The present invention relates to a method for expression of influenza virus PA and PB1 N-terminal polypeptide in bacteria, purification and crystallization. It also relates to the crystal three-dimensional structure of complex of C-terminal of PA and N-terminal polypeptide of PB1 and its application in drug design.
Influenza virus have already brought great disaster to human beings (Taubenberger and Morens 2007). Due to lacking enough treating means and frequent variation of the virus itself, the virus remains a threat to human beings. In recent years, frequent and severe avian influenza epidemic situation as well as transmission of avian influenza in human beings has constituted a great threat to health and economics of human beings, so investigation directed to this kind of virus is of great value to protect human health. Avian influenza virus belongs to influenza virus A type, which are all Orthomyxoviridae family members. The virus genome consists of 8 negatively charged single-stranded RNA. Through comparison and analysis of genes of Avian influenza virus origin and other influenza A viruses, it is found that there are sporadic mutations in primary struture, and these mutations result in differential pathogenicity of different influenza viruses. Now, it is considered that influenza virus can encode 11 proteins, wherein the replication of influenza virus genome RNA and mRNA transcription were completed by the RNA polymerase carried by that virus itself, and thus the polymerase has become a potentially important drug target. Recent research suggested that the high pathogenicity of some influenza viruses is directly correlated with the polymerase mutations (Hulse-Post, Franks et al. 2007; Munster, de Wit et 20 al. 2007), further illustrating the necessity of designing drugs aming at this complex. Investigation into this complex is of great significance to reveal the molecular mechanism underlying virus replication and to design drugs aming at this complex. The RNA polymerase is a complex composed of PB1, PB2 and PA subunits, wherein PB1 is a subunit with catalytic activity, PB2 is responsible for acquiring cellular mRNA cap (CAP structure) through a snatching mode as primers of virus mRNA transcription, but PB1 acts as an endonuclease in this process. A temperature sensitive mutant ts53 suggests that PA takes part in the replication process of virus genome, but its specific function is still unclear (Sugiura, Ueda et al. 1975; Kawaguchi, Naito et al. 2005). The polymerase has three kind of RNA activity which is needed in virus synthesis, i.e. mRNA, cRNA and vRNA, respectively. The mRNA synthesis starts from capped oligonucleotide primer and ends at the 15-17 nucleotides from vRNA terminal and a polyA tail is added. Polymerase can synthesize cRNA intermediate of the full-length virus de novo and further synthesize full-length vRNA. Respective subunits of the polymerase can be exprssed by insect cell expression system, thus forming three different complexes, wherein one is a ternary complex containg the three subunits PB1/PB2/PA of polymerase, and the other two are binary complexes: PB1/PB2 and PB1/PA binary complex respectively, but they can not form PB2/PA complex (Honda, Mizumoto et al. 2002). Wherein, 25 amino acids of PB1 N-terminal are sufficient to interact with PA C-terminal, whereas PB1 C-terminal is responsible for the interaction with PB2 N-terminal. A synthetical competive small peptide of PB1 N-terminal can significantly inhibit the activity of virus polymerase. RNA synthesis experiments using dinucleotide ApG as primers indicated that PB1/PA complex can effectively initiate the replication of virus genome RNA, and PB1/PB2 can synthesize virus mRNA in vitro (Honda, Mizumoto et al. 2002), but the recombinant polymerase which was expressed and purified using 293 cell revealed that the three subuits are all necessary for replication and transcription (Deng, Sharps et al. 2006). The idea that PA principally participates the replication process of virus RNA is derived from a finding that a tempreture sensitive mutant (L226P) can result in replication disorder of virus genome under non-permissible temperatures without affecting transcription activity (Kawaguchi, Naito et al. 2005); whereas PB2 is involved in virus mRNA transcription. Further studies found that PA can extensively take part in processes such as transcription, replication and virus stability (Hara, Schmidt et al. 2006). PB1/PA complex can bind the 5′ terminal virus promoter, but only PB1 fails to bind that promoter. Cross-linking experiments indicate that PA can bind vRNA and cRNA promoters (Fodor, Pritlove et al. 1994; Deng, Sharps et al. 2005; Hara, Schmidt et al. 2006)(Fodor 1994, Gonzalez 1999, Jung 2006, Hara 2006), but the specific binding sites are not clear. PA was found to have similar protease activity as chymotrypsins. Sanz-Ezquerro et al. (1996) found that about 250 amino acids at N-terminal are the active region of that protease (Sanz-Ezquerro, Zurcher et al. 1996). But subsequently the studies by Hara et al. (2001) showed that the Serine at position 624 of C-terminal was the active site of PA protease, and the mutation at that site resulted in loss of protease activity, therefore Ser624 may also consiste an active region of that protease (Hara, Shiota et al. 2001). There is still controversy about the effect of PA protease activity on polymerase function. Hara et al. (2006) reported that purified recombinant PA protein can be degraded into two fragments with molecular weight of ˜25 kDa and ˜55 kDa through trypsin hydrolysis (Hara, Schmidt et al. 2006). It is known that three-dimensional structure of protein is of great help to perform rational drug design, so revealing three-dimensional structure of PA is of important value to perform drug design and function studies. In addition, previous studies have not reported the expression and purification of influenza virus protein PA in bacteria, so expression and purification of proteins in bacteria is of important benefit to further explore the function of PA and to perform drug screening, thus saving much time and greatly decreasing job cost and labour intensity.
The present invention provides a method of separating the wild type or mutant protein of influenza virus polymerase complex subunit PA into N-terminal and C-terminal, and then cloning and expressing them respectively; and a method of expressing, purifying and crystallizating N-terminal of PA; and a method of expressing N-terminal short peptide of wild type or mutant protein of influenza virus polymerase subunit PB1; and a method of co-purification of PA C-terminal and PB1 N-terminal short peptides. The method of expressing and co-purifying the complex of the former 256 amino acids of the N-terminal of PA as well as 257-716 amino acids of C-terminal of PA and the 25 peptides of N-terminal of PB1 according to the invention, crystallization method of the protein complex of PA C-terminal and PB1 N-terminal peptide as well as crystal three-dimensional structure of the resulting complex.
In one aspect, the present invention provides a method of dividing the wild type or mutant protein of influenza virus polymerase complex subunit PA into N-terminal part and C-terminal part as well as cloning and expressing them respectively; and a method of expressing, purifying and crystalling N-terminal of PA; and a method of expressing N-terminal polypeptide of wild type or mutant protein of influenza virus polymerase subunit PB1 and co-purifying the complex of PA C-terminal and PB1 N-terminal short peptides for crystallization. The present invention preferably use prokaryotic cell expression system of E. coli (but other expression systems are not exclued, for example, expression can also be performed in other bacteria or other eukaryotic cells) to express the above-mentioned polypeptide as GST (glutathione-5-transferase) fusion protein, and mix two kind of expression bacteria which express PA C-terminal and PB1 N-terminal short peptide, and further co-purify the protein complex containing above-mentioned PA C-terminal and PB1 N-terminal short peptides from the bacteria, for use in crystallization of protein. According to the expression method of obtaining the former 256 amino acids of N-terminal of influenza virus polymerase subunit PA and 257-716 amino acids of C-terminal of influenza virus polymerase subunit PA through expression in E. coli and the method of obtaining microbial population of E. coli that express the polypeptide within 25 or 48 amino acids of N-terminal of influenza virus protein PB1 that are described in the invention, the methods can express the GST (glutathione-5-transferase)-fused fusion proteins by cloning corresponding genes into pGEX-6p vector.
In another aspect, the present invention provides a method of purifying the complex of PA C-terminal (PAc) and PB1N peptides, comprising: the microbial population expressing the 257-716 amino acids of C-terminal of influenza virus PA and the microbial population expressing a short peptide within 25 or 48 amino acids of the N-terminal of influenza virus PB1 were suspended with buffers respectively, and these two expression bacteria are mixed proportionally to reach a certain molar ratio between the total protein content of GST-PAc and GST-PB1N, thus expressing the protein mixture of these two proteins; the protein mixture was purified by affinity column and then cleaved by PreScission protease to cut GST fusion protein; and the complex of PA and PB1 N-terminal peptide through such methods as gel filtration and ion exchange chromatography; and the protein purity is determined by gel electrophoresis.
In another aspect, the present invention provides a method of crystallizing the complex of PAc and PB1N peptide obtained as described above, comprising: the complex of PAc and PB1N peptide is condensed to a concentration of 5-30 mg/ml; the crystal growth condition is screened by gas hanging drop at 4-30° C.; and crystal of the protein complex is obtained.
In another aspect, the present invention provides the crystal of the complex of PAc and PB1N peptides.
In another aspect, the present invention provides crystal three-dimensional structure of the complex of PAc and PB1N peptide, the structure describes interaction mode between PAc and PB1N and corresponding interaction sites, and also describes the composition of secondary structure, peptide chain direction and three-dimensional molecular structure of polypeptide in the complex, wherein X-ray crystal diffraction was performed based on the crystal of the complex of PAc and PB1N peptide to obtain the diffraction data from the protein crystal of the complex of PAc and PB1 N-terminal peptide, and then three-dimensional structure model of the complex of PAc and PB1N peptide was constructed by further performing a structure analysis process with the diffraction data from the protein crystal.
In one embodiment, the present invention provides crystal three-dimensional structure of complex of C-terminal of influenza virus polymerase subunit PA-PAc and N-terminal of influenza virus polymerase subunit PB1-PB1N, wherein the C-terminal of the influenza virus polymerase subunit PA-PAc is amino acids from amino acid positions about 201˜about 301 to about 650˜terminal, the N-terminal of influenza virus polymerase subunit PB1-PB1N is a short peptide within the 48 amino acids of the N-terminal of influenza virus polymerase subunit PB1-PB1N, wherein atoms of the crystal three-dimensional structure of the complex have at least part of atomic coordinates listed in table 1, or any structure that has average root mean square deviation (RMSD) smaller than or equal to 1.7 Angstrom with atomic coordinates of main chain carbon backbone of at least 40% amino acids in the crystal three-dimensional structure of complex.
Preferably, the crystal of complex of C-terminal of influenza virus polymerase subunit PA-PAc and N-terminal of influenza virus polymerase subunit PB1-PB1N has space group of P4(1)2(1)2, and the lattice parameters are about: a=b=122 Angstrom, c=133 Angstrom, α=β=γ=90°.
In one embodiment, the influenza virus is selected from influenza virus A, B and C type, preferably influenza virus A type: A/goose/Guangdong/1/96, A/Brevig Mission/1/1918; influenza virus B type: B/Ann Arbor/1/1966 or influenza virus C type: C/JJ/1950.
