_A433P
BG505
SOSIP, R6, 664, T332N
A433P
Disrupt CD4-bound sheet conf.





0007
A005
BG505.SOSIP.R6.664.T332N_Q432P
BG505
SOSIP, R6, 664, T332N
Q432P
Disrupt CD4-bound sheet conf.





0008
A006
BG505.SOSIP.R6.664.T332N_S174C/A319C
BG505
SOSIP, R6, 664, T332N
S174C/A319C
DS (disulfide)





0009
A007
BG505.SOSIP.R6.664.T332N_L175C/T320C
BG505
SOSIP, R6, 664, T332N
L175C/T320C
DS





0010
A008
BG505.SOSIP.R6.664.T332N_P220C/A578C
BG505
SOSIP, R6, 664, T332N
P220C/A578C
DS





0011
A009
BG505.SOSIP.R6.664.T332N_A221C/A582C
BG505
SOSIP, R6, 664, T332N
A221C/A582C
DS





0012
A010
BG505.SOSIP.R6.664.T332N_A200C/P313C
BG505
SOSIP, R6, 664, T332N
A200C/P313C
DS





0013
A011
BG505.SOSIP.R6.664.T332N_498C/W610C
BG505
SOSIP, R6, 664, T332N
498C/W610C
DS





0014
A012
BG505.IP.R6.664.T332N_G41C/Q540C
BG505
IP, R6, 664, T332N
G41C/Q540C
DS-non SOS context





0015
A013
BG505.IP.R6.664.T332N_P43C/A526C
BG505
IP, R6, 664, T332N
P43C/A526C
DS-non SOS context





0016
A014
BG505.IP.R6.664.T332N_A221C/A582C
BG505
IP, R6, 664, T332N
A221C/A582C
DS-non SOS





0017
A015
BG505.SOSIP.R6.664.T332N_G527C/N88C
BG505
SOSIP, R6, 664, T332N
G527C/N88C
DS





0018
A016
BG505.SOSIP.R6.664.T332N_Q540C/P43C
BG505
SOSIP, R6, 664, T332N
Q540C/P43C
DS





0019
A017
BG505.SOSIP.R6.664.T332N_E164C/N197C
BG505
SOSIP, R6, 664, T332N
E164C/N197C
DS





0020
A018
BG505.SOSIP.R6.664.T332N_P124C/R166C
BG505
SOSIP, R6, 664, T332N
P124C/R166C
DS





0021
A019
BG505.SOSIP.R6.664.T332N_D180C/I423C
BG505
SOSIP, R6, 664, T332N
D180C/I423C
DS





0022
A020
BG505.SOSIP.R6.664.T332N_N195C/I423C
BG505
SOSIP, R6, 664, T332N
N195C/I423C
DS





0023
A021
BG505.SOSIP.R6.664.T332N_N195C/A433C
BG505
SOSIP, R6, 664, T332N
N195C/A433C
DS





0024
A022
BG505.SOSIP.R6.664.T332N_S199C/A433C
BG505
SOSIP, R6, 664, T332N
S199C/A433C
DS





0025
A023
BG505.SOSIP.R6.664.T332N_S199C/G431C
BG505
SOSIP, R6, 664, T332N
S199C/G431C
DS





0026
A024
*BG505.SOSIP.R6.664.T332N_I201C/A433C
BG505
SOSIP, R6, 664, T332N
I201C/A433C
DS









AENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDK



KQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAcTQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMIRSENITNNAKNILVQFNT



PVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQ



IINMWQRIGQcMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQ



QQSNLLRAPEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD
















0027
A025
BG505.SOSIP.R6.664.T332N_T320C/P438C
BG505
SOSIP, R6, 664, T332N
T320C/P438C
DS





0028
A026
BG505.SOSIP.R6.664.T332N_D180C/K421C
BG505
SOSIP, R6, 664, T332N
D180C/K421C
DS





0029
A027
BG505.SOSIP.R6.664.T332N_M530W
BG505
SOSIP, R6, 664, T332N
M530W
CavF at gp41-tryptophan clasp.








Stabilize gp41-tryptophan clasp








interactions





0030
A028
BG505.SOSIP.R6.664.T332N_F159Y
BG505
SOSIP, R6, 664, T332N
F159Y
CavF at gp120 V1/V2. Substitute








Y or W, stabilize V1/V2/V3





0031
A029
BG505.SOSIP.R6.664.T332N_F223W
BG505
SOSIP, R6, 664, T332N
F223W
CavF at gp120 beta-5. Substitute








Y or W. stabilize gp120/gp41








interface





0032
A030
BG505.SOSIP.R6.664.T332N_L544Y_F223W
BG505
SOSIP, R6, 664, T332N
L544Y, F223W
CavF at gp41 tip of α-6. 544: F,








Y, or W 223: Y or W. stabilize








gp120/gp41 interface





0033
A031
BG505.SOSIP.R6.664.T332N_L523F
BG505
SOSIP, R6, 664, T332N
L523F
Fusion Peptide Cavity Fill





0034
A032
BG505.SOSIP.R6.664.T332N_F522Y
BG505
SOSIP, R6, 664, T332N
F522Y
Fusion Peptide Cavity Fill





0035
A033
BG505.SOSIP.R6.664.T332N_W35Q
BG505
SOSIP, R6, 664, T332N
W35Q
Exposed Nterm hydrophobic








resurfaced





0036
A034
BG505.SOSIP.R6.664.T332N_A200C/
BG505
SOSIP, R6, 664, T332N
A200C/P313C, A221C/A582C
nonSOS_multiple cyscys




P313C_A221C/A582C









0037
A035
BG505.SOSIP.R6.664.T332N_Q432E
BG505
SOSIP, R6, 664, T332N
Q432E
Disrupt CD4-bound sheet conf.





0038
A036
BG505.SOSIP.R6.664.T332N_Q432D
BG505
SOSIP, R6, 664, T332N
Q432D
Disrupt CD4-bound sheet conf.





0039
A037
BG505.SOSIP.R6.664.T332N_M434P
BG505
SOSIP, R6, 664, T332N
M434P
Disrupt CD4-bound sheet conf.





0040
A038
BG505.SOSIP.R6.664.T332N_Y435P
BG505
SOSIP, R6, 664, T332N
Y435P
Disrupt CD4-bound sheet conf.





0041
A039
BG505.SOSIP.R6.664.T332N_A436P
BG505
SOSIP, R6, 664, T332N
A436P
Disrupt CD4-bound sheet conf.





0042
A040
BG505.SOSIP.R6.664.T332N_P437A
BG505
SOSIP, R6, 664, T332N
P437A
proline removal





0043
A041
BG505.SOSIP.R6.664.T332N_P438A
BG505
SOSIP, R6, 664, T332N
P438A
proline removal





0044
A042
BG505.SOSIP.R6.664.T332N_P438A.P437A
BG505
SOSIP, R6, 664, T332N
P437A, P438A
proline removal





0045
A043
BG505.SOSIP.R6.664.T332N_T139W.I326R
BG505
SOSIP, R6, 664, T332N
T139W, I326R
CavF at the interface of V1V2








and V3 loops. Sustitute- T139:








F, M, I, Y; 1326: M, W, F, Y.








stabilize V1V2/V3 loop








interactions in mature closed








state





0046
A044
BG505.SOSIP.R6.664.T332N_L179W
BG505
SOSIP, R6, 664, T332N
L179W
CavF at V1V2 loop gp120 core








interface. Substitute- F, Y M, 








I. stabilize interaction between








V1V2 loop and gp120 core in








mature closed state





0047
A045
BG505.SOSIP.R6.664.T332N_Y39F.S534V
BG505
SOSIP, R6, 664, T332N
Y39F, S534V
CavF. add hydrophobicity at








gp120/gp41 interface Substitute-








S534: I, W, F, A, M; Y39: W,








M, I





0048
A046
BG505.SOSIP.R6.664.T332N_Y39W.S534A
BG505
SOSIP, R6, 664, T332N
Y39W, S534A
CavF. add hydrophobicity at








gp120/gp41 interface. A





0049
A047
BG505.SOSIP.R6.664.T332N_39F.S534V.
BG505
SOSIP, R6, 664, T332N
Y39F, S534V, T37V, T499V
CavF. add hydrophobicity at




T37V.T499V



gp120/gp41 interface





0050
A048 
BG505.SOSIP.R6.664.T332N_Y39F.Y40F.
BG505
SOSIP, R6, 664, T332N
Y39F, Y40F, S534V, T37V,
CavF. add hydrophobicity at




S534V.T37V.T499V


T499V
gp120/gp41 interface





0051
0
CAP256.SU
CAP256.SU








0052
A049
BG505.SOSIP.R6.664.T332N_N425C I430C
BG505
SOSIP, R6, 664, T332N
N425C/I430C
DS- Stabilizes CD4 binding loop





0053
A050
BG505.SOSIP.R6.664.T332N_Y318C P437C
BG505
SOSIP, R6, 664, T332N
Y318C/437C, G473A
DS- Restrain PGT122 bound




G473A



conformation; reduce CD4 binding





0054
A051
BG505.SOSIP.R6.664.T332N_M426W
BG505
SOSIP, R6, 664, T332N
M426W
CavF at CD4bs. Substitute- F, Y,








L, V, I. Constrains CD4 binding








loop





0055
A052 
BG505.SOSIP.R6.664.T332N_S174C A319C
BG505
SOSIP, R6, 664, T332N
S174C/A319C, G473A
DS- Restrain PGT122 bound




G473A



conformation; reduce CD4 binding





0056
A053 
BG505.SOSIP.R6.664.T332N_L175C T320C
BG505
SOSIP, R6, 664, T332N
L175C/T320C, G473A
DS- Restrain PGT122 bound




G473A



conformation; reduce CD4 binding





0057
A054 
BG505.SOSIP.R6.664.T332N_F176C D180C
BG505
SOSIP, R6, 664, T332N
F176C/D180C
DS- Restrain PGT122 bound








conformation





0058
A055
BG505.SOSIP.R6.664.T332N_A204C A436C
BG505
SOSIP, R6, 664, T332N
A204C/A436C, G473A
DS- Restrain PGT122 bound




G473A



conformation; reduce CD4 binding





0059
A056
BG505.SOSIP.R6.664.T332N_A204C M434C
BG505
SOSIP, R6, 664, T332N
A204C/M434C, G473A
DS- Restrain PGT122 bound




G473A



conformation; reduce CD4 binding





0060
A057
BG505.SOSIP.R6.664.T332N_P212C K252C
BG505
SOSIP, R6, 664, T332N
P212C/K252C
DS- Restrain PGT122 bound








conformation





0061
A058
BG505.SOSIP.R6.664.T332N_P220C A200C
BG505
SOSIP, R6, 664, T332N
P220C/A200C
DS- Restrain PGT122 bound








conformation





0062
A059
BG505.SOSIP.R6.664.T332N_G314C A200C
BG505
SOSIP, R6, 664, T332N
G314C/A200C
DS- Restrain PGT122 bound








conformation





0063
A060
BG505.SOSIP.R6.664.T332N_A204C M434C
BG505
SOSIP, R6, 664, T332N
A204C/M434C
DS- Restrain PGT122 bound








conformation





0064
A061 
BG505.SOSIP.R6.664.T332N_L122C L125C
BG505
SOSIP, R6, 664, T332N
L122C/L125C
DS- Restrain PGT122 bound








conformation





0065
A062
BG505.SOSIP.R6.664.T332N_G473A
BG505
SOSIP, R6, 664, T332N
G473A
CavF at CD4bs. Substitute- any.








sterically interfere with CD4








binding, without affecting Ab








binding





0066
A063
BG505.SOSIP.R6.664.T332N_G473S
BG505
SOSIP, R6, 664, T332N
G473S
Same as Seq_0065





0067
A064
BG505.SOSIP.R6.664.T332N_G473Y
BG505
SOSIP, R6, 664, T332N
G473Y
Same as Seq_0065





0068
A065
BG505.SOSIP.R6.664.T332N_G431P
BG505
SOSIP, R6, 664, T332N
G431P
Same as Seq_0065





0069
A066
BG505.SOSIP.R6.664.T332N_N425C A433C
BG505
SOSIP, R6, 664, T332N
N425C/A433C
DS- Fixes PGT122 bound state





0070
A067
BG505.SOSIP.R6.664.T332N_V120C Q315C
BG505
SOSIP, R6, 664, T332N
V120C/Q315C
DS- Fixes PGT122 bound state





0071
A068 
BG505.SOSIP.R6.664.T332N_P124C T164C
BG505
SOSIP, R6, 664, T332N
P124C/T164C
DS- Fixes PGT122 bound state





0072
A069
BG505.SOSIP.R6.664.T332N_T128C T167C
BG505
SOSIP, R6, 664, T332N
T128C/T167C, G473A
DS- Restrain PGT122 bound




G473A



conformation; reduce CD4 binding





0073
A070 
BG505.SOSIP.R6.664.T332N_I424C F382C
BG505
SOSIP, R6, 664, T332N
I424C/F382C
DS- Fixes PGT122 bound state





0074
A071 
BG505.SOSIP.R6.664.T332N_R298C A329C
BG505
SOSIP, R6, 664, T332N
R298C/A329C
DS- Fixes PGT122 bound state





0075
A072
BG505.SOSIP.R6.664.T332N_M426P
BG505
SOSIP, R6, 664, T332N
M426P
CavF at CD4bs. Substitute- P.








Rigidifies CD4 binding loop





0076
A073
BG505.SOSIP.R6.664.T332N_Y191W G473A
BG505
SOSIP, R6, 664, T332N
Y191W G473A
CavF at CD4bs and V1/V2 cap





0077
A074
BG505.SOSIP.R6.664.T332N_Q203C L122C
BG505
SOSIP, R6, 664, T332N
Q203C/L122C
DS- Fixes PGT122 bound state





0078
A075
BG505.SOSIP.R6.664.T332N_M426A
BG505
SOSIP, R6, 664, T332N
M426A
CavF at CD4bs. Substitute- G, V,








I, L, F, Y, W, R, K. prevents








triggering on CD4 binding





0079
A076
BG505.SOSIP.R6.664.T332N_Y191W A433P
BG505
SOSIP, R6, 664, T332N
Y191W A433P
CavF at CD4bs and V1/V2 cap





0080
A077
BG505.SOSIP.R6.664.T332N_T372C S364C
BG505
SOSIP, R6, 664, T332N
T372C/S364C
DS- Fixes PGT122 bound state





0081
0
BB201.B42
BB201.B42








0082
A078
BG505.SOSIP.R6.664.T332N_V36C V608C
BG505
SOSIP, R6, 664, T332N
V36C/V608C
DS- Fixes PGT122 bound state





0083
A079
BG505.SOSIP.R6.664.T332N_M426F
BG505
SOSIP, R6, 664, T332N
M426F
CavF at CD4bs. Substitute- Y, W,








L, I, V, R, K, G, A. Blocks








transition to CD4 bound








conformation





0084
A080
BG505.SOSIP.R6.664.T332N_W69P
BG505
SOSIP, R6, 664, T332N
W69P
helix 0 disruption





0085
A081
BG505.SOSIP.R6.664.T332N_V68P
BG505
SOSIP, R6, 664, T332N
V68P
helix 0 disruption





0086
A082
BG505.SOSIP.R6.664.T332N_T71P
BG505
SOSIP, R6, 664, T332N
T71P
helix 0 disruption





0087
A083
BG505.SOSIP.R6.664.T332N_H66C/K207C
BG505
SOSIP, R6, 664, T332N
H66C/K207C
disulfide





0088
A084
BG505.SOSIP.R6.664.T332N_A73C/G572C
BG505
SOSIP, R6, 664, T332N
A73C/G572C
disulfide





0089
A085 
BG505.SOSIP.R6.664.T332N_F53C/G575C
BG505
SOSIP, R6, 664, T332N
F53C/G575C
disulfide





0090
A086
BG505.SOSIP.R6.664.T332N_V75W
BG505
SOSIP, R6, 664, T332N
V75W
CavF at gp120/gp41 interface





0091
A087
BG505.SOSIP.R6.664.T332N_V75F
BG505
SOSIP, R6, 664, T332N
V75F
CavF at gp120/gp41 interface





0092
A088
BG505.SOSIP.R6.664.T332N_V75M
BG505
SOSIP, R6, 664, T332N
V75M
CavF at gp120/gp41 interface





0093
A089
BG505.SOSIP.R6.664.T332N_V208W
BG505
SOSIP, R6, 664, T332N
V208W
CavF between α1 and the strand








leading into what forms the








bridging sheet in the CD4-bound








form. Destabilize CD4-bound








state





0094
A090
BG505.SOSIP.R6.664.T332N_V208Y
BG505
SOSIP, R6, 664, T332N
V208Y
Same as Seq_0093





0095
A091
BG505.SOSIP.R6.664.T332N_V208F
BG505
SOSIP, R6, 664, T332N
V208F
Same as Seq_0093





0096
A092
BG505.SOSIP.R6.664.T332N_V208M
BG505
SOSIP, R6, 664, T332N
V208M
Same as Seq_0093





0097
A093
BG505.SOSIP.R6.664.T332N_A58C/T77C
BG505
SOSIP, R6, 664, T332N
A58C/T77C
helix 0 disruption





0098
A094
BG505.SOSIP.R6.664.T332N_D57C/T77C
BG505
SOSIP, R6, 664, T332N
D57C/T77C
helix 0 disruption





0099
A095
BG505.SOSIP.R6.664.T332N_V68C/S209C
BG505
SOSIP, R6, 664, T332N
V68C/S209C
helix 0 disruption





0100
A096
BG505.SOSIP.R6.664.T332N_V68C/V208C
BG505
SOSIP, R6, 664, T332N
V68C/208C
helix 0 disruption





0101
A097
BG505.SOSIP.R6.664.T332N_V66C/S209C
BG505
SOSIP, R6, 664, T332N
V66C/S209C
helix 0 disruption





0102
A098
BG505.SOSIP.R6.664.T332N_N67P
BG505
SOSIP, R6, 664, T332N
N67P
helix 0 disruption





0103
A099
BG505.SOSIP.R6.664.T332N_H66P
BG505
SOSIP, R6, 664, T332N
N66P
helix 0 disruption





0104
A100
BG505.SOSIP.R6.664.T332N_N67P/H66P
BG505
SOSIP, R6, 664, T332N
N67P/H66P
helix 0 disruption





0105
A101
BG505.SOSIP.R6.664.T332N_A58C/T77C/
BG505
SOSIP, R6, 664, T332N
A58C/T77C, N67P, H66P
helix 0 disruption




N67P/H66P









0106
A102
BG505.SOSIP.R6.664.T332N_D57C/T77C/
BG505
SOSIP, R6, 664, T332N
D57C/T77C, N67P, H66P
helix 0 disruption




N67P/H66P









0107
0
KER2018.11
KER2018.11








0108
A103 
BG505.SOSIP.R6.664.T332N_V68C/V208C/
BG505
SOSIP, R6, 664, T332N
V68C/V208C, N67P, H66P
helix 0 disruption




N67P/H66P









0109
A104
BG505.SOSIP.R6.664.T332N_V68C/S209C/
BG505
SOSIP, R6, 664, T332N
V68C/S209C, N67P, H66P
helix 0 disruption




N67P/H66P









0110
A105
BG505.SOSIP.R6.664.T332N_D474A/R476A
BG505
SOSIP, R6, 664, T332N
D474A,R476A
Destabilization of CD4 binding








site





0111
A106
BG505.SOSIP.R6.664.T332N_W112I
BG505
SOSIP, R6, 664, T332N
W112I
Destabilization of CD4 binding








site





0112
A107
BG505.SOSIP.R6.664.T332N_W112M
BG505
SOSIP, R6, 664, T332N
W112M
Destabilization of CD4 binding








site





0113
A108
BG505.SOSIP.R6.664.T332N_W427I
BG505
SOSIP, R6, 664, T332N
W427I
Destabilization of CD4 binding








site





0114
A109
BG505.SOSIP.R6.664.T332N_W427M
BG505
SOSIP, R6, 664, T332N
W427M
Destabilization of CD4 binding








site





0115
A110
BG505.SOSIP.R6.664.T332N_R429N
BG505
SOSIP, R6, 664, T332N
R429N
Destabilization of CD4 binding








site





0116
A111
BG505.SOSIP.R6.664.T332N_R429L
BG505
SOSIP, R6, 664, T332N
R429L
Destabilization of CD4 binding








site





0117
A112
BG505.SOSIP.R6.664.T332N_R429L/W427M
BG505
SOSIP, R6, 664, T332N
R429L, W427M
Destabilization of CD4 binding








site





0118
A113
BG505.SOSIP.R6.664.T332N_D474A
BG505
SOSIP, R6, 664, T332N
D474A
Destabilization of CD4 binding








site





0119
A114
BG505.SOSIP.R6.664.T332N_R476A
BG505
SOSIP, R6, 664, T332N
R476A






0120
A115
BG505.SOSIP.R6.664.T332N_I201C/
BG505
SOSIP, R6, 664, T332N
I201C/A433C, F159Y
DS and CavF at gp120 V1/V2.




A433C_F159Y



stabilize V1/V2/V3





0121
A116
BG505.SOSIP.R6.664.T332N_R166CG/V127C
BG505
SOSIP, R6, 664, T332N
R166CG/V127C
V1V2 disulfide stabilization.








prevent v1v2 from adopting cd4-








bound-conformation





0122
A117
BG505.SOSIP.R6.664.T332N_G314C/S199C/
BG505
SOSIP, R6, 664, T332N
G314C/S199C, R166CG/
V1V2V3 disulfide stabilization.




R166CG/V127C


V127C
prevent v1v2 from adopting cd4-








bound-conformation





0123
A118
BG505.SOSIP.R6.664.T332N_K421W.D180L
BG505
SOSIP, R6, 664, T332N
K421W, D180L
CavF at V1V2 interaction near








Res. 180 with V3 and base of








beta-21. substitute- 421: F, W,








Y; 180: L, V, I, M. prevent v1v2








to V3 along with B21 from








adopting cd4-bound-conformation





0124
A119
BG505.SOSIP.R6.664.T332N_G431.GC.S199C
BG505
SOSIP, R6, 664, T332N
G431GC/S199C
DS





0125
A120
BG505.SOSIP.R6.664.T332N_R166C.V127GC
BG505
SOSIP, R6, 664, T332N
R166C/V127GC
DS





0126
A121
BG505.SOSIP.R6.664.T332N_G314C.S199C
BG505
SOSIP, R6, 664, T332N
G314C/S199C
DS





0127
A122
BG505.SOSIP.R6.664.T332N_G314CG.S199C
BG505
SOSIP, R6, 664, T332N
G314CG/S199C
DS





0128
A123
BG505.SOSIP.R6.664.T332N_V120W
BG505
SOSIP, R6, 664, T332N
V120W
CavF at N-term of β-2. 








Substitute- F, W, Y, L, I, M.








β-2 extends in cd4-bound state,








this stabilizes small








hydrophobic pocket in ground








state





0129
A124
BG505.SOSIP.R6.664.T332N_V120W.Q203V
BG505
SOSIP, R6, 664, T332N
V120W, Q203V
Same as Seq_0128





0130
A125
BG505.SOSIP.R6.664.T332N_deltaP124
BG505
SOSIP, R6, 664, T332N
delP124
proline removal. Removal of








ground state destabilization/








flexibility





0131
A126
BG505.SOSIP.R6.664.T332N_L125W_
BG505
SOSIP, R6, 664, T332N
L125W, delP124
Proline removal and CavF at




deltaP124



Cavity between N-term of V1V2








domain and V3 near Res. 127 and








126-196 disulfide of V1V2.








Substitute- F, W, Y, L, I, M, V. 








Removal of ground state








destabilization/flexibility





0132
A127
BG505.SOSIP.R6.664.T332N_R151E.
BG505
SOSIP, R6, 664, T332N
R151E, E153W, Q328W
CavF at V1 loop at resi 153.




E153W.Q328W



Substitute- 153: F, W, Y, L, I,








M, V; 328 F, W, Y, L, I, M, V.








Adding hydrophobic patch at V1








loop to V3 loop





0133
A128
BG505.SOSIP.R6.664.T332N_F159W
BG505
SOSIP, R6, 664, T332N
F159W
CavF at Primary hydrophobic








pocket between V1V2 and V3 near








resi 159. Substitute- W or Y.








Stabilizing the hydrophobic core








of the V1V2-V3 interactions





0134
A129
BG505.SOSIP.R6.664.T332N_F317W
BG505
SOSIP, R6, 664, T332N
F317W
Same as Seq_0133





0135
A130
BG505.SOSIP.R6.664.T332N_M161W
BG505
SOSIP, R6, 664, T332N
M161W
CavF at Hydrophobic patch at








Cterm of V1V2 strand B.








Substitute- F, W, Y, L, I.








Stabilizing strand B to V3 near








trimeric interface





0136
A131
BG505.SOSIP.R6.664.T332N_I309W
BG505
SOSIP, R6, 664, T332N
I309W
Same as Seq_0135





0137
A132
BG505.SOSIP.R6.664.T332N_L125R.F317D
BG505
SOSIP, R6, 664, T332N
L125R, F317D
Salt bridge. Salt bridge








interaction in hyrophobiic shell





0138
A133
BG505.SOSIP.R6.664.T332N_L125WE.F317R
BG505
SOSIP, R6, 664, T332N
L125WE, F317R
Salt bridge. Salt bridge








interaction in hyrophobiic shell





0139
A134
BG505.SOSIP.R6.664.T332N_S115W
BG505
SOSIP, R6, 664, T332N
S115W
CavF at C-term of α-1. 








Substitute- F, W, Y, L, I, M, V.








Will fill cavity at top of α-1








which shifts conformation in








CD4-bound state





0140
A135
BG505.SOSIP.R6.664.T332N_P118W
BG505
SOSIP, R6, 664, T332N
P118W
CavF/proline removal at C-term








of α-1. Substitute- F, W, Y, L,








I, M, V. Will fill cavity at top








of α-1 which shifts conformation








in CD4-bound state





0141
A136
BG505.SOSIP.R6.664.T332N_P206A
BG505
SOSIP, R6, 664, T332N
P206A
proline removal. Removal of








ground state destabilization/








flexibility





0142
A137
BG505.SOSIP.R6.664.T332N_deltaP206
BG505
SOSIP, R6, 664, T332N
delP206
proline removal. Removal of








ground state destabilization/








flexibility





0143
A138
BG505.SOSIP.R6.664.T332N_A70Y
BG505
SOSIP, R6, 664, T332N
A70Y
CavF- extension of








hydrophobc/aromatic patch-








gp41/gp120 stabilization (a7/








a0cavity close to A70).








Substitute- F, Y, W





0144
A139
BG505.SOSIP.R6.664.T332N_A70F
BG505
SOSIP, R6, 664, T332N
A70F
Same as Seq_0143





0145
A140
BG505.SOSIP.R6.664.T332N_L111Y
BG505
SOSIP, R6, 664, T332N
L111Y
Same as Seq_0143





0146
A141
BG505.SOSIP.R6.664.T332N_L111F
BG505
SOSIP, R6, 664, T332N
L111F
Same as Seq_0143





0147
A142
BG505.SOSIP.R6.664.T332N_T202P
BG505
SOSIP, R6, 664, T332N
T202P
disrupt bridging sheet/








destabilizing CD4 bound state





0148
A143
BG505.SOSIP.R6.664.T332N_V120P
BG505
SOSIP, R6, 664, T332N
V120P
Same as Seq_0147





0149
A144
BG505.SOSIP.R6.664.T332N_V120T
BG505
SOSIP, R6, 664, T332N
V120T
Same as Seq_0147





0150
A145
BG505.SOSIP.R6.664.T332N_L122K
BG505
SOSIP, R6, 664, T332N
L122K
Same as Seq_0147





0151
A146
BG505.SOSIP.R6.664.T332N_P313C/A200C/
BG505
SOSIP, R6, 664, T332N
P313C/A200C, T51C/K574C
Ds




T51C/K574C









0152
A147
BG505.SOSIP.R6.664.T332N_P313C/A200C/
BG505
SOSIP, R6, 664, T332N
P313C/A200C, F53C/K574C
Ds




F53C/K574C









0153
A148
BG505.SOSIP.R6.664.T332N_P313C/A200C/
BG505
SOSIP, R6, 664, T332N
P313C/A200C, T51C/A578C
Ds




T51C/A578C









0154
A149
BG505.SOSIP.R6.664.T332N_T128C/L165C/
BG505
SOSIP, R6, 664, T332N
T128C/L165C, P313C/A200C,
Ds




P313C/A200C/T51C/K574C


T51C/K574C






0155
A150
BG505.SOSIP.R6.664.T332N_T128C/L165C/
BG505
SOSIP, R6, 664, T332N
T128C/L165C, P313C/A200C,
Ds




P313C/A200C/F53C/K574C


F53C/K574C






0156
A151
BG505.SOSIP.R6.664.T332N_T128C/L165C/
BG505
SOSIP, R6, 664, T332N
T128C/L165C, P313C/A200C,
Ds




P313C/A200C/T51C/A578C


T51C/A578C






0157
A152
BG505.SOSIP.R6.664.T332N_I573T
BG505
SOSIP, R6, 664, T332N
I573T
destabilize gp41 helix bundle





0158
A153
BG505.SOSIP.R6.664.T332N_G594N
BG505
SOSIP, R6, 664, T332N
G594N
destabilize gp41 helix bundle





0159
A154
BG505.SOSIP.R6.664.T332N_I573T-G594N
BG505
SOSIP, R6, 664, T332N
I573T-G594N
destabilize gp41 helix bundle





0160
A155
BG505.SOSIP.R6.664.T332N_I573T-G594N-
BG505
SOSIP, R6, 664, T332N
I573T-G594N-K574E
destabilize gp41 helix bundle




K574E









0161
A156
BG505.SOSIP.R6.664.T332N_I573T-G594N-
BG505
SOSIP, R6, 664, T332N
I573T-G594N-K574T
destabilize gp41 helix bundle




K574T









0162
A157
BG505.SOSIP.R6.664.T332N_A433C_L122C
BG505
SOSIP, R6, 664, T332N
A433C/L122C






0163
A158
BG505.SOSIP.R6.664.T332N_Q428C_E560C
BG505
SOSIP, R6, 664, T332N
Q428C/E560C






0164
A159
BG505.SOSIP.R6.664.T332N_Q428C_A561C
BG505
SOSIP, R6, 664, T332N
Q428C/A561C






0165
A160
BG505.SOSIP.R6.664.T332N_Q428C_Q562C
BG505
SOSIP, R6, 664, T332N
Q428C/Q562C






0166
A161
BG505.SOSIP.R6.664.T332N_K574C_D107C
BG505
SOSIP, R6, 664, T332N
K574C/D107C






0167
A162
BG505.SOSIP.R6.664.T332N_Q575C_Q550C
BG505
SOSIP, R6, 664, T332N
Q575C/Q550C






0168
A163
BG505.SOSIP.R6.664.T332N_Q575C_Q551C
BG505
SOSIP, R6, 664, T332N
Q575C/Q551C






0169
A164
BG505.SOSIP.R6.664.T332N_R579C_Q550C
BG505
SOSIP, R6, 664, T332N
R579C/Q550C






0170
A165
BG505.SOSIP.R6.664.T332N_M426C_E370C
BG505
SOSIP, R6, 664, T332N
M426C/E370C






0171
A166
BG505.SOSIP.R6.664.T332N_M426C_G380C
BG505
SOSIP, R6, 664, T332N
M426C/G380C






0172
A167
BG505.SOSIP.R6.664.T332N_T123W
BG505
SOSIP, R6, 664, T332N
T123W
CavF at trimer axis. Substitute-








F, Y, L, M, V. stabilize








prefusion axis interactions





0173
A168
BG505.SOSIP.R6.664.T332N_I423W_I201W
BG505
SOSIP, R6, 664, T332N
I423W, I201W
CavF at parallel b-strand #.








Substitute- F, Y, L, M, V.








prevent bridging sheet formation





0174
0
CH070.1
CH070.1








0175
A169
BG505.SOSIP.R6.664.T332N_K117W
BG505
SOSIP, R6, 664, T332N
K117W
CavF at trimer axis. Substitute-








F, Y, L, I, H, R, E, D, M, V.








stabilize prefusion axis








interactions





0176
A170
BG505.SOSIP.R6.664.T332N_K117E
BG505
SOSIP, R6, 664, T332N
K117E
CavF/charged at trimer axis.








Substitute- F, Y, L, I, H, R, E,








D, M, V. stabilize prefusion








axis interactions





0177
A171
BG505.SOSIP.R6.664.T332N_K121E
BG505
SOSIP, R6, 664, T332N
K121E
CavF/charged at trimer axis.








Substitute- F, Y, L, I, H, R, E,








D, M, V. stabilize prefusion








axis interactions





0178
A172
BG505.SOSIP.R6.664.T332N_S110W
BG505
SOSIP, R6, 664, T332N
S110W
CavF at trimer axis/gp41








interface boundary. Substitute-








F, Y, L, I, M, V. stabilize 








prefusion axis interactions/gp41








interface/prevent helix movement





0179
A173
BG505.SOSIP.R6.664.T332N_Q114W
BG505
SOSIP, R6, 664, T332N
Q114W
Same as Seq_0178





0180
A174
BG505.SOSIP.R6.664.T332N_P220W
BG505
SOSIP, R6, 664, T332N
P220W
CavF at gp41 interface.








Substitute- F, Y, L, I, M, V.








stabilize gp41 interface





0181
A175
BG505.SOSIP.R6.664.T332N_T50W
BG505
SOSIP, R6, 664, T332N
T50W
CavF at gp41 interface.








Substitute- F, Y, L, I, M, V.








stabilize gp41 interface





0182
A176
BG505.SOSIP.R6.664.T332N_R429W
BG505
SOSIP, R6, 664, T332N
R429W
CavF at parallel b-strand #. 








Substitute- F, Y, L, I, M, V.








prevent bridging sheet formation





0183
A177
BG505.SOSIP.R6.664.
BG505
SOSIP, R6, 664, T332N
V120W, I201C/A433C
ds/CavF under V1V2 cap.




T332N_V120W_I201C_A433C



Substitute- F, Y, L, I, H, R, E,








D, M, V. stabilize prefusion








axis interactions/combined








with DS





0184
A178
BG505.SOSIP.R6.664.
BG505
SOSIP, R6, 664, T332N
K121W, I201C/A433C
ds/CavF at trimer axis.




T332N_K121W_I201C_A433C



Substitute- F, Y, L, M, V.








stabilize prefusion axis








interactions/combined with DS





0185
A179
BG505.SOSIP.R6.664.
BG505
SOSIP, R6, 664, T332N
T123W, I201C/A433C
Same as Seq_0184




T332N_T123W_I201C_A433C









0186
A180
BG505.SOSIP.R6.664.
BG505
SOSIP, R6, 664, T332N
K117W, I201C/A433C
ds/CavF at trimer axis.




T332N_K117W_I201C_A433C



Substitute- F, Y, L, I, H, R, E,








D,M,V. stabilize prefusion axis








interactions/combined with DS





0187
A181
BG505.SOSIP.R6.664.
BG505
SOSIP, R6, 664, T332N
K117E, I201C/A433C
ds/CavF/charged at trimer axis.




T332N_K117E_I201C_A433C



Substitute- F, Y, L, I, H, R, E,








D, M, V. stabilize prefusion








axis interactions/combined








with DS





0188
A182
BG505.SOSIP.R6.664.
BG505
SOSIP, R6, 664, T332N
K121E, I201C/A433C
ds/CavF/charged at trimer axis.




T332N_K121E_I201C_A433C



Substitute- F, Y, L, I, H, R, E,








D, M, V. stabilize prefusion








axis interactions/combined








with DS





0189
A183
BG505.SOSIP.R6.664.
BG505
SOSIP, R6, 664, T332N
M426W, I201C/A433C
ds/CavF at parallel b-strand #.




T332N_M426W_I201C_A433C



Substitute- F, Y, L, I, H, R, E,








D, V. stabilize prefusion axis








interactions/combined with DS





0190
A184
BG505.SOSIP.R6.664.
BG505
SOSIP, R6, 664, T332N
S110W, I201C/A433C
ds/CavF at trimer axis/gp41




T332N_S110W_I201C_A433C



interface boundary. Substitute-








F, Y, L, I, M, V. stabilize








prefusion axis interactions/gp41








interface/prevent helix








movement/combined with DS





0191
A185
BG505.SOSIP.R6.664.
BG505
SOSIP, R6, 664, T332N
Q114W, I201C/A433C
Same as Seq_0190




T332N_Q114W_I201C_A433C









0192
A186
BG505.SOSIP.R6.664.
BG505
SOSIP, R6, 664, T332N
P220W, I201C/A433C
ds/CavF at gp41 interface. 




T332N_P220W_I201C_A433C



Substitute- F, Y, L, I, M, V.








stabilize gp41 interface/








combined with DS





0193
A187
BG505.SOSIP.R6.664.
BG505
SOSIP, R6, 664, T332N
T50W, I201C/A433C
ds/CavF at gp41 interface.




T332N_T50W_I201C_A433C



Substitute- F, Y, L, I, M, V.








stabilize gp41 interface/








combined with DS





0194
A188
BG505.SOSIP.R6.664.
BG505
SOSIP, R6, 664, T332N
R429W, I201C/A433C
ds/CavF at parallel b-strand #.




T332N_R429W_I201C_A433C



Substitute- F, Y, L, I, M, V.








prevent bridging sheet








formation/combined with DS





0195
A189
BG505.SOSIP.R6.664.T332N_Y61W
BG505
SOSIP, R6, 664, T332N
Y61W
CavF at Middle of α-1. Will








fill a cavity between gp120 and








gp41 to prevent CD4 induced α-1








disruption and α0 formation





0196
A190
BG505.SOSIP.R6.664.
BG505
SOSIP, R6, 664, T332N
S209R, V68L
CavF at Loop between α-1 and 




T332N_S209R_V68L



beta 0 and loop between beta 3








and beta 4. Substitute- F, W, Y,








L, I, M, V. Fills cavities that








are otherwise filled by CD4








induced α0 formation





0197
A191
BG505.SOSIP.R6.664.
BG505
SOSIP, R6, 664, T332N
F53W, Q246W
CavF at gp120-gp41 interface,




T332N_F53W_Q246W



N-term of beta-2, middle of








beta-8, Substitute- 246 F, W, Y,








L, I, M, V. Will fill a cavity








between gp120 and gp41 to








stabilize gp41 disordered region








and interaction between gp120








and gp41





0198
A192
BG505.SOSIP.R6.664.
BG505
SOSIP, R6, 664, T332N
Y177W, I323F
CavF at C-term of beta C, C-term




T332N_Y177W_I323F



of beta V3B. Substitute- 323 F,








Y, W. Fills cavity between V3








and gp120 core to stabilize








closed cap





0199
A193 
BG505SOS.R6.664.T332N_G41C A541C
BG505
SOS, R6, 664, T332N
G41C/A541C
DS- Fixes ground state, DS








between gp120 and gp41





0200
A194 
BG505.SOSIP.R6.664.T332N_G41C A541C
BG505
SOSIP, R6, 664, T332N
G41C/A541C
DS- Fixes ground state, DS








between gp120 and gp41





0201
A195
BG505.R6.664.T332N_G41C A541C
BG505
R6, 664, T332N
G41C/A541C
DS, non SOSIP- Fixes ground








state, DS between gp120 and gp41





0202
A196
BG505,SOS.R6.664.T332N_547-
BG505
SOS, R6, 664, T332N
547-GGPGGPGG-569
Prevent α6 to α7 transition




GGPGGPGG-569









0203
A197
BG505,SOS.R6.664.T332N_547-
BG505
SOS, R6, 664, T332N
547-GGGGPGGPG-569
Prevent α6 to α7 transition




GGGGPGGPG-569









0204
A198
BG505,SOS.R6.664.T332N_547-
BG505
SOS, R6, 664, T332N
547-GGGPGGG-569
Prevent α6 to α7 transition




GGGPGGG-569









0205
A199
BG505,SOS.R6.664.T332N_547-
BG505
SOS, R6, 664, T332N
547-GGPGGGGPGG-569
Prevent α6 to α7 transition




GGPGGGGPGG-569









0206
A200
BG505.SOSIP.R6.664.T332N_Q551P
BG505
SOSIP, R6, 664, T332N
Q551P
Prevent α6 to α7 transition





0207
A201
BG505.SOSIP.R6.664.T332N_L556P
BG505
SOSIP, R6, 664, T332N
L556P
Prevent α6 to α7 transition





0208
A202
BG505.SOSIP.R6.664.T332N_H564P
BG505
SOSIP, R6, 664, T332N
H564P
Prevent α6 to α7 transition





0209
A203 
BG505.SOSIP.R6.664.T332N_L568P
BG505
SOSIP, R6, 664, T332N
L568P
Prevent α6 to α7 transition





0210
B001
BG505,IP.664.T332N_bC-10In
BG505
IP, 664, T332N,
508(REKR)511 → 10 A.A. 
Single chain; no SOS; with 







linker
I559P





0211
B002
BG505,IP.664.T332N_bC-10ln_R166W
BG505
IP, 664, T332N
508(REKR)511 replaced by
Single chain; no SOS; with







10 A.A. linker, R166W
I559P; with R166W





0212
B003
BG505,IP.664.T332N_bC-11ln
BG505
IP, 664, T332N
508(REKR)511 → 11 A.A.
Single chain; no SOS; with







linker
I559P





0213
B004
BG505,IP.664.T332N_bC-11ln_R166W
BG505
IP, 664, T332N
508(REKR)511 → 11 A.A.
Same as Seq_211







linker, R166W






0214
B005
BG505,IP.664.T332N_bC-12ln
BG505
IP, 664, T332N
508(REKR)511 → 12 A.A.
Single chain; no SOS; with







linker
I559P





0215
B006
BG505,IP.664.T332N_bC-12ln_R166W
BG505
IP, 664, T332N
508(REKR)511 → 12 A.A.
Same as Seq_211







linker, R166W






0216
B007
BG505,IP.664.T332N_bC-13ln
BG505
IP, 664, T332N
508(REKR)511 → 13 A.A.
Single chain; no SOS; with







linker
I559P





0217
B008
BG505,IP.664.T332N_bC-13ln_R166W
BG505
IP, 664, T332N
508(REKR)511 → 13 A.A.
Same as Seq_211







linker, R166W






0218
B009
BG505,IP.664.T332N_bC-14ln
BG505
IP, 664, T332N
508(REKR)511 → 14 A.A.
Single chain; no SOS; with







linker
I559P





0219
B010
BG505,IP.664.T332N_bC-14ln_R166W
BG505
IP, 664, T332N
508(REKR)511 → 14 A.A.
Same as Seq_211







linker, R166W






0220
B011
BG505,IP.664.T332N_bC-15ln
BG505
IP, 664, T332N
508(REKR)511 → 15 A.A.
Single chain; no SOS; with







linker
I559P





0221
B012
BG505,IP.664.T332N_bC-15ln_R166W
BG505
IP, 664, T332N
508(REKR)511 → 15 A.A.
Same as Seq_211







linker, R166W






0222
B013
BG505,IP.664.T332N_bC-1ln
BG505
IP, 664, T332N
508(REKR)511 → 1 A.A.
Single chain; no SOS; with







linker
I559P





0223
B014
BG505,IP.664.T332N_bC-1ln_R166W
BG505
IP, 664, T332N
508(REKR)511 → 1 A.A.
Same as Seq_211







linker, R166W






0224
B015
BG505,1P.664.T332N_bC-20ln
BG505
IP, 664, T332N
508(REKR)511 → 20 A.A.
Single chain; no SOS; with







linker
I559P





0225
B016
BG505,IP.664.T332N_bC-20ln_R166W
BG505
IP, 664, T332N
508(REKR)511 → 20 A.A.
Same as Seq_211







linker, R166W






0226
B017
BG505,IP.664.T332N_bC-2ln
BG505
IP, 664, T332N
508(REKR)511 → 2 A.A.
Single chain; no SOS; with







linker
I559P





0227
B018
BG505,IP.664.T332N_bC-2ln_R166W
BG505
IP, 664, T332N
508(REKR)511 → 2 A.A.
Same as Seq_211







linker, R166W






0228
B019
BG505,IP.664.T332N_bC-3ln
BG505
IP, 664, T332N
508(REKR)511 → 3 A.A.
Single chain; no SOS; with







linker
I559P





0229
B020
BG505,IP.664.T332N_bC-3ln_R166W
BG505
IP, 664, T332N
508(REKR)511 → 3 A.A.
Same as Seq_211







linker, R166W






0230
B021
BG505,IP.664.T332N_bC-4ln
BG505
IP, 664, T332N
508(REKR)511 replaced by
Single chain; no SOS; with







4 A.A. linker
I559P





0231
B022
BG505,IP.664.T332N_bC-4ln_R166W
BG505
IP, 664, T332N
508(REKR)511 → 4 A.A.
Same as Seq_211







linker, R166W






0232
B023
BG505,IP.664.T332N_bC-5ln
BG505
IP, 664, T332N
508(REKR)511 → 5 A.A.
Single chain; no SOS; with







linker
I559P





0233
B024
BG505,IP.664.T332N_bC-5ln_R166W
BG505
IP, 664, T332N
508(REKR)511 → 5 A.A.
Same as Seq_211







linker, R166W






0234
B025
BG505,IP.664.T332N_bC-6ln
BG505
IP, 664, T332N
508(REKR)511 → 6 A.A.
Single chain; no SOS; with







linker
I559P





0235
B026
BG505,IP.664.T332N_bC-6ln_R166W
BG505
IP, 664, T332N
508(REKR)511 → 6 A.A.
Same as Seq_211







linker, R166W






0236
B027
BG505,IP.664.T332N_bC-7ln
BG505
IP, 664, T332N
508(REKR)511 → 7 A.A.
Single chain; no SOS; with







linker
I559P





0237
B028
BG505,IP.664.T332N_bC-7ln_R166W
BG505
IP, 664, T332N
508(REKR)511 → 7 A.A.
Same as Seq_211







linker, R166W






0238
B029
BG505,IP.664.T332N_bC-8ln
BG505
IP, 664, T332N
508(REKR)511 → 8 A.A.
Single chain; no SOS; with







linker
I559P





0239
B030
BG505,IP.664.T332N_bC-8ln_R166W
BG505
IP, 664, T332N
508(REKR)511 → 8 A.A.
Same as Seq_211







linker, R166W






0240
B031
BG505,IP.664.T332N_bC-9ln
BG505
IP, 664, T332N
508(REKR)511 → 9 A.A.
Single chain; no SOS; with







linker
I559P





0241
B032
BG505,IP.664.T332N_bC-9ln_R166W
BG505
IP, 664, T332N
508(REKR)511 → 9 A.A.
Same as Seq_211







linker, R166W






0242
B033
BG505.664.T332N_C-10ln
BG505
664, T332N
508(REKR)511 → 10 A.A.
Single chain; no SOSIP







linker






0243
B034
BG505.664.T332N_C-10ln_Q551F
BG505
664, T332N
508(REKR)511 → 10 A.A.
Single chain; no SOS; with







linker; Q551F
Q551F





0244
B035
BG505.664.T332N_C-11ln
BG505
664, T332N
508(REKR)511 → 11 A.A.
Single chain; no SOSIP







linker






0245
B036
BG505.664.T332N_C-12ln
BG505
664, T332N
508(REKR)511 → 12 A.A.
Single chain; no SOSIP







linker






0246
B037
BG505.664.T332N_C-13ln
BG505
664, T332N
508(REKR)511 → 13 A.A.
Single chain; no SOSIP







linker






0247
B038
BG505.664.T332N_C-14ln
BG505
664, T332N
508(REKR)511 → 14 A.A.
Single chain; no SOSIP







linker






0248
B039
BG505.664.T332N_C-15ln
BG505
664, T332N
508(REKR)511 → 15 A.A.
Single chain; no SOSIP







linker






0249
B040
BG505.664.T332N_C-1ln
BG505
664, T332N
508(REKR)511 → 1 A.A.
Single chain; no SOSIP







linker






0250
B041
BG505.664.T332N_C-2ln
BG505
664, T332N
508(REKR)511 → 2 A.A.
Single chain; no SOSIP







linker






0251
B042
BG505.664.T332N_C-3ln
BG505
664, T332N
508(REKR)511 → 3 A.A.
Single chain; no SOSIP







linker






0252
B043
BG505.664.T332N_C-4ln
BG505
664, T332N
508(REKR)511 → 4 A.A.
Single chain; no SOSIP







linker






0253
B044
BG505.664.T332N_C-5ln
BG505
664, T332N
508(REKR)511 → 5 A.A.
Single chain; no SOSIP







linker






0254
B045
BG505.664.T332N_C-6ln
BG505
664, T332N
508(REKR)511 → 6 A.A.
Single chain; no SOSIP







linker






0255
B046
BG505.664.T332N_C-7ln
BG505
664, T332N
508(REKR)511 → 7 A.A.
Single chain; no SOSIP







linker






0256
B047
BG505.664.T332N_C-8ln
BG505
664, T332N
508(REKR)511 → 8 A.A.
Single chain; no SOSIP







linker






0257
B048
BG505.664.T332N_C-9ln
BG505
664, T332N
508(REKR)511 → 9 A.A.
Single chain; no SOSIP







linker






0258
B049
BG505.IP.664.T332N_Gp120-HR2-HR1
BG505
IP, 664, T332N

circular permutant single chain





0259
B050
BG505.IP.664.T332N_Gp120-Linker-HR1-
BG505
IP, 664, T332N

linker gp120-HR1




GCN4









0260
B051
BG505.IP.664.T332N_SOScircuit2noC
BG505
IP, 664, T332N

circular permutant single chain





0261
B052
BG505.IP.664.T332N_SOScircuit3-noFus
BG505
IP, 664, T332N

circular permutant single chain





0262
B053
BG505.IP.664.T332N_SOScircuit4noC-noFus
BG505
IP, 664, T332N

circular permutant single chain





0263
B054
BG505.IP.664.T332N_SOScircuit9-
BG505
IP, 664, T332N

circular permutant single chain




GCN4coredownCC









0264
B055
BG505.IP.664.T332N_SOScircuit14-
BG505
IP, 664, T332N

circular permutant single chain




HR1envHR2-GCN4coredown









0265
B056
BG505.IP.664.T332N_SOScircuit15-
BG505
IP, 664, T332N

circular permutant single chain




HR1envHR2-GCN4coredown









0266
B057
BG505.IP.664.T332N_SOScircuit16-
BG505
IP, 664, T332N

circular permutant single chain




HR1envHR2-GCN4coredown









0267
B058
BG505.IP.664.T332N_SOScircuit17-
BG505
IP, 664, T332N

circular permutant single chain




HR1envHR2









0268
B059
BG505.IP.664.T332N_SOScircuit18-
BG505
IP, 664, T332N

circular permutant single chain




HR1envHR2









0269
B060
BG505.IP.664.T332N_SOScircuit4noC-
BG505
IP, 664, T332N

circular permutant single chain




noFus_CMVR-3c-His-R166W









0270
B061
BG505.IP.664.T332N_1.ZM53.R166W
BG505
IP, 664, T332N
R166W, circ. permut.
circ. Permut. single chain in








ZM53, with R166W





0271
B062
BG505.IP.664.T332N_10.ZM53.R166W
BG505
IP, 664, T332N
R166W, circ. permut.
circ. Permut. single chain in








ZM53, with R166W





0272
B063
BG505.IP.664.T332N_10_BG505_Nterm_H1
BG505
IP, 664, T332N
circ. permut.
circular permutant single chain





0273
B064
BG505.IP.664.T332N_10_BG505_Nterm_H1_
BG505
IP, 664, T332N
P313W, circ. permut.
circular permutant single chain




P313W









0274
B065
BG505.IP.664.T332N_10_BG505_Nterm_H1_
BG505
IP, 664, T332N
P313W, R166W, circ.
circular permutant single chain




P313W-R166W


permut.






0275
B066
BG505.IP.664.T332N_10_BG505_Nterm_H1_
BG505
IP, 664, T332N
R166W, circ. permut.
circular permutant single chain




R166W









0276
B067
BG505.IP.664.T332N_11.ZM53.R166W
BG505
IP, 664, T332N
R166W, circ. permut.
circular permutant single chain





0277
B068
BG505.IP.664.T332N_11_BG505_Nterm_H1
BG505
IP, 664, T332N
circ. permut.
circular permutant single chain





0278
B069
BG505.IP.664.T332N_11_BG505_Nterm_H1_
BG505
IP, 664, T332N
P313W, circ. permut.
circular permutant single chain




P313W









0279
B070
BG505.IP.664.T332N_11_BG505_Nterm_H1_
BG505
IP, 664, T332N
P313W, R166W, circ.
circular permutant single chain




P313W-R166W


permut.






0280
B071
BG505.IP.664.T332N_11_BG505_Nterm_H1_
BG505
IP, 664, T332N
R166W, circ. permut.
circular permutant single chain




R166W









0281
B072
BG505.IP.664.T332N_12.ZM53.R166W
BG505
IP, 664, T332N
R166W, circ. permut.
circular permutant single chain





0282
B073
BG505.IP.664.T332N_12_BG505_Nterm_H1
BG505
IP, 664, T332N
circ. permut.
circular permutant single chain





0283
B074
BG505.IP.664.T332N_12_BG505_Nterm_H1_
BG505
IP, 664, T332N
P313W, circ. permut.
circular permutant single chain




P313W









0284
B075
BG505.IP.664.T332N_12_BG505_Nterm_H1_
BG505
IP, 664, T332N
P313W, R166W, circ.
circular permutant single chain




P313W-R166W


permut.






