Patent Grant
11965001
The present disclosure relates to modular dimerization thermoswitches and related monomers, dimers, constructs, dimeric complexes, vectors, cells, surfaces and devices as well as related compositions, methods and systems, to spatiotemporally control formation of dimeric complexes through thermo-regulated dimerization.
Recent advances in synthetic biology are driving the development of biological switches for use in various applications wherein controlled formation of an association, of molecule of interest is desired.
For example, an important capability of biological switches for use in connection, with assays, as well as therapeutic and/or diagnostic applications, is the ability to control binding, and location of molecules such as proteins or other moiety one with another.
Despite development of approaches to control molecular associations, challenges remain for developing high-performance and/or tunable bioswitches to control complex formation with spatiotemporal regulation in a wide range of applications including biomedical and industrial applications.
Provided herein are modular temperature sensing dimers (herein also dimerization thermoswitches, thermomers, or thermomer dimers) and related monomers constructs, dimeric complexes, vectors, cells, surfaces, devices, as well as related compositions, methods and systems, which allow in several embodiments controlled thermo-regulated formation of molecular complexes.
According to a first aspect, a thermomer monomer is described comprising a temperature sensing region having temperature sensing sequence
wherein X111 X112, X161 X162 X182 and X183 are independently a negatively charged amino acid preferably a E and/or D or a positively charged amino acid preferably K and/or R,
or any derivative thereof configured to dimerize in a target environment at a target environment temperature Te below a bioswitch temperature Tbs in a temperature dependent manner to form a coiled coil temperature sensing domain.
According to a second aspect, a thermomer dimer is described. The thermomer dimer is formed by a first thermomer monomer of the disclosure having a first temperature sensing region and a second thermomer monomer of the disclosure having a second temperature sensing region.
In the thermomer dimer, the first thermomer monomer and the second thermomer monomer are configured to dimerize in a target environment at a target temperature Te<Tbs with a thermal Hill coefficient above 15, to form a coiled coil temperature sensing domain having comprising the first temperature sensing region and the second temperature sensing region and having a melting temperature Tm=Tbs−0° C. to 5° C.
In the preferred embodiments, at least one pair of corresponding residues forming non-covalent bonds between the first temperature sensing region and the second temperature sensing region, selected from
In the preferred embodiments,
According to a third aspect, a thermomer monomeric construct is described, comprising a thermomer monomer of the present disclosure configured to dimerize in a target environment to form a coiled coil temperature sensing domain at a target environment temperature Te<Tbs, the coiled coil temperature sensing domain having a melting temperature Tm=Tbs−0° C. to 5° C.
In the thermomer monomeric construct, the thermomer monomer has an N-terminus end and a C-terminus and is attached to a linker polypeptide having has an N-terminus end and a C-terminus and/or to a cargo moiety formed by a chemical moiety having a diameter of up to 1 micron.
In particular, in the thermomer monomeric construct, the thermomer monomer is attached to the linker polypeptide through attachment of one of the N-terminus end or a C-terminus of the thermomer monomer with one of the C-terminus end or N-terminus, of the linker polypeptide.
In the alternative, in the thermomer monomeric construct, the thermomer monomer is attached to the cargo moiety through
According to a fourth aspect, a thermomer dimeric complex is described. The thermomer dimeric complex comprises
In the thermomer dimeric complex, the first thermomer monomer and the second thermomer monomer are configured to dimerize in a target environment at a target temperature Te<Tbs with a thermal Hill coefficient above 15, to form a coiled coil temperature sensing domain having comprising the first temperature sensing region and the second temperature sensing region and having a melting temperature Tm=Tbs−0° C. to 5° C.
In the thermomer dimeric complex comprising a first cargo moiety and/or second cargo moiety, at least one of the first cargo moiety and the second cargo moiety is configured to have an interface with the target environment subjected to a Stokes' drag force up to 50 pN, preferably up to 20, pN more preferably 10 pN or even more preferably 6-7 pN or lower.
According to a fifth aspect, a thermomer vector is described comprising a thermomer gene expression cassette comprising a polynucleotide encoding for a thermomer monomer or a thermomer monomeric construct herein described comprising the linker polypeptide and/or a cargo moiety in which the chemical moiety comprises a polypeptide. In the thermomer gene expression cassette, the polynucleotide is under control of a promoter and additionally regulatory regions in a configuration allowing expression of the thermomer monomer or thermomer monomeric construct of the present disclosure in a target environment.
According to a sixth aspect, a thermomer cell is described comprising at least one of the thermomer monomer, thermomer dimer, thermomer monomeric construct, thermomer dimeric construct and thermomer vector herein described within a biological cell.
According to a seventh aspect, a thermomer surface is described comprising at least one of the thermomer monomer, thermomer dimer, thermomer monomeric construct, thermomer dimeric construct attached to a surface configured to directly or indirectly attach a polypeptide comprised in the linker polypeptide and/or the cargo moiety.
According to an eighth aspect, a thermomer device is described comprising at least one thermomer surface herein described and configured to allow performance of any one of the methods herein described wherein at least one thermomer monomeric construct and/or thermomer dimeric construct is attached to the thermomer surface.
According to a ninth aspect a method and a system are described to provide a thermomer monomer construct of the present disclosure; the method comprising providing a thermomer monomer of the present disclosure, the thermomer monomer having an N-terminus end and C-terminus,
The system to provide a thermomer monomer construct of the present disclosure, comprises
In embodiments, wherein the cargo moiety is formed by a polypeptide, the system can also comprise a polynucleotide encoding for the cargo moiety in addition or in the alternative to the cargo moiety as will be understood by a skilled person.
According to a tenth aspect, a method and a system are described to provide a thermomer dimeric complex of the present disclosure. The method comprises
In the method, the first thermomer monomer and the second thermomer monomer are configured to dimerize in a target environment at a target temperature Te<Tbs with a thermal Hill coefficient above 15, to form a coiled coil temperature sensing domain having comprising the first temperature sensing region and the second temperature sensing region and having a melting temperature Tm=Tbs−0° C. to 5° C.
In the method to provide a thermomer dimeric complex at least one of the first cargo moiety and the second cargo moiety has a Stokes' drag force acting on the interface between an aqueous fluid of the target environment and the cargo equal or lower than 6-7 pN.
The method to provide a thermomer dimeric complex of the present disclosure further comprises
In some embodiments the method can further comprise, attaching the N-terminus or C-terminus of the linker polypeptide or the cargo moiety of at least one of the first monomeric construct and second monomeric construct to a surface configured to allow the related binding before or after the contacting.
The system to provide a thermomer dimeric complex of the present disclosure, comprises
According to an eleventh aspect, a method and a system are described to control location of a first cargo moiety and/or second cargo moiety in a target environment having a target environment temperature Te. In the method and system, the first cargo moiety and optionally the second cargo moiety have a Stokes' drag force acting on the interface between an aqueous fluid of the target environment and the cargo up to 50 pN.
The method to control location of the cargo moiety and optionally the second cargo moiety, comprises
In the thermomer dimeric complex, the first thermomer monomer and the second thermomer monomer are configured to dimerize in a target environment at a target temperature Te<Tbs with a thermal Hill coefficient above 15, to form a coiled coil temperature sensing domain having comprising the first temperature sensing region and the second temperature sensing region and having a melting temperature Tm=Tbs−0° C. to 5° C.
The method further comprises changing the temperature Te to obtain Te<Tbs the changing performed to dimerize the first thermomer monomer and the second thermomer monomer thus obtaining the thermomer dimer complex in the target environment.
In some embodiments, the second thermomer monomeric construct herein described comprises the second thermomer monomer of the present disclosure attached to the second linker polypeptide and the second linker polypeptide is attached to a surface configured to bind the linker polypeptide.
The system to control location of a first cargo moiety and optionally a second cargo moiety in a target environment, comprises
According to an twelfth aspect, a method and systems to modify a bioswitch temperature Tbs0 of a thermomer dimer of the instant disclosure in a target environment and variants obtained thereby are described.
In the method to modify a bioswitch temperature Tbs0 of a thermomer dimer of the instant disclosure, the thermomer dimer has a melting temperature Tm0 with Tbs0=Tm+0° C. to 5° C.
In the method to modify a bioswitch temperature Tbs0 of a thermomer dimer of the instant disclosure, each thermomer monomer of the thermomer dimer has residues A1 to A291 arranged of the respect temperature sensing sequence arranged in consecutive uninterrupted series of heptad repeats a, b, c, d, e, f, or g, with at least two of the heptad repeats having a register in which no amino acid is missing, and up to 49 heptad repeats a register in which up to 5 consecutive amino acid residues are optionally missing.
The method to modify a bioswitch temperature Tbs of the thermomer dimer comprises
Additional aspects can comprise, i) a polynucleotide encoding for a thermomer monomer, thermomer dimer, thermomer monomeric constructs and/or a thermomer dimeric complexes, ii) a composition comprising a thermomer monomer, thermomer dimer, thermomer monomeric constructs and/or a thermomer dimeric complexes together with a suitable vehicle, iii) additional methods using a thermomer monomer, thermomer dimer, thermomer monomeric constructs and/or a thermomer dimeric complexes, and iv) additional systems comprising a thermomer monomer, thermomer dimer, thermomer monomeric constructs and/or a thermomer dimeric complexes, as well as additional aspects identifiable by a skilled person.
Thermomer monomers, thermomer dimers, thermomer monomeric construct, thermomer dimeric complexes of the instant disclosure, and related vectors, cells surface, devices, compositions, methods and systems herein described, allow in several embodiments to control spatial and/or temporal location of a cargo moiety in a target environment in a thermoregulated manner.
Thermomer monomers, thermomer dimers, thermomer monomeric construct, thermomer dimeric complexes of the instant disclosure, and related vectors, cells, surface, devices, compositions, methods and systems herein described, allow in several embodiments to thermally control interactions and binding of cargo moieties in a target environment.
Thermomer monomers, thermomer dimers, thermomer monomeric construct, thermomer dimeric complexes of the instant disclosure, and related vectors, cells, surface, devices, compositions, methods and systems herein described, allow in several embodiments to trigger formation and dissociation of dimer complexes in a thermally regulated manner.
Thermomer monomers, thermomer dimers, thermomer monomeric construct, thermomer dimeric complexes of the instant disclosure, and related vectors, cells, surface, devices, compositions, methods and systems herein described, can be used in connection with various applications wherein controlled location, interaction and/or binding of cargo moieties as well as controlled formation and dissociation of related complexes is desired. For example, thermomer monomers, thermomer dimers, thermomer monomeric constructs, thermomer dimeric complexes of the instant disclosure, and related vectors, cells compositions, methods and systems herein described can be used to provide spatially and/or temporally controlled location of therapeutics in medical applications, drug research and manufacturing, biological synthesis of chemicals and proteins such as enzymes or catalysts or polymers, as well diagnostics and/or clinical applications. In another example, thermomer monomers, thermomer dimers, thermomer monomeric constructs, thermomer dimeric complexes of the instant disclosure, and related vectors, cells compositions, methods and systems herein described can be used to control the activity of split proteins and/or protein-inhibitor complexes to regulate protein function in a temperature-dependent fashion.
Additional exemplary applications include uses of the monomers, thermomer dimers, thermomer monomeric construct, thermomer dimeric complexes of the instant disclosure, and related vectors, cells, surface, devices, compositions, methods and systems herein described in several fields including basic biology research, applied biology, bio-engineering, bio-energy, medical research, medical diagnostics, therapeutics, bio-fuels, and in additional fields identifiable by a skilled person upon reading of the present disclosure.
The details of one or more embodiments of the disclosure are set forth in the accompanying drawings and the description below. Other features, objects, and advantages will be apparent from the description and drawings, and from the claims
The accompanying drawings, which are incorporated into and constitute a part of this specification, illustrate one or more embodiments of the present disclosure and, together with the detailed description and the examples, serve to explain the principles and implementations of the disclosure.
Provided herein are modular temperature sensing dimers (herein also dimerization thermoswitches, thermomers, or thermomer dimers) formed by two monomer proteins and related monomers constructs, dimeric complexes, vectors, cells, compositions, methods and systems, which allow in several embodiments controlled thermo-regulated formation of molecular complexes
The term “dimer” as used herein indicates a macromolecular complex formed by two polymers and in particular by two proteins.
The term “protein” as used herein indicates a polypeptide with a particular secondary and tertiary structure that can interact with another molecule and in particular, with other biomolecules including other proteins, DNA, RNA, lipids, metabolites, hormones, chemokines, and/or small molecules. The term “polypeptide” as used herein indicates an organic linear, circular, or branched polymer composed of two or more amino acid monomers and/or analogs thereof. The term “polypeptide” includes amino acid polymers of any length including full-length proteins and peptides, as well as analogs and fragments thereof. A polypeptide of three or more amino acids is also called a protein oligomer, peptide, or oligopeptide. In particular, the terms “peptide” and “oligopeptide” usually indicate a polypeptide with less than 100 amino acid monomers. In particular, in a protein, the polypeptide provides the primary structure of the protein, wherein the term “primary structure” of a protein refers to the sequence of amino acids in the polypeptide chain covalently linked to form the polypeptide polymer. A protein “sequence” indicates the order of the amino acids that form the primary structure. Covalent bonds between amino acids within the primary structure can include peptide bonds or disulfide bonds, and additional bonds identifiable by a skilled person. Polypeptides in the sense of the present disclosure are usually composed of a linear chain of alpha-amino acid residues covalently linked by peptide bond or a synthetic covalent linkage. The two ends of the linear polypeptide chain encompassing the terminal residues and the adjacent segment are referred to as the carboxyl terminus (C-terminus) and the amino terminus (N-terminus) based on the nature of the free group on each extremity. Unless otherwise indicated, counting of residues in a polypeptide is performed from the N-terminal end (NH2-group), which is the end where the amino group is not involved in a peptide bond to the C-terminal end (—COOH group) which is the end where a COOH group is not involved in a peptide bond. Proteins and polypeptides can be identified by x-ray crystallography, direct sequencing, immunoprecipitation, and a variety of other methods as understood by a person skilled in the art. Proteins can be provided in vitro or in vivo by several methods identifiable by a skilled person. In some instances where the proteins are synthetic proteins in at least a portion of the polymer two or more amino acid monomers and/or analogs thereof are joined through chemically-mediated condensation of an organic acid (—COOH) and an amine (—NH2) to form an amide bond or a “peptide” bond.
The two ends of the linear polypeptide chain encompassing the terminal amino acid residues and the adjacent segment are referred to as the carboxyl terminus (C-terminus) and the amino terminus (N-terminus) based on the nature of the free group on each extremity. Unless otherwise indicated counting of residues in a polypeptide is performed from the N-terminal end (NH2-group), which is the end where the amino group is not involved in a peptide bond to the C-terminal end (—COOH group) which is the end where a COOH group is not involved in a peptide bond. A C-terminal end of a polypeptide can be comprised within a “tail” of the protein which indicates a segment formed by amino acid at the C-terminus of the protein
As used herein the term “amino acid”, “amino acid monomer”, or “amino acid residue” refers to organic compounds composed of amine and carboxylic acid functional groups, along with a side-chain specific to each amino acid. In particular, alpha- or α-amino acid refers to organic compounds composed of amine (—NH2) and carboxylic acid (—COOH), and a side-chain specific to each amino acid connected to an alpha carbon. Different amino acids have different side chains and have distinctive characteristics, such as charge, polarity, aromaticity, reduction potential, hydrophobicity, and pKa. Amino acids can be covalently linked to form a polymer through peptide bonds by reactions between the amine group of a first amino acid and the carboxylic acid group of a second amino acid. Amino acid in the sense of the disclosure refers to any of the twenty naturally occurring amino acids, non-natural amino acids, and includes both D an L optical isomers.
In a “dimer” in the sense of the disclosure, the two protein monomers bind to one another through covalent and/or non-covalent interactions as will be understood by a skilled person. Examples of non-covalent interactions comprise ionic bonds, Van der Waals interactions, polar interactions, salt bridges, coulombic attraction, coulombic repulsion, hydrophobic interaction, and others identifiable by a skilled person. An example of a non-covalently bound protein dimer is the enzyme reverse transcriptase. Examples of covalent interactions comprise any chemical bond that involves the sharing of electron pairs between such as disulfide bridges.
Dimers in the sense of the disclosure can be homodimers and heterodimers. The term “homodimer” means a dimer consisting of two monomers with identical polymer sequence, and in particular two polypeptide or protein monomers with identical amino acid sequence. Examples of protein homodimers include the enzyme cyclooxygenase (COX), the methionine repressor MetJ, TlpA, the lambda repressor cI, and others identifiable by a skilled person. The term “heterodimer” means a dimer of two monomers with non-identical polymer sequence, and in particular two polypeptide or protein monomers with non-identical amino acid sequence. Examples of protein heterodimers include the enzyme reverse transcriptase and others identifiable by a skilled person.
Accordingly, the term “monomer” in the sense of the disclosure indicates a polypeptide molecule capable of reversibly forming a dimer with another monomer of the same or different sequence. In particular, a monomer in the sense of the disclosure comprises a polypeptide having an N-terminus and a C-terminus, and configured to dimerize through a dimerizing region.
A “thermomer monomers” according to the disclosure, are polypeptide monomers in which the dimerizing region is a temperature sensing region having residues configured to form non-covalent bonds with corresponding residues of another thermomer monomer, to form a temperature sensing domain of dimer protein at a target temperature Te=Tm±10° C., wherein Tm is the melting temperature of the dimer protein, the melting temperature “Tm” the temperature, at which the temperature sensing binding domain of the dimer denaturates, as will be understood by a skilled person.
In embodiments herein described, a thermomer monomer in accordance with the present disclosure is a monomer comprising a temperature sensing region having a temperature sensing sequence
wherein X111 X112, X161 X162 X182 and X183 are independently a negatively charged amino acid preferably a E and/or D or a positively charged amino acid preferably K and/or R, or a derivative thereof comprising neutral substitution of at least one residue of the temperature sensing region.