In one embodiment, the C-terminal of influenza virus A polymerase subunit PA-PAc consists of the first portion (i.e. it constitutes the mouth section of the crystal structure, as shown in
In one embodiment, the C-terminal of influenza virus type A polymerase subunit PA-PAc interacts with N-terminal of PB1-PB1N mainly through α helix 8, α helix 10, α helix 11 and α helix 13, preferably through at least one amino acid selected from a group consisting of Leu666 of α helix 11, Phe710 of α helix 13, Val636 of α helix 10, Leu640 of α helix 10, Trp706 of α helix 13 and Gln670 of α helix 11, wherein fragments of influenza virus B and C type corresponding to α helixes of influenza virus A type are shown in
In one embodiment, wherein at least one amino acid selected from the group consisting of Ile621, Gly622, Glu623, Thr618 and Pro620 interacts with the influenza virus polymerase subunit PB1, the Ile621, Gly622, Glu623, Thr618 and Pro620 is in the ring peptide between α helix 9 and α helix 10 of C-terminal of influenza virus A polymerase subunit PA-PAc, wherein fragments of influenza virus B and C type corresponding to α helixes of influenza virus A type are shown in
In one embodiment, wherein at least one amino acid selected from the group consisting of Asn647, Gln408, Cys584, Gln587, Gln591, Lys643, Asn647, Ser659, Lys663, Trp699 and Asn703 of the C-terminal of influenza virus A polymerase subunit PA-PAc constitutes “pocket-shape” amino acid sites which bind the influenza virus polymerase subunit PB1N, wherein fragments of influenza virus B and C type corresponding to influenza virus A type are shown in
In one embodiment, wherein at least one amino acid selected from the group consisting of Trp406, Glu410, Lys461, Glu524, Phe525, Ser526, Lys536, Lys539, Tyr540, Leu563, Tyr564, Arg566 and Lys574 of the C-terminal of influenza virus A polymerase subunit PA-PAc constitutes “big groove” and “channel” structures which bind nucleotide, RNA or other small molecules or proteins, wherein fragments of influenza virus B and C type corresponding to influenza virus A type are shown in
In one embodiment, amino acid residues of 370˜405 positions of the C-terminal of PA-PAc constitutes a big ring, wherein corresponding fragments of influenza virus B and C type to influenza virus A type are shown in
In one embodiment, α helix 12 and α helix 13 interact with other proteins, preferably at least one amino acid selected from the group consisting of Ile690, Glu691, Glu692, Cys693 and Asn696 of the α helix 12 and α helix 13 interacts with other proteins.
In one embodiment, at least one amino acid selected from the group consisting of Lys506, Gly507, Arg508, Ser509, His510, Leu511, Arg512, Asn513 and Asp514 interacts with other proteins, wherein His510 constitutes a portion of the polymerase complex RNAse, wherein fragments of influenza virus B and C type corresponding to influenza virus A type are shown in
In one embodiment, the present invention provides a polypeptide, protein, inorganic compound or organic compound, which binds to at least one member selected from the group consisting of α helix 8, α helix 10, α helix 11 and α helix 13 of C-terminal of influenza virus subunit PA-PAc, preferably binds to the member selected from the group consisting of Leu666 in α helix 11, Phe710 in α helix 13, Val636 and Leu640 in α helix 10, Trp706 in α helix 13, Gln670 in α helix 11 of N-terminal of influenza virus subunit PA-PAc, wherein fragments of influenza virus B and C type corresponding to influenza virus A are shown in
In one embodiment, the present invention provides a polypeptide, protein, inorganic compound or organic compound, antibody or immune conjugate binding to at least one member selected from the group consisting of Ile621, Gly622, Glu623, Thr618 and Pro620 located at the circle peptide between α helix 9 and α helix 10 of the C-terminal of influenza virus polymerase subunit PA-PAc, wherein fragments of influenza virus B and C type corresponding to influenza virus A type are shown in
In one embodiment, the present invention provides a polypeptide, protein, inorganic compound or organic compound, antibody or immune conjugate binding to at least one amino acid selected from the group consisting of Asn647, Gln408, Cys584, Gln587, Gln591, Lys643, Asn647, Ser659, Lys663, Trp699 and Asn703 of the C-terminal of influenza virus A polymerase subunit PA-PAc, wherein fragments of influenza virus B and C type corresponding to influenza virus A type are shown in
In one embodiment, the present invention provides a polypeptide, protein, inorganic compound or organic compound, antibody or immune conjugate binding to at least one amino acid selected from the group consisting of Trp406, Glu410, Lys461, Glu524, Phe525, Ser526, Lys536, Lys539, Tyr540, Leu563, Tyr564, Arg566 and Lys574 of the C-terminal of influenza virus A polymerase subunit PA-PAc, wherein fragments of influenza virus B and C type corresponding to influenza virus A type are shown in
In one embodiment, the present invention provides a polypeptide, protein, inorganic compound or organic compound, antibody or immune conjugate binding to amino acids position 370˜405 of the C-terminal of influenza virus A polymerase subunit PA-PAc, wherein fragments of influenza virus B and C type corresponding to influenza virus A type are shown in
In one embodiment, the present invention provides a polypeptide, protein, inorganic compound or organic compound, antibody or immune conjugate binding to helix 12 and α helix 13 of the C-terminal of influenza virus A polymerase subunit PA-PAc, preferably to at least one amino acid selected from the group consisting of Ile690, Glu691, Glu692, Cys693 and Asn696 in α helix 12 and α helix 13, wherein corresponding fragments of influenza virus B and C type to influenza virus A type are shown in
In one embodiment, the present invention provides a polypeptide, protein, inorganic compound or organic compound, antibody or immune conjugate binding to at least one amino acid selected from the group consisting of Lys506, Gly507, Arg508, Ser509, His510, Leu511, Arg512, Asn513 and Asp514 located at ring region between sheet β 4 and sheet β 5 in the C-terminal of influenza virus A polymerase subunit PA-PAc, wherein fragments of influenza virus B and C type corresponding to influenza virus A type are shown in
In one embodiment, the present invention provides a polypeptide, protein, inorganic compound or organic compound, antibody or immune conjugate which competes with influenza virus polymerase subunit PB1 for binding PAc, wherein fragments of influenza virus B and C type corresponding to influenza virus A type are shown in
In one embodiment, the present invention provides an interaction with PAc through the hydrophobic core constituted by the α helix 8, α helix 11, α helix 13 and α helix 10, preferably interaction with PAc through Met595 in α helix 8, Leu666 in α helix 11, Trp706 and Phe710 in α helix 13, Val636 and Val640 in α helix 10, wherein fragments of influenza virus B and C type corresponding to influenza virus A type are shown in
In one embodiment, the present invention provides a polypeptide, protein, inorganic compound or organic compound, antibody or immune conjugate which competes with influenza virus polymerase subunit PB1 for binding PAc, wherein the amino acid sequence of the polypeptide, protein, antibody or immune conjugate comprises at least three amino acids which are identical to amino acids of corresponding position in short PTLLFL motif of the short helix domain constituted by the 5th˜10th residues Pro5, Thr6, Leu7, Leu8, Phe9 and Leu 10 of N-terminal of wild influenza virus polymerase subunit PB1-PB1N, when the polypeptide or protein is aligned with the PTLLFL motif.
In one embodiment, the present invention provides a composition comprising above-mentioned polypeptide, protein, inorganic compound or organic compound, antibody or immune conjugate.
In one embodiment, the present invention provides use of the above-mentioned composition in manufacturing the medicament used in the treatment of diseases caused by influenza virus.
In one embodiment, the present invention provides a method of expressing and purifying the complex of C-terminal of influenza virus polymerase subunit PA-PAc and N-terminal of influenza virus polymerase subunit PB1-PB1N, comprising: (a) construct a vector of gene sequence encoding amino acid positions about 201˜about 301 to about 650˜terminal of the C-terminal of influenza virus polymerase subunit PA-PAc, with a tag protein fused or not fused to the vector, prokaryotic cells or eukaryotic cells are transformed with said vector in order to express the PAc with the tag protein; (b) a method similar with that of expressing PAc was used to express the PB1N with or without a tag protein; (c) Proportionally mix the cell expressing influenza virus polymerase subunit PAc obtained from step (a) and the cell expressing amino acids within the 48 amino acids of the N-terminal of influenza virus polymerase subunit PB1 obtained from step (b), the resulting protein is separated through the specifically recognizing by the specific tag, the tag protein is removed from the protein through enzymolysis, the complex of PAc and PB1N is separated, and the concentration of the complex is determined;
The atoms of the Crystal three-dimensional structure of complex of C-terminal of influenza virus polymerase subunit PA-PAc and N-terminal of influenza virus polymerase subunit PB1-PB1N has at least 40% atomic coordinates listed in table 1, or atomic coordinates of main chain carbon backbone of at least 40% amino acids in the crystal three-dimensional structure of complex of C-terminal of influenza virus polymerase subunit PA-PAc and N-terminal of influenza virus polymerase subunit PB1-PB1N has average root mean square deviation smaller than or equal to 1.7 Angstrom with respect to the atomic coordinates listed in table 1.
In one embodiment, the present invention provides a method of expressing and purifying the complex of C-terminal of influenza virus polymerase subunit PA-PAc and N-terminal of influenza virus polymerase subunit PB1-PB1N, wherein the tag protein is selected from GST, Flag-tag, Myc-tag, MBP-tag, specific antibodies; the vector comprises selective marker gene, the proportional mixing in step (c) means that molar ratio of tag protein-PAc and tag protein-PB1N is 0.1:1˜1:0.1, preferably the molar ratio of tag protein-PAc and tag protein-PB1N is 0.5:1˜1:0.5, more preferably the molar ratio of tag protein-PAc and tag protein-PB1N is nearly 1:1; preferably the tag protein is GST, the method recognizing the specific tag is performed through affinity column, the method of removing tag is preformed by enzymolysis with proteinases, the method of separating the complex of PAc and PB1N is preformed through gel filtration or ion-exchange chromatography, the protein concentration is determined through gel electrophoresis.
In one embodiment, the present invention provides a method of expressing and purifying the complex of C-terminal of influenza virus polymerase subunit PA-PAc and N-terminal of influenza virus polymerase subunit PB1-PB1N, wherein the vector is pGEX-6p plasmid vector, and said selective marker gene is penicillin resistance gene, and the proteinase used in step (c) is ProScission proteinase; the restriction site in primers that is employed by the vector is a restriction site selected from a group consisting of SalI and NotI; the restriction site used where gene fragment is inserted is a restriction site selected from a group consisting of SalI and NotI; said gene fragment of C-terminal of influenza virus polymerase subunit PA-PAc is obtained from the genome of influenza virus A type: A/goose/Guangdong/1/96 by polymerase chain reaction (PCR) method; said vector and said inserted gene fragment are treated by corresponding DNA restriction enzyme respectively, such as those selected from a group consisting of BamHI and XhoI, and then the inserted gene and the vector is liagated by T4 DNA ligase, thus transfroming prokaryotic cells such as E. coli to obtain cloned plasimds. The cloned plasmid as described above is transformed into E. coli BL21, the resulting transformed bacteria are cultured and induced by using IPTG, wherein the preferred concentration of IPTG is 0.1 mM to 1 mM, and the cultured bacteria are centrifuged to obtain the microbial population that express said fusion protein.
In one embodiment, the present invention provides a method of co-crystallizing the complex of C-terminal of influenza virus polymerase subunit PA-PAc and N-terminal of influenza virus polymerase subunit PB1-PB1N, comprising: the protein concentration of the purified complex of PAc and PB1N is condensed to 5-30 mg/ml; the crystal growth condition is screened by gas sitting drop and hanging drop; and crystal of the complex of C-terminal of influenza virus polymerase subunit PA-PAc and N-terminal of influenza virus polymerase subunit PB1-PB1N is obtained.