0285
B076
BG505.IP.664.T332N_12_BG505_Nterm_H1_
BG505
IP, 664, T332N
R166W, circ. permut.
circular permutant single chain




R166W









0286
B077
BG505.IP.664.T332N_13_BG505_6RLinked
BG505
IP, 664, T332N
Linker at cleavage site
Linker at cleavage site





0287
B078
BG505.IP.664.T332N_14_BG505_6RLinked
BG505
IP, 664, T332N
Linker at cleavage site
Linker at cleavage site





0288
B079
BG505.IP.664.T332N_15_BG505_6RLinked
BG505
IP, 664, T332N
Linker at cleavage site
Linker at cleavage site





0289
B080
BG505.IP.664.T332N_16_BG505_6RLinked
BG505
IP, 664, T332N
Linker at cleavage site
Linker at cleavage site





0290
B081
BG505.IP.664.T332N_1_BG505_Nterm_H1
BG505
IP, 664, T332N
circ. permut.
circular permutant single chain





0291
B082
BG505.IP.664.T332N_1_BG505_Nterm_H1_
BG505
IP, 664,T332N
R166W, circ. permut.
circular permutant single chain




R166W









0292
B083
BG505.IP.664.T332N_2_BG505_Nterm_H1
BG505
IP, 664, T332N
circ. permut.
circular permutant single chain





0293
B084
BG505.IP.664.T332N_3_BG505_Nterm_H1
BG505
IP, 664, T332N
circ. permut.
circular permutant single chain





0294
B085
BG505.IP.664.T332N_4.ZM53.R166W
BG505
IP, 664, T332N
R166W, circ. permut.
circular permutant single chain








in ZM53, with R166W





0295
B086
BG505.IP.664.T332N_4_BG505_Nterm_H1
BG505
IP, 664, T332N
circ. permut.
Circular permutant single chain





0296
B087
BG505.IP.664.T332N_4_BG505_Nterm_H1_
BG505
IP, 664, T332N
R166W, circ. permut.
circular permutant single chain,




R166W



with R166W





0297
B088
BG505.IP.664.T332N_5_BG505_Nterm_H1
BG505
IP, 664, T332N
circ. permut.
Circular permutant single chain





0298
B089
BG505.IP.664.T332N_6_BG505_Nterm_H1
BG505
IP, 664, T332N
circ. permut.
Circular permutant single chain





0299
B090
BG505.IP.664.T332N_7_BG505_Nterm_H1
BG505
IP, 664, T332N
circ. permut.
Circular permutant single chain





0300
B091
BG505.IP.664.T332N_7_BG505_Nterm_H1_
BG505
IP, 664, T332N
R166Wcirc. permut.
circular permutant single chain,




R166W



with R166W





0301
B092
BG505.IP.664.T332N_8_BG505_Nterm_H1
BG505
IP, 664, T332N
circ. permut.
Circular permutant single chain





0302
B093
BG505.IP.664.T332N_9_BG505_Nterm_H1
BG505
IP, 664, T332N
circ. permut.
Circular permutant single chain





0303
B094
BG505.SOSIP.664.T332N_29_gp120-HR2_
BG505
SOSIP, 664, T332N
A433P, circ. permut.
circular permutant single chain,




A433P



with A433P





0304
B095
BG505.SOSIP.664.T332N_30_gp120-HR2_
BG505
SOSIP, 664, T332N
A433P, circ. permut.
circular permutant single chain,




A433P



with A433P





0305
B096
CH117.4_332N_IP_10ln
CH117.4
IP; 664; T332N
508(REKR)511 → 10 A.A.
Single chain; no SOS; with







linker; 332N
I559P





0306
B097
CNE58_1P_10ln
CNE58
IP; 664
508(REKR)511 → 10 A.A.
Single chain; no SOS; with







linker
I559P





0307
B098
Cap256-SU_IP_10ln
Cap256-SU
IP; 664
Same as Seq_307
Single chain; no SOS; with








I559P





0308
B099
SHIV-1157ipd3N4_IP_10ln
1157ipd3N4
IP; 664
Same as Seq_307
Single chain; no SOS; with








I559P





0309
B100
ZM53_IP_10ln
ZM53
IP; 664
Same as Seq_307
Single chain; no SOS; with








I559P





0310
B101
C-10ln_Q551F
BG505
664
664; 508(REKR)511 → 10
Single chain; no SOS; with







A.A. linker; Q551F
I559P; with Q551F





0311
B102
TF-B_THRO_TF1_10ln_Q551F
THRO_TF1
664
664; 508(REKR)511 → 10
Single chain; no SOS; with







A.A. linker; Q551F
Q551F





0312
B103
TF-C_1245045_10ln_Q551F
1245045
664
664; 508(REKR)511 → 10
Single chain; no SOS; with







A.A. linker; Q551F
Q551F





0313
B104
3301_V1_C24_10ln_Q551F
3301_V1_C24
664
664; 508(REKR)511 → 10
Single chain; no SOS; with







A.A. linker; Q551F
Q551F





0314
B105
TF-C_19157834_v1_10ln_Q551F_P162T
19157834_v1
664
664; 508(REKR)511 → 10
Single chain; no SOS; with







A.A. linker; Q551F; P162T
Q551F





0315
B106
25925-2.22_10ln_Q551F
25925-2.22
IP; 664
508(REKR)511 → 10 A.A.
Single chain; no SOS; with







linker; Q551F
Q551F





0316
B107
CAP210.E8_10ln_Q551F
CAP210.E8
IP; 664
508(REKR)511 → 10 A.A.
Single chain; no SOS; with







linker; Q551F
Q551F





0317
B108
CNE58_IP_10ln_SU-strandC
CNE58
IP; 664
664; 508(REKR)511 → 10
Single chain; no SOS; with







A.A. linker
I559P; strand-C from CAP256-SU





0318
B109
CNE58_10ln_Q551F_SU-strandC
CNE58
IP; 664
508(REKR)511 → 10 A.A.
Single chain; no SOS; with







linker; Q551F
Q551F; strand-C from CAP256-SU





0319
B110
TF-B_THRO_TF1_IP_10ln
THRO_TF1
IP; 664
Same as Seq_307
Single chain; no SOS; with








I559P





0320
B111
25925-2.22_IP_10ln
25925-2.22
IP; 664
508(REKR)511 → 10 A.A.
Single chain; no SOS; with







linker
I559P





0321
B112
CAP210.E8_IP_10ln
CAP210.E8
IP; 664
508(REKR)511 → 10 A.A.
Single chain; no SOS; with







linker
I559P





0322
B113
TF-C_19157834_v1_IP_10ln_P162T
19157834_v1
IP; 664
664; 508(REKR)511 → 10
Single chain; no SOS; with







A.A. linker, P162T
I559P





0323
B114
3301_V1_C24_IP_10ln
3301_V1_C24
IP; 664
664; 508(REKR)511 → 10
Single chain; no SOS; with







A.A. linker
I559P





0324
B115
TF-C_1245045_IP_10ln
1245045
IP; 664
664; 508(REKR)511 → 10
Single chain; no SOS; with







A.A. linker
I559P





0325
B116
00836-2.5_332N_IP_10ln
00836-2.5
IP; 664
664; 508(REKR)511 → 10
Single chain; no SOS; with







A.A. linker, 332N
I559P





0326
B117
6322_V4_C1_332N_IP_10ln
6322_V4_C1
IP; 664
664; 508(REKR)511 → 10
Single chain; no SOS; with







A.A. linker, 332N
I559P





0327
B118
ZM53-R166W_bC-10ln_IP
ZM53
IP; 664
664; 508(REKR)511 → 10
Single chain; no SOS; with







A.A. linker, R166W
I559P





0328
B119
ZM53-R166W_bC-15ln_IP
ZM53
IP; 664
664; 508(REKR)511 → 15
Single chain; no SOS; with







A.A. linker, R166W
I559P





0329
B120 
ZM53-R166W_bC-20ln_IP
ZM53
IP; 664
664; 508(REKR)511 → 20
Single chain; no SOS; with







A.A. linker, R166W
I559P





0330
B121
ZM53-R166W_bC-7ln_IP
ZM53
IP; 664
664; 508(REKR)511 → 7
Single chain; no SOS; with







A.A. linker, R166W
I559P





0331
B122
ZM53-R166W_C-10ln
BG505
664
508(REKR)511 → 10 A.A.
Single chain; no SOS







linker, R166W






0332
B123
ZM53-R166W_C-15ln
BG505
664
508(REKR)511 → 15 A.A.
Single chain; no SOS







linker, R166W






0333
B124
ZM53-R166W_C-20ln
BG505
664
508(REKR)511 → 20 A.A.
Single chain; no SOS







linker, R166W






0334
B125
ZM53-R166W_C-7ln
BG505
664
508(REKR)511 → 7 A.A.
Single chain; no SOS







linker, R166W






0335
B126
BG505.SOSIP.664.T332N_del504-5185ln
BG505
SOSIP, 664, T332N
504-518 → 5 A.A. linker
Single chain + N-term of gp41;








with SOS; with I559P





0336
B127
BG505.SOSIP.664.T332N_del504-518_10ln
BG505
SOSIP, 664, T332N
504-518 → 10 A.A. linker
Same as Seq_0335





0337
B128
BG505.SOSIP.664.T332N_del504-518_15ln
BG505
SOSIP, 664, T332N
segment 504-518 →
Same as Seq_0335







15 A.A. linker 






0338
B129
BG505.SOSIP.664.T332N_del504-518_20ln
BG505
SOSIP, 664, T332N
segment 504-518 →
Same as Seq_0335







20 A.A. linker 






0339
B130
BG505.SOSIP.664.T332N_del505-518_5ln
BG505
SOSIP, 664, T332N
segment 505-518 → 5 
Same as Seq_0335







A.A. linker






0340
B131
BG505.SOSIP.664.T332N_del505-518_10ln
BG505
SOSIP, 664, T332N
segment 505-518 → 10 
Same as Seq_0335







A.A. linker






0341
B132
BG505.SOSIP.664.T332N_del505-518_15ln
BG505
SOSIP, 664, T332N
segment 505-518 → 15 
Same as Seq_0335







A.A. linker






0342
B133
BG505.SOSIP.664.T332N_del505-518_20ln
BG505
SOSIP, 664, T332N
segment 505-518 →
Same as Seq_0335







20 A.A. linker






0343
B134
BG505.SOSIP.664.T332N_del504-521_5ln
BG505
SOSIP, 664, T332N
segment 504-521 →
Same as Seq_0335







5 A.A. linker






0344
B135
BG505.SOSIP.664.T332N_del504-521_10ln
BG505
SOSIP, 664, T332N
segment 504-521 →
Same as Seq_0335







10 A.A. linker






0345
B136
BG505.SOSIP.664.T332N_del504-521_15ln
BG505
SOSIP, 664, T332N
segment 504-521 →
Same as Seq_0335







15 A.A. linker






0346
B137
BG505.SOSIP.664.T332N_del504-521_20ln
BG505
SOSIP, 664, T332N
segment 504-521 →
Same as Seq_0335







20 A.A. linker






0347
B138
BG505.SOSIP.664.T332N_del505-521_5ln
BG505
SOSIP, 664, T332N
segment 505-521 →
Same as Seq_0335







5 A.A. linker






0348
B139
BG505.SOSIP.664.T332N_del505-521_10ln
BG505
SOSIP, 664, T332N
segment 505-521 →
Same as Seq_0335







10 A.A. linker






0349
B140
BG505.SOSIP.664.T332N_del505-521_15ln
BG505
SOSIP, 664, T332N
segment 505-521 →
Same as Seq_0335







15 A.A. linker






0350
B141
BG505.SOSIP.664.T332N_del505-521_20ln
BG505
SOSIP, 664, T332N
segment 505-521 →
Same as Seq_0335







20 A.A. linker






0351
B142
BG505.SOSIP.664.T332N_c5ln
BG505
SOSIP, 664, T332N
508(REKR)511 → 5 A.A.
Same as Seq_0335







linker






0352
B143
BG505.SOSIP.664.T332N_c10ln
BG505
SOSIP, 664, T332N
508(REKR)511 → 10 A.A.
Same as Seq_0335







linker






0353
B144
BG505.SOSIP.664.T332N_c15ln
BG505
SOSIP, 664, T332N
508(REKR)511 → 15 A.A.
Same as Seq_0335







linker






0354
B145
BG505.SOSIP.664.T332N_c20ln
BG505
SOSIP, 664, T332N
508(REKR)511 → 20 A.A.
Same as Seq_0335







linker






0355
B146 
BG505.1P.664.T332N_del505-521_5ln
BG505
IP,664, T332N
segment 505-521 → 5 A.A.
Single chain + N-term of gp41;







linker
no SOS; with I559P





0356
B147
BG505.1P.664.T332N_del505-521_10ln
BG505
IP,664, T332N
segment 505-521 →
Single chain + N-term of gp41;







10 A.A. linker
no SOS; with I559P





0357
B148
BG505.1P.664.T332N_del505-521_15ln
BG505
IP,664, T332N
segment 505-521 →
Single chain + N-term of gp41;







15 A.A. linker
no SOS; with I559P





0358
B149
BG505.1P.664.T332N_del505-521_20ln
BG505
IP,664, T332N
segment 505-521 →
Single chain + N-term of gp41;







20 A.A. linker
no SOS; with I559P





0359
B150
BG505.SOSIP.664.T332N_sc BZ1
BG505
SOSIP, 664, T332N
cleavage site and NT of
Same as Seq_0335







fusion peptide replaced








by a flexible linker






0360
B151
BG505.SOSIP.664.T332N_sc BZ2
BG505
SOSIP, 664, T332N
Same as Seq_0359
Same as Seq_0335





0361
B152
BG505.SOSIP.664.T332N_sc BZ3
BG505
SOSIP, 664, T332N
Same as Seq_0359
Same as Seq_0335





0362
B153
BG505.SOSIP.664.T332N_sc BZ4
BG505
SOSIP, 664, T332N
Same as Seq_0359
Same as Seq_0335





0363
B154
BG505.SOSIP.664.T332N_sc BZ5
BG505
SOSIP, 664, T332N
Same as Seq_0359
Same as Seq_0335





0364
B155
BG505.SOSIP.664.T332N_sc BZ6
BG505
SOSIP, 664, T332N
Same as Seq_0359
Same as Seq_0335





0365
B156
BG505.SOSIP.664.T332N_sc BZ7
BG505
SOSIP, 664, T332N
Same as Seq_0359
Same as Seq_0335





0366
B157
BG505.SOSIP.664.T332N_sc BZ8
BG505
SOSIP, 664, T332N
Same as Seq_0359
Same as Seq_0335





0367
B158
BG505.SOSIP.664.T332N_sc BZ9
BG505
SOSIP, 664, T332N
Same as Seq_0359
Same as Seq_0335





0368
B159
BG505.SOSIP.664.T332N_sc BZ10
BG505
SOSIP, 664, T332N
Same as Seq_0359
Same as Seq_0335





0369
B160
BG505.SOSIP.664.T332N_sc BZ11
BG505
SOSIP, 664, T332N
Same as Seq_0359
Same as Seq_0335





0370
B161
BG505.SOSIP.664.T332N_sc BZ12
BG505
SOSIP, 664, T332N
Same as Seq_0359
Same as Seq_0335





0371
B162
BG505.SOSIP.664.T332N_sc BZ2
BG505
SOSIP, 664, T332N
cleavage site and NT of
Same as Seq_0335




G312C/S199C/R166C/V127C


fusion peptide replaced








by a flexible linker;








G312C/S199C/R166C/V127C






0372
B163
BG505.SOSIP.664.T332N_sc BZ3
BG505
SOSIP, 664, T332N
cleavage site and NT of
Same as Seq_0335




G312C/S199C/R166C/V127C


fusion peptide replaced








by a flexible linker;








G312C/S199C/R166C/V127C






0373
B164
BG505.IP.664.T332N_bC10ln-5ln-
BG505
IP, 664, T332N
on ferritin with a 5-
ferritin for linker replacement




HpyFerritin


linker
of gp120-gp41 cleavage site;








no SOS; with I559P





0374
B165
BG505.IP.664.T332N_bC10ln-10ln-
BG505
IP, 664, T332N
on ferritin with a 10-
Same as Seq_0373




HpyFerritin


linker






0375
B166
BG505.IP.664.T332N_bC10ln-15ln-
BG505
IP, 664, T332N
on ferritin with a 15-
Same as Seq_0373




HpyFerritin


linker






0376
B167
BG505.664.T332N_FC10ln-5ln-
BG505
664, T332N
on ferritin with a 5-
ferritin for linker replacement




HpyFerritin


linker; Q551F
of gp120-gp41 cleavage site;








no SOS; with Q551F





0377
B168
BG505.664.T332N_FC10ln-10ln-HpyFerritin
BG505
664, T332N
on ferritin with a 10-
Same as Seq_0376







linker; Q551F






0378
B169
BG505.664.T332N_FC10ln-15ln-HpyFerritin
BG505
664, T332N
on ferritin with a 15-
Same as Seq_0376







linker; Q551F






0379
H009
Cap256-SU_bg505-NCgp120 + gp41.SOSIP
Cap256-SU/BG505
SOSIP; 664; R6
BG505 Platform,






chimera

remainder = Cap256-SU






0380
H010
1157ipd3N4_bg505-NCgp120 + gp41.SOSIP
1157ipd3N4/BG505
SOSIP; 664; R6
BG505 Platform,






chimera

remainder = 1157ipd3N4






0381
H011
CH117.4_332N_bg505-NCgp120 + gp41.SOSIP
CH117.4_332N/
SOSIP; 664; R6
BG505 Platform,






BG505 chimera

remainder = CH117.4_332N






0382
H012
CNE58_SU-strandC_bg505-NCgp120 +
CNE58_SU-
SOSIP; 664; R6
BG505 Platform, Res. 166-





gp41.SOSIP
strandC/

173 (strand C) from






BG505 chimera

CAP256-SU, remainder =








CNE58






0383
H013
25925-2.22_bg505-NCgp120 + gp41.SOSIP
25925-2.22/BG505
SOSIP; 664; R6
BG505 Platform,






chimera

remainder = 25925-2.22






0384
H014
3301_V1_C24_bg505-NCgp120 + gp41.SOSIP
3301_V1_C24/
SOSIP; 664; R6
BG505 Platform,






BG505 chimera

remainder = 3301_V1_C24






0385
H015
ZM53-R166W_bg505-NCgp120 + gp41.SOSIP
ZM53-R166W/BG505
SOSIP; 664; R6
BG505 Platform,






chimera

remainder = ZM53-R166W






0386
H016
ZM53_bg505-NCgp120 + gp41.SOSIP
ZM53/BG505
SOSIP; 664; R6
BG505 Platform,






chimera

remainder = ZM53 gp120






0387
B170
BG505.SOSIP.664.T332N_SC_1
BG505
SOSIP, 664, T332N
Circular permutant
Link gp120 Cterm to gp41 resi








664, and circ. permutate thru








rest of gp41, end at 518





0388
B171
BG505.SOSIP.664.T332N_SC_2
BG505
SOSIP, 664, T332N
Circular permutant
same as PA_SC_1 above, vary








linker





0389
B172
BG505.SOSIP.664.T332N_SC_3
BG505
SOSIP, 664, T332N
Circular permutant
same as PA_SC_1 and PA_SC_2








above, vary linker





0390
B173
BG505.SOSIP.664.T332N_SC_4
BG505
SOSIP, 664, T332N
Circular permutant
connects gp120 C term to region








around 606-609, and extends








forward, turncating at different








regions)





0391
B174
BG505.SOSIP.664.T332N_SC_5
BG505
SOSIP, 664, T332N
Circular permutant
only the inner circle of helices








to hold the trimer together





0392
B175
BG505.SOSIP.664.T332N_SC_6
BG505
SOSIP, 664, T332N
Circular permutant
Same as Seq_0391





0393
B176
BG505.SOSIP.664.T332N_SC_7
BG505
SOSIP, 664, T332N
Circular permutant
Same as Seq_0391





0394
B177
BG505.SOSIP.664.T332N_SC_8
BG505
SOSIP, 664, T332N
Circular permutant
Same as Seq_0391





0395
B178
BG505.SOSIP.664.T332N_SC_9
BG505
SOSIP, 664, T332N
Circular permutant
Start from resi 518, go to 664,








connect to C-term of gp120,








circ. permutate thru gp120





0396
B179
BG505.SOSIP.664.T332N_SC_10
BG505
SOSIP, 664, T332N
Circular permutant
same as PA_SC_9, change linker





0397
B180
BG505.SOSIP.664.T332N_SC_11
BG505
SOSIP, 664, T332N
Circular permutant
same as PA_SC_9, change linker





0398
B181
BG505.IP.664.T332N_1.2
BG505
SOSIP, 664, T332N
Circular permutant
Circular permutant single chain





0399
B182
BG505.IP.664.T332N_1.3
BG505
SOSIP, 664, T332N
Circular permutant
Circular permutant single chain





0400
B183
BG505.IP.664.T332N_2.1
BG505
SOSIP, 664, T332N
Circular permutant
Circular permutant single chain





0401
B184
BG505.IP.664.T332N_2.2
BG505
SOSIP, 664, T332N
Circular permutant
Circular permutant single chain





0402
B185
BG505.IP.664.T332N_2.3
BG505
SOSIP, 664, T332N
Circular permutant
Circular permutant single chain





0403
B186
BG505.IP.664.T332N_3.1
BG505
SOSIP, 664, T332N
Circular permutant
Circular permutant single chain





0404
B187
BG505.IP.664.T332N_3.3
BG505
SOSIP, 664, T332N
Circular permutant
Circular permutant single chain





0405
B188
BG505.IP.664.T332N.sc1
BG505
IP, 664, T332N
44-500-gsg-34-43-gsgg-
Circular permutant single chain







526-664






0406
B189
BG505.SOSIP.664.T332N.sc2
BG505
SOSIP, 664, T332N
44-502-ggsgg-34-43-gsgg-
Circular permutant single chain







526-664






0407
B190
BG505.IP.664.T332N.sc3
BG505
IP, 664, T332N
44-500-gsg-34-42-gsgg-
Circular permutant single chain







525-664






0408
B191
BG505.SOSIP.664.T332N.sc4
BG505
SOSIP, 664, T332N
44-502-ggsgg-34-42-gsgg-
Circular permutant single chain







525-664






0409
C001
BG505.SOSIP.R6.664.T332N_T90
BG505
SOSIP, R6, 664, T332N
T90C
gp140-35022complex-disulfide to








35O22_S80





0410
C002
BG505.SOSIP.R6.664.T332N_P238
BG505
SOSIP, R6, 664, T332N
P238C
gp140-35022complex-disulfide to








35O22_P77





0411
C003
BG505.SOSIP.R6.664.T332N_T529
BG505
SOSIP, R6, 664, T332N
T529C
gp140-35022complex-disulfide to








35O22_D111





0412
C004
BG505.SOSIP.R6.664.T332N_D624
BG505
SOSIP, R6, 664, T332N
D624C
gp140-35022complex-disulfide to








35O22_L109 or G112





0413
C005
BG505.SOSIP.R6.664.T332N_N625
BG505
SOSIP, R6, 664, T332N
N625C
gp140-35022complex-disulfide to








35O22_L109





0414
C006 
35O22_P77C
Ab 35O22

P77C
gp140-35O22complex-








BG505.SOSIP.R6.664.T332N_P238





0415
C007
35O22_S80C
Ab 35O22

S80C
gp140-35O22complex-








BG505.SOSIP.R6.664.T332N_T90





0416
C008 
35O22_L109C
Ab 35O22

L109C
gp140-35O22complex-








BG505.SOSIP.R6.664.T332N_D624 or








BG505.SOSIP.R6.664.T332N_N625





0417
C009
35O22_D111C
Ab 35O22

D111C
gp140-35O22complex-








BG505.SOSIP.R6.664.T332N_T529





0418
C010
35O22_G112C
Ab 35O22

G112C
gp140-35O22complex-








BG505.SOSIP.R6.664.T332N_D624





0419
C011
BG505.SOSIP.R6.664.T332N_D624C
BG505
SOSIP, R6, 664, T332N
D624C
gp140-35O22complex





0420
C012
BG505.SOSIP.R6.664.T332N_G459C
BG505
SOSIP, R6, 664, T332N
G459C
gp140-VRCO1complex





0421
C013
JRFL IP 3C Strep G459C
JRFL
IP
3C Strep G459C
gp140-VRCO1complex





0422
C014
BS208.61 SOSIP, R6, 664, G459C
BS208.61
SOSIP, R6, 664
G459C
gp140-VRCO1complex





0423
C015
KER2018.11 SOSIP, R6, 664, G459C
KER2018.11
SOSIP, R6, 664
G459C
gp140-VRCO1complex





0424
C016
C4118.09 SOSIP, R6, 664, G459C
C4118.09
SOSIP, R6, 664
G459C
gp140-VRCO1complex





0425
C017
TH966.8 SOSIP, R6, 664, G459C
TH966.8
SOSIP, R6, 664
G459C
gp140-VRCO1complex





0426
C018
WITO.33 SOSIP, R6, 664, G459C
WITO.33
SOSIP, R6, 664
G459C
gp140-VRCO1complex





0427
C019
CH181.12 SOSIP, R6, 664, G459C
CH181.12
SOSIP, R6, 664
G459C
gp140-VRCO1complex





0428
C020
BB201.B42 SOSIP, R6, 664, G459C
BB201.B42
SOSIP, R6, 664
G459C
gp140-VRCO1complex





0429
C021
Q842.d12 SOSIP, R6, 664, G459C
Q842.d12
SOSIP, R6, 664
G459C
gp140-VRCO1complex





0430
C022
AC10.29 SOSIP, R6, 664, G459C
AC10.29
SOSIP, R6, 664
G459C
gp140-VRCO1complex





0431
C023
BXO8_16 SOSIP, R6, 664, G459C
BXO8_16
SOSIP, R6, 664
G459C
gp140-VRCO1complex





0432
C024
257102.43 SOSIP, R6, 664, G459C
257102.43
SOSIP, R6, 664
G459C
gp140-VRCO1complex





0433
C025
259252.22 SOSIP, R6, 664, G459C
259252.22
SOSIP, R6, 664
G459C
gp140-VRCO1complex





0434
C026
SO18_18 SOSIP, R6, 664, G459C
SO18_18
SOSIP, R6, 664
G459C
gp140-VRCO1complex





0435
C027
X1193.c1 SOSIP, R6, 664, G459C
X1193.c1
SOSIP, R6, 664
G459C
gp140-VRCO1complex





0436
C028
SU SOSIP, R6, 664, G459C
SU
SOSIP, R6, 664
G459C
gp140-VRCO1complex





0437
C029
BG505.SOSIP G459C V1V2 Swap BB201.B42
BG505
SOSIP
G459C, V1V2 Swap
gp140-VRCO1complex







BB201.B42






0438
C030
BG505.SOSIP G459C V1V2 Swap KER2018.11
BG505
SOSIP
G459C, V1V2 Swap
gp140-VRCO1complex







KER2018.11






0439
C031
BG505.SOSIP G459C V1V2_Swap_CH070.1
BG505
SOSIP
G459C, V1V2 Swap CH070.1
gp140-VRCO1complex





0440
C032
BG505.SOSIP G459C V1V2_Swap_ZM233.6
BG505
SOSIP
G459C, V1V2 Swap ZM233.6
gp140-VRCO1complex





0441
C033
BG505.SOSIP G459C V1V2 Swap Q23.17
BG505
SOSIP
G459C, V1V2 Swap Q23.17
gp140-VRCO1complex





0442
C034
BG505.SOSIP G459C V1V2 Swap A244
BG505
SOSIP
G459C, V1V2 Swap A244
gp140-VRCO1complex





0443
C035
BG505.SOSIP G459C V1V2 Swap WIT0.33
BG505
SOSIP
G459C, V1V2 Swap WITO.33
gp140-VRCO1complex





0444
C036
BG505_Cap256_G459C SU_V1V2_swap
BG505
SOSIP
G459C, SU_V1V2_swap
gp140-VRCO1complex





0445
C037
VRCO1 H A60C-His
VRCO1 H Ab

A60C






0446
C038 
VRCO1 H R61C-His
VRCO1 H Ab

A61C






0447
C039
VRCO1 L
VRCO1 L Ab








0448
C040
VRCO1 H-His
VRCO1 H Ab








0449
C041
VRCO1LH scFv Tbn-His-Strep
VRCO1 Ab
GGGGSGGGGSGGGGS
GGGGSGGGGSGGGGS






0450
C042
VRCO1LH scFv Tbn-His
VRCO1 Ab
GGGGSGGGGSGGGGS
GGGGSGGGGSGGGGS






0451
C043
VRCO1LH scFv C60 Tbn-His
VRCO1 Ab
GGGGSGGGGSGGGGS
GGGGSGGGGSGGGGS






0452
C044
simVRCO1.2 (Thr) H
VRCO1 H Ab








0453
C045
simVRCO1.2 C60 (Thr) H
VRCO1 H Ab

A60C






0454
C046
simVRCO1.2 C60 (Thr) HS
VRCO1 H Ab

A60C






0455
C047
simVRCO1.2 L
VRCO1 L Ab








0456
C048
simVRCO1.2 C60 (Thr) H
VRCO1 H Ab

A60C






0457
C049
BG505.SOSIP.R6.664.T332N_I323C
BG505
SOSIP, R6, 664, T332N
I323C
covalently bonded gp140-








PGT122complex





0458
C050
BG505.SOSIP.R6.664.T332N_G324C
BG505
SOSIP, R6, 664, T332N
G324C
covalently bonded gp140-








PGT122complex





0459
C051
G122LH F67C
PGT122 H Ab

F67C






0460
C052
G122LH G29C
PGT122 H Ab

G29C






0461
D001
BG505.SOSIP.R6.664.T332N_Glyc504
BG505
SOSIP, R6, 664, T332N
504N/506T
Glycan at R504





0462
D002
BG505.SOSIP.R6.664.T332N_Glyc661
BG505
SOSIP, R6, 664, T332N
661N/663T
Glycan at L661





0463
D003
BG505.SOSIP.R6.664.T332N_Glyc504-661
BG505
SOSIP, R6, 664, T332N
504N/506T, 661N/663T
Glycans at R504 and L661





0464
D004
BG505, SOSIP.R6.664.T332N_K502N_R504T
BG505
SOSIP, R6, 664, T332N
K502N/R504T
Glycan at K502





0465
D005
BG505, SOSIP.R6.664.T332N_Q658N_L660T
BG505
SOSIP, R6, 664, T332N
Q658N/L660T
Glycan at Q658





0466
D006
BG505, SOSIP.R6.664.T332N_W35T
BG505
SOSIP, R6, 664, T332N
W35T
Glycan at N33





0467
D007
BG505, SOSIP.R6.664.T332N_W35N
BG505
SOSIP, R6, 664, T332N
W35N
Glycan at W35





0468
D008
BG505, SOSIP.R6.664.T332N_W35N_R504N_
BG505
SOSIP, R6, 664, T332N
W35N, R504N/V506T
Glycan at W35 and R504




V506T









0469
D009
BG505, SOSIP.R6.664.T332N_W35T_gly661
BG505
SOSIP, R6, 664, T332N
W35T, gly661
Glycan at N33 and L661





0470
D010
BG505, SOSIP.R6.664.T332N_W35T_K502N_
BG505
SOSIP, R6, 664, T332N
W35T, K502N/R504T, gly661
Glycan at K502 and L661




R504T_gly661









0471
F001
BG505.SOSIP.R6.664.T332N_ferritin
BG505
SOSIP, R6, 664, T332N
onto ferritin
HIV-1 En trimer on nanoparticles





0472
F002
BG505.SOSIP.R6.664.T332N_L5
BG505
SOSIP, R6, 664, T332N
onto Luminase synthase
HIV-1 En trimer on nanoparticles





0473
F003
BG505.SOSIP.R6.664.T332N_3bve_ferr-
BG505
SOSIP, R6, 664, T332N

Helicobacter pylori

SOSIP - linker - particle




24_1ln


ferritin






0474
F004
BG505.SOSIP.R6.664.T332N_3bve_ferr-
BG505
SOSIP, R6, 664, T332N

Helicobacter pylori

SOSIP - linker - particle




24_3ln


ferritin






0475
F005
BG505.SOSIP.R6.664.T332N_3bve_ferr-
BG505
SOSIP, R6, 664, T332N

Helicobacter pylori

SOSIP - linker - particle




24_15ln


ferritin






0476
F006
BG505.SOSIP.R6.664.T332N_1hqk_ls-60_3ln
BG505
SOSIP, R6, 664, T332N
lumazine synthase from
SOSIP - linker - particle







aquifex aeolicus






0477
F007
BG505.SOSIP.R6.664.T332N_1hqk_ls-60_15ln
BG505
SOSIP, R6, 664, T332N
lumazine synthase from
SOSIP - linker - particle







aquifex aeolicus






0478
F008
BG505.SOSIP.R6.664.T332N_1ohg_bph-hk97-
BG505
SOSIP, R6, 664, T332N
DSDNA bacteriophage HK97
SOSIP - linker - particle




420_1ln


mature empty capsid






0479
F009
BG505.SOSIP.R6.664.T332N_1ohg_bph-hk97-
BG505
SOSIP, R6, 664, T332N
DSDNA bacteriophage HK97
SOSIP - linker - particle




420_3ln


mature empty capsid






0480
F010
BG505.SOSIP.R6.664.T332N_1ohg_bph-hk97-
BG505
SOSIP, R6, 664, T332N
DSDNA bacteriophage HK97
SOSIP - linker - particle




420_5ln


mature empty capsid






0481
F011
BG505.SOSIP.R6.664.T332N_1ohg_bph-hk97-
BG505
SOSIP, R6, 664, T332N
DSDNA bacteriophage HK97
SOSIP - linker - particle




420_15ln


mature empty capsid






0482
F012
BG505.SOSIP.R6.664.T332N_1qbe_bph-qB-
BG505
SOSIP, R6, 664, T332N
BACTERIOPHAGE Q BETA
SOSIP - linker - particle




180_7ln


CAPSID






0483
F013
BG505.SOSIP.R6.664.T332N_1qbe_bph-qB-
BG505
SOSIP, R6, 664, T332N
BACTERIOPHAGE Q BETA
SOSIP - linker - particle




180_15ln


CAPSID






0484
F014
BG505.SOSIP.R6.664.T332N_1dwn_bph-pp7-
BG505
SOSIP, R6, 664, T332N
bacteriophage PP7 from
SOSIP - linker - particle




180_10ln



Pseudomonas aeruginosa







0485
F015
BG505.SOSIP.R6.664.T332N_1dwn_bph-pp7-
BG505
SOSIP, R6, 664, T332N
bacteriophage PP7 from
SOSIP - linker - particle




180_15ln



Pseudomonas aeruginosa







0486
F016
BG505.SOSIP.R6.664.T332N_2vf9_bph-prr1-
BG505
SOSIP, R6, 664, T332N
bacteriophage PRR1
SOSIP - linker - particle




180_10ln









0487
F017
BG505.SOSIP.R6.664.T332N_2vf9_bph-prr1-
BG505
SOSIP, R6, 664, T332N
bacteriophage PRR2
SOSIP - linker - particle




180_15ln









0488
F018
BG505.SOSIP.R6.664.T332N_1gav_bph-ga-
BG505
SOSIP, R6, 664, T332N
BACTERIOPHAGE GA PROTEIN
SOSIP - linker - particle




180_10ln


CAPSID






0489
F019
BG505.SOSIP.R6.664.T332N_1gav_bph-ga-
BG505
SOSIP, R6, 664, T332N
BACTERIOPHAGE GA PROTEIN
SOSIP - linker - particle




180_15ln


CAPSID






0490
F020
BG505.SOSIP.R6.664.T332N_2w4y_bph-5-
BG505
SOSIP, R6, 664, T332N
caulobacter bacteriophage
SOSIP - linker - particle




180_10ln


5- virus-like particle






0491
F021
BG505.SOSIP.R6.664.T332N_2w4y_bph-5-
BG505
SOSIP, R6, 664, T332N
caulobacter bacteriophage
SOSIP - linker - particle




180_15ln


5- virus-like particle






0492
F022
BG505.SOSIP.R6.664.T332N_1frs_bph-fr-
BG505
SOSIP, R6, 664, T332N
BACTERIOPHAGE FR CAPSID
SOSIP - linker - particle




180_10ln









0493
F023
BG505.SOSIP.R6.664.T332N_1frs_bph-fr-
BG505
SOSIP, R6, 664, T332N
BACTERIOPHAGE FR CAPSID
SOSIP - linker - particle




180_15ln









0494
F024
BG505.SOSIP.R6.664.T332N_1mva_ph-ms2-
BG505
SOSIP, R6, 664, T332N
PHAGE M52 PROTEIN CAPSID
SOSIP - linker - particle




180_7ln









0495
F025
BG505.SOSIP.R6.664.T332N_1mva_ph-ms2-
BG505
SOSIP, R6, 664, T332N
PHAGE M52 PROTEIN CAPSID
SOSIP - linker - particle




180_15ln









0496
F026
BG505.SOSIP.R6.664.T332N_2tbv_tom-v-
BG505
SOSIP, R6, 664, T332N
tomato bushy stunt virus.
particle - linker - SOSIP




180_7ln


v. coat protein






0497
F027
BG505.SOSIP.R6.664.T332N_2tbv_tom-v-
BG505
SOSIP, R6, 664, T332N
tomato bushy stunt virus.
particle - linker - SOSIP




180_15ln


v. coat protein






0498
F028
BG505.SOSIP.R6.664.T332N_1smv_sesb-mv-
BG505
SOSIP, R6, 664, T332N
SESBANIA MOSAIC VIRUS 
particle - linker - SOSIP




180_7ln


COAT PROTEIN






0499
F029
BG505.SOSIP.R6.664.T332N_ismv_sesb-mv-
BG505
SOSIP, R6, 664, T332N
SESBANIA MOSAIC VIRUS
particle - linker - SOSIP




180_15ln


COAT PROTEIN






0500
F030
BG505.SOSIP.R6.664.T332N_1f2n_rice-ymv-
BG505
SOSIP, R6, 664, T332N
RICE YELLOW MOTTLE VIRUS 
particle - linker - SOSIP




180_7ln









0501
F031
BG505.SOSIP.R6.664.T332N_1f2n_rice-ymv-
BG505
SOSIP, R6, 664, T332N
RICE YELLOW MOTTLE VIRUS
particle - linker - SOSIP




180_15ln









0502
F032
BG505.SOSIP.R6.664.T332N_1ng0_cfmv-
BG505
SOSIP, R6, 664, T332N
Cocksfoot mottle virus
particle - linker - SOSIP




180_7ln









0503
F033
BG505.SOSIP.R6.664.T332N_1ng0_cfmv-
BG505
SOSIP, R6, 664, T332N
Cocksfoot mottle virus
particle - linker - SOSIP




180_15ln









0504
F034
BG505.SOSIP.R6.664.T332N_2wqt_mhpd-
BG505
SOSIP, R6, 664, T332N
protein cage by
particle - linker - SOSIP




60_1ln



Escherichia coli 2-









hydroxypentadienoic acid








hydratase






0505
F035
BG505.SOSIP.R6.664.T332N_2wqt_mhpd-
BG505
SOSIP, R6, 664, T332N
Same as Seq_0504
particle - linker - SOSIP




60_3ln









0506
F036
BG505.SOSIP.R6.664.T332N_2wqt_mhpd-
BG505
SOSIP, R6, 664, T332N
Same as Seq_0504
particle - linker - SOSIP




60_5ln









0507
F037
BG505.SOSIP.R6.664.T332N_2wqt_mhpd-
BG505
SOSIP, R6, 664, T332N
Same as Seq_0504
particle - linker - SOSIP




60_15ln









0508
G001
BG505.SOSIP.R6.664.T332N_GGSGG_GCN4
BG505
SOSIP.R6.664.T332N
GGSGG_GCN4
Trimerization domain





0509
G002
BG505.SOSIP.R6.664.T332N_GGSGSGG_N_
BG505
SOSIP.R6.664.T332N
GGSGSGG_N_3HSH
Trimerization domain atgp120




3HSH



N-term





0510
G003
BG505.SOSIP.R6.664.T332N_GG_C_3HSH
BG505
SOSIP.R6.664.T332N
GG_C_3HSH
Trimerization domain at gp41








C-term





0511
H001
BG505.SOSIP.R6.664.T332N, V1V2 Swap
BG505
SOSIP.R6.664.T332N
V1V2 Swap CAP256.SU
V1V2 Swap CAP256.SU




CAP256.SU









0512
H002
BG505.SOSIP.R6.664.T332N, V1V2 Swap
BG505
SOSIP.R6.664.T332N
V1V2 Swap BB201.B42
V1V2 Swap BB201.B42




BB201.B42









0513
H003
BG505.SOSIP.R6.664.T332N, V1V2 Swap
BG505
SOSIP.R6.664.T332N
V1V2 Swap KER2018.11
V1V2 Swap KER2018.11




KER2018.11









0514
H004
BG505.SOSIP.R6.664.T332N, V1V2 Swap
BG505
SOSIP.R6.664.T332N
V1V2 Swap CH070.1
V1V2 Swap CH070.1




CH070.1









0515
H005
BG505.SOSIP.R6.664.T332N, V1V2 Swap
BG505
SOSIP.R6.664.T332N
V1V2 Swap ZM233.6
V1V2 Swap ZM233.6




ZM233.6









0516
H006
BG505.SOSIP.R6.664.T332N, V1V2 Swap
BG505
SOSIP.R6.664.T332N
V1V2 Swap Q23.17
V1V2 Swap Q23.17




Q23.17









0517
H007
BG505.SOSIP.R6.664.T332N, V1V2 Swap
BG505
SOSIP.R6.664.T332N
V1V2 Swap A244
V1V2 Swap A244




A244









0518
H008
BG505.SOSIP.R6.664.T332N, V1V2 Swap
BG505
SOSIP.R6.664.T332N
V1V2 Swap WIT0.33
V1V2 Swap WIT0.33




WIT0.33









0519
Z001










0520
Z002










0521
Z003










0522
Z004










0523
Z005










0524
Z006










0525
Z007










0526
Z008










0527
Z009










0528
Z010










0529
Z011










0530
Z012










0531
Z013










0532
Z014










0533
Z015










0534
Z016










0535
Z017










0536
Z018










0537
Z019










0538
Z020










0539
Z021










0540
Z022










0541
Z023










0542
Z024










0543
T001
BG505SOSIP.R6.664.T332N_C-6ln-HATM
BG505
SOSIP.R6.664.T332N

Transmembrane





0544
T002
BG505SOSIP.R6.664.T332N_C-10ln-HATM
BG505
SOSIP.R6.664.T332N

Transmembrane





0545
T003
bC-10ln_IP-6ln-HATM
BG505


Transmembrane





0546
T004
bC-10ln_IP-10ln-HATM
BG505


Transmembrane





0547
T005
BG505SOSIP.R6.664.T332N_N-NATM-6ln-C-
BG505
SOSIP.R6.664.T332N

Transmembrane




6ln-HATM









0548
T006
BG505SOSIP.R6.664.T332N_C-10ln-HATM
BG505
SOSIP.R6.664.T332N

Transmembrane





0549
T007
bC-10ln_IP-N-NATM-6ln-6ln-HATM
BG505


Transmembrane





0550
T008
bC-10ln_IP-10ln-HATM
BG505


Transmembrane





0551
T009
BG505SOSIP.R6.664.T332N_A201C/A433C-N-
BG505
SOSIP.R6.664.T332N
A201C/A433C
Transmembrane




NATM-6ln-C-6ln-HATM









0552
T010
BG505SOSIP.R6.664.T332N_A201C/A433C-C-
BG505
SOSIP.R6.664.T332N
A201C/A433C
Transmembrane




10ln-HATM









0553
T011
bC-10ln_IP-A201C/A433C--N-NATM-6ln-C-
BG505


Transmembrane




6ln-HATM









0554
T012
bC-10ln_IPA201C/A433C--10ln-HATM
BG505


Transmembrane





0555
T013
BG505SOSIP.R6.664.T332N_A201C/A433C-C-
BG505
SOSIP.R6.664.T332N
A201C/A433C
Transmembrane




6ln-HATM









0556
T014
BG505SOSIP.R6.664.T332N_A201C/A433C-C-
BG505
SOSIP.R6.664.T332N
A201C/A433C
Transmembrane




10ln-HATM









0557
T015
bC-10ln_IP-A201C/A433C-6ln-HATM
BG505


Transmembrane





0558
T016
bC-10ln_IP-A201C/A433C-10ln-HATM
BG505


Transmembrane





0559
T017
bC-10ln_IPA201C/A433C-N-NATM-6ln-C-
BG505


Transmembrane




6ln-HATM









0560
T018
BG505SOSIP.R6.664.T332N_N-NATM-6ln
BG505
SOSIP.R6.664.T332N

Transmembrane





0561
T019
BG505SOSIP.R6.664.T332N_N-10ln-NATM
BG505
SOSIP.R6.664.T332N

Transmembrane





0562
T020
bC-10ln_IP-6ln-N-NATM
BG505


Transmembrane





0563
T021
bC-10ln_IP-10ln-N-NATM
BG505


Transmembrane





0564
T022
BG505SOSIP.R6.664.T332N_A433P-N-NATM-
BG505
SOSIP.R6.664.T332N
A433P
Transmembrane




6ln-C-6ln-HATM









0565
T023
BG505SOSIP.R6.664.T332N_A433P-C-10ln-
BG505
SOSIP.R6.664.T332N
A433P
Transmembrane




HATM









0566
T024
bC-10ln_IPA433P--N-NATM-6ln-6ln-HATM
BG505


Transmembrane





0567
T025
bC-10ln_IPA433P--10ln-HATM
BG505


Transmembrane





0568
T026
BG505SOSIP.R6.664.T332N_A433P-C-6ln-HATM
BG505
SOSIP.R6.664.T332N
A433P
Transmembrane





0569
T027
BG505SOSIP.R6.664.T332N_A433P-C-10ln-
BG505
SOSIP.R6.664.T332N
A433P
Transmembrane




HATM









0570
T028
bC-10ln_IPA433P--6ln-HATM
BG505


Transmembrane





0571
T029
bC-10ln_IPA433P--10ln-HATM
BG505


Transmembrane





0572
Z025










0573
Z026










0574
Z027










0575
Z028




ferritin subunit





0576
Z029




lumazine synthase subunit





0577
Z030




Sulfer Oxygenase Reductase








subunit





0578
Z031




Foldon domain





0579
H017
Cap256-SU_bg505-NCgp120 + int +
CAP256-SU/BG505
SOSIP, R6, 664
BG505 Platform (Res. 31-
Chimeric gp140 with BG505




gp41.SOSIP
chimera

45, 478-507, 512-664),
gp41ecto/gp120-NC + Interface







BG505 Interface (Int.)
Res. set A “platform” and







Res. set A (Res. 46-54;
heterologous gp120







70-75; 84-89; 99; 102; 








106; 107; 114; 215; 220-








224; 226; 244; 471-473; 








476-477), remainder =








Cap256-SU






0580
H018
SHIV-1157ipd3N4_bg505-NCgp120 + int +
SHIV-1157ipd3N4/
SOSIP, R6, 664
BG505 Platform, BG505
Same as Seq_0579




gp41.SOSIP
BG505 chimera

Int. Res. set A;








remainder- 








SHIV-1157ipd3N4






0581
H019
CH117.4_332N_bg505-NCgp120 + int +
CH117.4/BG505
SOSIP, R6, 664
BG505 Platform, BG505
Same as Seq_0579




gp41.SOSIP
chimera

Int. Res. set A;








remainder- CH117.4 gp120






0582
H020
CNE58_SU-strandC_bg505-NCgp120 + int +
CNE58_SU-
SOSIP, R6, 664
BG505 Platform, BG505 
Same as Seq_0579




gp41.SOSIP
strandC/BG505

Int. Res. set A;






chimera

remainder-








CNE58_SU-strandC






0583
H021
25925-2.22_bg505-NCgp120 + int +
25925-2.22/
SOSIP, R6, 664
BG505 Platform, BG505
Same as Seq_0579




gp41.SOSIP
BG505 chimera

Int. Res. set A;








remainder- 25925-2.22






0584
H022
3301_V1_C24_bg505-NCgp120 + int +
3301_V1_C24/
SOSIP, R6, 664
BG505 Platform, BG505
Same as Seq_0579




gp41.SOSIP
BG505 chimera

Int. Res. set A;








remainder- 3301_V1_C24






0585
H023
ZM53-R166W_bg505-NCgp120 + int +
ZM53/BG505 
SOSIP, R6, 664
BG505 Platform, BG505
Same as Seq_0579




gp41.SOSIP
chimera

Int. Res. set A;








remainder- ZM53-








R166Wgp120






0586
H024
ZM53_bg505-NCgp120 + int + gp41.SOSIP
ZM53/BG505 
SOSIP, R6, 664
BG505 Platform, BG505
Same as Seq_0579





chimera

Int. Res. set A;;








remainder- ZM53






0587
H025
KER2018.11_bg505-NCgp120 + gp41.SOSIP
KER2018.11/BG505
SOSIP, R6, 664
BG505 Platform,
heterologous gp120 with (gp41 +





chimera

remainder = KER2018.11
gp120-NC (Res. 31-45; 478-507)








from BG505.SOSIP)





0588
H026
KER2018.11_bg505-NCgp120 + int +
KER2018.11/BG505
SOSIP, R6, 664
BG505 Platform, BG505
Same as Seq_0579




gp41.SOSIP
chimera

Int. Res. set A;;








remainder- KER2018.11






0589
H027
ZM233.6_bg505-NCgp120 + gp41.SOSIP
ZM233.6/BG505
SOSIP, R6, 664
BG505 Platform,
Same as Seq_0379





chimera

remainder = ZM233.6






0590
H028
ZM233.6_bg505-NCgp120 + int + gp41.
ZM233.6/BG505
SOSIP, R6, 664
BG505 Platform, BG505
Same as Seq_0579




SOSIP
chimera

Int. Res. set A;;








remainder- ZM233.6






0591
H029
UG037.8_bg505-NCgp120 + gp41.SOSIP
UG037.8/BG505
SOSIP, R6, 664
BG505 Platform, BG505
Same as Seq_0379





chimera

Int. Res. set A;;








remainder- UG037.8






0592
H030
C13_psv02_bg505-NCgp120 + gp41.SOSIP
C13/BG505
SOSIP, R6, 664
BG505 Platform, BG505
Same as Seq_0379





chimera

Int. Res. set A;;








remainder- C13






0593
H031
45_01dG5_bg505-NCgp120 + gp41.SOSIP
45_01dG5/BG505
SOSIP, R6, 664
BG505 Platform, BG505
Same as Seq_0379





chimera

Int. Res. set A;








remainder- 45_01dG5






0594
H032
ZM215.8-dCD4bsGlyc_bg505-NCgp120 +
ZM215.8/BG505
SOSIP, R6, 664
BG505 Platform, BG505
Same as Seq_0379




gp41.SOSIP
chimera

Int. Res. set A;;








remainder-








ZM215.8-dCD4bsGlyc






0595
H033
426c-dCD4bsGlyc_bg505-NCgp120 +
426c/BG505
SOSIP, R6, 664
BG505 Platform, BG505 
Same as Seq_0379




gp41.SOSIP
chimera

Int. Res. set A;;








remainder-








426c-dCD4bsGlyc






0596
F038
bg505.sosip_1dwn_bph-pp7-180_3-
BG505
SOSIP, R6, 664, T332N
bacteriophage PP7
sosip - linker - particle




127_5ln_mut1









0597
F039
bg505.sosip_1dwn_bph-pp7-180_3-
BG505
SOSIP, R6, 664, T332N
bacteriophage PP7
Same as Seq_0596




127_8ln_mut1









0598
F040
bg505.sosip_1dwn_bph-pp7-180_3-
BG505
SOSIP, R6, 664, T332N
bacteriophage PP7
Same as Seq_0596




127_8ln_mut1









0599
F041
bg505.sosip_1qbe_bph-qB-180_6-
BG505
SOSIP, R6, 664, T332N
BACTERIOPHAGE Q BETA
Same as Seq_0596




132_3ln_mut1


CAPSID






0600
F042
bg505.sosip_1qbe_bph-qB-180_6-
BG505
SOSIP, R6, 664, T332N
BACTERIOPHAGE Q BETA
Same as Seq_0596




132_5ln_mut1


CAPSID






0601
F043
bg505.sosip_1qbe_bph-qB-180_6-
BG505
SOSIP, R6, 664, T332N
BACTERIOPHAGE Q BETA
Same as Seq_0596




132_10ln_mut1


CAPSID






0602
F044
bg505.sosip_2vf9_bph-prr1-180_6-131-
BG505
SOSIP, R6, 664, T332N
bacteriophage PRR1
Same as Seq_0596




3ln_mut1









0603
F045
bg505.sosip_2vf9_bph-prr1-180_6-131-
BG505
SOSIP, R6, 664, T332N
bacteriophage PRR1
Same as Seq_0596




5ln_mut1









0604
F046
bg505.sosip_2vf9_bph-prr1-180_6-131-
BG505
SOSIP, R6, 664, T332N
bacteriophage PRR1
Same as Seq_0596




10ln_mut1









0605
F047
bg505.sosip_1gav_bph-ga-180_7-
BG505
SOSIP, R6, 664, T332N
BACTERIOPHAGE GA PROTEIN
Same as Seq_0596




129_3ln_mut1


CAPSID






0606
F048
bg505.sosip_1gav_bph-ga-180_7-
BG505
SOSIP, R6, 664, T332N
BACTERIOPHAGE GA PROTEIN
Same as Seq_0596




129_5ln_mut1


CAPSID






0607
F049
bg505.sosip_1gav_bph-ga-180_7-
BG505
SOSIP, R6, 664, T332N
BACTERIOPHAGE GA PROTEIN
Same as Seq_0596




129_10ln_mut1


CAPSID






0608
F050
bg505.sosip_1frs_bph-fr-180_7-
BG505
SOSIP, R6, 664, T332N
BACTERIOPHAGE FR CAPSID
Same as Seq_0596




129_5ln_mut1









0609
F051
bg505.sosip_1frs_bph-fr-180_7-
BG505
SOSIP, R6, 664, T332N
BACTERIOPHAGE FR CAPSID
Same as Seq_0596




129_10ln_mut1









0610
F052
bg505.sosip_1frs_bph-fr-180_7-
BG505
SOSIP, R6, 664, T332N
BACTERIOPHAGE FR CAPSID
Same as Seq_0596




129_15ln_mut1









0611
F053
bg505.sosip_1mva_ph-ms2-180_7-
BG505
SOSIP, R6, 664, T332N
PHAGE M52 PROTEIN CAPSID
Same as Seq_0596




129_5ln_mut1









0612
F054
bg505.sosip_1mva_ph-ms2-180_7-
BG505
SOSIP, R6, 664, T332N
PHAGE M52 PROTEIN CAPSID
Same as Seq_0596




129_10ln_mut1









0613
F055
bg505.sosip_1mva_ph-ms2-180_7-
BG505
SOSIP, R6, 664, T332N
PHAGE M52 PROTEIN CAPSID
Same as Seq_0596




129_15ln_mut1









0614
F056
bg505.sosip_1hqk_ls-60_9ln_mut1
BG505
SOSIP, R6, 664, T332N
LUMAZINE SYNTHASE FROM 
Same as Seq_0596







AQUIFEX AEOLICUS






0615
F057
bg505.sosip_3bve_ferr-24_9ln_mut1
BG505
SOSIP, R6, 664, T332N

Helicobacter pylori

Same as Seq_0596







ferritin






0616
F058
BG505.SOSIP.linker_1AA7_Ln9
BG505
SOSIP, R6, 664, T332N
M1 protein
sosip-self-assembling protein








cage





0617
F059
BG505.SOSIP.linker_1AA7_Ln12
BG505
SOSIP, R6, 664, T332N
M1 protein
sosip-self-assembling protein








cage





0618
F060
BG505.SOSIP.linker_1AA7_Ln15
BG505
SOSIP, R6, 664, T332N
M1 protein
sosip-self-assembling protein








cage





0619
F061
BG505.SOSIP.linker_1AA7_Ln18
BG505
SOSIP, R6, 664, T332N
M1 protein
sosip-self-assembling protein








cage





0620
F062
BG505SOSIP-linker3-3VDX
BG505
SOSIP, R6, 664, T332N
3VDX Cage
sosip-self-assembling protein








cage





0621
F063
BG505SOSIP-linker8-3VDX
BG505
SOSIP, R6, 664, T332N
3VDX Cage
sosip-self-assembling protein








cage





0622
F064
BG505SOSIP-linker9-3VDX
BG505
SOSIP, R6, 664, T332N
3VDX Cage
sosip-self-assembling protein








cage





0623
F065
BG505SOSIP-linker12-3VDX
BG505
SOSIP, R6, 664, T332N
3VDX Cage
sosip-self-assembling protein








cage





0624
F066
BG505SOSIP-linker15-3VDX
BG505
SOSIP, R6, 664, T332N
3VDX Cage
sosip-self-assembling protein








cage





0625
F067
BG505SOSIP-linker18-3VDX
BG505
SOSIP, R6, 664, T332N
3VDX Cage
sosip-self-assembling protein








cage





0626
F068
BG505.SOSIP.T332N_ZM233_NtermH1_4_
BG505
Circ. permut., SOSIP,

Circ. permut. V1V2 swap




Ferritin

T332N, 664, V1V2 swap,

nanoparticle






nanoparticle







0627
F069
BG505.SOSIP.T332N_Ker2018_NtermH1_
BG505
Same as Seq_0626

Same as Seq_0626




4_Ferritin









0628
F070
BG505.SOSIP.T332N_ZM233_201C433C_
BG505
Same as Seq_0626
201C, 433C
Same as Seq_0626




NtermH1_4_Ferritin









0629
F071
BG505.SOSIP.T332N_Ker2018_201C433C_
BG505
Same as Seq_0626
201C, 433C
Same as Seq_0626




NtermH1_4_Ferritin









0630
F072
BG505.SOSIP.T332N_ZM233_NtermH1_6_
BG505
Same as Seq_0626

Same as Seq_0626




Ferritin









0631
F073
BG505.SOSIP.T332N_KER2018_NtermH1_
BG505
Same as Seq_0626

Same as Seq_0626




6_Ferritin









0632
F074 
BG505.SOSIP.T332N_ZM233_NtermH1_
BG505
Same as Seq_0626

Same as Seq_0626




6_longer_Ferritin









0633
F075
BG505.SOSIP.T332N_KER2018_NtermH1_
BG505
Same as Seq_0626

Same as Seq_0626




6_longer_Ferritin









0634
F076
BG505.SOSIP.T332N_ZM233_NtermH1_
BG505
Same as Seq_0626

Same as Seq_0626




12_Ferritin









0635
F077
BG505.SOSIP.T332N_KER2018_NtermH1_
BG505
Same as Seq_0626

Same as Seq_0626




12_Ferritin









0636
F078 
BG505.SOSIP.T332N_ZM233_NtermH1_
BG505
Same as Seq_0626

Same as Seq_0626




Tri_Ferritin









0637
F079
BG505.SOSIP.T332N_KER2018_NtermH1_
BG505
Same as Seq_0626

Same as Seq_0626




Tri_Ferritin









0638
F080
BG505.SOSIP.T332N_KER2018_Circ_LS
BG505
Same as Seq_0626

Same as Seq_0626





0639
F081
BG505.SOSIP.T332N_KER2018_Circ_short_LS
BG505
Same as Seq_0626

Same as Seq_0626





0640
F082
BG505.SOSIP.T332N_KER2018_Circ_long_LS
BG505
Same as Seq_0626

Same as Seq_0626





0641
F083
BG505.SOSIP.T332N_ZM233_Circ_LS
BG505
Same as Seq_0626

Same as Seq_0626





0642
F084
BG505.SOSIP.T332N_ZM233_201C433C_Circ_LS
BG505
Same as Seq_0626
201C, 433C
Same as Seq_0626





0643
F085
BG505.SOSIP.T332N_ZM233_NtermH1_Tri_LS
BG505
Same as Seq_0626

Same as Seq_0626





0644
F086
BG505.SOSIP.T332N_KER2018_NtermH1_Tri_LS
BG505
Same as Seq_0626

Same as Seq_0626





0645
F087
BG505.SOSIP.T332N_ZM233_NtermH1_Tri_
BG505
Same as Seq_0626
201C, 433C
Same as Seq_0626




201C433C_LS









0646
A204
BG505.SOSIP.R6.664.T332N_I225C/V245C
BG505
SOSIP, R6, 664, T332N
I225C/V245C
DS





0647
A205
BG505.SOSIP.R6.664.T332N_V36C/T606C
BG505
SOSIP, R6, 664, T332N
V36C_T606C
DS





0648
A206
BG505.SOSIP.R6.664.T332N_T37C/T606C
BG505
SOSIP, R6, 664, T332N
T37C_T606C
DS





0649
A207
BG505.SOSIP.R6.664.T332N_V36C/V496C
BG505
SOSIP, R6, 664, T332N
V36C_V496C
DS





0650
A208
BG505.SOSIP.R6.664.T332N_V36C/P498C
BG505
SOSIP, R6, 664, T332N
V36C_P498C
DS





0651
A209
BG505.SOSIP.R6.664.T332N_T37C/A497C
BG505
SOSIP, R6, 664, T332N
T37C_A497C
DS





0652
A210
BG505.SOSIP.R6.664.T332N_V38C/V496C
BG505
SOSIP, R6, 664, T332N
V38C_V496C
DS





0653
A211
BG505.SOSIP.R6.664.T332N_A200C/Q432C
BG505
SOSIP, R6, 664, T332N
A200C/Q432C
DS





0654
A212
BG505.SOSIP.R6.664.T332N_T202C/M434C
BG505
SOSIP, R6, 664, T332N
T202C_M434C
DS





0655
A213
BG505.SOSIP.R6.664.T332N_T202C/M434C/
BG505
SOSIP, R6, 664, T332N
T202C_M434C_G431F
DS, CavF at gp120 C4 substitued




G431F



with F and stablize gp120,








interprotomer





0656
A214
BG505.SOSIP.R6.664.T332N_T202C_A433C
BG505
SOSIP, R6, 664, T332N
T202C_A433C
DS





0657
A215
BG505.SOSIP.R6.664.T332N_V182D
BG505
SOSIP, R6, 664 , T332N
V182D
salt bridge at gp120 V2 to








stablize V2 by subtitution of D,





0658
A216
BG505.SOSIP.R6.664.T332N_I251F/L260F
BG505
SOSIP, R6, 664, T332N
I251F/L260F
hydrophobic core betwwen gp120








V2/V3 with double F substitution








to stabilize V1/V2/V3





0659
A217
BG505.SOSIP.R6.664.T332N_I225C/V488C
BG505
SOSIP, R6, 664, T332N
I225C/V488C
DS





0660
A218
BG505.SOSIP.R6.664.T332N_N478F
BG505
SOSIP, R6, 664, T332N
N478F
CavF at gp120 C terminus








substitued with F and stablize








gp120 C terminus





0661
A219
BG505.SOSIP.R6.664.T332N_T163D_Q170R
BG505
SOSIP, R6, 664, T332N
T163D_Q17OR
salt bridge at gp120 V2 to








stablize V1/V2 with D and R








substitution





0662
A220
BG505.SOSIP.R6.664.T332N_T163C_Q170C
BG505
SOSIP, R6, 664, T332N
T163C_Q170C
DS





0663
A221
BG505.SOSIP.R6.664.T332N_I309R_Q315D
BG505
SOSIP, R6, 664, T332N
I309R_Q315D
salt bridge at gp120 V3 to








stablize V1/V2/V3 with D and R








subtitution





0664
A222
BG505.SOSIP.R6.664.T332N_I294C_V333C
BG505
SOSIP, R6, 664, T332N
I294C_V333C
DS





0665
A223
BG505.SOSIP.R6.664.T332N_I294D_V333R
BG505
SOSIP, R6, 664, T332N
I294D_V333R
salt bridge at gp120 V3 to








stablize V1/V2/V3 with D and R








subtitution





0666
A224
BG505.SOSIP.R6.664.T332N_G380F_P437F
BG505
SOSIP, R6, 664, T332N
G380F_P437F
hydrophobic core at gp120 C








terminus with double-F








substitution to stabilize gp120








C terminus





0667
A225
BG505.SOSIP.R6.664.T332N_G380F
BG505
SOSIP, R6, 664, T332N
G380F
CavF at gp120 C4 with F








substitution to stablize gp120





0668
A226
BG505.SOSIP.R6.664.T332N_P437F
BG505
SOSIP, R6, 664, T332N
P437F
CavF at gp120 C terminus with F








substitution and stablize gp120








C terminus





0669
A227
BG505.SOSIP.R6.664.T332N_V254F_L260F_
BG505
SOSIP, R6, 664, T332N
V254F_L260F_L261F_G263F
hydrophobic core at gp120 C2