The term “charged” as used herein means a molecule, and in particular an amino acid that has an ionically charged side chain at the pH of a target environment, e.g. at physiological pH of a cellular or intracellular cellular environment, as understood by a skilled person.
In particular, charged amino acid in the sense of the disclosure can be selected taking into account the fact that in an amino acid the α-carboxylic acid group of amino acids is a weak acid, meaning that it releases a proton at moderate pH values. In other words, carboxylic acid groups (—CO2H) can be deprotonated to become negative carboxylates (—CO2—). The negatively charged carboxylate ion predominates at pH values greater than the pKa of the carboxylic acid group. Also, in a cellular or intracellular cellular environment in a complementary fashion, the α-amine of amino acids is a weak base, meaning that it accepts a proton at moderate pH values. In other words, α-amino groups (NH2—) can be protonated to become positive α-ammonium groups (+NH3—). The positively charged α-ammonium group predominates at pH values less than the pKa of the α-ammonium group.
Therefore, a positively charged amino acid in the sense of the disclosure has a side chain positively charged at the pH defined by a target environment where the thermomer monomer is configured to operate.
A negatively charged amino acid in the sense of the disclosure, is an amino acid having a side chain positively charged at the pH defined by a target environment where the thermomer monomer is configured to operate.
The wording “target environment” as used herein indicates any a combination of structures and fluids where the thermomer monomers, dimers, construct and complexes of the disclosure are configured to operate. Typically, the target environment includes a combination of structures and fluid (herein also media) with a dielectric constant around 80. In particular, exemplary environment can have a dielectric constant ranging from 40 to 150, 50 to 80, 30 to 60, and higher than 15.
Exemplary target environments comprise cell free reactions mixture, cells, tissues, organs in vitro in vivo or ex vivo, collections of microorganisms in vitro as well as cells grown in an in vitro culture, including, primary mammalian, cells, immortalized cell lines, tumor cells, stem cells, and the like. Additional exemplary target environment include tissues and organs in an ex vivo culture and tissue, organs, or organ systems in a subject, for example, lungs, brain, kidney, liver, heart, the central nervous system, the peripheral nervous system, the gastrointestinal system, the circulatory system, the immune system, the skeletal system, the sensory system, within a body of an individual and additional environments identifiable by a skilled person. The term “individual” or “subject” or “patient” as used herein in the context of the present disclosure includes a single plant, fungus or animal and in particular higher plants or animals and in particular vertebrates such as mammals and more particularly human beings.
Exemplary pH values of exemplary target environments herein described comprise pH 7.2 (cytoplasm of most cells), 6.8-7.2 (cytoplasm of mammalian skeletal muscle), 5 (lysosomes), and 7.4 (standard PBS buffer).
Charges of natural amino acids can be determined by a skilled person upon identification of the target environment. For example, at pH=7.4 (e.g. in cellular or intracellular cellular environment), among the twenty common natural amino acids, five have a side chain which can be charged. At pH=7.4, two are negatively charged: aspartic acid (Asp, D) and glutamic acid (Glu, E) (acidic side chains), and three are positive charged: lysine (Lys, K), arginine (Arg, R) and histidine (His, H) (basic side chains).
Charged of non-natural amino acid such as noncanonical amino acids with sidechains that bear charges at their environmental pH can also be determined by a skilled person based on the related side chain. Exemplary charged noncanonical amino acids include α-aminoadipic acid (Aad) and γ-carboxyglutamic acid (Gla). Other non-canonical amino acids can contain positive charges harbored in moieties known to a skilled person to harbor positive charges such as a primary amine or guanidino group, or can contain negative charges harbored in moieties known to a skilled person to harbor negative charges such as carboxylate groups as will be understood by a skilled person.
Positively charged and negatively charged amino acids in the sense of the disclosure are therefore configured to have electrical interactions under pH conditions at which both species bear a charge (such as 7.2 in the cytoplasm of most cells), and under dielectric constants that permit coulombic interactions (such as 76 in the cytoplasm of most cells), and at distances between the charged moieties that permit significant force transmission between the charged moieties (such as <4 Angstroms in a dielectric constant of 76, as in the cytoplasm of most cells) >as will be understood by a skilled person.
The term “coulombic interactions” or “electrostatic interactions” as used herein, refers to interactions between static electrically charged particles, an in particular between amino acids, wherein amino acids can be coulombically attracting or coulombically repelling, according to Coulomb's law where ε0 is the vacuum permittivity, εr is the dielectric constant of the medium, and q1 and q2 are the respective charges on the participating atoms.
Electrostatic interactions comprise ionic interactions, hydrogen bonding, halogen bonding, Van der Waals forces, dipole-dipole, dipole-induced dipole, hydrophobic effects, and others as understood by a skilled person.
In particular, a thermomer monomer in accordance with the present disclosure the temperature sensing region is configured to dimerize in a target environment at a target temperature Te<Tbs in a temperature dependent manner to form a coiled coil temperature sensing domain. Preferably in accordance with the present disclosure the temperature sensing region is configured to dimerize in a target environment at a target temperature Te=Tbs−from 2° C. to 10° C.
The term “domain” as related to the protein indicates any continuous part of a protein sequence from single amino acid up to the full protein associated to an identifiable structure within the protein. An “identifiable structure” in the sense of the disclosure indicates a spatial arrangement of the primary structure or portions thereof which can be detected by techniques such as crystallography, hydrophobicity analysis or additional techniques known by a skilled person. In many instances, a protein domain comprises one or more secondary structures of the protein, which together form a tertiary or quaternary structure of a protein.
The “secondary structure” of a protein refers to local sub-structures with a repeating geometry identifiable within crystal structure of the protein, circular dichroism or by additional techniques identifiable by a skilled person. In some instances, a secondary structure of a protein can be identified by the patterns of hydrogen bonds between backbone amino and carboxyl groups. Secondary structures can also be defined based on a regular, repeating, geometry, being constrained to approximate values of the dihedral angles ψ and φ of the amino acids in the secondary structure unit on the Ramachandran plot. Two main types of secondary structure are the alpha helix and the beta strand or beta sheets as will be identifiable by a skilled person. Both the alpha helix and the beta sheet represent a way of establishing non-covalent hydrogen bonds between constituents of the peptide backbone, thus forming secondary structural features. Secondary structure formation can be promoted by formation of hydrogen bonds between backbone atoms. Amino acids that can minimize formation of a secondary structure by destabilizing the structure of the hydrogen bonding interactions are referred to as secondary structure breakers. Amino acids that can promote formation of a secondary structure by stabilizing formation of hydrogen bonding interactions are referred to as structure makers.
The term “tertiary structure” refers to the three-dimensional structure of a protein, stabilized by non-covalent interactions among non-adjacent segments of the protein and optionally by one or more additional compounds or ions interacting through covalent or non-covalent interactions with one or more segments of the proteins. Exemplary non-covalent interactions stabilizing the three dimensional structure of the proteins comprise non-specific hydrophobic interactions, burial of hydrophobic residues from water, specific tertiary interactions, such as salt bridges, hydrogen bonds, the tight packing of side chains, chelation and disulfide bonds and additional interactions identifiable by a skilled person. Exemplary covalent interactions among compounds or ions and segments of the protein comprise N-linked glycosylation, cytochrome C haem attachment and additional interaction identifiable by a skilled person.
The term “quaternary structure” when referred to a complex refers to the three-dimensional structure of a protein complex, also called a multimer, stabilized by non-transitory interactions between the two or more proteins forming the complex. Accordingly, the quaternary structure can be stabilized by some of the same types of non-covalent and covalent interactions as the tertiary structure as will be understood by a skilled person. Multimers made up of identical subunits are referred to with a prefix of “homo-” (e.g. a homotetramer) and those made up of different subunits are referred to with a prefix of “hetero-”, for example, a heterotetramer, such as the two alpha and two beta chains of hemoglobin. “Non-transitory interactions” as used herein indicates interactions between proteins or related segments that are detectable by laboratory techniques such as immunoprecipitation, crosslinking and Forster Resonance Energy Transfer (FRET) measurements, crystallography, Nuclear Magnetic Resonance (NMR) and additional techniques identifiable by a skilled person.
Detection of three-dimensional secondary, tertiary, or quaternary protein structure can be performed using techniques such as x-ray crystallography, NMR spectroscopy, dual polarization interferometry among others known to a skilled person. Using such techniques, the position of structural features comprising alpha-helices, beta strands, turns, beta bridges, bends, loops, coils, coiled coils, and others identifiable by a skilled person within the N-terminal to C-terminal primary sequence of a protein can be detected.
In particular, detection of repeated motifs in a protein domain in the sense of the disclosure can be performed using structure prediction servers COILS[2], Paircoil2[3], LOGICOIL[4] and JPred[5]. Structure of polypeptides and proteins can also be obtained from publicly available sources such as Protein Data Bank [6] and others known to a skilled person.
The term “temperature-sensing domain” refers to a protein or a portion thereof having a sequence configured to provide structural lability in response to temperature changes. This structural lability results in a change in the behavior of the switch between the “below threshold” and “above threshold” temperatures, where behavior means the output of the system controlled by the switch. In one embodiment, the output is a mRNA transcript whose production is blocked by binding of the switch to DNA at low temperature and enabled by unbinding of the switch from the DNA at high temperature.
A coiled coil temperature sensing domain in the sense of the disclosure indicates a temperature sensing domain comprising temperature sensing supercoiled motif of alpha-helical secondary structures. In particular, the term “coiled coil” indicates a structural motif in a protein in which two to seven alpha-helices are coiled together like the strands of a rope and interact with coiled coil structural motifs in one or more other proteins. Dimers and trimers are the most common types.
Coiled coils usually contain a repeated pattern, “hxxhcxc” (SEQ ID NO: 2), of hydrophobic (h) and charged or polar (c) amino-acid residues, referred to as a heptad repeat. The positions in the heptad repeat can be labeled “abcdefg”, according to a register where “a” and “d” are generally hydrophobic positions, often being occupied by isoleucine, leucine, or valine.
The term “register” as used herein in relation to a heptad repeat indicates the sequence of the positions a, b, c, d, e, f, g within the heptad repeat in an alpha-helical coiled coil. In particular a register indicates a series of consecutive positions among the possible consecutive a, b, c, d, e, f and g positions starting at any one of positions a, b, c, d, e, f, or g and can be interrupted by variation of the sequence such as deletion or insertions. A heptad coil register can be assigned based on consensus between previous literature [7] and structure prediction servers including COILS[2], Paircoil2[3], LOGICOIL[4], and Jpred[5]. Folding a sequence with this repeating pattern into an alpha-helical secondary structure causes the generally hydrophobic “a” and “d” residues to be presented as a stripe that coils around the alpha helix, forming an amphipathic structure as will be understood by a skilled person.
In a coiled coil temperature sensing domain, alpha helices of the coiled coil motif form a tertiary or quaternary structure in a water-filled environment such as the cytoplasm, and in particular the hydrophobic strands are wrapped against each other and are sandwiched between the hydrophilic amino acids. The alpha-helices can be parallel or anti-parallel, and can adopt either a left-handed or right-handed coiled coil. Coiled coils can be depicted using a ‘helical wheel’ diagram, in which the coiled coils are viewed down the axis of the alpha-helices from N-terminus to C-terminus such as the exemplary structure schematically illustrated in FIG. 16 of U.S. application Ser. No. 15,384,254 filed on Dec. 19, 2016 and published with publication number US2017/0928425 with reference to the coiled coil domain of TlpA, which shows a series of helical wheel representations of the homodimeric coiled-coil, with each monomer coil made up of heptad repeats.
In embodiment herein described, dimerization involves a dynamic process of forming a thermomer dimer of two thermomer monomers involving interactions between corresponding residues of the two thermomer monomers in their respective temperature sensing regions forming the temperature sensing domain of the thermomer dimers herein described.
The term “corresponding residues” as used herein indicates residues capable of interacting within a protein complex and typically forming through covalent or non-covalent binding or links.
The terms “covalent bond”, “covalent binding” or “covalent link” as used herein indicate an interaction by which two moieties are associated by formation of a covalent chemical bond. Exemplary covalent bonds comprise s disulfide bond, and amide bond of amino acid side chains of a peptide or protein.
The terms “non-covalent bond”, “non-covalent binding” or “non-covalent link” as used herein indicate to an interaction by which two moieties are associated by a non-covalent attractive force. Non-covalent interactions comprise hydrophobic interactions such as pi-pi interaction of aromatic groups, or van der Waals interaction of hydrophobic groups of amino acid side chain, electrostatic interactions such as polar interactions, coulombic attraction of opposite charge groups, coulombic repulsion of same charge group and others identifiable by a skilled person.
In embodiment herein described, dimerization of thermomer monomers involves a dynamic process of forming a coiled coil temperature sensing domain of a thermomer dimer involving non-covalent interactions between corresponding residues in positions a to g of heptad repeats in the temperature sensing region of each monomer protein as will be understood by a skilled person.
In particular, in dimerization of thermomer monomers herein described corresponding hydrophobic residues at positions a and d interact with each other and form the hydrophobic core or interface of the coiled coils, and are mainly responsible for the formation and stability of the coiled-coil. Electrostatic attractions at between corresponding residues in positions d-e and g-e can provide additional stability to the system by encouraging the salt bridge formation between the two coils.
Formation of these interchain salt bridges can also shield the non-polar core from solvent, further stabilizing the coiled-coils. Positions e and g of the heptad repeat flank the hydrophobic interface of the coiled-coil and can contribute to the hydrophobicity of the core by folding over the interface to interact with the hydrophobic residues through their side chain methylene groups, thereby shielding the core from water. Examples of proteins including coiled coil temperature domain include dimers such as lac repressor, TlpA protein, KfrA and others identifiable by a skilled person and other proteins not involved in regulation of gene expression, such as myosin, tropomyosin, and others as will be identified by a skilled person.
Structure prediction servers such as COILS[2], Paircoil2[3] and LOGICOIL[4] and Jpred among other as will be understood by a skilled person can be further used for analysis of coiled coil domains. Graphical depictions of coiled coils can be produced using software such as DrawCoil 1.0[8].
Examples of structural analysis results of thermomers derived from the TlpA coiled-coil domain using these programs are shown in
Thermomer monomers according to the disclosure and related configuration are based on the temperature sensing domain of the temperature sensing transcription factor TlpA
Temperature sensitive transcription factors” “thermal transcriptional bioswitches” or “transcriptional bioswitches” in the sense of the disclosure herein also indicated as “transcriptional bioswitches” are transcription factors that have a DNA-bound state or conformation in which the transcription factor is specifically bound to a corresponding DNA regulatory sequence through a DNA binding domain, and a DNA unbound state or conformation in which the transcription factor is not bound to a corresponding DNA regulatory sequence in particular.
A temperature sensitive transcription factor comprises a DNA binding domain and a temperature-sensing domain. In temperature sensing transcription factor, the factor can convert from a DNA-bound state to a DNA-unbound state with reference to corresponding DNA regulatory sequence at a bioswitch temperature Tbs through binding and dissociation of the temperature sensing domain of the transcription factor at the bioswitch temperature Tbs.
The thermomers of the present disclosure, are based on the surprising finding that the temperature sensing domain or the temperature sensing transcription factor TlpA maintain an ability to dimerize and disassociate in a temperature-controlled fashion at a bioswitch temperature Tbs even in absence of a related DNA binding.
Accordingly, thermomer monomers comprising a temperature sensing region from TlpA and in particular the temperature sensing region of SEQ ID NO: 1, can dimerize and disassociate in a temperature controlled fashion at a bioswitch temperature Tbs thus forming thermomer dimer having the ability to act as bioswitches a bioswitch temperature Tbs as will be understood by a skilled person.
In exemplary embodiments, the bioswitch temperature is, 39° C. to 42° C. range preferably 40° C. Accordingly, the target environment temperature can be from 25° C. to 40° C. preferably 36° C. to 38° C. and preferably Te is 37° C.
In particular, in a temperature sensing domain of a thermomer dimer of the disclosure, the coiled coil temperature sensing region of a first thermomer monomer and the coiled coil temperature sensing region of a second thermomer monomer are joined by non-covalent bounds of corresponding residues comprising
These corresponding residues and related interactions can be predicted using coiled-coil heptad register prediction software (e.g. COILS) and visualization software (e.g. DrawCoil 1.0) as discussed elsewhere in the document, and their functionality can be validated via circular dichroism spectroscopy as exemplified in
In in coiled coil temperature sensing domain of thermomer dimers herein described, the dimerization or de-dimerization of two monomers exhibits a cooperative behavior, also referred to as “cooperativity”. Cooperativity occurs in molecular structures containing multiple binding sites. In general, cooperativity describes the changes in conformation or binding energy that occur when a binding site of one of these structures is activated or deactivated effecting the other binding sites in the same molecule. It can also be described as the increasing (positive cooperativity) or decreasing (negative cooperativity) affinity for binding of the other sites affected by the original binding site. Cooperativity can occur in enzymes, receptors, DNA and many molecules that are made of identical or near identical subunits. An example of positive cooperativity can be seen on the binding of oxygen to hemoglobin to form oxyhemoglobin. Another example is the unwinding of DNA in which sections of DNA first unwind followed by the process of unwinding another group of adjacent nucleotides. Similar processes also apply to other types of chain molecules, such as the folding and unfolding of alpha-helices in coiled-coils of the temperature-sensing domain.
In embodiments herein described, the cooperativity of a temperature-sensing domain can be quantified by a single parameter referred to as “Hill coefficient”. The Hill coefficient is a measure for the cooperative of the temperature-sensing domain de-dimerization transition. High Hill coefficients go together with sharp de-dimerization transitions while low Hill coefficients indicate a gradual transition from the folded dimer to unfolded two monomer conformation. The Hill coefficient can be mathematically calculated from fitting a circular dichroism (CD) melting curves as follow:
where Tm is the melting temperature of a temperature-sensing domain of a thermomer dimer, a the amplitude, T the temperature in units of Celsius or and b the Hill coefficient.