In one embodiment, the present invention provides a method of expressing wild type or mutant protein of N-terminal of PA-PAN, wherein PAN is amino acids from positions 1˜ about 50 to about 200˜ about 300, the method comprising: construct a expression vector of gene sequence encoding amino acid positions 1˜ about 50 to about 200˜ about 300 of the N-terminal of influenza virus polymerase subunit PA-PAN, with a gene of tag protein fused to the vector, and cells are transformed with the expression vector in order to express the PAN with the maker protein, wherein the N-terminal of PA-PAN has at least 40% sequence identity with the amino acids listed in
In one embodiment, the present invention provides a method of expressing wild type or mutant protein of N-terminal of PA-PAN, wherein the gene sequence of N-terminal of polymerase subunit PA-PAN is cloned into plasmind vectors for example, a series of pGEX vectors such as pGEX-6p, pGEX-4 T (Amersham Pharmacia), a series of pET vectors (Novagen) and a series of pMAL-c2 (Invitrogen) to express a fusion protein GST-PAN which N-terminal of PAN is fused with GST; the plasmid vector comprises the penicillin resistance gene and the restriction site that is employed by vector when cloning the polypeptide gene of N-terminal of PA-PAN is a restriction site selected from a group consisting of BamHI and XhoI from multiple cloning sites in pGEX-6p; the restriction site used in PAN gene cloning fragment is BamHI and XhoI; gene fragment of PAN protein is amplified from the genome of influenza virus A type: A/goose/Guangdong/1/96 by polymerase chain reaction (PCR) method; the vector and the inserted gene fragment are treated by corresponding DNA restriction enzyme respectively, such as those selected from a group consisting of BamHI and XhoI, and then the inserted gene and the vector is liagated by T4 DNA ligase, thus transfroming E. coli to obtain cloned plasimds. The cloned plasmid as described above is transformed into E. coli BL21, the resulting transformed bacteria are cultured and induced by using 0.1 mM to 1 mM IPTG, and the cultured bacteria are centrifuged to obtain the microbial population that express said fusion protein.
In one embodiment, the present invention provides a method of screening candidate compounds which compete with PB1N for binding PAc, the method comprising: (a) combine PAc to surface of the fixed support; (b) contact the excess tagged PB1N with the fixed PAc; (c) thoroughly elute with eluent in order to remove unbound PB1N; (d) contact the candidate compound solutions to be detected with the fixed PAc binding to the PB1N in step (b); (e) thoroughly elute with the eluent in order to obtain solution to be detected; (f) measure concentration of free tagged PB1N in the solution to be detected; (g) calculate the binding capability of the candidate compound to be detected with PAc according to the concentration of free tagged PB1N in the solution.
In one embodiment, the present invention provides a method of screening candidate compounds which compete with PB1N for binding PAc, wherein combining PAc to surface of the fixed support in step (a) is accomplished through covalently crosslinking or through binding PAc with affinity matrix, wherein there is a binding group of affinity matrix on the surface of the fixed support.
In one embodiment, the present invention provides a method of screening candidate compounds which compete with PB1N for binding PAc, wherein the affinity matrix can be other polypeptides such as GST, Flag-tag, Myc-tag, MBP-tag and specific antibody, whereas there is corresponding binding group on the surface of the fixed support.
In one embodiment, the present invention provides a method of screening candidate compounds compete with PB1N for binding PAc, wherein the tagged PB1N polypeptide is selected from the protein tagged with isotope or the protein tagged with other chemical molecule, preferably, the other chemical molecular tag is green fluorescent protein or various fusion polypeptides, eg. binding peroxidase, phosphohydrolase, protien kinase, various group transferase.
In one embodiment, the present invention provides a method of screening candidate compounds which compete with PB1N for binding PAc, wherein the fixed surface can be affinity chromatography columns
In one embodiment, the present invention provides use of the crystal three-dimensional structure of complex of C-terminal of influenza virus polymerase subunit PA-PAc and N-terminal of influenza virus polymerase subunit PB1-PB1N in designing and screening polypeptide, protein, inorganic compound or organic compound, antibody or immune conjugate used in the treatment of diseases caused by the influenza virus infection.
Drug screening can be performed based on the above method of expressing and purifying PAc protein; the above method of expressing and purifying the complex of PAc and PB1N polypeptide and the above method of obtaining protein crystal, and drug design can be performed based on the three-dimensional structure of PAc and PB1N.
In one embodiment, the present invention provides use of the crystal three-dimensional structure of complex of C-terminal of influenza virus polymerase subunit PA-PAc and N-terminal of influenza virus polymerase subunit PB1-PB1N in designing and screening polypeptide, protein, inorganic compound or organic compound, antibody or immune conjugate used in the treatment of diseases caused by the influenza virus infection, comprising:
design polypeptide, protein, inorganic compound or organic compound, antibody or immune conjugate binding to specific portion through computer simulation technology according to coordinates of three-dimensional structure of protein;
search for potential polypeptide, protein, inorganic compound or organic compound, antibody or immune conjugate binding to specific portion through computer simulation technology according to coordinates of three-dimensional structure of the protein;
the designed or searched polypeptide, protein, inorganic compound or organic compound, antibody or immune conjugate according to coordinates of three-dimensional structure of the protein bind to any subtype of influenza virus polymerase protein which have at least 50% sequence identity with the PAc and the PB1N sequence, binding information is then analyzed;
the designed or searched polypeptide, protein, inorganic compound or organic compound, antibody or immune conjugate according to coordinates of three-dimensional structure of the protein bind to any subtype of influenza virus polymerase protein which have at least 50% sequence identity with the PAc and the PB1N sequence, and then crystallization is preformed, the binding information of polypeptide or compound molecule to protein is analyzed through crystal diffraction method;
wherein the polypeptide, protein, inorganic compound or organic compound, antibody or immune conjugate that bind to any subtype of influenza virus polymerase protein which had at least 50% sequence identity with the PAc and the PB1N sequence are candidate compounds.
To reveal the role of PA in polymerase and its fine three-dimensional structure, the inventors analyzed the crystal structure with a resolution of 2.9 Angstrom of the complex of a fragment of 257-716 residue in the C-terminal of PA (PAC) and 25 peptides in the N-terminal of PB1 (PB1N). This structure clearly indicates the interaction mode between the C-terminal of PA and N-terminal of PB1 as well as the composition of amino acid residues that participate in the interaction and their relative spatial position; reveals the three-dimensional structure model of the complex of C-terminal of PA and N-terminal of PB1, the composition of secondary structure in that protein, the binding sites of nucleic acid in PA protein molecule, small-molecule channel in PA protein molecule and the charge distribution of PA protein surface, providing structure basis for investigating the role of PA in the complex of virus RNA polymerase, and providing protein crystal platform and three-dimensional platform for designing drugs aming at interaction between PA and PB1 as well as interaction between PA and RNA and other proteins to inhibit the activity of influenza virus polymerase.
It should be noted that the amino acid sequence of corresponding fragments in influenza virus B and C type to α helixes and β sheets of influenza virus A type are shown in
The present invention provides a method of expressing fragments of wild type or mutant protein of influenza virus polymerase subunit PA, wherein N-terminal part and C-terminal part are expressed and purified in E. coli respectively, including: a method of only using N-terminal of PA for crystallization experiment; a method of expressing and purifying a fragment containing the 257-716 residue in the C-terminal of the PA as well as the wild type and mutant protein of the N-terminal of influenza virus subunit PB1 in E. coli respectively. It also provides a method of crystallizating the complex of C-terminal of PA and N-terminal peptide of PB1, and the crystal structure of complex of PAc/PB1N short peptide obtained therefrom, and drug screening based on these crystallization methods as well as drug design based on these crystal structures.
In one embodiment, the present invention provides crystal three-dimensional structure of complex of C-terminal of influenza virus polymerase subunit PA-PAc and N-terminal of influenza virus polymerase subunit PB1-PB1N, wherein the C-terminal of the influenza virus polymerase subunit PA-PAc is amino acids from amino acid positions about 201˜ about 301 to about 650˜ terminal, the N-terminal of influenza virus polymerase subunit PB1-PB1N is a short peptide within the 48 amino acids of the N-terminal of influenza virus polymerase subunit PB1-PB1N, wherein atoms of the crystal three-dimensional structure has at least 40% atomic coordinates listed in table 1, or atomic coordinates of main chain carbon backbone of at least 40% amino acids in the crystal three-dimensional structure of complex of C-terminal of influenza virus polymerase subunit PA-PAc and N-terminal of influenza virus polymerase subunit PB1-PB1N has an average root mean square deviation smaller than or equal to 1.7 Angstrom with respect to the atomic coordinates listed in table 1.
In one embodiment, the present invention provides crystal three-dimensional structure of complex of C-terminal of influenza virus polymerase subunit PA-PAc and N-terminal of influenza virus polymerase subunit PB1-PB1N, wherein the influenza virus is selected from influenza virus A, B and C type, preferably influenza virus A type: A/goose/Guangdong/1/96, A/Brevig Mission/1/1918; influenza virus B type: B/Ann Arbor/1/1966 or influenza virus C type: C/JJ/1950.
In a preferred embodiment, the present invention provides crystal three-dimensional structure of complex of C-terminal of influenza virus polymerase subunit PA-PAc and N-terminal of influenza virus polymerase subunit PB1-PB1N, wherein the crystal of the complex has space group of P4(1)2(1)2, and the lattice parameters are about: a=b=122 Angstrom, c=133 Angstrom, α=β=γ=90°.
