Discovery of novel anti-HIV-1 agents based on a broadly neutralizing antibody against the envelope gp120 V3 loop: a computational study

References

• Ablameyko, S. V., Abramov, S. M., Anishchanka, U. V., Medvedev, S. V., Paramonov, N. N., & Tchij, O. P. (2005). SKIF supercomputer configurations. Minsk: United Institute of Informatics Problems.
   Google Scholar
• Almond, D., Kimura, T., Kong, X., Swetnam, J., Zolla-Pazner, S., & Cardozo, T. (2010). Structural conservation predominates over sequence variability in the crown of HIV type 1’s V3 loop. AIDS Research and Human Retroviruses, 26, 717–723.
   PubMed Web of Science ®Google Scholar
• Anandakrishnan, R., Aguilar, B., & Onufriev, A. V. (2012). H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulation. Nucleic Acids Research, 40, W537–W541.
   PubMed Web of Science ®Google Scholar
• Andrianov, A. M. (2011). HIV-1 gp120 V3 loop for anti-AIDS drug discovery: Computer-aided approaches to the problem solving. Expert Opinion on Drug Discovery, 6, 419–435.
   PubMed Web of Science ®Google Scholar
• Andrianov, A. M., Anishchenko, I. V., & Tuzikov, A. V. (2011). Discovery of novel promising targets for anti-AIDS drug developments by computer modeling: application to the HIV-1 gp120 V3 loop. Journal of Chemical Information and Modeling, 51, 2760–2767.
   PubMed Web of Science ®Google Scholar
• Andrianov, A. M., Kornoushenko, Yu V, Anishchenko, I. V., Eremin, V. F., & Tuzikov, A. V. (2013). Structural analysis of the envelope gp120 V3 loop for some HIV-1 variants circulating in the countries of Eastern Europe. Journal of Biomolecular Structure and Dynamics, 31, 665–683.
   PubMed Web of Science ®Google Scholar
• Ballester, P. J., & Richards, W. G. (2007). Ultrafast shape recognition to search compound databases for similar molecular shapes. Journal of Computational Chemistry, 28, 1711–1723.
   PubMed Web of Science ®Google Scholar
• Basmaciogullari, S., Babcock, G. J., Van Ryk, D., Wojtowicz, W., & Sodroski, J. (2002). Identification of conserved and variable structures in the human immunodeficiency virus gp120 glycoprotein of importance for CXCR4 binding. Journal of Virology, 76, 10791–10800.
   PubMed Web of Science ®Google Scholar
• Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., DiNola, A., & Haak, J. R. (1984). Molecular dynamics with coupling to an external bath. Journal of Chemical Physics, 81, 3684–3690.
   Web of Science ®Google Scholar
• Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., … Bourne, P. E. (2000). The protein data bank. Nucleic Acids Research, 28, 235–242.
   PubMed Web of Science ®Google Scholar
• Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Brice, M. D., Rodgers, J. R., … Tasumi, M. (1977). The protein data bank. A computer-based archival file for macromolecular structures. Journal of Molecular Biology, 112, 535–542.
   PubMed Web of Science ®Google Scholar
• Binley, J. M., Lybarger, E. A., Crooks, E. T., Seaman, M. S., Gray, E., Davis, K. L., … Mascola, J. R. (2008). Profiling the specificity of neutralizing antibodies in a large panel of plasmas from patients chronically infected with human immunodeficiency virus type 1 subtypes B and C. Journal of Virology, 82, 11651–11668.
   PubMed Web of Science ®Google Scholar
• Bou-Habib, D. C., Roderiquez, G., Oravecz, T., Berman, P. W., Lusso, P., & Norcross, M. A. (1994). Cryptic nature of envelope V3 region epitopes protects primary monocytotropic human immunodeficiency virus type 1 from antibody neutralization. Journal of Virology, 68, 6006–6013.
   PubMed Web of Science ®Google Scholar
• Burke, V. J., Kim, S., Williams, C., Gorny, M. K., Zolla-Pazner, S., & Kong, X. (2008). Structural characterization of neutralizing human anti-V3 monoclonal antibodies 3074 and 268-D. AIDS Research & Human Retroviruses, 24, 46.