The melting temperature “Tm” of a temperature sensing binding domain is the temperature, at which the temperature sensing binding domain desaturates. The change in size or structure that accompanies the protein denaturation can be identified using DLS techniques, CD techniques and other techniques identifiable by a skilled person. Factors affecting the Tm of a temperature sensing domain comprise the primary sequence of amino acids and environment conditions, e.g. pH and salt concentration, as well as post translational modifications, e.g. glycosylation, and formation of complex with other molecules (proteins or DNA) or other factors that can affect the stability of the protein structure and hence the melting temperature as will be understood by a skilled person.
As a person skilled in the art would understand, CD and other spectroscopic measurements that measure changes in absorption and fluorescence collected as a function of temperature can determine the thermodynamics of protein unfolding and binding interaction. For example, measuring CD as a function of temperature can be used to determine the effects of mutations on protein stability, as well as the binding constants of interacting proteins and protein-ligand complexes.
In some embodiments, a CD melting curve can be recorded using spectroscopic technique for following the de-dimerization and dimerization of temperature-sensing domains as a function of temperature, as will be understood by a person skilled in the art.
Coiled coil temperature temperature-sensing domains in the sense of the current disclosure contain a two-stranded α-helical coiled-coil structure that have sharp uncoiling transitions with a Hill coefficient above 15. In some embodiments, the two monomer proteins of the coiled coil temperature sensing domain are further configured to bind to one another in the target environment with a thermal Hill coefficient from 15 to 40 to form the dimer in a temperature dependent manner. For example, the coiled-coil domain of thermomer dimers herein described can have a Hill coefficient of from about 15 to 25.
For example, a sharp transition of thermomer dimerization between coiled coil domains of each monomer features cooperative binding, as indicated by the Hill coefficient. The Hill coefficient can be identified by fitting a circular dichroism melting curve dataset of any thermomer to the thermal Hill equation, with signal normalized from 0 to 1 on the Y-axis and temperature in units of ° C. on the x axis. As a representative example, the thermal Hill coefficient of the G1A/G1B thermomer in
In coiled coil temperature sensing dimers, the Tm of the temperature sensing domain also controls the temperature of the target environment at which the temperature sensitive monomers specifically bind to one another forming a dimer, herein also bioswitch temperature or Tbs), determined by the melting temperature Tm of the temperature sensitive binding domain.
In particular, in temperature sensing coiled-coil interaction domain essentially consisting of supercoiled alpha-helical structure, cooperative unfolding of the coil results in a loss of the ability to correctly position the two halves of the DNA binding domain found at the N-termini of each protein chain.
In particular, in coiled coil temperature sensing domain, the Tm of the temperature sensing domain defines the bioswitch temperature of the temperature sensitive dimer (Tbs) herein also indicated as threshold temperature, the Tbs being a temperature of the target environment at which the temperature sensitive monomers bind to form a dimer, with Tbs=Tm+0° C. to 5° C. In particular, Tbs=Tm+0° C. to 5° C. in a target environment with a net concentration of monomer proteins from 2 to 20 uM.
In some embodiments, the melting temperature Tm of a coiled coil temperature sensing domain herein described can be Tm=from 20 to 80° C. In some embodiments, the melting temperature Tm of the coiled coil temperature sensing domain herein described can be Tm=from 25 to 60° C. In some embodiments the melting temperature Tm of the coiled coil temperature sensing domain herein described can be Tm=from 30 to 50° C. In some embodiments, the melting temperature Tm of the coiled coil temperature sensing domain herein described can be Tm=from 32 to 46° C.
In some embodiments, the Tbs can be Tbs=Tm+2.5 to 5° C., wherein the temperature sensitive dimer is encoded in the target environment by a polynucleotide in a number from 100 to 1000 copies per cell. In some embodiments, the Tbs can be Tbs=Tm+1 to 3.5° C., wherein the temperature sensitive dimer is encoded in the target environment by a polynucleotide in a number from 10 to 100 copies per cell. In some embodiments, the Tbs can be Tbs=Tm+0 to 1.5° C., wherein the temperature sensitive dimer is encoded in the target environment by a polynucleotide in a number below 10 copies per cell.
In some embodiments, association of adjacent thermomer cargoes may increase the Tbs above the value set by independent thermoswitches. Affinity between cargo 1 and cargo 2 may stabilize the overall structure, as will be understood by a skilled person, resulting in a shift of Tbs by up to 10° C.
Accordingly, a skilled person upon reading of the present disclosure will understand that thermomer monomer of the instant disclosure encompass not only polypeptide of SEQ ID NO: 1 but also by any derivative thereof.
, The term “derivative” as used herein in connection with the temperature sensitive region indicates a polypeptide having a same length of the temperature sensitive region and comprising a neutral substitution of at least one of the amino acid residues of the temperature sensing region.
The term “neutral substitution” as used herein indicates amino acid replacement in a polypeptide that changes a given amino acid to a different amino acid resulting in maintenance of the structural properties of the polypeptide. Accordingly, one or more neutral substitutions in temperature sensitive region of thermomer monomer herein described result in a polypeptide having same structural properties of the temperature sensing region of SEQ ID NO: 1 as will be understood by a skilled person.
Accordingly, in a thermomer monomer with SEQ ID NO: 1 neutral substitution of one or more residues of the temperature sensing region are amino acid substitutions that do not perturb the structural stability of the thermomers (e.g. their affinity for each other, and the Tm of the resulting dimer). A substitution can be defined as “neutral” relative to the original thermomer if the circular dichroism spectrum of the substitution product (in complex with the same partner thermomer as the partner of the original thermomer, and at the same concentration as the original thermomer) is superimposable upon the circular dichroism spectrum of the original thermomer with its original partner, to within a margin of error of 5% for any given data point, when normalized from the minimal value to the maximal value, setting the bounds at 0 and 1 respectively. Additionally, the neutral substitution, under the same conditions, do display a melting curve at 222 nm that is superimposable upon the circular dichroism spectrum of the original thermomer with its original partner, to within a margin of error of 5% for any given data point, when normalized from the minimal value to the maximal value, setting the bounds at 0 and 1 respectively.
In view of their ability to associate and disassociate in a temperature dependent manner, thermomer monomers of the present disclosure and related thermomer dimers can be used as modular dimerization thermoswitches, in which the bioswitch temperature of the coiled coil temperature sensing dimers affects the related thermoswitch properties in a target environment wherein the thermomer conversion from monomer state to heterodimer state can be used to control spatiotemporal locations of cargo moieties as will be understood by a skilled person upon reading of the present disclosure.
In particular, in application where thermomer monomers and related thermomer dimers of the instant disclosure are used as dimerization thermoswitches, the coiled coil temperature sensing domain of the thermomer dimers are configured so that the coiled coil temperature sensing dimers exhibit an ON or OFF state at a particular temperature range of interest while still retaining a sharp thermal transition resulting in a large change in activity. For example, thermomer dimers of the disclosure can have a >100-fold difference between an on and off state, and a 10-fold switching over a temperature range less than 5° C. in some exemplary embodiments, fold switching lower that 10-fold switching, and in particular to a 4-fold switching, or even lower such as a 2-fold switching. (see
In a preferred embodiment, the first thermomer monomer and the second thermomer monomer have X111=R, X112=E, X161=E, X162=R, X182=E, X183=R and the thermomer monomer comprise the sequence of wild type TlpA.
In preferred embodiments, thermomers of the present disclosure are also based on the surprising finding that engineering in the temperature sensing region of a first thermomer monomer and a second thermomer monomer forming a thermomer dimer herein descried, of at least one of the following pair of corresponding residues
In the preferred embodiments,
Exemplary oppositely charged residues used in the thermomer monomers and dimers herein described comprise glutamic acid (E, negative) and arginine (R, positive), and glutamic acid (E, negative) and lysine (K, positive). Additional possible oppositely charged residue interactions may consist of aspartic acid (D, negative) and arginine (R, positive), and aspartic acid (D, negative) and lysine (K, positive) as well as additional combinations identifiable by a skilled person.
Accordingly, in thermomers of the present disclosure, inclusion of the above corresponding residues in a thermomer monomer with SEQ ID NO: 1, the thermomer bioswitches of the present disclosure are heterodimeric.
Heterodimer formation occurs when the affinity of two different thermomers for each other exceeds the affinity of two copies of the same thermomer for each other. In cases where the thermomers are produced in separate enclosures (e.g. cells) and the homodimer interaction energy exceeds the ambient energy at the temperature of storage, the homodimers may be mixed at an equimolar ratio, heated to above their Tm and cooled back to their ambient storage temperature to escape from their kinetically trapped conformation and relax to their thermodynamically favored conformation.
Heterodimer formation can be detected by obtaining the circular dichroism spectrum and melting curve at 222 nm, as exemplified for the wild type TlpA coiled-coil in
In a preferred embodiment, an heterodimeric thermomer dimers comprise, the thermomer dimer wherein the first thermomer monomer is (R179), in which X111=E, X112=E, X161=E, X162=R X182=E, and X183=R and the second thermomer monomer is (E180R) in which X111=R X112=R X161=E X162=R X182=E X183=R
In another preferred embodiment, an heterodimeric thermomer dimers comprises, the thermomer dimer wherein the first thermomer monomer is (E229R) in which X111=R, X112=E, X161=R, X162=R, X182=E, X183=R and in the second thermomer monomer is (R230E) in which X111=R, X112=E, X161=E, X162=E, X182=E, X183=R,
In another preferred embodiment, an heterodimeric thermomer dimers comprises, the thermomer dimer wherein the first thermomer monomer is (E250R) in which X111=R, X112=E, X161=E, X162=R, X182=R, X183=R, and in the second thermomer monomer is (R251E) in which X111=R, X112=E, X161=E X162=R, X182=E X183=E.
In another preferred embodiment, an heterodimeric thermomer dimers comprises, the thermomer dimer wherein the first thermomer monomer is (E180R, E229R) in which X111=R, X112=R, X161=R, X162=R, X182=E, X183=R, G2A1 and the second thermomer monomer is (R179E, R230E) in which X111=E, X112=E, X161=E, X162=E, X182=E, X183=R, G2B1.
In another preferred embodiment, an heterodimeric thermomer dimers comprises, the thermomer dimer wherein the first thermomer monomer is (E180R, R230E) X111=R, X112=R, X161=E, X162=E, X182=E, X183=R, G2A2 and the second thermomer monomer is (R179E) E229R) in which X111=E, X112=E, X161=R, X162=R, X182=E, X183=R, G2B2
In another preferred embodiment, a heterodimeric thermomer dimers comprises, the thermomer dimer wherein the first thermomer monomer is (E180R, E250R), X111=R, X112=R, X161=E, X162=R, X182=R, X183=R, G2A3 and in the second thermomer monomer is (R179E, R251E) in which X111=E, X112=E, X161=E, X162=R, X182=E, X183=E, G2B3
In another preferred embodiment, an heterodimeric thermomer dimers comprises, the thermomer dimer wherein the first thermomer monomer is (E180R, R251E), in which X111=R, X112=R, X161=E, X162=R, X182=E, X183=E, G2A4 and in the second thermomer monomer is (R179E), E250R) in which X111=E, X112=E, X161=E, X162=R, X182=R, X183=R, G2B4.
In another preferred embodiment, an heterodimeric thermomer dimers comprises, the thermomer dimer wherein the first thermomer monomer is (E229R, E250R) in which X111=R, X112=E, X161=R, X162=R, X182=R, X183=R G2A5 and in the second thermomer monomer is (R230E, R251E) in which X111=R, X112=E, X161=E, X162=E, X182=E, X183=E, G2B5.
In another preferred embodiment, a heterodimeric thermomer dimers comprises, the thermomer dimer wherein the first thermomer monomer is (E229R, R251E), in which X111=R, X112=E, X161=R, X162=R, X182=E, X183=E, G2A6 and in the second thermomer monomer is (R230E, E250R) in which X111=R, X112=E, X161=E, X162=E, X182=R, X183=R, G2B6
In particular in applications where thermomer monomers and related thermomer dimers of the instant disclosure are used as dimerization thermoswitches, the unexpected modularity of the thermomer monomers and dimers allow to build thermomer constructs where the thermomer monomers are linked to cargo moieties and to use the thermomer dimers herein described are used as thermoswitches to control spatiotemporal location of the cargo moiety as well formation and dissociation of dimer complexes comprising the cargo moieties in a thermally regulated manner.
In particular it has been surprisingly found that the temperature sensing region of a TlpA monomer retain an ability to dimerize in a temperature controlled manner also in a construct if the TlpA temperature sensing region is linked to the construct through a linker polypeptide attached at the N-terminus or the C-terminus of the TlpA temperature sensing region.
The term “linker polypeptide” as used herein indicates a short peptide sequences that occur between protein domains. A linker polypeptide in accordance with the disclosure can have a length that can be selected in view of the target environment and the construct where the thermomer monomer of the instant disclosure is to be included and the experimental design.
The term “attach” or “attached” as used herein, refers to connecting or uniting by a bond, link, force, or tie in order to keep two or more components together, which encompasses either direct or indirect attachment. For example, “direct attachment” refers to a first molecule directly bound to a second molecule or material, while “indirect attachment” in refers to one or more intermediate molecules being disposed between the first molecule and the second molecule or material. Attachment between two referenced molecules therefore comprises connecting or uniting the two referenced molecules by covalent bonds, or non-covalent bonds between the two molecules introduced and by chemical modification of the molecules (such as with a maleimide-cysteine conjugation) or by creation of a precursor of the two molecules which will provide the two molecules attached one to the other (e.g. by creating a fusion gene comprising polynucleotides encoding for two polypeptide to be attached.)
In thermomer monomer herein described, attachment of a linker polypeptide can occur at the N-terminus the C-terminus of the thermomer monomer which in embodiments herein described the N-terminus and the C-terminus are typically range independently from 5 to 12 amino acids long as will be understood by a skilled person. In particular, one of the N-terminus or the C-terminus can attach to one of the C-terminus and N-terminus of a linker polypeptide to for a stable construct in the target environment as will be understood by a skilled person.
In embodiments here described, a linker polypeptide allows attachment of a thermomer monomer of the disclosure to a cargo and/or a surface configured to bind a polypeptide. In some embodiments, the linker polypeptide can be part of the cargo as will be understood by a skilled person upon reading of the present disclosure.
The term “cargo” refers to any chemical moiety having a diameter up to 1 micron configured to be attached to a polypeptide either directly or through a linker described herein. Exemplary cargo moiety can have a diameter of 100-200 nm or lower than 100-nm as will be understood by a skilled person upon reading of the present disclosure. Accordingly, the term “cargo” as used herein indicates any group of atoms linked to one another to form a compound molecule substance or material that can be attached to a polypeptide or any portions thereof.
Cargo moieties in the sense of the disclosure typically have an identifiable chemical or physical property associated thereto In particular, chemical moieties forming cargo according to the disclosure can have chemical properties such as chemical reactivity (e.g. a gold nanoparticle to form a S—Au bond with a thiol group (—SH)) and physical properties such as, radioactivity (e.g. radioactive isotope moiety), fluorescence (e.g. fluorophore moiety, chemiluminescence (e.g. a chemiluminescent dye moiety), light absorption (a chromophore moiety), catalytic activity (e.g. enzymatic activity), binding activity (e.g. scFvs or Fabs), signaling activity (e.g. adaptor protein domains such as SH2 and SH3), or combinations thereof (e.g. antibodies, nanobodies, natural cell surface receptors, chimeric cell surface receptors, and similar) or a Stokes' drag force for a cargo moiety in including a bead as used in the present application.
In some embodiments, the cargo can have a molecular weight of less than 500 kD. Typical cargoes and associated molecular weights include proteins (5-100 kD), large proteins and protein complexes (100-500 kD), small molecules (0.05-1.5 kDa), and peptides (1-5 kDa). Oligonucleotides of <100 kD, and additional cargos identifiable by a skilled person.
Exemplary cargo moieties in the sense of the disclosure polypeptides, polynucleotides nanomaterial such as beads
In some embodiments, the cargo can be attached to the thermomer through a covalent bond such as a peptide bond or a non-covalent bond.
In some embodiments, the cargo can be a protein, polynucleotide or macromolecular complex such as a bead, that is covalently fused to the thermoswitch by chemical modification (such as with a maleimide-cysteine conjugation)
In some embodiments, herein described, a thermomer monomer of the disclosure is covalently attached to a suitable cargo moiety directly or through a linker polypeptide to provide a thermomer monomeric construct herein described
In embodiments, wherein a cargo is comprised in a thermomer monomeric construct, selection of the correct linker can be aided by approximating the cargo as a sphere of hydrodynamic radius R based on known structural information regarding the cargo, drawing the two spheres so as to touch each other tangentially, and drawing straight lines toward from the expected attachment sites on the cargo to the same point in space (which represents the attachment site on the coiled coil). The length of the resulting lines indicates the minimal required length of the linkers, and can be converted into number of amino acids by the relationship 1 aa=3.5 Angstroms. Typically, a linker polypeptide for a thermomer monomeric construct herein described can be shorter than 50 amino acids and most often shorter than 30 amino acids
In some embodiments, a linker polypeptide in thermomer monomeric construct can be a flexible linker polypeptide, and therefore polypeptide predicted to be unstructured using software known to someone skilled in the art, such as Jpred, or selected from published lists of such linker sequences. linkers can be categorized as short (such as the representative example GGSGGS (SEQ ID NO: 3) used to fuse the palmitoylation domain to one strand of an exemplar thermoswitch (G2A3 of the disclosure), or long (such as the representative example GGGGSGGGGSGGGGSGGGGSGGGGS (SEQ ID NO: 34) used to fuse the RFP to the other strand of an exemplary thermoswitch (G2B3 in
Exemplary linkers further include GGGGS (SEQ ID NO: 4), GSGSG (SEQ ID NO: 5), GGGG (SEQ ID NO: 6), GGG (SEQ ID NO: 7), GG (SEQ ID NO 8), GS (SEQ ID NO: 9), GSGS(SEQ ID NO: 10), GGGS(SEQ ID NO: 11), GGS(SEQ ID NO: 12), GTS (SEQ ID NO: 13) GGSGGS (SEQ ID NO 14), GGG (SEQ ID NO: 15), GGGGGG (SEQ ID NO: 16), GGGGGGGGG (SEQ ID NO: 17), GGGGGGGGGGGG (SEQ ID NO:18), GGGGGGGGGGGGGGG (SEQ ID NO: 19), GGS(SEQ ID NO: 20), GGSGGS(SEQ ID NO: 21), GGSGGSGGS (SEQ ID NO 22), GGSGGSGGSGGS (SEQ ID NO: 23), GGSGGSGGSGGSGGS (SEQ ID NO: 24), GSG (SEQ ID NO: 25), GSGGSG (SEQ ID NO: 26), GSGGSGGSG (SEQ ID NO: 27), GSGGSGGSGGSG (SEQ ID NO: 28), GSGGSGGSGGSGGSG (SEQ ID NO:29), GGGGS(SEQ ID NO: 30), GGGGSGGGGS (SEQ ID NO: 31), GGGGSGGGGSGGGGS (SEQ ID NO: 32), GGGGSGGGGSGGGGSGGGGS (SEQ ID NO: 33), GGGGSGGGGSGGGGSGGGGSGGGGS (SEQ ID NO:34) and additional polypeptide linkers identifiable by a skilled person.