In a preferred embodiment, the present invention provides crystal three-dimensional structure of complex of C-terminal of influenza virus polymerase subunit PA-PAc and N-terminal of influenza virus polymerase subunit PB1-PB1N, wherein the C-terminal of influenza virus A polymerase subunit PA-PAc consists of the first portion and the second portion, wherein the first portion consists of α helix 4, i.e. amino acids fragment of 406-414 positions, α helix 5, i.e. amino acids fragment of 440-450 positions, α helix 8, i.e. amino acids fragment of 583-603 positions, α helix 9, i.e. amino acids fragment of 608-613 positions, α helix 10, i.e. amino acids fragment of 633-649 positions, α helix 11, i.e. amino acids fragment of 653-673 positions, α helix 12, i.e. amino acids fragment of 683-691 positions, α helix 13, i.e. amino acids fragment of 698-714 positions, β sheet 8, i.e. amino acids fragment of 619-623 positions and β sheet 9, i.e. amino acids fragment of 628-631 positions; wherein the second portion mainly consists of β sheet 1, i.e. amino acids fragment of 290-292 positions, β sheet 2, i.e. amino acids fragment of 317-324 positions, β sheet 3, i.e. amino acids fragment of 480-491 positions, β sheet 4, i.e. amino acids fragment of 496-506 positions, β sheet 5, i.e. amino acids fragment of 517-526 positions, β sheet 6, i.e. amino acids fragment of 541-550 positions and β sheet 7, i.e. amino acids fragment of 557-571 positions; wherein the β sheets of the second portion of the C-terminal of influenza virus polymerase A polymerase subunit PA-PAc is surrounded by α helix 1, i.e. amino acids fragment of 303-311 positions, α helix 2, i.e. amino acids fragment of 331-349 positions, α helix 3, i.e. amino acids fragment of 364-369 positions, α helix 6, i.e. amino acids fragment of 454-475 positions and α helix 7, i.e. amino acids fragment of 572-578 positions, wherein amino acids of fragments of influenza virus B and C type corresponding to influenza virus A type are shown in
In a preferred embodiment, the present invention provides crystal three-dimensional structure of complex of C-terminal of influenza virus polymerase subunit PA-PAc and N-terminal of influenza virus polymerase subunit PB1-PB1N, wherein the C-terminal of influenza virus A polymerase subunit PA-PAc interacts with N-terminal of PB1-PB1N mainly through α helix 8, α helix 10, α helix 11 and α helix 13, preferably through at least one amino acid selected from a group consisting of Leu666 of α helix 11, Phe710 of α helix 13, Val636 of α helix 10, Leu640 of α helix 10, Trp706 of α helix 13 and Gln670 of α helix 11, wherein amino acids of fragments of influenza virus B and C type corresponding to influenza virus A type are shown in
In a preferred embodiment, the present invention provides crystal three-dimensional structure of complex of C-terminal of influenza virus polymerase subunit PA-PAc and N-terminal of influenza virus polymerase subunit PB1-PB1N, wherein at least one amino acid selected from the group consisting of Ile621, Gly622, Glu623, Thr618 and Pro620 interacts with the influenza virus polymerase subunit PB1, the Ile621, Gly622, Glu623, Thr618 and Pro620 is in the ring peptide between α helix 9 and α helix 10 of C-terminal of influenza virus A polymerase subunit PA-PAc, wherein amino acids of fragments of influenza virus B and C type corresponding to influenza virus A type are shown in
In a preferred embodiment, the present invention provides crystal three-dimensional structure of complex of C-terminal of influenza virus polymerase subunit PA-PAc and N-terminal of influenza virus polymerase subunit PB1-PB1N, wherein at least one amino acid selected from the group consisting of Asn647, Gln408, Cys584, Gln587, Gln591, Lys643, Asn647, Ser659, Lys663, Trp699 and Asn703 of the C-terminal of influenza virus A polymerase subunit PA-PAc constitutes “pocket” amino acid sites which bind the influenza virus polymerase subunit PB1N, wherein amino acids of fragments of influenza virus B and C type corresponding to influenza virus A type are shown in
In a preferred embodiment, the present invention provides crystal three-dimensional structure of complex of C-terminal of influenza virus polymerase subunit PA-PAc and N-terminal of influenza virus polymerase subunit PB1-PB1N, wherein at least one amino acid selected from the group consisting of Trp406, Glu410, Lys461, Glu524, Phe525, Ser526, Lys536, Lys539, Tyr540, Leu563, Tyr564, Arg566 and Lys574 of the C-terminal of influenza virus A polymerase subunit PA-PAc constitutes “big groove” and “channel” structures which bind nucleotide, RNA or other small molecules or proteins, wherein amino acids of fragments of influenza virus B and C type corresponding to the influenza virus A type are shown in
In a preferred embodiment, the present invention provides crystal three-dimensional structure of complex of C-terminal of influenza virus polymerase subunit PA-PAc and N-terminal of influenza virus polymerase subunit PB1-PB1N, wherein amino acid residues of 370-405 positions of the C-terminal of influenza virus A polymerase subunit PA-PAc constitutes a big ring, wherein amino acids of fragments of influenza virus B and C type corresponding to the influenza virus A type are shown in
In a preferred embodiment, the present invention provides crystal three-dimensional structure of complex of C-terminal of influenza virus polymerase subunit PA-PAc and N-terminal of influenza virus polymerase subunit PB1-PB1N, wherein α helix 12 and α helix 13 of C-terminal of influenza virus polymerase subunit PA-PAc interact with other proteins, preferably at least one amino acid selected from the group consisting of Ile690, Glu691, Glu692, Cys693 and Asn696 of the α helix 12 and α helix 13 interacts with other proteins, and amino acids of fragments of influenza virus B and C type corresponding to the influenza virus A type are shown in
In a preferred embodiment, the present invention provides crystal three-dimensional structure of complex of C-terminal of influenza virus polymerase subunit PA-PAc and N-terminal of influenza virus polymerase subunit PB1-PB1N, wherein at least one amino acid of C-terminal of influenza virus polymerase subunit PA-PAc that is selected from the group consisting of Lys506, Gly507, Arg508, Ser509, His510, Leu511, Arg512, Asn513 and Asp514 interacts with other proteins, wherein His510 constitutes a portion of the polymerase complex RNAse, and amino acids of fragments of influenza virus B and C type corresponding to the influenza virus A type are shown in
In another embodiment, the present invention provides a polypeptide, protein, inorganic compound or organic compound binding to at least one member selected from the group consisting of α helix 8, α helix 10, α helix 11 and α helix 13 of C-terminal of influenza virus polymerase subunit PA-PAc, wherein the influenza virus is selected from influenza virus A, B and C type, preferably influenza virus A type: A/goose/Guangdong/1/96, A/Brevig Mission/1/1918; influenza virus B type: B/Ann Arbor/1/1966 or influenza virus C type: C/JJ/1950; wherein the polypeptide, protein, inorganic compound or organic compound, antibody or immune conjugate preferably bind to the member selected from the group consisting of Leu666 in α helix 11, Phe710 in α helix 13, Val636 and Leu640 in α helix 10, Trp706 in α helix 13, Gln670 in α helix 11 of C-terminal of influenza virus polymerase subunit PA-PAc, wherein amino acids of fragments of influenza virus B and C type corresponding to the influenza virus A type are shown in
In another embodiment, the present invention provides a polypeptide, protein, inorganic compound or organic compound, antibody or immune conjugate binding to at least one member selected from the group consisting of Ile621, Gly622, Glu623, Thr618 and Pro620 located at the circle peptide between α helix 9 and α helix 10 of the C-terminal of influenza virus polymerase subunit PA-PAc, wherein amino acids of fragments of influenza virus B and C type corresponding to the influenza virus A type are shown in
In another embodiment, the present invention provides a polypeptide, protein, inorganic compound or organic compound, antibody or immune conjugate binding to at least one amino acid selected from the group consisting of Asn647, Gln408, Cys584, Gln587, Gln591, Lys643, Asn647, Ser659, Lys663, Trp699 and Asn703 of the C-terminal of influenza virus A polymerase subunit PA-PAc, wherein amino acids of fragments of influenza virus B and C type corresponding to influenza virus A type are shown in
In another embodiment, the present invention provides a polypeptide, protein, inorganic compound or organic compound, antibody or immune conjugate binding to at least one amino acid selected from the group consisting of Trp406, Glu410, Lys461, Glu524, Phe525, Ser526, Lys536, Lys539, Tyr540, Leu563, Tyr564, Arg566 and Lys574 of the C-terminal of influenza virus A polymerase subunit PA-PAc, wherein amino acids of fragments of influenza virus B and C type corresponding to influenza virus A type are shown in
In another embodiment, the present invention provides a polypeptide, protein, inorganic compound or organic compound, antibody or immune conjugate binding to amino acids position 370˜405 of the C-terminal of influenza virus A polymerase subunit PA-PAc, wherein amino acids of fragments of influenza virus B and C type corresponding to influenza virus A type are shown in
In another embodiment, the present invention provides a polypeptide, protein, inorganic compound or organic compound, antibody or immune conjugate binding to helix 12 and a helix 13 of the C-terminal of influenza virus A polymerase subunit PA-Pac, preferably to at least one amino acid selected from the group consisting of Ile690, Glu691, Glu692, Cys693 and Asn696 in α helix 12 and α helix 13, wherein amino acids of fragments of influenza virus B and C type corresponding to influenza virus A type are shown in
In another embodiment, the present invention provides a polypeptide, protein, inorganic compound or organic compound, antibody or immune conjugate binding to at least one amino acid selected from the group consisting of Lys506, Gly507, Arg508, Ser509, His510, Leu511, Arg512, Asn513 and Asp514 located at ring region between β sheet 4 and β sheet 5 in the C-terminal of influenza virus A polymerase subunit PA-PAc, wherein amino acids of fragments of influenza virus B and C type corresponding to influenza virus A type are shown in
In another embodiment, the present invention provides a polypeptide, protein, inorganic compound or organic compound, antibody or immune conjugate which competes with influenza virus polymerase subunit PB1 for binding PAc.
In a preferred embodiment, the present invention provides the polypeptide, protein, inorganic compound or organic compound, antibody or immune conjugate which competes with influenza virus polymerase subunit PB1 for binding PAc predominantly by an interaction with PAc through the hydrophobic core constituted by the α helix 8, α helix 11, α helix 13 and α helix 10, preferably interaction with PAc through Met595 in α helix 8, Leu666 in α helix 11, Trp706 and Phe710 in α helix 13, Val636 and Val640 in α helix 10, wherein amino acids of corresponding fragments of influenza virus B and C type to influenza virus A type are shown in
In a preferred embodiment, the present invention provides a polypeptide, protein, inorganic compound or organic compound, antibody or immune conjugate which competes with influenza virus polymerase subunit PB1 for binding PAc, wherein the amino acid sequence of the polypeptide or protein comprises at least three amino acids which are identical to amino acids of corresponding position of short PTLLFL motif of the short helix domain constituted by the 5th-10th residues Pro5, Thr6, Leu7, Leu8, Phe9 and Leu10 of N-terminal of wild influenza virus polymerase subunit PB1-PB1N, when the polypeptide or protein is aligned with the PTLLFL motif
In another embodiment, the present invention provides a composition comprising above-mentioned polypeptide, protein, inorganic compound or organic compound, antibody or immune conjugates, and optionally comprising an carrier and an excipient.
In another embodiment, the present invention provides use of the composition in manufacturing medicaments used in the treatment of diseases caused by influenza virus.
In another embodiment, the present invention provides a method of expressing and purifying the complex of C-terminal of influenza virus polymerase subunit PA-PAc and N-terminal of influenza virus polymerase subunit PB1-PB1N, comprising:
(a) Construct a vector of gene sequence encoding amino acid positions about 201˜ about 301 to about 650˜ terminal of the C-terminal of influenza virus polymerase subunit PA-PAc, with a tag protein fused or not fused to the vector, prokaryotic cells or eukaryotic cells are transformed with said vector in order to express the PAc with the tag protein;
(b) A method similar with that of expressing PAc was used to express the PB1N with or without a tag;
(c) Proportionally mix cells expressing the influenza virus PAc obtained from step (a) and cells expressing amino acids sequence within the 48 amino acids of the N-terminal of influenza virus PB1 obtained from step (b), the resulting protein is separated through the specifically recognizing the specific tag, the tag protein is removed from the protein through enzymolysis, the complex of PAc and PB1N is separated, the concentration of the complex is determined;
Wherein the atoms of the crystal three-dimensional structure of complex of C-terminal of influenza virus polymerase subunit PA-PAc and N-terminal of influenza virus polymerase subunit PB1-PB1N has at least 40% atomic coordinates listed in table 1, or atomic coordinates of main chain carbon backbone of at least 40% amino acids in the crystal three-dimensional structure of complex of C-terminal of influenza virus polymerase subunit PA-PAc and N-terminal of influenza virus polymerase subunit PB1-PB1N has average root mean square deviation smaller than or equal to 1.7 Angstrom with respect to the atomic coordinates listed in table 1.