L261F_G263F



with four-F substitution to








stabilize gp120





0670
A228
BG505.SOSIP.R6.664.T332N_V254F
BG505
SOSIP, R6, 664, T332N
V254F
CavF at gp120 C2 with F








substitution to stablize gp120





0671
A229
BG505.SOSIP.R6.664.T332N_L260F
BG505
SOSIP, R6, 664, T332N
L260F
CavF at gp120 C2 with F








substitution to stablize gp120





0672
A230 
BG505.SOSIP.R6.664.T332N_L261F
BG505
SOSIP, R6, 664, T332N
L261F
CavF at gp120 C2 with F








substitution to stablize gp120,








interprotomer





0673
A231
BG505.SOSIP.R6.664.T332N_G263W
BG505
SOSIP, R6, 664, T332N
G263W
CavF at gp120 C2 with W








substitution to stablize gp120,








interprotomer





0674
A232
BG505.SOSIP.R6.664.T332N_A55F_V75F
BG505
SOSIP, R6, 664, T332N
A55F_V75F
hydrophobic core at gp120 C1








with double-F substitution to








stabilize gp120 N terminus





0675
A233
BG505.SOSIP.R6.664.T332N_T77F_V245F
BG505
SOSIP, R6, 664, T332N
T77F_V245F
hydrophobic core at gp120 C1/C2








with double-F substitution to








stabilize gp120 N terminus





0676
A234
BG505.SOSIP.R6.664.T332N_T77F
BG505
SOSIP, R6, 664, T332N
T77F
CavF at gp120 Cl with F








substitution to stablize gp120








N terminus





0677
A235
BG505.SOSIP.R6.664.T332N_S56H_P76E
BG505
SOSIP, R6, 664, T332N
S56H_P76E
salt bridge at gp120 C1 to








stablize gp120 N terminus with 








H and E subtitution





0678
A236
BG505.SOSIP.R6.664.T332N_A55F
BG505
SOSIP, R6, 664, T332N
A55F
CavF at gp120 C1 with F








substitution C to stablize








gp120 N terminus





0679
A237
BG505.SOSIP.R6.664.T332N_A55F_P81W
BG505
SOSIP, R6, 664, T332N
A55F_P81W
hydrophobic core at gp120 C1








with F and W substitution to








stabilize gp120 N terminus





0680
A238
BG505.SOSIP.R6.664.T332N_L52F_I215W
BG505
SOSIP, R6, 664, T332N
L52F_I215W
hydrophobic core at gp120 C1/C2








with double-F substitution to








stabilize gp120 N terminus





0681
A239
BG505.SOSIP.R6.664.T332N_I109K_Q428E
BG505
SOSIP, R6, 664, T332N
I109K_Q428E
salt bridge at gp120 C1/C4 to








stablize gp120 N/C terminus with








K and E substitution





0682
A240
BG505.SOSIP.R6.664.T332N_T257C_S375C
BG505
SOSIP, R6, 664, T332N
T257C_S375C
DS





0683
A241
BG505.SOSIP.R6.664.T332N_A55C_T77C
BG505
SOSIP, R6, 664, T332N
A55C_T77C
DS





0684
A242
BG505.SOSIP.R6.664.T332N_L125F_L193W
BG505
SOSIP, R6, 664, T332N
L125F_L193W
hydrophobic core at gp120 V1/V2








with F or W substitution to








stabilize gp120 V1/V2





0685
A243
BG505.SOSIP.R6.664.T332N_L125F
BG505
SOSIP, R6, 664, T332N
L125F
CavF at gp120 V1/V2. Substitute








F to stabilize V1/V2/V3





0686
A244
BG505.SOSIP.R6.664.T332N_N136W
BG505
SOSIP, R6, 664, T332N
N136W
CavF at gp120 V1. Substitute W








to stabilize V1/V2/V3





0687
A245
BG505.SOSIP.R6.664.T332N_N136W_L154W
BG505
SOSIP, R6, 664, T332N
N136W_L154W
hydrophobic core at gp120 V1








with double W substitution to








stabilize gp120 V1/V2





0688
A246
BG505.SOSIP.R6.664.T332N_L193F_
BG505
SOSIP, R6, 664, T332N
L193F_N195C_I423C
DS, CavF at gp120 V1 substituted




N195C_I423C



with F and stabilize V1/V2,








interprotomer





0689
A247
BG505.SOSIP.R6.664.T332N_I323W_I326F
BG505
SOSIP, R6, 664, T332N
I323W_I326F
hydrophobic core at gp120 V3








with W or F substitution to








stabilize gp120 V1/V2/V3





0690
A248
BG505.SOSIP.R6.664.T332N_I323W
BG505
SOSIP, R6, 664, T332N
I323W
CavF at gp120 V3. Substitute F








to stabilize V1/V2/V3





0691
A249
BG505.SOSIP.R6.664.T332N_I326F
BG505
SOSIP, R6, 664, T332N
I326F
CavF at gp120 V3. Substitute F








to stabilize V1/V2/V3





0692
A250
BG505.SOSIP.R6.664.T332N_M475F_N478F
BG505
SOSIP, R6, 664, T332N
M475F_N478F
hydrophobic core at gp120 V3








with W or F substitution to








stabilize gp120 V1/V2/V3





0693
A251
BG505.SOSIP.R6.664.T332N_Q130H
BG505
SOSIP, R6, 664, T332N
Q130H
salt bridge at gp120 C1 to








stabilize gp120 N/C terminus








with H substitution





0694
A252
BG505.SOSIP.R6.664.T332N_Q103D_T106K
BG505
SOSIP, R6, 664, T332N
Q103D_T106K
salt bridge at gp120 C1 to








stabilize gp120 N/C terminus








with K and D substitution





0695
A253
BG505.SOSIP.R6.664.T332N_S110H_Q114E
BG505
SOSIP, R6, 664, T332N
S110H_Q114E
salt bridge at gp120 C1 to








stabilize gp120 N/C terminus








with H and E substitution





0696
A254
BG505.SOSIP.R6.664.T332N_M150F_I326W
BG505
SOSIP, R6, 664, T332N
M150F_I326W
hydrophobic core at gp120 V1/V3








with W or F substitution to








stabilize gp120 V1/V2/V3





0697
A255
BG505.SOSIP.R6.664.T332N_L111W
BG505
SOSIP, R6, 664, T332N
L111W
CavF at gp120 C1. Substitute W








to stabilize gp120 terminus





0698
A256
BG505.SOSIP.R6.664.T332N_A204F_V208W
BG505
SOSIP, R6, 664, T332N
A204F_V208W
hydrophobic core at gp120 C2








with W or F substitution to








stabilize gp120 V1/V2/V3,








interprotomer





0699
A257
BG505.SOSIP.R6.664.T332N_L537C_G41C
BG505
SOSIP, R6, 664, T332N
L537C_G41C
DS





0700
A258
BG505.SOSIP.R6.664.T332N_V245F
BG505
SOSIP, R6, 664, T332N
V245F
CavF at gp120 C2. Substitute F








to stabilize gp120 V1/V2/V3,








interprotomer





0701
A259
BG505.SOSIP.R6.664.T332N_L125W.I195W
BG505
SOSIP, R6, 664, T332N
L125W, I195W
Cavity filling of V1V2-V3








interface near 126-196








disulfide bond





0702
A260
BG505.SOSIP.R6.664.T332N_V2V3_Hyd2
BG505
SOSIP, R6, 664, T332N
T139W,D140I,G324I,D325W
hydrophobic patch between V1V2








and V3 near base of V3 and








Variable loop 1 in V1V2





0703
A261
BG505.SOSIP.R6.664.T332N_Y173W
BG505
SOSIP, R6, 664, T332N
Y173W
CavF at gp120 V1/V2/V3. 173:








Substitute W or F





0704
A262
BG505.SOSIP.R6.664.T332N_L179W
BG505
SOSIP, R6, 664, T332N
L179W
Stabilized V1V2 cap





0705
A263
BG505.SOSIP.R6.664.T332N_L175F
BG505
SOSIP, R6, 664, T332N
L175F
CavF: V1V2-V3 interface,








Substitute F or W,





0706
A264
BG505.SOSIP.R6.664.T332N_L175W
BG505
SOSIP, R6, 664, T332N
L175W
CavF: V1V2-V3 interface,








Substitute F or W,





0707
A265
BG505.SOSIP.R6.664.T332N_E153F
BG505
SOSIP, R6, 664, T332N
E153F
CavF: V1V2-V3/gp120core








interface, Substitute F or W,





0708
A266
BG505.SOSIP.R6.664.T332N_E153W
BG505
SOSIP, R6, 664, T332N
E153W
CavF: V1V2-V3/gp120core








interface, Substitute F or W,





0709
A267
BG505.SOSIP.R6.664.T332N_L154F
BG505
SOSIP, R6, 664, T332N
L154F
CavF at gp120 V1/V2. Substitute








F, Y or W, stabilize V1/V2/V3





0710
A268
BG505.SOSIP.R6.664.T332N_L154W
BG505
SOSIP, R6, 664, T332N
L154W
CavF at gp120 V1/V2. Substitute








F, Y or W, stabilize V1/V2/V3





0711
A269
BG505.SOSIP.R6.664.T332N_E164F
BG505
SOSIP, R6, 664, T332N
E164F
CavF: inter-protomer, Substitute








F or W,





0712
A270
BG505.SOSIP.R6.664.T332N_E164W
BG505
SOSIP, R6, 664, T332N
E164W
CavF: inter-protomer, Substitute








F or W,





0713
A271
BG505.SOSIP.R6.664.T332N_T198F
BG505
SOSIP, R6, 664, T332N
T198F
CavF: V1V2-gp120core interface





0714
A272
BG505.SOSIP.R6.664.T332N_T202F
BG505
SOSIP, R6, 664, T332N
T202F
CavF: V1V2-gp120core interface,








Substitute F or W,





0715
A273
BG505.SOSIP.R6.664.T332N_T202W
BG505
SOSIP, R6, 664, T332N
T202W
CavF: V1V2-gp120core interface





0716
A274
BG505.SOSIP.R6.664.T332N_A204F
BG505
SOSIP, R6, 664, T332N
A204F
CavF: V1V2-gp120core interface,








Substitute F or W,





0717
A275
BG505.SOSIP.R6.664.T332N_I423F
BG505
SOSIP, R6, 664, T332N
I423F
CavF: gp120core-V1V2 interface,








Substitute F or W,





0718
A276
BG505.SOSIP.R6.664.T332N_I423W
BG505
SOSIP, R6, 664, T332N
I423W
CavF: gp120core-V1V2 interface





0719
A277
BG505.SOSIP.R6.664.T332N_Q432F
BG505
SOSIP, R6, 664, T332N
Q432F
CavF: stabilize unliganded








conformation of bridging sheet








region, Substitute F or W,





0720
A278
BG505.SOSIP.R6.664.T332N_Q432W
BG505
SOSIP, R6, 664, T332N
Q432W,
CavF: stabilize unliganded








conformation of bridging sheet








region





0721
A279
BG505.SOSIP.R6.664.T332N_A436M
BG505
SOSIP, R6, 664, T332N
A436M
CavF: stabilize unliganded








conformation of bridging sheet








region, Substitute F, M or W,





0722
A280
BG505.SOSIP.R6.664.T332N_A436F
BG505
SOSIP, R6, 664, T332N
A436F
Same as Seq_0721





0723
A281
BG505.SOSIP.R6.664.T332N_A436W
BG505
SOSIP, R6, 664, T332N
A436W
Same as Seq_0721





0724
A282
BG505.SOSIP.R6.664.T332N_A204W
BG505
SOSIP, R6, 664, T332N
A204W
CavF: V1V2-gp120core interface,








Substitute F or W,





0725
A283
BG505.SOSIP.R6.664.T332N_N302F
BG505
SOSIP, R6, 664, T332N
N302F
CavF: V3-V1V2/gp120core








interface, Substitute F or W,





0726
A284
BG505.SOSIP.R6.664.T332N_N302W
BG505
SOSIP, R6, 664, T332N
N302W
CavF: V3-V1V2/gp120core








interface, Substitute F or W,





0727
A285
BG505.SOSIP.R6.664.T332N_I307W
BG505
SOSIP, R6, 664, T332N
I307W
V1V2/V3 stabilization/packing,








Substitute F or W,





0728
A286
BG505.SOSIP.R6.664.T332N_I307F
BG505
SOSIP, R6, 664, T332N
I307F
V1V2/V3 stabilization/packing/








non-bridging sheet, Substitute








F or W,





0729
A287
BG505.SOSIP.R6.664.T332N_F210A
BG505
SOSIP, R6, 664, T332N
F210A
α-1 helix/destablize CD4-bound








conformation





0730
A288
BG505.SOSIP.R6.664.T332N_F176W_I323Y
BG505
SOSIP, R6, 664, T332N
F176W/I323Y
CavF at gp120 V1/V2/V3. 176:








Substitute Y or W; 323: F, Y,








or W; stabilize V1/V2/V3





0731
A289
BG505.SOSIP.R6.664.T332N_F176W_L154W
BG505
SOSIP, R6, 664, T332N
F176W/L154W
CavF at gp120 V1/V2. 176:








Substitute Y or W; 154: F, Y,








or W; stabilize V1/V2/V3





0732
A290
BG505.SOSIP.R6.664.T332N_F159Y_L154W
BG505
SOSIP, R6, 664, T332N
F159Y/L154W
CavF at gp120 V1/V2. 159:








Substitute Y or W; 154: F, Y,








or W; stabilize V1/V2/V3





0733
A291
BG505.SOSIP.R6.664.T332N_F176W
BG505
SOSIP, R6, 664, T332N
F176W
CavF at gp120 V1/V2. Substitute








Y or W, stabilize V1/V2/V3





0734
A292
BG505.R6.664_G41C_L537C
BG505
R6, 664
G41C_L537C
DS between gp120 and gp41





0735
A293
BG505.R6.664_G41C_A541C
BG505
R6, 664
G41C_A541C
DS between gp120 and gp41





0736
A294
BG505.R6.664_P43C_A526C
BG505
R6, 664
P43C_A526C
DS between gp120 and gp41





0737
A295
BG505.R6.664_A73C_G572C
BG505
R6, 664
A73C_G572C
DS between gp120 and gp41





0738
A296
BG505.R6.664_I84C_G521C
BG505
R6, 664
I84C_G521C
DS between gp120 and gp41





0739
A297
BG505.R6.664_V89C_G527C
BG505
R6, 664
V89C_G527C
DS between gp120 and gp41





0740
A298
BG505.IP.R6.664.T332N_A73C_G572C
BG505
IP, R6, 664, T332N
A73C_G572C
DS between gp120 and gp41





0741
A299
BG505.1P.R6.664.T332N_I84C_G521C
BG505
IP, R6, 664, T332N
I84C_G521C
DS between gp120 and gp41





0742
A300
BG505.IP.R6.664.T332N_V89C_G527C
BG505
IP, R6, 664, T332N
V89C_G527C
DS between gp120 and gp41





0743
A301
BG505.SOSIP.R6.664.T332N_R304C/Q440C
BG505
IP, R6, 664, T332N
R304C/Q440C
DS





0744
F088
BG505.SOSIP.R6.664.T332N_I201C/
BG505
SOSIP, R6, 664, T332N
I201C/A433C
Polymeric Fc-fusion protein




A433C_polymer hFc fusion









0745
0
ZM233.6
ZM233.6








0746
0
Q23.17
Q23.17








0747
0
A244
A244








0748
0
WITO.33
WITO.33








0749
0
ZM53.12
ZM53.12








0750
0
CNE58
CNE58








0751
0
3301_V1_C24
3301_V1_C24








0752
Z032
foldon domain









0753
Z033
foldon domain









0754
Z034
foldon domain









0755
Z035
foldon domain









0756
Z036
Encapsulin subunit









0757
Z037
DNA encoding SEQ ID NO: 352









0758
Z038 
BG505 transmembrane domain









0759
Z039
DNA encoding BG505 transmembrane domain









0760
Z040
Influenza A Hemagglutinin transmembrane








domain









0761
Z041
DNA encoding Influenza A Hemagglutinin








transmembrane domain









0762
Z042
Influenza A Neuraminidase transmembrane








domain









0763
Z043
DNA encoding Influenza A Neuraminidase








transmembrane domain









0764
H034
Cap256-SU_bg505-NCgp120 + gp41.
CAP256-SU/BG505
SOSIP, R6, 664
CAP256-SU gp120 with 
heterologous gp120 with (gp41 +




SOSIP_ds201-433
chimera

(gp41 + gp120-NC from
gp120-NC (Res. 31-45; 478-507)







BG505.SOSIP)
from BG505.SOSIP





0765
H035
3301_bg505-NCgp120 + gp41.
3301_V1_C24/
SOSIP, R6, 664
3301_V1_C24 gp120 with
Same as Seq_0764




SOSIP_ds201-433
BG505 chimera

(gp41 + gp120-NC from








BG505.SOSIP)






0766
H036
ZM53_bg505-NCgp120 + gp41.
ZM53/BG505
SOSIP, R6, 664
ZM53 gp120 with (gp41 +
Same as Seq_0764




SOSIP_ds201-433
chimera

gp120-NC from








BG505.SOSIP)






0767
H037
Cap256-SU_bg505-NCgp120 + gp41.SOSIP +
CAP256-SU/BG505
SOSIP, R6, 664
CAP256-SU gp120 with 
BG505 Platform + Int. Res.




int_ds201-433
chimera

(gp41 + gp120-NC
Set A







from BG505.SOSIP)






0768
H038
3301_bg505-NCgp120 + gp41.SOSIP +
3301_V1_C24/
SOSIP, R6, 664
3301_V1_C24 gp120 with
Same as Seq_0767




int_ds201-433
BG505 chimera

(gp41 + gp120-NC








from BG505.SOSIP)






0769
H039
ZM53_bg505-NCgp120 + gp41.SOSIP +
ZM53/BG505
SOSIP, R6, 664
ZM53 gp120 with
Same as Seq_0767




int_ds201-433
chimera

(gp41 + gp120-NC








from BG505.SOSIP)






0770
H040
CNE58-SUstrandC_bg505-NCgp120 +
CNE58/BG505
SOSIP, R6, 664
CNE58 gp120 with
BG505 Platform and Res. 166-173




gp41.SOSIP_ds201-433
chimera

(gp41 + gp120-NC
from CAP256-SU







from BG505.SOSIP) and








(strand C from CAP256-SU)






0771
H041
CNE58-SUstrandC_bg505-NCgp120 +
CNE58/BG505
SOSIP, R6, 664
CNE58 gp120 with
BG505 Platform and Res. 166-173




gp41.SOSIP_d5304-440
chimera

(gp41 + gp120-NC
from CAP256-SU







from BG505.SOSIP) and 








(strand C from CAP256-SU)






0772
H042
BG505.SOSIP.664.R6.T332N
BG505/CAP45
SOSIP, R6, 664, T332N
CAP45 as gp41 sequence
BG505.SOSIP.664.R6.T332N





chimera


construct with gp41 from CAP45





0773
A302
JR-FLgp140.6R.SOSIP.664.E168K_I201C/
JR-FL
SOSIP, R6, 664, E168K
I201C/A433C





A433C









0774
A303
JR-FLgp140.6R.SOSIP.664.E168K_A433P
JR-FL
SOSIP, R6, 664, E168K
A433P






0775
A304
JR-FLgp140.6R.SOSIP.664.E168K_Q432P
JR-FL
SOSIP, R6, 664, E168K
Q432P






0776
A305
JR-FLgp140.6R.SOSIP.664.E168K_S174C/
JR-FL
SOSIP, R6, 664, E168K
S174C/A319C





A319C









0777
A306
JR-FLgp140.6R.SOSIP.664.E168K_N195C/
JR-FL
SOSIP, R6, 664, E168K
N195C/A433C





A433C









0778
A307
JR-FLgp140.6R.SOSIP.664.E168K_S199C/
JR-FL
SOSIP, R6, 664, E168K
S199C/A433C





A433C









0779
A308
JR-FLgp140.6R.SOSIP.664.E168K_R304C/
JR-FL
SOSIP, R6, 664, E168K
R304C/Q440C





Q440C









0780
A309
JR-FLgp140.6R.SOSIP.664.E168K_F223W
JR-FL
SOSIP, R6, 664, E168K
F223W






0781
A310
JR-FLgp140.6R.SOSIP.664.E168K_G473Y
JR-FL
SOSIP, R6, 664, E168K
G473Y






0782
A311
JR-FLgp140.6R.SOSIP.664.E168K_G431P
JR-FL
SOSIP, R6, 664, E168K
G431P






0783
A312
JR-FLgp140.6R.SOSIP.664.E168K_N425C_
JR-FL
SOSIP, R6, 664, E168K
N425C_A433C





A433C









0784
A313
JR-FLgp140.6R.SOSIP.664.E168K_V120C_
JR-FL
SOSIP, R6, 664, E168K
V120C_Q315C





Q315C









0785
A314
JR-FLgp140.6R.SOSIP.664.E168K_Q203C_
JR-FL
SOSIP, R6, 664, E168K
Q203C_L122C





L122C









0786
A315
JR-FLgp140.6R.SOSIP.664.E168K_I201C/
JR-FL
SOSIP, R6, 664, E168K
I201C/A433C/R304C/Q440C





A433C/R304C/Q440C









0787
A316
JR-FLgp140.6R.SOSIP.664.E168K_R304C/
JR-FL
SOSIP, R6, 664, E168K
R304C/R440C
Lock V3 to gp120 to prevent




R440C



exposure/opening





0788
A317
JR-FLgp140.6R.SOSIP.664.E168K_Q203C/
JR-FL
SOSIP, R6, 664, E168K
Q203C/F317C
Same as Seq_0787




F317C









0789
A318
JR-FLgp140.6R.SOSIP.664.E168K_L122C/
JR-FL
SOSIP, R6, 664, E168K
L122C/F317C
Same as Seq_0787




F317C









0790
A319
JR-FLgp140.6R.SOSIP.664.E168K_P437C/
JR-FL
SOSIP, R6, 664, E168K
P437C/Y318C
Same as Seq_0787




Y318C









0791
A320
JR-FLgp140.6R.SOSIP.664.E168K_E172C/
JR-FL
SOSIP, R6, 664, E168K
E172C/I307C
Locking V3 V3 to V1V2 to




I307C



prevent exposure/opening





0792
A321
JR-FLgp140.6R.SOSIP.664.E168K_P206C/
JR-FL
SOSIP, R6, 664, E168K
P206C/Y318C
Same as Seq_0787




Y318C









0793
A322
JR-FLgp140.6R.SOSIP.664.E168K_A174C/
JR-FL
SOSIP, R6, 664, E168K
A174C/T319C
Same as Seq_0791




T319C









0794
A323
JR-FLgp140.6R.SOSIP.664.E168K_S164C/
JR-FL
SOSIP, R6, 664, E168K
S164C/H308C
Same as Seq_0791




H308C









0795
A324
JR-FLgp140.6R.SOSIP.664.E168K_T320C/
JR-FL
SOSIP, R6, 664, E168K
T320C/L175C
Same as Seq_0791




L175C









0796
A325
JR-FLgp140.6R.SOSIP.664.E168K_T320C/
JR-FL
SOSIP, R6, 664, E168K
T320C/P438C
Same as Seq_0791




P438C









0797
F089
KER2008.12_V1V2V3CAP_fer_15ln_gyc
KER2008

V1V2V3 nanoparticle circ.
V1V2V3 constructed at distances







permut., inter-subunit
defined by the 4TVP structure







disulfide, ferritin






0798
F090
KER2008.12_V1V2V3CAP_fer_10ln_gyc
KER2008

Same as Seq_0797
Same as Seq_0797





0799
F091
KER2008.12_V1V2V3CAP_fer_10ln_gyc
KER2008

Same as Seq_0797
Same as Seq_0797





0800
F092
Q23.17_V1V2V3CAP_fer_15ln_gyc
Q23.17

Same as Seq_0797
Same as Seq_0797





0801
F093
Q23.17_V1V2V3CAP_fer_10ln_gyc
Q23.17

Same as Seq_0797
Same as Seq_0797





0802
F094
Q23.17_V1V2V3CAP_fer_5ln_gyc
Q23.17

Same as Seq_0797
Same as Seq_0797





0803
F095
KER2008.12_V1V2V3CAP_LS_15ln_gyc
KER2008

V1V2V3 nanoparticle circ.
Same as Seq_0797







permut., inter-subunit








disulfide, lumazine








synthase






0804
F096
KER2008.12_V1V2V3CAP_LS_10ln_gyc
KER2008

Same as Seq_0803
Same as Seq_0797





0805
F097
KER2008.12_V1V2V3CAP_LS_10ln_gyc
KER2008

Same as Seq_0803
Same as Seq_0797





0806
F098
Q23.17_V1V2V3CAP_LS_15ln_gyc
Q23.17

Same as Seq_0803
Same as Seq_0797





0807
F099
Q23.17_V1V2V3CAP_LS_10ln_gyc
Q23.17

Same as Seq_0803
Same as Seq_0797





0808
F100
Q23.17_V1V2V3CAP_LS_5ln_gyc
Q23.17

Same as Seq_0803
Same as Seq_0797





0809
F101
KER2008.12_ds175_320_V1V2V3CAP_fer_
KER2008

V1V2V3 nanoparticle circ.
Same as Seq_0797




15ln_gyc


permut., inter-subunit 








disulfide, intra-subunit








disulfide, ferritin






0810
F102
KER2008.12_ds175_320_V1V2V3CAP_fer_
KER2008

Same as Seq_0809
Same as Seq_0797




10ln_gyc









0811
F103
KER2008.12_ds175_320_V1V2V3CAP_fer_
KER2008

Same as Seq_0809
Same as Seq_0797




10ln_gyc









0812
F104
Q23.17_ds174_319_V1V2V3CAP_fer_15ln_gyc
Q23.17

Same as Seq_0809
Same as Seq_0797





0813
F105
Q23.17_ds174_319_V1V2V3CAP_fer_10ln_gyc
Q23.17

Same as Seq_0809
Same as Seq_0797





0814
F106
Q23.17_ds174_319_V1V2V3CAP_fer_5ln_gyc
Q23.17

Same as Seq_0809
Same as Seq_0797





0815
F107
KER2008.12_ds175_320_V1V2V3CAP_LS_
KER2008

V1V2V3 nanoparticle circ.
Same as Seq_0797




15ln_gyc


permut., inter-subunit 








disulfide, lumazine








synthase, intra-subunit








disulfide






0816
F108
KER2008.12_ds175_320_V1V2V3CAP_LS_
KER2008

Same as Seq_0815
Same as Seq_0797




10ln_gyc









0817
F109
KER2008.12_ds175_320_V1V2V3CAP_LS_
KER2008

Same as Seq_0815
Same as Seq_0797




10ln_gyc









0818
F110
Q23.17_ds174_319_V1V2V3CAP_LS_15ln_gyc
Q23.17

Same as Seq_0815
Same as Seq_0797





0819
F111
Q23.17_ds174_319_V1V2V3CAP_LS_10ln_gyc
Q23.17

Same as Seq_0815
Same as Seq_0797





0820
F112
Q23.17_ds174_319_V1V2V3CAP_LS_5ln_gyc
Q23.17

Same as Seq_0815
Same as Seq_0797





0821
F113
BG505_119-136 + ln + 296-331 + ln +
BG505

V1V2V3 nanoparticle circ.
Same as Seq_0797




151-205 + 1ln + ferr


permut.






0822
F114
CNE58_SU-strandC_119-136 + ln +
CNE58

V1V2V3 nanoparticle circ.
Same as Seq_0797




296-331 + ln + 151-205 + 1ln + ferr


permut.






0823
F115
3301_V1_C24_119-136 + ln + 296-331 +
3301

V1V2V3 nanoparticle circ.
Same as Seq_0797




ln + 151-205 + 1ln + ferr


permut.






0824
F116
ZM53-R166W_119-136 + ln + 296-331 +
ZM53

V1V2V3 nanoparticle circ.
Same as Seq_0797




ln + 151-205 + 1ln + ferr


permut.






0825
F117
ZM233.6_119-136 + ln + 296-331 + ln +
ZM233

V1V2V3 nanoparticle circ.
Same as Seq_0797




151-205 + 1ln + ferr


permut.






0826
F118
BG505_119-136 + ln + 296-331 + ln +
BG505

V1V2V3 nanoparticle circ.
Same as Seq_0797




151-205 + 5ln + ferr


permut.






0827
F119
CNE58_SU-strandC 119-136 + ln +
CNE58

V1V2V3 nanoparticle circ.
Same as Seq_0797




296-331 + ln + 151-205 + 5ln + ferr


permut.






0828
F120
3301_V1_C24_119-136 + ln + 296-331 +
3301

V1V2V3 nanoparticle circ.
Same as Seq_0797




ln + 151-205 + 5ln + ferr


permut.






0829
F121 
ZM53-R166W_119-136 + ln + 296-331 +
ZM53

V1V2V3 nanoparticle circ.
Same as Seq_0797




ln + 151-205 + 5ln + ferr


permut.






0830
F122
ZM233.6_119-136 + ln + 296-331 + ln +
ZM233

V1V2V3 nanoparticle circ.
Same as Seq_0797




151-205 + 5ln + ferr


permut.






0831
F123
BG505_119-136 + ln + 296-331 + ln +
BG505

V1V2V3 nanoparticle circ.
Same as Seq_0797




151-205 + 10ln + ferr


permut.






0832
F124
CNE58_SU-strandC_119-136 + ln +
CNE58

V1V2V3 nanoparticle circ.
Same as Seq_0797




296-331 + ln + 151-205 + 10ln + ferr


permut.






0833
F125
3301_V1_C24_119-136 + ln + 296-331 +
3301

V1V2V3 nanoparticle circ.
Same as Seq_0797




ln + 151-205 + 10ln + ferr


permut.






0834
F126
ZM53-R166W_119-136 + ln + 296-331 +
ZM53

V1V2V3 nanoparticle circ.
Same as Seq_0797




ln + 151-205 + 10ln + ferr


permut.






0835
F127
ZM233.6_119-136 + ln + 296-331 + ln +
ZM233

V1V2V3 nanoparticle circ.
Same as Seq_0797




151-205 + 10ln + ferr


permut.






0836
E001
KER2008.12_V1V2V3CAP_1VH8cp_10ln_gyc
KER2008

V1V2V3 scaffold circ.
Same as Seq_0797







permut., inter-subunit








disulfide, 1VH8






0837
E002
KER2008.12_V1V2V3CAP_1VH8cp_15ln_gyc
KER2008

V1V2V3 scaffold circ.
Same as Seq_0797







permut., inter-subunit








disulfide, 1VH8






0838
E003
Q23.17_V1V2V3CAP_1VH8cp_10ln_gyc
Q23.17

V1V2V3 scaffold circ.
Same as Seq_0797







permut., inter-subunit








disulfide, 1VH8






0839
E004
Q23.17_V1V2V3CAP_1VH8cp_15ln_gyc
Q23.17

V1V2V3 scaffold circ.
Same as Seq_0797







permut., inter-subunit








disulfide, 1VH8






0840
E005
KER2008.12_ds175_320_V1V2V3CAP_
KER2008

V1V2V3 scaffold circ.
Same as Seq_0797




1VH8cp_10ln_gyc


permut., inter-subunit








disulfide, 1VH8, intra-








subunit disulfide






0841
E006
KER2008.12_ds175_320_V1V2V3CAP_
KER2008

V1V2V3 scaffold circ.
Same as Seq_0797




1VH8cp_15ln_gyc


permut., inter-subunit








disulfide, 1VH8, intra-








subunit disulfide






0842
E007
Q23.17_ds174_319_V1V2V3CAP_1VH8cp_
Q23.17

V1V2V3 scaffold circ.
Same as Seq_0797




10ln_gyc


permut., inter-subunit








disulfide, 1VH8, intra-








subunit disulfide






0843
E008
Q23.17_ds174_319_V1V2V3CAP_1VH8cp_
Q23.17

V1V2V3 scaffold circ.
Same as Seq_0797




15ln_gyc


permut., inter-subunit








disulfide, 1VH8, intra-








subunit disulfide






0844
G004
BG505_119-136 + ln + 296-331 + ln +
BG505

V1V2V3 trimerization-
Same as Seq_0797




151-205 + 3ln + foldon


domain circ. permut.






0845
G005
CNE58_SU-strandC_119-136 + ln +
CNE58

V1V2V3 trimerization-
Same as Seq_0797




296-331 + ln + 151-205 + 3ln + foldon


domain circ. permut.






0846
G006
3301_V1_C24_119-136 + ln + 296-331 +
3301

V1V2V3 trimerization-
Same as Seq_0797




ln + 151-205 + 3ln + foldon


domain circ. permut.






0847
G007
ZM53-R166W_119-136 + ln + 296-331 +
ZM53

V1V2V3 trimerization-
Same as Seq_0797




ln + 151-205 + 3ln + foldon


domain circ. permut.






0848
G008
ZM233.6_119-136 + ln + 296-331 + ln +
ZM233

V1V2V3 trimerization-
Same as Seq_0797




151-205 + 3ln + foldon


domain circ. permut.






0849
G009
BG505_119-136 + ln + 296-331 + ln +
BG505

V1V2V3 trimerization-
Same as Seq_0797




151-205 + 7ln + foldon


domain circ. permut.






0850
G010
CNE58_SU-strandC_119-136 + ln +
CNE58

V1V2V3 trimerization-
Same as Seq_0797




296-331 + ln + 151-205 + 7ln + foldon


domain circ. permut.






0851
G011
3301_V1_C24_119-136 + ln + 296-331 +
3301

V1V2V3 trimerization-
Same as Seq_0797




ln + 151-205 + 7ln + foldon


domain circ. permut.






0852
G012
ZM53-R166W_119-136 + ln + 296-331 +
ZM53

V1V2V3 trimerization-
Same as Seq_0797




ln + 151-205 + 7ln + foldon


domain circ. permut.






0853
G013
ZM233.6_119-136 + ln + 296-331 + ln +
ZM233

V1V2V3 trimerization-
Same as Seq_0797




151-205 + 7ln + foldon


domain circ. permut.






0854
Z
Linker









0855
Z
1VH8 Scaffold
1VH8








0856
H043
*286.36-chim_d7324.201C-433C
286.36/BG505
SOSIP, R6, 664,
Res. 31-45, 478-507, 512-
Same as Seq_0379





chimera
201C/433C
664 from BG505 (“BG505








Platform”), remainder =








286.36






0857
H044
288.38-chim_d7324.201C-433C
288.38/BG505
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





chimera
201C/433C
remainder = 288.38






0858
H045
3988.25-chim_d7324.201C-433C
3988.25/BG505
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





chimera
201C/433C
remainder = 3988.25






0859
H046
5768.04-chim_d7324.201C-433C
5768.04/BG505
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





chimera
201C/433C
remainder from 5768.04






0860
H047
6101.1-chim_d7324.201C-433C
6101.1/BG505
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





chimera
201C/433C
remainder = 6101.1






0861
H048
6535.3-chim_d7324.201C-433C
6535.3/BG505
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





chimera
201C/433C
remainder = 6535.3






0862
H049
7165.18-chim_d7324.201C-433C
7165.18/BG505 
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





chimera
201C/433C
remainder = 7165.18






0863
H050
0013095-2.11-chim_d7324.201C-433C
0013095-2.11/
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





BG505 chimera
201C/433C
remainder = 0013095-2.11






0864
H051
001428-2.42-chim_d7324.201C-433C
001428-2.42/
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





BG505 chimera
201C/433C
remainder = 001428-2.42






0865
H052
0077_V1.C16-chim _d7324.201C-433C
0077_V1.C16/
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





BG505 chimera
201C/433C
remainder = 0077V1.C16






0866
H053
00836-2.5-chim_d7324.201C-433C
00836-2.5/BG505
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





chimera
201C/433C
remainder = 00836-2.5






0867
H054
0260.v5.c36-chim_d7324.201C-433C
0260.v5.c36/
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





BG505 chimera
201C/433C
remainder = 0260.v5.c36






0868
H055
0330.v4.c3-chim_d7324.201C-433C
0330.v4.c3/
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





BG505 chimera
201C/433C
remainder = 0330.v4.c3






0869
H056
0439.v5.c1-chim_d7324.201C-433C
0439.v5.c1/
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





BG505 chimera
201C/433C
remainder = 0439.v5.c1






0870
H057
0815.V3.C3-chim_d7324.201C-433C
0815.V3.C3/
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





BG505 chimera
201C/433C
remainder = 0815.V3.C3






0871
H058
*0921.V2.C14-chim_d7324.201C-433C
0921.V2.C14/
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





BG505 chimera
201C/433C
remainder = 0921.V2.C14






0872
H059
*16055-2.3-chim_d7324.201C-433C
16055-2.3/BG505
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





chimera
201C/433C
remainder = 16055-2.3






0873
H060
16845-2.22-chim_d7324.201C-433C
16845-2.22/BG505
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





chimera
201C/433C
remainder = 16845-2.22






0874
H061
16936-2.21-chim_d7324.201C-433C
16936-2.21/BG505
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





chimera
201C/433C
remainder = 16936-2.21






0875
H062
231965.c1-chim_d7324.201C-433C
231965.c1/BG505
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





chimera
201C/433C
remainder = 231965.c1






0876
H063
235-47-chim_d7324.201C-433C
235-47/BG505
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





chimera
201C/433C
remainder = 235-47






0877
H064
242-14-chim_d7324.201C-433C
242-14/BG505
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





chimera
201C/433C
remainder = 242-14






0878
H065
247-23-chim_d7324.201C-433C
247-23/BG505
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





chimera
201C/433C
remainder = 247-23






0879
H066
25710-2.43-chim_d7324.201C-433C
25710-2.43/BG505
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





chimera
201C/433C
remainder = 25710-2.43






0880
H067
25711-2.4-chim_d7324.201C-433C
25711-2.4/BG505
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





chimera
201C/433C
remainder = 25711-2.4






0881
H068
*25925-2.22-chim_d7324.201C-433C
25925-2.22/BG505
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





chimera
201C/433C
remainder = 25925-2.22






0882
H069
26191-2.48-chim_d7324.201C-433C
26191-2.48/BG505
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





chimera
201C/433C
remainder = 26191-2.48






0883
H070
263-8-chim_d7324.201C-433C
263-8/BG505
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





chimera
201C/433C
remainder = 263-8






0884
H071
269-12-chim_d7324.201C-433C
269-12/BG505
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





chimera
201C/433C
remainder = 269-12






0885
H072
271-11-chim_d7324.201C-433C
271-11/BG505
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





chimera
201C/433C
remainder = 271-11






0886
H073
3016.v5.c45-chim_d7324.201C-433C
3016.v5.c45/
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





BG505 chimera
201C/433C
remainder = 3016.v5.c45






0887
H074
3168.V4.C10-chim_d7324.201C-433C
3168.V4.C10/
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





BG505 chimera
201C/433C
remainder = 3168.V4.C10






0888
H075
*3301.V1.C24-chim_d7324.201C-433C
3301.V1.C24/
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





BG505 chimera
201C/433C
remainder = 3301.V1.C24






0889
H076
3326.V4.C3-chim_d7324.201C-433C
3326.V4.C3/
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





BG505 chimera
201C/433C
remainder = 3326.V4.C3






0890
H077
3337.V2.C6-chim_d7324.201C-433C
3337.V2.C6/
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





BG505 chimera
201C/433C
remainder = 3337.V2.C6






0891
H078
3365.v2.c20-chim_d7324.201C-433C
3365.v2.c20/
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





BG505 chimera
201C/433C
remainder = 3365.v2.c20






0892
H079
3415.v1.c1-chim_d7324.201C-433C
3415.v1.c1/BG505
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





chimera
201C/433C
remainder = 3415.v1.c1






0893
H080
3468.V1.C12-chim_d7324.201C-433C
3468.V1.C12/
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





BG505 chimera
201C/433C
remainder = 3468.V1.C12






0894
H081
3589.V1.C4-chim_d7324.201C-433C
3589.V1.C4/BG505
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





chimera
201C/433C
remainder = 3589.V1.C4






0895
H082
3637.V5.C3-chim_d7324.201C-433C
3637.V5.C3/BG505
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





chimera
201C/433C
remainder = 3637.V5.C3






0896
H083
3718.v3.c11-chim_d7324.201C-433C
3718.v3.c11/
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





BG505 chimera
201C/433C
remainder = 3718.v3.c11






0897
H084
3817.v2.c59-chim_d7324.201C-433C
3817.v2.c59/
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





BG505 chimera
201C/433C
remainder = 3817.v2.c59






0898
H085
3873.V1.C24-chim_d7324.201C-433C
3873.V1.C24/
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





BG505 chimera
201C/433C
remainder = 3873.V1.C24






0899
H086
398-F1_F6_20-chim_d7324.201C-433C
398-F1_F6_20/
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





BG505 chimera
201C/433C
remainder = 398-F1_F6_20






0900
H087
57128.vrc15-chim_d7324.201C-433C
57128.vrc15/
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





BG505 chimera
201C/433C
remainder = 57128.vrc15






0901
H088
6095.V1.C10-chim_d7324.201C-433C
6095.V1.C10/
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





BG505 chimera
201C/433C
remainder = 6095.V1.C10






0902
H089
*620345.c1-chim_d7324.201C-433C
620345.c1/BG505
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





chimera
201C/433C
remainder = 620345.c1






0903
H090
6322.V4.C1-chim_d7324.201C-433C
6322.V4.C1/BG505
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





chimera
201C/433C
remainder = 6322.V4.C1






0904
H091
6405.v4.c34-chim_d7324.201C-433C
6405.v4.c34/
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





BG505 chimera
201C/433C
remainder = 6405.v4.c34






0905
H092
6471.V1.C16-chim_d7324.201C-433C
6471.V1.C16/
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





BG505 chimera
201C/433C
remainder = 6471.V1.C16






0906
H093
6540.v4.c1-chim_d7324.201C-433C
6540.v4.c1/BG505
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





chimera
201C/433C
remainder = 6540.v4.c1






0907
H094
6545.V3.C13-chim_d7324.201C-433C
6545.V3.C13/
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





BG505 chimera
201C/433C
remainder = 6545.V3.C13






0908
H095
6545.V4.C1-chim_d7324.201C-433C
6545.V4.C1/BG505
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





chimera
201C/433C
remainder = 6545.V4.C1






0909
H096
6631.V3.C10-chim_d7324.201C-433C
6631.V3.C10/
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





BG505 chimera
201C/433C
remainder = 6631.V3.C10






0910
H097
6644.V2.C33-chim_d7324.201C-433C
6644.V2.C33/
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





BG505 chimera
201C/433C
remainder = 6644.V2.C33






0911
H098
6785.V5.C14-chim_d7324.201C-433C
6785.V5.C14/
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





BG505 chimera
201C/433C
remainder = 6785.V5.C14






0912
H099
6838.V1.C35-chim_d7324.201C-433C
6838.V1.C35/
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





BG505 chimera
201C/433C
remainder = 6838.V1.C35






0913
H100
89.6.DG-chim_d7324.201C-433C
89.6.DG/BG505
SOSIP, R6, 664,
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = 89.6.DG






0914
H101
928-28-chim_d7324.201C-433C
928-28/BG505
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





chimera
201C/433C
remainder = 928-28






0915
H102
962M651.02-chim_d7324.201C-433C
96ZM651.02/
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





BG505 chimera
201C/433C
remainder = 962M651.02






0916
H103
A03349M1.vrc4a-chim_d7324.201C-433C
A03349M1.vrc4a/
SOSIP, R6, 664,
BG505 Platform, 
Same as Seq_0379





BG505 chimera
201C/433C
remainder =








A03349M1.vrc4a






0917
H104
*AC10.29-chim_d7324.201C-433C
AC10.29/BG505
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





chimera
201C/433C
remainder = AC10.29






0918
H105
ADA.DG-chim_d7324.201C-433C
ADA.DG/BG505
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





chimera
201C/433C
remainder = ADA.DG






0919
H106
Bal.01-chim_d7324.201C-433C
Bal.01/BG505 
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





chimera
201C/433C
remainder = Bal.01






0920
H107
BaL.26-chim_d7324.201C-433C
BaL.26/BG505
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





chimera
201C/433C
remainder = BaL.26






0921
H108
BB201.1342-chim_d7324.201C-433C
BB201.1342/BG505
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





chimera
201C/433C
remainder = BB201.B42






0922
H109
BB539.21313-chim_d7324.201C-433C
BB539.21313/
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





BG505 chimera
201C/433C
remainder = B13539.21313






0923
H110
BG1168.01-chim_d7324.201C-433C
BG1168.01/BG505
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





chimera
201C/433C
remainder = BG1168.01






0924
H111
*B1369.9A-chim_d7324.201C-433C
B1369.9A/BG505 
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





chimera
201C/433C
remainder = B1369.9A






0925
H112
BLO1.DG-chim_d7324.201C-433C
BLO1.DG/BG505
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





chimera
201C/433C
remainder = BL01.DG






0926
H113
BR025.9-chim_d7324.201C-433C
BR025.9/BG505 
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





chimera
201C/433C
remainder = BR025.9






0927
H114
BR07.DG-chim_d7324.201C-433C
BR07.DG/BG505 
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





chimera
201C/433C
remainder = BR07.DG






0928
H115
BS208.131-chim_d7324.201C-433C
BS208.131/BG505 
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





chimera
201C/433C
remainder = BS208.61






0929
H116
BX08.16-chim_d7324.201C-433C
BX08.16/BG505 
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





chimera
201C/433C
remainder = BX08.16






0930
H117
*C1080.c3-chim_d7324.201C-433C
C1080.c3/BG505 
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





chimera
201C/433C
remainder = C1080.c3






0931
H118
C2101.c1-chim_d7324.201C-433C
C2101.c1/BG505 
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





chimera
201C/433C
remainder = C2101.c1






0932
H119
C3347.c11-chim_d7324.201C-433C
C3347.c11/BG505 
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





chimera
201C/433C
remainder = C3347.c11






0933
H120
*C4118.09-chim_d7324.201C-433C
C4118.09/BG505 
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





chimera
201C/433C
remainder = C4118.09






0934
H121
CAAN.A2-chim_d7324.201C-433C
CAAN.A2/BG505 
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





chimera
201C/433C
remainder = CAAN.A2






0935
H122
CAP210.E8-chim_d7324.201C-433C
CAP210.E8/BG505 
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





chimera
201C/433C
remainder = CAP210.E8






0936
H123
CAP244.D3-chim_d7324.201C-433C
CAP244.D3/BG505 
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





chimera
201C/433C
remainder = CAP244.D3






0937
H124
*CAP45.G3-chim_d7324.201C-433C
CAP45.G3/BG505 
SOSIP, R6, 664,
BG505 Platform,
Same as Seq_0379





chimera
201C/433C
remainder = CAP45.G3






0938
H125
*CH038.12-chim_d7324.201C-433C
CH038.12/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = CH038.12






0939
H126
CH070.1-chim_d7324.201C-433C
CH070.1/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = CH070.1






0940
H127
*CH117.4-chim_d7324.201C-433C
CH117.4/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = CH117.4






0941
H128
CH181.12-chim_d7324.201C-433C
CH181.12/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = CH181.12






0942
H129
CNE10-chim_d7324.201C-433C
CNE10/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = CNE10






0943
H130
CNE12-chim_d7324.201C-433C
CNE12/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = CNE12






0944
H131
CNE14-chim_d7324.201C-433C
CNE14/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = CNE14






0945
H132
CNE15-chim_d7324.201C-433C
CNE15/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = CNE15






0946
H133
CNE3-chim_d7324.201C-433C
CNE3/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = CNE3






0947
H134
CNE30-chim_d7324.201C-433C
CNE30/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = CNE30






0948
H135
CNE31-chim_d7324.201C-433C
CNE31/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = CNE31






0949
H136
CNE4-chim_d7324.201C-433C
CNE4/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = CNE4






0950
H137
CNE40-chim_d7324.201C-433C
CNE40/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = CNE40






0951
H138
CNE5-chim_d7324.201C-433C
CNE5/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = CNE5






0952
H139
CNE53-chim_d7324.201C-433C
CNE53/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = CNE53






0953
H140
*CNE55-chim_d7324.201C-433C
CNE55/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = CNE55






0954
H141
CNE56-chim_d7324.201C-433C
CNE56/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = CNE56






0955
H142
CNE57-chim_d7324.201C-433C
CNE57/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = CNE57






0956
H143
CNE58-chim_d7324.201C-433C
CNE58/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = CNE58






0957
H144
CNE59-chim_d7324.201C-433C
CNE59/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = CNE59






0958
H145
CNE7-chim_d7324.201C-433C
CNE7/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = CNE7






0959
H146
DJ263.8-chim_d7324.201C-433C
DJ263.8/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = DJ263.8






0960
H147
DU123.06-chim_d7324.201C-433C
DU123.06/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = DU123.06






0961
H148
DU151.02-chim_d7324.201C-433C
DU151.02/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = DU151.02






0962
H149
*DU156.12-chim_d7324.201C-433C
DU156.12/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = DU156.12






0963
H150
DU172.17-chim_d7324.201C-433C
DU172.17/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = DU172.17






0964
H151
*DU422.01-chim_d7324.201C-433C
DU422.01/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = DU422.01






0965
H152
H086.8-chim_d7324.201C-433C
H086.8/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = H086.8






0966
H153
HT593.1-chim_d7324.201C-433C
HT593.1/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = HT593.1






0967
H154
JRCSF.JB-chim_d7324.201C-433C
JRCSF.JB/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = JRCSF.JB






0968
H155
JRFLIB-chim_d7324.201C-433C
JRFL.JB/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = JRFL.JB






0969
H156
KER2008.12-chim_d7324.201C-433C
KER2008.12/
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





BG505 chimera
201C/433C
remainder = KER2008.12






0970
H157
KER2018.11-chim_d7324.201C-433C
KER2018.11/
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





BG505 chimera
201C/433C
remainder = KER2018.11






0971
H158
KNH1209.18-ch1m_d7324.201C-433C
KNH1209.18/
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





BG505 chimera
201C/433C
remainder = KNH1209.18






0972
H159
M02138-chim_d7324.201C-433C
M02138/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = M02138






0973
H160
*MB201.A1-chim_d7324.201C-433C
MB201.A1/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = MB201.A1






0974
H161
MB539.2137-chim_d7324.201C-433C
MB539.2137/
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





BG505 chimera
201C/433C
remainder = MB539.267






0975
H162
MI369.A5-chim_d7324.201C-433C
MI369.A5/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = MI369.A5






0976
H163
MN.3-chim_d7324.201C-433C
MN.3/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = MN.3






0977
H164
M5208.A1-chim_d7324.201C-433C
M5208.A1/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = M5208.A1






0978
H165
*MW965.26-chim_d7324.201C-433C
MW965.26/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = MW965.26






0979 
H166
NKU3006.ec1-chim_d7324.201C-433C
NKU3006.ec1/
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





BG505 chimera
201C/433C
remainder = NKU3006.ec1






0980
H167
PVO.04-chim_d7324.201C-433C
PVO.04/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = PVO.04






0981
H168
Q168.a2-chim_d7324.201C-433C
Q168.a2/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = Q168.a2






0982
H169
Q23.17-chim_d7324.201C-433C
Q23.17/BG505 
SOSIP, R6, 664, 
BG505 Platform,
Same as Seq_0379





chimera
201C/433C
remainder = Q23.17






0983
H170
Q259.17-chim_d7324.201C-433C
Q259.17/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = Q259.17






0984
H171
Q461.e2-chim_d7324.201C-433C
Q461.e2/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = Q461.e2






0985
H172
Q769.d22-chim_d7324.201C-433C
Q769.d22/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = Q769.d22






0986
H173
Q769.h5-chim_d7324.201C-433C
Q769.h5/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = Q769.h5






0987
H174
Q842.d12-chim_d7324.201C-433C
Q842.d12/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = Q842.d12






0988
H175
QH0515.01-chim_d7324.201C-433C
QH0515.01/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = QH0515.01






0989
H176
QH0692.42-chim_d7324.201C-433C
QH0692.42/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = QH0692.42






0990
H177
*QH209.14M.A2-chim_d7324.201C-433C
QH209.14M.A2/
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





BG505 chimera
201C/433C
remainder = QH209.14M.A2






0991
H178
R1166.c1-chim_d7324.201C-433C
R1166.c1/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = R1166.c1






0992
H179
R2184.c4-chim_d7324.201C-433C
R2184.c4/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = R2184.c4






0993
H180
R3265.c6-chim_d7324.201C-433C
R3265.c6/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = R3265.c6






0994
H181
REJ0.67-chim_d7324.201C-433C
REJO.67/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = REJO.67






0995
H182
RHPA.7-chim_d7324.201C-433C
RHPA.7/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = RHPA.7






0996
H183
RWO20.2-chim_d7324.201C-433C
RWO20.2/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = RWO20.2






0997
H184
SC422.8-chim_d7324.201C-433C
SC422.8/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = SC422.8






0998
H185
SF162.LS-chim_d7324.201C-433C
SF162.LS/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = SF162.LS






0999
H186
SO18.18-chim_d7324.201C-433C
SO18.18/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = SO18.18






1000
H187
SS1196.01-chim_d7324.201C-433C
SS1196.01/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = SS1196.01






1001
H188
T250-4-chim_d7324.201C-433C
T250-4/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = T250-4






1002
H189
T251-18-chim_d7324.201C-433C
T251-18/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = T251-18






1003
H190
T253-11-chim_d7324.201C-433C
T253-11/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = T253-11






1004
H191
T255-34-chim_d7324.201C-433C
T255-34/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = T255-34






1005
H192
T257-31-chim_d7324.201C-433C
T257-31/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = T257-31






1006
H193
T266-60-chim_d7324.201C-433C
T266-60/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = T266-60






1007
H194
T278-50-chim_d7324.201C-433C
T278-50/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = T278-50






1008
H195
T280-5-ch1m_d7324.201C-433C
T280-5/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = T280-5






1009
H196
T33-7-chim_d7324.201C-433C
T33-7/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = T33-7






1010
H197
*TH966.8-chim_d7324.201C-433C
TH966.8/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = TH966.8






1011
H198
TH976.17-chim_d7324.201C-433C
TH976.17/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = TH976.17






1012
H199
THRO.18-chim_d7324.201C-433C
THRO.18/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = THRO.18






1013
H200
TRJO.58-chim_d7324.201C-433C
TRJO.58/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = TRJO.58






1014
H201
TRO.11-chim_d7324.201C-433C
TRO.11/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = TRO.11






1015
H202
TV1.29-chim_d7324.201C-433C
TV1.29/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = TV1.29






1016
H203
TZA125.17-chim_d7324.201C-433C
TZA125.17/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = TZA125.17






1017
H204
TZBD.02-chim_d7324.201C-433C
TZBD.02/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = TZBD.02






1018
H205
UG021.16-chim_d7324.201C-433C
UG021.16/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = UG021.16






1019
H206
UG024.2-chim_d7324.201C-433C
UG024.2/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = UG024.2






1020
H207
UG037.8-chim_d7324.201C-433C
UG037.8/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = UG037.8






1021
H208
WITO.33-chim_d7324.201C-433C
WITO.33/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = WITO.33






1022
H209
X2088.c9-chim_d7324.201C-433C
X2088.c9/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = X2088.c9






1023
H210
YU2.DG-chim_d7324.201C-433C
YU2.DG/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = YU2.DG






1024
H211
ZA012.29-chim_d7324.201C-433C
ZA012.29/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = ZA012.29






1025
H212
*ZM106.9-chim_d7324.201C-433C
ZM106.9/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = ZM106.9






1026
H213
ZM109.4-chim_d7324.201C-433C
ZM109.4/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = ZM109.4






1027
H214
ZM135.10a-chim_d7324.201C-433C
ZM135.10a/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = ZM135.10a






1028
H215
ZM176.66-chim_d7324.201C-433C
ZM176.66/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = ZM176.66






1029
H216
ZM197.7-chim_d7324.201C-433C
ZM197.7/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = ZM197.7






1030
H217
ZM214.15-chim_d7324.201C-433C
ZM214.15/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = ZM214.15






1031
H218
ZM215.8-chim_d7324.201C-433C
ZM215.8/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = ZM215.8






1032
H219
ZM233.6-chim_d7324.201C-433C
ZM233.6/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = ZM233.6






1033
H220
ZM249.1-chim_d7324.201C-433C
ZM249.1/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = ZM249.1






1034
H221
*ZM53.12-chim_d7324.201C-433C
ZM53.12/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = ZM53.12






1035
H222
*ZM55.28a-chim_d7324.201C-433C
ZM55.28a/BG505 
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_0379





chimera
201C/433C
remainder = ZM55.28a






1036
H223
6101.1-chim + int_d7324.201C-433C
6101.1 + int/
SOSIP, R6, 664, 
BG505: Res. 31-45,
Same as Seq_0579





BG505 chimera
201C/433C
478-507, 512-664








and Int. Res. set A;








remainder- 6101.1






1037
H224
Bal.01-chim + int_d7324.201C-433C
Bal.01 + int/
SOSIP, R6, 664, 
BG505: Res. 31-45, 
Same as Seq_0579





BG505 chimera
201C/433C
478-507, 512-664 and Int.








Res. set A; remainder- 








Bal.01






1038
H225
BG1168.01-chim + int_d7324.201C-433C
BG1168.01 + int/
SOSIP, R6, 664, 
BG505: Res. 31-45,
Same as Seq_0579





BG505 chimera
201C/433C
478-507, 512-664 and Int.








Res. set A; remainder-








BG1168.01






1039
H226
CAAN.A2-chim + int_d7324.201C-433C
CAAN.A2 + int/
SOSIP, R6, 664 , 
BG505: Res. 31-45, 
Same as Seq_0579





BG505 chimera
201C/433C
478-507, 512-664 and Int.








Res. set A; remainder- 








CAAN.A2






1040
H227
DU156.12-chim + int d7324.201C-433C
DU156.12 + int/
SOSIP, R6, 664, 
BG505: Res. 31-45, 
Same as Seq_0579





BG505 chimera
201C/433C
478-507, 512-664 and Int.








Res. set A; remainder- 








DU156.12






1041
H228
DU422.01-chim + int d7324.201C-433C
DU422.01 + int/
SOSIP, R6, 664, 
BG505: Res. 31-45, 
Same as Seq_0579





BG505 chimera
201C/433C
478-507, 512-664 and Int.








Res. set A; remainder- 








DU422.01






1042
H229
JRCSF.JB-chim + int_d7324.201C-433C
JRCSF.JB + int/
SOSIP, R6, 664, 
BG505: Res. 31-45, 
Same as Seq_0579





BG505 chimera
201C/433C
478-507, 512-664 and Int.








Res. set A; remainder- 








JRCSF.JB






1043
H230
JRFL.JB-chim + int_d7324.201C-433C
JRFL.JB + int/
SOSIP, R6, 664, 
BG505: Res. 31-45, 
Same as Seq_0579





BG505 chimera
201C/433C
478-507, 512-664 and Int.








Res. set A; remainder- 








JRFL.JB






1044
H231
KER2018.11-chim + int_d7324.201C-433C
KER2018.11 +
SOSIP, R6, 664, 
BG505: Res. 31-45,
Same as Seq_0579





int/BG505 
201C/433C
478-507, 512-664 and Int.






chimera

Res. set A; remainder-








KER2018.11






1045
H232
PVO.04-chim + int_d7324.201C-433C
PVO.04 + int/
SOSIP, R6, 664, 
BG505: Res. 31-45, 
Same as Seq_0579





BG505 chimera
201C/433C
478-507, 512-664 and Int.








Res. set A; remainder- 








PVO.04






1046
H233
Q168.a2-chim + int_d7324.201C-433C
Q168.a2 + int/
SOSIP, R6, 664, 
BG505: Res. 31-45, 
Same as Seq_0579





BG505 chimera
201C/433C
478-507, 512-664 and Int.








Res. set A; remainder- 








Q168.a2






1047
H234
Q23.17-chim + int_d7324.201C-433C
Q23.17 + int/
SOSIP, R6, 664, 
BG505: Res. 31-45, 
Same as Seq_0579





BG505 chimera
201C/433C
478-507, 512-664 and Int.








Res. set A; remainder- 








Q23.17






1048
H235
Q769.h5-chim + int_d7324.201C-433C
Q769.h5 + int/
SOSIP, R6, 664, 
BG505: Res. 31-45, 
Same as Seq_0579





BG505 chimera
201C/433C
478-507, 512-664 and Int.








Res. set A; remainder- 








Q769.h5






1049
H236
RW020.2-chim + int_d7324.201C-433C
RW020.2 + int/
SOSIP, R6, 664, 
BG505: Res. 31-45, 
Same as Seq_0579





BG505 chimera
201C/433C
478-507, 512-664 and Int.








Res. set A; remainder- 








RW020.2






1050
H237
THRO.18-chim + int_d7324.201C-433C
THRO.18 + int/
SOSIP, R6, 664, 
BG505: Res. 31-45, 
Same as Seq_0579





BG505 chimera
201C/433C
478-507, 512-664 and Int.








Res. set A; remainder- 








THRO.18






1051
H238
TRJO.58-chim + int_d7324.201C-433C
TRJO.58 + int/
SOSIP, R6, 664, 
BG505: Res. 31-45, 
Same as Seq_0579





BG505 chimera
201C/433C
478-507, 512-664 and Int.








Res. set A; remainder- 








TRJO.58






1052
H239
TRO.11-chim + int_d7324.201C-433C
TRO.11 + int/
SOSIP, R6, 664, 
BG505: Res. 31-45,
Same as Seq_0579





BG505 chimera
201C/433C
478-507, 512-664 and Int.








Res. set A; remainder- 








TRO.11






1053
H240
YU2.DG-chim + int_d7324.201C-433C
YU2.DG + int/
SOSIP, R6, 664, 
BG505: Res. 31-45,
Same as Seq_0579





BG505 chimera
201C/433C
478-507, 512-664 and Int.








Res. set A; remainder- 








YU2.DG






1054
H241
ZA012.29-chim + int_d7324.201C-433C
ZA012.29 + int/
SOSIP, R6, 664, 
BG505: Res. 31-45, 
Same as Seq_0579





BG505 chimera
201C/433C
478-507, 512-664 and Int.








Res. set A; remainder- 








ZA012.29






1055
H242
ZM106.9-chim + int_d7324.201C-433C
ZM106.9 + int/
SOSIP, R6, 664, 
BG505: Res. 31-45, 
Same as Seq_0579





BG505 chimera
201C/433C
478-507, 512-664 and Int.