In some embodiments, a linker polypeptide in thermomer monomeric construct can be a rigid linker polypeptide, and therefore can comprise amino acids predicted to assemble into rigid sequences (most often alpha helices). Examples of rigid linkers include one or more (typically <10) repeats of the motif EAAAK (SEQ ID NO: 35), which fold into alpha helices.
In some of the embodiments wherein a linker polypeptide is used to provide thermomer monomeric construct of the disclosure, the combination of cargo and a linker enables the correct spacing of the coiled-coil terminus. The spacing of the coiled-coil terminus can be estimated from the crystal structure of any coiled-coil. For example, for the coiled-coil Tropomyosin, the N-terminus to N-terminus distance is 6.5 Angstroms. The size of the cargos and the location of the linker fusion can be selected to maintain such distance.
In other exemplary embodiments, for example for certain cargo moieties wherein the chemical moiety is formed by a protein, the cargo can be directly attached to the thermomers, without an intervening linker sequence. This can occur when the cargo itself contains a flexible region that can serve as the linker. For example, in the case where the palmitoylation motif is fused to the N-terminus of a thermomer in the context of the full-length TlpA protein, residues SQSTVVTEPVAELPVEV (SEQ ID NO 36): which are predicted via Jpred to be unstructured are presumed to comprise the linker between the folded domain and the thermomer.
Accordingly, in a thermomer monomeric construct the cargo moiety can be attached to one of the N-terminus end or a C-terminus of the thermomer monomer. In the alternative in a thermomer monomeric construct the cargo moiety can be attached to one of the N-terminus end or a C-terminus, of the linker polypeptide and the thermomer monomer is attached to the other one of the N-terminus end and C-terminus of the linker polypeptide.
The thermomer herein described can be attached to a cargo comprising transcription factor domains. The cargo coupled or linked to one monomer of a thermomer in the sense of the present disclosure can comprise a transactivation domain of a transcription factor or a functional fragment thereof, while the cargo coupled or linked to the other monomer of the thermomer can comprise a DNA binding domain of a transcription factor or a functional fragment thereof.
The thermomer herein described can also be attached to a cargo comprising molecules that mediate signaling, e.g., the intracellular signaling domain(s) through proliferation pathways, e.g., the P13K or AKT pathway. Accordingly, in some embodiments the cargo can be a protein kinase.
The thermomer herein described can also be attached to a cargo comprising molecules that regulate protein translocation to a membrane of a cell. Accordingly, in some embodiments, the thermomers can be coupled or fused to a membrane anchoring domain such as a molecule that is localized to the plasma membrane such as a myristoyl group, or a myristoylation site, or a transmembrane domain.
The thermomer herein described can also be attached to a cargo comprising molecules that regulate protein translocation to and from the nucleus of a cell. Accordingly, in some embodiments, the thermomers can be coupled or fused to nuclear localization signaling sequence for nuclear import or nuclear export signaling sequence for export to form a transport complex that is passed through the nuclear pore complex.
The thermomer herein described can also be attached to a cargo comprising gene editing systems that can regulate gene editing by modifying the nucleic acids of a target gene and/or for modulating the expression of a target gene. The gene editing systems typically comprise a DNA binding domain and a DND modifying domain. For example, in some embodiments, one of two monomers of a thermomer can be coupled or fused to a DNA binding domain while the other monomer can be coupled or fused to a DNA modifying domain.
A “DNA-modifying domain” of the present invention is a molecule or domain of a molecule that is capable of causing a change to the covalent structure of a DNA molecule. In some aspects, the change to the covalent structure of a DNA molecule is a cleavage (a breakage, of the covalent backbone of a DNA molecule). The association of the two monomers will cause the association of the DNA-binding domain and the DNA-modifying domain thereby enabling the gene editing functionality. Exemplary gene editing systems include TALEN gene editing system, CRISPR/Cas gene editing system, Zinc Finger nuclease gene editing system, meganuclease gene editing system, and others identifiable to a person skilled in the art.
Exemplary cargo moieties in the sense of the disclosure further comprise Chimeric antigen receptors, Engineered GPCRs such as TanGo, Engineered enzymes such as Cellobiohydrolase, Cellulase, Lignase, Immunological receptors such as Toll-Like receptors, Antibodies and fragments thereof, Viruses and exosomes, and protein Gas vesicles
Additional cargo molecules that can be coupled or fused to thermomers herein described can be found in Table 5 of WO 2016/098078 incorporated herein by reference in its entirety and further cargo moieties identifiable by a skilled person
Additional preferred cargos comprise the cargo moiety is selected from a chimeric Antigen Receptor, Cas9, split Cas9, dCas9, split dCas9, anti-CRISPR, Cpf1, split Cpf1, dCpf1, split dCpf1, TALENs and split TALENs, and Chimeric GPCR (e.g. TanGo, DREADDs).
In some embodiments herein described, a thermomer monomeric construct can be provided by selecting suitable thermomer monomer in view of the cargo, the target environment and the target temperature Tbs where the thermomer monomeric construct is to be operated. to be attached to a cargo moiety, optionally through a linker polypeptide
In those embodiments, a first thermomer monomer can be provided configured to dimerize with a second thermomer monomer in the target environment at a target temperature Tbs with a thermal Hill coefficient above 15, to form a thermomer dimer of the present disclosure having a melting temperature Tm=Tbs−0° C. to 5° C.
In methods to provide a thermomer monomeric construct of the present disclosure the methods comprising attaching the cargo moiety to the thermomer monomer directly or through a linker polypeptide as will be understood by a skilled person.
In some embodiments, the attaching can be performed by translational conjugation via generation of a fusion protein gene, Untargeted chemical conjugation e.g. via (maleimide, iodoacetamide, 2-thiopyridine, 3-arylpropiolonitrile) binding to one or more cysteine residues, (NHS, isocyanate, isothiocyanate, or benzoyl fluoride) conjugation to one or more lysine residues, (diazonium salts, PTAD, or mannich reaction) to one or more tyrosine residues, N-terminal serine or threonine conjugation via NaIO4, N-terminal cysteine conjugation via iodoacetamides, N-terminal conjugation via pyridoxal phosphate (PLP), Native chemical ligation.
In some embodiments, the attaching can also be performed by targeted chemical conjugation via click reaction to an introduced noncanonical amino acid at any position that demonstrates evidence of being a neutral substitution as herein described,
In some embodiments, the attaching can also be performed by any other conjugation method described in [9], by Introduction of specific sequences for chemical reaction such as FlAsH and ReAsH and/or by Fusion of a biotinylation sequence for modification via BirA.
In some embodiments, the attaching can also be performed by Translational fusion to antibodies or other dimerization/oligomerization domains and/or Fusion to SpyTag or SpyCatcher (or related systems such as SnoopTag-SnoopCatcher and SpyLigase or SnoopLigase) for covalent bond formation
In some embodiments providing, the attaching can be performed by providing a thermomer gene expression cassette comprising a polynucleotide encoding for a thermomer monomer herein described under control of a promoter and additionally regulatory regions in a configuration allowing expression of the monomer of the present disclosure in a target environment.
In those embodiment, where construct comprises a linker polypeptide and/or a cargo moiety is formed by or comprising a protein, the polynucleotide encoding for a thermomer monomer herein described can be a fusion gene comprising the thermomer monomer, the cargo and/or the linker polypeptide in a configuration allowing expression of a polypeptide forming the thermomer monomeric construct as will be understood by a skilled person
The term “gene cassette” as used herein indicated a mobile genetic element that contains at least one gene and a recombination site. Accordingly, a gene cassette can contain a single gene or multiple genes possibly organized in an operon structure A gene cassette can be transferred from one DNA sequence (usually on a vector) to another by ‘cutting’ the fragment out using restriction enzymes or transposase, cripr, viral and/or recombinase enzymes and other nucleases and ‘pasting’ it back into the new context or other molecular biology and cloning techniques (e.g. per, CRISPR, TALENs, ZFN). Gene cassettes can move around within an organism's genome or be transferred to another organism in the environment via horizontal gene transfer.
A “gene expression cassette” is a gene cassette comprising regulatory sequence to be expressed by a transfected cell. Following transformation, the expression cassette directs the cell's machinery to make RNA and proteins. Some expression cassettes are designed for modular cloning of protein-encoding sequences so that the same cassette can easily be altered to make different proteins. An expression cassette is composed of one or more genes and the sequences controlling their expression. An expression cassette typically comprises at least three components: a promoter sequence, an open reading frame, and a 3′ untranslated region that, in eukaryotes, usually contains a polyadenylation site. An expression cassette can be formed by manipulable fragment of DNA carrying, and capable of expressing, one or more genes of interest optionally located between one or more sets of restriction sites Gene expression cassettes as used herein typically comprise further regulatory sequences additional to the prompter to regulated the expression of the gene or genes within the open reading frame herein also indicated as coding region of the cassette.
The term “regulatory sequence” or “regulatory regions” as described herein indicate a segment of a nucleic acid molecule which is capable of increasing or decreasing transcription or translation of a gene within an organism either in vitro or in vivo. In particular, coding regions of the GV genes herein described comprise one or more protein coding regions which when transcribed and translated produce a polypeptide. Regulatory regions of a gene herein described comprise promoters, transcription factor binding sites, operators, activator binding sites, repressor binding sites, enhancers, protein-protein binding domains, RNA binding domains, DNA binding domains, silencers, insulators and additional regulatory regions that can alter gene expression in response to developmental and/or external stimuli as will be recognized by a person skilled in the art.
The term “operative connection” as used herein indicate an arrangement of elements in a combination enabling production of an appropriate effect. With respect to genes and regulatory sequences an operative connection indicates a configuration of the genes with respect to the regulatory sequence allowing the regulatory sequences to directly or indirectly increase or decrease transcription or translation of the genes.
Accordingly, in some embodiments, a thermomer monomeric construct can comprise thermomer monomer attached to its cargo in the form of a fusion protein with or without an intervening linker. The term “fusion protein” as used herein refers to proteins expressed through the joined two or more genes or gene fragments which originally code for separate proteins. Translation of the joined two or more genes results in a single fusion protein with retained functional properties derived from each of the original proteins.
In embodiments wherein providing and/or attaching thermomer monomers of the present disclosure are performed through gene expression cassettes, the cassettes can be comprised in a thermomer vector comprising a thermomer gene expression cassette comprising a polynucleotide encoding for a thermomer monomer herein described under control of a promoter and additionally regulatory regions in a configuration allowing expression of the monomer of the present disclosure in a target environment.
The term “vector” indicates a molecule configured to be used as a vehicle to artificially carry foreign genetic material into a cell, where it can be replicated and/or expressed. An expression vector is configured to carry and express the material in a cell under appropriate conditions. In some embodiments, a suitable vector can comprise a recombinant plasmid, a recombinant non-viral vector, or a recombinant viral vector. Vectors described herein can comprise suitable promoters, enhancers, post-transcriptional and post-translational elements for expression in mammalian that are identifiable by those skilled in the art. Vectors suitable for transduction of mammalian cells, are known to those skilled in the art.
Vectors for establishing heterodimer performance can consist of one or more TlpA DNA binding domain-thermomer open reading frames along with a TlpA promoter controlling expression of one or more fluorescent proteins, as depicted in
In some embodiments, the vector can be a selected from lentiviral vectors, AAV vectors, Sleeping Beauty, and PiggyBac.
In embodiments herein described thermomer monomeric constructs can administered to the target environment for a time and under condition to form a thermomer dimeric complex. In particular, in those embodiments which
In particular, the first thermomer monomer and the second thermomer monomer can be selected that are configured to dimerize in a target environment at a target temperature Tbs with a thermal Hill coefficient above 15, to form a thermomer dimer of the present disclosure having a melting temperature Tm=Tbs−0° C. to 5° C.
In embodiments of the present disclosure the temperature of the target environment Te can be modified in accordance with the experimental design. In particular, the temperature of the target environment Te can be changed to have Te=Tbs to dimerize and/or have Te<Tbs to disassociate the complex in the target environment. Lowering the Te can be accomplished using a peltier cooler, refrigerator, or placing the medium in contact with a colder medium. Raising the Te can be accomplished via microwaving, exposing to other forms of radiation that can be absorbed by the environment including solar, radiofrequency, and ultrasonic, or by placing the medium in contact with a warmer medium.
In thermomer dimeric complexes of the present disclosure at least one of the first cargo moiety and the second cargo moiety is formed by a chemical moiety configured to have an interface with the target environment subjected to a Stokes' drag force up to 50 pN, preferably equal or lower than 6-7 pN.
The wording “stokes' drag force” as used herein indicate the drag force F on a sphere of radius R moving through a fluid of viscosity μ at speed ν is given by:
Fd=6πμRv [Eq. 3]
wherein Fd is the frictional force known as Stokes' drag acting on the interface between the fluid and the spherical object; μ is the dynamic viscosity; R is the radius of the spherical object; and ν is the flow velocity relative to the spherical object.
In particular, the cargos are selected to ensure that the coiled-coil structure of the thermomer will not be pulled apart due to the Stokes' drag as the molecule moves through its surroundings. The force applied to the coiled coil can be estimated from the Stokes' drag of its cargo as will be understood by a person skilled in the art. In some embodiments, the combined stoke's drag of the cargo coupled or fused to one monomer and the cargo coupled or fused to the other monomer cannot exceed up to 50 pN preferably 6-7 pN.
Accordingly, in an exemplary embodiment the first cargo moiety is a bead which produces 1000 pN of, and the second thermomer constructs comprises no second cargo moiety.
In another exemplary, embodiment the first cargo moiety is a bead which produces 1000 pN a do the second cargo moiety can be a small protein that produces 1 pN of force with a maximum force pulling in opposite direction being 1 pN.
Accordingly, in some embodiments, no more than ono more than one cargo (or the combination of the N-terminal and C-terminal cargo) can induce an SDF up to 50 pN and preferably induce a stoke's draft force of 6-7 pN or lower.
In some embodiments, the target environment is a cell and the cell comprises at least one of the thermomer monomer, thermomer dimer, thermomer monomeric construct, and thermomer dimeric construct and thermomer vector herein described.
In some embodiments, deposition of thermal energy to activate thermomer dimers is guided spatially by magnetic resonance imaging (MRI). Additionally, MRI can be used to monitor the temperature of the target region and adjust the energy source to achieve the desired local temperature (FIG. 9b of U.S. application Ser. No. 15/384,254 filed on Dec. 19, 20176 and published with publication number US2017/0928425 incorporated herein by reference in its entirety).
In an exemplary embodiment, a fluorescent protein is covalently fused to one polypeptide of the thermomer while a plasma membrane-localization signal is covalently fused to the other strand of the thermomer, resulting in a fluorescent indicator that is localized to the plasma membrane at low temperature and released to diffuse freely in the cell at high temperature.
In another exemplary embodiment, one strand of the thermomer can be covalently fused to an enzyme while the other strand can be covalently fused to an inhibitor, resulting in the activation of that enzyme upon an increase in temperature.
In another exemplary embodiment, one strand of the thermomer can be fused to an arbitrary molecular binding domain (defined as a domain that can bind to a biological or non-biological macromolecule such as DNA, RNA, or a protein) while another strand can be fused to another arbitrary molecular binding domain, resulting in a temperature-dependent bridging system that holds two molecules in close proximity at low temperature and releases them to diffuse freely at high temperature. This embodiment can be used in the creation of new temperature-sensitive transcriptional transactivators or repressors which can bind to a specific DNA sequence only when two halves of the DNA binding domain are brought in close proximity. A naturally occurring example of a repressor that can only bind to a specific DNA sequence only when two halves of the DNA binding domain are brought in close proximity is TlpA. Another potential use of this embodiment is the covalent fusion of an intact DNA binding domain to one polypeptide strand of the thermomer and a transactivation domain (such as VP16) or repression domain (such as KRAB) on the other strand of the thermomer, which would be recognizable to someone skilled in the art as a “two hybrid system” with temperature-mediated control imparted by the thermomers.
In an exemplary embodiments, thermomer dimers herein described, a fluorescent protein is covalent fused to one of the two bioswitch polypeptides in a heterodimeric coiled-coil bioswitch. The other polypeptide in the heterodimer is covalently fused to a peptide region that undergoes enzymatic palmitoylation using endogenous cellular machinery, resulting in its insertion into the cell membrane via hydrophobic interaction. The resulting bioswitch confines the fluorescent protein to the vicinity of the plasma membrane at low temperature, and releases it to diffuse throughout the cell at high temperature.