In a preferred embodiment, wherein the tag protein is selected from GST, Flag-tag, Myc-tag, MBP-tag, specific antibodies; the vector comprises selective marker gene, the Proportional mixing in step (c) means that molar ratio of tag protein-PAc and tag protein-PB1N is 0.1:1˜1:0.1, preferably the molar ratio of tag protein-PAc and tag protein-PB1N is 0.5:1˜1:0.5, more preferably the molar ratio of tag protein-PAc and tag protein-PB1N is nearly 1:1; more preferably the tag protein is GST, the method of recognizing the specific tag is performed through affinity column, the method of removing tag is preformed with a protease, the method of separating the complex of PAc and PB1N is preformed through gel filtration or ion-exchange chromatography, the protein concentration is determined through gel electrophoresis.
In a more preferable embodiment, wherein the procaryotic cell is E coli.
In another embodiment, the present invention provides a method of cocrystallizing the complex of C-terminal of influenza virus polymerase subunit PA-PAc and N-terminal of influenza virus polymerase subunit PB1-PB1N, comprising:
the protein concentration of the purified complex of PAc and PB1N is condensed to 5-30 mg/ml;
the crystal growth condition is screened by gas sitting drop and hanging drop;
crystal of the complex of C-terminal of influenza virus polymerase subunit PA-PAc and N-terminal of influenza virus polymerase subunit PB1-PB1N is obtained.
In another embodiment, the present invention provides a method of expressing wild type or mutant protein of N-terminal of PA-PAN, wherein PAN is amino acids from positions 1˜ about 50 to about 200˜ about 300, the method comprising: construct an expression vector of gene sequence encoding amino acid positions 1˜ about 50 to about 200˜ about 300 of the N-terminal of influenza virus polymerase subunit PA-PAN, with a gene of tag protein fused or not fused to the vector, and eukaryotic cells or prokaryotic cell are transformed with the vector in order to express the PAN with or without the tag protein, wherein the amino acid sequence of the N-terminal of PA-PAN has at least 40% sequence identity with the amino acids listed in
In a preferred embodiment, the procaryotic cell is E coli.
In another embodiment, the present invention provides a method of screening candidate compounds which compete with PB1N for binding PAc, the method comprising:
(a) combine PAc to surface of the fixed support;
(b) contact the excess tagged PB1N with the combined PAc;
(c) thoroughly elute with eluent in order to remove unbound PB1N;
(d) contact the candidate compound solutions to be detected with the fixed PAc binding to the PB1N;
(e) thoroughly elute with the eluent in order to obtain solution to be detected;
(f) measure concentration of free tagged PB1N in the solution to be detected;
(g) calculate the binding capability of the candidate compound to be detected with PAc according to the concentration of free tagged PB1N in the solution.
In a preferred embodiment, combining PAc to surface of the fixed support in step (a) is accomplished through covalently crosslinking or through binding PAc with affinity matrix, wherein there is a binding group of affinity matrix on the surface of the fixed support.
Preferably, the affinity matrix can be selected from GST, Flag-tag, Myc-tag, MBP-tag and specific antibody, whereas there is corresponding binding group of the affinity matrix on the surface of the fixed support.
Preferably, the tagged PB1N polypeptide is selected from the protein tagged with isotope or the protein tagged with other chemical molecule, preferably, the other chemical molecular tag is green fluorescent protein or various fusion polypeptides.
Preferably, the fixed surface can be affinity chromatography columns
In one embodiment, the present invention provides use of the crystal three-dimensional structure of complex of C-terminal of influenza virus polymerase subunit PA-PAc and N-terminal of influenza virus polymerase subunit PB1-PB1N in designing and screening polypeptide, protein, inorganic compound or organic compound, antibody or immune conjugates used in the treatment of diseases caused by the influenza virus infection, comprising:
design polypeptide, protein, inorganic compound or organic compound, antibody or immune conjugates binding to specific portion through computer simulation technology according to coordinates of three-dimensional structure of protein;
search for potential polypeptide, protein, inorganic compound or organic compound, antibody or immune conjugates binding to specific portion through computer simulation technology according to coordinates of three-dimensional structure of the protein;
the designed or searched polypeptide, protein, inorganic compound or organic compound, antibody or immune conjugates according to coordinates of three-dimensional structure of the protein bind to any subtype of influenza virus polymerase protein which have at least 50% sequence identity with the PAc and the PB1N sequence, binding information is then analyzed;
the designed or searched polypeptide, protein, inorganic compound or organic compound, antibody or immune conjugates according to coordinates of three-dimensional structure of the protein bind to any subtype of influenza virus polymerase protein which have at least 50% sequence identity with the PAc and the PB1N sequence, and then crystallization is preformed, the binding information of polypeptide or compound molecule to protein is analyzed through crystal diffraction method;
wherein the polypeptide, protein, inorganic compound or organic compound, antibody or immune conjugates that bind to any subtype of influenza virus polymerase protein which had at least 50% sequence identity with the PAc and the PB1N sequence are candidate compounds.
In one embodiment, the present invention provides structure of the three subunits i.e. PA, PB1, PB2 of any subtype of influenza virus polymerase or the complex of PA, PB1 and PB2, wherein a protein contained in it or a fragment thereof has 40% identical sequence with the PAc protein.
In one embodiment, the present invention provides three-dimensional stereochemical structure of the three subunits i.e. PA, PB1, PB2 of any subtype of influenza virus polymerase or that of the complex of PA, PB1 and PB2, wherein the coordinates of three-dimensional structure in main chain of a protein contained in it or a fragment thereof has an average root mean square deviation smaller than or equal to 1.7 Angstrom with respect to three-dimensional atomic coordinates of a main chain carbon backbone having at least 40% amino acid residues of the PAc protein sequence.
In one embodiment, the present invention provides structure of subunit PA, PB1, PB2 or that of the complex of subunit PA, PB1 and PB2 from any subtype of influenza virus, wherein a protein fragment contained in it has 20% sequcne homology with the fragment of amnio acid 1-11 in the PB1N polypeptide, preferably 40% sequence homology.
In one embodiment, the present invention provides a polypeptide or a small molecule, characterized in that it interacts with any amino acid of the influenza virus subunit PA.
In one embodiment, the present invention provides use of the crystal three-dimensional structure in drug screening and drug design.
In one embodiment, the present invention provides a method of screening a polypeptide, protein, inorganic compound or organic compound, antibody or immune conjugate which binds to the protein based on crystal three-dimensional structure of PAc and PB1N protein, comprising: obtaining PAc-containing crystal by protein crystallization method, or obtaining the coordinates of crystal three-dimensional structure of the protein complex containing PAc and PB1N; wherein the three-dimensional structure contains any structure that has an average root mean square deviation smaller than or equal to 1.7 Angstrom with respect to three-dimensional coordinates of a main chain carbon backbone having at least 40% amino acid residues of the coordinates.
In one embodiment, the present invention provides a method of expressing and purifying the influenza virus subunit PA through expressing PA fragments in bacteria and eukaryotic cell expression systems.
In one embodiment, the present invention provides a polypeptide, protein, inorganic compound or organic compound, antibody or immune conjugate that interacts with amino-acid residues on a protein, wherein the protein has at least 40% identical amino acids with any fragment of α helix 8, 10, 11 and 13 in complex of C-terminal of influenza virus polymerase subunit PA-PAc and N-terminal of influenza virus polymerase subunit PB1-PB1N.
It should be noted that the fragments in influenza virus B and C type corresponding to α helix and β sheet of influenza virus A are shown in
The protein sequences encoded by virus gene derived from Avian influenza virus A/goose/Guangdong/1/96 are respectively as follows:
(1) Protein sequence of PA:
(2) Protein sequence of PB1:
The gene of influenza virus subunit PA was separated into C-terminal part and N-terminal part, and then the C-terminal part and the N-terminal part were cloned by molecular cloning techniques, wherein the N-terminal part contains the first 256 amino acids and the C-terminal part contains 257-716 amino acids. The two parts were cloned into pGEX-6p vector (from Amersham Pharmacia Inc.) respectively so as to express fusion proteins of N-terminal fused with GST (GST-PAN and GST-PAc). The cloned plasmids were transformed into E. coli BL21 respectively, and E. coli are induced by using 0.1 to 1 mM IPTG(isopropyl-β-thiogalactoside) in BL21 to express these two proteins respectively, thus obtaining respectively expressing bacteria of these two protein, for details see Example 1.
The gene encoding within 48 amino acids of N-terminal of PB1 (including the former 25 amino acids peptide) was also cloned into pGEX-6p vector, so as to express fusion protein of fused GST-PB1 peptide.
Likewise, the short peptide of GST fused the former 25 amino acids or former 48 amino acids of PB1N was expressed respectively. The vectors were transformed into E. coli BL21 in the same way. E. coli were induced by using 0.1 to 1 mM IPTG in BL21 to express proteins, thus obtaining expression bacteria of the protein.
The bacteria that express GST-PA-N were suspended with buffer, lysed and centrifuged to obtain supernatant. Then affinity chromatographic column was used to purify GST-PA-N fusion protein from the supernatant.
The GST-PAc expressing bacteria and the GST-PB1 expressing bacteria were suspended with a buffer (which contains about 20 mM Tris-HCl (pH8.0) and 250 mM NaCl) respectively and mixed with a molar ratio between the protein content of GST-PAc and GST-PB1N is 0.1:1˜1:0.1, preferably the molar ratio between the protein content of GST-PAc and GST-PB1N is 0.5:1˜1:0.5, more preferably the molar ratio between the protein content of GST-PAc and GST-PB1N is near 1:1.
Subsequently, Glutathione-Sepharose affinity column (from Amersham Pharmacia Inc.) was used to purify the GST fusion protein. After enzymolysis with PreScission protease (from Amersham Pharmacia Inc.), the complex of PAc/PB1 short peptide was separated and purified through such methods as gel filtration Superdex-200 and ion exchange chromatography (Q sepharose), wherein complex can be used for further crystallization experiment after determining the protein concentration by SDS-PAGE gel electrophoresis.
The complex that has been expressed and purified through above methods was condensed to a concentration of 5-30 mg/ml, and crystal growth condition is screened with crystallization reagents (from Hampton Research) by gas hanging drop so as to obtain original crystals under conditions of multiple crystallization reagents.
Through further optimization, crystals with good appearance were obtained in solution containing about 1M sodium acetate with different buffer conditions under pH 4-9, wherein larger triangle-cone crystal was obtained in solution containing about 1-1.3M sodium acetate (Sigma) with different buffers under pH 4-9, and the resolution of said crystal is about 4 Angstrom.
When collecting X-ray diffraction data, the crystal required by diffraction was transferred from hanging drops to about 10 μl corresponding crystallization buffer containing 1.4 M sodium acetate and 10% glycerol (Sigma). After the fluid drops are left open for air dehydration for more than one hour, parent crystal and selenium-containing crystal with a resolution of about 3 Angstrom as well as corresponding X-ray diffraction data were obtained.