Res. set A; remainder- 








ZM106.9






1056
H243
ZM55.28a-chim + int_d7324.201C-433C
ZM55.28a + int/
SOSIP, R6, 664, 
BG505: Res. 31-45, 
Same as Seq_0579





BG505 chimera
201C/433C
478-507, 512-664 and Int.








Res. set A; remainder-








ZM55.28a






1057
A326
*6101.1.sosip_d7324.201C-433C
6101.1
SOSIP, R6, 664,
201C, 433C






1058
A327
*Bal.01.sosip_d7324.201C-433C
Bal.01
SOSIP, R6, 664,
201C, 433C






1059
A328
*BG1168.01.sosip_d7324.201C-433C
BG1168.01
SOSIP, R6, 664,
201C, 433C






1060
A329
*CAAN.A2.sosip_d7324.201C-433C
CAAN.A2
SOSIP, R6, 664,
201C, 433C






1061
A330
*DU156.12.sosip_d7324.201C-433C
DU156.12
SOSIP, R6, 664,
201C, 433C






1062
A331
*DU422.01.sosip_d7324.201C-433C
DU422.01
SOSIP, R6, 664,
201C, 433C






1063
A332
*JRC5F.JB.sosip_d7324.201C-433C
JRCSF.JB
SOSIP, R6, 664,
201C, 433C






1064
A333
*JRFLIB.sosip_d7324.201C-433C
JRFL.JB
SOSIP, R6, 664,
201C, 433C






1065
A334
*KER2018.11.sosip_d7324.201C-433C
KER2018.11
SOSIP, R6, 664,
201C, 433C






1066
A335
*PVO.04.sosip_d7324.201C-433C
PVO.04
SOSIP, R6, 664,
201C, 433C5






1067
A336
*Q168.a2.sosip_d7324.201C-433C
Q168.a2
SOSIP, R6, 664,
201C, 433C






1068
A337
*Q23.17.sosip_d7324.201C-433C
Q23.17
SOSIP, R6, 664,
201C, 433C






1069
A338
*Q769.h5.sosip_d7324.201C-433C
Q769.h5
SOSIP, R6, 664,
201C, 433C5






1070
A339
*RW020.2.sosip_d7324.201C-433C
RW020.2
SOSIP, R6, 664,
201C, 433C






1071
A340
*THRO.18.sosip_d7324.201C-433C
THRO.18
SOSIP, R6, 664,
201C, 433C






1072
A341
*TRJO.58.sosip_d7324.201C-433C
TRJO.58
SOSIP, R6, 664,
201C, 433C






1073
A342
*TRO.11.sosip_d7324.201C-433C
TRO.11
SOSIP, R6, 664,
201C, 433C






1074
A343
*YU2.DG.sosip_d7324.201C-433C
YU2.DG
SOSIP, R6, 664,
201C, 433C






1075
A344
*ZA012.29.sosip_d7324.201C-433C
ZA012.29
SOSIP, R6, 664,
201C, 433C






1076
A345
*ZM106.9.sosip_d7324.201C-433C
ZM106.9
SOSIP, R6, 664,
201C, 433C






1077
A346
*ZM55.28a.sosip_d7324.201C-433C
ZM55.28a
SOSIP, R6, 664,
201C, 433C






1078
H244
6101.1-chim-sc_d7324.201C-433C
6101.1/BG505 
SOSIP, R6, 664, 
Seq_0534 linker between
Chimeric single chain Env with





chimera
201C/433C
508-511, BG505 Platform,
BG505gp41ecto/gp120-NC







remainder = ZM55.28a
“platform” and heterologous








gp120





1079
H245
Bal.01-chim-sc_d7324.201C-433C
Bal.01/BG505 
SOSIP, R6, 664, 
Seq_0534 linker between
Same as Seq_1078





chimera
201C/433C
508-511, BG505 Platform,








remainder = Bal.01






1080
H246
BG1168.01-chim-sc_d7324.201C-433C
BG1168.01/BG505
SOSIP, R6, 664, 
Seq_0534 linker between
Same as Seq_1078





chimera
201C/433C
508-511, BG505 Platform,








remainder = BG1168.01






1081
H247
CAAN.A2-chim-sc_d7324.201C-433C
CAAN.A2/BG505 
SOSIP, R6, 664, 
Seq_0534 linker between
Same as Seq_1078





chimera
201C/433C
508-511, Res. 31-45,








478-507, 512-664 from








BG505, remainder =








CAAN.A2






1082
H248
DU156.12-chim-sc_d7324.201C-433C
DU156.12/BG505
SOSIP, R6, 664,
Seq_0534 linker between
Same as Seq_1078





chimera
201C/433C
508-511, BG505 Platform,








remainder = DU156.12






1083
H249
DU422.01-chim-sc_d7324.201C-433C
DU422.01/BG505 
SOSIP, R6, 664, 
Seq_0534 linker between
Same as Seq_1078





chimera
201C/433C
508-511, BG505 Platform,








remainder = DU422.01






1084
H250
JRCSF.JB-chim-sc_d7324.201C-433C
JRCSF.JB/BG505
SOSIP, R6, 664,
Seq_0534 linker between
Same as Seq_1078





chimera
201C/433C
508-511, BG505 Platform,








remainder = JRCSF.JB






1085
H251
JRFL.JB-chim-sc_d7324.201C-433C
JRFL.JB/BG505 
SOSIP, R6, 664, 
Seq_0534 linker between
Same as Seq_1078





chimera
201C/433C
508-511, Res. 31-45,








478-507, 512-664 from








BG505, remainder =








JRFL.JB






1086
H252
KER2018.11-chim-sc_d7324.201C-433C
KER2018.11/
SOSIP, R6, 664, 
Seq_0534 linker between
Same as Seq_1078





BG505 chimera
201C/433C
508-511, BG505 Platform,








remainder = KER2018.11






1087
H253
PVO.04-chim-sc_d7324.201C-433C
PVO.04/BG505 
SOSIP, R6, 664, 
Seq_0534 linker between
Same as Seq_1078





chimera
201C/433C
508-511, BG505 Platform,








Platform, remainder =








PVO.04






1088
H254
Q168.a2-chim-sc_d7324.201C-433C
Q168.a2/BG505 
SOSIP, R6, 664, 
Seq_0534 linker between
Same as Seq_1078





chimera
201C/433C
508-511, BG505 Platform,








remainder = Q168.a2






1089
H255
Q23.17-chim-sc_d7324.201C-433C
Q23.17/BG505 
SOSIP, R6, 664, 
Seq_0534 linker between
Same as Seq_1078





chimera
201C/433C
508-511, BG505 Platform,








remainder = Q23.17






1090
H256
Q769.h5-chim-sc_d7324.201C-433C
Q769.h5/BG505 
SOSIP, R6, 664, 
Seq_0534 linker between
Same as Seq_1078





chimera
201C/433C
508-511, BG505 Platform,








remainder = Q769.h5






1091
H257
RW020.2-chim-sc_d7324.201C-433C
RW020.2/BG505 
SOSIP, R6, 664, 
Seq_0534 linker between
Same as Seq_1078





chimera
201C/433C
508-511, BG505 Platform,








remainder = RW020.2






1092
H258
THRO.18-chim-sc_d7324.201C-433C
THRO.18/BG505 
SOSIP, R6, 664, 
Seq_0534 linker between
Same as Seq_1078





chimera
201C/433C
508-511, BG505 Platform,








remainder = THRO.18






1093
H259
TRJO.58-chim-sc_d7324.201C-433C
TRJO.58/BG505 
SOSIP, R6, 664, 
Seq_0534 linker between
Same as Seq_1078





chimera
201C/433C
508-511, BG505 Platform,








remainder = TRJO.58






1094
H260
TRO.11-chim-sc_d7324.201C-433C
TRO.11/BG505 
SOSIP, R6, 664, 
Seq_0534 linker between
Same as Seq_1078





chimera
201C/433C
508-511, BG505 Platform,








remainder = TRO.11






1095
H261
YU2.DG-chim-sc_d7324.201C-433C
YU2.DG/BG505 
SOSIP, R6, 664, 
Seq_0534 linker between
Same as Seq_1078





chimera
201C/433C
508-511, BG505 Platform,








remainder = YU2.DG






1096
H262
ZA012.29-chim-sc_d7324.201C-433C
ZA012.29/BG505 
SOSIP, R6, 664, 
Seq_0534 linker between
Same as Seq_1078





chimera
201C/433C
508-511, BG505 Platform,








remainder = ZA012.29






1097
H263
ZM106.9-chim-sc_d7324.201C-433C
ZM106.9/BG505 
SOSIP, R6, 664, 
Seq_0534 linker between
Same as Seq_1078





chimera
201C/433C
508-511, BG505 Platform,








remainder = ZM106.9






1098
H264
ZM55.28a-chim-sc_d7324.201C-433C
ZM55.28a/BG505 
SOSIP, R6, 664, 
Seq_0534 linker between
Same as Seq_1078





chimera
201C/433C
508-511, BG505 Platform,








remainder = ZM55.28a






1099
H265
ZM53_bg505-NCgp120 + gp41.SOSIP_ds201-
ZM53/BG505 
SOSIP, R6, 664, 
BG505 Platform,
Ferritin particle with Chimeric




433_3bve-5ln
chimera
201C/433C; 332N
remainder = ZM53,
gp140 with BG505 gp41ecto/







ferritin linked to
gp120-NC “platform” and







gp41-C
heterologous gp120





1100
H266
CNE55-glyc332_bg505-NCgp120 +
CNE55/BG505 
SOSIP, R6, 664, 
BG505 Platform,
Same as Seq_1099




gp41.SOSIP_ds201-433_ferr-5ln
chimera
201C/433C
remainder = CNE55,








ferritin linked to








gp41-C






1101
H267
P0402_C1_bg505-NCgp120 +
P0402_C11/BG505 
SOSIP, R6, 664, 
BG505 Platform,
Same as Seq_1099




gp41.SOSIP_ds201-433_ferr-5ln
chimera
201C/433C
remainder = P0402_C11,








ferritin linked to








gp41-C






1102
H268
X1193_C1_bg505-NCgp120 +
X1193_C1/BG505 
SOSIP, R6, 664, 
BG505 Platform,
Same as Seq_1099




gp41.SOSIP_ds201-433_ferr-5ln
chimera
201C/433C
remainder = X1193_C1,








ferritin linked to








gp41-C






1103
H269
DU156.12_bg505-NCgp120 +
DU156.12/BG505 
SOSIP, R6, 664, 
BG505 Platform,
Same as Seq_1099




gp41.SOSIP_ds201-433_ferr-5ln
chimera
201C/433C
remainder = DU156.12,








ferritin linked to








gp41-C






1104
H270
DU422.01_bg505-NCgp120 +
DU422.01/BG505 
SOSIP, R6, 664, 
BG505 Platform,
Same as Seq_1099




gp41.SOSIP_ds201-433_ferr-5ln
chimera
201C/433C
remainder = DU422.01,








ferritin linked to








gp41-C






1105
H271
25925-2.22_bg505-NCgp120 +
25925-2.22/BG505
SOSIP, R6, 664, 
BG505 Platform, 
Same as Seq_1099




gp41.SOSIP_ds201-433_3bve-5ln
chimera
201C/433C
remainder = 25925-2.22,








ferritin linked to








gp41-C






1106
H272
3301_V1_C24_bg505-NCgp120 +
3301_V1_C24/
SOSIP, R6, 664, 
BG505 Platform,
Same as Seq_1099




gp41.SOSIP_ds201-433_3bve-5ln
BG505 chimera
201C/433C
remainder= 3301_V1_C24,








ferritin linked to








gp41-C






1107
H273
Cap256-SU_bg505-NCgp120 +
Cap256-SU/BG505
SOSIP, R6, 664, 
BG505 Platform,
Same as Seq_1099




gp41.SOSIP_ds201-433_3bve-5ln
chimera
201C/433C
remainder = Cap256-SU,








ferritin linked to








gp41-C






1108
H274
CH117.4_332N_bg505-NCgp120 +
CH117.4_332N/
SOSIP, R6, 664,  
BG505 Platform, 
Same as Seq_1099




gp41.SOSIP_ds201-433_3bve-5ln
BG505 chimera
201C/433C
remainder = CH117.4_332N,








ferritin linked to








gp41-C






1109
H275
CNE58_SU-strandC_bg505-NCgp120 +
CNE58_SU-
SOSIP, R6, 664, 
BG505 Platform , Res.
Same as Seq_1099




gp41.SOSIP_ds201-433_3bve-5ln
strandC/
201C/433C
166-173 (strand C) from






BG505 chimera

CAP256-SU, remainder =








CNE58, ferritin linked








to gp41-C






1110
H276
KER2018.11_bg505-NCgp120 +
KER2018.11/
SOSIP, R6, 664, 
BG505 Platform,
Same as Seq_1099




gp41.SOSIP_ds201-433_3bve-5ln
BG505 chimera
201C/433C
remainder = KER2018.11,








ferritin linked to








gp41-C






1111
H277
ZM233.6_bg505-NCgp120 + int +
ZM233.6/BG505 
SOSIP, R6, 664, 
BG505 Platform,
Same as Seq_1099




gp41.SOSIP_ds201-433_3bve-5ln
chimera
201C/433C
remainder = ZM233.6








ferritin linked to








gp41-C






1112
H278
ZM53_bg505-NCgp120 +
ZM53/BG505 
SOSIP, R6, 664, 
BG505 Platform,
Same as Seq_1099




gp41.SOSIP_ds201-433_3bve-5ln
chimera
201C/433C
remainder = ZM53,








ferritin linked to








gp41-C






1113
H279
45_01dG5_bg505-NCgp120 +
G5 from d45/
SOSIP, R6, 664, 
BG505 Platform,
Same as Seq_1099




gp41.SOSIP_ds201-433_3bve-5ln
BG505 chimera
201C/433C
remainder = dG5,








ferritin linked to








gp41-C






1114
H280
231965.c1-chim_d7324.201C-433C.
231965.c1/BG505
SOSIP, R6, 664, 
BG505 Platform, Res. Set 
Chimeric gp140 with gp41ecto/




mi-cl-min
chimera
201C/433C
B (Res. 133; 134; 164;
gp120-NC “platform” and







169; 308; 316) from BG505
BG505 Res. Set B, and







(“BG505 Res. Set B”),
heterologous gp120







remainder = 231965.c1






1115
H281
288.38-chim_d7324.201C-433C.mi-cl-min
288.38/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505
Same as Seq_1114





chimera
201C/433C
Res. Set B,








remainder = 288.38






1116
H282
3415.v1.c1-chim_d7324.201C-433C.mi-
3415.v1.c1/BG505
SOSIP, R6, 664, 
BG505 Platform, BG505
Same as Seq_1114




cl-min
chimera
201C/433C
Res. Set B,








remainder = 3415.v1.c1






1117
H283
3817.v2.c59-chim_d7324.201C-433C.mi-
3817.v2.c59/
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1114




cl-min
BG505 chimera
201C/433C
Res. Set B,








remainder = 3817.v2.c59






1118
H284
57128.vrc15-chim_d7324.201C-433C.mi-
57128.vrc15/
SOSIP, R6, 664, 
BG505 Platform, BG505
Same as Seq_1114




cl-min
BG505 chimera
201C/433C
Res. Set B,








remainder = 57128.vrc15






1119
H285
6535.3-chim_d7324.201C-433C.mi-cl-min
6535.3/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505
Same as Seq_1114





chimera
201C/433C
Res. Set B,








remainder = 6535.3






1120
H286
89.6.DG-chim_d7324.201C-433C.mi-cl-min
89.6.DG/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505
Same as Seq_1114





chimera
201C/433C
Res. Set B,








remainder = 89.6.DG






1121
H287
A03349M1.vrc4a-chim_d7324.201C-433C.
A03349M1.vrc4a/
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1114




mi-cl-min
BG505 chimera
201C/433C
Res. Set B, remainder =








A03349M1.vrc4a






1122
H288
Bal.01-chim_d7324.201C-433C.mi-cl-min
Bal.01/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505
Same as Seq_1114





chimera
201C/433C
Res. Set B,








remainder = Bal.01






1123
H289
BaL.26-chim_d7324.201C-433C.mi-cl-min
BaL.26/BG505
SOSIP, R6, 664, 
BG505 Platform, BG505
Same as Seq_1114





chimera
201C/433C
Res. Set B,








remainder = BaL.26






1124
H290
BG1168.01-chim_d7324.201C-433C.mi-
BG1168.01/BG505
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1114




cl-min
chimera
201C/433C
Res. Set B,








remainder = BG1168.01






1125
H291
BR07.DG-chim_d7324.201C-433C.mi-cl-min
BR07.DG/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505
Same as Seq_1114





chimera
201C/433C
Res. Set B,








remainder = BR07.DG






1126
H292
CNE10-chim_d7324.201C-433C.mi-cl-min
CNE10/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1114





chimera
201C/433C
Res. Set B,








remainder = CNE10






1127
H293
CNE30-chim_d7324.201C-433C.mi-cl-min
CNE30/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1114





chimera
201C/433C
Res. Set B,








remainder = CNE30






1128
H294
CNE4-chim_d7324.201C-433C.mi-cl-min
CNE4/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1114





chimera
201C/433C
Res. Set B,








remainder = CNE4






1129
H295
JRCSF.JB-chim_d7324.201C-433C.mi-cl-min
JRCSF.JB/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1114





chimera
201C/433C
Res. Set B,








remainder = JRCSF.JB






1130
H296
JRFLIB-chim_d7324.201C-433C.mi-cl-min
JRFLIB/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1114





chimera
201C/433C
Res. Set B,








remainder = JRFL.JB






1131
H297
MB539.2137-chim_d7324.201C-433C.mi-
MB539.2137/BG505
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1114




cl-min
chimera
201C/433C
Res. Set B,








remainder = MB539.267






1132
H298
MN.3-chim_d7324.201C-433C.mi-cl-min
MN.3/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1114





chimera
201C/433C
Res. Set B,








remainder = MN.3






1133
H299
NKU3006.ec1-chim_d7324.201C-433C.mi-
NKU3006.ec1/
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1114




cl-min
BG505 chimera
201C/433C
Res. Set B,








remainder = NKU3006.ec1






1134
H300
PVO.04-chim_d7324.201C-433C.mi-cl-min
PVO.04/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1114





chimera
201C/433C
Res. Set B,








remainder = PVO.04






1135
H301
Q259.17-chim_d7324.201C-433C.mi-cl-min
Q259.17/BG505
SOSIP, R6, 664,
BG505 Platform, BG505 
Same as Seq_1114





chimera
201C/433C
Res. Set B,








remainder = Q259.17






1136
H302
QH0692.42-chim_d7324.201C-433C.mi-
QH0692.42/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1114




cl-min
chimera
201C/433C
Res. Set B,








remainder = QH0692.42






1137
H303
SF162.LS-chim_d7324.201C-433C.mi-
SF162.LS/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1114




cl-min
chimera
201C/433C
Res. Set B,








remainder = SF162.LS






1138
H304
551196.01-chim_d7324.201C-433C.mi-
551196.01/BG505
SOSIP, R6, 664, 
BG505 Platform, BG505
Same as Seq_1114




cl-min
chimera
201C/433C
Res. Set B,








remainder = SS1196.01






1139
H305
T266-60-chim_d7324.201C-433C.mi-cl-min
T266-60/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1114





chimera
201C/433C
Res. Set B,








remainder = T266-60






1140
H306
T280-5-chim_d7324.201C-433C.mi-cl-min
T280-5/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505
Same as Seq_1114





chimera
201C/433C
Res. Set B,








remainder = T280-5






1141
H307
UG024.2-chim_d7324.201C-433C.mi-cl-min
UG024.2/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1114





chimera
201C/433C
Res. Set B,








remainder = UG024.2






1142
H308
ZM215.8-chim_d7324.201C-433C.mi-cl-min
ZM215.8/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1114





chimera
201C/433C
Res. Set B,








remainder = ZM215.8






1143
H309
231965.c1-chim_d7324.201C-433C.mi-cl1
231965.c1/BG505 
SOSIP, R6, 664, 
BG505 Platform, Res. Set
Chimeric gp140 with





chimera
201C/433C
C (Res. 49; 133; 134;
gp41ecto/gp120-NC “platform”







149; 150; 151; 152; 164;
and Res. Set C from BG505, and







169; 188; 190; 211; 223;
heterologous gp120







252; 281; 293; 308; 316;








336; 340; 352; 360; 362;








363; 369; 372; 393; 410;








432; 442; 444; 446; 474;








476) from BG505 (“BG505








Res. Set C”), remainder =








ZM215.8






1144
H310
288.38-chim_d7324.201C-433C.mi-cl1
288.38/BG505 
SOSIP, R6, 664, 
BG505 Platform, Res. Set 
Same as Seq_1143





chimera
201C/433C
C from BG505, remainder =








288.38






1145
H311
3415.v1.c1-chim_d7324.201C-433C.mi-cl1
3415.v1.c1/BG505
SOSIP, R6, 664,
BG505 Platform, BG505
Same as Seq_1143





chimera
201C/433C
Res. Set C, remainder =








3415.v1.c1






1146
H312
3817.v2.c59-chim_d7324.201C-433C.mi-cl1
3817.v2.c59/
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1143





BG505 chimera
201C/433C
Res. Set C, remainder =








3817.v2.c59






1147
H313
57128.vrc15-chim_d7324.201C-433C.mi-cl1
57128.vrc15/
SOSIP, R6, 664, 
BG505 Platform, BG505
Same as Seq_1143





BG505 chimera
201C/433C
Res. Set C, remainder =








57128.vrc15






1148
H314
6535.3-chim_d7324.201C-433C.mi-cl1
6535.3/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505
Same as Seq_1143





chimera
201C/433C
Res. Set C, remainder =








6535.3






1149
H315
89.6.DG-chim_d7324.201C-433C.mi-cl1
89.6.DG/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505
Same as Seq_1143





chimera
201C/433C
Res. Set C, remainder =








89.6.DG






1150
H316
A03349M1.vrc4a-chim_d7324.201C-
A03349M1.vrc4a/
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1143




433C.mi-cl1
BG505 chimera
201C/433C
Res. Set C, remainder =








A03349M1.vrc4a






1151
H317
Bal.01-chim_d7324.201C-433C.mi-cl1
Bal.01/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1143





chimera
201C/433C
Res. Set C, remainder =








Bal.01






1152
H318
BaL.26-chim_d7324.201C-433C.mi-cl1
BaL.26/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1143





chimera
201C/433C
Res. Set C, remainder =








BaL.26






1153
H319
BG1168.01-chim_d7324.201C-433C.mi-cl1
BG1168.01/BG505
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1143





chimera
201C/433C
Res. Set C, remainder =








BG1168.01






1154
H320
BR07.DG-chim_d7324.201C-433C.mi-cl1
BR07.DG/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1143





chimera
201C/433C
Res. Set C, remainder =








BR07.DG






1155
H321
CNE10-chim_d7324.201C-433C.mi-cl1
CNE10/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1143





chimera
201C/433C
Res. Set C, remainder =








CNE10






1156
H322
CNE30-chim_d7324.201C-433C.mi-cl1
CNE30/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1143





chimera
201C/433C
Res. Set C, remainder =








CNE30






1157
H323
CNE4-chim_d7324.201C-433C.mi-cl1
CNE4/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1143





chimera
201C/433C
Res. Set C, remainder =








CNE4






1158
H324
JRCSF.JB-chim_d7324.201C-433C.mi-cl1
JRCSF.JB/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1143





chimera
201C/433C
Res. Set C, remainder =








JRCSF.JB






1159
H325
JRFL.JB-chim_d7324.201C-433C.mi-cl1
JRFL.JB/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1143





chimera
201C/433C
Res. Set C, remainder =








JRFL.JB






1160
H326
MB539.2137-chim_d7324.201C-433C.mi-cl1
MB539.2137/BG505
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1143





chimera
201C/433C
Res. Set C, remainder =








MB539.267






1161
H327
MN.3-chim_d7324.201C-433C.mi-cl1
MN.3/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1143





chimera
201C/433C
Res. Set C, remainder =








MN.3






1162
H328
NKU3006.ec1-chim_d7324.201C-433C.mi-cl1
NKU3006.ec1/
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1143





BG505 chimera
201C/433C
Res. Set C, remainder =








NKU3006.ec1






1163
H329
PVO.04-chim_d7324.201C-433C.mi-cl1
PVO.04/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1143





chimera
201C/433C
Res. Set C, remainder =








PVO.04






1164
H330
Q259.17-chim_d7324.201C-433C.mi-cl1
Q259.17/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1143





chimera
201C/433C
Res. Set C, remainder =








Q259.17






1165
H331
QH0692.42-chim_d7324.201C-433C.mi-cl1
QH0692.42/BG505
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1143





chimera
201C/433C
Res. Set C, remainder =








QH0692.42






1166
H332
SF162.LS-chim_d7324.201C-433C.mi-cl1
SF162.LS/BG505
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1143





chimera
201C/433C
Res. Set C, remainder =








SF162.LS






1167
H333
SS1196.01-chim_d7324.201C-433C.mi-cl1
SS1196.01/BG505
SOSIP, R6, 664,
BG505 Platform, BG505 
Same as Seq_1143





chimera
201C/433C
Res. Set C, remainder =








SS1196.01






1168
H334
T266-60-chim_d7324.201C-433C.mi-cl1
T266-60/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1143





chimera
201C/433C
Res. Set C, remainder =








T266-60






1169
H335
T280-5-chim_d7324.201C-433C.mi-cl1
T280-5/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1143





chimera
201C/433C
Res. Set C, remainder =








T280-5






1170
H336
UG024.2-chim_d7324.201C-433C.mi-cl1
UG024.2/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1143





chimera
201C/433C
Res. Set C, remainder =








UG024.2






1171
H337
ZM215.8-chim_d7324.201C-433C.mi-cl1
ZM215.8/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1143





chimera
201C/433C
Res. Set C, remainder =








ZM215.8






1172
H338
231965.c1-chim_d7324.201C-433C.mi-c11-2
231965.c1/BG505
SOSIP, R6, 664,
BG505 Platform, Res. Set
Chimeric gp140 with





chimera
201C/433C
C, + Res. Set D (46; 60;
gp41ecto/gp120-NC “platform”







62; 63; 84; 85; 87; 99;
and Res. Sets C and D from







102; 130; 132; 135; 153;
BG505, and heterologous gp120







158; 160; 161; 165; 166;








167; 171; 172; 173; 175;








177; 178; 181; 184; 185;








189; 202; 232; 234; 236;








240; 268; 269; 270; 271;








275; 277; 287; 289; 292;








295; 297; 305; 315; 317;








319; 322; 328; 330; 332;








333; 334; 335; 337; 339;








343; 344; 345; 346; 347;








350; 351; 357; 371; 375;








379; 387; 389; 394; 411;








412; 413; 415; 424; 426;








429; 440; 460; 461; 465;








475; 477) from BG505








(“BG505 Res. Set D”),








remainder = 231965.c1






1173
H339
288.38-chim_d7324.201C-433C.mi-cl1-2
288.38/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1172





chimera
201C/433C
Res. Sets C +D,








remainder = 288.38






1174
H340
3415.v1.c1-chim_d7324.201C-433C.mi-
3415.v1.c1/
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1172




cl1-2
BG505 chimera
201C/433C
Res. Sets C + D,








remainder = 3415.v1.c1






1175
H341
3817.v2.c59-chim_d7324.201C-433C.mi-
3817.v2.c59/
SOSIP, R6, 664, 
BG505 Platform, BG505
Same as Seq_1172




cl1-2
BG505 chimera
201C/433C
Res. Sets C + D,








remainder = 3817.v2.c59






1176
H342
57128.vrc15-chim_d7324.201C-433C.mi-
57128.vrc15/
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1172




cl1-2
BG505 chimera
201C/433C
Res. Sets C + D,








remainder = 57128.vrc15






1177
H343
6535.3-chim_d7324.201C-433C.mi-cl1-2
6535.3/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1172





chimera
201C/433C
Res. Sets C + D,








remainder = 6535.3






1178
H344
89.6.DG-chim_d7324.201C-433C.mi-cl1-2
89.6.DG/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1172





chimera
201C/433C
Res. Sets C + D,








remainder = 89.6.DG






1179
H345
A03349M1.vrc4a-chim_d7324.201C-
A03349M1.vrc4a/
SOSIP, R6, 664, 
BG505 Platform, BG505
Same as Seq_1172




433C.mi-c11-2
BG505  chimera
201C/433C
Res. Sets C + D,








remainder =








A03349M1.vrc4a






1180
H346
Bal.01-chim_d7324.201C-433C.mi-cl1-2
Bal.01/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505
Same as Seq_1172





chimera
201C/433C
Res. Sets C + D,








remainder = Bal.01






1181
H347
BaL.26-chim_d7324.201C-433C.mi-cl1-2
BaL.26/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1172





chimera
201C/433C
Res. Sets C + D,








remainder = BaL.26






1182
H348
BG1168.01-chim_d7324.201C-433C.mi-cl1-2
BG1168.01/BG505
SOSIP, R6, 664, 
BG505 Platform, BG505
Same as Seq_1172





chimera
201C/433C
Res. Sets C + D,








remainder = BG1168.01






1183
H349
BRO7.DG-chim_d7324.201C-433C.mi-cl1-2
BRO7.DG/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1172





chimera
201C/433C
Res. Sets C + D,








remainder = BRO7.DG






1184
H350
CNE10-chim_d7324.201C-433C.mi-cl1-2
CNE10/BG505 
SOSIP, R6, 664, 
BG505 Platform BG505 
Same as Seq_1172





chimera
201C/433C
Res. Sets C + D,








remainder = CNE10






1185
H351
CNE30-chim_d7324.201C-433C.mi-cl1-2
CNE30/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1172





chimera
201C/433C
Res. Sets C + D,








remainder = CNE30






1186
H352
CNE4-chim_d7324.201C-433C.mi-cl1-2
CNE4/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1172





chimera
201C/433C
Res. Sets C + D,








remainder = CNE4






1187
H353
JRCSF.JB-chim_d7324.201C-433C.mi-cl1-2
JRCSF.JB/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1172





chimera
201C/433C
Res. Sets C + D,








remainder = JRCSF.JB






1188
H354
JRFL.JB-chim_d7324.201C-433C.mi-cl1-2
JRFLIB/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1172





chimera
201C/433C
Res. Sets C + D,








remainder = JRFL.JB






1189
H355
MB539.2137-chim_d7324.201C-433C.mi-
MB539.2137/
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1172




cl1-2
BG505 chimera
201C/433C
Res. Sets C + D,








remainder = MB539.267






1190
H356
MN.3-chim_d7324.201C-433C.mi-cl1-2
MN.3/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1172





chimera
201C/433C
Res. Sets C + D,








remainder = MN.3






1191
H357
NKU3006.ec1-chim_d7324.201C-433C.mi-
NKU3006.ec1/
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1172




cl1-2
BG505 chimera
201C/433C
Res. Sets C + D,








remainder = NKU3006.ec1






1192
H358
PVO.04-chim_d7324.201C-433C.mi-cl1-2
PVO.04/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1172





chimera
201C/433C
Res. Sets C + D,








remainder = PVO.04






1193
H359
Q259.17-chim_d7324.201C-433C.mi-cl1-2
Q259.17/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1172





chimera
201C/433C
Res. Sets C + D,








remainder = Q259.17






1194
H360
QH0692.42-chim_d7324.201C-433C.mi-
QH0692.42/BG505
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1172




cl1-2
chimera
201C/433C
Res. Sets C + D,








remainder = QH0692.42






1195
H361
SF162.LS-chim_d7324.201C-433C.mi-cl1-2
SF162.LS/BG505
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1172





chimera
201C/433C
Res. Sets C + D,








remainder = SF162.LS






1196
H362
SS1196.01-chim_d7324.201C-433C.mi-
SS1196.01/BG505
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1172




cl1-2
chimera
201C/433C
Res. Sets C + D,








remainder = SS1196.01






1197
H363
T266-60-chim_d7324.201C-433C.mi-cl1-2
T266-60/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1172





chimera
201C/433C
Res. Sets C + D,








remainder = T266-60






1198
H364
T280-5-chim_d7324.201C-433C.mi-cl1-2
T280-5/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1172





chimera
201C/433C
Res. Sets C + D,








remainder = T280-5






1199
H365
UG024.2-chim_d7324.201C-433C.mi-cl1-2
UG024.2/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1172





chimera
201C/433C
Res. Sets C + D,








remainder = UG024.2






1200
H366
ZM215.8-chim_d7324.201C-433C.mi-cl1-2
ZM215.8/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1172





chimera
201C/433C
Res. Sets C + D,








remainder = ZM215.8






1201
H367
0921.V2.C14-chim_201C-433C_5ln-ferr
0921.V2.C14/
SOSIP, R6, 664, 
BG505 Platform, gp140
Same as Seq_1099





BG505 chimera
201C/433C
remainder = 0921.V2.C14,








ferritin linked to








gp41-C






1202
H368
16055-2.3-chim_201C-433C_5ln-ferr
16055-2.3/BG505
SOSIP, R6, 664, 
BG505 Platform, gp140
Same as Seq_1099





chimera
201C/433C
remainder = 16055-2.3,








ferritin linked to








gp41-C






1203
H369
286.36-chim_201C-433C_5ln-ferr
286.36/BG505 
SOSIP, R6, 664, 
BG505 Platform, gp140
Same as Seq_1099





chimera
201C/433C
remainder = 286.36,








ferritin linked to








gp41-C






1204
H370
620345.c1-chim_201C-433C_5ln-ferr
620345.cl/BG505
SOSIP, R6, 664,
BG505 Platform, gp140
Same as Seq_1099





chimera
201C/433C
remainder = 620345.c1,








ferritin linked to








gp41-C






1205
H371
6545.V4.C1-chim_201C-433C_5ln-ferr
6545.V4.C1/BG505
SOSIP, R6, 664, 
BG505 Platform, gp140
Same as Seq_1099





chimera
201C/433C
remainder = 6545.V4.C1,








ferritin linked to








gp41-C






1206
H372
AC10.29-chim_201C-433C_5ln-ferr
AC10.29/BG505 
SOSIP, R6, 664, 
BG505 Platform, gp140
Same as Seq_1099





chimera
201C/433C
remainder = AC10.29,








ferritin linked to








gp41-C






1207
H373
B1369.9A-chim_201C-433C_5ln-ferr
B1369.9A/BG505
SOSIP, R6, 664, 
BG505 Platform, gp140
Same as Seq_1099





chimera
201C/433C
remainder = B1369.9A,








ferritin linked to








gp41-C






1208
H374
C1080.c3-chim_201C-433C_5ln-ferr
C1080.c3/BG505
SOSIP, R6, 664, 
BG505 Platform, gp140
Same as Seq_1099





chimera
201C/433C
remainder = C1080.c3,








ferritin linked to








gp41-C






1209
H375
C4118.09-chim_201C-433C_5ln-ferr
C4118.09/BG505
SOSIP, R6, 664, 
BG505 Platform, gp140
Same as Seq_1099





chimera
201C/433C
remainder = C4118.09,








ferritin linked to








gp41-C






1210
H376
CAP45.G3-chim_201C-433C_5ln-ferr
CAP45.G3/BG505 
SOSIP, R6, 664, 
BG505 Platform, gp140
Same as Seq_1099





chimera
201C/433C
remainder = CAP45.G3,








ferritin linked to








gp41-C






1211
H377
CH038.12-chim_201C-433C_5ln-ferr
CH038.12/BG505 
SOSIP, R6, 664,
BG505 Platform, gp140
Same as Seq_1099





chimera
201C/433C
remainder = CH038.12,








ferritin linked to








gp41-C






1212
H378
CH117.4-chim_201C-433C_5ln-ferr
CH117.4/BG505
SOSIP, R6, 664, 
BG505 Platform, gp140
Same as Seq_1099





chimera
201C/433C
remainder = CH117.4,








ferritin linked to








gp41-C






1213
H379
MB201.A1-chim_201C-433C_5ln-ferr
MB201.A1/BG505
SOSIP, R6, 664, 
BG505 Platform, gp140
Same as Seq_1099





chimera
201C/433C
remainder = MB201.A1,








ferritin linked to








gp41-C






1214
H380
MW965.26-chim_201C-433C_5ln-ferr
MW965.26/BG505
SOSIP, R6, 664, 
BG505 Platform, gp140
Same as Seq_1099





chimera
201C/433C
remainder = MW965.26,








ferritin linked to








gp41-C






1215
H381
QH209.14M.A2-chim_201C-433C_5ln-ferr
QH209.14M.A2/
SOSIP, R6, 664, 
BG505 Platform, gp140 
Same as Seq_1099





BG505 chimera
201C/433C
remainder = QH209.14M.A2,








ferritin linked to








gp41-C






1216
H382
TH966.8-chim_201C-433C_5ln-ferr
TH966.8/BG505
SOSIP, R6, 664, 
BG505 Platform, gp140
Same as Seq_1099





chimera
201C/433C
remainder = TH966.8,








ferritin linked to








gp41-C






1217
H383
ZM106.9-chim_201C-433C_5ln-ferr
ZM106.9/BG505
SOSIP, R6, 664, 
BG505 Platform, gp140
Same as Seq_1099





chimera
201C/433C
remainder = ZM106.9,








ferritin linked to








gp41-C






1218
H384
ZM55.28a-chim_201C-433C_5ln-ferr
ZM55.28a/BG505
SOSIP, R6, 664, 
BG505 Platform, gp140
Same as Seq_1099





chimera
201C/433C
remainder = ZM55.28a,








ferritin linked to








gp41-C






1219
0
B1369.9A
B1369.9A








1220
0
MB201.A1
MB201.A1








1221
0
QH209.14M.A2
QH209.14M.A2








1222
0
0921.V2.C14
0921.V2.C14








1223
0
16055-2.3
16055-2.3








1224
0
25925-2.22
25925-2.22








1225
0
286.36
286.36








1226
0
CAP45.G3
CAP45.G3








1227
0
CNE58
CNE58








1228
0
DU156.12
DU156.12








1229
0
DU422.01
DU422.01








1230
0
MW965.26
MW965.26








1231
0
ZM53.12
ZM53.12








1232
0
ZM55.28a
ZM55.28a








1233
0
ZM106.9
ZM106.9








1234
0
3301.V1.C24
3301.V1.C24








1235
0
6545.V4.C1
6545.V4.C1








1236
0
620345.c1
620345.c1








1237
0
C1080.c3
C1080.c3








1238
0
C4118.09
C4118.09








1239
0
CNE55
CNE55








1240
0
TH966.8
TH966.8








1241
0
AC10.29
AC10.29








1242
0
CH038.12
CH038.12








1243
0
CH117.4
CH117.4








1244
A347
*CH505, BG505 chimera,
CH505/BG505 
SOSIP, R6, 664, T332N
I201C/A433C





SOSIP.R6.664_I201C/A433C
chimera












AENLWVTVYYGVPVWKEAKTTLFCASDAKAYEKEVHNVWATHACVPTDPNPQEMVLKNVTENFNMWKNDMVDQMHEDVISLWDQSLKPCVKLTPLCVTLNCTNATASNSSIIEGMKNCSFNITTELRDKR



EKKNALFYKLDIVQLDGNSSQYRLINCNTSVCTQACPKVSFDPIPIHYCAPAGYAILKCNNKTFTGTGPCNNVSTVQCTHGIKPVVSTQLLLNGSLAEGEIIIRSENITNNVKTIIVHLNESVKIECTRP



NNKTRTSIRIGPGQAFYATGQVIGDIREAYCNINESKWNETLQRVSKKLKEYFPHKNITFQPSSGGDLEITTHSFNCGGEFFYCNTSSLFNRTYMANSTDMANSTETNSTRTITIHCRIKQIINMWQEVG



RCMYAPPIAGNITCISNITGLLLTRDGGKNNTETFRPGGGNMKDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEA



QQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD
















1245
A348
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
SOSIP, R6, 664, T332N,
V134F/L175M/I322M/I326M
Cavity Filling/Hydrophobic core




V134F/L175M/I322M/I326M

I201C/A433C







1246
A349
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
V134F/I322Y/I326M
Cavity Filling/Hydrophobic core




V134F/I322Y/I326M









1247
A350
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
V134I/L175W/I322F/I326M
Cavity Filling/Hydrophobic core




V134I/L175W/I322F/I326M









1248
A351
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
V134F/N136W/M150H/I326M
Cavity Filling/Hydrophobic core




V134F/N136W/M150H/I326M









1249
A352
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
V134F/N136W/M150F/I326L
Cavity Filling/Hydrophobic core




V134F/N136W/M150F/I326L









1250
A353
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
V1341/N136W/M150F/I326L
Cavity Filling/Hydrophobic core




V134I/N136W/M150F/I326L









1251
A354
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
V134F/N136F/M150L/I326M
Cavity Filling/Hydrophobic core




V134F/N136F/M150L/I326M









1252
A355
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
L154M/N300M/N302M/T320L
Cavity Filling/Hydrophobic core




L154M/N300M/N302M/T320L









1253
A356
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
L154F/N300L/N302M/T320L
Cavity Filling/Hydrophobic core




L154F/N300L/N302M/T320L









1254
A357
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
L154W/N300L/N302G/T320F
Cavity Filling/Hydrophobic core




L154W/N300L/N302G/T320F









1255
A358
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
V120F/Q203M/Y318M
Cavity Filling/Hydrophobic core




V120F/Q203M/Y318M









1256
A359
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
V120I/Q203M/Y318W
Cavity Filling/Hydrophobic core




V120I/Q203M/Y318W









1257
A360
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
V120W/Q203M/Y318W
Cavity Filling/Hydrophobic core




V120W/Q203M/Y318W









1258
A361
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
V120F/Q315M
Cavity Filling/Hydrophobic core




V120F/Q315M









1259
A362
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
V120W/Q315F
Cavity Filling/Hydrophobic core




V120W/Q315F









1260
A363
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
Y177W/I420M
Cavity Filling/Hydrophobic core




Y177W/I420M









1261
A364
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
Y177W/Q328F/I420M
Cavity Filling/Hydrophobic core




Y177W/Q328F/I420M









1262
A365
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
L116M/M426F/Q432M
Cavity Filling/Hydrophobic core




L116M/M426F/Q432M









1263
A366
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
L116M/M426F/Q432W
Cavity Filling/Hydrophobic core




L116M/M426F/Q432W









1264
A367
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
M426F/Q432L
Cavity Filling/Hydrophobic core




M426F/Q432L









1265
A368
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
V134F/L175M/I322M/I326M/
Cavity Filling/Hydrophobic core




V134F/L175M/I322M/I326M/N136W/M150H


N136W/M150H






1266
A369
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
V134I/L175W/I322F/I326L/
Cavity Filling/Hydrophobic core




V134I/L175W/I322F/I326L/N136W/M150F


N136W/M150F






1267
A370
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
V120F/Q203M/Y318M/Q315M
Cavity Filling/Hydrophobic core




V120F/Q203M/Y318M/Q315M









1268
A371
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
V120W/Q203M/Y318W/Q315F
Cavity Filling/Hydrophobic core




V120W/Q203M/Y318W/Q315F









1269
A372
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
L154M/N300M/N302M/T320L/
Cavity Filling/Hydrophobic core




L154M/N300M/N302M/T320L/Y177W/I420M


Y177W/I420M






1270
A373
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
L154W/N300L/N302G/T320F/
Cavity Filling/Hydrophobic core




L154W/N300L/N302G/T320F/Y177W/Q328F/


Y177W/Q328F/I420M





I420M









1271
A374
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
E153F
Cavity Filling




E153F









1272
A375
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
E153W
Cavity Filling




E153W









1273
A376
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
L154F
Cavity Filling




L154F









1274
A377
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
L154W
Cavity Filling




L154W









1275
A378
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
E164F
Cavity Filling




E164F









1276
A379
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
E164W
Cavity Filling




E164W









1277
A380
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
V172F
Cavity Filling




V172F









1278
A381
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
V172W
Cavity Filling




V172W









1279
A382
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
L175F
Cavity Filling




L175F









1280
A383
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
F176W
Cavity Filling




F176W









1281
A384
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
L179F
Cavity Filling




L179F









1282
A385
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
L179W
Cavity Filling




L179W









1283
A386
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
Y191F
Cavity Filling




Y191F









1284
A387
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
Y191W
Cavity Filling




Y191W









1285
A388
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
L193F
Cavity Filling




L193F









1286
A389
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
L193W
Cavity Filling




L193W









1287
A390
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
I194W
Cavity Filling




I194W









1288
A391
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
T198F
Cavity Filling




T198F









1289
A392
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
T198W
Cavity Filling




T198W









1290
A393
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
T202F
Cavity Filling




T202F









1291
A394
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
T202W
Cavity Filling




T202W









1292
A395
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
A204F
Cavity Filling




A204F









1293
A396
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
A204W
Cavity Filling




A204W









1294
A397
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
N302F
Cavity Filling




N302F









1295
A398
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
N302W
Cavity Filling




N302W









1296
A399
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
R304F
Cavity Filling




R304F









1297
A400
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
R304W
Cavity Filling




R304W









1298
A401
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
I307F
Cavity Filling




I307F









1299
A402
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
I307W
Cavity Filling




I307W









1300
A403
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
Q315F
Cavity Filling




Q315F









1301
A404
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
Q315W
Cavity Filling




Q315W









1302
A405
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
I423F
Cavity Filling




I423F









1303
A406
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
I430F
Cavity Filling




I430F









1304
A407
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
I430W
Cavity Filling




I430W









1305
A408
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
Q432F
Cavity Filling




Q432F









1306
A409
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
Q432W
Cavity Filling




Q432W









1307
A410
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
A436M
Cavity Filling




A436M









1308
A411
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
A436F
Cavity Filling




A436F









1309
A412
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
A436W
Cavity Filling




A436W









1310
A413
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
L125W/I194W
Cavity Filling




L125W/I194W









1311
A414
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
T139W/D1401/G324I/D325W
Cavity Filling




T139W/D140I/G324I/D325W









1312
A415
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
F210A
Destabilization of CD4-induced




F210A



conformation





1313
A416
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
F2105
Destabilization of CD4-induced




F2105



conformation





1314
A417
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
Q432P
Destabilization of CD4-induced




Q432P



conformation





1315
A418
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
T538C/Q652C
Disulfide




T538C/Q652C









1316
A419
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
R304C/Q440C
Disulfide




R304C/Q440C









1317
A420
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
F159Y
Cavity Filling




F159Y









1318
A421
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
I323Y
Cavity Filling




I323Y









1319
A422
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
F159Y/I323Y
Cavity Filling




F159Y/I323Y









1320
A423
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
F223W
Cavity Filling




F223W









1321
A424
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
V580L
Cavity Filling




V580L









1322
A425
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
V583L
Cavity Filling




V583L









1323
A426
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
V580L/V583L
Cavity Filling




V580L/V583L









1324
A427
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
W69P
helix 0 disruption




W69P









1325
A428
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
V68P
helix 0 disruption




V68P









1326
A429
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
T71P
helix 0 disruption




T71P









1327
A430
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
V75W
Cavity Filling




V75W









1328
A431
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
V75F
Cavity Filling




V75F









1329
A432
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
V75M
Cavity Filling




V75M









1330
A433
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
V208W
Cavity Filling




V208W









1331
A434
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
V208F
Cavity Filling




V208F









1332
A435
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
A58C/T77C
Disulfide




A58C/T77C









1333
A436
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
D57C/T77C
Disulfide




D57C/T77C









1334
A437
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
N67P
helix 0 disruption




N67P









1335
A438
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
H66P
helix 0 disruption




H66P









1336
A439
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
N67P/H66P
helix 0 disruption




N67P/H66P









1337
A440
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
W112I
Cavity Filling




W112I









1338
A441
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
W112M
Cavity Filling




W112M









1339
A442
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
W427I
Cavity Filling




W427I









1340
A443
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
W427M
Cavity Filling




W427M









1341
A444
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
R429N
Destabilization of CD4 binding




R429N



site





1342
A445
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
R429L
Destabilization of CD4 binding




R429L



site





1343
A446
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
R429L/W427M
Destabilization of CD4 binding




R429L/W427M



site





1344
A447
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
G431GC/S199C
Disulfide




G431GC/S199C









1345
A448
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
V120W
Cavity Filling




V120W









1346
A449
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
A316W
Cavity Filling




A316W









1347
A450
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
I309W
Cavity Filling




I309W









1348
A451
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
S115W
Cavity Filling




S115W









1349
A452
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
P118W
Cavity Filling




P118W









1350
A453
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
A70Y
Cavity Filling




A70Y









1351
A454
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
A70F
Cavity Filling




A70F









1352
A455
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
L111Y
Cavity Filling




L111Y









1353
A456
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
L111F
Cavity Filling




L111F









1354
A457
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
T202P
disrupt bridging sheet/




T202P



destabilizing CD4 bound state





1355
A458
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
V120T
disrupt bridging sheet/




V120T



destabilizing CD4 bound state





1356
A459
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
I573T
destabilize gp41 helix bundle




I573T









1357
A460
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
G594N
destabilize gp41 helix bundle




G594N









1358
A461
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
I573T/G594N
destabilize gp41 helix bundle




I573T/G594N









1359
A462
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
I573T/G594N/K574E
destabilize gp41 helix bundle




I573T/G594N/K574E









1360
A463
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
I573T/G594N/K574T
destabilize gp41 helix bundle




I573T/G594N/K574T









1361
A464
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
K117W
Cavity Filling




K117W









1362
A465
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
SHOW
Cavity Filling




S110W









1363
A466
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
L544Y
Cavity Filling




L544Y









1364
A467
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
L544Y/L537Y
Cavity Filling




L544Y/L537Y









1365
A468
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
L544Y/F223W
Cavity Filling




L544Y/F223W









1366
A469
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
L544Y/L537Y/F223W
Cavity Filling




L544Y/L537Y/F223W









1367
A470
BG505.SOSIP.R6.664.T332N_I201C/A433C/
BG505
Same as Seq_1245
Delta P206
proline removal. Removal of




Delta_P206



ground state destabilization/








flexibility





1368
A471
BG505.SOSIP.R6.664.T332N_I194W/T198M/
BG505
SOSIP, R6, 664, T332N
I194W/T198M/N425F
Cavity Filling/Hydrophobic core




N425F









1369
A472
BG505.SOSIP.R6.664.T332N_T198M/N425F
BG505
SOSIP, R6, 664, T332N
T198M/N425F
Cavity Filling/Hydrophobic core





1370
A473
BG505.SOSIP.R6.664.T332N_I194W/T198Y/
BG505
SOSIP, R6, 664, T332N
I194W/T198Y/N425F
Cavity Filling/Hydrophobic core




N425F









1371
A474
BG505.SOSIP.R6.664.T332N_I194F/T198L/
BG505
SOSIP, R6, 664, T332N
I194F/T198L/N425W
Cavity Filling/Hydrophobic core




N425W









1372
A475
BG505.SOSIP.R6.664.T332N_V134F/L175M/
BG505
SOSIP, R6, 664, T332N
V134F/L175M/I322M/I326M
Cavity Filling/Hydrophobic core




I322M/I326M









1373
A476
BG505.SOSIP.R6.664.T332N_V134F/I322Y/
BG505
SOSIP, R6, 664, T332N
V134F/I322Y/I326M
Cavity Filling/Hydrophobic core




I326M









1374
A477
BG505.SOSIP.R6.664.T332N_V134I/L175W/
BG505
SOSIP, R6, 664, T332N
V134I/L175W/I322F/I326M
Cavity Filling/Hydrophobic core




I322F/I326M









1375
A478
BG505.SOSIP.R6.664.T332N_V134F/N136W/
BG505
SOSIP, R6, 664, T332N
V134F/N136W/M150H/I326M
Cavity Filling/Hydrophobic core




M150H/I326M









1376
A479
BG505.SOSIP.R6.664.T332N_V134F/N136W/
BG505
SOSIP, R6, 664, T332N
V134F/N136W/M150F/I326L
Cavity Filling/Hydrophobic core




M150F/I326L









1377
A480
BG505.SOSIP.R6.664.T332N_V134I/N136W/
BG505
SOSIP, R6, 664, T332N
V134I/N136W/M150F/I326L
Cavity Filling/Hydrophobic core




M150F/I326L









1378
A481
BG505.SOSIP.R6.664.T332N_V134F/N136F/
BG505
SOSIP, R6, 664, T332N
V134F/N136F/M150L/I326M
Cavity Filling/Hydrophobic core




M150L/I326M









1379
A482
BG505.SOSIP.R6.664.T332N_L154M/N300M/
BG505
SOSIP, R6, 664, T332N
L154M/N300M/N302M/T320L
Cavity Filling/Hydrophobic core




N302M/T320L









1380
A483
BG505.SOSIP.R6.664.T332N_L154F/N300L/
BG505
SOSIP, R6, 664, T332N
L154F/N300L/N302M/T320L
Cavity Filling/Hydrophobic core




N302M/T320L









1381
A484
BG505.SOSIP.R6.664.T332N_L154W/N300L/
BG505
SOSIP, R6, 664, T332N
L154W/N300L/N302G/T320F
Cavity Filling/Hydrophobic core




N302G/T320F









1382
A485
BG505.SOSIP.R6.664.T332N_V120F/Q203M/
BG505
SOSIP, R6, 664, T332N
V120F/Q203M/Y318M
Cavity Filling/Hydrophobic core




Y318M









1383
A486
BG505.SOSIP.R6.664.T332N_V120I/Q203M/
BG505
SOSIP, R6, 664, T332N
V120I/Q203M/Y318W
Cavity Filling/Hydrophobic core




Y318W









1384
A487
BG505.SOSIP.R6.664.T332N_V120W/Q203M/
BG505
SOSIP, R6, 664, T332N
V120W/Q203M/Y318W
Cavity Filling/Hydrophobic core




Y318W









1385
A488
BG505.SOSIP.R6.664.T332N_V120F/Q315M
BG505
SOSIP, R6, 664, T332N
V120F/Q315M
Cavity Filling/Hydrophobic core





1386
A489
BG505.SOSIP.R6.664.T332N_V120W/Q315F
BG505
SOSIP, R6, 664, T332N
V120W/Q315F
Cavity Filling/Hydrophobic core





1387
A490
BG505.SOSIP.R6.664.T332N_Y177W/1420M
BG505
SOSIP, R6, 664, T332N
Y177W/1420M
Cavity Filling/Hydrophobic core





1388
A491
BG505.SOSIP.R6.664.T332N_Y177W/Q328F/
BG505
SOSIP, R6, 664, T332N
Y177W/Q328F/I420M
Cavity Filling/Hydrophobic core




I420M









1389
A492
BG505.SOSIP.R6.664.T332N_L116M/M426F/
BG505
SOSIP, R6, 664, T332N
L116M/M426F/Q432M
Cavity Filling/Hydrophobic core




Q432M









1390
A493
BG505.SOSIP.R6.664.T332N_L116M/M426F/
BG505
SOSIP, R6, 664, T332N
L116M/M426F/Q432W
Cavity Filling/Hydrophobic core




Q432W









1391
A494
BG505.SOSIP.R6.664.T332N_M426F/Q432L
BG505
SOSIP, R6, 664, T332N
M426F/Q432L
Cavity Filling/Hydrophobic core





1392
A495
BG505.SOSIP.R6.664.T332N_V134F/L175M/
BG505
SOSIP, R6, 664, T332N
V134F/L175M/I322M/I326M/
Cavity Filling/Hydrophobic core




I322M/I326M/N136W/M150H


N136W/M150H






1393
A496
BG505.SOSIP.R6.664.T332N_V134I/L175W/
BG505
SOSIP, R6, 664, T332N
V134I/L175W/I322F/I326L/
Cavity Filling/Hydrophobic core




I322F/I326L/N136W/M150F


N136W/M150F






1394
A497
BG505.SOSIP.R6.664.T332N_V120F/Q203M/
BG505
SOSIP, R6, 664, T332N
V120F/Q203M/Y318M/Q315M
Cavity Filling/Hydrophobic core




Y318M/Q315M









1395
A498
BG505.SOSIP.R6.664.T332N_V120W/Q203M/
BG505
SOSIP, R6, 664, T332N
V120W/Q203M/Y318W/Q315F
Cavity Filling/Hydrophobic core




Y318W/Q315F









1396
A499
BG505.SOSIP.R6.664.T332N_L154M/N300M/
BG505
SOSIP, R6, 664, T332N
L154M/N300M/N302M/T320L/
Cavity Filling/Hydrophobic core




N302M/T320L/Y177W/I420M


Y177W/I420M






1397
A500
BG505.SOSIP.R6.664.T332N_L154W/N300L/
BG505
SOSIP, R6, 664, T332N
L154W/N300L/N302G/T320F/
Cavity Filling/Hydrophobic core