In some embodiments, each monomer of the protein of the coiled coil temperature sensing dimer can be fused to another protein, protein domain, or protein motif, either directly or via a linker sequence. The term “motif” as related to the protein indicates any continuous part of a protein sequence, regardless of whether or not it folds into a defined tertiary structure, that can be robustly associated with a function. Motifs are typically short (<50 amino acids). A representative motif is the GAP43 palmitoylation sequence MLCCMRRTKQVEKNDEDQKI which is recognized by endogenous mammalian cellular machinery and covalently fused to a lipid macromolecule. The thermoswitchable protein system (which is comprised of two or more proteins, domains, and/or motifs fused via the N-terminus or the C-terminus to the coiled-coil bioswitch) is regulated in response to temperature. This regulation is made apparent by the change in activity of one or more domains fused to the bioswitch (such as a change in the rate of catalysis of an enzyme protein or domain fused to the bioswitch), or by the change in intracellular localization of one or more of the domains fused to the bioswitch (such as the change in the apparent membrane localization of a fluorescent protein fused to the bioswitch).
Additional exemplary embodiments comprise temperature-dependent reconstitution catalytically active Cas9, catalytically inactive Cas9 (dCas9), analogous variants of other Cas proteins. Other potential examples include temperature-dependent reconstitution of split enzymes. Other examples include temperature-dependent activation by temperature-inducible release of an inhibitor from an enzyme. Other examples include temperature-dependent reconstitution of split signaling molecules such as chimeric antigen receptors.
In some embodiments, in a thermomer dimeric complex herein described, the first cargo moiety is Split CAR (N-terminal half) and the second cargo moiety is Split CAR (C-terminal half)
In some embodiments, in a thermomer dimeric complex herein described, the first cargo moiety is Cas9 and the second cargo moiety is anti-CRISPR.
In some embodiments, in a thermomer dimeric complex herein described, the first cargo moiety is Split Cas9 (N-terminal half) and the second cargo moiety is Split Cas9 (C-terminal half).
In some embodiments, in a thermomer dimeric complex herein described, the first cargo moiety is Cpf1 and the second cargo moiety is anti-CRISPR
In some embodiments, in a thermomer dimeric complex herein described, the first cargo moiety is Split Cpf1 (N-terminal half) and the second cargo moiety is Split Cpf1 (C-terminal half)
In some embodiments, in a thermomer dimeric complex herein described, the first cargo moiety is Split dCpf1 (N-terminal half) and the second cargo moiety is Split Cpf1 (C-terminal half).
In some embodiments, in a thermomer dimeric complex herein described, the first cargo moiety is Split TALEN (N-terminal half) and the second cargo moiety is +Split TALEN (C-terminal half)
In some embodiments, in a thermomer dimeric complex herein described, the first cargo moiety is Gal4 DBD and the second cargo moiety is VP16.
In some embodiments, in a thermomer dimeric complex herein described, the first cargo moiety is Gal4 DBD and the second cargo moiety is VP64.
Thermomer monomers, thermomer monomeric constructs and/or thermomer dimeric complexes can be attached to a surface and/or be part of a device as will be understood by a skilled person.
A suitable surface encompasses any surface configured to bind a polypeptide as will be understood by a skilled person upon reading of the present disclosure. Such as surface can be functionalized with chemical handles to facilitate reactions with biological or and/or organic molecules including direct conjugation to the thermomer or its cargo, or via a bridging moiety that serves to chemically link the functionalized surface to the thermomer or its cargo. Additionally, the thermomer may be attached to the surface noncovalently, such as by fusing the thermomer to streptavidin and coating the surface with biotin. Additionally, the thermomer may be attached to the surface nonspecifically, such as via adsorption.
A further description of thermomer surfaces and thermomer devices in accordance with the disclosure is provided herein in connection with the schematic illustration of
In some embodiments, the bioswitch temperature of the coiled coil temperature sensing dimers herein described can be increased or decreased through modification of the amino acid sequences of the temperature sensing domain to obtain temperature sensitive dimers that can operate at controlled temperatures.
In particular, coiled coil temperature sensing dimers operating at controlled temperature can be created by modifying the thermomer to result in modulation of the temperature response profile to higher or lower temperatures, as well as in changing the profile from a cooperative, switch-like induction to a linear “analog” transition.
In some of those embodiments, a coiled coil temperature sensing dimers can be mutated and “tuned” in the sense of the disclosure, to increase or decrease their bioswitch temperature Tbs and activate at different transition temperatures. In particular, in some embodiments, the coiled coil temperature sensing dimers can be tuned to activate at new temperatures while retaining sharp, robust switching performance.
In particular, temperature sensing domain of the coiled coil temperature sensing dimers obtainable with methods herein described can be configured so that the coiled coil temperature sensing dimers can be tuned to exhibit an ON or OFF state at a particular temperature range while still retaining a sharp thermal transition resulting in a large change in activity. For example, modification of the thermomer can be performed to obtain a >100-fold difference between an on and off state, and a 10-fold switching over a temperature range less than 5° C.
A modification of the a coiled coil temperature sensing dimer herein described can be performed to obtain a dimer with a Tbs bioswitch temperature that selected for specific application such as tunable thresholds within a biomedically relevant range of 32° C. to 46° C. Accordingly, one or more coiled coil temperature sensing dimers can be provided starting from coiled coil temperature sensing dimers for use within a cell can be provided that are orthogonal to endogenous cellular machinery and compatible with other thermos-responsive components and a Tbs compatible with the cell physiological temperature to allow multiplexed thermal logic.
In some embodiments, tuning of the thermal response curve is achieved by modulating the affinity of the two coiled coil strands for each other. In those embodiments modification of a bioswitch temperature Tbs of a coiled coil temperature sensing dimer can be performed by providing a coiled coil temperature sensing dimer herein described having a starting bioswitch temperature Tbs0 in the target environment and two monomer proteins configured to form a coiled coil temperature sensing dimer in the target environment with a starting melting temperature Tm0; and replacing in at least one monomer protein of the two monomer proteins forming the t one or more residues in positions a, b, d, e and g of a heptad repeat in the temperature sensing amino acid sequence of the provided coiled coil temperature sensing dimer.
In particular in some embodiments the replacing can be performed by replacing at least one of a hydrophobic amino acid in a position a and/or d of an heptad repeat of the temperature sensitive amino acid sequence of the temperature sensing domain with residues configured to increase or decrease hydrophobic packing between corresponding amino acid residues in positions a and/or d of the two monomer forming temperature sensing domain.
The term “hydrophobic packing” as used herein relates to the aggregating together of nonpolar molecules, and in particular, amino acids, to reduce the surface area exposed to water and minimize their disruptive effect. The efficiency of hydrophobic packing can be quantified by measuring the partition coefficients of non-polar molecules between water and non-polar solvents. The partition coefficients can be transformed to free energy of transfer which includes enthalpic and entropic components:
ΔG=ΔH−TΔS Eq. 4
where G is the Gibbs free energy of protein folding, H is the total enthalpy of a system, T is temperature, and S is entropy. These components can be experimentally determined using techniques such as calorimetry, circular dichroism or NMR, where an increase in ΔG indicates a decrease in efficiency of hydrophobic packing
Hydrophobicity refers to the property of thermodynamically unfavorable interaction with water. In contrast, hydrophilicity refers to the property of thermodynamically favorable interaction with water.
Thus, hydrophobic effect represents the tendency of water to exclude non-polar molecules. The effect originates from the disruption of hydrogen bonds between water molecules. Hydrophobic molecules tend to be nonpolar and, thus, prefer other neutral molecules and nonpolar solvents. Because water molecules are polar, hydrophobic molecules do not dissolve well among them. Hydrophobic molecules in water often cluster together.
There are different hydrophobicity scales (or alternatively, hydropathy indices) of amino acid residues, based on measurement of the level of disruption of hydrogen bonds between water molecules, such as that of Kyte and Doolittle [10] as shown in FIG. 24 of U.S. application Ser. No. 15/384,254 filed on Dec. 19, 2016 and published as US 2017/0298425 incorporated herein by referenced in its entirety.
Exemplary hydrophobic amino acids include alanine, valine, leucine, isoleucine, proline, phenylalanine, tryptophan, cysteine and methionine.
Hydrophobicity scales or hydropathy indices are values that can be used to define relative hydrophobicity or conversely relative polarity (hydrophilicity) of amino acid residues, wherein, the more positive the value, the more hydrophobic the amino acid, and conversely the more negative the value, the more polar the amino acid.
Techniques of measuring amino acid hydrophobicity or polarity comprise wet lab methods such as partitioning between two immiscible phases or reverse phase liquid chromatographic methods, or computer-based methods such as calculation of solvent accessible surface area.
In some embodiments the replacing can be performed by replacing at least one polar or charged amino acid in position b e, and/or g of at least one heptad repeat of the temperature sensing domain amino acid sequence, with a hydrophobic residue,
In some embodiments the replacing can be performed by replacing at least one polar or charged amino acid in positions e and/or g of at least one heptad repeat of the temperature sensing domain amino acid sequence with a residue configured to increase or decrease coulombic repulsion between corresponding residues in positions a, d, e and/or g of at least one heptad repeat of the temperature sensing domain amino acid sequence of the two monomers forming the temperature sensing domain.
In some embodiments the replacing can be performed by replacing one or more amino acid residues in anyone of positions a, b, d, e and/or g of at least one heptad repeat of the temperature sensing domain amino acid sequence as indicated above in combination one with the other.
In embodiments of the method to modify the amino acid sequences of the temperature sensing domain of coiled coil temperature sensing dimers herein described, the replacing is performed to obtain a variant of the coiled coil temperature sensing dimer with a melting temperature of the temperature sensing domain Tmm lower or higher than Tm0 in the target environment, the obtained variant having a bioswitch temperature Tbsm lower or higher than Tbs0 in the target environment.
In particular, some of those embodiments coiled coil temperature sensing dimers of the disclosure can be engineered to lower the bioswitch temperature Tbs of a starting coiled coil temperature sensing dimer, by replacing
where ke is Coulomb's constant (ke=8.99×109 N m2 C−2), q1 and q2 are the signed magnitudes of the charges on each amino acid residue of the pair of residues, and the scalar r is the distance between the charges
Accordingly, an amino acid substitution that changes the coulombic force (in pN) between two amino acids residues by changing from positive to negative or vice-versa, or increases the coulombic force in either direction, can change the structure of a polypeptide or protein, or protein-protein interactions, and related functional characteristics of the polypeptide or protein.
Exemplary variants of coiled coil temperature sensing dimers herein described having a lower bioswitch temperature with respect to a starting coiled coil temperature sensitive dimer, and obtainable methods herein described comprise TlpA39 coiled coil temperature sensing homodimer in which each monomer has sequence MRPATYEPEQIIEAGLALQAEGRNITGFALRNQVGGGNPTRLRQIWDEYQASQSTVVTE PVAELPVEVAEEVKAVSAALSERITQLATELNDKAVRAAERRVAEVTRAAGEQTAQAE RELADAAQTVDDLEEKLVELQDRYDSLTLALESERSLRQQHDVEMAQLKERLAAAEEN TRQREERYQEQKTVLQDALNAEQAQHKNTREDLQKRLEQISVEANARTEELKSERDKV NTFLTRLESQENALASERQQHLATRETLQQRLEQAIADTQARAGEIALERDRVSSLTARL ESQEKASSEQLVRMGSEIASLTERCTQLENQRDDARLETMGEKETVAALRGEAEALKRQ NQSLMAALSGNKQTGGQNA (SEQ ID NO: 37) and TlpA36 oiled coil temperature sensing homodimer in which each monomer has sequence
In some embodiments coiled coil temperature sensing dimers herein described can be engineered to increase the bioswitch temperature Tbs of a starting coiled coil temperature sensing dimers, by replacing
Exemplary variants of coiled coil temperature sensing dimers herein described having a higher bioswitch temperature with respect to a starting coiled coil temperature sensing dimers, and obtainable methods herein described comprise dimers comprising a coiled coil temperature sensing domain of sequence SEQ ID NO: 1 possibly with a 0% to 20% variation and including at least one of the replacement herein described in one or more of the amino acid residues in positions a, b, d e and g of at least one heptad repeat in the sequence that increases the bioswitch temperature Tbs of the coiled coil transcriptional bioswitch dimers.
The structure of the resulting variant and structure of related temperature sensitive amino acid sequence, of temperature sensing domain herein described can be performed to detect can be arranged in heptad repeats each with a register that begins with either a, b, c, d, e, f or g to verify maintenance of the variant's ability to form coiled coil dimerization domains Accordingly, an uninterrupted series of heptad repeats without modification of any one of the a to g positions beginning at position a has a heptad repeat register of [a, b, c, d, e, f, g]n; beginning at position b has a heptad repeat register of [b, c, d, e, f, g, a]n; beginning at position c has a heptad repeat register of [c, d, e, f, g, a, b]n; beginning at position d has a heptad repeat register of [d, e, f, g, a, b, c]n; beginning at position e has a heptad repeat register of [e, f, g, a, b, c, d]n; beginning at position f has a heptad repeat register of [f, g, a, b, c, d, e,]n; and beginning at position g has a heptad repeat register of [g, a, b, c, d, e, f]n.
Detection of heptad repeats within a coiled coil amino acid sequence can be performed using structure prediction servers COILS[2], Paircoil2[3], LOGICOIL[4], among others identifiable by a skilled person. In particular, COILS[2] detects predicted heptad repeats within an amino acid sequence and provides a probability score for each amino acid relative to the position a, b, c, d, e, f, or g within the heptad.
In a thermomer variant herein described heptad repeats in a register can have up to 5 consecutive amino acid residues missing in view of possible deletion or insertion in the sequence within a 0% to 20% percent variation range.
The term “percent variation” or “percentage variation” as used herein means the difference between two amino acid residue sequences, expressed as a percentage, wherein the difference between two amino acid sequences is measured by a process that comprises the steps of aligning the two amino acid sequences, then detecting one or more differences between the aligned sequences, and calculating the total number of differences divided by the total number of aligned amino acids in each amino acid sequence, including gaps with the result expressed as a percentage. The term “alignment” as used herein means aligning the positions of structural features of statistically significant structural similarity between two amino acid sequences, where “statistically significant structural similarity” means greater than 95% probability that two structural features are structurally homologous, for example, alpha-helix. The term “difference” indicates mismatches in the position of structural features in the position of structural features in the two amino acid sequences, whereby each amino acid that comprises part of a mismatched structural feature is counted as one difference between the two aligned amino acid sequences. Mismatches between aligned sequences can comprise an insertion, a deletion, and/or a replacement of one or more structural features in one amino acid sequence compared to the other aligned amino acid sequence as would be understood by a skilled person. Several publicly available online servers can be used to detect protein structure alignment and calculate percent variation, such as FATCAT [11], SuperPose [12], iPBA [13], MAPSCI [14], and others known to a person skilled in the art.
In some embodiments, variation in the temperature sensing amino acid sequence SEQ ID NO: 1 can result in having a total of 2 to 49 consecutive uninterrupted heptad repeats in the temperature sensing amino acid sequence within the 0% to 20% variation range,
In some embodiments, variation in the temperature sensing amino acid sequence SEQ ID NO: 1 can result in having a total of 10 to 30 consecutive uninterrupted heptad repeats in the temperature sensing amino acid sequence within the 0% to 20% variation range
In some embodiments, variation in the temperature sensing amino acid sequence SEQ ID NO: 1 can result in having heptad repeats interrupted by one or more insertions distributed unevenly throughout the system.
In some embodiments, a Minimum and Maximum number of amino acids residues can be inserted in the coiled coil temperature sensitive amino acid sequence, wherein—Minimum=1. Maximum=maximum number of amino acids−(minimum number of heptad repeats*7) to provide the temperature sensitive amino acid sequence with breaks that can be distributed unevenly throughout the coil, with long stretches of heptads and short puncta of heptads. Accordingly in some embodiments the number of uninterrupted heptad repeats in the coiled coil temperature sensitive amino acid sequence can be 2 to 30, in some embodiments the number of uninterrupted heptad repeats in the coiled coil temperature sensitive amino acid sequence can be 5-20 based on the consensus coiled coil prediction for TlpA.
Additional embodiments can comprise a thermomer cell is described comprising at least one of the thermomer monomer, thermomer dimer, thermomer monomeric construct, thermomer dimeric construct and thermomer vector herein described within a biological cell.
A “biological cell or “cell” as used herein indicates the basic structural, functional, and biological unit of all known organism. Cells consist of cytoplasm enclosed within a membrane, which contains many biomolecules such as proteins and nucleic acids had has dimensions typically between 1 and 100 micrometers. Exemplary cells comprise eukaryotic cells, prokaryotic cells identifiable by a skilled person.
Exemplary cells in the sense of the disclosure comprise a plurality of bacterial cells such as E. coli, Salmonella, Bacteroides, Lactobacillus. The cells can be natural cells or they can be genetically modified cells that have been engineered for enhanced disease homing, proliferation, and additional properties identifiable by a skilled person.
Exemplary cells in the sense of the disclosure can comprise a plurality of eukaryotic cells. In some embodiments, the eukaryotic cells are unicellular organisms. Exemplary unicellular eukaryotes comprise protozoa, such as ciliates such as Paramecia, Stentors and Vorticella, amoebas such as Physarum and Entamoeba, unicellular algae such as euglenophyta, chlorophyte, diatoms, dinoflagellates, unicellular fungi such as yeasts such as Saccharomyces and Candida species.
Exemplary cells in the sense of the disclosure comprise cells in or isolated from multicellular eukaryotic species. Multicellular eukaryotic species comprise mammalian species such as animals, plants, and multicellular fungi. In some embodiments, multicellular eukaryotes comprise species such as Homo sapiens and Mus musculus, for example, among others. In some embodiments, cells comprise stem cells, progenitor cells, induced pluripotent stem cells, and others identifiable by a skilled person. In some embodiments, cells comprise genetically engineered mammalian stem cells, for or example, genetically engineered stem cells that have been designed to secrete therapeutic substance after introduction into a host, such as a human.