A set data of parent crystal with a resolution of 2.9 Angstrom from the complex crystal of PA-PB1 N-terminal (this PB1 N-terminal contains 25 amino acids) was first collected by using FR-E X-ray diffractometer (Rigaku) under a wave length 1.5418 Angstrom. Then under wave length of 0.9783 and 0.9785 Angstrom, two sets of data from derivative crystal of selenium atom were collected, i.e. peak and edge, using synchrotron radiometer located at APS, Chicago, USA (station number: SBC 19ID; detection screen: ADSC Q315), the resolution of said crystal is about 3.3 Angstrom. The three sets of data were treated by HKL2000 (Otwinowski 1997) and found to have spacegroup of P4(1)2(1)2. Phase was calculated by multi-wavelength anomalous scattering (Hendrickson 1991), and sas file resulted from treatment was searched for selenium atoms by SHELXD (Sheldrick 1998). The protein itself has 14 methionines, and the inventors found 14 selenium atoms in all. Coordinates of selenium atoms and two sets of data (i.e. Peak and Edge) were input into Program autoSHARP (Vonrhein, Blanc et al. 2007) to calculate phase and to modify the electron density map, and several secondary structures (including α helixes and (β sheets) can be clearly found from the calculated electron density map. Then phase can be expanded by Program CAD, and the phase was expanded to 2.9 Angstrom by collected parent data so as to construct a structure model, wherein the Programs used to construt model are ARP/wARP (Perrakis, Morris et al. 1999) and Phenix (Adams, Grosse-Kunstleve et al. 2002). Automatic model construction performed by these two programs can amount to 60% of the whole structure, and the rest is manually constructed through Program COOT (Emsley and Cowtan 2004).
Finally, the resulting model was modified by Program CNS (Brunger, Adams et al. 1998) and REFMAC5(Murshudov, Vagin et al. 1997) to achieve the protein structure analysis, and the final factor R and factor R-free for modify structure are 0.22 and 0.26 respectively.
Atomic coordinates in crystal structure of protein complex of PAc/PB1N short peptide, see Table 1.
In one embodiment of the present invention, PA was divided into two fragments so as to express former 256 amino acid residues fragments and 257-716 amino acid residues fragments of the PA, respectively, and two gene fragments encoding these two protein polypeptides were cloned into an Escherichia coli expression vector, respectively so as to expressing proteins in a bacteria. The PA N-terminal polypeptides were purified from a PA N-terminal (1-256 amino acids) expressing bacteria and used for protein crystallization. C-terminal of PA expressing bacteria was centrifugally collected for later use so as to be co-purified with the N-terminal of PB1 polypeptides.
Polypeptide containing former 25 or no more than 48 amino acids of the N-terminal of PB1 (not containing first-position methionine) was expressed in the form of GST fusion protein in a bacteria. The influenza virus polymerase protein subunit PA was expressed by fragments in a bacteria or other eukaryotic cells such that at least 50% fragments were part of amino acid fragments of positions 257-716 of the PA protein.
Expression and Purification of N-Terminal of Influenza Virus PA in Escherichia coli
The N-terminal of the influenza virus PA (amino acids 1-256) was cloned into a pGEX-6p vector (from Amersham Pharmacia Inc.) via a molecular cloning technique, the cloning sites thereof being BamHI and XhoI. Expression plasmids with a PA N-terminal gene, obtained by cloning, were transformed into Escherichia coli BL21 for protein expression, such that the bacteria could express the N-terminal (amino terminal) of the PA protein which was connected with the GST fusion protein and has protease cleavage sites cleaved by ProScission protease to further separate a GST protein tag from the target protein-PA polypeptide. IPTG with a final concentration of about 0.1-1 mM was used in the cultured Escherichia coli BL21 cells to induce Escherichia coli in order to obtain the expressing bacteria of said protein. The used vector contained an ampicillin-resistance gene. After the cloning-constructed expression plasmids of the fusion protein were transformed into Escherichia coli such as BL21 (Novagen), bacterium were cultured overnight using bacteria culture media such as LB and so on at 37, and after about 12 hours transferred to a mass culture medium in a proportion of about 1:100, and cultured in a shake flask at 37 until OD is approximately 1.0, and then added 0.1-1 mM IPTG for inducing expression. After about 3 to 6 hours, the bacterium were collected centrifugally, and the collected precipitated bacterium could be stored at −20 to −80 in a refrigerator for later use or be used directly for purification of the PA N-terminal protein.
Expression and Purification of Complex of C-Terminal of Influenza Virus PA and PB1 Polypeptide
The C-terminal (amino acids 257-716) of the influenza virus PA was cloned into a pGEX-6p vector (from Amersham Pharmacia Inc.) via a molecular cloning technique, the cloning sites thereof being BamHI and NhoI. Expression plasmids with a PA C-terminal gene, obtained by cloning, were transformed into Escherichia coli BL21 for protein expression, such that the bacteria could express the N-terminal (amino terminal) of the protein which was connected with the GST fusion protein and has protease cleavage sites cleaved by ProScission protease to further separate a GST protein tag from the target protein-PA polypeptide. IPTG with a final concentration of about 0.1-1 mM was used in the cultured Escherichia coli BL21 cells to induce Escherichia coli in order to obtain the expressing bacteria of said protein. The used vector contained an ampicillin-resistance gene. After the cloning-constructed expression plasmids of the fusion protein were transformed into Escherichia coli such as BL21 (Novagen), bacterium were cultured overnight using bacteria culture media such as LB and so on at 37, and after about 12 hours transferred to a mass culture medium in a proportion of about 1:100, and cultured in a shake flask at 37 until OD is approximately 1.0, and then added 0.1-1 mM IPTG for inducing expression after the culture temperature is lowered to 16. After about 12 to 24 hours, the bacterium were collected centrifugally, and the collected precipitated bacterium could be stored at −20 to −80 in a refrigerator for later use or be used directly for purification.
The gene of the N-terminal of PB1 with no more than 48 amino acids (the inventor had expressed the former 48-amino acid polypeptide and the former 25-amino acid polypeptide of the N-terminal of PB1) was likewise cloned into multiple cloning sites of the pGEX-6p vector, wherein the used cloning sites were BamHI and XhoI, such that the bacteria could express a fusion protein containing GST, there is protease cleavage sites cleaved by ProScission protease in the fusion protein in order to further separate a GST protein tag from the target protein of PB1 polypeptide. The fusion protein of a GST-PB1N peptide was expressed in Escherichia coli BL21 in the same way as the PA fusion protein was expressed above. The resistance gene was ampicillin-resistance gene. The protein expression was carried out at 37° C., and the used inducer was IPTG. Finally, the expressing bacterium were collected centrifugally, used directly for protein purification and could be stored temporarily at −20° C. to −80° C. in a refrigerator.
The centrifugally collected expressing bacteria expressing the GST-PA N-terminal polypeptide was suspended using a buffer solution containing 20 mM Tris-HCl (pH8.0) and 250 mM NaCl or a buffer solution of 1×PBS (pH7.4) phosphoric acid. An ultrasonic breaker was used to break cells. The insoluble precipitation was centrifugally separated and removed in order to collect soluble supernatant. A Glutathione affinity chromatographic column was used to purify the GST-PA-N-terminal polypeptide, and the ProScission protease was further used to enzymolyze the fusion protein into two fragments of GST (glutathione S-transferase) and PA-N. Ion exchange chromatography and gel exclusion chromatography were then used to purify the PA-N protein polypeptide. The protein was concentrated to 5-30 mg/mL for crystal growth.
The expressing bacteria expressing the GST-PAC C-terminal polypeptide and the expressing bacteria expressing the GST-PB1N short peptide were suspended using a buffer solution containing 20 mM Tris-HCl (pH8.0) and 250 mM NaCl or a buffer solution of 1×PBS (pH7.4) phosphoric acid, and then mixed in proportion, such that the molar ratio of the total protein of GST-PA to GST-PB1 was 0.1:1 to 1:0.1, preferably 0.5:1 to 1:0.5, most preferably close to 1:1.
The cell in the mixed bacterial suspension was lysed using ultrasonic wave or other cell lysing methods. An insoluble portion and a soluble portion of the bacterial lysates were centrifugally separated. The supernatant obtained by high speed centrifugation (about 20,000 g) was preliminarily separated using a Glutathione-Sepharose affinity column (from Amersham Pharmacia Inc.) to purify such mixed protein. The protein containing a GST tag could bind to the Glutathione-Sepharose affinity column, while other proteins could not bind to said affinity column. The above mentioned bacterial suspension buffer solution was used to rinse impurity after the protein bound to the affinity column. A suitable amount of ProScission protease (from Amersham Pharmacia Inc.) was used to enzymolyze the mixed GST fusion protein of the affinity column. This process generally needs about 24 hours. Then, the enzymatically cleaved PAC and PB1N proteins were further separated using methods of gel filtration superdex-200 (from Amersham Pharmacia Inc.), Q sepharose ion exchange chromatography (from Amersham Pharmacia Inc.) and so on to purify the PAC/PB1N short peptide complex (the chromatography column comes from Amersham Pharmacia Inc.). The protein purity was determined via SDS-PAGE gel electrophoresis, and the purity generally reached more than 90%. The protein purified by the above steps was concentrated to about 5-30 mg/mL using an evaporating pipe (coming from Millipore Inc.) for a further crystallization experiment.
The person skilled in the art would know that, the N-terminal of influenza virus PA-PAN and the C-terminal of influenza virus PA-PAC as well as the N-terminal of PB1-PBN could be expressed not only in the prokaryotic cell such as Escherichia coli described hereinabove but also in an eukaryotic cell such as insect cells; any other endonuclease, protease cleavage site, and ligase could be used; the target polypeptide to be purified may be fused with other tags such as GST, and the corresponding separating and purifying method was then selected for purification, and finally the tag fused into the target polypeptide was removed. Various change and modification of the present invention as described above fall within the scope of protection of the present invention.
It shall be noted that, the fragments of an α helix and a β sheet of type B or type C influenza corresponding to type A influenza virus are as shown in
The complex of the PA and PB1 polypeptides expressed and purified with the above method was concentrated to about 5 to 30 mg/mL. A crystallization reagent (from reagent kits such as Screen Kit I/II, Index, and so on from Hampton Research incorporation, etc.) was used in gas sitting drop to screen crystal growth conditions. Upon preliminary screening, the inventor could obtain an original crystal with multiple different crystallization reagents.
Upon further optimization, a crystal with a fairly good appearance was obtained using a solution containing about 1M of sodium acetate in cases of using buffer solutions with different PH values (PH 4-9). A relatively larger triangle-cone crystal was obtained in a sodium acetate buffer solution (PH4-9) with a concentration of 1 to 1.3 M (from Sigma Inc.), the resolution being about 4 Angstrom.
When X-ray diffraction was performed to collect data, crystal needed for the diffraction was transferred from suspension drops to a 10 microliter corresponding crystal buffer solution containing 1.4M sodium acetate and 10% glycerol (from Sigma). The liquid drops were placed in the air for dehydration for more than one hour to obtain a protein crystal with a high resolution, and the resolution of parental and selenium-containing (selenium substituted) protein crystal could reach more than 2.9 Angstrom.