N302G/T320F/Y177W/Q328F/I420M


Y177W/Q328F/I420M






1398
A501
703010505.TF.sosip_d7324, R6, 664,
703010505.TF
SOSIP, R6, 664
I201C/A433C





I201C/A433C









1399
A502
703010505.TF.sosip_d7324_tad, R6, 664,
703010505.TF
SOSIP, R6, 664
I201C/A433C
trimer association domain




I201C/A433C/E47D/K49E/V65K/E106T/E429R/



mutations




R432Q/E500R









1400
A503
286.36.sosip_d7324
286.36
SOSIP, R6, 664
I201C/A433C






1401
A504
288.38.sosip_d7324
288.38
SOSIP, R6, 664
I201C/A433C






1402
A505
3988.25.sosip_d7324
3988.25
SOSIP, R6, 664
I201C/A433C






1403
A506
5768.04.sosip_d7324
5768.04
SOSIP, R6, 664
I201C/A433C






1404
A507
6101.1.sosip_d7324
6101.1
SOSIP, R6, 664
I201C/A433C






1405
A508
6535.3.sosip_d7324
6535.3
SOSIP, R6, 664
I201C/A433C






1406
A509
7165.18.sosip_d7324
7165.18
SOSIP, R6, 664
I201C/A433C






1407
A510
00130952.11.sosip_d7324
130952.11
SOSIP, R6, 664
I201C/A433C






1408
A511
0014282.42.sosip_d7324
14282.42
SOSIP, R6, 664
I201C/A433C






1409
A512
0077_V1.C16.sosip_d7324
0077_V1.C16
SOSIP, R6, 664
I201C/A433C






1410
A513
008362.5.sosip_d7324
8362.5
SOSIP, R6, 664
I201C/A433C






1411
A514
0260.v5.c36.sosip_d7324
0260.v5.c36
SOSIP, R6, 664
I201C/A433C






1412
A515
0330.v4.c3.sosip_d7324
0330.v4.c3
SOSIP, R6, 664
I201C/A433C






1413
A516
0439.v5.c1.sosip_d7324
0439.v5.c1
SOSIP, R6, 664
I201C/A433C






1414
A517
0815.V3.C3.sosip_d7324
0815.V3.C3
SOSIP, R6, 664
I201C/A433C






1415
A518
0921.V2.C14.sosip_d7324
0921.V2.C14
SOSIP, R6, 664
I201C/A433C






1416
A519
160552.3.sosip_d7324
160552.3
SOSIP, R6, 664
I201C/A433C






1417
A520
168452.22.sosip_d7324
168452.22
SOSIP, R6, 664
I201C/A433C






1418
A521
169362.21.sosip_d7324
169362.21
SOSIP, R6, 664
I201C/A433C






1419
A522
231965.c1.sosip_d7324
231965.c1
SOSIP, R6, 664
I201C/A433C






1420
A523
23547.sosip_d7324
23547
SOSIP, R6, 664
I201C/A433C






1421
A524
24214.sosip_d7324
24214
SOSIP, R6, 664
I201C/A433C






1422
A525
24723.sosip_d7324
24723
SOSIP, R6, 664
I201C/A433C






1423
A526
257102.43.sosip_d7324
257102.43
SOSIP, R6, 664
I201C/A433C






1424
A527
257112.4.sosip_d7324
257112.4
SOSIP, R6, 664
I201C/A433C






1425
A528
259252.22.sosip_d7324
259252.22
SOSIP, R6, 664
I201C/A433C






1426
A529
261912.48.sosip_d7324
261912.48
SOSIP, R6, 664
I201C/A433C






1427
A530
2638.sosip_d7324
2638
SOSIP, R6, 664
I201C/A433C






1428
A531
26912.sosip_d7324
26912
SOSIP, R6, 664
I201C/A433C






1429
A532
27111.sosip_d7324
27111
SOSIP, R6, 664
I201C/A433C






1430
A533
3016.v5.c45.sosip_d7324
3016.v5.c45
SOSIP, R6, 664
I201C/A433C






1431
A534
3168.V4.C10.sosip_d7324
3168.V4.C10
SOSIP, R6, 664
I201C/A433C






1432
A535
3301.V1.C24.sosip_d7324
3301.V1.C24
SOSIP, R6, 664
I201C/A433C






1433
A536
3326.V4.C3.sosip_d7324
3326.V4.C3
SOSIP, R6, 664
I201C/A433C






1434
A537
3337.V2.C6.sosip_d7324
3337.V2.C6
SOSIP, R6, 664
I201C/A433C






1435
A538
3365.v2.c20.sosip_d7324
3365.v2.c20
SOSIP, R6, 664
I201C/A433C






1436
A539
3415.v1.c1.sosip_d7324
3415.v1.c1
SOSIP, R6, 664
I201C/A433C






1437
A540
3468.V1.C12.sosip_d7324
3468.V1.C12
SOSIP, R6, 664
I201C/A433C






1438
A541
3589.V1.C4.sosip_d7324
3589.V1.C4
SOSIP, R6, 664
I201C/A433C






1439
A542
3637.V5.C3.sosip_d7324
3637.V5.C3
SOSIP, R6, 664
I201C/A433C






1440
A543
3718.v3.c11.sosip_d7324
3718.v3.c11
SOSIP, R6, 664
I201C/A433C






1441
A544
3817.v2.c59.sosip_d7324
3817.v2.c59
SOSIP, R6, 664
I201C/A433C






1442
A545
3873.V1.C24.sosip_d7324
3873.V1.C24
SOSIP, R6, 664
I201C/A433C






1443
A546
398F1_F6_20.sosip_d7324
398F1_F6_20
SOSIP, R6, 664
I201C/A433C






1444
A547
57128.vrc15.sosip_d7324
57128.vrc15
SOSIP, R6, 664
I201C/A433C






1445
A548
6095.V1.C10.sosip_d7324
6095.V1.C10
SOSIP, R6, 664
I201C/A433C






1446
A549
620345.c1.sosip_d7324
620345.c1
SOSIP, R6, 664
I201C/A433C






1447
A550
6322.V4.C1.sosip_d7324
6322.V4.C1
SOSIP, R6, 664
I201C/A433C






1448
A551
6405.v4.c34.sosip_d7324
6405.v4.c34
SOSIP, R6, 664
I201C/A433C






1449
A552
6471.V1.C16.sosip_d7324
6471.V1.C16
SOSIP, R6, 664
I201C/A433C






1450
A553
6540.v4.c1.sosip_d7324
6540.v4.c1
SOSIP, R6, 664
I201C/A433C






1451
A554
6545.V3.C13.sosip_d7324
6545.V3.C13
SOSIP, R6, 664
I201C/A433C






1452
A555
6545.V4.C1.sosip_d7324
6545.V4.C1
SOSIP, R6, 664
I201C/A433C






1453
A556
6631.V3.C10.sosip_d7324
6631.V3.C10
SOSIP, R6, 664
I201C/A433C






1454
A557
6644.V2.C33.sosip_d7324
6644.V2.C33
SOSIP, R6, 664
I201C/A433C






1455
A558
6785.V5.C14.sosip_d7324
6785.V5.C14
SOSIP, R6, 664
I201C/A433C






1456
A559
6838.V1.C35.sosip_d7324
6838.V1.C35
SOSIP, R6, 664
I201C/A433C






1457
A560
89.6.DG.sosip_d7324
89.6.DG
SOSIP, R6, 664
I201C/A433C






1458
A561
92828.sosip_d7324
92828
SOSIP, R6, 664
I201C/A433C






1459
A562
96ZM651.02.sosip_d7324
96ZM651.02
SOSIP, R6, 664
I201C/A433C






1460
A563
A03349M1.vrc4a.sosip_d7324
A03349M1.vrc4a
SOSIP, R6, 664
I201C/A433C






1461
A564
AC10.29.sosip_d7324
AC10.29
SOSIP, R6, 664
I201C/A433C






1462
A565
ADA.DG.sosip_d7324
ADA.DG
SOSIP, R6, 664
I201C/A433C






1463
A566
Bal.01.sosip_d7324
Bal.01
SOSIP, R6, 664
I201C/A433C






1464
A567
BaL.26.sosip_d7324
BaL.26
SOSIP, R6, 664
I201C/A433C






1465
A568
BB201.1342.sosip_d7324
BB201.B42
SOSIP, R6, 664
I201C/A433C






1466
A569
BB539.21313.sosip_d7324
B13539.21313
SOSIP, R6, 664
I201C/A433C






1467
A570
BG1168.01.sosip_d7324
BG1168.01
SOSIP, R6, 664
I201C/A433C






1468
A571
B1369.9A.sosip_d7324
B1369.9A
SOSIP, R6, 664
I201C/A433C






1469
A572
BL01.DG.sosip_d7324
BL01.DG
SOSIP, R6, 664
I201C/A433C






1470
A573
BR025.9.sosip_d7324
BR025.9
SOSIP, R6, 664
I201C/A433C






1471
A574
BR07.DG.sosip_d7324
BR07.DG
SOSIP, R6, 664
I201C/A433C






1472
A575
BS208.131.sosip_d7324
BS208.81
SOSIP, R6, 664
I201C/A433C






1473
A576
BX08.16.sosip_d7324
BX08.16
SOSIP, R6, 664
I201C/A433C






1474
A577
C1080.c3.sosip_d7324
C1080.c3
SOSIP, R6, 664
I201C/A433C






1475
A578
C2101.c1.sosip_d7324
C2101.c1
SOSIP, R6, 664
I201C/A433C






1476
A579
C3347.c11.sosip_d7324
C3347.c11
SOSIP, R6, 664
I201C/A433C






1477
A580
C4118.09.sosip_d7324
C4118.09
SOSIP, R6, 664
I201C/A433C






1478
A581
CAAN.A2.sosip_d7324
CAAN.A2
SOSIP, R6, 664
I201C/A433C






1479
A582
CAP210.E8.sosip_d7324
CAP210.E8
SOSIP, R6, 664
I201C/A433C






1480
A583
CAP244.D3.sosip_d7324
CAP244.D3
SOSIP, R6, 664
I201C/A433C






1481
A584
CAP45.G3.sosip_d7324
CAP45.G3
SOSIP, R6, 664
I201C/A433C






1482
A585
CH038.12.sosip_d7324
CH038.12
SOSIP, R6, 664
I201C/A433C






1483
A586
CH070.1.sosip_d7324
CH070.1
SOSIP, R6, 664
I201C/A433C






1484
A587
CH117.4.sosip_d7324
CH117.4
SOSIP, R6, 664
I201C/A433C






1485
A588
CH181.12.sosip_d7324
CH181.12
SOSIP, R6, 664
I201C/A433C






1486
A589
CNE10.sosip_d7324
CNE10
SOSIP, R6, 664
I201C/A433C






1487
A590
CNE12.sosip_d7324
CNE12
SOSIP, R6, 664
I201C/A433C






1488
A591
CNE14.sosip_d7324
CNE14
SOSIP, R6, 664
I201C/A433C






1489
A592
CNE15.sosip_d7324
CNE15
SOSIP, R6, 664
I201C/A433C






1490
A593
CNE3.sosip_d7324
CNE3
SOSIP, R6, 664
I201C/A433C






1491
A594
CNE30.sosip_d7324
CNE30
SOSIP, R6, 664
I201C/A433C






1492
A595
CNE31.sosip_d7324
CNE31
SOSIP, R6, 664
I201C/A433C






1493
A596
CNE4.sosip_d7324
CNE4
SOSIP, R6, 664
I201C/A433C






1494
A597
CNE40.sosip_d7324
CNE40
SOSIP, R6, 664
I201C/A433C






1495
A598
CNE5.sosip_d7324
CNE5
SOSIP, R6, 664
I201C/A433C






1496
A599
CNE53.sosip_d7324
CNE53
SOSIP, R6, 664
I201C/A433C






1497
A600
CNE55.sosip_d7324
CNE55
SOSIP, R6, 664
I201C/A433C






1498
A601
CNE56.sosip_d7324
CNE56
SOSIP, R6, 664
I201C/A433C






1499
A602
CNE57.sosip_d7324
CNE57
SOSIP, R6, 664
I201C/A433C






1500
A603
CNE58.sosip_d7324
CNE58
SOSIP, R6, 664
I201C/A433C






1501
A604
CNE59.sosip_d7324
CNE59
SOSIP, R6, 664
I201C/A433C






1502
A605
CNE7.sosip_d7324
CNE7
SOSIP, R6, 664
I201C/A433C






1503
A606
DJ263.8.sosip_d7324
DJ263.8
SOSIP, R6, 664
I201C/A433C






1504
A607
DU123.06.sosip_d7324
DU123.06
SOSIP, R6, 664
I201C/A433C






1505
A608
DU151.02.sosip_d7324
DU151.02
SOSIP, R6, 664
I201C/A433C






1506
A609
DU156.12.sosip_d7324
DU156.12
SOSIP, R6, 664
I201C/A433C






1507
A610
DU172.17.sosip_d7324
DU172.17
SOSIP, R6, 664
I201C/A433C






1508
A611
DU422.01.sosip_d7324
DU422.01
SOSIP, R6, 664
I201C/A433C






1509
A612
HO86.8.sosip_d7324
HO86.8
SOSIP, R6, 664
I201C/A433C






1510
A613
HT593.1.sosip_d7324
HT593.1
SOSIP, R6, 664
I201C/A433C






1511
A614
JRCSF.JB.sosip_d7324
JRCSF.JB
SOSIP, R6, 664
I201C/A433C






1512
A615
JRFL.JB.sosip_d7324
JRFL.JB
SOSIP, R6, 664
I201C/A433C






1513
A616
KER2008.12.sosip_d7324
KER2008.12
SOSIP, R6, 664
I201C/A433C






1514
A617
KER2018.11.sosip_d7324
KER2018.11
SOSIP, R6, 664
I201C/A433C






1515
A618
KNH1209.18.sosip_d7324
KNH1209.18
SOSIP, R6, 664
I201C/A433C






1516
A619
M02138.sosip_d7324
M02138
SOSIP, R6, 664
I201C/A433C






1517
A620
MB201.A1.sosip_d7324
MB201.A1
SOSIP, R6, 664
I201C/A433C






1518
A621
MB539.2137.sosip_d7324
MB539.287
SOSIP, R6, 664
I201C/A433C






1519
A622
MI369.A5.sosip_d7324
MI369.A5
SOSIP, R6, 664
I201C/A433C






1520
A623
MN.3.sosip_d7324
MN.3
SOSIP, R6, 664
I201C/A433C






1521
A624
MS208.A1.sosip_d7324
MS208.A1
SOSIP, R6, 664
I201C/A433C






1522
A625
MW965.26.sosip_d7324
MW965.26
SOSIP, R6, 664
I201C/A433C






1523
A626
NKU3006.ec1.sosip_d7324
NKU3006.ec1
SOSIP, R6, 664
I201C/A433C






1524
A627
PVO.04.sosip_d7324
PVO.04
SOSIP, R6, 664
I201C/A433C






1525
A628
Q168.a2.sosip_d7324
Q168.a2
SOSIP, R6, 664
I201C/A433C






1526
A629
Q23.17.sosip_d7324
Q23.17
SOSIP, R6, 664
I201C/A433C






1527
A630
Q259.17.sosip_d7324
Q259.17
SOSIP, R6, 664
I201C/A433C






1528
A631
Q461.e2.sosip_d7324
Q461.e2
SOSIP, R6, 664
I201C/A433C






1529
A632
Q769.d22.sosip_d7324
Q769.d22
SOSIP, R6, 664
I201C/A433C






1530
A633
Q769.h5.sosip_d7324
Q769.h5
SOSIP, R6, 664
I201C/A433C






1531
A634
Q842.d12.sosip_d7324
Q842.d12
SOSIP, R6, 664
I201C/A433C






1532
A635
QH0515.01.sosip_d7324
QH0515.01
SOSIP, R6, 664
I201C/A433C






1533
A636
QH0692.42.sosip_d7324
QH0692.42
SOSIP, R6, 664
I201C/A433C






1534
A637
QH209.14M.A2.sosip_d7324
QH209.14M.A2
SOSIP, R6, 664
I201C/A433C






1535
A638
R1166.c1.sosip_d7324
R1166.c1
SOSIP, R6, 664
I201C/A433C






1536
A639
R2184.c4.sosip_d7324
R2184.c4
SOSIP, R6, 664
I201C/A433C






1537
A640
R3265.c6.sosip_d7324
R3265.c6
SOSIP, R6, 664
I201C/A433C






1538
A641
REJO.67.sosip_d7324
REJO.67
SOSIP, R6, 664
I201C/A433C






1539
A642
RHPA.7.sosip_d7324
RHPA.7
SOSIP, R6, 664
I201C/A433C






1540
A643
RW020.2.sosip_d7324
RW020.2
SOSIP, R6, 664
I201C/A433C






1541
A644
SC422.8.sosip_d7324
SC422.8
SOSIP, R6, 664
I201C/A433C






1542
A645
SF162.LS.sosip_d7324
SF162.LS
SOSIP, R6, 664
I201C/A433C






1543
A646
SO18.18.sosip_d7324
SO18.18
SOSIP, R6, 664
I201C/A433C






1544
A647
SS1196.01.sosip_d7324
SS1196.01
SOSIP, R6, 664
I201C/A433C






1545
A648
T2504.sosip_d7324
T2504
SOSIP, R6, 664
I201C/A433C






1546
A649
T25118.sosip_d7324
T25118
SOSIP, R6, 664
I201C/A433C






1547
A650
T25311.sosip_d7324
T25311
SOSIP, R6, 664
I201C/A433C






1548
A651
T25534.sosip_d7324
T25534
SOSIP, R6, 664
I201C/A433C






1549
A652
T25731.sosip_d7324
T25731
SOSIP, R6, 664
I201C/A433C






1550
A653
T26660.sosip_d7324
T26660
SOSIP, R6, 664
I201C/A433C






1551
A654
T27850.sosip_d7324
T27850
SOSIP, R6, 664
I201C/A433C






1552
A655
T2805.sosip_d7324
T2805
SOSIP, R6, 664
I201C/A433C






1553
A656
T337.sosip_d7324
T337
SOSIP, R6, 664
I201C/A433C






1554
A657
TH966.8.sosip_d7324
TH966.8
SOSIP, R6, 664
I201C/A433C






1555
A658
TH976.17.sosip_d7324
TH976.17
SOSIP, R6, 664
I201C/A433C






1556
A659
THRO.18.sosip_d7324
THRO.18
SOSIP, R6, 664
I201C/A433C






1557
A660
TRJO.58.sosip_d7324
TRJO.58
SOSIP, R6, 664
I201C/A433C






1558
A661
TRO.11.sosip_d7324
TRO.11
SOSIP, R6, 664
I201C/A433C






1559
A662
TV1.29.sosip_d7324
TV1.29
SOSIP, R6, 664
I201C/A433C






1560
A663
TZA125.17.sosip_d7324
TZA125.17
SOSIP, R6, 664
I201C/A433C






1561
A664
TZBD.02.sosip_d7324
TZBD.02
SOSIP, R6, 664
I201C/A433C






1562
A665
UG021.16.sosip_d7324
UG021.16
SOSIP, R6, 664
I201C/A433C






1563
A666
UG024.2.sosip_d7324
UG024.2
SOSIP, R6, 664
I201C/A433C






1564
A667
UG037.8.sosip_d7324
UG037.8
SOSIP, R6, 664
I201C/A433C






1565
A668
WITO.33.sosip_d7324
WITO.33
SOSIP, R6, 664
I201C/A433C






1566
A669
X2088.c9.sosip_d7324
X2088.c9
SOSIP, R6, 664
I201C/A433C






1567
A670
YU2.DG.sosip_d7324
YU2.DG
SOSIP, R6, 664
I201C/A433C






1568
A671
ZA012.29.sosip_d7324
ZA012.29
SOSIP, R6, 664
I201C/A433C






1569
A672
ZM106.9.sosip_d7324
ZM106.9
SOSIP, R6, 664
I201C/A433C






1570
A673
ZM109.4.sosip_d7324
ZM109.4
SOSIP, R6, 664
I201C/A433C






1571
A674
ZM135.10a.sosip_d7324
ZM135.10a
SOSIP, R6, 664
I201C/A433C






1572
A675
ZM176.66.sosip_d7324
ZM176.66
SOSIP, R6, 664
I201C/A433C






1573
A676
ZM197.7.sosip_d7324
ZM197.7
SOSIP, R6, 664
I201C/A433C






1574
A677
ZM214.15.sosip_d7324
ZM214.15
SOSIP, R6, 664
I201C/A433C






1575
A678
ZM215.8.sosip_d7324
ZM215.8
SOSIP, R6, 664
I201C/A433C






1576
A679
ZM233.6.sosip_d7324
ZM233.6
SOSIP, R6, 664
I201C/A433C






1577
A680
ZM249.1.sosip_d7324
ZM249.1
SOSIP, R6, 664
I201C/A433C






1578
A681
ZM53.12.sosip_d7324
ZM53.12
SOSIP, R6, 664
I201C/A433C






1579
A682
ZM55.28a.sosip_d7324
ZM55.28a
SOSIP, R6, 664
I201C/A433C






1580
A683
JRFLgp140.6R.SOSIP.664.E168K, BG505 
JRFLgp140/BG505
SOSIP, R6, 664
E168K, I201C-A433C,
stability




gp41 chim, I201C-A433C, Y191W
chimera

Y191W






1581
A684
JRFLgp140.6R.SOSIP.664.E168K,Y191W
JRFLgp140/BG505 
SOSIP, R6, 664
E168K, Y191W
stability





chimera








1582
A685
JRFLgp140.6R.SOSIP.664.E168K, BG505 
JRFLgp140/BG505
SOSIP, R6, 664
E168K, I201C-A433C,
VRC26 binding




gp41 chim, I201C-A433C, R315Q
chimera

R315Q






1583
A686
JRFLgp140.6R.SOSIP.664.E168K, BG505
JRFLgp140/BG505
SOSIP, R6, 664
E168K, I201C-A433C, 
VRC26 binding




gp41 chim, I201C-A433C, 161-170SU
chimera

residues 161-170 from








CAP256 SU strain






1584
A687
JRFLgp140.6R.SOSIP.664.E168K, BG505
JRFLgp140/BG505
SOSIP, R6, 664
E168K, I201C-A433C, 
VRC26 binding




gp41 chim, I201C-A433C, 161-170SU,
chimera

residues 161-170 from





R313Q


CAP256 SU strain, R313Q






1585
A688
JRFLgp140.6R.SOSIP.664.E168K,R315Q
JRFLgp140/BG505
SOSIP, R6, 664
E168K,R315Q
VRC26 binding





chimera








1586
A689
JRFLgp140.6R.SOSIP.664.E168K,161-170,
JRFLgp140/BG505
SOSIP, R6, 664
E168K,residues 161-170
VRC26 binding




SUstrandC 
chimera

from CAP256 SU strain






1587
A690
JRFLgp140.6R.SOSIP.664.E168K,161-1705U,
JRFLgp140/BG505
SOSIP, R6, 664
E168K,residues 161-170
VRC26 binding




R313Q
chimera

from CAP256 SU strain,








R313Q






1588
A691
JRFLgp140.6R.SOSIP.664.E168K, BG505
JRFLgp140/BG505
SOSIP, R6, 664
E168K, I201C-A433C, 
Interprotomer DS




gp41 chim, I201C-A433C, T128C, D167C
chimera

T128C, D167C






1589
A692
JRFLgp140.6R.SOSIP.664.E168K, BG505
JRFLgp140/BG505
SOSIP, R6, 664
E168K, I201C-A433C,
Interprotomer DS




gp41 chim, I201C-A433C, V127C, D167C
chimera

V127C, D167C






1590
A693
JRFLgp140.6R.SOSIP.664.E168K,T128C, 
JRFLgp140/BG505
SOSIP, R6, 664
E168K,T128C, D167C
Interprotomer DS




D167C
chimera








1591
A694
JRFLgp140.6R.SOSIP.664.E168K,V127C, 
JRFLgp140/BG505
SOSIP, R6, 664
E168K,V127C, D167C
Interprotomer DS




D167C
chimera








1592
A695
JRFLgp140.6R.SOSIP.664.E168K, BG505
JRFLgp140/BG505
SOSIP, R6, 664
E168K, I201C-A433C, 
Interprotomer DS




gp41 chim, I201C-A433C, I165C, C196S
chimera

I165C, C196S






1593
A696
JRFLgp140.6R.SOSIP.664.E168K, BG505
JRFLgp140/BG505
SOSIP, R6, 664
E168K, I201C-A433C, 
Interprotomer DS




gp41 chim, I201C-A433C, I165C, C196F
chimera

I165C, C196F






1594
A697
JRFLgp140.6R.SOSIP.664.E168K, BG505 
JRFLgp140/BG505
SOSIP, R6, 664
E168K, I201C-A433C, 
Interprotomer DS




gp41 chim, I201C-A433C, I165C, C196L
chimera

I165C, C196L






1595
A698
JRFLgp140.6R.SOSIP.664.E168K,I165C, 
JRFLgp140/BG505
SOSIP, R6, 664
E168K, I165C, C196S
Interprotomer DS




C196S
chimera








1596
A699
JRFLgp140.6R.SOSIP.664.E168K,I165C, 
JRFLgp140/BG505
SOSIP, R6, 664
E168K, I165C, C196F
Interprotomer DS




C196F
chimera








1597
A700
JRFLgp140.6R.SOSIP.664.E168K,I165C, 
JRFLgp140/BG505
SOSIP, R6, 664
E168K, I165C, C196L
Interprotomer DS




C196L
chimera








1598
A701
JRFLgp140.6R.SOSIP.664.E168K, BG505 
JRFLgp140/BG505
SOSIP, R6, 664
E168K, I201C-A433C,
DDS




gp41 chim, I201C-A433C, R304C/R440C
chimera

R304C/R440C






1599
A702
JRFLgp140.6R.SOSIP.664.E168K, BG505
JRFLgp140/BG505
SOSIP, R6, 664
E168K, I201C-A433C,
DDS




gp41 chim, I201C-A433C, A174C/T319C
chimera

A174C/T319C






1600
A703
JRFLgp140.6R.SOSIP.664.E168K, BG505
JRFLgp140/BG505
SOSIP, R6, 664
E168K, I201C-A433C,
DDS




gp41 chim, I201C-A433C, S164C/H308C
chimera

S164C/H308C






1601
A704
JRFLgp140.6R.SOSIP.664.E168K, BG505
JRFLgp140/BG505
SOSIP, R6, 664
E168K, I201C-A433C, 
Interprotomer DS




gp41 chim, I201C-A433C, S110C/L556C
chimera

S110C/L556C






1602
A705
JRFLgp140.6R.SOSIP.664.E168K,S110C/
JRFLgp140/BG505
SOSIP, R6, 664
E168K,S110C/L556C
Interprotomer DS




L556C
chimera








1603
A706
JRFLgp140.6R.SOSIP.664.E168K, BG505
JRFLgp140/BG505
SOSIP, R6, 664
E168K, I201C-A433C, 
Interprotomer DS




gp41 chim, I201C-A433C, A558C/D113C
chimera

A558C/D113C






1604
A707
JRFLgp140.6R.SOSIP.664.E168K,A558C/
JRFLgp140/BG505
SOSIP, R6, 664
E168K,A558C/D113C
Interprotomer DS




D113C
chimera








1605
A708
JRFLgp140.6R.SOSIP.664.E168K,E561W
JRFLgp140/BG505
SOSIP, R6, 664
E168K,E561W
Cav





chimera








1606
A709
JRFLgp140.6R.SOSIP.664.E168K,E561F
JRFLgp140/BG505
SOSIP, R6, 664
E168K,E561F
Cav





chimera








1607
A710
JRFLgp140.6R.SOSIP.664.E168K,E561W/
JRFLgp140/BG505
SOSIP, R6, 664
E168K,E561W/K121F
Cav




K121F
chimera








1608
A711
JRFLgp140.6R.SOSIP.664.E168K,E561F/
JRFLgp140/BG505
SOSIP, R6, 664
E168K,E561F/K121F
Cav




K121F
chimera








1609
A712
JRFLgp140.6R.SOSIP.664.E168K,E561W/
JRFLgp140/BG505
SOSIP, R6, 664
E168K,E561W/K121W
Cav




K121W
chimera








1610
A713
JRFLgp140.6R.SOSIP.664.E168K,E561F/
JRFLgp140/BG505
SOSIP, R6, 664
E168K,E561F/K121W
Cav




K121W
chimera








1611
A714
BG505gp140.6R.SOSIP.664.T332N.D7325
BG505
SOSIP, R6, 664
T332N.D7325 Q315C





Q315C









1612
A715
BG505gp140.6R.SOSIP.664.T332N.D7324
BG505
SOSIP, R6, 664
T332N.D7324 V120C





V120C









1613
A716
JRFLgp140.6R.SOSIP.664.E168K_Q315C
JRFL
SOSIP, R6, 664
E168K_Q315C






1614
A717
JRFLgp140.6R.SOSIP.664.E168K_V120C
JRFL
SOSIP, R6, 664
E168K_V120C






1615
A718
JRFLgp140.6R.SOSIP.664.E168K
JRFL
SOSIP, R6, 664
E168K






1616
A719
JRFLgp140.6R.SOSIP.664.E168K_I201C/
JRFL
SOSIP, R6, 664
E168K_I201C/A433C
DS




A433C









1617
A720
JRFLgp140.6R.SOSIP.664.E168K_A433P
JRFL
SOSIP, R6, 664
E168K_A433P
stability





1618
A721
JRFLgp140.6R.SOSIP.664.E168K_Q432P
JRFL
SOSIP, R6, 664
E168K_Q432P
stability





1619
A722
JRFLgp140.6R.SOSIP.664.E168K_S174C/
JRFL
SOSIP, R6, 664
E168K_S174C/A319C





A319C









1620
A723
JRFLgp140.6R.SOSIP.664.E168K_N195C/
JRFL
SOSIP, R6, 664
E168K_N195C/A433C





A433C









1621
A724
JRFLgp140.6R.SOSIP.664.E168K_S199C/
JRFL
SOSIP, R6, 664
E168K_S199C/A433C





A433C









1622
A725
JRFLgp140.6R.SOSIP.664.E168K_R304C/
JRFL
SOSIP, R6, 664
E168K_R304C/Q440C





Q440C









1623
A726
JRFLgp140.6R.SOSIP.664.E168K_F223W
JRFL
SOSIP, R6, 664
E168K_F223W
Cav





1624
A727
JRFLgp140.6R.SOSIP.664.E168K_G473Y
JRFL
SOSIP, R6, 664
E168K_G473Y
Cav





1625
A728
JRFLgp140.6R.SOSIP.664.E168K_G431P
JRFL
SOSIP, R6, 664
E168K_G431P
stability





1626
A729
JRFLgp140.6R.SOSIP.664.E168K_N425C_
JRFL
SOSIP, R6, 664
E168K_N425C_A433C





A433C









1627
A730
JRFLgp140.6R.SOSIP.664.E168K_V120C_
JRFL
SOSIP, R6, 664
E168K_V120C_Q315C





Q315C









1628
A731
JRFLgp140.6R.SOSIP.664.E168K_Q203C_
JRFL
SOSIP, R6, 664
E168K_Q203C_L122C





L122C









1629
A732
JRFLgp140.6R.SOSIP.664.E168K_I201C/
JRFL
SOSIP, R6, 664
E168K_I201C/A433C/





A433C/R304C/Q440C


R304C/Q440C






1630
A733
JRFLgp140.6R.SOSIP.664.E168K_R304C/
JRFL
SOSIP, R6, 664
E168K_R304C/R440C





R440C









1631
A734
JRFLgp140.6R.SOSIP.664.E168K_Q203C/
JRFL
SOSIP, R6, 664
E168K_Q203C/F317C





F317C









1632
A735
JRFLgp140.6R.SOSIP.664.E168K_L122C/
JRFL
SOSIP, R6, 664
E168K_L122C/F317C





F317C









1633
A736
JRFLgp140.6R.SOSIP.664.E168K_P437C/
JRFL
SOSIP, R6, 664
E168K_P437C/Y318C





Y318C









1634
A737
JRFLgp140.6R.SOSIP.664.E168K_E172C/
JRFL
SOSIP, R6, 664
E168K_E172C/I307C





I307C









1635
A738
JRFLgp140.6R.SOSIP.664.E168K_P206C/
JRFL
SOSIP, R6, 664
E168K_P206C/Y318C





Y318C









1636
A739
JRFLgp140.6R.SOSIP.664.E168K_A174C/
JRFL
SOSIP, R6, 664
E168K_A174C/T319C





T319C









1637
A740
JRFLgp140.6R.SOSIP.664.E168K_S164C/
JRFL
SOSIP, R6, 664
E168K_S164C/H308C





H308C









1638
A741
JRFLgp140.6R.SOSIP.664.E168K_T320C/
JRFL
SOSIP, R6, 664
E168K_T320C/L175C





L175C









1639
A742
JRFLgp140.6R.SOSIP.664.E168K_T320C/
JRFL
SOSIP, R6, 664
E168K_T320C/P438C





P438C









1640
A743
JRFLgp140.6R.SOS.664.E168K
JRFL
6R.SOS.664
E168K
stability





1641
A744
JRFLgp140.6R.IP.664.E168K
JRFL
6R.IP.664
E168K
stability





1642
A745
JRFLgp140.6R.664.E168K
JRFL
6R.664
E168K
stability





1643
B192
*703010505.TF-chim-sc d7324, R6, 664,
703010505.TF/
SOSIP, sc15ln, 664
I201C/A433C





I201C/A433C
BG505 chimera












AENLWVTVYYGVPVWKEAKTTLFCASDAKAYEKEVHNVWATHACVPTDPNPQEMVLKNVTENFNMWKNDMVDQMHEDVISLWDQSLKPCVKLTPLCVTLNCTNATASNSSIIEGMKNCSFNITTELRDKR



EKKNALFYKLDIVQLDGNSSQYRLINCNTSVITQACPKVSFDPIPIHYCAPAGYAILKCNNKTFTGTGPCNNVSTVQCTHGIKPVVSTQLLLNGSLAEGEIIIRSENITNNVKTIIVHLNESVKIECTRP



NNKTRTSIRIGPGQAFYATGQVIGDIREAYCNINESKWNETLQRVSKKLKEYFPHKNITFQPSSGGDLEITTHSFNCGGEFFYCNTSSLFNRTYMANSTDMANSTETNSTRTITIHCRIKQIINMWQEVG



RAMYAPPIAGNITCISNITGLLLTRDGGKNNTETFRPGGGNMKDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGggsggggsggggsggAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQ



SNLLRAPEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD
















1644
B193
703010505.TF-chim-sc_d7324_tad, sc15ln,
703010505.TF/
SOSIP, sc15ln, 664
I201C/A433C/E47D/K49E/
single chain 15 amino acid 




664, I201C/A433C/E47D/K49E/V65K/E106T/
BG505 chimera

V65K/E106T/E429R/R432Q/
linker, trimer association 




E429R/R432Q/E500R


E500R
domain mutations





1645
B194
bg505.sosip_c15ln.DS_gly3
BG505
SOSIP; 664, 201C, 433C
508(REKR)511 replaced by
Increase CD4-binding site







linker of length 15,
accessibility by removing







278A, 365A, 464A
glycans around it





1646
B195
bg505.sosip_c15ln.DS_gly4
BG505
SOSIP; 664; 201C, 433C
508(REKR)511 replaced by
Same as Seq_1645







linker of length 15, 








S199A, 278A, 365A, 464A






1647
B196
bg505.sosip_c15ln.DS_gly5
BG505
SOSIP; 664; 201C, 433C
508(REKR)511 replaced by
Same as Seq_1645







linker of length 15, 








S199A, 278A, 365A, 388A,








464A






1648
B197
ZM55.28a-chim-sc_DS_gly3
ZM55/BG505 
SOSIP; 664; 201C, 433C
Seq_0534 linker between
Same as Seq_1645





chimera

508-511, BG505 Platform,








BG505 Res. Set B,








remainder = ZM55.28a,








278A, 463A, 467A






1649
B198
ZM55.28a-chim-sc_DS_gly4
ZM55/BG505 
SOSIP; 664; 201C, 433C
Seq_0534 linker between
Same as Seq_1645





chimera

508-511, BG505 Platform,








BG505 Res. Set B,








remainder = ZM55.28a,








S199A, 278A, 463A, 467A






1650
B199
ZM55.28a-chim-sc_DS_gly5
ZM55/BG505 
SOSIP; 664; 201C, 433C
Seq_0534 linker between
Same as Seq_1645





chimera

508-511,BG505 Platform,








BG505 Res. Set B,








remainder = ZM55.28a,








S199A, 278A, 388A, 463A,








467A






1651
D011
BG505sosip_ig_I201C/A433C.STOP-gly3
BG505
SOSIP, R6, 664, 
278A, 365A, 464A
Same as Seq_1645






201C/433C







1652
D012
BG505sosip_ig_I201C/A433C.STOP-gly4
BG505
SOSIP, R6, 664, 
S199A, 278A, 365A, 464A
Same as Seq_1645






201C/433C







1653
D013
BG505sosip_ig_I201C/A433C.STOP-gly5
BG505
SOSIP, R6, 664, 
S199A, 278A, 365A, 388A,
Same as Seq_1645






201C/433C
464A






1654
D014
CH505SOSIP_DS_degly3
CH505
SOSIP, R6, 664,
278A, 463A
Same as Seq_1645






201C/433C







1655
D015
CH505SOSIP_DS_degly4
CH505
SOSIP, R6, 664, 
199A, 278A, 463A
Same as Seq_1645






201C/433C







1656
D016
CH505SOSIP_DS_degly5
CH505
SOSIP, R6, 664,
199A, 278A, 388A, 463A
Same as Seq_1645






201C/433C







1657
D017
ZM55.28a-chim_DS_gly3
ZM55/BG505 
SOSIP, R6, 664, 
BG505 Platform,
Same as Seq_1645





chimera
201C/433C
BG505 Res. Set B,








remainder = ZM55.28a,








278A, 463A, 467A






1658
D018
ZM55.28a-chim_DS_gly4
ZM55/BG505 
SOSIP, R6, 664, 
BG505 Platform,
Same as Seq_1645





chimera
201C/433C
BG505 Res. Set B,








remainder = ZM55.28a, 








S199A, 278A, 463A, 467A






1659
D019
ZM55.28a-chim_DS_gly5
ZM55/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505
Same as Seq_1645





chimera
201C/433C
Res. Set B, remainder =








ZM55.28a, S199A, 278A,








388A, 463A, 467A






1660
D020
ZM106.9.sosip_DS_gly3
Zm1096.9
SOSIP, R6, 664, 
278A, 466A
Same as Seq_1645






201C/433C







1661
D021
ZM106.9.sosip_DS_gly4
Zm1096.9
SOSIP, R6, 664, 
S199A, 278A, 466A
Same as Seq_1645






201C/433C







1662
D022
ZM106.9.sosip_DS_gly5
Zm1096.9
SOSIP, R6, 664, 
S199A, 278A, 388A, 466A
Same as Seq_1645






201C/433C







1663
D023
CH038.12-chim_DS_gly3
CH038/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505
Same as Seq_1645





chimera
201C/433C
Res. Set B, remainder =








CH038, 278A, 464A, 467A






1664
D024
CH038.12-chim_DS_gly4
CH038/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505
Same as Seq_1645





chimera
201C/433C
Res. Set B, remainder =








CH038, 199A, 278A, 464A,








467A






1665
D025
CH038.12-chim_DS_gly5
CH038/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505
Same as Seq_1645





chimera
201C/433C
Res. Set B, remainder =








CH038, 199A, 278A, 388A,








464A, 467A






1666
D026
ZM106.9-chim_DS_gly3
ZM106/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505
Same as Seq_1645





chimera
201C/433C
Res. Set B, remainder =








ZM106.9, 278A, 466A






1667
D027
ZM106.9-chim_DS_gly4
ZM106/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505
Same as Seq_1645





chimera
201C/433C
Res. Set B, remainder =








ZM106.9, S199A, 278A,








466A






1668
D028
ZM106.9-chim_DS_gly5
ZM106/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505
Same as Seq_1645





chimera
201C/433C
Res. Set B, remainder =








ZM106.9, S199A, 278A,








388A, 466A






1669
D029
16055-2.3-chim_DS_gly3
10655/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505
Same as Seq_1645





chimera
201C/433C
Res. Set B, remainder =








10655, 278A, 465A






1670
D030
16055-2.3-chim_DS_gly4
10655/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505
Same as Seq_1645





chimera
201C/433C
Res. Set B, remainder =








10655, S199A, 278A, 465A






1671
D031
16055-2.3-chim_DS_gly5
10655/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505
Same as Seq_1645





chimera
201C/433C
Res. Set B, remainder =








10655, S199A, 278A,








388A, 465A






1672
D032
45_01dG5_bg505-NCgp120 +
45-01dG5/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1645




gp41.SOSIP_DS_gly3
chimera
201C/433C
Res. Set B, remainder =








45_01dG5, 364A






1673
D033
45_01dG5_bg505-NCgp120 +
45-01dG5/BG505 
SOSIP, R6, 664, 
BG505 Platform, BG505 
Same as Seq_1645




gp41.SOSIP_DS_gly4
chimera
201C/433C
Res. Set B, remainder =








45_01dG5, S199A, 364A






1674
D034
426c_degly3DS
426c
SOSIP, R6, 664, 
278A, 462A
Same as Seq_1645






201C/433C







1675
D035
426c_degly4DS
426c
SOSIP, R6, 664, 
S199A, 278A, 462A
Same as Seq_1645






201C/433C







1676
H385
*426c-v1v2-WITO-degly4-S199A/I201C/
426c/WITO-
SOSIP, R6, 664,

BG505 chimera, V1V2 chimera,




A433C/N276D/N460D/N463D/R504N/
V1v2/BG505
S199A/I201C/A433C/N276

glycan shielding at residues




V506T/L661N/L663T
chimera
D/N460D/N463D/R504N/

504, 661






V506T/L661N/L663T











AENLWVTVYYGVPVWKEAKTTLFCASDAKAYEKEVHNVWATHACVPTDPNPQEVVLENVTENFNMWKNDMVDQMQEDVISIWDQSLKPCVKLTPLCVTLHCTNVTISSTNGSTANVTMREEMKNCSFNTT



TVIRDKIQKEYALFYKLDIVPIEGKNTNTGYRLINCNTATCTQACPKVTFDPIPIHYCAPAGYAILKCNNKTFNGKGPCNNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIVIRSKNLADNAKIIIVQLNK



SVEIVCTRPNNNTRRSIRIGPGQTFYATDIIGDIRQAYCNISGRNWSEAVNQVKKKLKEHFPHKNISFQSSSGGDLEITTHSFNCGGEFFYCNTSGLFNDTISNATIMLPCRIKQIINMWQEVGKCIYAP



PIKGNITCKSDITGLLLLRDGGNTANNAEIFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRnvtGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHL



LKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIYGLLEESQNQQEKNEQDLnAtD
















1677
H386
*426c-v1v2-WITO-degly3-I201C/A433C/
426c/WITO-
SOSIP, R6, 664,

BG505 chimera, V1V2 chimera,




N276D/N460D/N463D/R504N/V506T/
V1v2/BG505
I201C/A433C/N276D/

glycan shielding at residues




L661N/L663T
chimera
N460D/N463D/R504N/

504, 662






V506T/L661N/L663T











AENLWVTVYYGVPVWKEAKTTLFCASDAKAYEKEVHNVWATHACVPTDPNPQEVVLENVTENFNMWKNDMVDQMQEDVISIWDQSLKPCVKLTPLCVTLHCTNVTISSTNGSTANVTMREEMKNCSFNTT



TVIRDKIQKEYALFYKLDIVPIEGKNTNTGYRLINCNTsTCTQACPKVTFDPIPIHYCAPAGYAILKCNNKTFNGKGPCNNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIVIRSKNLADNAKIIIVQLNK



SVEIVCTRPNNNTRRSIRIGPGQTFYATDIIGDIRQAYNISGRNWSEAVNQVKKKLKEHFPHKNISFQSSSGGDLEITTHSFNCGGEFFYCNTSGLFNDTISNATIMLPCRIKQIINMWQEVGKCIYAPP



IKGNITCKSDITGLLLLRDGGNTANNAEIFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRnvtGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLL



KLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLnAtD
















1678
H387
*426c-v1v2-ZM233-degly4-S199A/I201C/
426c/ZM233-
SOSIP R6, 664,

BG505 chimera, V1V2 chimera,




A433C/N276D/N460D/N463D/R504N/
V1v2/BG505
S199A/I201C/A433C/

glycan shielding at residues




V506T/L661N/L663T
chimera
N276D/N460D/N463D/

504, 663






R504N/V506T/L661N/








L663T











AENLWVTVYYGVPVWKEAKTTLFCASDAKAYEKEVHNVWATHACVPTDPNPQEVVLENVTENFNMWKNDMVDQMQEDVISIWDQSLKPCVKLTPLCVTLDCSTYNNTHNISKEMKICSFNMTTELRDKKR



KVNVLFYKLDLVPLTNSSNTTNYRLISCNTATCTQACPKVTFDPIPIHYCAPAGYAILKCNNKTFNGKGPCNNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIVIRSKNLADNAKIIIVQLNKSVEIVCTR



PNNNTRRSIRIGPGQTFYATDIIGDIRQAYCNISGRNWSEAVNQVKKKLKEHFPHKNISFQSSSGGDLEITTHSFNCGGEFFYCNTSGLFNDTISNATIMLPCRIKQIINMWQEVGKCIYAPPIKGNITC



KSDITGLLLLRDGGNTANNAEIFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRnvtGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLKLTVWGI



KQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLEESQNQQEKNEQDLnAtD
















1679
H388
*426c-v1v2-ZM233-degly3-I201C/A433C/
426c/ZM233-
SOSIP, R6, 664,

BG505 chimera, V1V2 chimera,




N276D/N460D/N463D/R504N/V506T/
V1v2/BG505
I201C/A433C/N276D/

glycan shielding at residues




L661N/L663T
chimera
N460D/N463D/R504N/

504, 664






V506T/L661N/L663T











AENLWVTVYYGVPVWKEAKTTLFCASDAKAYEKEVHNVWATHACVPTDPNPQEVVLENVTENFNMWKNDMVDQMQEDVISIWDQSLKPCVKLTPLCVTLDCSTYNNTHNISKEMKICSFNMTTELRDKKR



KVNVLFYKLDLVPLTNSSNTTNYRLISCNTsTCTQACPKVTFDPIPIHYCAPAGYAILKCNNKTFNGKGPCNNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIVIRSKNLADNAKIIIVQLNKSVEIVCTR



PNNNTRRSIRIGPGQTFYATDIIGDIRQAYCNISGRNWSEAVNQVKKKLKEHFPHKNISFQSSSGGDLEITTHSFNCGGEFFYCNTSGLFNDTISNATIMLPCRIKQIINMWQEVGKCIYAPPIKGNITC



KSDITGLLLLRDGGNTANNAEIFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRnvtGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLKLTVWGI



KQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLnAtD
















1680
H389
*d45-01dG5chim-v1v2-WITO-
donor45-
SOSIP, R6, 664,

BG505 chimera, V1V2 chimera,




I201C/A433C/R504N/V506T/L661N/L663T
01dG5/WITO-
I201C/A433C/R504N/

glycan shielding at residues





V1v2/BG505
V506T/L661N/L663T

504, 665





chimera












AENLWVTVYYGVPVWKEATATLFCASDAKAYETEVHNVWATHACVPTDPNPQEVVLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLHCTNVTISSTNGSTANVTMREEMKNCSFNTT



TVIRDKIQKEYALFYKLDIVPIEGKNTNTGYRLINCNTsVCTQACPKISFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENIKDNAKIIIVQLNE



TVEINCTRPNNNTRKSIPIGPGRAFYTTGAIIGDIRQAHCNISKAKWENTLKQIARKLREHFKNETIAFNQsSGGDPEIVMHSFNCGGEFFYCNSTQLFNSTWTWNDTEVVNNTEKNINITLPCRIKQII



NMWQEVGKCMYAPPIKGQIRCSSNITGLLLTRDGGSSTNGTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRnVtGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQ



QSNLLRAPEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLnAtD
















1681
H390
*d45-01dG5chim-v1v2-WITO-01dG5chim-
donor45-
SOSIP, R6, 664,

BG505 chimera, V1V2 chimera,




degly3-I201C/5364A/A433C/R504N/V506T/
01dG5/WITO-
I201C/S364A/A433C/

glycan shielding at residues




L661N/L663T
V1v2/BG505
R504N/V506T/L661N/

504, 666





chimera
L663T











AENLWVTVYYGVPVWKEATATLFCASDAKAYETEVHNVWATHACVPTDPNPQEVVLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLHCTNVTISSTNGSTANVTMREEMKNCSFNTT



TVIRDKIQKEYALFYKLDIVPIEGKNTNTGYRLINCNTsVCTQACPKISFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENIKDNAKIIIVQLNE



TVEINCTRPNNNTRKSIPIGPGRAFYTTGAIIGDIRQAHCNISKAKWENTLKQIARKLREHFKNETIAFNQaSGGDPEIVMHSFNCGGEFFYCNSTQLFNSTWTWNDTEVVNNTEKNINITLPCRIKQII



NMWQEVGKCMYAPPIKGQIRCSSNITGLLLTRDGGSSTNGTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRnVtGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQ



QSNLLRAPEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLnAtD
















1682
H391
*d45-01dG5chim-v1v2-WITO-01dG5chim-
d0n0r45-
SOSIP, R6, 664,

BG505 chimera, V1V2 chimera,




degly4-S199A/I201C/S364A/A433C/R504N/
01dG5/WITO-
S199A/I201C/S364A/

glycan shielding at residues




V506T/L661N/L663T
V1v2/BG505
A433C/R504N/V506T/

504, 667





chimera
L661N/L663T











AENLWVTVYYGVPVWKEATATLFCASDAKAYETEVHNVWATHACVPTDPNPQEVVLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLHCTNVTISSTNGSTANVTMREEMKNCSFNTT



TVIRDKIQKEYALFYKLDIVPIEGKNTNTGYRLINCNTaVCTQACPKISFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENIKDNAKIIIVQLNE



TVEINCTRPNNNTRKSIPIGPGRAFYTTGAIIGDIRQAHCINISKAKWENTLKQIARKLREHFKNETIAFNQaSGGDPEIVMHSFNCGGEFFYCNSTQLFNSTWTWNDTEVVNNTEKNINITLPCRIKQI



INMWQEVGKCMYAPPIKGQIRCSSNITGLLLTRDGGSSTNGTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRnVtGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQ



QQSNLLRAPEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLnAtD
















1683
H392
*d45-01dG5chim-v1v2-ZM233-
d0n0r45-
SOSIP, R6, 664,

BG505 chimera, V1V2 chimera,




I201C/A433C/R504N/V506T/L661N/L663T
01dG5/ZM233-
I201C/A433C/R504N/

glycan shielding at residues





V1v2/BG505
V506T/L661N/L663T

504, 668





chimera












AENLWVTVYYGVPVWKEATATLFCASDAKAYETEVHNVWATHACVPTDPNPQEVVLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLDCSTYNNTHNISKEMKICSFNMTTELRDKKR



KVNVLFYKLDLVPLTNSSNTTNYRLISCNTsVCTQACPKISFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENIKDNAKIIIVQLNETVEINCTR



PNNNTRKSIPIGPGRAFYTTGAIIGDIRQAHCNISKAKWENTLKQIARKLREHFKNETIAFNQsSGGDPEIVMHSFNCGGEFFYCNSTQLFNSTWTWNDTEVVNNTEKNINITLPCRIKQIINMWQEVGK



CMYAPPIKGQIRCSSNITGLLLTRDGGSSTNGTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRnVtGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAP



EAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLnAtD
















1684
H393
*d45-01dG5chim-v1v2-ZM233-degly3-
donor45-
SOSIP, R6, 664,

BG505 chimera, V1V2 chimera,




I201C/S364A/A433C/R504N/V506T/L661N/
01dG5/ZM233-
I201C/S364A/A433C/

glycan shielding at residues




L663T
V1v2/BG505
R504N/V506T/L661N/

504, 669





chimera
L663T











AENLWVTVYYGVPVWKEATATLFCASDAKAYETEVHNVWATHACVPTDPNPQEVVLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLDCSTYNNTHNISKEMKICSFNMTTELRDKKR



KVNVLFYKLDLVPLTNSSNTTNYRLISCNTsVCTQACPKISFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENIKDNAKIIIVQLNETVEINCTR



PNNNTRKSIPIGPGRAFYTTGAIIGDIRQAHCNISKAKWENTLKQIARKLREHFKNETIAFNQaSGGDPEIVMHSFNCGGEFFYCNSTQLFNSTWTWNDTEVVNNTEKNINITLPCRIKQIINMWQEVGK



CMYAPPIKGQIRCSSNITGLLLTRDGGSSTNGTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRnVtGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAP



EAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLnAtD
















1685
H394
*d45-01dG5chim-v1v2-ZM233-degly4-
donor45-
SOSIP, R6, 664,

BG505 chimera, V1V2 chimera,




S199A/201C/S364A/A433C/R504N/V506T/
01dG5/ZM233-
S199A/201C/S364A/A433

glycan shielding at residues




L661N/L663T
V1v2/BG505
C/R504N/V506T/L661N/

504, 670





chimera
L663T











AENLWVTVYYGVPVWKEATATLFCASDAKAYETEVHNVWATHACVPTDPNPQEVVLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLDCSTYNNTHNISKEMKICSFNMTTELRDKKR



KVNVLFYKLDLVPLTNSSNTTNYRLISCNTaVCTQACPKISFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENIKDNAKIIIVQLNETVEINCTR



PNNNTRKSIPIGPGRAFYTTGAIIGDIRQAHCNISKAKWENTLKQIARKLREHFKNETIAFNQaSGGDPEIVMHSFNCGGEFFYCNSTQLFNSTWTWNDTEVVNNTEKNINITLPCRIKQIINMWQEVGK



CMYAPPIKGQIRCSSNITGLLLTRDGGSSTNGTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRnVtGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAP



EAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLnAtD
















1686
H395
*426c-v1v2-WITO-degly4-
426c/WITO-
SOSIP, R6, 664,

BG505 chimera, V1V2 chimera,




S199A/I201C/A433C/N276D/N460D/N463D
V1v2/BG505
S199A/I201C/A433C/

glycan shielding at residues





chimera
N276D/N460D/N463D

504, 661









AENLWVTVYYGVPVWKEAKTTLFCASDAKAYEKEVHNVWATHACVPTDPNPQEVVLENVTENFNMWKNDMVDQMQEDVISIWDQSLKPCVKLTPLCVTLHCTNVTISSTNGSTANVTMREEMKNCSFNTT



TVIRDKIQKEYALFYKLDIVPIEGKNTNTGYRLINCNTATCTQACPKVTFDPIPIHYCAPAGYAILKCNNKTFNGKGPCNNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIVIRSKNLADNAKIIIVQLNK



SVEIVCTRPNNNTRRSIRIGPGQTFYATDIIGDIRQAYCNISGRNWSEAVNQVKKKLKEHFPHKNISFQSSSGGDLEITTHSFNCGGEFFYCNTSGLFNDTISNATIMLPCRIKQIINMWQEVGKCIYAP



PIKGNITCKSDITGLLLLRDGGNTANNAEIFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRvVGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLL



KLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIYGLLEESQNQQEKNEQDLLALD
















1687
H396
*426c-v1v2-WITO-degly3-
426c/WITO-
SOSIP, R6, 664,

BG505 chimera, V1V2 chimera,




I201C/A433C/N276D/N460D/N463D
V1v2/BG505
I201C/A433C/N276D/

glycan shielding at residues





chimera
N460D/N463D

504, 662









AENLWVTVYYGVPVWKEAKTTLFCASDAKAYEKEVHNVWATHACVPTDPNPQEVVLENVTENFNMWKNDMVDQMQEDVISIWDQSLKPCVKLTPLCVTLHCTNVTISSTNGSTANVTMREEMKNCSFNTT



TVIRDKIQKEYALFYKLDIVPIEGKNTNTGYRLINCNTsTCTQACPKVTFDPIPIHYCAPAGYAILKCNNKTFNGKGPCNNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIVIRSKNLADNAKIIIVQLNK



SVEIVCTRPNNNTRRSIRIGPGQTFYATDIIGDIRQAYCNISGRNWSEAVNQVKKKLKEHFPHKNISFQSSSGGDLEITTHSFNCGGEFFYCNTSGLFNDTISNATIMLPCRIKQIINMWQEVGKCIYAP



PIKGNITCKSDITGLLLLRDGGNTANNAEIFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRvVGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHL



LKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIYGLLEESQNQQEKNEQDLLALD
















1688
H397
*426c-v1v2-ZM233-degly4-
426c/ZM233-
SOSIP, R6, 664,

BG505 chimera, V1V2 chimera,




S199A/I201C/A433C/N276D/N460D/N463D
V1v2/BG505
S199A/I201C/A433C/

glycan shielding at residues





chimera
N276D/N460D/N463D

504, 663









AENLWVTVYYGVPVWKEAKTTLFCASDAKAYEKEVHNVWATHACVPTDPNPQEVVLENVTENFNMWKNDMVDQMQEDVISIWDQSLKPCVKLTPLCVTLDCSTYNNTHNISKEMKICSFNMTTELRDKKR



KVNVLFYKLDLVPLTNSSNTTNYRLISCNTATCTQACPKVTFDPIPIHYCAPAGYAILKCNNKTFNGKGPCNNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIVIRSKNLADNAKIIIVQLNKSVEIVCTR



PNNNTRRSIRIGPGQTFYATDIIGDIRQAYCNISGRNWSEAVNQVKKKLKEHFPHKNISFQSSSGGDLEITTHSFNCGGEFFYCNTSGLFNDTISNATIMLPCRIKQIINMWQEVGKCIYAPPIKGNITC



KSDITGLLLLRDGGNTANNAEIFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRvVGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLKLTVWGI



KQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD
















1689
H398
*426c-v1v2-ZM233-degly3-
426c/ZM233-
SOSIP, R6, 664,

BG505 chimera, V1V2 chimera,




I201C/A433C/N276D/N460D/N463D
V1v2/BG505
I201C/A433C/N276D/

glycan shielding at residues





chimera
N460D/N463D

504, 664









AENLWVTVYYGVPVWKEAKTTLFCASDAKAYEKEVHNVWATHACVPTDPNPQEVVLENVTENFNMWKNDMVDQMQEDVISIWDQSLKPCVKLTPLCVTLDCSTYNNTHNISKEMKICSFNMTTELRDKKR



KVNVLFYKLDLVPLTNSSNTTNYRLISCNTsTCTQACPKVTFDPIPIHYCAPAGYAILKCNNKTFNGKGPCNNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIVIRSKNLADNAKIIIVQLNKSVEIVCTR



PNNNTRRSIRIGPGQTFYATDIIGDIRQAYCNISGRNWSEAVNQVKKKLKEHFPHKNISFQSSSGGDLEITTHSFNCGGEFFYCNTSGLFNDTISNATIMLPCRIKQIINMWQEVGKCIYAPPIKGNITC



KSDITGLLLLRDGGNTANNAEIFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRvVGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLKLTVWGI



KQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD
















1690
H399
*d45-01dG5chim-v1v2-WITO-I201C/A433C
d0n0r45-
SOSIP, R6, 664,

BG505 chimera, V1V2 chimera,





01dG5/WITO-
I201C/A433C

glycan shielding at residues





V1v2/BG505


504, 665





chimera












AENLWVTVYYGVPVWKEATATLFCASDAKAYETEVHNVWATHACVPTDPNPQEVVLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLHCTNVTISSTNGSTANVTMREEMKNCSFNTT



TVIRDKIQKEYALFYKLDIVPIEGKNTNTGYRLINCNTsVCTQACPKISFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENIKDNAKIIIVQLNE



TVEINCTRPNNNTRKSIPIGPGRAFYTTGAIIGDIRQAHCNISKAKWENTLKQIARKLREHFKNETIAFNQsSGGDPEIVMHSFNCGGEFFYCNSTQLFNSTWTWNDTEVVNNTEKNINITLPCRIKQII



NMWQEVGKCMYAPPIKGQIRCSSNITGLLLTRDGGSSTNGTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQ



QSNLLRAPEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD
















1691
H400
*d45-01dG5chim-v1v2-WITO-degly3-
d0n0r45-
SOSIP, R6, 664,

BG505 chimera, V1V2 chimera,




I201C/S364A/A433C
01dG5/WITO-
I201C/S364A/A433C

glycan shielding at residues





V1v2/BG505


504, 666





chimera












AENLWVTVYYGVPVWKEATATLFCASDAKAYETEVHNVWATHACVPTDPNPQEVVLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLHCTNVTISSTNGSTANVTMREEMKNCSFNTT



TVIRDKIQKEYALFYKLDIVPIEGKNTNTGYRLINCNTsVCTQACPKISFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENIKDNAKIIIVQLNE



TVEINCTRPNNNTRKSIPIGPGRAFYTTGAIIGDIRQAHCNISKAKWENTLKQIARKLREHFKNETIAFNQaSGGDPEIVMHSFNCGGEFFYCNSTQLFNSTWTWNDTEVVNNTEKNINITLPCRIKQII



NMWQEVGKCMYAPPIKGQIRCSSNITGLLLTRDGGSSTNGTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQ



QSNLLRAPEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD
















1692
H401
*d45-01dG5chim-v1v2-WITO-degly4-
d0n0r45-
SOSIP, R6, 664,

BG505 chimera, V1V2 chimera,




S199A/I201C/S364A
01dG5/WITO-
S199A/I201C/S364A/

glycan shielding at residues





V1v2/BG505
A433C

504, 667





chimera












AENLWVTVYYGVPVWKEATATLFCASDAKAYETEVHNVWATHACVPTDPNPQEVVLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLHCTNVTISSTNGSTANVTMREEMKNCSFNTT



TVIRDKIQKEYALFYKLDIVPIEGKNTNTGYRLINCNTaVCTQACPKISFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENIKDNAKIIIVQLNE



TVEINCTRPNNNTRKSIPIGPGRAFYTTGAIIGDIRQAHCNISKAKWENTLKQIARKLREHFKNETIAFNQaSGGDPEIVMHSFNCGGEFFYCNSTQLFNSTWTWNDTEVVNNTEKNINITLPCRIKQII



NMWQEVGKCMYAPPIKGQIRCSSNITGLLLTRDGGSSTNGTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQ



QSNLLRAPEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD
















1693
H402
*d45-01dG5chim-v1v2-ZM233-I201C/A433C
d0n0r45-
SOSIP, R6, 664,

BG505 chimera, V1V2 chimera,





01dG5/ZM233-
I201C/A433C

glycan shielding at residues





V1v2/BG505


504, 668





chimera












AENLWVTVYYGVPVWKEATATLFCASDAKAYETEVHNVWATHACVPTDPNPQEVVLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLDCSTYNNTHNISKEMKICSFNMTTELRDKKR



KVNVLFYKLDLVPLTNSSNTTNYRLISCNTsVCTQACPKISFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENIKDNAKIIIVQLNETVEINCTR



PNNNTRKSIPIGPGRAFYTTGAIIGDIRQAHCNISKAKWENTLKQIARKLREHFKNETIAFNQsSGGDPEIVMHSFNCGGEFFYCNSTQLFNSTWTWNDTEVVNNTEKNINITLPCRIKQIINMWQEVGK



CMYAPPIKGQIRCSSNITGLLLTRDGGSSTNGTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAP



EAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD
















1694
H403
*d45-01dG5chim-v1v2-ZM233-degly3-
d0n0r45-
SOSIP, R6, 664,

BG505 chimera, V1V2 chimera,




I201C/S364A/A433C
01dG5/ZM233-
I201C/S364A/A433C

glycan shielding at residues





V1v2/BG505


504, 669





chimera












AENLWVTVYYGVPVWKEATATLFCASDAKAYETEVHNVWATHACVPTDPNPQEVVLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLDCSTYNNTHNISKEMKICSFNMTTELRDKKR