Exemplary cells comprise further comprises plants and animal cells such as a human cell, an immune cell, a neural cells, Stem cells, T-cells, Neuron cell and additional cell identifiable by a skilled person.
As mentioned above, thermomer monomers, linker polypeptides, cargo moieties, thermomer dimer, thermomer monomeric constructs, thermomer dimeric complex, and related polypeptides, polynucleotidic constructs, vectors, cells and compositions herein described can be provided as a part of systems to perform any of the above mentioned methods. The systems can be provided in the form of kits of parts. In a kit of parts, one or more thermomer monomers, linker polypeptides, cargo moieties, thermomer dimer, thermomer monomeric constructs, thermomer dimeric complex, and related polypeptides, polynucleotidic constructs, vectors, and cells as well as other reagents to perform the methods herein described are comprised in the kit independently. thermomer monomers, linker polypeptides, cargo moieties, thermomer dimer, thermomer monomeric constructs, thermomer dimeric complex, and related polypeptides, polynucleotidic constructs, vectors, and cells and other reagents can be included in one or more compositions, and each thermomer monomers, linker polypeptides, cargo moieties, thermomer dimer, thermomer monomeric constructs, thermomer dimeric complex, and related polypeptides, polynucleotidic constructs, vectors, cells and reagents is in a composition together with a suitable vehicle.
Additional components can include labeled polynucleotides, labeled antibodies, labels, microfluidic chip, reference standards, and additional components identifiable by a skilled person upon reading of the present disclosure.
The terms “label” and “labeled molecule” as used herein refer to a molecule capable of detection, including but not limited to radioactive isotopes, fluorophores, chemiluminescent dyes, chromophores, enzymes, enzymes substrates, enzyme cofactors, enzyme inhibitors, dyes, metal ions, nanoparticles, metal sols, ligands (such as biotin, avidin, streptavidin or haptens) and the like. The term “fluorophore” refers to a substance or a portion thereof which is capable of exhibiting fluorescence in a detectable image. As a consequence, the wording “labeling signal” as used herein indicates the signal emitted from the label that allows detection of the label, including but not limited to radioactivity, fluorescence, chemoluminescence, production of a compound in outcome of an enzymatic reaction and the like.
In embodiments herein described, the components of the kit can be provided, with suitable instructions and other necessary reagents, in order to perform the methods here disclosed. The kit will normally contain the compositions in separate containers. Instructions, for example written or audio instructions, on paper or electronic support such as tapes, CD-ROMs, flash drives, or by indication of a Uniform Resource Locator (URL), which contains a pdf copy of the instructions for carrying out the assay, will usually be included in the kit. The kit can also contain, depending on the particular method used, other packaged reagents and materials (i.e. wash buffers and the like).
Further details concerning the thermal bioswitches, and related thermal genetic circuits, therapeutic cells, systems and methods of the present disclosure will become more apparent hereinafter from the following detailed disclosure of examples by way of illustration only with reference to an experimental section.
The thermal bioswitches and related systems and methods herein disclosed are further illustrated in the following examples, which are provided by way of illustration and are not intended to be limiting.
In particular, the following examples illustrate exemplary methods and protocols for preparing sets of polynucleotides and polypeptides, testing and characterizing these sets of polynucleotides and polypeptides, building genetic circuits, and testing genetic circuits in vivo and in vitro. A person skilled in the art will appreciate the applicability and the necessary modifications to adapt the features described in detail in the present section, to additional tunable thermal bioswitches, genetic circuits and therapeutic cells and related methods and systems according to embodiments of the present disclosure.
Plasmid Construction and Molecular Biology. All plasmids were designed using SnapGene (GSL Biotech) and assembled via KLD mutagenesis or Gibson Assembly using enzymes from New England Biolabs. All plasmids and sequences will be deposited to Addgene. After assembly, constructs were transformed into NEB Turbo and NEB Stable E. coli (New England Biolabs) for growth and plasmid preparation. Constructs containing long homologous regions such, including all plasmids containing two TlpA ORFs, were propagated using NEB Stable. Thermal gene expression assays were performed in NEB Stable E. coli. Bacterial reporters of gene expression referred to in the text as GFP and RFP are mWasabi[15] and mCherry[16], respectively. The mammalian fusion protein fluorophore referred to in the text and figures as RFP is mScarlet-I[17]. TlpA, mCherry and mWasabi were obtained from our previous work[18]. mScarlet-I was obtained from Addgene (pmScarlet-i_C1, plasmid #85044). Coiled-coil structure prediction and helical wheel diagram annotation was performed using the software DrawCoil 1.0[8]. In the creation of dual-expression GFP/RFP thermal reporter plasmids such as that described in
Bacterial Thermal Regulation Assay. Determination of temperature-dependent gene expression was performed as described previously[18]. Briefly, saturated precultures were diluted to OD600=0.1 and propagated at 30° C. until reaching OD600=0.3 as measured via Nanodrop 2000c (Thermo Scientific), at which point 25 uL aliquots were dispensed into PCR tubes with transparent caps (Bio-Rad) and incubated for 12 hours in a thermal gradient using a Bio-Rad C1000 Touch thermocycler. After thermal stimulus, fluorescence was measured using a Stratagene MX3005p qPCR (Agilent), after which cultures were diluted 4×, transferred into microplates (Costar black/clear bottom), and measured for OD600 using a Molecular Devices SpectraMax M5 plate reader. The background-corrected F/OD is reported as described previously [18].
Protein Expression and Purification for CD Spectroscopy. pET26b-based expression constructs were transformed into BL21-DE3 E. coli and grown on kanamycin-selective plates. Saturated overnight cultures were diluted 1 mL into 400 mL expression cultures and induced with a final IPTG (Sigma Aldrich) concentration of 1 mM at OD600=0.6. After 24 hours of expression at 25° C., cultures were harvested by centrifugation using a JLA-16.250 rotor (Beckman Coulter) at 6,000 rpm and 4° C. for 8 minutes. Pellets were lysed using the detergent Solulyse in Tris Buffer (Genlantis) and debris was pelleted by centrifugation at 35,343 rcf in a JS-24.38 rotor (Beckman Coulter). Polyhistidine-tagged proteins were purified on an AKTA purifier (GE Healthcare) using 1 mL cOmplete columns (Roche) and buffer exchanged into 1×PBS (Corning) using Zeba spin desalting columns. Concentration was determined using the Pierce 660 nm Protein Assay (Thermo Fisher Scientific) and proteins were stored at 4° C. until use. Proteins were subsequently analyzed within 24 hours of purification.
Circular Dichroism Spectroscopy. CD melting curves were taken using an Aviv Circular Dichroism Spectrophotometer (Model 60DS) at 222 nm with 0.1 minute equilibration time and 5 second averaging time. Purified proteins were diluted to 3 μM in 1×PBS and measured in a 1 mm quartz cuvette.
Temperature-dependent protein fluorescence measurement. Fluorescent proteins were purified as described above and diluted to 1 μM for analysis. 25 μL samples were placed in N=3 replicates in PCR strips with optically transparent caps (Bio Rad) into a Stratagene MX3005p qPCR (Agilent) for intensity measurements. Filter sets used for red, green, and blue proteins were ROX, FAM, and ATTO, respectively. Sample fluorescence was measured continuously as temperature was ramped from 25° C. to 50° C. in 1° C. increments and with 1 minute of equilibration time at each increment.
Mass-based validation of heterodimerization. Dual TlpA expression constructs were transformed into BL21-DE3 cells (NEB) and grown as 1 mL precultures in 2×YT/ampicillin for 20-24 hours at 30° C. in an Infors Multitron with shaking at 250 rpm. 10 μL saturated cultures were diluted into 4 mL 2×YT/ampicillin and returned to 30° C. At OD600—0.6 to 0.7, cultures were induced with 4 μL of 1 M IPTG (Sigma Aldrich) and returned to 30° C. for 12 hours, at which point they were transferred into 2 mL centrifuge tubes (USA Scientific) and pelleted in a Beckman Microfuge 20 at maximum speed for 1 minute. Supernatant was carefully and completely aspirated with a pipette, and the pellet was weighed and frozen at −20° C. for at least 20 minutes. After thawing, Solulyse in Tris Buffer (Genlantis) was added at 10 μL per 1 mg. Pellets were gently resuspended via pipetting and shaken in an Eppendorf ThermoMixer at room temperature (800 rpm for 20 minutes). Subsequently the tubes were spun at 13,000 rcf for 10 minutes and the lysate was diluted 5-fold in Solulyse in Tris Buffer. A pilot Western blot was performed and total TlpA band intensity was quantified for each variant, after which loading amounts for all variants were normalized to that of the wild type via dilution in Solulyse. For crosslinking, 1 μL of 50 mM CuCl2 (Sigma Aldrich) was added to 10 μL lysate in an Eppendorf microcentrifuge tube. The lysate and CuCl2 solution were pre-heated separately for 5 minutes prior to co-incubation. Subsequently, the lysate and crosslinker mixture was shaken at 800 rpm for 10 minutes in an Eppendorf ThermoMixer at the desired temperature. After 10 minutes of CuCl2-catalyzed crosslinking, the reaction was quenched with 11 μL Laemmli buffer (Bio Rad). For uncrosslinked samples, 10 uL Laemmli buffer was added to the lysate at the appropriate temperature. SDS-PAGE was performed using 7.5% pre-cast polyacrylamide gels (Bio Rad) run at 75 V for 140 minutes. Western blotting was performed using the Transblot Turbo apparatus and nitrocellulose membrane kit (Bio Rad). Transfer was performed at 25 V for 7 minutes. Membranes were blocked with 5% w/v Blotto milk (Santa Cruz Biotechnology) in 0.05% TBS-Tween for 1 hour at room temperature. Primary staining was performed using the mouse anti-HA sc-7392 antibody (Santa Cruz Biotech) overnight at 4° C. Blots were then washed three times for 15 minutes at 4° C. with 0.05% TBS-Tween and stained for 4 hours with goat anti-mouse IgG-HRP sc-2005 (Santa Cruz Biotech) at room temperature. After three 15-minute washes, HRP visualization was performed using Supersignal West Pico PLUS reagent (Thermo Fisher Scientific). Imaging was performed in a Bio-Rad ChemiDoc MP gel imager.
Mammalian cell culture. K562 cells (gift of D. Baltimore) were cultured in RPMI 1640 media (Thermo Fisher Scientific) with 1×Penicillin/Streptomycin (Corning). Transient transfection was performed using Lonza 4D nucleofection with SF Cell Line buffer and the pre-programmed K562 protocol. Lentivirus was prepared using a third-generation viral vector and helper plasmids (gifts of D. Baltimore). Virus was packaged in HEK293T cells grown in 10 cm dishes after 2 days of transfection and concentrated via the Lenti-X reagent (Takara Bio). Infection was performed by resuspending viral pellets in 250 uL RPMI and spinfecting 1E6 K562 cells in 1 mL RPMI with 10 μL virus at 800×g, 30° C., for 90 minutes. Experiments were performed at least five passages after infection.
Live cell microscopy. Delta-T dishes (Bioptechs) were coated with 400 μL 0.1 mg/mL Poly-D Lysine (Sigma Aldrich) for 30 minutes. Meanwhile, 1E6 K562 cells were pelleted at 300 rcf for 5 minutes and resuspended in staining solution (1×PBS or HBSS with 2.5 μg/mL Hoechst 33342, Thermo Fisher Scientific). For Golgi staining, the solution (in HBSS) also contained BODIPY FL C5-Ceramide complexed to BSA (Thermo Fisher Scientific, 50 nM final concentration). Cells were stained at room temperature for 10 minutes before being pelleted and resuspended in 1 mL RPMI 1640. For co-localization experiments, the staining solution (in HBSS) also contained CellBrite Fix 488 at 1×concentration as described in the product manual, and staining was performed at 37° C. for 10 minutes. After at least 20 minutes of coating, PDL was aspirated from the Delta-T dishes, which were then rinsed once with 1×PBS and dried. Cells were then transferred to the Delta-T dishes, which where adhesively affixed to the swinging plates of an Allegra X-12 centrifuge with SX4750 rotor (Beckman Coulter) and centrifugated at 30° C. for 15 minutes at 300 rcf. Imaging was performed at the California Institute of Technology confocal microscopy facility using an LSM880 (Zeiss) with Airyscan. Cells with sufficient overall brightness to discern membrane contrast were imaged; the membrane localization of dimmer cells could not be discerned in our thermal imaging configuration but was observable under higher magnification on a conventional glass slide (
Image analysis. Image analysis was performed using the Zeiss Zen Black software for pre-processing and CellProfiler[19] for correlation quantification. Images were manually cropped to include only a single cell per ROI, with approximately 408×408 pixel FOVs. For cells with poor attachment to the plate, resulting in position offsets between the red, blue, and green channels, frame alignment between the red and green channels was performed in Zen Black. All available transformations were sampled and the best-aligned transformation on a per-cell basis was used. Blue channel alignment was performed in CellProfiler on a per-cell basis for images with obvious displacement of the nucleus using the Mutual Information module, correlating the blue channel image with the inverted red channel image. Exported images were then loaded in CellProfiler and analyzed using a custom pipeline. Briefly, cell boundaries were determined from red channel using Hoescht 33342-stained nuclei as primary seed objects. Colocalization was calculated for the ROI defined between the outer cell membrane and the nucleus. The nucleus was excluded because it acts as a diffusion barrier to TlpA-RFP but not to free mScarlet-I. For the free mScarlet-I cell line in
Most applications of inducible dimerization systems require the interacting modules to be heterodimeric to enforce selective binding between two desired molecular partners [20]. To redesign the wild type TlpA into a pair of heterodimeric coiled-coil species (
Coiled-coil domains typically consist of repetitive seven-amino acid residue sequences known as heptad repeats[21]. Applicant used a published annotation of the TlpA sequence[7], cross-referenced against a computational annotation from the COILS[2] prediction server, to establish the register of heptad repeats within the TlpA primary sequence. Charge-complementary pairs of residues [22] predicted either at conventional g-to-e′ contacts or at alternative g-to-d′ interfaces were then introduced to disfavor homodimerization and favor heterodimerization (
To maintain the highly switch-like thermal dissociation behavior of TlpA, Applicant reasoned that the least perturbative positions for mutagenesis would be at existing interfacial ionic interaction sites in the wild-type protein, which are present due to the C2 symmetry of the parallel coiled-coil structure. All such positions were mutated one by one, replacing cationic residues with glutamate and anionic side chains with arginine or lysine. The resulting coiled-coil domains were expressed in E. coli, the proteins purified via affinity chromatography, and their helical content assayed over a relevant thermal range using circular dichroism spectroscopy (
From this initial screen a pair of charge-complemented mutants was obtained, dubbed TlpA-G1A (E180R) and TlpA-G1B (R179E), that demonstrated a sharp, sigmoidal thermal response profile with a notable upshift in the temperature threshold for an equimolar mixture of the mutant pair relative to pure solutions of either species (
To validate the in cellulo functionality of the TlpA-G1A and G1B mutants, the ability of TlpA was utilized to modulate the expression of a fluorescent reporter gene in E. coli[18].
A temperature-inducible circuit was constructed containing two separate copies of the TlpA gene, with TlpA operators upstream of a green fluorescent protein (GFP) and a red fluorescent protein (RFP). To compare the repression efficiency of the G1A/G1A and G1B/G1B homodimers to that of the G1A/G1B heterodimer, circuit variants was generated containing two copies of TlpA-G1A, two copies of TlpA-G1B, or one copy of each TlpA variant (
The thermal gene expression profiles of GFP showed all three circuits to produce a highly switch-like cooperative activation. However, the two homodimeric constructs had a clear downshift in their transition temperature compared to the heterodimeric construct containing both TlpA variants (
While the first-generation variants shown in Examples 1-2 demonstrated the ability to engineer a heterodimerization preference, it was noted that the G1A/G1A and G1B/G1B circuit constructs still had a transition setpoint above 37° C., indicating that these mutants retained the ability to homodimerize under typical mammalian homeostatic conditions.
Therefore, thermal GFP expression assay was used to evaluate a subset of additional rational mutant pairs selected from the original panel (
In the bacterial bioswitch assay, all the heterodimeric circuits combining G2An with its complementary G2Bn displayed switch-like activation of reporter fluorescence (
To confirm the dimerization preference of the engineered coiled-coils, a biochemical assay was designed based on covalent crosslinking and size-based gel separation.
TlpA dimers can be crosslinked via CuCl2-catalyzed oxidation of the protein's single cysteine residue[26]. To distinguish hetero- from homodimerization, one of the two TlpA sequences was truncated by removing its DNA binding domain, thereby altering its electrophoretic mobility on a polyacrylamide gel without perturbing its ability to dimerize (
Substituting the wild type coiled-coils with the first-generation heterodimerizing mutants resulted in preferential accumulation of the TlpA heterodimer at 37° C. (
After validating the temperature-dependent association of the engineered heterodimeric TlpA thermomers, Applicant set out to demonstrate their ability to be fused with other proteins and confer controlled protein-protein association in mammalian cells.