It shall be noted that, the fragments of an α helix and a β sheet of type B or type C influenza corresponding to type A influenza virus are as shown in
A set data of parent crystal with a resolution of 2.9 Angstrom from the complex crystal of PA-PB1 N-terminal (this PB1 N-terminal contains 25 amino acids) was first collected by using FR-E X-ray diffractometer (Rigaku) under a wave length 1.5418 Angstrom. Then under wave length of 0.9783 and 0.9785 Angstrom, two sets of data from derivative crystal of selenium atom were collected, i.e. peak and edge, using synchrotron radiometer located at APS, Chicago, USA (station number: SBC 19ID; detection screen: ADSC Q315), the resolution of said crystal is about 3.3 Angstrom. The three sets of data were treated by HKL2000 (Otwinowski 1997) and found to have spacegroup of P4(1)2(1)2. Phase was calculated by multi-wavelength anomalous scattering (Hendrickson 1991), and sas file resulted from treatment was searched for selenium atoms by SHELXD (Sheldrick 1998). The protein itself has 14 methionines, and the inventors found 14 selenium atoms in all. Coordinates of selenium atoms and two sets of data (i.e. Peak and Edge) were input into Program autoSHARP (Vonrhein, Blanc et al. 2007) to calculate phase and to modify the electron density map, and several secondary structures (including α helixes and β sheets) can be clearly found from the calculated electron density map. Then phase can be expanded by Program CAD, and the phase was expanded to 2.9 Angstrom by collected parent data so as to construct a structure model, wherein the Programs used to construt model are ARP/wARP (Perrakis, Morris et al. 1999) and Phenix (Adams, Grosse-Kunstleve et al. 2002). Automatic model construction performed by these two programs can amount to 60% of the whole structure, and the rest is manually constructed through Program COOT (Emsley and Cowtan 2004).
Finally, the resulting model was modified by Program CNS (Brunger, Adams et al. 1998) and REFMAC5(Murshudov, Vagin et al. 1997) to achieve the protein structure analysis, and the final factor R and factor R-free for modify structure are 0.23 and 0.26 respectively.
The PA N-terminal polypeptide complex expressed and purified by the above method was concentrated to about 5 to 30 mg/mL. A crystal agent (kits such as Screen Kit I/II, Index, and so on from Hampton Research Incorporation, etc.) was used in gas sitting drop to screen crystal growth conditions. Upon preliminary screening, the inventor obtained an original crystal with different crystal agents.
For further optimization, a crystal well diffracted by an X-ray was obtained from a solution containing about 20% PEG 8000 or 20% PEG 3350 and 0.1 M magnesium chloride or 0.1 M magnesium acetate in a case of using a MES buffer solution with PH 6.5 (all the used regents came from Sigma Inc.) (see A and B crystal pictures and C and D diffraction pictures in
During a process of screening a small molecular medicament capable of disintegrating the PAC/PB1N short peptide complex, the PB1N short peptide gene was fused with a gene expressing GFP (green fluorescent protein). The PB1N short peptide protein fused with GFP was expressed as an indicator molecule during a small molecular compound disintegrating a protein complex. The PB1 short peptide gene fragment was connected to the GFP gene fragment using a molecular cloning method so as to express PB1 small peptide fusion protein of which one N-terminal or C-terminal was connected with GFP.
Method 1: a complex of PA C-terminal fusion protein with the N-terminal fused GST, viz. GST-PAC fusion protein, and GFP-PB1N short peptide fusion protein was expressed with the above method of expressing and purifying the C-terminal of PA and the PB1 short peptide.
The complex of the GST-PAC fusion protein and the GFP-PB1N short peptide fusion protein flew through and bound to the Glutathione affinity column Since said complex contained the GFP protein, the GFP-PB1N fusion protein binding to GST-PAC enabled the affinity column to show a green color after GST-PAC bound to the affinity column. The affinity column binding with the complex protein of GST-PAC and GFP-PB1N was rinsed sufficiently with a buffer solution to thoroughly elute and remove unbound proteins. Then, a mixture of small molecular compounds to be screened flew through the affinity column (said mixture should not contain Glutathione or other eluted compounds for detaching GST from the affinity column). If the mixture contained small molecules substituted for the PB1N polypeptide to bind to the PAC, part of the GFP-PB1N polypeptide fusion protein binding to PAc was replaced and eluted. The eluted solution flowing out showed a green color due to containing said GFP fusion protein when observed under a fixed wavelength fluorescent microscope. The small molecules were further sequentially separated and purified from the mixture, and the components substituted for the PB1N polypeptide were traced by the above green GFP protein tracing method to finally determine a small molecular compound interfering with the binding of PA to the PB1 small peptide. In the above method, besides using GST as an affinity matrix, other polypeptides such as Flag-tag, Myc-tag, MBP (Maltose binding protein)-tag, specific antibody, etc. could be used as combining groups of affinity matrix. Correspondingly, the affinity chromatographic column needs a corresponding affinity matrix, for example, if the Flag-tag was used, an antibody against the Flag-tag (e.g. an anti-flag monoclonal antibody from Sigma Inc.) was used to be fixed to the affinity chromatographic column as a gel medium binding to the Flag. The compound molecules binding to PA and replacing a PB1 small peptide (specific structure) could be determined via methods such as mass spectrometry, etc.
Method 2: PAC was purified separately (fusion protein or non-fusion protein) and covalently crosslinked to a gel medium by chemical crosslinking, but protein was not denatured. GFP-PB1N flew through the covalently binding gel column GFP-PB1N bound to the PAC protein such that the gel column presents a green fluorescent light of GFP. The solution of the small molecular mixture flew through the gel column, if a compound substituted for GFP-PB1N to bind to PAC was present, the GFP-PB1N fusion protein was eluted. The eluent showed a green color by stimulation of a specific-wavelength light, and the compound molecules substituted for GFP-PB1N bound to the PAC molecules of the gel column. A buffer solution was used to elute the gel column to remove impurities, and urea and the like was then used to denature PAC in order that the small molecules binding thereto were eluted. Methods of mass spectrometry and the like were used to analyze small molecules binding to PA to obtain structural information of the small molecules. The compound may be a small molecular medicament capable of disintegrating the PAC/PB1N short peptide complex.
A crystal three-dimensional structure of a complex of the C-terminal of influenza virus polymerase subunit PA-PAC and the N-terminal of influenza virus polymerase subunit PB1-PB1N was used to design and screen various polypeptides, proteins, or inorganic or organic compounds for treating diseases caused by influenza virus infection. The specific steps are as follows: polypeptides and compound molecules binding to specific portion were designed through computer stimulation technology according to coordinates of three-dimensional structure of protein; potential polypeptides and compound molecules binding to specific portion were searched for through computer stimulation technology according to coordinates of three-dimensional structure of protein; the polypeptides and compound molecules designed or searched according to the coordinates of three-dimensional structure of protein bound to any type of influenza virus polymerase protein which has at least 50% sequence identity with the PAC and PB1N sequences, and binding information was then analysed; the polypeptides and compound molecules designed or searched according to the coordinates of three-dimensional structure of protein bound to any type of influenza virus polymerase protein which has at least 50% sequence identity with the PAC and the PB1N sequences, and then crystallized; and the binding information of the polypeptides or compound molecules to protein is analyzed through a crystal diffraction method.
Upon verification by experiment, a short peptide containing M1, D2, V3, N4, P5, T6, L7, L8, F9, L10, and K11 bound to the C-terminal of PA. The inventors cloned gene encoding PB1N polypeptide containing the first-position M1 to the eleventh-position K11 into a pFEX-6p vector, purified said GST-PB1N fusion protein, and used the fusion protein fixed to the affinity chromatographic gel column to bind to PA-C in a solution through an in vitro binding experiment. The inventors found that said fusion protein maintained the PB1N's capability of binding to PA-C.
Using the same experimental method, the inventors found that a fusion protein containing M1, D2, V3, N4, P5, T6, L7, L8, F9, L10, K11, V12 and p13 also maintained the PB1N's capability of binding to PA-C. Thus, these two short peptides had a capacity of binding to PA-C to make themselves potential polypeptide medicaments interfering with influenza virus polymerase activity or models for further medicament design.
Likewise, the selected polypeptide having at least three amino acid sequence alignment identical with the above polypeptide might be a potential polypeptide medicament interfering with influenza virus polymerase activity.
The structure of subunits PA, PB1, PB2 or the complex of PA, PB1 and PB2 of any type of influenza virus polymerase contains one protein or one fragment thereof having at least 40% sequences identical with those of the PAC protein.
In the structure of subunits PA, PB1, PB2 or the complex of PA, PB1 and PB2 of any type of influenza virus polymerase, at least 40% coordinates of main chain carbon backbone of three-dimensional structure of one protein or one fragment thereof has average root mean square deviation smaller than or equal to 1.7 Angstrom with respect to the atomic coordinates of PAC.
In the structure of subunit PA, PB1, PB2 or the complex of PA, PB1 and PB2 of any type of influenza virus polymerase, the protein fragment has 40% sequence identity of 2-12 amino acid fragments of the PB1N polypeptide.
Any polypeptide or small molecule that interacts with key amino acids of the influenza virus subunit PA is included in the invention.
The structure is used in medicament screening and medicament designing.
A method for screening a compound or polypeptide binding to a protein based on the three-dimensional structure of the PAC and PB1N comprises: obtaining a crystal of the complex of PAC and PB1N proteins by protein crystallization, wherein the crystal of the complex protein has a spacegroup of P4(1)2(1)2, and the crystal cell parameters are: a=b=122 Angstrom, c=133 Angstrom, and α=β=γ=90°; obtaining the coordinate of the three-dimensional structure of the complex of the PAC and PB1N proteins by an X-ray diffracting crystal technique, wherein any structure containing at least 40% amino acid residues of which coordinates of main chain carbon backbone have average root mean square deviation smaller than or equal to 1.7 Angstrom with respect to said coordinate is included.
A method of expressing and purifying influenza virus subunit PA comprises expressing PA in segments in a bacteria or a eukaryotic expressing system, and the method is used to express and purify any protein fragments which has 40% sequence identity with PA.
In a preferred embodiment, the PAC/PB1N complex is used in designing and screening polypeptides, proteins, compounds, or medicaments in the treatment of diseases caused by influenza virus infection.
In a preferred embodiment, polypeptides for treating diseases caused by the influenza virus infection comprises polypeptides interacting with the above complex, at least one of the α helix or β sheet, and at least one amino acid site.
In a preferred embodiment, proteins for treating diseases caused by the influenza virus infection comprises proteins interacting with the above complex, at least one of the α helix or β sheet, and at least one amino acid site.
In a preferred embodiment, compounds for treating diseases caused by the influenza virus infection comprises compounds interacting with the above complex, at least one of the α helix or β sheet, and at least one amino acid site.
In a preferred embodiment, a pharmaceutical composition comprises the above polypeptides, proteins, or compounds.
The pharmaceutical composition of the present invention generally includes one carrier or excipient. An antibody and/or immune conjugate are dissolved in a pharmaceutically acceptable carrier, wherein an aqueous carrier is preferred. Many types of aqueous carriers can be applied, e.g. buffer saline, etc. These solutions are sterilized and generally free from undesired substances. These components can be disinfected through a conventional, well-known disinfecting technique. These components may include auxiliary substances required by physiological conditions, such as a buffering agent adjusting PH, toxicity regulator, sodium acetate, sodium chloride, potassium chloride, calcium chloride, sodium lactate, etc. The fusion proteins of these components vary greatly in concentration mainly depending on the selected administration manner, the liquid amount and viscosity required by a patient, body weight, etc.