KVNVLFYKLDLVPLTNSSNTTNYRLISCNTsVCTQACPKISFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENIKDNAKIIIVQLNETVEINCTR



PNNNTRKSIPIGPGRAFYTTGAIIGDIRQAHCNISKAKWENTLKQIARKLREHFKNETIAFNQaSGGDPEIVMHSFNCGGEFFYCNSTQLFNSTWTWNDTEVVNNTEKNINITLPCRIKQIINMWQEVGK



CMYAPPIKGQIRCSSNITGLLLTRDGGSSTNGTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAP



EAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD
















1695
H404
*d45-01dG5chim-v1v2-ZM233-degly4-
donor45-
SOSIP, R6, 664,

BG505 chimera, V1V2 chimera,




S199A/201C/S364A/A433C
01dG5/ZM233-
S199A/201C/S364A/

glycan shielding at residues





V1v2/BG505
A433C

504, 670





chimera












AENLWVTVYYGVPVWKEATATLFCASDAKAYETEVHNVWATHACVPTDPNPQEVVLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLDCSTYNNTHNISKEMKICSFNMTTELRDKKR



KVNVLFYKLDLVPLTNSSNTTNYRLISCNTaVCTQACPKISFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENIKDNAKIIIVQLNETVEINCTR



PNNNTRKSIPIGPGRAFYTTGAIIGDIRQAHCNISKAKWENTLKQIARKLREHFKNETIAFNQaSGGDPEIVMHSFNCGGEFFYCNSTQLFNSTWTWNDTEVVNNTEKNINITLPCRIKQIINMWQEVGK



CMYAPPIKGQIRCSSNITGLLLTRDGGSSTNGTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAP



EAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD
















1696
H405
*ZM106.9-chim_DS_THS_v1v2-KER2018.11-
ZM106.9/BG505
V1V2SOSIP; 664; R6; 
V1V2 Swap





201C/D368R/433C/R504T/V506T/L661N/L663T
chimera
201C, D368R, 433C, 
KER2018.11, gly504-661







glycan504, glycan661











AENLWVTVYYGVPVWKEAKTTLFCASDAKSYEREVHNVWATHACVPTDPDPQELVMANVTENFNMWKNDMVDQMHEDIISLWDQSLKPCVKLTPLCVTLNCINANVTNSSMTNSSMMEGEIKNCSYNMTT



ELRDKKRKVFSLFYKLDVVPMNENNSEYRLISCNTSTCTQACPKVSFDPIPIHYCAPAGYAILKCNNKTFSGKGPCSNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENLTDNAKTIIVHLNKSVE



IECIRPGNNTRKSIRLGPGQTFYATGDVIGDIRKAYCKINGSEWNETLTKVSEKLKEYFNKTIRFAQHSGGRLEVTTHSFNCRGEFFYCNTSELFNSNATESNITLPCRIKQIINMWQGVGRCMYAPPIR



GEIKCTSNITGLLLTRDGGNNNNSTEEIFRPEGGNMRDNWRSELYKYKVVKIEPLGVAPTRCKRnvtGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLK



LTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLNATD
















1697
H406
*ZM106.9-chim_DS_THS_v1v2-CH070.1-
ZM106.9/BG505
V1V2SOSIP; 664; R6; 
V1V2 Swap





201C/D368R/433C/R504T/V506T/L661N/
chimera
201C, D368R, 433C, 
CH070.1, gly504-661





L663T

glycan504, glycan661











AENLWVTVYYGVPVWKEAKTTLFCASDAKSYEREVHNVWATHACVPTDPDPQELVMANVTENFNMWKNDMVDQMHEDIISLWDQSLKPCVKLTPLCVTLKCKDVSINNGNVSSSNGSTSHNNSSIDNETL



NEGMKEMKNCSFNATTVLRDKKQKVHALFYRLISCNTSTCTQACPKVSFDPIPIHYCAPAGYAILKCNNKTFSGKGPCSNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENLTDNAKTIIVHLNKS



VEIECIRPGNNTRKSIRLGPGQTFYATGDVIGDIRKAYCKINGSEWNETLTKVSEKLKEYFNKTIRFAQHSGGRLEVTTHSFNCRGEFFYCNTSELFNSNATESNITLPCRIKQIINMWQGVGRCMYAPP



IRGEIKCTSNITGLLLTRDGGNNNNSTEEIFRPEGGNMRDNWRSELYKYKVVKIEPLGVAPTRCKRnvtGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHL



LKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLNATD
















1698
H407
*ZM106.9-chim_DS_THS_v1v2-ZM233.6-
ZM106.9/BG505
V1V2SOSIP; 664; R6; 
V1V2 Swap





201C/D368R/433C/R504T/V506T/L661N/
chimera
201C, D368R, 433C,
ZM233.6, gly504-661





L663T

glycan504, glycan661











AENLWVTVYYGVPVWKEAKTTLFCASDAKSYEREVHNVWATHACVPTDPDPQELVMANVTENFNMWKNDMVDQMHEDIISLWDQSLKPCVKLTPLCVTLDCSTYNNTHNISKEMKICSFNMTTELRDKKR



KVNVLFYKLDLVPLTNSSNTTNYRLISCNTSTCTQACPKVSFDPIPIHYCAPAGYAILKCNNKTFSGKGPCSNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENLTDNAKTIIVHLNKSVEIECIR



PGNNTRKSIRLGPGQTFYATGDVIGDIRKAYCKINGSEWNETLTKVSEKLKEYFNKTIRFAQHSGGRLEVTTHSFNCRGEFFYCNTSELFNSNATESNITLPCRIKQIINMWQGVGRCMYAPPIRGEIKC



TSNITGLLLTRDGGNNNNSTEEIFRPEGGNMRDNWRSELYKYKVVKIEPLGVAPTRCKRnvtGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLKLTVWG



IKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLNATD
















1699
H408
*ZM106.9-chim_DS_THS_v1v2-Q23-
ZM106.9/BG505
V1V2SOSIP; 664; R6;
V1V2 Swap Q23, 





201C/D368R/433C/V506T/R504T/L661N/
chimera
201C, D368R, 433C,
gly504-661





L663T

glycan504, glycan661











AENLWVTVYYGVPVWKEAKTTLFCASDAKSYEREVHNVWATHACVPTDPDPQELVMANVTENFNMWKNDMVDQMHEDIISLWDQSLKPCVKLTPLCVTLHCTNVTSVNTTGDREGLKNCSFNMTTELRDK



RQKVYSLFYRLDIVPINENQGSEYRLISCNTSTCTQACPKVSFDPIPIHYCAPAGYAILKCNNKTFSGKGPCSNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENLTDNAKTIIVHLNKSVEIECI



RPGNNTRKSIRLGPGQTFYATGDVIGDIRKAYCKINGSEWNETLTKVSEKLKEYFNKTIRFAQHSGGRLEVTTHSFNCRGEFFYCNTSELFNSNATESNITLPCRIKQIINMWQGVGRCMYAPPIRGEIK



CTSNITGLLLTRDGGNNNNSTEEIFRPEGGNMRDNWRSELYKYKVVKIEPLGVAPTRCKRnvtGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLKLTVW



GIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLNATD
















1700
H409
*ZM106.9-chim_DS_THS_v1v2-A244-
ZM106.9/BG505
V1V2SOSIP; 664; R6; 
V1V2 Swap A244,





201C/D368R/433C/R504T/V506T/L661N/
chimera
201C, D368R, 433C,
gly504-661





L663T

glycan504, glycan661











AENLWVTVYYGVPVWKEAKTTLFCASDAKSYEREVHNVWATHACVPTDPDPQELVMANVTENFNMWKNDMVDQMHEDIISLWDQSLKPCVKLTPLCVTLHCTNANLTKANLTNVNNRTNVSNIIGNITDE



VRNCSFNMTTELRDKKQKVHALFYKLDIVPIEDNNDNSKYRLISCNTSTCTQACPKVSFDPIPIHYCAPAGYAILKCNNKTFSGKGPCSNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENLTDNA



KTIIVHLNKSVEIECIRPGNNTRKSIRLGPGQTFYATGDVIGDIRKAYCKINGSEWNETLTKVSEKLKEYFNKTIRFAQHSGGRLEVTTHSFNCRGEFFYCNTSELFNSNATESNITLPCRIKQIINMWQ



GVGRCMYAPPIRGElKCTSNITGLLLTRDGGNNNNSTEElFRPEGGNMRDNWRSELYKYKVVKIEPLGVAPTRCKRnvtGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNL



LRAPEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLNATD
















1701
H410
*ZM106.9-chim_DS_THS_v1v2-WITO-
ZM106.9/BG505 
V1V2SOSIP; 664; R6;
V1V2 Swap WITO, 





201C/D368R/433C/R504T/V506T/L661N/
chimera
201C, D368R, 433C, 
gly504-661





L663T

glycan504, glycan661











AENLWVTVYYGVPVWKEAKTTLFCASDAKSYEREVHNVWATHACVPTDPDPQELVMANVTENFNMWKNDMVDQMHEDIISLWDQSLKPCVKLTPLCVTLHCTNVTISSTNGSTANVTMREEMKNCSFNTT



TVIRDKIQKEYALFYKLDIVPIEGKNTNTGYRLISCNTSTCTQACPKVSFDPIPIHYCAPAGYAILKCNNKTFSGKGPCSNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENLTDNAKTIIVHLNK



SVEIECIRPGNNTRKSIRLGPGQTFYATGDVIGDIRKAYCKINGSEWNETLTKVSEKLKEYFNKTIRFAQHSGGRLEVTTHSFNCRGEFFYCNTSELFNSNATESNITLPCRIKQIINMWQGVGRCMYAP



PIRGElKCTSNITGLLLTRDGGNNNNSTEEIFRPEGGNMRDNWRSELYKYKVVKIEPLGVAPTRCKRnvtGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQH



LLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIYGLLEESQNQQEKNEQDLNATD
















1702
H411
*ZM106.9-chim_DS_THS_v1v2-Cap256-SU-
ZM106.9/BG505 
V1V2SOSIP; 664; R6; 
V1V2 Swap CAP256-SU,





201C/D368R/433C/R504T/V506T/L661N/
chimera
201C, D368R, 433C, 
gly504-661





L663T

glycan504, glycan661











AENLWVTVYYGVPVWKEAKTTLFCASDAKSYEREVHNVWATHACVPTDPDPQELVMANVTENFNMWKNDMVDQMHEDIISLWDQSLKPCVKLTPLCVTLNCSDAKVNINATYNGTREEIKNCSFNATTEL



RDKKKKEYALFYRLDIVPLNKEGNNNSEYRLISCNTSTCTQACPKVSFDPIPIHYCAPAGYAILKCNNKTFSGKGPCSNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENLTDNAKTIIVHLNKSV



EIECIRPGNNTRKSIRLGPGQTFYATGDVIGDIRKAYCKNGSEWNETLTKVSEKLKEYFNKTIRFAQHSGGRLEVTTHSFNCRGEFFYCNTSELFNSNATESNITLPCRIKQIINMWQGVGRCMYAPPIR



GEIKCTSNITGLLLTRDGGNNNNSTEEIFRPEGGNMRDNWRSELYKYKVVKIEPLGVAPTRCKRnvtGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLK



LTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLNATD
















1703
H412
*ZM106.9-chim_DS_THS_v1v2-T250.4-
ZM106.9/BG505 
V1V2SOSIP; 664; R6; 
V1V2 Swap T250.4,





201C/D368R/433C/R504T/V506T/L661N/
chimera
201C, D368R, 433C, 
gly504-661





L663T

glycan504, glycan661











AENLWVTVYYGVPVWKEAKTTLFCASDAKSYEREVHNVWATHACVPTDPDPQELVMANVTENFNMWKNDMVDQMHEDIISLWDQSLKPCVKLTPLCVTLDCQAFNSSSHTNSSIAMQEMKNCSFNVTTEL



RDKKKKEYSFFYKTDIEQINKNGRQYRLISCNTSTCTQACPKVSFDPIPIHYCAPAGYAILKCNNKTFSGKGPCSNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENLTDNAKTIIVHLNKSVEIE



CIRPGNNTRKSIRLGPGQTFYATGDVIGDIRKAYCKINGSEWNETLTKVSEKLKEYFNKTIRFAQHSGGRLEVTTHSFNCRGEFFYCNTSELFNSNATESNITLPCRIKQIINMWQGVGRCMYAPPIRGE



IKCTSNITGLLLTRDGGNNNNSTEElFRPEGGNMRDNWRSELYKYKVVKIEPLGVAPTRCKRnvtGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLKLT



VWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLNATD
















1704
H413
*ZM106.9-chim_DS_THS_v1v2-BB201.B42-
ZM106.9/BG505 
V1V2SOSIP; 664; R6;
V1V2 Swap BB201.B42, 





201C/D368R/433C/R504T/V506T/L661N/
chimera
201C, D368R, 433C,
gly504-661





L663T

glycan504, glycan661











AENLWVTVYYGVPVWKEAKTTLFCASDAKSYEREVHNVWATHACVPTDPDPQELVMANVTENFNMWKNDMVDQMHEDIISLWDQSLKPCVKLTPLCVTLECRNITGVNISEGKEEIKNCSFNITTELRDK



RKKVYSLFYRLDVVQIDEGDKNSTQYRLISCNTSTCTQACPKVSFDPIPIHYCAPAGYAILKCNNKTFSGKGPCSNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENLTDNAKTIIVHLNKSVEIE



CIRPGNNTRKSIRLGPGQTFYATGDVIGDIRKAYCKINGSEWNETLTKVSEKLKEYFNKTIRFAQHSGGRLEVTTHSFNCRGEFFYCNTSELFNSNATESNITLPCRIKQIINMWQGVGRCMYAPPIRGE



IKCTSNITGLLLTRDGGNNNNSTEEIFRPEGGNMRDNWRSELYKYKVVKIEPLGVAPTRCKRnvtGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLKLT



VWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGILLEESQNQQEKNEQDLNATD
















1705
H414
*cap256-su-chim_ds_THS-Avi
cap256-su
SOSIP, R6, 664, 








201C/433C











AENLWVTVYYGVPVWREAKTTLFCASDAKSYEKEVHNVWATHACVPTDPNPQELVLKNVTENFNMWKNDMVDQMHEDIISLWDQSLKPCVKLTPLCVTLNCSDAKVNINATYNGTREEIKNCSFNATTEL



RDKKKKEYALFYRLDIVPLNKEGNNNSEYRLINCNTSVCTQACPKVTFDPIPIHYCAPAGYAILKCNNKTFNGTGPCNNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTDNVKTIIVHLNESV



EINCTRPNNNTRKSIRIGPGQTFYATGDIIGDIRQAHCNISEIKWEKTLQRVSEKLREHFNKTIIFNQSSGGDLEITTHSFNCGGEFFYCNTSDLFFNKTFDETYSTGSNSTNSTITLPCRIKQIINMWQ



EVGRCMYASPIAGEITCKSNITGLLLTRDGGGNNSTEETFRPGGGNMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLL



RAPEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD
















1706
H415
*cap256-su-chim + int_ds_THS-Avi
cap256-su
SOSIP, R6, 664, 
Interacting residues







201C/433
between the gp41 and








gp120










AENLWVTVYYGVPVWKDAETTLFCASDAKSYEKEVHNVWATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLNCSDAKVNINATYNGTREEIKNCSFNATTEL



RDKKKKEYALFYRLDIVPLNKEGNNNSEYRLINCNTSVCTQACPKVTFDPIPIHYCAPAGFAILKCNNKTFNGTGPCNNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTDNVKTIIVHLNESV



EINCTRPNNNTRKSIRIGPGQTFYATGDIIGDIRQAHCNISEIKWEKTLQRVSEKLREHFNKTIIFNQSSGGDLEITTHSFNCGGEFFYCNTSDLFFNKTFDETYSTGSNSTNSTITLPCRIKQIINMWQ



EVGRCMYASPIAGEITCKSNITGLLLTRDGGGNNSTEETFRPGGGNMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLL



RAPEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD
















1707
H416
*426c-native_bg505-NCgp120 + gp41.SOSIP
426c/BG505
SOSIP; 664; R6







chimera












AENLWVTVYYGVPVWKEAKTTLFCASDAKAYEKEVHNVWATHACVPTDPNPQEVVLENVTENFNMWKNDMVDQMQEDVISIWDQSLKPCVKLTPLCVTLNCTNVNVTSNSTNVNSSSTDNTTLGEIKNCS



FDITTEIRDKTRKEYALFYRLDIVPLDNSSNPNSSNTYRLINCNTSTLTQACPKVTFDPIPIHYCAPAGYAILKCNNKTFNGKGPCNNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIVIRSKNLSDNAKI



IIVQLNKSVEIVCTRPNNNTRRSIRIGPGQTFYATDIIGDIRQAYCNISGRNWSEAVNQVKKKLKEHFPHKNISFQSSSGGDLEITTHSFNCGGEFFYCNTSGLFNDTISNATIMLPCRIKQIINMWQEV



GKAIYAPPIKGNITCKSDITGLLLLRDGGNTTNNTEIFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRA



PEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD
















1708
H417
*426c-del276-460_bg505-NCgp120 +
426c/BG505 
SOSIP; 664; R6
removal of glycan 276





gp41.SOSIP
chimera












AENLWVTVYYGVPVWKEAKTTLFCASDAKAYEKEVHNVWATHACVPTDPNPQEVVLENVTENFNMWKNDMVDQMQEDVISIWDQSLKPCVKLTPLCVTLNCTNVNVTSNSTNVNSSSTDNTTLGEIKNCS



FDITTEIRDKTRKEYALFYRLDIVPLDNSSNPNSSNTYRLINCNTSTLTQACPKVTFDPIPIHYCAPAGYAILKCNNKTFNGKGPCNNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIVIRSKNLaDNAKI



IIVQLNKSVEIVCTRPNNNTRRSIRIGPGQTFYATDIIGDIRQAYCNISGRNWSEAVNQVKKKLKEHFPHKNISFQSSSGGDLEITTHSFNCGGEFFYCNTSGLFNDTISNATIMLPCRIKQIINMWQEV



GKAIYAPPIKGNITCKSDITGLLLLRDGGNTaNNTEIFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRA



PEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD
















1709
H418
*426c-del276_bg505-NCgp120 + gp41.SOSIP
426c/BG505 
SOSIP; 664
removal of glycan 276






chimera












AENLWVTVYYGVPVWKEAKTTLFCASDAKAYEKEVHNVWATHACVPTDPNPQEVVLENVTENFNMWKNDMVDQMQEDVISIWDQSLKPCVKLTPLCVTLNCTNVNVTSNSTNVNSSSTDNTTLGEIKNCS



FDITTEIRDKTRKEYALFYRLDIVPLDNSSNPNSSNTYRLINCNTSTLTQACPKVTFDPIPIHYCAPAGYAILKCNNKTFNGKGPCNNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIVIRSKNLaDNAKI



IIVQLNKSVEIVCTRPNNNTRRSIRIGPGQTFYATDIIGDIRQAYCNISGRNWSEAVNQVKKKLKEHFPHKNISFQSSSGGDLEITTHSFNCGGEFFYCNTSGLFNDTISNATIMLPCRIKQIINMWQEV



GKAIYAPPIKGNITCKSDITGLLLLRDGGNTTNNTEIFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRA



PEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD
















1710
H419
*426c-del276-460_DS bg505-NCgp120 +
426c/BG505
SOSIP, R6, 664, 
removal of glycan 276





gp41.SOSIP
chimera
201C/433C
and glycan 460










AENLWVTVYYGVPVWKEAKTTLFCASDAKAYEKEVHNVWATHACVPTDPNPQEVVLENVTENFNMWKNDMVDQMQEDVISIWDQSLKPCVKLTPLCVTLNCTNVNVTSNSTNVNSSSTDNTTLGEIKNCS



FDITTEIRDKTRKEYALFYRLDIVPLDNSSNPNSSNTYRLINCNTSTCTQACPKVTFDPIPIHYCAPAGYAILKCNNKTFNGKGPCNNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIVIRSKNLaDNAKI



IIVQLNKSVEIVCTRPNNNTRRSIRIGPGQTFYATDIIGDIRQAYCNISGRNWSEAVNQVKKKLKEHFPHKNISFQSSSGGDLEITTHSFNCGGEFFYCNTSGLFNDTISNATIMLPCRIKQIINMWQEV



GKCIYAPPIKGNITCKSDITGLLLLRDGGNTaNNTEIFRPGGGDMRDNWRSELYKYKVV1KIEPLGVAPTRCKRRVVGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLR



APEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD
















1711
H420
*426c-de1276 DS bg505-NCgp120 +
426c/BG505 
SOSIP, R6, 664, 
removal of glycan 276





gp41.SOSIP
chimera
201C/433C











AENLWVTVYYGVPVWKEAKTTLFCASDAKAYEKEVHNVWATHACVPTDPNPQEVVLENVTENFNMWKNDMVDQMQEDVISIWDQSLKPCVKLTPLCVTLNCTNVNVTSNSTNVNSSSTDNTTLGEIKNCS



FDITTEIRDKTRKEYALFYRLDIVPLDNSSNPNSSNTYRLINCNTSTCTQACPKVTFDPIPIHYCAPAGYAILKCNNKTFNGKGPCNNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIVIRSKNLaDNAKI



IIVQLNKSVEIVCTRPNNNTRRSIRIGPGQTFYATDIIGDIRQAYCNISGRNWSEAVNQVKKKLKEHFPHKNISFQSSSGGDLEITTHSFNCGGEFFYCNTSGLFNDTISNATIMLPCRIKQIINMWQEV



GKCIYAPPIKGNITCKSDITGLLLLRDGGNTTNNTEIFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRA



PEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD
















1712
H421
*426c-native DS bg505-NCgp120 +
426c/BG505 
SOSIP, R6, 664, 






gp41.SOSIP
chimera
201C/433C











AENLWVTVYYGVPVWKEAKTTLFCASDAKAYEKEVHNVWATHACVPTDPNPQEVVLENVTENFNMWKNDMVDQMQEDVISIWDQSLKPCVKLTPLCVTLNCTNVNVTSNSTNVNSSSTDNTTLGEIKNCS



FDITTEIRDKTRKEYALFYRLDIVPLDNSSNPNSSNTYRLINCNTSTCTQACPKVTFDPIPIHYCAPAGYAILKCNNKTFNGKGPCNNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIVIRSKNLSDNAKI



IIVQLNKSVEIVCTRPNNNTRRSIRIGPGQTFYATDIIGDIRQAYCNISGRNWSEAVNQVKKKLKEHFPHKNISFQSSSGGDLEITTHSFNCGGEFFYCNTSGLFNDTISNATIMLPCRIKQIINMWQEV



GKCIYAPPIKGNITCKSDITGLLLLRDGGNTTNNTEIFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRA



PEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD
















1713
H422
*426c-d3GLY-SUstrC_bg505-NCgp120 +
426c/BG505 
SOSIP; 664; R6
Introduction of cap256





gp41.SOSIP
chimera

su strand c










AENLWVTVYYGVPVWKEAKTTLFCASDAKAYEKEVHNVWATHACVPTDPNPQEVVLENVTENFNMWKNDMVDQMQEDVISIWDQSLKPCVKLTPLCVTLNCTNVNVTSNSTNVNSSSTDNTTLGEIKNCS



FnattelrdkkkKEYALFYRLDIVPLDNSSNPNSSNTYRLINCNTSTLTQACPKVTFDPIPIHYCAPAGYAILKCNNKTFNGKGPCNNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIVIRSKNLaDNAKI



IIVQLNKSVEIVCTRPNNNTRRSIRIGPGQTFYATDIIGDIRQAYCNISGRNWSEAVNQVKKKLKEHFPHKNISFQSSSGGDLEITTHSFNCGGEFFYCNTSGLFNDTISNATIMLPCRIKQIINMWQEV



GKAIYAPPIKGNITCKSDITGLLLLRDGGNTaNNaElFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRA



PEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD
















1714
H423
*426c-d3GLY-SUstrC_DS bg505-
426c/BG505 
SOSIP, R6, 664, 
Introduction of cap256





NCgp120 + 30gp41.SOSIP
chimera
201C/433C
su strand c










AENLWVTVYYGVPVWKEAKTTLFCASDAKAYEKEVHNVWATHACVPTDPNPQEVVLENVTENFNMWKNDMVDQMQEDVISIWDQSLKPCVKLTPLCVTLNCTNVNVTSNSTNVNSSSTDNTTLGEIKNCS



FnattelrdkkkKEYALFYRLDIVPLDNSSNPNSSNTYRLINCNTSTCTQACPKVTFDPIPIHYCAPAGYAILKCNNKTFNGKGPCNNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIVIRSKNLaDNAKI



IIVQLNKSVEIVCTRPNNNTRRSIRIGPGQTFYATDIIGDIRQAYCNISGRNWSEAVNQVKKKLKEHFPHKNISFQSSSGGDLEITTHSFNCGGEFFYCNTSGLFNDTISNATIMLPCRIKQIINMWQEV



GKCIYAPPIKGNITCKSDITGLLLLRDGGNTaNNaElFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRA



PEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD
















1715
H424
*703010505.TF-chim_d7324, R6, 664,
703010505.TF/
SOSIP, R6, 664
I201C/A433C





I201C/A433C
BG505 chimera












AENLWVTVYYGVPVWKEAKTTLFCASDAKAYEKEVHNVWATHACVPTDPNPQEMVLKNVTENFNMWKNDMVDQMHEDVISLWDQSLKPCVKLTPLCVTLNCTNATASNSSIIEGMKNCSFNITTELRDKR



EKKNALFYKLDIVQLDGNSSQYRLINCNTSVITQACPKVSFDPIPIHYCAPAGYAILKCNNKTFTGTGPCNNVSTVQCTHGIKPVVSTQLLLNGSLAEGEIIIRSENITNNVKTIIVHLNESVKIECTRP



NNKTRTSIRIGPGQAFYATGQVIGDIREAYCNINESKWNETLQRVSKKLKEYFPHKNITFQPSSGGDLEITTHSFNCGGEFFYCNTSSLFNRTYMANSTDMANSTETNSTRTITIHCRIKQIINMWQEVG



RAMYAPPIAGNITCISNITGLLLTRDGGKNNTETFRPGGGNMKDNWRSELYKYKVVKCeIEPLGVAPTRCKRRVVGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAP



EAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD
















1716
H425
703010505.TF-chim + int_d7324, R6, 664,
703010505.TF/
SOSIP, R6, 664
I201C/A433C
interface mutations




I201C/A433C
BG505 chimera








1717
H426
703010505.TF_cl-small-sel_d7324, R6,
703010505.TF/
SOSIP, R6, 664
I201C/A433C





664, I201C/A433C
BG505 chimera








1718
H427
703010505.TF_cl1-2_d7324, R6, 664,
703010505.TF/
SOSIP, R6, 664
I201C/A433C





I201C/A433C
BG505 chimera








1719
H428
703010505.TF_cl1_0324, R6, 664,
703010505.TF/
SOSIP, R6, 664
I201C/A433C





I201C/A433C
BG505 chimera








1720
H429
703010505.TF-chim_d7324_tad, R6, 664,
703010505.TF/
SOSIP, R6, 664
I201C/A433C
trimer association domain




I201C/A433C/E47D/K49E/V65K/E106T/
BG505 chimera


mutations




E429R/R432Q/E500R









1721
H430
703010505.TF_cl-small-sel_d7324_tad,
703010505.TF/
SOSIP, R6, 664
I201C/A433C
trimer association domain




R6, 664, I201C/A433C/E47D/K49E/V65K/
BG505 chimera


mutations




E106T/E429R/R432Q/E500R









1722
H431
703010505.TF_cl1-2_d7324_tad, R6, 664,
703010505.TF/
SOSIP, R6, 664
I201C/A433C
trimer association domain




I201C/A433C/E47D/K49E/V65K/E106T/
BG505 chimera


mutations




E429R/R432Q/E500R









1723
H432
703010505.TF_cl1_0324_tad, R6, 664,
703010505.TF/
SOSIP, R6, 664
I201C/A433C
trimer association domain




I201C/A433C/E47D/K49E/V65K/E106T/
BG505 chimera


mutations




E429R/R432Q/E5OOR









1724
H433
703010505.TF-chim + int_d7324_tad, R6, 
703010505.TF/
SOSIP, R6, 664
I201C/A433C
interface mutations, trimer




664, I201C/A433C/E47D/K49E/V65K/E106T/
BG505 chimera







E429R/R432Q/E500R



association domain mutations





1725
H434
JRFLgp140.6R.SOSIP.664.E168K, BG505
JRFL/BG505 chim
SOSIP, R6, 664
E168K, I201C, A433C,
DS




gp41 chim, I201C, A433C,









1726
H435
JRFLgp140.6R.SOSIP.664.E168K, BG505 
JRFL/BG505 chim
SOSIP, R6, 664
E168K, + interface





gp41 chim, + int I201C, A433C,


residues, I201C, A433C,






1727
H436
JRFLgp140.6R.SOSIP.664.E168K, BG505
JRFL/BG505 chim
SOSIP, R6, 664
E168K,, I201C, 
V2 from BG505




gp41 chim, I201C, A433C,_v2


A433C,_BG505 V2








(residues 154-205),






1728
H437
JRFLgp140.6R.SOSIP.664.E168K, BG505 
JRFL/BG505 chim
SOSIP, R6, 664
E168K,, I201C, A433C,_
V1, 191-205 from BG505




gp41 chim, I201C, A433C,_v1_191-205


BG505 V1 (residues








119-153),_191-205






1729
H438
JRFLgp140.6R.SOSIP.664.E168K, BG505 
JRFL/BG505 chim
SOSIP, R6, 664
E168K,, + interface
V1 from BG505




gp41 chim, + int I201C, A433C,_v1


residues, I201C, A433C,_








BG505 V1 (residues








119-153),






1730
H439
JRFLgp140.6R.SOSIP.664.E168K, BG505
JRFL/BG505 chim
SOSIP, R6, 664
E168K,, I201C,
166-173 from BG505




gp41 chim, I201C, A433C,_strC


A433C,_strC






1731
H440
JRFLgp140.6R.SOSIP.664.E168K, BG505
JRFL/BG505 chim
SOSIP, R6, 664
E168K,, + interface 
166-173 from BG505




gp41 chim, + int I201C, A433C,_strC


residues, I201C, 








A433C,_strC






1732
H441
*JRFLgp140.6R.SOSIP.664.E168K, BG505 
JRFL/BG505 chim
SOSIP, R6, 664
E168K, I201C, A433C,
V2, V3 from BG505




gp41 chim, I201C, A433C,_v2_v3


BG505 V2 (residues 154-








205), _BG505 V3 (residues








296-331),










AENLWVTVYYGVPVWKEATTTLFCASDAKAYDTEVHNVWATHACVPTDPNPQEVVLENVTEHFNMWKNNMVEQMQEDIISLWDQSLKPCVKLTPLCVTLNCKDVNATNTTNDSEGTMERGELKNCSFNMT



TELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQACPKISFEPIPIHYCAPAGFAILKCNDKTFNGKGPCKNVSTVQCTHGIRPVVSTQLLLNGSLAEEEVVIRSDNFTNNAKTI



IVQLKESVEINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNISRAKWNDTLKQIVIKLREQFENKTIVFNHSSGGDPEIVMHSFNCGGEFFYCNSTQLFNSTWNNNTEGSNNTEGNTITLPCRI



KQIINMWQEVGKCMYAPPIRGQIRCSSNITGLLLTRDGGINENGTEIFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGI



VQQQSNLLRAPEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD
















1733
H442
JRFLgp140.6R.SOSIP.664.E168K, BG505 
JRFL/BG505 chim
SOSIP, R6, 664
E168K, I201C, A433C,_
V1, 191-205, 166-173 from 




gp41 chim, I201C, A433C,_v1_strC_


BG505 V1 (residues 119-
BG505




191-205


153), _strC_191-205






1734
H443
JRFLgp140.6R.SOSIP.664.E168K, BG505
JRFL/BG505 chim
SOSIP, R6, 664
E168K,, + interface
V1, 166-173 from BG505




gp41 chim, + int I201C, A433C,_v1_strC


residues, I201C, A433C,_








BG505 V1 (residues








119-153),_strC






1735 
H444
*JRFLgp140.6R.SOSIP.664.E168K, BG505 
JRFL/BG505 chim
SOSIP, R6, 664
E168K, I201C, A433C,_
V3 from BG505




gp41 chim, I201C, A433C,_v3


BG505 V3 (residues 296-








331),










AENLWVTVYYGVPVWKEATTTLFCASDAKAYDTEVHNVWATHACVPTDPNPQEVVLENVTEHFNMWKNNMVEQMQEDIISLWDQSLKPCVKLTPLCVTLNCKDVNATNTTNDSEGTMERGEIKNCSFNIT



TSIRDKVQKEYALFYKLDVVPIDNNNTSYRLISCDTSVCTQACPKISFEPIPIHYCAPAGFAILKCNDKTFNGKGPCKNVSTVQCTHGIRPVVSTQLLLNGSLAEEEVVIRSDNFTNNAKTIIVQLKESV



EINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNISRAKWNDTLKQIVIKLREQFENKTIVFNHSSGGDPEIVMHSFNCGGEFFYCNSTQLFNSTWNNNTEGSNNTEGNTITLPCRIKQIINMWQ



EVGKCMYAPPIRGQIRCSSNITGLLLTRDGGINENGTEIFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLL



RAPEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD
















1736
H445
*JRFLgp140.6R.SOSIP.664.E168K, BG505 
JRFL/BG505 chim
SOSIP, R6, 664
E168K, + interface
166-173, V3 from BG505




gp41 chim, + int I201C, A433C,_strC_v3


residue set A, I201C,








A433C,_strC_BG505 V3








(residues 296-331),










AENLWVTVYYGVPVWKDAETTLFCASDAKAYDTEVHNVWATHACVPTDPNPQEIHLENVTEHFNMWKNNMVEQMQTDIISLWDQSLKPCVKLTPLCVTLNCKDVNATNTTNDSEGTMERGEIKNCSFNIT



TSIRDKKQKVYALFYKLDVVPIDNNNTSYRLISCDTSVCTQACPKISFEPIPIHYCAPAGFAILKCNDKTFNGKGPCKNVSTVQCTHGIRPVVSTQLLLNGSLAEEEVVIRSDNFTNNAKTIIVQLKESV



EINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNISRAKWNDTLKQIVIKLREQFENKTIVFNHSSGGDPEIVMHSFNCGGEFFYCNSTQLFNSTWNNNTEGSNNTEGNTITLPCRIKQIINMWQ



EVGKCMYAPPIRGQIRCSSNITGLLLTRDGGINENGTEIFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLL



RAPEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD
















1737
H446
JRFLgp140.6R.SOSIP.664.E168K, BG505 
JRFL/BG505 chim
SOSIP, R6, 664
E168K, + interface
V2 from BG505




gp41 chim, + int I201C, A433C,_v2


residues, I201C, A433C,_








BG505 V2 (residues 154-








205),






1738
H447
*JRFLgp140.6R.SOSIP.664.E168K, BG505 
JRFL/BG505 chim
SOSIP, R6, 664
E168K, + interface
191-205, V3 from BG505




gp41 chim, + int I201C, A433C,_191-


residue set A, I201C,





205_v3


A433C,_191-205_BG505 V3








(residues 296-331),










AENLWVTVYYGVPVWKDAETTLFCASDAKAYDTEVHNVWATHACVPTDPNPQEIHLENVTEHFNMWKNNMVEQMQTDIISLWDQSLKPCVKLTPLCVTLNCKDVNATNTTNDSEGTMERGEIKNCSFNIT



TSIRDKVQKEYALFYKLDVVPIDNNNTSYRLINCNTSAITQACPKISFEPIPIHYCAPAGFAILKCNDKTFNGKGPCKNVSTVQCTHGIRPVVSTQLLLNGSLAEEEVVIRSDNFTNNAKTIIVQLKESV



EINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNISRAKWNDTLKQIVIKLREQFENKTIVFNHSSGGDPEIVMHSFNCGGEFFYCNSTQLFNSTWNNNTEGSNNTEGNTITLPCRIKQIINMWQ



EVGKCMYAPPIRGQIRCSSNITGLLLTRDGGINENGTEIFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLL



RAPEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD
















1739
H448
*JRFLgp140.6R.SOSIP.664.E168K, BG505 
JRFL/BG505 chim
SOSIP, R6, 664
E168K, + interface
V1, V3 from BG505




gp41 chim, + int I201C, A433C,_v1_v3


residue set A, I201C,








A433C,_BG505 V1 (residues








119-153),_ BG505 V3








(residues 296-331),










AENLWVTVYYGVPVWKDAETTLFCASDAKAYDTEVHNVWATHACVPTDPNPQEIHLENVTEHFNMWKNNMVEQMQTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGElKNCSFNITTSIRDK



VQKEYALFYKLDVVPIDNNNTSYRLISCDTSVCTQACPKISFEPIPIHYCAPAGFAILKCNDKTFNGKGPCKNVSTVQCTHGIRPVVSTQLLLNGSLAEEEVVIRSDNFTNNAKTIIVQLKESVEINCTR



PNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNISRAKWNDTLKQIVIKLREQFENKTIVFNHSSGGDPEIVMHSFNCGGEFFYCNSTQLFNSTWNNNTEGSNNTEGNTITLPCRIKQIINMWQEVGKCM



YAPPIRGQIRCSSNITGLLLTRDGGINENGTEIFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQ



QHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD
















1740
H449
*JRFLgp140.6R.SOSIP.664.E168K, BG505 
JRFL/BG505 chim
SOSIP, R6, 664
E168K, I201C, A433C,_
166-173, V3 from BG505




gp41 chim, I201C, A433C,_strC_v3


strC_BG505 V3








(residues 296-331),










AENLWVTVYYGVPVWKEATTTLFCASDAKAYDTEVHNVWATHACVPTDPNPQEVVLENVTEHFNMWKNNMVEQMQEDIISLWDQSLKPCVKLTPLCVTLNCKDVNATNTTNDSEGTMERGElKNCSFNIT



TSIRDKKQKVYALFYKLDVVPIDNNNTSYRLISCDTSVCTQACPKISFEPIPIHYCAPAGFAILKCNDKTFNGKGPCKNVSTVQCTHGIRPVVSTQLLLNGSLAEEEVVIRSDNFTNNAKTIIVQLKESV



EINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNISRAKWNDTLKQIVIKLREQFENKTIVFNHSSGGDPEIVMHSFNCGGEFFYCNSTQLFNSTWNNNTEGSNNTEGNTITLPCRIKQIINMWQ



EVGKCMYAPPIRGQIRCSSNITGLLLTRDGGINENGTEIFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLL



RAPEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD
















1741 
H450
*JRFLgp140.6R.SOSIP.664.E168K, BG505 
JRFL/BG505 chim
SOSIP, R6, 664
E168K, + interface
V3 from BG505




gp41 chim, + int I201C, A433C,_v3


residue set A, I201C,








A433C,_BG505 V3 (residues








296-331),










AENLWVTVYYGVPVWKDAETTLFCASDAKAYDTEVHNVWATHACVPTDPNPQEIHLENVTEHFNMWKNNMVEQMQTDIISLWDQSLKPCVKLTPLCVTLNCKDVNATNTTNDSEGTMERGEIKNCSFNIT



TSIRDKVQKEYALFYKLDVVPIDNNNTSYRLISCDTSVCTQACPKISFEPIPIHYCAPAGFAILKCNDKTFNGKGPCKNVSTVQCTHGIRPVVSTQLLLNGSLAEEEVVIRSDNFTNNAKTIIVQLKESV



EINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNISRAKWNDTLKQIVIKLREQFENKTIVFNHSSGGDPEIVMHSFNCGGEFFYCNSTQLFNSTWNNNTEGSNNTEGNTITLPCRIKQIINMWQ



EVGKCMYAPPIRGQIRCSSNITGLLLTRDGGINENGTEIFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLL



RAPEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD
















1742
H451
*JRFLgp140.6R.SOSIP.664.E168K, BG505 
JRFL/BG505 chim
SOSIP, R6, 664
E168K, + interface
V2, V3 from BG505




gp41 chim, + int I201C, A433C,_v2_v3


residue set A, I201C,








A433C,_BG505 V2 (residues








154-205),_ BG505 V3








(residues 296-331)










AENLWVTVYYGVPVWKDAETTLFCASDAKAYDTEVHNVWATHACVPTDPNPQEIHLENVTEHFNMWKNNMVEQMQTDIISLWDQSLKPCVKLTPLCVTLNCKDVNATNTTNDSEGTMERGELKNCSFNMT



TELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQACPKISFEPIPIHYCAPAGFAILKCNDKTFNGKGPCKNVSTVQCTHGIRPVVSTQLLLNGSLAEEEVVIRSDNFTNNAKTI



IVQLKESVEINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNISRAKWNDTLKQIVIKLREQFENKTIVFNHSSGGDPEIVMHSFNCGGEFFYCNSTQLFNSTWNNNTEGSNNTEGNTITLPCRI



KQIINMWQEVGKCMYAPPIRGQIRCSSNITGLLLTRDGGINENGTEIFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGI



VQQQSNLLRAPEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD



















1743
H452
JRFLgp140.6R.SOSIP.664.E168K, BG505
JRFL/BG505 chim
SOSIP, R6, 664
E168K, I201C, A433C,_
V1, 166-173, 191-205, V3 from 




gp41 chim, I201C, A433C,_v1_strC_


BG505 V1 (residues 119-
BG505




191-205_v3


153), _strC_191-205_








BG505 V3 (residues








296-331),






1744
H453
*JRFLgp140.6R.SOSIP.664.E168K, BG505 
JRFL/BG505 chim
SOSIP, R6, 664
E168K, + interface
V1, 166-173, V3 from BG505




gp41 chim, + int I201C, A433C,_


residue set A, I201C,





v1_strC_v3


A433C,_BG505 V1 (residues








119-153),_strC_ BG505 V3








(residues 296-331)










AENLWVTVYYGVPVWKDAETTLFCASDAKAYDTEVHNVWATHACVPTDPNPQEIHLENVTEHFNMWKNNMVEQMQTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGEIKNCSFNITTSIRDK



KQKVYALFYKLDVVPIDNNNTSYRLISCDTSVCTQACPKISFEPIPIHYCAPAGFAILKCNDKTFNGKGPCKNVSTVQCTHGIRPVVSTQLLLNGSLAEEEVVIRSDNFTNNAKTIIVQLKESVEINCTR



PNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNISRAKWNDTLKQIVIKLREQFENKTIVFNHSSGGDPEIVMHSFNCGGEFFYCNSTQLFNSTWNNNTEGSNNTEGNTITLPCRIKQIINMWQEVGKCM



YAPPIRGQIRCSSNITGLLLTRDGGINENGTEIFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQ



QHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD
















1745
H454
JRFLgp140.6R.SOSIP.664.E168K, BG505
JRFL/BG505 chim
SOSIP, R6, 664
E168K, I201C, A433C,_
191-205 from BG505




gp41 chim, I201C, A433C,_191-205


191-205






1746
H455
JRFLgp140.6R.SOSIP.664.E168K, BG505 
JRFL/BG505 chim
SOSIP, R6, 664
E168K, + interface 
191-205 from BG505




gp41 chim, + int I201C, A433C,_191-205


residues, I201C, A433C,_








191-205






1747
H456
JRFLgp140.6R.SOSIP.664.E168K, BG505
JRFL/BG505 chim
SOSIP, R6, 664
E168K, I201C, A433C,_
V1, V2 from BG505




gp41 chim, I201C, A433C,_v1_v2


BG505 V1 (residues 119-








153), _BG505 V2








(residues 154-205),






1748
H457
JRFLgp140.6R.SOSIP.664.E168K, BG505
JRFL/BG505 chim
SOSIP, R6, 664
E168K, I201C, A433C,_
V1 from BG505




gp41 chim, I201C, A433C,_v1


BG505 V1 (residues 119-








153),






1749
H458
JRFLgp140.6R.SOSIP.664.E168K, BG505 
JRFL/BG505 chim
SOSIP, R6, 664
E168K, + interface
V1, 191-205 from BG505




gp41 chim, + int I201C, A433C,_


residue set A, I201C, 





v1_191-205


A433C,_BG505 V1 (residues








119-153),_191-205






1750
H459
JRFLgp140.6R.SOSIP.664.E168K, BG505
JRFL/BG505 chim
SOSIP, R6, 664
E168K, I201C, A433C,_
166-173, 191-205 from BG505




gp41 chim, I201C, A433C,_strC_191-205


strC_191-205






1751
H460
JRFLgp140.6R.SOSIP.664.E168K, BG505 
JRFL/BG505 chim
SOSIP, R6, 664
E168K, + interface
166-173, 191-205 from BG505




gp41 chim, + int I201C, A433C,_strC_


residue set A, I201C,





191-205


A433C,_strC_191-205






1752
H461
JRFLgp140.6R.SOSIP.664.E168K, BG505
JRFL/BG505 chim
SOSIP, R6, 664
E168K,I201C, A433C,_BG505
V1, V2, V3 from BG505




gp41 chim, I201C, A433C,_v1_v2_v3


V1 (residues 119-153),_








BG505 V2 (residues 154-








205),_ BG505 V3 (residues








296-331)










AENLWVTVYYGVPVWKEATTTLFCASDAKAYDTEVHNVWATHACVPTDPNPQEVVLENVTEHFNMWKNNMVEQMQEDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDK



KQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQACPKISFEPIPIHYCAPAGFAILKCNDKTFNGKGPCKNVSTVQCTHGIRPVVSTQLLLNGSLAEEEVVIRSDNFTNNAKTIIVQLKE



SVEINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNISRAKWNDTLKQIVIKLREQFENKTIVFNHSSGGDPEIVMHSFNCGGEFFYCNSTQLFNSTWNNNTEGSNNTEGNTITLPCRIKQIINM



WQEVGKCMYAPPIRGQIRCSSNITGLLLTRDGGINENGTEIFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSN



LLRAPEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD
















1753
H462
JRFLgp140.6R.SOSIP.664.E168K, BG505 
JRFL/BG505 chim
SOSIP, R6, 664
E168K, I201C, A433C,_
V1, 166-173 from BG505




gp41 chim, I201C, A433C,_v1_strC


BG505 V1 (residues 119-








153), _strC






1754
H463
JRFLgp140.6R.SOSIP.664.E168K, BG505 
JRFL/BG505 chim
SOSIP, R6, 664
E168K, + interface 
V1, 166-173, 191-205 from BG505




gp41 chim, + int I201C, A433C,_


residue set A, I201C,





v1_strC_191-205


A433C,_BG505 V1 (residues








119-153), _strC_191-205






1755
H464
JRFLgp140.6R.SOSIP.664.E168K, BG505 
JRFL/BG505 chim
SOSIP, R6, 664
E168K,I201C, A433C,_
166-173, 191-205, V3 from BG505




gp41 chim, I201C, A433C,_strC_191-


strC_191-205_ BG505 V3





205_v3


(residues 296-331),






1756
H465
JRFLgp140.6R.SOSIP.664.E168K, BG505
JRFL/BG505 chim
SOSIP, R6, 664
E168K, I201C, A433C,_
V1, 191-205, V3 from BG505




gp41 chim, I201C, A433C,_v1_191-205_v3


BG505 V1 (residues 119-








153), _191-205_BG505 V3 








(residues 296-331),






1757
H466
JRFLgp140.6R.SOSIP.664.E168K, BG505
JRFL/BG505 chim
SOSIP, R6, 664
E168K, + interface 
V1, V2 from BG505




gp41 chim, + int I201C, A433C,_v1_v2


residues, I201C, A433C,_








BG505 V1 (residues 119-








153),_BG505 V2 (residues








154-205),






1758
H467
*JRFLgp140.6R.SOSIP.664.E168K, BG505 
JRFL/BG505 chim
SOSIP, R6, 664
E168K, I201C, A433C,_
V1, V3 from BG505




gp41 chim, I201C, A433C,_v1_v3


BG505 V1 (residues 119-








153), _BG505 V3 (residues








296-331),










AENLWVTVYYGVPVWKEATTTLFCASDAKAYDTEVHNVWATHACVPTDPNPQEVVLENVTEHFNMWKNNMVEQMQEDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGEIKNCSFNITTSIRDK



VQKEYALFYKLDVVPIDNNNTSYRLISCDTSVCTQACPKISFEPIPIHYCAPAGFAILKCNDKTFNGKGPCKNVSTVQCTHGIRPVVSTQLLLNGSLAEEEVVIRSDNFTNNAKTIIVQLKESVEINCTR



PNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNISRAKWNDTLKQIVIKLREQFENKTIVFNHSSGGDPEIVMHSFNCGGEFFYCNSTQLFNSTWNNNTEGSNNTEGNTITLPCRIKQIINMWQEVGKCM



YAPPIRGQIRCSSNITGLLLTRDGGINENGTEIFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQ



QHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD
















1759 
H468
*JRFLgp140.6R.SOSIP.664.E168K, BG505 
JRFL/BG505 chim
SOSIP, R6, 664
E168K, + interface
V1, 191-205, V3 from BG505




gp41 chim, + int I201C, A433C,_v1_191-


residues, I201C, A433C,_





205_v3


BG505 V1 (residues








119-153),_191-205_BG505








V3 (residues 296-331),










AENLWVTVYYGVPVWKDAETTLFCASDAKAYDTEVHNVWATHACVPTDPNPQEIHLENVTEHFNMWKNNMVEQMQTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGEIKNCSFNITTSIRDK



VQKEYALFYKLDVVPIDNNNTSYRLINCNTSAITQACPKISFEPIPIHYCAPAGFAILKCNDKTFNGKGPCKNVSTVQCTHGIRPVVSTQLLLNGSLAEEEVVIRSDNFTNNAKTIIVQLKESVEINCTR



PNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNISRAKWNDTLKQIVIKLREQFENKTIVFNHSSGGDPEIVMHSFNCGGEFFYCNSTQLFNSTWNNNTEGSNNTEGNTITLPCRIKQIINMWQEVGKCM



YAPPIRGQIRCSSNITGLLLTRDGGINENGTEIFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQ



QHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD
















1760
H469
*JRFLgp140.6R.SOSIP.664.E168K, BG505 
JRFL/BG505 chim
SOSIP, R6, 664
E168K, I201C, A433C,_191-
191-205, V3 from BG505




gp41 chim, I201C, A433C,_191-205_v3


205_BG505 V3 (residues








296-331),










AENLWVTVYYGVPVWKEATTTLFCASDAKAYDTEVHNVWATHACVPTDPNPQEVVLENVTEHFNMWKNNMVEQMQEDIISLWDQSLKPCVKLTPLCVTLNCKDVNATNTTNDSEGTMERGEIKNCSFNIT



TSIRDKVQKEYALFYKLDVVPIDNNNTSYRLINCNTSAITQACPKISFEPIPIHYCAPAGFAILKCNDKTFNGKGPCKNVSTVQCTHGIRPVVSTQLLLNGSLAEEEVVIRSDNFTNNAKTIIVQLKESV



EINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNISRAKWNDTLKQIVIKLREQFENKTIVFNHSSGGDPEIVMHSFNCGGEFFYCNSTQLFNSTWNNNTEGSNNTEGNTITLPCRIKQIINMWQ



EVGKCMYAPPIRGQIRCSSNITGLLLTRDGGINENGTEIFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLL



RAPEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD
















1761
H470
*JRFLgp140.6R.SOSIP.664.E168K, BG505 
JRFL/BG505 chim
SOSIP, R6, 664
E168K, + interface
166-173, 191-205, V3 from BG505




gp41 chim, + int I201C, A433C,_strC_191-


residues, I201C, A433C,_





205_v3


strC_191-205_BG505 V3








(residues 296-331),










AENLWVTVYYGVPVWKDAETTLFCASDAKAYDTEVHNVWATHACVPTDPNPQEIHLENVTEHFNMWKNNMVEQMQTDIISLWDQSLKPCVKLTPLCVTLNCKDVNATNTTNDSEGTMERGEIKNCSFNIT



TSIRDKKQKVYALFYKLDVVPIDNNNTSYRLINCNTSAITQACPKISFEPIPIHYCAPAGFAILKCNDKTFNGKGPCKNVSTVQCTHGIRPVVSTQLLLNGSLAEEEVVIRSDNFTNNAKTIIVQLKESV



EINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNISRAKWNDTLKQIVIKLREQFENKTIVFNHSSGGDPEIVMHSFNCGGEFFYCNSTQLFNSTWNNNTEGSNNTEGNTITLPCRIKQIINMWQ



EVGKCMYAPPIRGQIRCSSNITGLLLTRDGGINENGTEIFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLL



RAPEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD
















1762
H471
*JRFLgp140.6R.SOSIP.664.E168K, BG505 
JRFL/BG505 chim
SOSIP, R6, 664
E168K, + interface 
V1, V2, V3 from BG505




gp41 chim, + int I201C, A433C,_v1_v2_v3


residues, I201C, A433C,_ 








BG505V1 (residues 119-








153),_BG505 V2 (residues








154-205), _BG505 V3








(residues 296-331),










AENLWVTVYYGVPVWKDAETTLFCASDAKAYDTEVHNVWATHACVPTDPNPQEIHLENVTEHFNMWKNNMVEQMQTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDK



KQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQACPKISFEPIPIHYCAPAGFAILKCNDKTFNGKGPCKNVSTVQCTHGIRPVVSTQLLLNGSLAEEEVVIRSDNFTNNAKTIIVQLKE



SVEINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNISRAKWNDTLKQIVIKLREQFENKTIVFNHSSGGDPEIVMHSFNCGGEFFYCNSTQLFNSTWNNNTEGSNNTEGNTITLPCRIKQIINM



WQEVGKCMYAPPIRGQIRCSSNITGLLLTRDGGINENGTEIFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSN



LLRAPEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD
















1763
H472
*JRFLgp140.6R.SOSIP.664.E168K, BG505 
JRFL/BG505 chim
SOSIP, R6, 664
E168K, I201C, A433C,_
V1, 166-173, V3 from BG505




gp41 chim, I201C, A433C,_v1_strCv3


BG505 V1 (residues 119-








153),_strC_BG505 V3








(residues 296-331),










AENLWVTVYYGVPVWKEATTTLFCASDAKAYDTEVHNVWATHACVPTDPNPQEVVLENVTEHFNMWKNNMVEQMQEDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGElKNCSFNITTSIRDK



KQKVYALFYKLDVVPIDNNNTSYRLISCDTSVCTQACPKISFEPIPIHYCAPAGFAILKCNDKTFNGKGPCKNVSTVQCTHGIRPVVSTQLLLNGSLAEEEVVIRSDNFTNNAKTIIVQLKESVEINCTR



PNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNISRAKWNDTLKQIVIKLREQFENKTIVFNHSSGGDPEIVMHSFNCGGEFFYCNSTQLFNSTWNNNTEGSNNTEGNTITLPCRIKQIINMWQEVGKCM



YAPPIRGQIRCSSNITGLLLTRDGGINENGTEIFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQ



QHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD
















1764
H473
JRFLgp140.6R.SOSIP.664.E168K, BG505
JRFL/BG505 chim
SOSIP, R6, 664
E168K, + interface 
V1, 166-173, 191-205, V3 from




gp41 chim, + int I201C, A433C,_


residues, I201C, 
BG505




v1_strC_191-205_v3


A433C,_BG505 V1 (residues








119-153),_strC_191-205_








BG505 V3 (residues








296-331),






1765
T030
TH966.8-chim_sc10ln-IP-10ln-HATM
TH966.8/BG505 
sc10ln-IP-10ln-HATM







chimera








1766
T031
6545.V4.C1-chim_sc10ln-IP-10ln-HATM
6545.V4.C1/BG505
sc10ln-IP-10ln-HATM







chimera








1767
T032
R2184.c4-chim_sc10ln-IP-10ln-HATM
R2184.c4/BG505 
sc10ln-IP-10ln-HATM







chimera








1768
T033
ZM197.7-chim_sc10ln-IP-10ln-HATM
ZM197.7/BG505 
sc10ln-IP-10ln-HATM







chimera








1769
T034
ZM106.9-chim_sc10ln-IP-10ln-HATM
ZM106.9/BG505 
sc10ln-IP-10ln-HATM







chimera








1770
T035
ZM53.12-chim_sc10ln-IP-10ln-HATM
ZM53.12/BG505 
sc10ln-IP-10ln-HATM







chimera








1771
T036
R2184.c4-chim_sc10ln-IP-MPER-TM
R2184.c4/BG505 
sc10ln-IP-MPER-TM







chimera








1772
T037
CNE55-chim_sc10ln-IP-10ln-HATM
CNE55/BG505 
sc10ln-IP-10ln-HATM







chimera








1773
T038
6545.V4.C1-chim_sc10ln-IP-MPER-TM
6545.V4.C1/BG505
sc10ln-IP-MPER-TM







chimera








1774
T039
DU422.01-chim_sc10ln-IP-10ln-HATM
DU422.01/BG505 
sc10ln-IP-10ln-HATM







chimera








1775
T040
25925-2.22-chim_sc10ln-IP-10ln-HATM
25925-2.22/BG505
sc10ln-IP-10ln-HATM







chimera








1776
T041
CNE58-chim_sc10ln-IP-10ln-HATM
CNE58/BG505 
sc10ln-IP-10ln-HATM







chimera








1777
T042
16055-2.3-chim_sc10ln-IP-10ln-HATM
16055-2.3/BG505
sc10ln-IP-10ln-HATM







chimera








1778
T043
TH966.8-chim_sc10ln-IP-MPER-TM
TH966.8/BG505 
sc10ln-IP-MPER-TM







chimera








1779
T044
ZM55.28a-chim_sc10ln-IP-MPER-TM
ZM55.28a/BG505 
sc10ln-IP-MPER-TM







chimera








1780
T045
ZM53.12-chim_sc10ln-IP-MPER-TM
ZM53.12/BG505 
sc10ln-IP-MPER-TM







chimera








1781
T046
B1369.9A-chim_sc10ln-IP-10ln-HATM
B1369.9A/BG505 
sc10ln-IP-10ln-HATM







chimera








1782
T047
ZM197.7-chim_sc10ln-IP-MPER-TM
ZM197.7/BG505 
sc10ln-IP-MPER-TM







chimera








1783
T048
16055-2.3-chim_sc10ln-IP-MPER-TM
16055-2.3/BG505
sc10ln-IP-MPER-TM







chimera








1784
T049
ZM55.28a-chim_sc151n-SOS-DS-10ln-HATM
ZM55.28a/BG505 
sc151n-SOS-DS-10ln-







chimera
HATM







1785
T050
ZM106.9-chim_SOS-DS-10ln-HATM
ZM106.9/BG505 
SOS-DS-10ln-HATM







chimera








1786
T051
AC10.29-chim_SOS-DS-10ln-HATM
AC10.29/BG505 
SOS-DS-10ln-HATM







chimera








1787
T052
CH038.12-chim_SOS-DS-10ln-HATM
CH038.12/BG505 
SOS-DS-10ln-HATM







chimera








1788
T053
TRO.11-chim_SOS-DS-10ln-HATM
TRO.11/BG505 
SOS-DS-10ln-HATM







chimera








1789
T054
QH209.14M.A2-chimSOS-DS-10ln-HATM
QH209.14M.A2/
SOS-DS-10ln-HATM







BG505 chimera








1790
T055
6545.V4.C1-chim_SOS-DS-10ln-HATM
6545.V4.C1/BG505
SOS-DS-10ln-HATM







chimera








1791
T056
KER2018.11-chim_SOS-DS-10ln-HATM
KER2018.11/BG505
SOS-DS-10ln-HATM







chimera








1792
T057
MB201.A1-chim_SOS-DS-10ln-HATM
MB201.A1/BG505 
SOS-DS-10ln-HATM







chimera








1793
T058
B1369.9A-chim_SOS-DS-10ln-HATM
B1369.9A/BG505 
SOS-DS-10ln-HATM







chimera








1794
T059
CNE55-chim_SOS-DS-10ln-HATM
CNE55/BG505 
SOS-DS-10ln-HATM







chimera








1795
T060
TH966.8-chim_SOS-DS-10ln-HATM
TH966.8/BG505 
SOS-DS-10ln-HATM







chimera








1796
T061
R2184.c4-chim_SOS-DS-10ln-HATM
R2184.c4/BG505 
SOS-DS-10ln-HATM







chimera








1797
T062
DU422.01-chim_SOS-DS-10ln-HATM
DU422.01/BG505 
SOS-DS-10ln-HATM







chimera








1798
T063
16055-2.3-chim_SOS-DS-10ln-HATM
16055-2.3/BG505
SOS-DS-10ln-HATM







chimera








1799
T064
ZM55.28a-chim_SOS-DS-10ln-HATM
ZM55.28a/BG505 
SOS-DS-10ln-HATM







chimera








1800
T065
CH117.4-chim_SOS-DS-10ln-HATM
CH117.4/BG505 
SOS-DS-10ln-HATM







chimera








1801
T066
CNE58-chim_SOS-DS-10ln-HATM
CNE58/BG505 
SOS-DS-10ln-HATM







chimera








1802
T067
ZM53.12-chim_SOS-DS-10ln-HATM
ZM53.12/BG505 
SOS-DS-10ln-HATM







chimera








1803
T068
ZM197.7-chim_SOS-DS-10ln-HATM
ZM197.7/BG505 
SOS-DS-10ln-HATM







chimera








1804
T069
25925-2.22-chim_SOS-DS-10ln-HATM
25925-2.22/BG505
SOS-DS-10ln-HATM







chimera








1805
T070
ZM106.9-chim_SOS-DS-MPER-TM
ZM106.9/BG505 
SOS-DS-MPER-TM







chimera








1806
T071
AC10.29-chim_SOS-DS-MPER-TM
AC10.29/BG505 
SOS-DS-MPER-TM







chimera








1807
T072
CH038.12-chim_SOS-DS-MPER-TM
CH038.12/BG505 
SOS-DS-MPER-TM







chimera








1808
T073
TRO.11-chim_SOS-DS-MPER-TM
TRO.11/BG505 
SOS-DS-MPER-TM







chimera








1809
T074
QH209.14M.A2-chimSOS-DS-MPER-TM
QH209.14M.A2/
SOS-DS-MPER-TM







BG505 chimera








1810
T075
6545.V4.C1-chim_SOS-DS-MPER-TM
6545.V4.C1/BG505
SOS-DS-MPER-TM







chimera








1811
T076
KER2018.11-chim_SOS-DS-MPER-TM
KER2018.11/BG505
SOS-DS-MPER-TM







chimera








1812
T077
MB201.A1-chim_SOS-DS-MPER-TM
MB201.A1/BG505 
SOS-DS-MPER-TM







chimera








1813
T078
B1369.9A-chim_SOS-DS-MPER-TM
B1369.9A/BG505 
SOS-DS-MPER-TM







chimera








1814
T079
CNE55-chim_SOS-DS-MPER-TM
CNE55/BG505 
SOS-DS-MPER-TM







chimera








1815
T080
TH966.8-chim_SOS-DS-MPER-TM
TH966.8/BG505 
SOS-DS-MPER-TM







chimera








1816
T081
R2184.c4-chim_SOS-DS-MPER-TM
R2184.c4/BG505 
SOS-DS-MPER-TM







chimera








1817
T082
DU422.01-chim_SOS-DS-MPER-TM
DU422.01/BG505 
SOS-DS-MPER-TM







chimera








1818
T083
16055-2.3-chim_SOS-DS-MPER-TM
16055-2.3/BG505 
SOS-DS-MPER-TM







chimera








1819
T084
ZM55.28a-chim_SOS-DS-MPER-TM
ZM55.28a/BG505 
SOS-DS-MPER-TM







chimera








1820
T085
CH117.4-chim_SOS-DS-MPER-TM
CH117.4/BG505 
SOS-DS-MPER-TM







chimera








1821
T086
CNE58-chim_SOS-DS-MPER-TM
CNE58/BG505 
SOS-DS-MPER-TM







chimera








1822
T087
ZM53.12-chim_SOS-DS-MPER-TM
ZM53.12/BG505 
SOS-DS-MPER-TM







chimera








1823
T088
ZM197.7-chim_SOS-DS-MPER-TM
ZM197.7/BG505 
SOS-DS-MPER-TM







chimera








1824
T089
25925-2.22-chim_SOS-DS-MPER-TM
25925-2.22/BG505
SOS-DS-MPER-TM







chimera








1825
T090
ZM106.9-chim_SOS-DS-MPER-TM-cyto
ZM106.9/BG505 
SOS-DS-MPER-TM-cyto







chimera








1826
T091
AC10.29-chim_SOS-DS-MPER-TM-cyto
AC10.29/BG505 
SOS-DS-MPER-TM-cyto







chimera








1827
T092
CH038.12-chim_SOS-DS-MPER-TM-cyto
CH038.12/BG505 
SOS-DS-MPER-TM-cyto







chimera








1828
T093
TRO.11-chim_SOS-DS-MPER-TM-cyto
TRO.11/BG505 
SOS-DS-MPER-TM-cyto







chimera








1829
T094
QH209.14M.A2-chim_SOS-DS-MPER-TM-cyto
QH209.14M.A2/
SOS-DS-MPER-TM-cyto







BG505 chimera








1830
T095
6545.V4.C1-chim_SOS-DS-MPER-TM-cyto
6545.V4.C1/BG505
SOS-DS-MPER-TM-cyto







chimera








1831
T096
KER2018.11-chim_SOS-DS-MPER-TM-cyto
KER2018.11/BG505
SOS-DS-MPER-TM-cyto







chimera








1832
T097
MB201.A1-chim_SOS-DS-MPER-TM-cyto
MB201.A1/BG505 
SOS-DS-MPER-TM-cyto







chimera








1833
T098
B1369.9A-chim_SOS-DS-MPER-TM-cyto
B1369.9A/BG505 
SOS-DS-MPER-TM-cyto







chimera








1834
T099
CNE55-chim_SOS-DS-MPER-TM-cyto
CNE55/BG505 
SOS-DS-MPER-TM-cyto







chimera








1835
T100
TH966.8-chim_SOS-DS-MPER-TM-cyto
TH966.8/BG505 
SOS-DS-MPER-TM-cyto







chimera








1836
T101
R2184.c4-chim_SOS-DS-MPER-TM-cyto
R2184.c4/BG505 
SOS-DS-MPER-TM-cyto







chimera








1837
T102
DU422.01-chim_SOS-DS-MPER-TM-cyto
DU422.01/BG505 
SOS-DS-MPER-TM-cyto







chimera








1838
T103
16055-2.3-chim_SOS-DS-MPER-TM-cyto
16055-2.3/BG505
SOS-DS-MPER-TM-cyto







chimera








1839
T104
ZM55.28a-chim_SOS-DS-MPER-TM-cyto
ZM55.28a/BG505 
SOS-DS-MPER-TM-cyto







chimera








1840
T105
CH117.4-chim_SOS-DS-MPER-TM-cyto
CH117.4/BG505 
SOS-DS-MPER-TM-cyto







chimera








1841
T106
CNE58-chim_SOS-DS-MPER-TM-cyto
CNE58/BG505 
SOS-DS-MPER-TM-cyto







chimera








1842
T107
ZM53.12-chim_SOS-DS-MPER-TM-cyto
ZM53.12/BG505 
SOS-DS-MPER-TM-cyto







chimera








1843
T108
ZM197.7-chim_SOS-DS-MPER-TM-cyto
ZM197.7/BG505 
SOS-DS-MPER-TM-cyto







chimera








1844
T109
25925-2.22-chim_SOS-DS-MPER-TM-cyto
25925-2.22/BG505
SOS-DS-MPER-TM-cyto







chimera








1845
T110
AC10.29-chim_sc10ln-IP-10ln-HATM
AC10.29/BG505 
sc10ln-IP-10ln-HATM







chimera








1846
T111
CH038.12-chim_sc10ln-IP-10ln-HATM
CH038.12/BG505 
sc10ln-IP-10ln-HATM







chimera








1847
T112 
TRO.11-chim_sc10ln-IP-10ln-HATM
TRO.11/BG505 
sc10ln-IP-10ln-HATM







chimera








1848
T113
QH209.14M.A2-chimsc10ln-IP-10ln-HATM
QH209.14M.A2/
sc10ln-IP-10ln-HATM







BG505 chimera








1849
T114
KER2018.11-chim_sc10ln-IP-10ln-HATM
KER2018.11/BG505
sc10ln-IP-10ln-HATM







chimera








1850
T115
MB201.A1-chim_sc10ln-IP-10ln-HATM
MB201.A1/BG505 
sc10ln-IP-10ln-HATM







chimera








1851
T116
ZM55.28a-chim_sc10ln-IP-10ln-HATM
ZM55.28a/BG505 
sc10ln-IP-10ln-HATM







chimera








1852
T117
CH117.4-chim_sc10ln-IP-10ln-HATM
CH117.4/BG505 
sc10ln-IP-10ln-HATM







chimera








1853
T118
CNE58-chim_sc10ln-IP-10ln-HATM
CNE58/BG505 
sc10ln-IP-10ln-HATM







chimera








1854
T119
ZM106.9-chim_sc10ln-IP-MPER-TM
ZM106.9/BG505 
sc10ln-IP-MPER-TM







chimera








1855
T120
AC10.29-chim_sc10ln-IP-MPER-TM
AC10.29/BG505 
sc10ln-IP-MPER-TM







chimera








1856
T121
CH038.12-chim_sc10ln-IP-MPER-TM
CH038.12/BG505 
sc10ln-IP-MPER-TM







chimera








1857
T122
TRO.11-chim_sc10ln-IP-MPER-TM
TRO.11/BG505 
sc10ln-IP-MPER-TM







chimera








1858
T123
QH209.14M.A2-chimsc10ln-IP-MPER-TM
QH209.14M.A2/
sc10ln-IP-MPER-TM







BG505 chimera








1859
T124
KER2018.11-chim_sc10ln-IP-MPER-TM
KER2018.11/BG505
sc10ln-IP-MPER-TM







chimera








1860
T125
MB201.A1-chim_sc10ln-IP-MPER-TM
MB201.A1/BG505 
sc10ln-IP-MPER-TM







chimera








1861
T126
B1369.9A-chim_sc10ln-IP-MPER-TM
B1369.9A/BG505 
sc10ln-IP-MPER-TM







chimera








1862
T127
CNE55-chim_sc10ln-IP-MPER-TM
CNE55/BG505 
sc10ln-IP-MPER-TM







chimera








1863
T128
DU422.01-chim_sc10ln-IP-MPER-TM
DU422.01/BG505 
sc10ln-IP-MPER-TM







chimera








1864
T129
CH117.4-chim_sc10ln-IP-MPER-TM
CH117.4/BG505 
sc10ln-IP-MPER-TM







chimera








1865
T130
CNE58-chim_sc10ln-IP-MPER-TM
CNE58/BG505 
sc10ln-IP-MPER-TM







chimera








1866
T131
25925-2.22-chim_sc10ln-IP-MPER-TM
25925-2.22/BG505
sc10ln-IP-MPER-TM







chimera








1867
T132
ZM106.9-chim_sc10ln-IP-MPER-TM-cyto
ZM106.9/BG505 
sc10ln-IP-MPER-TM-cyto







chimera








1868
T133
AC10.29-chim_sc10ln-IP-MPER-TM-cyto
AC10.29/BG505 
sc10ln-IP-MPER-TM-cyto







chimera








1869
T134
CH038.12-chim_sc10ln-IP-MPER-TM-cyto
CH038.12/BG505 
sc10ln-IP-MPER-TM-cyto







chimera








1870
T135
TRO.11-chim_sc10ln-IP-MPER-TM-cyto
TRO.11/BG505 
sc10ln-IP-MPER-TM-cyto







chimera








1871
T136
QH209.14M.A2-chim_sc10ln-IP-MPER-TM-cyto
QH209.14M.A2/
sc10ln-IP-MPER-TM-cyto







BG505 chimera








1872
T137
6545.V4.C1-chim_sc10ln-IP-MPER-TM-cyto
6545.V4.C1/BG505
sc10ln-IP-MPER-TM-cyto







chimera








1873
T138
KER2018.11-chim_sc10ln-IP-MPER-TM-cyto
KER2018.11/BG505
sc10ln-IP-MPER-TM-cyto







chimera








1874
T139
MB201.A1-chim_sc10ln-IP-MPER-TM-cyto
MB201.A1/BG505 
sc10ln-IP-MPER-TM-cyto







chimera








1875
T140
B1369.9A-chim_sc10ln-IP-MPER-TM-cyto
B1369.9A/BG505 
sc10ln-IP-MPER-TM-cyto







chimera








1876
T141
CNE55-chim_sc10ln-IP-MPER-TM-cyto
CNE55/BG505 
sc10ln-IP-MPER-TM-cyto







chimera








1877
T142
TH966.8-chim_sc10ln-IP-MPER-TM-cyto
TH966.8/BG505 
sc10ln-IP-MPER-TM-cyto







chimera








1878
T143
R2184.c4-chim_sc10ln-IP-MPER-TM-cyto
R2184.c4/BG505 
sc10ln-IP-MPER-TM-cyto







chimera








1879
T144
DU422.01-chim_sc10ln-IP-MPER-TM-cyto
DU422.01/BG505 
sc10ln-IP-MPER-TM-cyto







chimera








1880
T145
16055-2.3-chim_sc10ln-IP-MPER-TM-cyto
16055-2.3/BG505
sc10ln-IP-MPER-TM-cyto







chimera








1881
T146
ZM55.28a-chim_sc10ln-IP-MPER-TM-cyto
ZM55.28a/BG505 
sc10ln-IP-MPER-TM-cyto







chimera








1882
T147
CH117.4-chim_sc10ln-IP-MPER-TM-cyto
CH117.4/BG505 
sc10ln-IP-MPER-TM-cyto







chimera








1883
T148
CNE58-chim_sc10ln-IP-MPER-TM-cyto
CNE58/BG505 
sc10ln-IP-MPER-TM-cyto







chimera








1884
T149
ZM53.12-chim_sc10ln-IP-MPER-TM-cyto
ZM53.12/BG505 
sc10ln-IP-MPER-TM-cyto







chimera








1885
T150
ZM197.7-chim_sc10ln-IP-MPER-TM-cyto
ZM197.7/BG505 
sc10ln-IP-MPER-TM-cyto







chimera








1886
T151
25925-2.22-chim_sc10ln-IP-MPER-TM-cyto
25925-2.22/BG505
sc10ln-IP-MPER-TM-cyto







chimera








1887
T152
ZM106.9-chim_sc15ln-SOS-DS-10ln-HATM
ZM106.9/BG505 
sc15ln-SOS-DS-10ln-HATM







chimera








1888
T153
AC10.29-chim_sc15ln-SOS-DS-10ln-HATM
AC10.29/BG505 
sc15ln-SOS-DS-10ln-HATM







chimera








1889
T154
CH038.12-chim_sc15ln-SOS-DS-10ln-HATM
CH038.12/BG505 
sc15ln-SOS-DS-10ln-HATM







chimera








1890
T155
TRO.11-chim_sc15ln-SOS-DS-10ln-HATM
TRO.11/BG505 
sc15ln-SOS-DS-10ln-HATM







chimera








1891
T156
QH209.14M.A2-chim_sc15ln-SOS-DS-10ln-
QH209.14M.A2/
sc15ln-SOS-DS-10ln-HATM






HATM
BG505 chimera








1892
T157
6545.V4.C1-chim_sc15ln-SOS-DS-10ln-HATM
6545.V4.C1/
sc15ln-SOS-DS-10ln-HATM







BG505 chimera








1893
T158
KER2018.11-chim_sc15ln-SOS-DS-10ln-HATM
KER2018.11/
sc15ln-SOS-DS-10ln-HATM







BG505 chimera








1894
T159
MB201.A1-chim_sc15ln-SOS-DS-10ln-HATM
MB201.A1/BG505 
sc15ln-SOS-DS-10ln-HATM







chimera








1895
T160
B1369.9A-chim_sc15ln-SOS-DS-10ln-HATM
B1369.9A/BG505 
sc15ln-SOS-DS-10ln-HATM







chimera








1896
T161
CNE55-chim_sc15ln-SOS-DS-10ln-HATM
CNE55/BG505 
sc15ln-SOS-DS-10ln-HATM







chimera








1897
T162
TH966.8-chim_sc15ln-SOS-DS-10ln-HATM
TH966.8/BG505 
sc15ln-SOS-DS-10ln-HATM







chimera








1898
T163
R2184.c4-chim_sc15ln-SOS-DS-10ln-HATM
R2184.c4/BG505 
sc15ln-SOS-DS-10ln-HATM







chimera








1899
T164
DU422.01-chim_sc15ln-SOS-DS-10ln-HATM
DU422.01/BG505 
sc15ln-SOS-DS-10ln-HATM







chimera








1900
T165
16055-2.3-chim_sc15ln-SOS-DS-10ln-HATM
16055-2.3/BG505 
sc15ln-SOS-DS-10ln-HATM







chimera








1901
T166
CH117.4-chim_sc15ln-SOS-DS-10ln-HATM
CH117.4/BG505 
sc15ln-SOS-DS-10ln-HATM







chimera








1902
T167
CNE58-chim_sc15ln-SOS-DS-10ln-HATM
CNE58/BG505 
sc15ln-SOS-DS-10ln-HATM







chimera








1903
T168
ZM53.12-chim_sc15ln-SOS-DS-10ln-HATM
ZM53.12/BG505 
sc15ln-SOS-DS-10ln-HATM







chimera








1904
T169
ZM197.7-chim_sc15ln-SOS-DS-10ln-HATM
ZM197.7/BG505 
sc15ln-SOS-DS-10ln-HATM







chimera








1905
T170
25925-2.22-chim_sc15ln-SOS-DS-10ln-HATM
25925-2.22/BG505
sc15ln-SOS-DS-10ln-HATM







chimera








1906
T171
ZM106.9-chim_sc15ln-SOS-DS-MPER-TM
ZM106.9/BG505 
sc15ln-SOS-DS-MPER-TM







chimera








1907
T172
AC10.29-chim_sc15ln-SOS-DS-MPER-TM
AC10.29/BG505 
sc15ln-SOS-DS-MPER-TM







chimera








1908
T173
CH038.12-chim_sc15ln-SOS-DS-MPER-TM
CH038.12/BG505 
sc15ln-SOS-DS-MPER-TM







chimera








1909
T174
TRO.11-chim_sc15ln-SOS-DS-MPER-TM
TRO.11/BG505 
sc15ln-SOS-DS-MPER-TM







chimera








1910
T175
QH209.14M.A2-chim_sc15ln-SOS-DS-MPER-TM
QH209.14M.A2/
sc15ln-SOS-DS-MPER-TM







BG505 chimera








1911
T176
6545.V4.C1-chim_sc15ln-SOS-DS-MPER-TM
6545.V4.C1/
sc15ln-SOS-DS-MPER-TM







BG505 chimera








1912
T177
KER2018.11-chim_sc15ln-SOS-DS-MPER-TM
KER2018.11/
sc15ln-SOS-DS-MPER-TM







BG505 chimera








1913
T178
MB201.A1-chim_sc15ln-SOS-DS-MPER-TM
MB201.A1/BG505 
sc15ln-SOS-DS-MPER-TM







chimera








1914
T179
B1369.9A-chim_sc15ln-SOS-DS-MPER-TM
B1369.9A/BG505 
sc15ln-SOS-DS-MPER-TM







chimera








1915
T180
CNE55-chim_sc15ln-SOS-DS-MPER-TM
CNE55/BG505 
sc15ln-SOS-DS-MPER-TM







chimera








1916
T181
TH966.8-chim_sc15ln-SOS-DS-MPER-TM
TH966.8/BG505 
sc15ln-SOS-DS-MPER-TM







chimera








1917
T182
_sc15ln-SOS-DS-MPER-TM
R2184.c4/BG505 
sc15ln-SOS-DS-MPER-TM







chimera








1918
T183
DU422.01-chim_sc15ln-SOS-DS-MPER-TM
DU422.01/BG505 
sc15ln-SOS-DS-MPER-TM







chimera








1919
T184
16055-2.3-chim_sc15ln-SOS-DS-MPER-TM
16055-2.3/BG505 
sc15ln-SOS-DS-MPER-TM







chimera








1920
T185
ZM55.28a-chim_sc15ln-SOS-DS-MPER-TM
ZM55.28a/BG505 
sc15ln-SOS-DS-MPER-TM







chimera








1921
T186
CH117.4-chim_sc15ln-SOS-DS-MPER-TM
CH117.4/BG505 
sc15ln-SOS-DS-MPER-TM







chimera








1922
T187
CNE58-chim_sc15ln-SOS-DS-MPER-TM
CNE58/BG505 
sc15ln-SOS-DS-MPER-TM







chimera








1923
T188
ZM53.12-chim_sc15ln-SOS-DS-MPER-TM
ZM53.12/BG505 
sc15ln-SOS-DS-MPER-TM







chimera








1924
T189
ZM197.7-chim_sc15ln-SOS-DS-MPER-TM
ZM197.7/BG505 
sc15ln-SOS-DS-MPER-TM







chimera








1925
T190
25925-2.22-chim_sc15ln-SOS-DS-MPER-TM
25925-2.22/BG505 
sc15ln-SOS-DS-MPER-TM







chimera








1926
T191
ZM106.9-chim_sc151n-SOS-DS-MPER-TM-cyto
ZM106.9/BG505 
sc15ln-SOS-DS-MPER-TM-







chimera
cyto







1927
T192
AC10.29-chim_sc15ln-SOS-DS-MPER-TM-cyto
AC10.29/BG505 
sc15ln-SOS-DS-MPER-TM-







chimera
cyto







1928
T193
CH038.12-chim_sc15ln-SOS-DS-MPER-TM-
CH038.12/BG505 
sc15ln-SOS-DS-MPER-TM-






cyto
chimera
cyto







1929
T194
TRO.11-chim_sc15ln-SOS-DS-MPER-TM-cyto
TRO.11/BG505 
sc15ln-SOS-DS-MPER-TM-







chimera
cyto







1930
T195
QH209.14M.A2-chim_sc15ln-SOS-DS-MPER-
QH209.14M.A2/
sc15ln-SOS-DS-MPER-TM-






TM-cyto
BG505 chimera
cyto







1931
T196
6545.V4.C1-chim_sc15ln-SOS-DS-MPER-TM-
6545.V4.C1/
sc15ln-SOS-DS-MPER-TM-






cyto
BG505 chimera
cyto







1932
T197
KER2018.11-chim_sc15ln-SOS-DS-MPER-TM-
KER2018.11/
sc15ln-SOS-DS-MPER-TM-






cyto
BG505 chimera
cyto







1933
T198
MB201.A1-chim_sc15ln-SOS-DS-MPER-TM-
MB201.A1/BG505 
sc15ln-SOS-DS-MPER-TM-






cyto
chimera
cyto







1934
T199
B1369.9A-chim_sc15ln-SOS-DS-MPER-TM-
B1369.9A/BG505 
sc15ln-SOS-DS-MPER-TM-






cyto
chimera
cyto







1935
T200
CNE55-chim_sc15ln-SOS-DS-MPER-TM-cyto
CNE55/BG505 
sc15ln-SOS-DS-MPER-TM-







chimera
cyto







1936
T201
TH966.8-chim_sc15ln-SOS-DS-MPER-TM-
TH966.8/BG505 
sc15ln-SOS-DS-MPER-TM-






cyto
chimera
cyto







1937
T202
R2184.c4-chim_sc15ln-SOS-DS-MPER-TM-
R2184.c4/BG505 
sc15ln-SOS-DS-MPER-TM-






cyto
chimera
cyto







1938
T203
DU422.01-chim_sc15ln-SOS-DS-MPER-TM-
DU422.01/BG505 
sc15ln-SOS-DS-MPER-TM-






cyto
chimera
cyto







1939
T204
16055-2.3-chim_sc15ln-SOS-DS-MPER-TM-
16055-2.3/BG505 
sc15ln-SOS-DS-MPER-TM-






cyto
chimera
cyto







1940
T205
ZM55.28a-chim_sc15ln-SOS-DS-MPER-TM-
ZM55.28a/BG505 
sc15ln-SOS-DS-MPER-TM-






cyto
chimera
cyto







1941
T206
CH117.4-chim_sc15ln-SOS-DS-MPER-TM-cyto
CH117.4/BG505 
sc15ln-SOS-DS-MPER-TM-







chimera
cyto







1942
T207
CNE58-chim_sc15ln-SOS-DS-MPER-TM-cyto
CNE58/BG505 
sc15ln-SOS-DS-MPER-TM-







chimera
cyto







1943
T208
ZM53.12-chim_sc15ln-SOS-DS-MPER-TM-cyto
ZM53.12/BG505 
sc15ln-SOS-DS-MPER-TM-







chimera
cyto







1944
T209
ZM197.7-chim_sc15ln-SOS-DS-MPER-TM-cyto
ZM197.7/BG505 
sc15ln-SOS-DS-MPER-TM-







chimera
cyto







1945
T210
25925-2.22-chim_sc15ln-SOS-DS-MPER-TM-
25925-2.22/
sc15ln-SOS-DS-MPER-TM-






cyto
BG505 chimera
cyto







1946
T211
ZM106.9-chim_IP-DS-10ln-HATM
ZM106.9/BG505 
IP-DS-10ln-HATM







chimera








1947
T212
AC10.29-chim_IP-DS-10ln-HATM
AC10.29/BG505 
IP-DS-10ln-HATM







chimera








1948
T213
CH038.12-chim_IP-DS-10ln-HATM
CH038.12/BG505 
IP-DS-10ln-HATM







chimera








1949
T214
TRO.11-chim_IP-DS-10ln-HATM
TRO.11/BG505 
IP-DS-10ln-HATM







chimera








1950
T215
QH209.14M.A2-chimIP-DS-10ln-HATM
QH209.14M.A2/
IP-DS-10ln-HATM







BG505 chimera








1951
T216
6545.V4.C1-chim_IP-DS-10ln-HATM
6545.V4.C1/
IP-DS-10ln-HATM







BG505 chimera








1952
T217
KER2018.11-chim_IP-DS-10ln-HATM
KER2018.11/
IP-DS-10ln-HATM







BG505 chimera








1953
T218
MB201.A1-chim_IP-DS-10ln-HATM
MB201.A1/BG505 
IP-DS-10ln-HATM







chimera








1954
T219
B1369.9A-chim_IP-DS-10ln-HATM
B1369.9A/BG505 
IP-DS-10ln-HATM







chimera








1955
T220
CNE55-chim_IP-DS-10ln-HATM
CNE55/BG505 
IP-DS-10ln-HATM







chimera








1956
T221
TH966.8-chim_IP-DS-10ln-HATM
TH966.8/BG505 
IP-DS-10ln-HATM







chimera








1957
T222
R2184.c4-chim_IP-DS-10ln-HATM
R2184.c4/BG505 
IP-DS-10ln-HATM







chimera








1958
T223
DU422.01-chim_IP-DS-10ln-HATM
DU422.01/BG505 
IP-DS-10ln-HATM







chimera








1959
T224
16055-2.3-chim_IP-DS-10ln-HATM
16055-2.3/BG505 
IP-DS-10ln-HATM







chimera








1960
T225
ZM55.28a-chim_IP-DS-10ln-HATM
ZM55.28a/BG505 
IP-DS-10ln-HATM







chimera








1961
T226
CH117.4-chim_IP-DS-10ln-HATM
CH117.4/BG505 
IP-DS-10ln-HATM







chimera








1962
T227
CNE58-chim_IP-DS-10ln-HATM
CNE58/BG505 
IP-DS-10ln-HATM







chimera








1963
T228
ZM53.12-chim_IP-DS-10ln-HATM
ZM53.12/BG505 
IP-DS-10ln-HATM







chimera








1964
T229
ZM197.7-chim_IP-DS-10ln-HATM
ZM197.7/BG505 
IP-DS-10ln-HATM







chimera








1965
T230
25925-2.22-chim_IP-DS-10ln-HATM
25925-2.22/
IP-DS-10ln-HATM







BG505 chimera








1966
T231
ZM106.9-chim_IP-DS-MPER-TM
ZM106.9/BG505 
IP-DS-MPER-TM







chimera








1967
T232
AC10.29-chim_IP-DS-MPER-TM
AC10.29/BG505 
IP-DS-MPER-TM







chimera








1968
T233
CH038.12-chim_IP-DS-MPER-TM
CH038.12/BG505 
IP-DS-MPER-TM







chimera








1969
T234
TRO.11-chim_IP-DS-MPER-TM
TRO.11/BG505 
IP-DS-MPER-TM







chimera








1970
T235
QH209.14M.A2-chim_IP-DS-MPER-TM
QH209.14M.A2/
IP-DS-MPER-TM







BG505 chimera








1971
T236
6545.V4.C1-chim_IP-DS-MPER-TM
6545.V4.C1/
IP-DS-MPER-TM







BG505 chimera








1972
T237
KER2018.11-chim_IP-DS-MPER-TM
KER2018.11/
IP-DS-MPER-TM







BG505 chimera








1973
T238
MB201.A1-chim_IP-DS-MPER-TM
MB201.A1/BG505 
IP-DS-MPER-TM







chimera








1974
T239
B1369.9A-chim_IP-DS-MPER-TM
B1369.9A/BG505 
IP-DS-MPER-TM







chimera








1975
T240
CNE55-chim_IP-DS-MPER-TM
CNE55/BG505 
IP-DS-MPER-TM







chimera








1976
T241
TH966.8-chim_IP-DS-MPER-TM
TH966.8/BG505 
IP-DS-MPER-TM







chimera








1977
T242
R2184.c4-chim_IP-DS-MPER-TM
R2184.c4/BG505 
IP-DS-MPER-TM







chimera








1978
T243
DU422.01-chim_IP-DS-MPER-TM
DU422.01/BG505 
IP-DS-MPER-TM







chimera








1979
T244
16055-2.3-chim_IP-DS-MPER-TM
16055-2.3/BG505 
IP-DS-MPER-TM







chimera








1980
T245
ZM55.28a-chim_IP-DS-MPER-TM
ZM55.28a/BG505 
IP-DS-MPER-TM







chimera








1981
T246
CH117.4-chim_IP-DS-MPER-TM
CH117.4/BG505 
IP-DS-MPER-TM







chimera








1982
T247
CNE58-chim_IP-DS-MPER-TM
CNE58/BG505 
IP-DS-MPER-TM







chimera








1983
T248
ZM53.12-chim_IP-DS-MPER-TM
ZM53.12/BG505 
IP-DS-MPER-TM







chimera








1984
T249
ZM197.7-chim_IP-DS-MPER-TM
ZM197.7/BG505 
IP-DS-MPER-TM







chimera








1985
T250
25925-2.22-chim_IP-DS-MPER-TM
25925-2.22/
IP-DS-MPER-TM







BG505 chimera








1986
T251
ZM106.9-chim_IP-DS-MPER-TM-cyto
ZM106.9/BG505 
IP-DS-MPER-TM-cyto







chimera








1987
T252
AC10.29-chim_IP-DS-MPER-TM-cyto
AC10.29/BG505 
IP-DS-MPER-TM-cyto







chimera








1988
T253
CH038.12-chim_IP-DS-MPER-TM-cyto
CH038.12/BG505 
IP-DS-MPER-TM-cyto







chimera








1989
T254
TRO.11-chim_IP-DS-MPER-TM-cyto
TRO.11/BG505 
IP-DS-MPER-TM-cyto







chimera








1990
T255
QH209.14M.A2-chim_IP-DS-MPER-TM-cyto
QH209.14M.A2/
IP-DS-MPER-TM-cyto







BG505 chimera








1991
T256
6545.V4.C1-chim_IP-DS-MPER-TM-cyto
6545.V4.C1/
IP-DS-MPER-TM-cyto







BG505 chimera








1992
T257
KER2018.11-chim_IP-DS-MPER-TM-cyto
KER2018.11/
IP-DS-MPER-TM-cyto







BG505 chimera








1993
T258
MB201.A1-chim_IP-DS-MPER-TM-cyto
MB201.A1/BG505 
IP-DS-MPER-TM-cyto







chimera








1994
T259
B1369.9A-chim_IP-DS-MPER-TM-cyto
B1369.9A/BG505 
IP-DS-MPER-TM-cyto







chimera








1995
T260
CNE55-chim_IP-DS-MPER-TM-cyto
CNE55/BG505 
IP-DS-MPER-TM-cyto







chimera








1996
T261
TH966.8-chim_IP-DS-MPER-TM-cyto
TH966.8/BG505 
IP-DS-MPER-TM-cyto







chimera








1997
T262
R2184.c4-chim_IP-DS-MPER-TM-cyto
R2184.c4/BG505 
IP-DS-MPER-TM-cyto







chimera








1998
T263
DU422.01-chim_IP-DS-MPER-TM-cyto
DU422.01/BG505 
IP-DS-MPER-TM-cyto







chimera








1999
T264
16055-2.3-chim_SOS-DS-MPER-TM-cyto
16055-2.3/BG505 
SOS-DS-MPER-TM-cyto







chimera








2000
T265
ZM55.28a-chim_SOS-DS-MPER-TM-cyto
ZM55.28a/BG505 
SOS-DS-MPER-TM-cyto







chimera








2001
T266
CH117.4-chim_SOS-DS-MPER-TM-cyto
CH117.4/BG505 
SOS-DS-MPER-TM-cyto







chimera








2002
T267
CNE58-chim_SOS-DS-MPER-TM-cyto
CNE58/BG505 
SOS-DS-MPER-TM-cyto







chimera








2003
T268
ZM53.12-chim_SOS-DS-MPER-TM-cyto
ZM53.12/BG505 
SOS-DS-MPER-TM-cyto







chimera








2004
T269
ZM197.7-chim_SOS-DS-MPER-TM-cyto
ZM197.7/BG505 
SOS-DS-MPER-TM-cyto







chimera








2005
T270
25925-2.22-chim_SOS-DS-MPER-TM-cyto
25925-2.22/
SOS-DS-MPER-TM-cyto







BG505 chimera








2006
T271
TH966.8-chim_sc10ln-IP-MPER-TM-full-
TH966.8/BG505 
sc10ln-IP-MPER-TM-full-
single-chain 10 amino 





cytoplasmic domain
chimera
cytoplasmic domain
acid replace cleavage 








site and I559P mutation






2007
T272
6545.V4.C1-chim sc10ln-IP-MPER-TM-full-
6545.V4.C1/
sc10ln-IP-MPER-TM-full-
single-chain 10 amino 





cytoplasmic domain
BG505 chimera
cytoplasmic domain
acid replace cleavage 








site and I559P mutation






2008
T273
cR2184.c4-chim_sc10ln-IP-MPER-TM-full-
R2184.c4/BG505 
sc10ln-IP-MPER-TM-full-
single-chain 10 amino 





cytoplasmic domain
chimera
cytoplasmic domain
acid replace cleavage 








site and I559P mutation






2009
T274
ZM197.7-chim_sc10ln-IP-MPER-TM-full-
ZM197.7/BG505 
sc10ln-IP-MPER-TM-full-
single-chain 10 amino 





cytoplasmic domain
chimera
cytoplasmic domain
acid replace cleavage 








site and I559P mutation






2010
T275
ZM106.9-chim_sc10ln-IP-MPER-TM-full-
ZM106.9/BG505 
sc10ln-IP-MPER-TM-full-
single-chain 10 amino 





cytoplasmic domain
chimera
cytoplasmic domain
acid replace cleavage 








site and I559P mutation






2011
T276
ZM53.12-chim_sc10ln-IP-MPER-TM-full-
ZM53.12/BG505 
sc10ln-IP-MPER-TM-full-
single-chain 10 amino 





cytoplasmic domain
chimera
cytoplasmic domain
acid replace cleavage 








site and I559P mutation






2012
T277
CNE55-chim_sc10ln-IP-MPER-TM-full-
CNE55/BG505 
sc10ln-IP-MPER-TM-full-
single-chain 10 amino 





cytoplasmic domain
chimera
cytoplasmic domain
acid replace cleavage 








site and I559P mutation






2013
T278
DU422.01-chim_sc10ln-IP-MPER-TM-full-
DU422.01/BG505 
sc10ln-IP-MPER-TM-full-
single-chain 10 amino 





cytoplasmic domain
chimera
cytoplasmic domain
acid replace cleavage 








site and I559P mutation






2014
T279
25925-2.22-chim_sc10ln-IP-MPER-TM-full-
25925-2.22/
sc10ln-IP-MPER-TM-full-
single-chain 10 amino 





cytoplasmic domain
BG505 chimera
cytoplasmic domain
acid replace cleavage 








site and I559P mutation






2015
T280
CNE58-chim_sc10ln-IP-MPER-TM-full-
CNE58/BG505 
sc10ln-IP-MPER-TM-full-
single-chain 10 amino 





cytoplasmic domain
chimera
cytoplasmic domain
acid replace cleavage 








site and I559P mutation






2016
T281
16055-2.3-chim_sc10ln-IP-MPER-TM-full-
16055-2.3/BG505 
sc10ln-IP-MPER-TM-full-
single-chain 10 amino 





cytoplasmic domain
chimera
cytoplasmic domain
acid replace cleavage 








site and I559P mutation






2017
T282
ZM55.28a-chim_sc10ln-IP-MPER-TM-full-
ZM55.28a/BG505 
sc10ln-IP-MPER-TM-full-
single-chain 10 amino 





cytoplasmic domain
chimera
cytoplasmic domain
acid replace cleavage 








site and I559P mutation






2018
T283
BI369.9A-chim_sc10ln-IP-MPER-TM-full-
BI369.9A/BG505 
sc10ln-IP-MPER-TM-full-
single-chain 10 amino 





cytoplasmic domain
chimera
cytoplasmic domain
acid replace cleavage 








site and I559P mutation






2019
T284
TH966.8-chim_sc10ln-a433p-IP-10ln-HATM
TH966.8/BG505 
sc10ln-IP-10ln-HATM
a433p






chimera








2020
T285
6545.V4.C1-chim_sc10ln-a433p-IP-10ln-
6545.V4.C1/
sc10ln-IP-10ln-HATM
a433p





HATM
BG505 chimera








2021
T286
R2184.c4-chim_sc10ln-a433p-IP-10ln-HATM
R2184.c4/BG505 
sc10ln-IP-10ln-HATM
a433p






chimera








2022
T287
ZM197.7-chim_sc10ln-a433p-IP-10ln-HATM
ZM197.7/BG505 
sc10ln-IP-10ln-HATM
a433p






chimera








2023
T288
ZM106.9-chim_sc10ln-a433p-IP-10ln-HATM
ZM106.9/BG505 
sc10ln-IP-10ln-HATM
a433p






chimera








2024
T289
ZM53.12-chim_sc10ln-a433p-IP-10ln-HATM
ZM53.12/BG505 
sc10ln-IP-10ln-HATM
a433p






chimera








2025
T290
R2184.c4-chim_sc10ln-a433p-IP-MPER-TM
R2184.c4/BG505 
sc10ln-IP-MPER-TM
a433p






chimera








2026
T291
CNE55-chim_sc10ln-a433p-IP-10ln-HATM
CNE55/BG505 
sc10ln-IP-10ln-HATM
a433p






chimera








2027
T292
6545.V4.C1-chim_sc10In-a433p-IP-MPER-TM
6545.V4.C1/
sc10ln-IP-MPER-TM
a433p






BG505 chimera








2028
T293
DU422.01-chim_sc10ln-a433p-IP-10ln-HATM
DU422.01/BG505 
sc10ln-IP-10ln-HATM
a433p






chimera








2029
T294
25925-2.22-chim_sc10ln-a433p-IP-10ln-
25925-2.22/
sc10ln-IP-10ln-HATM
a433p





HATM
BG505 chimera








2030
T295
CNE58-chim_sc10ln-a433p-IP-10ln-HATM
CNE58/BG505 
sc10ln-IP-10ln-HATM
a433p






chimera








2031
T296
16055-2.3-chim_sc10ln-a433p-IP-10ln-HATM
16055-2.3/BG505 
sc10ln-IP-10ln-HATM
a433p






chimera








2032
T297
TH966.8-chim_sc10ln-a433p-IP-MPER-TM
TH966.8/BG505 
sc10ln-IP-MPER-TM
a433p






chimera








2033
T298
ZM55.28a-chim_sc10ln-a433p-IP-MPER-TM
ZM55.28a/BG505 
sc10ln-IP-MPER-TM
a433p






chimera








2034
T299
ZM53.12-chim_sc10ln-a433p-IP-MPER-TM
ZM53.12/BG505 
sc10ln-IP-MPER-TM
a433p






chimera








2035
T300
B1369.9A-chim_sc10lna433p--IP-10ln-HATM
B1369.9A/BG505 
sc10ln-IP-10ln-HATM
a433p






chimera








2036
T301
ZM197.7-chim_sc10ln-a433p-IP-MPER-TM
ZM197.7/BG505 
sc10ln-IP-MPER-TM
a433p






chimera








2037
T302
16055-2.3-chim_sc10ln-a433p-IP-MPER-TM
16055-2.3/BG505 
sc10ln-IP-MPER-TM
a433p






chimera








2038
T303
ZM55.28a-chim_sc15ln-SOS-a433p-10ln-HATM
ZM55.28a/BG505 
sc15ln-SOS-10ln-HATM
a433p






chimera








2039
T304
TH966.8-chim_sc10ln-IP-10ln-HATM-173-
TH966.8/BG505 
sc10ln-IP-10ln-HATM
173-177 mutated to YSLFE
Increase the negative charge in




yslfe-177
chimera


the V2 region to stabilize V2








to V3 interactions





2040
T305
6545.V4.C1-chim_sc10ln-IP-10ln-HATM-173-
6545.V4.C1/
sc10ln-IP-10ln-HATM
173-177 mutated to YSLFE
Same as Seq_2039




yslfe-177
BG505 chimera








2041
T306
R2184.c4-chim_sc10ln-IP-10ln-HATM-173-
R2184.c4/BG505 
sc10ln-IP-10ln-HATM
173-177 mutated to YSLFE
Same as Seq_2039




yslfe-177
chimera








2042
T307
ZM197.7-chim_sc10ln-IP-10ln-HATM-173-
ZM197.7/BG505 
sc10ln-IP-10ln-HATM
173-177 mutated to YSLFE
Same as Seq_2039




yslfe-177
chimera








2043
T308
ZM106.9-chim_sc10ln-IP-10ln-HATM-173-
ZM106.9/BG505 
sc10ln-IP-10ln-HATM
173-177 mutated to YSLFE
Same as Seq_2039




yslfe-177
chimera








2044
T309
ZM53.12-chim_sc10ln-IP-10ln-HATM-173-
ZM53.12/BG505 
sc10ln-IP-10ln-HATM
173-177 mutated to YSLFE
Same as Seq_2039




yslfe-177
chimera








2045
T310
R2184.c4-chim_sc10ln-IP-MPER-TM-173-
R2184.c4/BG505 
sc10ln-IP-MPER-TM
173-177 mutated to YSLFE
Same as Seq_2039




yslfe-177
chimera








2046
T311
CNE55-chim_sc10ln-IP-10ln-HATM-173-
CNE55/BG505 
sc10ln-IP-10ln-HATM
173-177 mutated to YSLFE
Same as Seq_2039




yslfe-177
chimera








2047
T312
6545.V4.C1-chim_sc10ln-IP-MPER-TM-173-
6545.V4.C1/
sc10ln-IP-MPER-TM
173-177 mutated to YSLFE
Same as Seq_2039




yslfe-177
BG505 chimera








2048
T313
DU422.01-chim_sc10ln-IP-10ln-HATM-173-
DU422.01/BG505 
sc10ln-IP-10ln-HATM
173-177 mutated to YSLFE
Same as Seq_2039




yslfe-177
chimera








2049
T314
25925-2.22-chim_sc10ln-IP-10ln-HATM-173-
25925-2.22/
sc10ln-IP-10ln-HATM
173-177 mutated to YSLFE
Same as Seq_2039




yslfe-177
BG505 chimera








2050
T315
CNE58-chim_sc10ln-IP-10ln-HATM-173-
CNE58/BG505 
sc10ln-IP-10ln-HATM
173-177 mutated to YSLFE
Same as Seq_2039




yslfe-177
chimera








2051
T316
16055-2.3-chim_sc10ln-IP-10ln-HATM-173-
16055-2.3/BG505 
sc10ln-IP-10ln-HATM
173-177 mutated to YSLFE
Same as Seq_2039




yslfe-177
chimera








2052
T317
TH966.8-chim_sc10ln-IP-MPER-TM-173-
TH966.8/BG505 
sc10ln-IP-MPER-TM
173-177 mutated to YSLFE
Same as Seq_2039




yslfe-177
chimera








2053
T318
ZM55.28a-chim_sc10ln-IP-MPER-TM-173-
ZM55.28a/BG505 
sc10ln-IP-MPER-TM
173-177 mutated to YSLFE
Same as Seq_2039




yslfe-177
chimera








2054
T319
ZM53.12-chim_sc10ln-IP-MPER-TM-173-
ZM53.12/BG505 
sc10ln-IP-MPER-TM
173-177 mutated to YSLFE
Same as Seq_2039




yslfe-177
chimera








2055
T320
B1369.9A-chim_sc10ln-IP-10ln-HATM-173-
B1369.9A/BG505 
sc10ln-IP-10ln-HATM
173-177 mutated to YSLFE
Same as Seq_2039




yslfe-177
chimera








2056
T321
ZM197.7-chim_sc10ln-IP-MPER-TM-173-
ZM197.7/BG505 
sc10ln-IP-MPER-TM
173-177 mutated to YSLFE
Same as Seq_2039




yslfe-177
chimera








2057
T322
16055-2.3-chim_sc10ln-IP-MPER-TM-173-
16055-2.3/BG505 
sc10ln-IP-MPER-TM
173-177 mutated to YSLFE
Same as Seq_2039




yslfe-177
chimera








2058
T323
ZM55.28a-chim_sc15ln-SOS-DS-10ln-HATM-
ZM55.28a/BG505 
sc15ln-SOS-DS-10ln-
173-177 mutated to YSLFE
Same as Seq_2039




173-yslfe-177
chimera
HATM







2059
T324
TH966.8-chim_sc10ln-IP-10ln-HATM-173-
TH966.8/BG505 
sc10ln-IP-10ln-HATM
173-177 mutated to ESLFE
Same as Seq_2039




eslfe-177
chimera








2060
T325
6545.V4.C1-chim sc10ln-IP-10ln-HATM-173-
6545.V4.C1/
sc10ln-IP-10ln-HATM
173-177 mutated to ESLFE
Same as Seq_2039




eslfe-177
BG505 chimera








2061
T326
R2184.c4-chim_sc10ln-IP-10ln-HATM-173-
R2184.c4/BG505 
sc10ln-IP-10ln-HATM
173-177 mutated to ESLFE
Same as Seq_2039




eslfe-177
chimera








2062
T327
ZM197.7-chim_sc10ln-IP-10ln-HATM-173-
ZM197.7/BG505 
sc10ln-IP-10ln-HATM
173-177 mutated to ESLFE
Same as Seq_2039




eslfe-177
chimera








2063
T328
ZM106.9-chim_sc10ln-IP-10ln-HATM-173-
ZM106.9/BG505 
sc10ln-IP-10ln-HATM
173-177 mutated to ESLFE
Same as Seq_2039




eslfe-177
chimera








2064
T329
ZM53.12-chim_sc10ln-IP-10ln-HATM-173-
ZM53.12/BG505 
sc10ln-IP-10ln-HATM
173-177 mutated to ESLFE
Same as Seq_2039




eslfe-177
chimera








2065
T330
R2184.c4-chim_sc10ln-IP-MPER-TM-173-
R2184.c4/BG505 
sc10ln-IP-MPER-TM
173-177 mutated to ESLFE
Same as Seq_2039




eslfe-177
chimera








2066
T331
CNE55-chim_sc10ln-IP-10ln-HATM-173-
CNE55/BG505 
sc10ln-IP-10ln-HATM
173-177 mutated to ESLFE
Same as Seq_2039




eslfe-177
chimera








2067
T332
6545.V4.C1-chim_sc10ln-IP-MPER-TM-173-
6545.V4.C1/
sc10ln-IP-MPER-TM
173-177 mutated to ESLFE
Same as Seq_2039




eslfe-177
BG505 chimera








2068
T333
DU422.01-chim_sc10ln-IP-10ln-HATM-173-
DU422.01/BG505 
sc10ln-IP-10ln-HATM
173-177 mutated to ESLFE
Same as Seq_2039




eslfe-177
chimera








2069
T334
25925-2.22-chim sc10ln-IP-10ln-HATM-173-
25925-2.22/
sc10ln-IP-10ln-HATM
173-177 mutated to ESLFE
Same as Seq_2039




eslfe-177
BG505 chimera








2070
T335
CNE58-chim_sc10ln-IP-10ln-HATM-173-
CNE58/BG505 
sc10ln-IP-10ln-HATM
173-177 mutated to ESLFE
Same as Seq_2039




eslfe-177
chimera








2071
T336
16055-2.3-chim_sc10ln-IP-10ln-HATM-173-
16055-2.3/BG505 
sc10ln-IP-10ln-HATM
173-177 mutated to ESLFE
Same as Seq_2039




eslfe-177
chimera








2072
T337
TH966.8-chim_sc10ln-IP-MPER-TM-173-
TH966.8/BG505 
sc10ln-IP-MPER-TM
173-177 mutated to ESLFE
Same as Seq_2039




eslfe-177
chimera








2073
T338
ZM55.28a-chim_sc10ln-IP-MPER-TM-173-
ZM55.28a/BG505 
sc10ln-IP-MPER-TM
173-177 mutated to ESLFE
Same as Seq_2039




eslfe-177
chimera








2074
T339
ZM53.12-chim_sc10ln-IP-MPER-TM-173-
ZM53.12/BG505 
sc10ln-IP-MPER-TM
173-177 mutated to ESLFE
Same as Seq_2039




eslfe-177
chimera








2075
T340
B1369.9A-chim_sc10ln-IP-10ln-HATM-173-
B1369.9A/BG505 
sc10ln-IP-10ln-HATM
173-177 mutated to ESLFE
Same as Seq_2039




eslfe-177
chimera








2076
T341
ZM197.7-chim_sc10ln-IP-MPER-TM-173-
ZM197.7/BG505 
sc10ln-IP-MPER-TM
173-177 mutated to ESLFE
Same as Seq_2039




eslfe-177
chimera








2077
T342
16055-2.3-chim_sc10ln-IP-MPER-TM-173-
16055-2.3/BG505 
sc10ln-IP-MPER-TM
173-177 mutated to ESLFE
Same as Seq_2039




eslfe-177
chimera








2078
T343
ZM55.28a-chim_sc15ln-SOS-DS-10ln-HATM-
ZM55.28a/BG505 
sc15ln-SOS-DS-10ln-
173-177 mutated to ESLFE
Same as Seq_2039




173-eslfe-177
chimera
HATM







2079
T344
TH966.8-chim_sc10ln-IP-10ln-HATM-173-
TH966.8/BG505 
sc10ln-IP-10ln-HATM
173-177 mutated to ESLFY
Same as Seq_2039




eslfy-177
chimera








2080
T345
6545.V4.C1-chim_sc10ln-IP-10ln-HATM-173-
6545.V4.C1/
sc10ln-IP-10ln-HATM
173-177 mutated to ESLFY
Same as Seq_2039




eslfy-177
BG505 chimera








2081
T346
R2184.c4-chim_sc10ln-IP-10ln-HATM-173-
R2184.c4/BG505 
sc10ln-IP-10ln-HATM
173-177 mutated to ESLFY
Same as Seq_2039




eslfy-177
chimera








2082
T347
ZM197.7-chim_sc10ln-IP-10ln-HATM-173-
ZM197.7/BG505 
sc10ln-IP-10ln-HATM
173-177 mutated to ESLFY
Same as Seq_2039




eslfy-177 
chimera








2083
T348
ZM106.9-chim_sc10ln-IP-10ln-HATM-173-
ZM106.9/BG505 
sc10ln-IP-10ln-HATM
173-177 mutated to ESLFY
Same as Seq_2039




eslfy-177
chimera








2084
T349
ZM53.12-chim_sc10ln-IP-10ln-HATM-173-
ZM53.12/BG505 
sc10ln-IP-10ln-HATM
173-177 mutated to ESLFY
Same as Seq_2039




eslfy-177
chimera








2085
T350
R2184.c4-chim_sc10ln-IP-MPER-TM-173-
R2184.c4/BG505 
sc10ln-IP-MPER-TM
173-177 mutated to ESLFY
Same as Seq_2039




eslfy-177
chimera








2086
T351
CNE55-chim_sc10ln-IP-10ln-HATM-173-
CNE55/BG505 
sc10ln-IP-10ln-HATM
173-177 mutated to ESLFY
Same as Seq_2039




eslfy-177
chimera








2087
T352
6545.V4.C1-chim_sc10ln-IP-MPER-TM-173-
6545.V4.C1/
sc10ln-IP-MPER-TM
173-177 mutated to ESLFY
Same as Seq_2039




eslfy-177
BG505 chimera








2088
T353
DU422.01-chim_sc10ln-IP-10ln-HATM-173-
DU422.01/BG505 
sc10ln-IP-10ln-HATM
173-177 mutated to ESLFY
Same as Seq_2039




eslfy-177
chimera








2089
T354
25925-2.22-chim_sc10ln-IP-10ln-HATM-173-
25925-2.22/
sc10ln-IP-10ln-HATM
173-177 mutated to ESLFY
Same as Seq_2039




eslfy-177
BG505 chimera








2090
T355
CNE58-chim_sc10ln-IP-10ln-HATM-173-
CNE58/BG505 
sc10ln-IP-10ln-HATM
173-177 mutated to ESLFY
Same as Seq_2039




eslfy-177
chimera








2091
T356
16055-2.3-chim_sc10ln-IP-10ln-HATM-173-
16055-2.3/BG505 
sc10ln-IP-10ln-HATM
173-177 mutated to ESLFY
Same as Seq_2039




eslfy-177
chimera








2092
T357
TH966.8-chim_sc10ln-IP-MPER-TM-173-
TH966.8/BG505 
sc10ln-IP-MPER-TM
173-177 mutated to ESLFY
Same as Seq_2039




eslfy-177
chimera








2093
T358
ZM55.28a-chim_sc10ln-IP-MPER-TM-173-
ZM55.28a/BG505 
sc10ln-IP-MPER-TM
173-177 mutated to ESLFY
Same as Seq_2039




eslfy-177
chimera








2094
T359
ZM53.12-chim_sc10ln-IP-MPER-TM-173-
ZM53.12/BG505 
sc10ln-IP-MPER-TM
173-177 mutated to ESLFY
Same as Seq_2039




eslfy-177
chimera








2095
T360
B1369.9A-chim_sc10ln-IP-10ln-HATM-173-
B1369.9A/BG505 
sc10ln-IP-10ln-HATM
173-177 mutated to ESLFY
Same as Seq_2039




eslfy-177
chimera








2096
T361
ZM197.7-chim_sc10ln-IP-MPER-TM-173-
ZM197.7/BG505 
sc10ln-IP-MPER-TM
173-177 mutated to ESLFY
Same as Seq_2039




eslfy-177
chimera








2097
T362
16055-2.3-chim_sc10ln-IP-MPER-TM-173-
16055-2.3/BG505 
sc10ln-IP-MPER-TM
173-177 mutated to ESLFY
Same as Seq_2039




eslfy-177
chimera








2098
T363
ZM55.28a-chim_sc15ln-SOS-DS-10ln-HATM-
ZM55.28a/BG505 
sc15ln-S0S-DS-10ln-
173-177 mutated to ESLFY
Same as Seq_2039




173-eslfy-177
chimera
HATM







2099
z
35O22 VH









2100
z
35O22 VL









2101
z
coat protein subunit



#NAME?