A construct was designed wherein one TlpA-G2-3 strand was N-terminally fused with the palmitoylation sequence of GAP43, thereby compartmentalizing it to the plasma membrane. The complementary TlpA-G2-3 strand was fused at the C-terminus to mScarlet-I (
Using live cell confocal microscopy of transiently transfected K562 cells, at physiological temperature strong localization of fluorescence to the plasma membrane (
To enable the use of the thermomer system with viral gene delivery and genomic integration, Applicant generated a nonhomologous variant of the TlpA G2A3 strand (nhTlpA G2A3) in which all degenerate codons were mutagenized to synonymous triplets with minimal identity to the original sequence. This mutagenesis helps avoid template switching-mediated recombination during viral delivery of high-homology constructs[27]. The resulting open reading frame had 57.48% sequence identity to the parent sequence, with no more than 5 consecutive homologous nucleotides. Lentiviral delivery of a construct containing palmitoylated nhTlpA G2A3 and mScarlet-fused TlpA G2B3 resulted in robust temperature-induced dissociation of fluorescence from the plasma membrane (
This virally-engineered K562 cell line was used to quantify the co-localization of RFP fluorescence intensity with signal from the plasma membrane, as delineated by CellBrite Fix 488 staining (
The TlpA reporter cell line was also used to evaluate the reversibility of TlpA-mediated membrane localization after heating. Membrane localization was released by a 5-minute incubation at 42° C. Upon cooling back to 37° C., TlpA re-partitioned to the plasma membrane, indicating reversibility, albeit with slower kinetics than observed for dissociation (
Exemplary monomers and monomeric structure are listed in Table 2 below, wherein the cargo moiety is indicated with brackets, the linker is indicated with underlined fonts and the thermomer monomer is indicated with italic fonts
VSAALSERITQLATELNDKAVRAAERRVAEVTRAAGEQTAQ
AERELADAAQTVDDLEEKLDELQDRYDSLTLALESERSLR
QQHDVEMAQLKERLAAAEENTRQREERYQEQKTVLQDAL
NAEQAQHKNTREDLQKRLEQISAEANARTEELKSERDKVN
TLLTRLESQENALASERQQHLATRETLQQRLEQAIADTQAR
AGEIALERDRVSSLTARLESQEKASSEQLVRMGSEIASLTER
CTQLENQRDDARLETMGEKETVAALRGEAEALKRQNQSL
MAALSGNKQTGGQNA
VSAALSERITQLATELNDKAVRAAERRVAEVTRAAGEQTAQ
AERELADAAQTVDDLEEKL
V
ELQDRYDSLTLALESERSLR
QQHDVEMAQLKERLAAAEENTRQREERYQEQKTVLQDAL
T
F
LTRLESQENALASERQQHLATRETLQQRLEQAIADTQA
RAGEIALERDRVSSLTARLESQEKASSEQLVRMGSEIASLTE
RCTQLENQRDDARLETMGEKETVAALRGEAEALKRQNQS
LMAALSGNKQTGGQNA
VSAALSERITQLATELNDKAVRAAERRVAEVTRAAGEQTAQ
AERELADAAQTVDDLEEKLDELQDRYDSLTLALESERSLR
QQHDVEMAQLKERLAAAEENTRQR
R
ERYQEQKTVLQDAL
NAEQAQHKNTREDLQKRLEQISAEANARTEELKSERDKVN
TLLTRLESQENALASERQQHLATRETLQQRLEQAIADTQAR
AGEIALERDRVSSLTARLESQEKASSEQLVRMGSEIASLTER
CTQLENQRDDARLETMGEKETVAALRGEAEALKRQNQSL
MAALSGNKQTGGQNA
VSAALSERITQLATELNDKAVRAAERRVAEVTRAAGEQTAQ
AERELADAAQTVDDLEEKLDELQDRYDSLTLALESERSLR
QQHDVEMAQLKERLAAAEENTRQ
E
EEERYQEQKTVLQDAL
NAEQAQHKNTREDLQKRLEQISAEANARTEELKSERDKVN
TLLTRLESQENALASERQQHLATRETLQQRLEQAIADTQAR
AGEIALERDRVSSLTARLESQEKASSEQLVRMGSEIASLTER
CTQLENQRDDARLETMGEKETVAALRGEAEALKRQNQSL
MAALSGNKQTGGQNA
VSAALSERITQLATELNDKAVRAAERRVAEVTRAAGEQTAQ
AERELADAAQTVDDLEEKLDELQDRYDSLTLALESERSLR
QQHDVEMAQLKERLAAAEENTRQR
R
ERYQEQKTVLQDAL
NAEQAQHKNTREDLQKRLEQISAEANARTEELKS
R
RDKVN
TLLTRLESQENALASERQQHLATRETLQQRLEQAIADTQAR
AGEIALERDRVSSLTARLESQEKASSEQLVRMGSEIASLTER
CTQLENQRDDARLETMGEKETVAALRGEAEALKRQNQSL
MAALSGNKQTGGQNA
VSAALSERITQLATELNDKAVRAAERRVAEVTRAAGEQTAQ
AERELADAAQTVDDLEEKLDELQDRYDSLTLALESERSLR
NAEQAQHKNTREDLQKRLEQISAEANARTEELKSE
E
DKVN
TLLTRLESQENALASERQQHLATRETLQQRLEQAIADTQAR
AGEIALERDRVSSLTARLESQEKASSEQLVRMGSEIASLTER
CTQLENQRDDARLETMGEKETVAALRGEAEALKRQNQSL
MAALSGNKQTGGQNA
VSAALSERITQLATELNDKAVRAAERRVAEVTRAAGEQTAQ
AERELADAAQTVDDLEEKLDELQDRYDSLTLALESERSLR
QQHDVEMAQLKERLAAAEENTRQR
R
ERYQEQKTVLQDAL
NAEQAQHKNTREDLQKRLEQISAEANARTEELKSE
E
DKVN
TLLTRLESQENALASERQQHLATRETLQQRLEQAIADTQAR
AGEIALERDRVSSLTARLESQEKASSEQLVRMGSEIASLTER
CTQLENQRDDARLETMGEKETVAALRGEAEALKRQNQSL
MAALSGNKQTGGQNA
VSAALSERITQLATELNDKAVRAAERRVAEVTRAAGEQTAQ
AERELADAAQTVDDLEEKLDELQDRYDSLTLALESERSLR
QQHDVEMAQLKERLAAAEENTRQ
E
EERYQEQKTVLQDAL
NAEQAQHKNTREDLQKRLEQISAEANARTEELKS
R
RDKVN
TLLTRLESQENALASERQQHLATRETLQQRLEQAIADTQAR
AGEIALERDRVSSLTARLESQEKASSEQLVRMGSEIASLTER
CTQLENQRDDARLETMGEKETVAALRGEAEALKRQNQSL
MAALSGNKQTGGQNA
VSAALSERITQLATELNDKAVRAAERRVAEVTRAAGEQTAQ
AERELADAAQTVDDLEEKLDELQDRYDSLTLALESERSLR
QQHDVEMAQLKERLAAAEENTRQR
R
ERYQEQKTVLQDAL
NAEQAQHKNTREDLQKRLEQISAEANARTEELKSERDKVN
TLLTRLESQENALAS
R
RQQHLATRETLQQRLEQAIADTQAR
AGEIALERDRVSSLTARLESQEKASSEQLVRMGSEIASLTER
CTQLENQRDDARLETMGEKETVAALRGEAEALKRQNQSL
MAALSGNKQTGGQNA
VSAALSERITQLATELNDKAVRAAERRVAEVTRAAGEQTAQ
AERELADAAQTVDDLEEKLDELQDRYDSLTLALESERSLR
QQHDVEMAQLKERLAAAEENTRQ
E
EERYQEQKTVLQDAL
NAEQAQHKNTREDLQKRLEQISAEANARTEELKSERDKVN
TLLTRLESQENALASE
E
QQHLATRETLQQRLEQAIADTQAR
AGEIALERDRVSSLTARLESQEKASSEQLVRMGSEIASLTER
CTQLENQRDDARLETMGEKETVAALRGEAEALKRQNQSL
MAALSGNKQTGGQNA
VSAALSERITQLATELNDKAVRAAERRVAEVTRAAGEQTAQ
AERELADAAQTVDDLEEKLDELQDRYDSLTLALESERSLR
QQHDVEMAQLKERLAAAEENTRQR
R
ERYQEQKTVLQDAL
NAEQAQHKNTREDLQKRLEQISAEANARTEELKSERDKVN
TLLTRLESQENALASE
E
QQHLATRETLQQRLEQAIADTQAR
AGEIALERDRVSSLTARLESQEKASSEQLVRMGSEIASLTER
CTQLENQRDDARLETMGEKETVAALRGEAEALKRQNQSL
MAALSGNKQTGGQNA
VSAALSERITQLATELNDKAVRAAERRVAEVTRAAGEQTAQ
AERELADAAQTVDDLEEKLDELQDRYDSLTLALESERSLR
QQHDVEMAQLKERLAAAEENTRQ
E
EERYQEQKTVLQDAL
NAEQAQHKNTREDLQKRLEQISAEANARTEELKSERDKVN
TLLTRLESQENALAS
R
RQQHLATRETLQQRLEQAIADTQAR
AGEIALERDRVSSLTARLESQEKASSEQLVRMGSEIASLTER
CTQLENQRDDARLETMGEKETVAALRGEAEALKRQNQSL
MAALSGNKQTGGQNA
VSAALSERITQLATELNDKAVRAAERRVAEVTRAAGEQTAQ
AERELADAAQTVDDLEEKLDELQDRYDSLTLALESERSLR
QQHDVEMAQLKERLAAAEENTRQREERYQEQKTVLQDAL
NAEQAQHKNTREDLQKRLEQISAEANARTEELKSE
E
DKVN
TLLTRLESQENALASE
E
QQHLATRETLQQRLEQAIADTQAR
AGEIALERDRVSSLTARLESQEKASSEQLVRMGSEIASLTER
CTQLENQRDDARLETMGEKETVAALRGEAEALKRQNQSL
MAALSGNKQTGGQNA
VSAALSERITQLATELNDKAVRAAERRVAEVTRAAGEQTAQ
AERELADAAQTVDDLEEKLDELQDRYDSLTLALESERSLR
QQHDVEMAQLKERLAAAEENTRQREERYQEQKTVLQDAL
NAEQAQHKNTREDLQKRLEQISAEANARTEELKS
R
RDKVN
TLLTRLESQENALAS
R
RQQHLATRETLQQRLEQAIADTQAR
AGEIALERDRVSSLTARLESQEKASSEQLVRMGSEIASLTER
CTQLENQRDDARLETMGEKETVAALRGEAEALKRQNQSL
MAALSGNKQTGGQNA
VSAALSERITQLATELNDKAVRAAERRVAEVTRAAGEQTAQ
AERELADAAQTVDDLEEKLDELQDRYDSLTLALESERSLR
QQHDVEMAQLKERLAAAEENTRQREERYQEQKTVLQDAL
NAEQAQHKNTREDLQKRLEQISAEANARTEELKS
R
RDKVN
TLLTRLESQENALASE
E
QQHLATRETLQQRLEQAIADTQAR
AGEIALERDRVSSLTARLESQEKASSEQLVRMGSEIASLTER
CTQLENQRDDARLETMGEKETVAALRGEAEALKRQNQSL
MAALSGNKQTGGQNA
VSAALSERITQLATELNDKAVRAAERRVAEVTRAAGEQTAQ
AERELADAAQTVDDLEEKLDELQDRYDSLTLALESERSLR
QQHDVEMAQLKERLAAAEENTRQREERYQEQKTVLQDAL
NAEQAQHKNTREDLQKRLEQISAEANARTEELKSE
E
DKVN
TLLTRLESQENALAS
R
RQQHLATRETLQQRLEQAIADTQAR
AGEIALERDRVSSLTARLESQEKASSEQLVRMGSEIASLTER
CTQLENQRDDARLETMGEKETVAALRGEAEALKRQNQSL
MAALSGNKQTGGQNA
AGEQTAQAERELADAAQTVDDLEEKLDELQDRYDSLTLAL
ES
R
RSLRQQHDVEMAQLKERLAAAEENTRQREERYQEQK
TVLQDALNAEQAQHKNTREDLQKRLEQISAEANARTEELK
SERDKVNTLLTRLESQENALASERQQHLATRETLQQRLEQ
AIADTQARAGEIALERDRVSSLTARLESQEKASSEQLVRMG
SEIASLTERCTQLENQRDDARLETMGEKETVAALRGEAEA
LKRQNQSLMAALGHHHHHH
AGEQTAQAERELADAAQTVDDLEEKLDELQDRYDSLTLAL
ESE
E
SLRQQHDVEMAQLKERLAAAEENTRQREERYQEQK
TVLQDALNAEQAQHKNTREDLQKRLEQISAEANARTEELK
SERDKVNTLLTRLESQENALASERQQHLATRETLQQRLEQ
AIADTQARAGEIALERDRVSSLTARLESQEKASSEQLVRMG
SEIASLTERCTQLENQRDDARLETMGEKETVAALRGEAEA
LKRQNQSLMAALGHHHHHH
AGEQTAQAERELADAAQTVDDLEEKLDELQDRYDSLTLAL
ESERSLRQQHDVEMAQLKE
E
LAAAEENTRQREERYQEQK
TVLQDALNAEQAQHKNTREDLQKRLEQISAEANARTEELK
SERDKVNTLLTRLESQENALASERQQHLATRETLQQRLEQ
AIADTQARAGEIALERDRVSSLTARLESQEKASSEQLVRMG
SEIASLTERCTQLENQRDDARLETMGEKETVAALRGEAEA
LKRQNQSLMAALGHHHHHH
AGEQTAQAERELADAAQTVDDLEEKLDELQDRYDSLTLAL
ESERSLRQQHDVEMAQLKERLAAA
R
ENTRQREERYQEQK
TVLQDALNAEQAQHKNTREDLQKRLEQISAEANARTEELK
SERDKVNTLLTRLESQENALASERQQHLATRETLQQRLEQ
AIADTQARAGEIALERDRVSSLTARLESQEKASSEQLVRMG
SEIASLTERCTQLENQRDDARLETMGEKETVAALRGEAEA
LKRQNQSLMAALGHHHHHH
AGEQTAQAERELADAAQTVDDLEEKLDELQDRYDSLTLAL
ESERSLRQQHDVEMAQLKERLAAAEENTRQ
E
EERYQEQK
TVLQDALNAEQAQHKNTREDLQKRLEQISAEANARTEELK
SERDKVNTLLTRLESQENALASERQQHLATRETLQQRLEQ
AIADTQARAGEIALERDRVSSLTARLESQEKASSEQLVRMG
SEIASLTERCTQLENQRDDARLETMGEKETVAALRGEAEA
LKRQNQSLMAALGHHHHHH
AGEQTAQAERELADAAQTVDDLEEKLDELQDRYDSLTLAL
ESERSLRQQHDVEMAQLKERLAAAEENTRQR
R
ERYQEQK
TVLQDALNAEQAQHKNTREDLQKRLEQISAEANARTEELK
SERDKVNTLLTRLESQENALASERQQHLATRETLQQRLEQ
AIADTQARAGEIALERDRVSSLTARLESQEKASSEQLVRMG
SEIASLTERCTQLENQRDDARLETMGEKETVAALRGEAEA
LKRQNQSLMAALGHHHHHH
AGEQTAQAERELADAAQTVDDLEEKLDELQDRYDSLTLAL
ESERSLRQQHDVEMAQLKERLAAAEENTRQREERYQEQK
TVLQDALNAEQAQHKNTREDLQKRLEQISAEANARTE
R
LK
SERDKVNTLLTRLESQENALASERQQHLATRETLQQRLEQ
AIADTQARAGEIALERDRVSSLTARLESQEKASSEQLVRMG
SEIASLTERCTQLENQRDDARLETMGEKETVAALRGEAEA
LKRQNQSLMAALGHHHHHH
AGEQTAQAERELADAAQTVDDLEEKLDELQDRYDSLTLAL
ESERSLRQQHDVEMAQLKERLAAAEENTRQREERYQEQK
TVLQDALNAEQAQHKNTREDLQKRLEQISAEANARTEELK
SE
E
DKVNTLLTRLESQENALASERQQHLATRETLQQRLEQ
AIADTQARAGEIALERDRVSSLTARLESQEKASSEQLVRMG
SEIASLTERCTQLENQRDDARLETMGEKETVAALRGEAEA
LKRQNQSLMAALGHHHHHH
AGEQTAQAERELADAAQTVDDLEEKLDELQDRYDSLTLAL
ESERSLRQQHDVEMAQLKERLAAAEENTRQREERYQEQK
TVLQDALNAEQAQHKNTREDLQKRLEQISAEANARTEELK
S
R
RDKVNTLLTRLESQENALASERQQHLATRETLQQRLEQ
AIADTQARAGEIALERDRVSSLTARLESQEKASSEQLVRMG
SEIASLTERCTQLENQRDDARLETMGEKETVAALRGEAEA
LKRQNQSLMAALGHHHHHH
AGEQTAQAERELADAAQTVDDLEEKLDELQDRYDSLTLAL
ESERSLRQQHDVEMAQLKERLAAAEENTRQREERYQEQK
TVLQDALNAEQAQHKNTREDLQKRLEQISAEANARTEELK
SERDKVNTLLTRLESQENALAS
R
RQQHLATRETLQQRLEQ
AIADTQARAGEIALERDRVSSLTARLESQEKASSEQLVRMG
SEIASLTERCTQLENQRDDARLETMGEKETVAALRGEAEA
LKRQNQSLMAALGHHHHHH
AGEQTAQAERELADAAQTVDDLEEKLDELQDRYDSLTLAL
ESERSLRQQHDVEMAQLKERLAAAEENTRQREERYQEQK
TVLQDALNAEQAQHKNTREDLQKRLEQISAEANARTEELK
SERDKVNTLLTRLESQENALASE
E
QQHLATRETLQQRLEQ
AIADTQARAGEIALERDRVSSLTARLESQEKASSEQLVRMG
SEIASLTERCTQLENQRDDARLETMGEKETVAALRGEAEA
LKRQNQSLMAALGHHHHHH
ELNDKAVRAAERRVAEVTRAAGEQTAQAERELADAAQTV
DDLEEKL
V
ELQDRYDSLTLALESERSLRQQHDVEMAQLK
ERLAAAEENTRQR
R
ERYQEQKTVLQDALNAEQAQHKNTR
EDLQKRLEQIS
R
EANARTEELKSERDKVNT
F
LTRLESQENA
LASR
R
QQHLATRETLQQRLEQAIADTQARAGEIALERDRVS
LPVEV
AEEVKAVSAALSERITQLATELNDKAVRAAERRVA
EVTRAAGEQTAQAERELADAAQTVDDLEEKL
ELQDRYD
SLTLALESERSLRQQHDVEMAQLKERLAAAEENTRQ
EER
YQEQKTVLQDALNAEQAQHKNTREDLQKRLEQIS
EANA
RTEELKSERDKVNT
LTRLESQENALASE
QQHLATRETL
QQRLEQAIADTQARAGEIALERDRVSSLTARLESQEKASSE
QLVRMGSEIASLTERCTQLENQRDDARLETMGEKETVAAL
RGEAEALKRQNQSLMAALSGNKQTGGQNA
GGGGSGGGGSGGGGS
GGGSGGGS[MVSKGEAVIKEFMRFKVHMEGSMNGHEFEIEGEGE
Additional monomers are listed in Table 3 below wherein
TRAAGEQTAQAERELADAAQTVDDLEEKLDELQDRY
DSLTLALESERSLRQQHDV
K
MAQLKERLAAAEENTRQ
REERYQEQKTVLQDALNAEQAQHKNTREDLQKRLEQI
SAEANARTEELKSERDKVNTLLTRLESQENALASERQQ
HLATRETLQQRLEQAIADTQARAGEIALERDRVSSLTA
RLESQEKASSEQLVRMGSEIASLTERCTQLENQRDDAR
LETMGEKETVAALRGEAEALKRQNQSLMAALGHHHH
TRAAGEQTAQAERELADAAQTVDDLEEKLDELQDRY
DSLTLALESERSLRQQHDVEMAQL
E
ERLAAAEENTRQ
REERYQEQKTVLQDALNAEQAQHKNTREDLQKRLEQ
ISAEANARTEELKSERDKVNTLLTRLESQENALASERQ
QHLATRETLQQRLEQAIADTQARAGEIALERDRVSSLT
ARLESQEKASSEQLVRMGSEIASLTERCTQLENQRDD
ARLETMGEKETVAALRGEAEALKRQNQSLMAALGHH
TRAAGEQTAQAERELADAAQTVDDLEEKLDELQDRY
ISAEANARTE
R
LKS
RRDKVNTLLTRLESQENALASERQ
QHLATRETLQQRLEQAIADTQARAGEIALERDRVSSLT
ARLESQEKASSEQLVRMGSEIASLTERCTQLENQRDD
ARLETMGEKETVAALRGEAEALKRQNQSLMAALGHH
TRAAGEQTAQAERELADAAQTVDDLEEKLDELQDRY
DSLTLALESERSLRQQHDVEMAQLKERLAAAEENTRQ
REERYQEQKTVLQDALNAEQAQHKNTREDLQKRLEQ
ISAEANARTEELKSERDKVNTLLT
E
LESQENALASERQ
QHLATRETLQQRLEQAIADTQARAGEIALERDRVSSLT
ARLESQEKASSEQLVRMGSEIASLTERCTQLENQRDD
ARLETMGEKETVAALRGEAEALKRQNQSLMAALGHH
TRAAGEQTAQAERELADAAQTVDDLEEKLDELQDRY
DSLTLALESERSLRQQHDVEMAQLKERLAAAEENTRQ
REERYQEQKTVLQDALNAEQAQHKNTREDLQKRLEQ
ISAEANARTEELKSERDKVNTLLTRLESQ
R
NALASERQ
QHLATRETLQQRLEQAIADTQARAGEIALERDRVSSLT
ARLESQEKASSEQLVRMGSEIASLTERCTQLENQRDD
ARLETMGEKETVAALRGEAEALKRQNQSLMAALGHH
TRAAGEQTAQAERELADAAQTVDDLEEKLDELQDRY
DSLTLALESERSLRQQHDVEMAQLKERLAAAEENTRQ
REERYQEQKTVLQDALNAEQAQHKNTREDLQKRLEQ
ISAEANARTEELKSERDKVNTLLTRLESQENALASERQ
QHLATRETLQQRLEQAIADTQARAGEIAL
R
RDRVSSLT
ARLESQEKASSEQLVRMGSEIASLTERCTQLENQRDD
ARLETMGEKETVAALRGEAEALKRQNQSLMAALGHH
TRAAGEQTAQAERELADAAQTVDDLEEKLDELQDRY
DSLTLALESERSLRQQHDVEMAQLKERLAAAEENTRQ
REERYQEQKTVLQDALNAEQAQHKNTREDLQKRLEQ
ISAEANARTEELKSERDKVNTLLTRLESQENALASERQ
QHLATRETLQQRLEQAIADTQARAGEIALE
E
DRVSSLT
ARLESQEKASSEQLVRMGSEIASLTERCTQLENQRDD
ARLETMGEKETVAALRGEAEALKRQNQSLMAALGHH
TRAAGEQTAQAERELADAAQTVDDLEEKLDELQDRY
DSLTLALESERSLRQQHDVEMAQLKERLAAAEENTRQ
REERYQEQKTVLQDALNAEQAQHKNTREDLQKRLEQ
ISAEANARTEELKSERDKVNTLLTRLESQENALASERQ
QHLATRETLQQRLEQAIADTQARAGEIALERDRVSSLT
A
E
LESQEKASSEQLVRMGSEIASLTERCTQLENQRDD
ARLETMGEKETVAALRGEAEALKRQNQSLMAALGHH
TRAAGEQTAQAERELADAAQTVDDLEEKLDELQDRY