Therefore, about 1.2 to 1200 μg of one typical pharmaceutical immunotoxin component in the present invention shall be applied daily for brain administration. One typical component for treating neoplasms of breast, ovary and lung via intravenous administration shall be applied to one patient 0.1 to 10 mg per day. The dosage of 0.1 to 100 mg per day for one person may be allowed, especially in a case that the medicament is administrated to a closed position without entering blood circulation or a lymphatic system, for example, it is administrated to a body cavity or an organ lacuna. The actual procedures for preparing applicable medical components are understood or acquired by the person skilled in the art and are described in detail in some publications, e.g. Remington's PHARMACETUTICAL SCIENCE, 19th ed., Mack Publishing Company, Easton, Pa. (1995).
The components of the present invention can be used for a treatment. In treatment application, the components are applied to a patient suffering from a certain disease (for example, glioblastoma, breast cancer, ovarian cancer, and lung cancer), the dosage of which shall be enough to at least alleviate or partially control said disease and the complications thereof. The dosage enough to complete these tasks is called as “therapeutically effective dosage”. The applied effective dosage depends on illness severity and patient's general health conditions. The effective dosage of the component can achieve subjectively-recognized alleviation of a certain symptom or objective improvement recorded by a clinician or other qualified observer.
Whether to be administrate once only or for several times depends on desired and tolerated dose and frequency by a patient. Nevertheless, an adequate amount of the immunotoxin shall be provided to treat a patient effectively. Preferably, the medical dosage might be administrated only once or administrated periodically until a certain therapy efficacy or an adverse reaction inhibits continuation of the treatment. Generally, these dosages are enough to treat or improve disease conditions without incurring unbearable toxicity for a patient.
The immune conjugates of the present invention can be prepared into gastrointestinal sustained release formulations (e.g. an implant, an oil injection, or a microparticle system). A protein delivery system can be fully understood by referring to Banga, A. J., THERAPEUTIC PEPTIDES AND PROTEINS: FORMULATION, PROCESSING, AND DELIVERY SYSTEMS, Technomic Publishing Company, Inc., Lancaster, Pa., (1995). The microparticle system includes microspheres, particles, microcapsules, nano-microcapsules, nano-microspheres, and nano-particles. The microcapsule uses therapeutic protein as a core. In globules, therapeutic substances are dispersed in the particles. Particles, microspheres, and microcapsues which are smaller than about 1 μm are generally called as nano-microparticles, nano-spheres, and nano-microcapsules. Capillary vessels are about 5 μm in diameter. Therefore, only nano-particles are intravenously administrated. The microparticles are about 100 μm in diameter and are intravenously and intramuscularly administrated. Examples are Kreuter, J., COLLOIDAL DRUG DELIVERY SYSTEMS, J. Kreuter, ed., Marcel Dekker, Inc., New York, N.Y., pp. 219-342 (1994); and Tice&Tabibi, TREATISE ON CONTROLLED DRUG DELIVERY, A. Kydonieus, ed., Marcel Dekker, Inc. New York, N.Y., pp. 315-339, (1992), both of which are cited herein.
Polymers can be used for ion controlled release of immune conjugate components in the present invention. Multiple degradable and nondegradable polymers for drug controlled release are well-known in the art (Langer, R., Accounts Chem. Res. 26:537-542 (1993)), for example, a retarding polymer polaxamer 407 is viscous and flowable at low temperature, but is formed as a semisolid gel at body temperature, and is proved to be an effective carrier for forming and delivering continuously recombinant interleukin-2 and urease (Johnston etc., Pharm. Res. 9:425-434 (1992)) and Pec etc., J. Parent. Sci. Tech. 44(2):58-65 (1990)). Likewise, hydroxyapatite can be used as a microcarrier for protein controlled release (Ijntema etc., Int. J. Pharm. 112:215-224 (1994)), while liposome is used for controlled release and targeting transport processes of a liplid-coated medicament (Betageri, etc., LIPOSOME DRUG DELIVERY SYSTEMS, Technomic Publishing Co., Inc., Lancaster, Pa. (1993)). Many other therapeutic protein controlled release systems have been known, for example, U.S. Pat. Nos. 5,055,303, 5,188,837, 4,235,871, 4,501,728, 4,837,028, 4,957,735, 5,019,369, 5,055,303, 5,514,670, 5,413,797, 5,268,164, 5,004,697, 4,902,505, 5,506,206, 5,271,961, 5,254,342, and 5,534,496, any of which is cited herein.
Experimental Results
The atomic coordinate of the structure of the complex of PAC and PB1N is shown in the following Table 1.
Polymerase subunit PA protein derived from avian H5N1 influenza virus strains A/goose/Guangdong/1/96 is compared with PA protein sequences of type A influenza virus strains A/BrevigMission/1/1918 that outbreaks on a large scale in Europe, 1998, and two types of type B influenza virus strains B/Ann Arbor/1/1966 and type C influenza virus strains C/JJ/1950, the results of which are as shown in
PA is divided by the inventor into two parts, and multiple fragments of varying lengths of two parts of a PA gene are cloned and expressed in Escherichia coli, wherein residues 1-256 (see
A preliminary crystallization experiment shows that the C-terminal of PA fails to obtain a crystal despite a lot of efforts has been made. Therefore, the inventor also uses a GST fusion method to express PB1 N-terminal peptides of 25 amino acids and 48 amino acids (see
The in vitro binding experiment shows that the expressing bacterium of the corresponding polypeptides of PA and PB1 are mixed in proportion, and then these two proteins are co-purified through the Glutathione affinity columnand gel exclusion chromatograph, and so on. It is determined therefrom that the co-purification of the two can be realized, indicating the purified 460 amino acids of the C-terminal of PA may form a stable complex with the GST-PB1 polypeptide.
Further, the PAC/PB1N polypeptide complex is separated and purified after using protease to cleave the GST fusion peptide and then used in a crystallization experiment to obtain a crystal under multiple conditions, wherein a well-diffracted crystal is obtained under one condition. However, the separately purified PA C-terminal protein fails to obtain a crystal, implying that the addition of PB1 polypeptide helps to stabilize the PA protein.
Three-Dimensional Structure of PAC/PB1N Polypeptide Complex
A method of MAD is used to analyze a crystal structure of a complex of PA C-terminal 460 amino acids and PB1 N-terminal 25 amino acids, wherein the resolution is 2.9 Angstrom, the finally corrected R factor is 23%, and the Rfree factor is 26%. In general, if the structure is indicated by lines, the PA part is, vividly speaking, like a wolf's head viewed from the side, which has an extruding mouth, a skull thereafter and a ringed neck (
Interaction Between PA and PB1 Polypeptide
Helixes binding to the PB1 polypeptide in domain I are helix 4 (406-415), 8 (582-604aa), (633-650aa), 11 (653-674aa), and 13 (698-714aa), wherein three helixes (8, 11, 13) extend outwards nearly in parallel to form a nearly right-angled triangle viewed from α helix axis direction, the fourth helix (10) extends obliquely, the PB1 polypeptide is interposed therebetween (
It is found from the results of analyzing the PA structure that a large groove (domain III) is provided at the conjunction of two domains below domain I (
RNA promoter binding capacity. In terms of the structure analyzed by the inventors, the inventors find that the large groove is a binding site for nucleotide or RNA, wherein the sites of K539, E538, and K328 are highly conserved across the three types of influenza viruses. The inventors deem that these amino acids are involved in binding to RNA nucleotide, especially in binding to RNA, indicating that the PA subunit plays an important role in binding to a promoter, RNA, and a process of RNA synthesis.
Between domain I and domain II, the helixes of domain I and the β sheets of domain II form a channel with a diameter of about 8 Angstrom to 15 Angstrom (
In a specific embodiment, there is provided in the present invention a polypeptide, a protein, an inorganic compound, or an organic compound competing with the influenza virus polymerase PB1 to bind to PAC, wherein the amino acid sequences of the polypeptide or protein contain a short LLFL motif of the short helix region formed by the PB1N residues 5 to 11 of wild type influenza virus polymerase PB1.
Herein, part of atoms between Met595 and Val12, between Leu666 and Phe9, between Leu640 and Leu8, between Leu636 and Leu8, between Met628 and Leu7, between Phe710 and Thr6, between Trp706 and Thr6, between Trp706 and Pro5, between Phe411 and Pro5, and between Trp706 and Asn4 are involved in interaction within the scope of 4 Angstrom. Therefore, it can be seen that they bind to one another by means of hydrophobic interaction. Thus, polypeptides or compounds involved in hydrophobic interaction with the corresponding amino acids of the C-terminal of PA can be used as medicaments for inhibiting influenza virus.
There are many successful examples for designing a medicament based on a structure of target protein (Schneider, G. and Fechner, U., Nature Reviews Drug Discovery 2005, 4, 649). The LigBuilder program developed by the research group set up by Professor Lu Hua from Peking University has more than 700 worldwide registration users (Wang, R. X.; Gao, Y.; Lai, L. H., LigBuilder: A multi-purpose program for structure-based drug design. J. Mol. Mod. 2000, 6, 498). Many examples has been reported of designing a highly active inhibitor successfully using the LigBuilder program, for example, the Boehringer Ingelheim pharmaceutical company uses LigBuilder 1.2 to access and implement aided design for optimizing a highly active kinase inhibitor (Goldberg D R, Hao, M-H., et al., J. Med. Chem. 2007, 50, 4016).
Novel medicament design and calculation is conducted using the LigBuilder 2.0 program according to the crystal structure of the PAC-PB1N complex of the H5N1 virus RNA polymerase. First, directed at the PAC protein, an analysis of binding sites is made, wherein two binding sites wining highest scores are located in the “mouth” region and the “channel” region of the structure. Novel medicament design and calculation for these two sites are conducted using the LigBuilder 2.0 program to obtain some easily-synthesized compounds with high prediction activity.
Molecules binding to the “channel” region of the PA molecules are exemplified as follows:
R1=—CH3, —CH2CH3
R2=—CH3, —CH2NH2, —CH(OH)CH3, —CH(CH3)2
Predicted Kd: 8.64 to 9.60
R1=—NH2
R2=—COCH3, —CH2COCH3, —CO, —OCH2CH3
R3=—CH2NH2, —CH2(NH2)CH2CH3, —CH2(NH2)CH2CH2CH3
Predicted Kd: 8.51 to 9.65
Molecules binding to the “mouth” region of the PA molecule are exemplified as follows:
R1=—OH
R2=—OH, —CO, —CONH2, —CONHCH3, COOH
R3=—COOH, —NH2, —C(NH2)2+
R4=—CH(OH)CH3, CONH2, CH(NH2)CH2OH
Predicted Kd: 8.52 to 8.96
R1=—OH, —NHCO
R2=—CH2(OH)CH3, —NHCH3, —CH2OH, —CH2NH2, —NH2, —C(NH2)2+
R3=—NH2, —C(NH2)2+, —CH2OH, —CO, —CH2CO, —NHCO
R4=—OH, —OCH3
Number | Date | Country | Kind |
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200810100840.X | Feb 2008 | CN | national |
200810083994.2 | May 2008 | CN | national |
Filing Document | Filing Date | Country | Kind | 371c Date |
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PCT/CN09/70498 | 2/22/2009 | WO | 00 | 11/4/2010 |