2102
z
coat protein subunit









2103
z
coat protein subunit









2104
z
coat protein subunit









2105
z
coat protein subunit









2106
z
coat protein subunit









2107
z
coat protein subunit









2108
z
coat protein subunit









2109
z
coat protein subunit









2110
z
coat protein subunit









2111
z
coat protein subunit









2112
z
coat protein subunit









2113
z
coat protein subunit









2114
0
T250-4
T250-4








2115
0
JRFL
JRFL








2116
H474
T2504.SOSIP.6R.201C433C
T2504.SOSIP.6R.








201C433C








2117

bg505.sosip_c15ln.201C-433C
bg505.sosip_








c15ln.201C-433C








2118

soluble CD4 (sCD4
soluble CD4 (sCD4








2119

BG505.SOSIP.R6.664.T332N_I201C/A433C
BG505 DNA







(VRC4571)









2120

BG505 WT DNA









2121
H475
*BG505.SOSIP.R6.664.T332N.D368R.V1V2.
BG505 chimera
V1V2SOSIP; 664; R6; 
V1V2 Swap CAP256-SU
SOSIP, V1V2 swap, 201-422 




CAP256_SU

201C, D368R, 433C, 

disulfide stabilization, cd4 






T332N

binding site KO,





2122
H476
*BG505.SOSIP.R6.664.T332N.D368R.V1V2.
BG505 chimera
V1V2SOSIP; 664; R6; 
V1V2 Swap BB201.B42
SOSIP, V1V2 swap, 201-422 




66201.B42

201C, D368R, 433C, 

disulfide stabilization, cd4 






T332N

binding site KO,





2123
H477
*BG505.SOSIP.R6.664.T332N.D368R.V1V2.
BG505 chimera
V1V2SOSIP; 664; R6; 
V1V2 Swap KER2018.11
SOSIP, V1V2 swap, 201-422 




KER2018.11

201C, D368R, 433C, 

disulfide stabilization, cd4 






T332N

binding site KO,





2124
H478
*BG505.SOSIP.R6.664.T332N.D368R.V1V2.
BG505 chimera
V1V2SOSIP; 664; R6; 
V1V2 Swap CH070.1
SOSIP, V1V2 swap, 201-422 




CH070.1

201C, D368R, 433C, 

disulfide stabilization, cd4 






T332N

binding site KO,





2125
H479
*BG505.SOSIP.R6.664.T332N.D368R.V1V2.
BG505 chimera
V1V2SOSIP; 664; R6; 
V1V2 Swap ZM233.6
SOSIP, V1V2 swap, 201-422 




ZM233.6

201C, D368R, 433C, 

disulfide stabilization, cd4 






T332N

binding site KO,





2126
H480
*BG505.SOSIP.R6.664.T332N.D368R.V1V2.
BG505 chimera
V1V2SOSIP; 664; R6; 
V1V2 Swap Q23
SOSIP, V1V2 swap, 201-422 




Q23

201C, D368R, 433C, 

disulfide stabilization, cd4 






T332N

binding site KO,





2127
H481
*BG505.SOSIP.R6.664.T332N.D368R.V1V2.
BG505 chimera
V1V2SOSIP; 664; R6; 
V1V2 Swap A244
SOSIP, V1V2 swap, 201-422 




A244

201C, D368R, 433C, 

disulfide stabilization, cd4 






T332N

binding site KO,





2128
H482
*BG505.SOSIP.R6.664.T332N.D368R.V1V2.
BG505 chimera
V1V2SOSIP; 664; R6; 
V1V2 Swap WITO
SOSIP, V1V2 swap, 201-422 




WITO

201C, D368R, 433C, 

disulfide stabilization, cd4 






T332N

binding site KO,





2129
H483 
*BG505.SOSIP.R6.664.T332N.D368R.V1V2.
BG505 chimera
V1V2SOSIP; 664; R6; 
V1V2 Swap T250.4
SOSIP, V1V2 swap, 201-422 




T250.4

201C, D368R, 433C, 

disulfide stabilization, cd4 






T332N

binding site KO,





2130
H484 
*BG505.SOSIP.R6.664.T332N.D368R.V1V2.
BG505 chimera
V1V2SOSIP; 664; R6; 
V1V2 Swap CAP256-SU. 
SOSIP, V1V2 swap, 201-422 




CAP256_SU.W34.77

201C, D368R, 433C, 
Week34.clone77
disulfide stabilization, cd4 






T332N

binding site KO,





2131
H485
*BG505.SOSIP.R6.664.T332N.D368R.V1V2.
BG505 chimera
V1V2SOSIP; 664; R6; 
V1V2 Swap CAP256-SU. 
SOSIP, V1V2 swap, 201-422 




CAP256_SU.W34.80

201C, D368R, 433C, 
Week34.clone80
disulfide stabilization, cd4 






T332N

binding site KO,





2132
H486 
*BG505.SOSIP.R6.664.T332N.D368R.V1V2.
BG505 chimera
V1V2SOSIP; 664; R6; 
V1V2 Swap CAP256-SU. 
SOSIP, V1V2 swap, 201-422 




CAP256_SU.W34.781

201C, D368R, 433C, 
Week34.clone81
disulfide stabilization, cd4 






T332N

binding site KO,





2133
H487
*CNE58.SOSIP.R6.V1V2.CAP256_SU
CNE58/136505 
V1V2SOSIP; 664; R6; 
V1V2 Swap CAP256-SU
SOSIP, V1V2 swap, 201-422 





chimera
201C, 433C

disulfide stabilization, on 








chimeric backbone





2134
H488
*CNE58.SOSIP.R6.V1V2.BB201.1342
CNE58/136505 
V1V2SOSIP; 664; R6; 
V1V2 Swap BB201.1342
SOSIP, V1V2 swap, 201-422 





chimera
201C, 433C

disulfide stabilization, on 








chimeric backbone





2135
H489
*CNE58.SOSIP.R6.V1V2.KER2018.11
CNE58/BG505 
V1V2SOSIP; 664; R6; 
V1V2 Swap KER2018.11
SOSIP, V1V2 swap, 201-422 





chimera
201C, 433C

disulfide stabilization, on 








chimeric backbone





2136
H490
*CNE58.SOSIP.R6.V1V2.CH070.1
CNE58/BG505 
V1V2SOSIP; 664; R6; 
V1V2 Swap CH070.1
SOSIP, V1V2 swap, 201-422 





chimera
201C, 433C

disulfide stabilization, on 








chimeric backbone





2137
H491
*CNE58.SOSIP.R6.V1V2.ZM233.6
CNE58/BG505 
V1V2SOSIP; 664; R6; 
V1V2 Swap ZM233.6
SOSIP, V1V2 swap, 201-422 





chimera
201C, 433C

disulfide stabilization, on 








chimeric backbone





2138
H492
*CNE58.SOSIP.R6.V1V2.Q23
CNE58/BG505 
V1V2SOSIP; 664; R6; 
V1V2 Swap Q23
SOSIP, V1V2 swap, 201-422 





chimera
201C, 433C

disulfide stabilization, on 








chimeric backbone





2139
H493
*CNE58.SOSIP.R6.V1V2.A244
CNE58/BG505 
V1V2SOSIP; 664; R6; 
V1V2 Swap A244
SOSIP, V1V2 swap, 201-422 





chimera
201C, 433C

disulfide stabilization, on 








chimeric backbone





2140
H494
*CNE58.SOSIP.R6.V1V2.WITO
CNE58/BG505 
V1V2SOSIP; 664; R6; 
V1V2 Swap WITO
SOSIP, V1V2 swap, 201-422 





chimera
201C, 433C

disulfide stabilization, on








chimeric backbone





2141
H495
*CNE58.SOSIP.R6.V1V2.T250.4
CNE58/BG505 
V1V2SOSIP; 664; R6; 
V1V2 Swap T250.4
SOSIP, V1V2 swap, 201-422 





chimera
201C, 433C

disulfide stabilization, on 








chimeric backbone















2142
0
426c


GenBank: KC769518.1, incorporated by reference herein as







present in GenBank on September 3, 2015









MDAMKRGLCCVLLLCGAVFVSPSASVGNLWVTVYYGVPVWKEAKTTLFCASDAKAYEKEVHNVWATHACVPTDPNPQEVVLENVTENFNMWKNDMVDQMQEDVISIWDQSLKPCVKLTPLCVTLNCTNVN



VTSNSTNVNSSSTDNTTLGElKNCSFDITTEIRDKTRKEYALFYRLDIVPLDNSSNPNSSNTYRLINCNTSTLTQACPKVTFDPIPIHYCAPAGYAILKCNNKTFNGKGPCNNVSTVQCTHGIKPVVSTQ



LLLNGSLAEEEIVIRSKNLSDNAKIIIVQLNKSVEIVCTRPNNNTRRSIRIGPGQTFYATDIIGDIRQAYCNISGRNWSEAVNQVKKKLKEHFPHKNISFQSSSGGDLEITTHSFNCGGEFFYCNTSGLF



NDTISNATIMLPCRIKQIINMWQEVGKAIYAPPIKGNITCKSDITGLLLLRDGGNTTNNTEIFRPGGGDMRDNWRSELYKYKVVEIKPLGVAPTDAKSSVVESNKSAVGIGAVFLGFLGAAGSTMGAASI



TLTVQARQLLSGIVQQQSNLLRAIEAQQHMLQLTVWGIKQLQTRVLAIERYLKDQQLLGLWGCSGKLICTTAVPWNISWSNKSKEEIWENMTWMQWDREINNYTNTIYRLLEESQNQQENNEKDLLALDS



WNNLWNWFNITNWLWYIK
















2143
0
426c DNA



















2144
0
426c.N276D.N460D.N463D


GenBank: KC769519.1, incorporated by reference herein as







present in GenBank on September 3, 2015









MDAMKRGLCCVLLLCGAVFVSPSASVGNLWVTVYYGVPVWKEAKTTLFCASDAKAYEKEVHNVWATHACVPTDPNPQEVVLENVTENFNMWKNDMVDQMQEDVISIWDQSLKPCVKLTPLCVTLNCTNVN



VTSNSTNVNSSSTDNTTLGEIKNCSFDITTEIRDKTRKEYALFYRLDIVPLDNSSNPNSSNTYRLINCNTSTLTQACPKVTFDPIPIHYCAPAGYAILKCNNKTFNGKGPCNNVSTVQCTHGIKPVVSTQ



LLLNGSLAEEEIVIRSKDLSDNAKIIIVQLNKSVEIVCTRPNNNTRRSIRIGPGQTFYATDIIGDIRQAYCNISGRNWSEAVNQVKKKLKEHFPHKNISFQSSSGGDLEITTHSFNCGGEFFYCNTSGLF



NDTISNATIMLPCRIKQIINMWQEVGKAIYAPPIKGNITCKSDITGLLLLRDGGDTTDNTEIFRPGGGDMRDNWRSELYKYKVVEIKPLGVAPTDAISSVVESNKSAVGIGAVFLGFLGAAGSTMGAASI



TLTVQARQLLSGIVQQQSNLLRAIEAQQHMLQLTVWGIKQLQTRVLAIERYLKDQQLLGLWGCSGKLICTTAVPWNISWSNKSKEEIWENMTWMQWDREINNYTNTIYRLLEESQNQQENNEKDLLALDS



WNNLWNWFNITNWLWYIK















2145
0
45_01dG5


GenBank: JQ609687.1, incorporated by reference herein as







present in GenBank on September 3, 2015









MRVMGIRKNCQRLWRGGTLFLGILMIFSAAENLWVTVYYGVPVWKEATATLFCASDAKAYETEVHNVWATHACVPTDPNPQEVVLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLNC



TDYLGNATNTTSSSGGAMEGGEIKNCSFNITTSMRDKMQKEYALFYKLDVVSIDNDNASTNYRLISCNTSVITQACPKISFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQL



LLNGSLAEEEIVIRSENIKDNAKIIIVQLNETVEINCTRPNNNTRKSIPIGPGRAFYTTGAIIGDIRQAHCNISKAKWENTLKQIARKLREHFKNETIAFNQSSGGDPEIVMHSFNCGGEFFYCNSTQLF



NSTWTWNDTEVVNNTEKNINITLPCRIKQIINMWQEVGKAMYAPPIKGQIRCSSNITGLLLTRDGGSSTNGTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGLAPTRAKRRVVQREKRAVGIGAVFLGF



LGAAGSTMGAASMTLTVQARLLLSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARVLAVERYLKDQQLLGIWGCSGKLICTTAVPWNASWSNKSLDKIWNNMTWMEWEREINNYTGLIYNLIEESQNQ



QEKNEQELLELDKWASLWNWFDITKWLWYIKIFIMIVGGLVGLRIIFTVLSIVNRVRQGYSPLSFQTHLPAPRGPDRPEGIGEEGGEQDRDRSDRLVTGFLAIFWVDLRSLCLFSYHRLRDLLLIVTRIV



ELLGRRGWEILKYWWNLLQYWNQELKNSAVSLLNATAIVVAEGTDRVIEVLQRAFRAVLNIPTRIRQGLERALL















2146
H496
*426c-v1v2-WITO-degly4-DS-gly504-gly661


BG505 platform; heterologous V1V2; remainder 426c with







N276, N460 and N463 glycan mutations; 201C/433C; add







504/661 sequons for glycosylation of membrane proximal







region









AENLWVTVYYGVPVWKEAKTTLFCASDAKAYEKEVHNVWATHACVPTDPNPQEVVLENVTENFNMWKNDMVDQMQEDVISIWDQSLKPCVKLTPLCVTLHCTNVTISSTNGSTANVTMREEMKNCSFNTT



TVIRDKIQKEYALFYKLDIVPIEGKNTNTGYRLINCNTATCTQACPKVTFDPIPIHYCAPAGYAILKCNNKTFNGKGPCNNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIVIRSKNLADNAKIIIVQLNK



SVEIVCTRPNNNTRRSIRIGPGQTFYATDIIGDIRQAYCNISGRNWSEAVNQVKKKLKEHFPHKNISFQSSSGGDLEITTHSFNCGGEFFYCNTSGLFNDTISNATIMLPCRIKQIINMWQEVGKCIYAP



PIKGNITCKSDITGLLLLRDGGNTANNAEIFRPGGGDMRDNWRSELYKYKVVKIEPLGGVAPTRCKRnvtGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQH



LLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIYGLLEESQNQQEKNEQDLnAtD















2147
H497
*426c-v1v2-WITO-degly3-DS-gly504-gly661


BG505 platform; heterologous V1V2; remainder 426c with







N276, N460 and N463 glycan mutations; 201C/433C; add







504/661 sequons for glycosylation of membrane proximal







region









AENLWVTVYYGVPVWKEAKTTLFCASDAKAYEKEVHNVWATHACVPTDPNPQEVVLENVTENFNMWKNDMVDQMQEDVISIWDQSLKPCVKLTPLCVTLHCTNVTISSTNGSTANVTMREEMKNCSFNTT



TVIRDKIQKEYALFYKLDIVPIEGKNTNTGYRLINCNTsTCTQACPKVTFDPIPIHYCAPAGYAILKCNNKTFNGKGPCNNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIVIRSKNLADNAKIIIVQLNK



SVEIVCTRPNNNTRRSIRIGPGQTFYATDIIGDIRQAYNISGRNWSEAVNQVKKKLKEHFPHKNISFQSSSGGDLEITTHSFNCGGEFFYCNTSGLFNDTISNATIMLPCRIKQIINMWQEVGKCIYAPP



IKGNITCKSDITGLLLLRDGGNTANNAEIFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRnvtGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLL



KLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLnAtD















2148
H498
*426c-v1v2-ZM233-degly4-DS-gly504-gly661


BG505 platform; heterologous V1V2; remainder 426c with







N276, N460 and N463 glycan mutations; 201C/433C; add







504/661 sequons for glycosylation of membrane proximal







region









AENLWVTVYYGVPVWKEAKTTLFCASDAKAYEKEVHNVWATHACVPTDPNPQEVVLENVTENFNMWKNDMVDQMQEDVISIWDQSLKPCVKLTPLCVTLDCSTYNNTHNISKEMKICSFNMTTELRDKKR



KVNVLFYKLDLVPLTNSSNTTNYRLISCNTATCTQACPKVTFDPIPIHYCAPAGYAILKCNNKTFNGKGPCNNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIVIRSKNLADNAKIIIVQLNKSVEIVCTR



PNNNTRRSIRIGPGQTFYATDIIGDIRQAYCNISGRNWSEAVNQVKKKLKEHFPHKNISFQSSSGGDLEITTHSFNCGGEFFYCNTSGLFNDTISNATIMLPCRIKQIINMWQEVGKCIYAPPIKGNITC



KSDITGLLLLRDGGNTANNAEIFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRnvtGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLKLTVWGI



KQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLEESQNQQEKNEQDLnAtD















2149
H499
*426c-v1v2-ZM233-degly3-DS-gly504-gly661


BG505 platform; heterologous V1V2; remainder 426c with







N276, N460 and N463 glycan mutations; 201C/433C; add







504/661 sequons for glycosylation of membrane proximal







region









AENLWVTVYYGVPVWKEAKTTLFCASDAKAYEKEVHNVWATHACVPTDPNPQEVVLENVTENFNMWKNDMVDQMQEDVISIWDQSLKPCVKLTPLCVTLDCSTYNNTHNISKEMKICSFNMTTELRDKKR



KVNVLFYKLDLVPLTNSSNTTNYRLISCNTsTCTQACPKVTFDPIPIHYCAPAGYAILKCNNKTFNGKGPCNNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIVIRSKNLADNAKIIIVQLNKSVEIVCTR



PNNNTRRSIRIGPGQTFYATDIIGDIRQAYCNISGRNWSEAVNQVKKKLKEHFPHKNISFQSSSGGDLEITTHSFNCGGEFFYCNTSGLFNDTISNATIMLPCRIKQIINMWQEVGKCIYAPPIKGNITC



KSDITGLLLLRDGGNTANNAEIFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRnvtGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLKLTVWGI



KQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLnAtD















2150
H500
*d45-v1v2-WITO-01dG5chim-DS-gly504-


BG505 platform; heterologous V1V2; remainder 45_01dG5,




gly661


201C/433C; add 504/661 sequons for glycosylation of







membrane proximal region









AENLWVTVYYGVPVWKEATATLFCASDAKAYETEVHNVWATHACVPTDPNPQEVVLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLHCTNVTISSTNGSTANVTMREEMKNCSFNTT



TVIRDKIQKEYALFYKLDIVPIEGKNTNTGYRLINCNTsVCTQACPKISFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENIKDNAKIIIVQLNE



TVEINCTRPNNNTRKSIPIGPGRAFYTTGAIIGDIRQAHCNISKAKWENTLKQIARKLREHFKNETIAFNQsSGGDPEIVMHSFNCGGEFFYCNSTQLFNSTWTWNDTEVVNNTEKNINITLPCRIKQII



NMWQEVGKCMYAPPIKGQIRCSSNITGLLLTRDGGSSTNGTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRnVtGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQ



QSNLLRAPEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLnAtD















2151
H501
*d45-v1v2-WITO-01dG5chim-degly3-DS-


BG505 platform; heterologous V1V2; remainder 45_01dG5,




gly504-gly661


201C/433C; add 504/661 sequons for glycosylation of







membrane proximal region









AENLWVTVYYGVPVWKEATATLFCASDAKAYETEVHNVWATHACVPTDPNPQEVVLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLHCTNVTISSTNGSTANVTMREEMKNCSFNTT



TVIRDKIQKEYALFYKLDIVPIEGKNTNTGYRLINCNTsVCTQACPKISFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENIKDNAKIIIVQLNE



TVEINCTRPNNNTRKSIPIGPGRAFYTTGAIIGDIRQAHCNISKAKWENTLKQIARKLREHFKNETIAFNQaSGGDPEIVMHSFNCGGEFFYCNSTQLFNSTWTWNDTEVVNNTEKNINITLPCRIKQII



NMWQEVGKCMYAPPIKGQIRCSSNITGLLLTRDGGSSTNGTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRnVtGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQ



QSNLLRAPEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLnAtD















2152
H502
*d45-v1v2-WITO-01dG5chim-degly4-DS-


BG505 platform; heterologous V1V2; remainder 45_01dG5,




gly504-gly661


201C/433C; add 504/661 sequons for glycosylation of







membrane proximal region









AENLWVTVYYGVPVWKEATATLFCASDAKAYETEVHNVWATHACVPTDPNPQEVVLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLHCTNVTISSTNGSTANVTMREEMKNCSFNTT



TVIRDKIQKEYALFYKLDIVPIEGKNTNTGYRLINCNTaVCTQACPKISFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENIKDNAKIIIVQLNE



TVEINCTRPNNNTRKSIPIGPGRAFYTTGAIIGDIRQAHCNISKAKWENTLKQIARKLREHFKNETIAFNQaSGGDPEIVMHSFNCGGEFFYCNSTQLFNSTWTWNDTEVVNNTEKNINITLPCRIKQII



NMWQEVGKCMYAPPIKGQIRCSSNITGLLLTRDGGSSTNGTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRnVtGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQ



QSNLLRAPEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLnAtD















2153
H503
*d45-v1v2-ZM233-01dG5chim-DS-gly504-


BG505 platform; heterologous V1V2; remainder 45_01dG5,




gly661


201C/433C; add 504/661 sequons for glycosylation of







membrane proximal region









AENLWVTVYYGVPVWKEATATLFCASDAKAYETEVHNVWATHACVPTDPNPQEVVLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLDCSTYNNTHNISKEMKICSFNMTTELRDKKR



KVNVLFYKLDLVPLTNSSNTTNYRLISCNTsVCTQACPKISFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENIKDNAKIIIVQLNETVEINCTR



PNNNTRKSIPIGPGRAFYTTGAIIGDIRQAHCNISKAKWENTLKQIARKLREHFKNETIAFNQsSGGDPEIVMHSFNCGGEFFYCNSTQLFNSTWTWNDTEVVNNTEKNINITLPCRIKQIINMWQEVGK



CMYAPPIKGQIRCSSNITGLLLTRDGGSSTNGTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRnVtGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAP



EAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLnAtD















2154
H504
*d45-v1v2-ZM233-01dG5chim-degly3-DS-


BG505 platform; heterologous V1V2; remainder 45_01dG5,




gly504-gly661


201C/433C; add 504/661 sequons for glycosylation of







membrane proximal region









AENLWVTVYYGVPVWKEATATLFCASDAKAYETEVHNVWATHACVPTDPNPQEVVLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLDCSTYNNTHNISKEMKICSFNMTTELRDKKR



KVNVLFYKLDLVPLTNSSNTTNYRLISCNTsVCTQACPKISFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENIKDNAKIIIVQLNETVEINCTR



PNNNTRKSIPIGPGRAFYTTGAIIGDIRQAHCNISKAKWENTLKQIARKLREHFKNETIAFNQaSGGDPEIVMHSFNCGGEFFYCNSTQLFNSTWTWNDTEVVNNTEKNINITLPCRIKQIINMWQEVGK



CMYAPPIKGQIRCSSNITGLLLTRDGGSSTNGTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRnVtGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAP



EAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLnAtD















2155
H505
*d45-v1v2-ZM233-01dG5chim-degly4-DS-


BG505 platform; heterologous V1V2; remainder 45_01dG5,




gly504-gly661


201C/433C; add 504/661 sequons for glycosylation of







membrane proximal region









AENLWVTVYYGVPVWKEATATLFCASDAKAYETEVHNVWATHACVPTDPNPQEVVLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLDCSTYNNTHNISKEMKICSFNMTTELRDKKR



KVNVLFYKLDLVPLTNSSNTTNYRLISCNTaVCTQACPKISFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENIKDNAKIIIVQLNETVEINCTR



PNNNTRKSIPIGPGRAFYTTGAIIGDIRQAHCNISKAKWENTLKQIARKLREHFKNETIAFNQaSGGDPEIVMHSFNCGGEFFYCNSTQLFNSTWTWNDTEVVNNTEKNINITLPCRIKQIINMWQEVGK



CMYAPPIKGQIRCSSNITGLLLTRDGGSSTNGTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRnVtGRRRRRRAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAP



EAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLnAtD















2156
H506
*Sc15ln 426c-v1v2-WITO-degly4-DS-


BG505 platform; heterologous V1V2; remainder 426c with




gly504-gly661


N276, N460 and N463 glycan mutations; 201C/433C, single







chain format with 15 AA linker; add 504/661 sequons for







glycosylation of membrane proximal region









AENLWVTVYYGVPVWKEAKTTLFCASDAKAYEKEVHNVWATHACVPTDPNPQEVVLENVTENFNMWKNDMVDQMQEDVISIWDQSLKPCVKLTPLCVTLHCTNVTISSTNGSTANVTMREEMKNCSFNTT



TVIRDKIQKEYALFYKLDIVPIEGKNTNTGYRLINCNTATCTQACPKVTFDPIPIHYCAPAGYAILKCNNKTFNGKGPCNNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIVIRSKNLADNAKIIIVQLNK



SVEIVCTRPNNNTRRSIRIGPGQTFYATDIIGDIRQAYCNISGRNWSEAVNQVKKKLKEHFPHKNISFQSSSGGDLEITTHSFNCGGEFFYCNTSGLFNDTISNATIMLPCRIKQIINMWQEVGKCIYAP



PIKGNITCKSDITGLLLLRDGGNTANNAEIFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRnvtGGGSGGGGSGGGGSGGAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLL



RAPEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLnAtD















2157
H507
*Sc10ln 426c-v1v2-WITO-degly4-DS-


BG505 platform; heterologous V1V2; remainder 426c with




gly504-gly661


N276, N460 and N463 glycan mutations; 201C/433C, single







chain format with 10 AA linker; add 504/661 sequons for







glycosylation of membrane proximal region









AENLWVTVYYGVPVWKEAKTTLFCASDAKAYEKEVHNVWATHACVPTDPNPQEVVLENVTENFNMWKNDMVDQMQEDVISIWDQSLKPCVKLTPLCVTLHCTNVTISSTNGSTANVTMREEMKNCSFNTT



TVIRDKIQKEYALFYKLDIVPIEGKNTNTGYRLINCNTATCTQACPKVTFDPIPIHYCAPAGYAILKCNNKTFNGKGPCNNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIVIRSKNLADNAKIIIVQLNK



SVEIVCTRPNNNTRRSIRIGPGQTFYATDIIGDIRQAYCNISGRNWSEAVNQVKKKLKEHFPHKNISFQSSSGGDLEITTHSFNCGGEFFYCNTSGLFNDTISNATIMLPCRIKQIINMWQEVGKCIYAP



PIKGNITCKSDITGLLLLRDGGNTANNAEIFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRnvtGGGSGGGGSGGAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEA



QQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLnAtD















2158
H508
*Sc15ln d45-v1v2-ZM233-01dG5chim-DS-g1y504-


BG505 platform; heterologous V1V2; remainder 45_01dG5; 201C/433C, single




gly661


chain format with 15 AA linker; add 504/661 sequons for glycosylation of







membrane proximal region









AENLWVTVYYGVPVWKEATATLFCASDAKAYETEVHNVWATHACVPTDPNPQEVVLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLDCSTYNNTHNISKEMKICSFNMTTELRDKKR



KVNVLFYKLDLVPLTNSSNTTNYRLISCNTsVCTQACPKISFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENIKDNAKIIIVQLNETVEINCTR



PNNNTRKSIPIGPGRAFYTTGAIIGDIRQAHCNISKAKWENTLKQIARKLREHFKNETIAFNQsSGGDPEIVMHSFNCGGEFFYCNSTQLFNSTWTWNDTEVVNNTEKNINITLPCRIKQIINMWQEVGK



CMYAPPIKGQIRCSSNITGLLLTRDGGSSTNGTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRnVtGGGSGGGGSGGGGSGGAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQ



QQSNLLRAPEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLnAtD















2159
H509
*Sc10ln d45-v1v2-ZM233-01dG5chim-DS-


BG505 platform; heterologous V1V2; remainder 45_01dG5; 




gly504-gly661


201C/433C, single chain format with 10 AA linker; add 







504/661 sequons for glycosylation of membrane proximal







region









AENLWVTVYYGVPVWKEATATLFCASDAKAYETEVHNVWATHACVPTDPNPQEVVLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLDCSTYNNTHNISKEMKICSFNMTTELRDKKR



KVNVLFYKLDLVPLTNSSNTTNYRLISCNTsVCTQACPKISFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENIKDNAKIIIVQLNETVEINCTR



PNNNTRKSIPIGPGRAFYTTGAIIGDIRQAHCNISKAKWENTLKQIARKLREHFKNETIAFNQsSGGDPEIVMHSFNCGGEFFYCNSTQLFNSTWTWNDTEVVNNTEKNINITLPCRIKQIINMWQEVGK



CMYAPPIKGQIRCSSNITGLLLTRDGGSSTNGTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRnVtGGGSGGGGSGGAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNL



LRAPEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLnAtD









It will be apparent that the precise details of the methods or compositions described may be varied or modified without departing from the spirit of the described embodiments. We claim all such modifications and variations that fall within the scope and spirit of the claims below. Unless indicated otherwise, HIV-1 Env amino acid positions listed in the following claims correspond to the HXB2 numbering system using the HXB2 reference sequence set forth as SEQ ID NO: 1

Claims
  • 1. An isolated immunogen, comprising: a recombinant HIV-1 Env ectodomain trimer stabilized in a prefusion mature closed conformation by a non-natural disulfide bond between cysteine substitutions at positions 201 and 433, wherein the HIV-1 Env positions correspond to a HXB2 reference sequence set forth as SEQ ID NO: 1.
  • 2. The immunogen of claim 1, wherein: (A) the recombinant HIV-1 Env ectodomain trimer further comprises a proline substitution at position 559; a non-natural disulfide bond between cysteine substitutions at positions 501 and 605; or a non-natural disulfide bond between cysteine substitutions at positions 501 and 605 and a proline substitution at position 559; to stabilize the recombinant HIV-1 Env ectodomain trimer or immunogenic fragment in the prefusion mature closed conformation;(B) the HIV-1 Env ectodomain trimer specifically binds to VRC26 mAb and/or PGT145 mAb, and does not specifically bind to 17b mAb when incubated with a molar excess of sCD4.(C) the HIV-1 Env ectodomain trimer comprises three gp120-gp41 protomers comprising a gp120 polypeptide comprising or consisting of HIV-1 Env positions 31-507 and a gp41 ectodomain comprising or consisting of HIV-1 Env positions 512-664(D) the recombinant HIV-1 Env ectodomain trimer comprises a BG505 Env ectodomain trimer modified to comprise the one or more amino acid substitutions; and/or(E) the recombinant HIV-1 Env ectodomain trimer is a chimera comprising: (i) a V1V2 domain of an HIV-1 Env protein from any one of a CAP256.SU, a BB201.B42, a KER2018.11, a CH070.1, a ZM233.6, a Q23.17, a A244, a T250-4, or a WITO.33, strain of HIV-1; gp120 positions 31-45 and 478-508 and a gp41 ectodomain from a BG505 strain of HIV-1; and the remaining gp120 positions from a 45_01dG5 strain of HIV-1;(ii) a V1V2 domain of an HIV-1 Env protein from any one of a CAP256.SU, a BB201.B42, a KER2018.11, a CH070.1, a ZM233.6, a Q23.17, a A244, a T250-4, or a WITO.33, strain of HIV-1; gp120 positions 31-45 and 478-508 and a gp41 ectodomain from a BG505 strain of HIV-1; and the remaining gp120 positions from a 426c strain further comprising amino acid substitutions to remove N-linked glycan sequons at positions 276, 460, 463; or(iii) a V1V2 domain of an HIV-1 Env protein from any one of a CAP256.SU, a BB201.B42, a KER2018.11, a CH070.1, a ZM233.6, a Q23.17, a A244, a T250-4, or a WITO.33, strain of HIV-1; and the remaining gp120 positions from a BG505 strain of HIV-1; andwherein the chimera further comprises the one or more amino acid substitutions that stabilize the recombinant HIV-1 Env ectodomain trimer in the prefusion mature closed conformation
  • 3-6. (canceled)
  • 7. An isolated immunogen, comprising: a recombinant HIV-1 Env ectodomain trimer or immunogenic fragment thereof stabilized in a prefusion mature closed conformation by one or more amino acid substitutions compared to a native HIV-1 Env sequence; whereinthe recombinant HIV-1 Env ectodomain trimer comprises three gp120-gp41 protomers comprising a gp120 polypeptide and a gp41 ectodomain; andthe recombinant HIV-1 Env ectodomain trimer does not specifically bind to a CD4-induced antibody when incubated with a molar excess of sCD4.
  • 8. The immunogen of claim 7, wherein the gp41 ectodomain comprise an α7 helix that forms C-terminal to position 570; andthe distance between positions 200 and 313 of the gp120 polypeptides in the trimer is less than five angstroms, wherein the HIV-1 Env positions correspond to a HXB2 reference sequence set forth as SEQ ID NO: 1.
  • 9. The immunogen of claim 7, wherein the HIV-1 Env ectodomain trimer or immunogenic fragment specifically binds to PGT145 mAb and/or VRC26 mAb, and does not specifically bind to 17b mAb when incubated with a molar excess of sCD4; and optionally binds to a unmutated common ancestor (UCA) of a broadly neutralizing antibody related to a VRC26 antibody, a VRC01 antibody, a CH01 antibody, a PG9 antibody, and/or a PGT145 antibody, with a KD of less than 10−5.
  • 10. The immunogen of claim 7, wherein: the N-terminal residue of the gp120 polypeptide is one of HIV-1 Env positions 1-35;the C-terminal residue of the gp120 polypeptide is one of HIV-1 Env positions 503-512;the N-terminal residue of the gp41 ectodomain is one of HIV-1 Env positions 512-522; and/orthe C-terminal residue of the gp41 ectodomain is one of HIV-1 Env positions 624-705, andwherein the HIV-Env positions correspond to a HXB2 reference sequence set forth as SEQ ID NO: 1.
  • 11. The immunogen of claim 10, wherein the gp120 polypeptide comprises or consists of HIV-1 Env positions 31-507, and the gp41 ectodomain comprises or consists of HIV-1 Env positions 512-664, wherein the HIV-Env positions correspond to a HXB2 reference sequence set forth as SEQ ID NO: 1.
  • 12. The immunogen of claim 7, wherein the gp120 polypeptide and the gp41 ectodomain comprise amino acid sequences of positions 31-511 and 512-664 (HXB2 numbering), respectively, of the HIV-1 Env amino acid sequence set forth as SEQ ID NO: 2 (BG505), SEQ ID NO: 51 (CAP256.SU), SEQ ID NO: 81 (BB201.B42), SEQ ID NO: 107 (KER2018.11), SEQ ID NO: 174 (CH070.1), SEQ ID NO: 745 (ZM233.6), SEQ ID NO: 746 (Q23.17), SEQ ID NO: 747 (A244), SEQ ID NO: 2114 (T250-4), or SEQ ID NO: 748 (WITO.33), or sequences at least 80% identical thereto that comprise the at least one amino acid substitution that stabilizes the recombinant HIV-1 Env ectodomain in the prefusion mature closed conformation.
  • 13. The immunogen of claim 7, wherein the recombinant HIV-1 Env ectodomain trimer is a chimera comprising amino acid sequences from at least two HIV-1 strains, wherein the gp41 ectodomain, an N-terminal region of the gp120 polypeptide comprising a β-4 strand, and a C-terminal region of the gp120 polypeptide comprising a β26 strand, are from a first strain of HIV-1; andthe remaining sequence of the gp120 polypeptide are from a heterologous strain of HIV-1; andthe sequences of the first and heterologous strains have been modified to comprise one or more amino acid substitutions that stabilize the recombinant HIV-1 Env ectodomain trimer in the prefusion mature closed conformation.
  • 14. The immunogen of claim 13, wherein: (A) the N-terminal region of the gp120 polypeptide further comprises a β-3 strand from the first HIV-1 strain; and the C-terminal region of the gp120 polypeptide further comprises a β25 strand or a β25 strand and a α5 helix from the first HIV-1 strain;(B) the N- and C-terminal regions of the gp120 polypeptide comprise gp120 positions 31-45 and 478-508, respectively;(C) the gp120 polypeptide further comprises the sequence of positions 46-54, 70-75, 84-89, 99, 102, 106, 107, 114, 215, 220-224, 226, 244, 471-473, and 476-477 from the first HIV-1 strain;(D) the gp120 polypeptide further comprises the sequence of one of the following from the first HIV-1 strain: a V1 loop; a V2 loop; a Strand C of the V1V2 domain; a V3 domain; Positions 191-205; a V2 loop and a V3 loop; a Strand C of the V1V2 domain and a V3 domain; Positions 191-205 and a Strand C of the V1V2 domain; a V1 loop and a V3 domain; a V1 loop, a Strand C of the V1V2 domain, and a V3 domain; a V1 loop, a V2 loop, and a V3 domain; or a V1V2 domain;(E) the V1 loop comprises gp120 positions 119-153, the V2 loop comprises gp120 positions 154-205, the Strand C of the V1V2 domain comprises gp120 positions 166-173, the V3 domain comprises gp120 positions 296-331, and the V1V2 domain comprises gp120 positions 126-196;(F) the first strain is BG505; and/or(G) the heterologous strain is selected from one of the following HIV-1 strains: BI369.9A, MB201.A1, QH209.14M.A2, 0921.V2.C14, 16055-2.3, 25925-2.22, 286.36, CAP45.G3, DU156.12, DU422.01, MW965.26, ZM53.12, ZM55.28a, ZM106.9, 3301.V1.C24, 6545.V4.C1, 620345.c1, C1080.c3, C4118.09, CNE55, TH966.8, AC10.29, CH038.12, CNE58, CH117.4, CAP256.SU, BB201.B42, KER2018.11, CH070.1, ZM233.6, Q23.17, A244, T250-4, WITO.33, 426c, 45_01dG5, and JRFL, strain of HIV-1, particularly wherein the heterologous strain is the JRFL strain of HIV-1.
  • 15-18. (canceled)
  • 19. The immunogen of claim 7, wherein the recombinant HIV-1 Env ectodomain trimer is a chimera comprising amino acid sequences from at least two HIV-1 strains, wherein the recombinant HIV-1 Env ectodomain trimer comprises a V1V2 domain of an HIV-1 Env protein from a heterologous HIV-1 strain, and the remainder of the recombinant HIV-1 Env ectodomain is from a first strain of HIV-1, optionally wherein the V1V2 domain comprises positions 126-196.
  • 20-21. (canceled)
  • 22. The immunogen of claim 7, wherein the recombinant HIV-1 Env ectodomain trimer is a chimera comprising amino acid sequences from at least three HIV-1 strains, wherein the gp41 ectodomain, an N-terminal region of the gp120 polypeptide comprising a β-4 strand, and a C-terminal region of the gp120 polypeptide comprising a β26 strand, are from a first strain of HIV-1;a V1V2 domain of the gp120 polypeptide is from a second strain of HIV-1; andthe remaining sequence of the gp120 polypeptide is from a heterologous strain of HIV-1; andthe sequences of the first, second, and heterologous strains have been modified to comprise the one or more amino acid substitutions that stabilize the recombinant HIV-1 Env ectodomain trimer in the prefusion mature closed conformation.
  • 23. The immunogen of claim 22, wherein: (A) the N-terminal region of the gp120 polypeptide further comprises a β-3 strand from the first HIV-1 strain; and the C-terminal region of the gp120 polypeptide further comprises a β25 strand or a β25 strand and a α5 helix from the first HIV-1 strain;(B) the N- and C-terminal regions of the gp120 polypeptide comprise gp120 positions 31-45 and 478-508, respectively;(C) the V1V2 domain comprises gp120 positions 126-196;(D) the gp120 polypeptide further comprises positions 46-54, 70-75, 84-89, 99, 102, 106, 107, 114, 215, 220-224, 226, 244, 471-473, and 476-477 from the first HIV-1 strain;(E) the first strain is BG505;(F) the second strain is selected from one of the following HIV-1 strains: BI369.9A, MB201.A1, QH209.14M.A2, 0921.V2.C14, 16055-2.3, 25925-2.22, 286.36, CAP45.G3, DU156.12, DU422.01, MW965.26, ZM53.12, ZM55.28a, ZM106.9, 3301.V1.C24, 6545.V4.C1, 620345.c1, C1080.c3, C4118.09, CNE55, TH966.8, AC10.29, CH038.12, CNE58, CH117.4, CAP256.SU, BB201.B42, KER2018.11, CH070.1, ZM233.6, Q23.17, A244, T250-4, WITO.33, and JRFL, strain of HIV-1;(G) the second strain is one of CAP256.SU, BB201.B42, KER2018.11, CH070.1, ZM233.6, Q23.17, A244, T250-4, WITO.33, and JRFL;(H) the heterologous strain is a 45_01dG5 strain;(I) the heterologous strain is a 426c strain further comprising amino acid substitutions to remove the N-linked glycan sequons at positions 276, 460, 463; and/or(J) the second and heterologous strains are respectively one of: CAP256.SU and 426c; BB201.B42 and 426c; KER2018.11 and 426c; CH070.1 and 426c; ZM233.6 and 426c; Q23.17 and 426c; A244 and 426c; T250-4 and 426c; WITO.33 and 426c; CAP256.SU and 45_01dG5; BB201.B42 and 45_01dG5; KER2018.11 and 45_01dG5; CH070.1 and 45_01dG5: ZM233.6 and 45_01dG5; 023.17 and 45_01dG5: A244 and 45_01dG5; T250-4 and 45_01dG5: or WITO.33 and 45_01dG5; and wherein the 426c strain further comprises amino acid substitutions to remove the N-linked glycan sequons at positions 276, 460, 463.
  • 24-32. (canceled)
  • 33. The immunogen of claim 7, wherein the one or more amino acid substitutions that stabilize the HIV-1 Env ectodomain trimer in the prefusion mature closed conformation comprise cysteine substitutions in a V2 domain and a β21 sheet of the recombinant HIV-1 ectodomain trimer to form a non-native disulfide bond between the V2 domain and the β21 sheet that stabilizes the HIV-1 Env ectodomain trimer in the prefusion mature closed conformation.
  • 34. The immunogen of claim 7, wherein the one or more amino acid substitutions that stabilize the HIV-1 Env ectodomain trimer in the prefusion mature closed conformation comprise cysteine amino acid substitutions to introduce a non-natural disulfide bond between any one of: one of gp120 positions 179-180 and one of gp120 positions 420-423;one of gp120 positions 190-210 and one of gp120 positions 425-437;one of gp120 positions 198-202 and one of gp120 positions 428-437;one of gp120 positions 179-180 and one of gp120 positions 421-423; orone of gp120 positions 195-201 and one of gp120 positions 423-433, wherein the non-natural disulfide bond stabilizes the HIV-1 Env ectodomain in the prefusion mature closed conformation;particularly wherein the one or more amino acid substitutions comprise cysteine amino acid substitutions to introduce a non-natural disulfide bond between one of gp120 positions 195-201 and one of gp120 positions 423-433, wherein the non-natural disulfide bond stabilizes the HIV-1 Env ectodomain in the prefusion mature closed conformation.
  • 35. The immunogen of claim 7, wherein the one or more amino acid substitutions that stabilize the HIV-1 Env ectodomain trimer in the prefusion mature closed conformation comprise cysteine substitutions to introduce a non-natural disulfide bond between any one of HIV-1 Env positions 36 and 496, 36 and 498, 37 and 497, 38 and 496, 36 and 608, 55 and 77, 57 and 77, 58 and 77, 66 and 209, 68 and 208, 68 and 209, 120 and 315, 122 and 125, 122 and 203, 122 and 317, 122 and 433, 124 and 164, 124 and 166, 128 and 165, 128 and 167, 163 and 170, 164 and 197, 164 and 308, 172 and 307, 174 and 318, 174 and 319, 175 and 319, 176 and 180, 180 and 421, 180 and 423, 195 and 423, 195 and 433, 199 and 431, 199 and 433, 200 and 313, 200 and 432, 201 and 433, 202 and 434, 202 and 433, 204 and 434, 204 and 436, 206 and 318, 212 and 252, 225 and 245, 225 and 488, 257 and 375, 294 and 333, 298 and 329, 304 and 440, 318 and 437, 320 and 438, 364 and 372, 370 and 426, 380 and 426, 382 and 424, 425 and 433, and 425 and 430, wherein the non-natural disulfide bond stabilizes the HIV-1 Env ectodomain in the prefusion mature closed conformation;particularly wherein the one or more amino acid substitutions comprise cysteine amino acid substitutions to introduce a non-natural disulfide bond between one of:HIV-1 Env positions 120 and 315;HIV-1 Env positions 195 and 433;HIV-1 Env positions 199 and 433;HIV-1 Env positions 201 and 433; orHIV-1 Env positions 425 and 433.
  • 36. The immunogen of claim 35, wherein the one or more amino acid substitutions comprise one of V36C and V496C, V36C and P498C, T37C and A497C, V38C and V496C, V36C and V608C, A55C and T77C, D57C and T77C, A58C and T77C, V66C and S209C, V68C and V208C, V68C and S209C, V120C and Q315C, L122C and L125C, L122C and Q203C, L122C and A433C, P124C and T164C, P124C and R166C, T128C and L165C, T128C and T167C, T163C and Q170C, E164C and N197C, S174C and A319C, L175C and T320C, F176C and D180C, D180C and K421C, D180C and I423C, N195C and I423C, N195C and A433C, S199C and G431C, S199C and A433C, A200C and P313C, A200C and Q432C, I201C and A433C, T202C and M434C, T202C and A433C, A204C and M434C, A204C and A436C, P212C and K252C, I225C and V245C, I225C and V488C, T257C and S375C, I294C and V333C, R298C and A329C, R304C and Q440C, Y318C and P437C, T320C and P438C, S364C and T372C, E370C and M426C, G380C and M426C, F382C and I424C, N425C and A433C, and N425C and I430C, to introduce a non-natural disulfide bond that stabilizes the HIV-1 Env ectodomain in the prefusion mature closed conformation.
  • 37. The immunogen of claim 7, wherein the one or more amino acid substitutions that stabilize the HIV-1 Env ectodomain trimer in the prefusion mature closed conformation comprise any one or more of the following: 112I, 112M, 120T, 122K, 120P, 202P, 427I, 427M, 429N, 429L, 432P, 432E, 432D, 433P, 434P, 435P, 436P, 437A, 438A, 474A, 476A, or a combination of two or more thereof.
  • 38. The immunogen of claim 7, wherein the HIV-1 Env ectodomain comprises a proline amino acid substitution at position 66, position 67, or positions 66 and 67, wherein the proline amino acid substitution inhibits formation of a c0 helix in the HIV-1 Env ectodomain to stabilize the HIV-1 Env ectodomain in the prefusion mature closed conformation.
  • 39. The immunogen of claim 7, wherein the one or more amino acid substitutions that stabilize the HIV-1 Env ectodomain trimer in the prefusion mature closed conformation comprise a cavity filling amino acid substitution at any one or more of HIV-1 Env positions 39, 50, 53, 55, 61, 68, 70, 75, 77, 110, 111, 114, 115, 117, 118, 120, 121, 123, 125, 136, 139, 151, 153, 154, 159, 161, 164, 173, 175, 176, 177, 179, 180, 191, 198, 201, 202, 203, 204, 208, 209, 220, 223, 245, 246, 254, 260, 261, 263, 302, 309, 317, 323, 326, 328, 332, 380, 421, 423, 426, 429, 431, 432, 436, 437, 473, 478, 522, 523, 530, 534, or 544, wherein the cavity filling substitution stabilizes the recombinant HIV-1 Env ectodomain trimer in the prefusion mature closed conformation.
  • 40. The immunogen of claim 39, wherein the cavity filling substitution comprises a 50W, 53W, 55F, 61W, 68L, 70F, 70Y, 75W, 75F, 75M, 77F, 110W, 111Y, 111F, 111W, 114W, 115W, 117E, 117W, 118W, 120W, 121E, 123W, 125W, 125F, 136W, 139W, 151E, 153F, 153W, 154F, 154W, 159W, 159Y, 161W, 164F, 164W, 173W, 175F, 175W, 176W, 177W, 179W, 180L, 191W, 191F, 198F, 201W, 202F, 202W, 203V, 204F, 204W, 208W, 208Y, 208F, 208M, 209R, 220W, 223W, 245F, 246W, 254F, 260F, 261F, 263W, 302F, 302W, 309W, 317W, 326R, 328W, 323W, 326F, 332F, 380F, 421W, 423F, 423W, 426W, 426A, 426F, 426P, 429W, 431P, 432F, 432W, 436M, 436F, 436W, 437F, 473A, 473S, 473Y, 478F, 522Y, 523F, 530W, 534V, 534A, or 544Y substitution, or a combination of two or more thereof; or wherein the cavity filling substitution comprises a T50W, A55F, F53W, Y61W, V68L, A70F, A70Y, V75W, V75F, V75M, T77F, S110W, L111W, L111Y, L111F, Q114W, S115W, K117E, K117W, P118W, V120W, K121E, T123W, L125W, L125F, N136W, T139W, R151E, E153F, E153W, L154F, L154W F159W, F159Y, M161W, E164F, E164W, Y173W, L175F, L175W, F176W Y177W, L179W, D180L, Y191W, Y191F, T198F, I201W, T202F, T202W, Q203V, A204F, A204W, V208W, V208Y, V208F, V208, S209R, P220W, F223W, V245F, Q246W, V254F, L260F, L261F, G263W, N302F, N302W, I309W, F317W, I323W, I326F, I326R, Q328W, I332F, G380F, K421W, I423W, I423F, M426W, M426A, M426F, M426P, R429W, G431P, Q432F, Q432W, A436M, A436F, A436W, P437F, G473A, G473S, G473Y, N478F, F522Y, L523F, M530W, S534V, S534A, or L544Y substitution, or a combination of two or more thereof.
  • 41. The immunogen of claim 7, wherein the one or more amino acid substitutions that stabilize the HIV-1 Env ectodomain trimer in the prefusion mature closed conformation comprise: (a) a non-natural disulfide bond between cysteine substitutions at one of positions 174 and 319, 195 and 433, 199 and 433, 199 and 431, 201 and 433, 221 and 582, or 304 and 440;(b) non-natural disulfide bonds between cysteine substitutions at positions: (i) 195 and 433, and 304 and 440;(ii) 195 and 433, and 174 and 319;(iii) 199 and 433, and 304 and 440;(iv) 199 and 433, and 174 and 319;(v) 201 and 433, and 304 and 440; or(vi) 201 and 433, and 174 and 319;(c) a tryptophan substitution at position 223 and a non-natural disulfide bond between cysteine substitutions at one of positions 195 and 433, 199 and 433, or 201 and 433; or(d) a proline substitution at position 432 or 433; andwherein the HIV-Env positions correspond to a HXB2 reference sequence set forth as SEQ ID NO: 1.
  • 42. The immunogen of claim 7, wherein the one or more amino acid substitutions that stabilize the HIV-1 Env ectodomain trimer in the prefusion mature closed conformation further comprise: (a) a non-natural disulfide bond between cysteine substitutions at positions 501 and 605;(b) a proline substitution at position 559; or(c) a combination of (a) and (b); andwherein the HIV-Env positions correspond to a HXB2 reference sequence set forth as SEQ ID NO: 1.
  • 43. The immunogen of claim 7, wherein the HIV-1 Env ectodomain further comprises a non-natural disulfide bond between a pair of cysteine substitutions at positions 41 and 540, 41 and 541, 43 and 526, 51 and 574, 53 and 574, 51 and 578, 43 and 540, 88 and 527, 107 and 574, 220 and 578, 221 and 582, 428 and 560, 428 and 561, 428 and 562, 498 and 610, 550 and 575, or 551 and 575, 36 and 606, 37 and 606, 41 and 537, 73 and 572, 84 and 521, 89 and 527, or a combination of two or more non-natural disulfide bonds between the pairs of cysteines, wherein the non-natural disulfide bond or combination thereof stabilizes the HIV-1 Env ectodomain; and wherein the HIV-Env positions correspond to a HXB2 reference sequence set forth as SEQ ID NO: 1.
  • 44. The immunogen of claim 7, wherein: the recombinant HIV-1 Env ectodomain further comprises one or more amino acid substitutions that introduce an N-linked glycosylation site at the N-terminus of the gp120 polypeptide, the C-terminus of the gp120 polypeptide, and/or the C-terminus of the gp41 polypeptide.the recombinant HIV-1 Env ectodomain further comprises one or more amino acid substitutions that introduce an N-linked glycosylation site at one of position 33, 35, 502, 504, 658, or 661, or a combination of two or more thereof;the recombinant HIV-1 Env ectodomain further comprises one or more amino acid substitutions that introduce N-linked glycosylation sites at positions 35 and 504, 33 and 661, 504 and 661, or 502 and 661; and/orthe recombinant HIV-1 Env ectodomain further comprises one or more amino acid substitutions that introduce N-linked glycosylation sites at positions 504 and 661, and wherein the HIV-Env positions correspond to a HXB2 reference sequence set forth as SEQ ID NO: 1
  • 45. (canceled)
  • 46. The immunogen of claim 7, wherein the gp120-gp41 protomers are single chain HIV-1 Env ectodomains, and wherein the N-terminal residue of the gp120 polypeptide is linked to the C-terminal residue of the gp41 ectodomain by a heterologous peptide linker.
  • 47. The immunogen of claim 46, wherein: (A) the heterologous peptide linker joins gp120 and gp41 positions 507 and 512, 503 and 519, 504 and 519, 503 and 522, or 504 and 522, respectfully.(B) the heterologous peptide linker joins gp120 and gp41 positions 507 and 512, respectfully(C) the heterologous peptide linker comprises a 10 amino acid glycine-serine linker; and/or(D) the heterologous peptide linker comprises the amino acid sequence set forth as SEQ ID NOs: 528 (GGSGGGGSGG)
  • 48-50. (canceled)
  • 51. The immunogen of claim 7, wherein the gp120-gp41 protomers in the recombinant HIV-1 Env ectodomain trimer are linked to a transmembrane domain.
  • 52. The immunogen of claim 51, wherein: (A) the N-terminal residue of the gp120 polypeptide is linked to the transmembrane domain and/or the C-terminal residue of the gp41 ectodomain is linked to the transmembrane domain.(B) the gp120-gp41 protomers in the recombinant HIV-1 Env ectodomain trimer are linked to the transmembrane domain by a heterologous peptide linker or by a native HIV-1 Env MPER sequence;(C) the peptide linker comprises a 10 amino acid glycine-serine peptide linker;(D) the heterologous peptide linker comprises the amino acid sequence set forth as SEQ ID NOs: 528 (GGSGGGGSGG); and/or(E) the transmembrane domains comprises the amino acid sequence set forth as one of SEQ ID NOs: 568, 560, 562, 758, 760, 762, or an amino acid sequence at least 80% identical thereto
  • 53-56. (canceled)
  • 57. The immunogen of claim 7, wherein the recombinant HIV-1 Env ectodomain comprises: (A) a cysteine substitution at position 90, 238, 529, 624, or 625 that can form a non-natural disulfide bond with a cysteine residue on a 35O22 antibody or clonal variant thereof;(B) a cysteine substitution at position 449 that can form a non-natural disulfide bond with a cysteine residue on a VRC01 antibody or clonal variant thereof;(C) a cysteine substitution at position 323 that can form a non-natural disulfide bond with a cysteine residue on a PGT122 antibody or clonal variant thereof;(D) a combination of (B) or (C), and (A); or(E) a combination of (A), (B), and (C); andwherein the HIV-Env positions correspond to a HXB2 reference sequence set forth as SEQ ID NO: 1.
  • 58. The immunogen of claim 57, comprising: (A) the recombinant HIV-1 Env ectodomain crosslinked to a 35O22 antibody by a non-natural disulfide bond between the 90C substitution on the HIV-1 ectodomain and a 80C substitution (kabat numbering) on a heavy chain variable region of the 35O22 antibody;(B) the recombinant HIV-1 Env ectodomain crosslinked to a 35O22 antibody by a non-natural disulfide bond between the 238C substitution on the HIV-1 ectodomain and a 77C substitution (kabat numbering) on a heavy chain variable region of the 35O22 antibody;(C) the recombinant HIV-1 Env ectodomain crosslinked to a 35O22 antibody by a non-natural disulfide bond between the 529C substitution on the HIV-1 ectodomain and a 111C substitution (kabat numbering) on a heavy chain variable region of the 35O22 antibody;(D) the recombinant HIV-1 Env ectodomain crosslinked to a 35O22 antibody by a non-natural disulfide bond between the 624C substitution on the HIV-1 ectodomain and a 109C or 112C substitution (kabat numbering) on a heavy chain variable region of the 35O22 antibody;(E) the recombinant HIV-1 Env ectodomain crosslinked to a 35O22 antibody by a non-natural disulfide bond between the 625C substitution on the HIV-1 ectodomain and a 109C substitution (kabat numbering) on a heavy chain variable region of the 35O22 antibody;(F) the recombinant HIV-1 Env ectodomain crosslinked to a VRC01 antibody by a non-natural disulfide bond between the 449C substitution on the HIV-1 ectodomain and a 60C or 61C substitution (kabat numbering) on a heavy chain variable region of the VRC01 antibody;(G) the recombinant HIV-1 Env ectodomain crosslinked to a PGT122 antibody by a non-natural disulfide bond between the 323C substitution on the HIV-1 ectodomain and a 29C or 67C substitution (kabat numbering) on a heavy chain variable region of the PGT122 antibody;(H) a combination of (F) or (G), and one of (A)-(E); or(G) a combination of (F), (G), and one of (A)-(E).
  • 59. An isolated immunogen, comprising: a recombinant polypeptide comprising a V1, V2, and V3 domain of HIV-1 Env stabilized in a prefusion mature closed conformation and linked to a heterologous scaffold protein,optionally wherein the heterologous scaffold protein is a heterologous HIV-1 ectodomain stabilized in a prefusion mature closed conformation by one or more amino acid substitutions;optionally wherein the recombinant polypeptide comprises the amino acid sequence set forth as any one of SEQ ID NOs: 836-843, or an amino acid sequence at least 80% identical thereto.
  • 60. The immunogen of claim 7, wherein the one or more amino acid substitutions that stabilize the recombinant HIV-1 Env ectodomain trimer in the prefusion mature closed conformation comprise: cysteine substitutions at positions 201 and 433 substitutions to introduce a disulfide bond in the HIV-1 Env ectodomain trimer;cysteine substitutions at positions 501 and 605 to introduce a disulfide bond in the HIV-1 Env ectodomain trimer; anda proline substitution at position 559.
  • 61. The immunogen of claim 60, wherein the gp120-gp41 protomers in the recombinant HIV-1 Env ectodomain trimer comprise the amino acid sequence set forth as one of SEQ ID NOs: 26, 1057-1077, 1400-1579.
  • 62. The immunogen of claim 61, comprising BG505.SOSIP.R6.664.T332N_I201C/A433C.
  • 63. The immunogen of claim 7, further comprising a D368R substitution, an N-linked glycosylation site at position 332, an R6 substitution, or a combination thereof.
  • 64. The immunogen of claim 7, wherein the gp120-gp41 protomers in the recombinant HIV-1 Env ectodomain trimer comprise: the amino acid sequence set forth as one of SEQ ID NO: 26, 856, 871, 872, 881, 888, 902, 908, 917, 924, 930, 933, 937, 938, 940, 953, 962, 964, 973, 978, 990, 1010, 1025, 1034, 1035, 1057, 1058, 1059, 1060, 1061, 1062, 1063, 1064, 1065, 1066, 1067, 1068, 1069, 1070, 1071, 1072, 1073, 1074, 1075, 1076, 1077, 1244, 1643, 1676, 1677, 1678, 1679, 1680, 1681, 1682, 1683, 1684, 1685, 1686, 1687, 1688, 1689, 1690, 1691, 1692, 1693, 1694, 1695, 1696, 1697, 1698, 1699, 1700, 1701, 1702, 1703, 1704, 1705, 1706, 1707, 1708, 1709, 1710, 1711, 1712, 1713, 1714, 1715, 1732, 1735, 1736, 1738, 1739, 1740, 1741, 1742, 1744, 1752, 1758, 1759, 1760, 1761, 1762, 1763, 2121, 2122, 2123, 2124, 2125, 2126, 2127, 2128, 2129, 2130, 2131, 2132, 2133, 2134, 2135, 2136, 2137, 2138, 2139, 2140, 2141, 2146, 2147, 2148, 2149, 2150, 2151, 2152, 2153, 2154, 2155, 2156, 2157, 2158, or 2159, or an amino acid sequence at least 90% identical thereto;the amino acid sequence set forth as one of SEQ ID NOs: 1244-1764, or an amino acid sequence at least 90% identical thereto; orthe amino acid sequence set forth as one of SEQ ID NOs: 1765-2098, or an amino acid sequence at least 90% identical thereto.
  • 65-66. (canceled)
  • 67. The immunogen of claim 7, wherein the gp120-gp41 protomers in the recombinant HIV-1 Env ectodomain trimer are linked to trimerization domains, optionally wherein the trimerization domains are Foldon domains, optionally wherein the gp120-gp41 protomers linked to the trimerization domains comprise an amino acid sequence set forth as any one of SEQ ID NOs: 508-510, or 844-853, or an amino acid sequence at least 80% identical thereto.
  • 68. A protein nanoparticle comprising the recombinant HIV-1 Env ectodomain trimer or immunogenic fragment of claim 7.
  • 69. The protein nanoparticle of claim 69, wherein: (A) the protein nanoparticle is a ferritin nanoparticle, an encapsulin nanoparticle, a Sulfur Oxygenase Reductase (SOR) nanoparticle, a lumazine synthase nanoparticle or a pyruvate dehydrogenase nanoparticle;(B) the protein nanoparticle comprises two or more of the recombinant HIV-1 Env proteins, and wherein the two or more recombinant HIV-1 Env proteins are from two or more different strains of HIV-1; and/or(C) the recombinant HIV-1 Env ectodomain trimer or immunogenic fragment comprises gp120/gp41 protomers linked to a protein nanoparticle subunit that comprise an amino acid sequence set forth as any one of 471-507, 596-645, 797-835, 1099-1113, or 1201-1218, or an amino acid sequence at least 80% identical thereto.
  • 70-71. (canceled)
  • 72. An isolated nucleic acid molecule encoding the recombinant HIV-1 Env ectodomain trimer or the immunogenic fragment thereof of claim 7.
  • 73. The nucleic acid molecule of claim 72, wherein the nucleic acid molecule encodes a precursor protein of the gp120/gp41 protomers in the recombinant HIV-1 Env ectodomain trimer.
  • 74. The nucleic acid molecule of claim 72, operably linked to a promoter.
  • 75. A vector comprising the nucleic acid molecule of claim 74.
  • 76. An isolated host cell comprising the vector of claim 75.
  • 77. (canceled)
  • 78. An immunogenic composition comprising an effective amount of the immunogen of claim 7, and a pharmaceutically acceptable carrier.
  • 79. The immunogenic composition of claim 78, further comprising an adjuvant.
  • 80. A method for generating an immune response to Human Immunodeficiency Virus type 1 (HIV-1) gp120 in a subject, comprising administering to the subject an effective amount of the immunogenic composition of claim 78, thereby generating the immune response.
  • 81. A method for treating or preventing a Human Immunodeficiency Virus type 1 (HIV-1) infection in a subject, comprising administering to the subject a therapeutically effective amount of the immunogenic composition of claim 78, thereby treating the subject or preventing HIV-1 infection of the subject.
  • 82. The method of claim 80, comprising a prime-boost administration of the immunogenic composition.
  • 83. A method for detecting or isolating an antibody that specifically binds to HIV-1 Env from a subject, comprising: providing an effective amount of the immunogen of claim 7;contacting a biological sample from the subject with the immunogen under conditions sufficient to form an immune complex between the immunogen and the antibody that specifically binds to HIV-1 Env; anddetecting the immune complex, thereby detecting or isolating the antibody from the subject.
  • 84. The method of claim 80, wherein the subject is at risk of or has an HIV-1 infection.
  • 85-87. (canceled)
  • 88. The immunogen of claim 1, wherein the one or more amino acid substitutions that stabilize the recombinant HIV-1 Env ectodomain trimer in the prefusion mature closed conformation comprise cysteine substitutions at positions 201 and 433 to introduce a disulfide bond in the HIV-1 Env ectodomain trimer.
CROSS REFERENCE TO RELATED APPLICATIONS

This application claims priority to U.S. Provisional Application Nos. 62/046,059, filed Sep. 4, 2014, and 62/136,480, filed Mar. 21, 2015, each of which is incorporated by reference in its entirety.

PCT Information
Filing Document Filing Date Country Kind
PCT/US2015/048729 9/4/2015 WO 00
Provisional Applications (2)
Number Date Country
62046059 Sep 2014 US
62136480 Mar 2015 US