DSLTLALESERSLRQQHDVEMAQLKERLAAAEENTRQ
REERYQEQKTVLQDALNAEQAQHKNTREDLQKRLEQ
ISAEANARTEELKSERDKVNTLLTRLESQENALASERQ
QHLATRETLQQRLEQAIADTQARAGEIALERDRVSSLT
ARLESQ
R
KASSEQLVRMGSEIASLTERCTQLENQRDD
ARLETMGEKETVAALRGEAEALKRQNQSLMAALGHH
TRAAGEQTAQAERELADAAQTVDDLEEKLDELQDRY
DSLTLALESERSLRQQHDVEMAQLKERLAAAEENTRQ
REERYQEQKTVLQDALNAEQAQHKNTREDLQKRLEQ
ISAEANARTEELKSERDKVNTLLTRLESQENALASERQ
QHLATRETLQQRLEQAIADTQARAGEIALERDRVSSLT
ARLESQEKASSEQLVRMGSEIASLTE
E
CTQLENQRDD
ARLETMGEKETVAALRGEAEALKRQNQSLMAALGHH
TRAAGEQTAQAERELADAAQTVDDLEEKLDELQDRY
DSLTLALESERSLRQQHDVEMAQLKERLAAAEENTRQ
REERYQEQKTVLQDALNAEQAQHKNTREDLQKRLEQ
ISAEANARTEELKSERDKVNTLLTRLESQENALASERQ
QHLATRETLQQRLEQAIADTQARAGEIALERDRVSSLT
ARLESQEKASSEQLVRMGSEIASLTERCTQL
R
NQRDD
ARLETMGEKETVAALRGEAEALKRQNQSLMAALGHH
TRAAGEQTAQAERELADAAQTVDDLEEKLDELQDRY
DSLTLALESERSLRQQHDVEMAQLKERLAAAEENTRQ
REERYQEQKTVLQDALNAEQAQHKNTREDLQKRLEQ
ISAEANARTEELKSERDKVNTLLTRLESQENALASERQ
QHLATRETLQQRLEQAIADTQARAGEIALERDRVSSLT
ARLESQEKASSEQLVRMGSEIASLTERCTQLENQRDD
ARL
K
TMGEKETVAALRGEAEALKRQNQSLMAALGHH
TRAAGEQTAQAERELADAAQTVDDLEEKLDELQDRY
DSLTLALESERSLRQQHDVEMAQLKERLAAAEENTRQ
REERYQEQKTVLQDALNAEQAQHKNTREDLQKRLEQ
ISAEANARTEELKSERDKVNTLLTRLESQENALASERQ
QHLATRETLQQRLEQAIADTQARAGEIALERDRVSSLT
ARLESQEKASSEQLVRMGSEIASLTERCTQLENQRDD
TRAAGEQTAQAERELADAAQTVDDLEEKLDELQDRY
DSLTLALESERSLRQQHDVEMAQLKERLAAAEENTRQ
REERYQEQKTVLQDALNAEQAQHKNTREDLQKRLEQ
ISAEANARTEELKSERDKVNTLLTRLESQENALASERQ
QHLATRETLQQRLEQAIADTQARAGEIALERDRVSSLT
ARLESQEKASSEQLVRMGSEIASLTERCTQLENQRDD
ARLETMGE
E
ETVAALR
GEAEALKRQNQSLMAA
LGHH
TRAAGEQTAQAERELADAAQTVDDLEEKLDELQDRY
DSLTLALESERSLRQQHDVEMAQLKERLAAAEENTRQ
REERYQEQKTVLQDALNAEQAQHKNTREDLQKRLEQ
ISAEANARTEELKSERDKVNTLLTRLESQENALASERQ
QHLATRETLQQRLEQAIADTQARAGEIALERDRVSSLT
ARLESQEKASSEQLVRMGSEIASLTERCTQLENQRDD
ARL
K
TMG
K
KETVAALRGEAEALKRQNQSLMAALGHH
TRAAGEQTAQAERELADAAQTVDDLEEKLDELQDRY
DSLTLALESERSLRQQHDVEMAQLKERLAAAEENTRQ
REERYQEQKTVLQDALNAEQAQHKNTREDLQKRLEQ
ISAEANARTEELKSERDKVNTLLTRLESQENALASERQ
QHLATRETLQQRLEQAIADTQARAGEIALERDRVSSLT
ARLESQEKASSEQLVRMGSEIASLTERCTQLENQRDD
ARLETMGEKETVAALRG
K
AEALKRQNQSLMAALGHH
TRAAGEQTAQAERELADAAQTVDDLEEKLDELQDRY
DSLTLALESERSLRQQHDVEMAQLKERLAAAEENTRQ
REERYQEQKTVLQDALNAEQAQHKNTREDLQKRLEQ
ISAEANARTEELKSERDKVNTLLTRLESQENALASERQ
QHLATRETLQQRLEQAIADTQARAGEIALERDRVSSLT
ARLESQEKASSEQLVRMGSEIASLTERCTQLENQRDD
ARLETMGEKETVAALRGEAEAL
E
RQNQSLMAALGHH
From a comparison with the results shown in
Applicant however expect this apparent negative result to be due to aggregation resulting from a combination of the specific monomer and protocols used to produce the Circular Dichroism spectra shown in
This protocol presents a solubility challenge to the thermomers of SEQ ID NO: 1 as will be understood by a skilled person, in view of the positions of charged residues in the thermomers.
In particular, the charged residues are within a string of hydrophobic corresponding residues in each thermomer monomer of the thermomer dimer attaching one with the other through non-covalent bonds to provide interlinked the quaternary structure of the coiled coil temperature sensitive domain.
Accordingly, separate production of thermomer monomers followed by assembly can result in aggregation of the monomers, depending on the specific experimental settings, as will be understood by a skilled person.
Applicant expects that different protocols such as co expression in a same bacteria will overcome this issue and show functionality of the monomers of Table 3 as heterodimers in view of their structure and results related to the monomers of Table 2.
Applicant also indicates that when thermomer monomers of the disclosure are provided through in cell or cell free expression, protocols avoiding separate expression of the monomers should be used in providing the thermomer dimer here described, as well as in screening neutral substitutions, as well as variants as will be understood by a skilled person.
The following steps can be performed to evaluate the structural properties of a derivative or variant of a thermomer monomer and dimers according to the present disclosure.
First, a coiled-coil construct is tested for alpha helical content. If the construct contains predicted heterodimerizing mutations, then an equimolar combination of each strand is prepared. Furthermore, if the construct contains predicted heterodimerizing mutations and the two polypeptides were expressed in separate cells (allowing the potential formation of homodimers due to the absence of the other polypeptide), the mixture is heated to Tbs+10° C. and then cooled to at least Tbs−10° C. to facilitate strand exchange and generation of the most stable (e.g. heterodimeric) product.
If a construct is derived from TlpA or one of its claimed variants (e.g. TlpA or variant containing a limited number of temperature-shifting, heterodimerizing, or neutral mutations generated via directed evolution or rational mutagenesis), then alpha helical content is interpreted as being indicative of dimerization because when coiled-coils disassemble they do not maintain an alpha helical secondary structure (they transition into random coil). Evaluation of secondary structure is performed via circular dichroism spectroscopy at a temperature at least 10° C. below the predicted Tbs. The presence of a peak at both 208 nm+/−3 nm and 222 nm+/−3 nm (note: I'm estimating the error here but 3 nm seems reasonable) indicates alpha helical secondary structure.
Representative examples of circular dichroism spectra is shown in
Next, the same sample is incubated at a temperature range from at least Tbs−5° C. to Tbs+5° C. (with a greater range being desirable). The circular dichroism at 222 nm is tracked throughout this range and the resulting data is fit to the Hill equation. If the Hill coefficient is >15, then the switch is deemed a functional thermomer. An illustration of this process is shown below (sample=wild type TlpA). Note that above Tbs, the value at 222 nm approaches 0, as is the case for “Extended” (unstructured) proteins in the chart shown in
Note that in some cases, candidate coiled-coils will fails to adopt an alpha helical CD spectrum. In such cases, the temperature scan does not need to be performed. In other cases, we have observed that candidate coiled-coils adopt an alpha helical CD spectrum but have a non-switch-like (e.g. low Hill-coefficient) thermal transition. Either failure disqualifies the candidate from being a thermomer. This was the primary test that we used to establish the functionality of thermomers. More rigorous tests can be performed as described by inserting the thermomers into a thermal gene regulation vector as exemplified in
In summary, described herein are thermomer monomer, thermomer dimers, thermomer monomeric constructs, thermomer dimeric complexes, and related gene expression cassette vectors, cells, surfaces devices, compositions methods and systems, that provide a thermobioswitch suitable to control location and/or binding of cargo moiety of interest in a temperature regulated manner.
The examples set forth above are provided to give those of ordinary skill in the art a complete disclosure and description of how to make and use the embodiments of the materials, compositions, systems and methods of the disclosure, and are not intended to limit the scope of what the inventors regard as their disclosure. Those skilled in the art will recognize how to adapt the features of the exemplified methods and arrangements to additional genetic circuit, related nodes, molecular components, sets of polynucleotides, polypeptides and/or metabolites, in according to various embodiments and scope of the claims.
All patents and publications mentioned in the specification are indicative of the levels of skill of those skilled in the art to which the disclosure pertains.
The entire disclosure of each document cited (including patents, patent applications, journal articles, abstracts, laboratory manuals, books, or other disclosures) in the Background, Summary, Detailed Description, and Examples is hereby incorporated herein by reference. All references cited in this disclosure are incorporated by reference to the same extent as if each reference had been incorporated by reference in its entirety individually. However, if any inconsistency arises between a cited reference and the present disclosure, the present disclosure takes precedence. Further, the computer readable form of the sequence listing of the ASCII text file P2503-US-Sequence-Listing_ST25 is incorporated herein by reference in its entirety.
The terms and expressions which have been employed herein are used as terms of description and not of limitation, and there is no intention in the use of such terms and expressions of excluding any equivalents of the features shown and described or portions thereof, but it is recognized that various modifications are possible within the scope of the disclosure claimed. Thus, it should be understood that although the disclosure has been specifically disclosed by embodiments, exemplary embodiments and optional features, modification and variation of the concepts herein disclosed can be resorted to by those skilled in the art, and that such modifications and variations are considered to be within the scope of this disclosure as defined by the appended claims.
It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to be limiting. As used in this specification and the appended claims, the singular forms “a,” “an,” and “the” include plural referents unless the content clearly dictates otherwise. The term “plurality” includes two or more referents unless the content clearly dictates otherwise. Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which the disclosure pertains.
When a Markush group or other grouping is used herein, all individual members of the group and all combinations and possible subcombinations of the group are intended to be individually included in the disclosure. Every combination of components or materials described or exemplified herein can be used to practice the disclosure, unless otherwise stated. One of ordinary skill in the art will appreciate that methods, device elements, and materials other than those specifically exemplified may be employed in the practice of the disclosure without resort to undue experimentation. All art-known functional equivalents, of any such methods, device elements, and materials are intended to be included in this disclosure. Whenever a range is given in the specification, for example, a temperature range, a frequency range, a time range, or a composition range, all intermediate ranges and all subranges, as well as, all individual values included in the ranges given are intended to be included in the disclosure. Any one or more individual members of a range or group disclosed herein may be excluded from a claim of this disclosure. The disclosure illustratively described herein suitably may be practiced in the absence of any element or elements, limitation or limitations which is not specifically disclosed herein.
A number of embodiments of the disclosure have been described. The specific embodiments provided herein are examples of useful embodiments of the invention and it will be apparent to one skilled in the art that the disclosure can be carried out using a large number of variations of the devices, device components, methods steps set forth in the present description. As will be obvious to one of skill in the art, methods and devices useful for the present methods may include a large number of optional composition and processing elements and steps.
In particular, it will be understood that various modifications may be made without departing from the spirit and scope of the present disclosure. Accordingly, other embodiments are within the scope of the following claims.
The present application claims priority to U.S. Provisional Application No. 62/873,482, entitled “Modular Temperature Dependent Protein Association Domains” filed on Jul. 12, 2019, which is incorporated herein by reference in its entirety.
This invention was made with government support under Grant No. W911NF-19-D-0001 awarded by the Army and Grant No. HR0011-14-1-0780 (DOI: D14AP0050) awarded by DARPA. The government has certain rights in the invention.
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| Number | Date | Country | |
|---|---|---|---|
| 20210040161 A1 | Feb 2021 | US |
| Number | Date | Country | |
|---|---|---|---|
| 62873482 | Jul 2019 | US |