   Web of Science ®Google Scholar
• Case, D. A., Darden, T. A., Cheatham, T. E., Simmerling, C. L., Wang, J., Duke, R. E., … Kollman, P. A. (2010). AMBER 11. San Francisco: University of California.
   Google Scholar
• Cavacini, L. A., Duval, M., Robinson, J., & Posner, M. R. (2002). Interactions of human antibodies, epitope exposure, antibody binding and neutralization of primary isolate HIV-1 virions. AIDS, 16, 2409–2417.
   Google Scholar
• Chesebro, B., Wehrly, K., Nishio, J., & Perryman, S. (1992). Macrophage-tropic human immunodeficiency virus isolates from different patients exhibit unusual V3 envelope sequence homogeneity in comparison with T-cell-tropic isolates: Definition of critical amino acids involved in cell tropism. Journal of Virology, 66, 6547–6554.
   PubMed Web of Science ®Google Scholar
• Cormier, E. G., & Dragic, T. (2002). The crown and stem of the V3 loop play distinct roles in human immunodeficiency virus type 1 envelope glycoprotein interactions with the CCR5 coreceptor. Journal of Virology, 76, 8953–8957.
   PubMed Web of Science ®Google Scholar
• Cormier, E. G., Tran, D. N., Yukhayeva, L., Olson, W. C., & Dragic, T. (2001). Mapping the determinants of the CCR5 amino-terminal sulfopeptide interaction with soluble human immunodeficiency virus type 1 gp120–CD4 complexes. Journal of Virology, 75, 5541–5549.
   PubMed Web of Science ®Google Scholar
• Del Prete, G. Q., Leslie, G. J., Haggarty, B., Jordan, A. P., Romano, J., & Hoxie, J. A. (2010). Distinct molecular pathways to X4 tropism for a V3-truncated human immunodeficiency virus type 1 lead to differential coreceptor interactions and sensitivity to a CXCR4 antagonist. Journal of Virology, 84, 8777–8789.
   PubMed Web of Science ®Google Scholar
• De Jong, J.-J., De Ronde, A., Keulen, W., Tersmette, M., & Goudsmit, J. (1992). Minimal requirements for the human immunodeficiency virus type 1 V3 domain to support the syncytium-inducing phenotype: Analysis by single amino acid substitution. Journal of Virology, 66, 6777–6780.
   PubMed Web of Science ®Google Scholar
• Durrant, J. D., & McCammon, J. A. (2011). BINANA: A novel algorithm for ligand-binding characterization. Journal of Molecular Graphics and Modelling, 29, 888–893.
   PubMed Web of Science ®Google Scholar
• Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., & Pedersen, L. G. (1995). A smooth particle mesh Ewald method. Journal of Chemical Physics, 103, 8577–8592.
   Web of Science ®Google Scholar
• Floris, M., Masciocchi, J., Fanton, M., & Moro, S. (2011). Swimming into peptidomimetic chemical space using pepMMsMIMIC. Nucleic Acids Research, 39, W261–W269.
   PubMed Web of Science ®Google Scholar
• Fouchier, R. A., Groenink, M., Kootstra, N. A., Tersmette, M., Huisman, H. G., Miedema, F., & Schuitemaker, H. (1992). Phenotype-associated sequence variation in the third variable domain of the human immunodeficiency virus type 1 gp120 molecule. Journal of Virology, 66, 3183–3187.
   PubMed Web of Science ®Google Scholar
• Freed, E. O., Myers, D. J., & Risser, R. (1991). Identification of the principal neutralizing determinant of human immunodeficiency virus type 1 as a fusion domain. Journal of Virology, 65, 190–194.
   PubMed Web of Science ®Google Scholar
• Gorny, M. K., Williams, C., Volsky, B., Revesz, K., Wang, X.-H., Burda, S., … Zolla-Pazner, S. (2006). Cross-clade neutralizing activity of human anti-V3 monoclonal antibodies derived from the cells of individuals infected with non-B clades of human immunodeficiency virus type 1. Journal of Virology, 80, 6865–6872.
   PubMed Web of Science ®Google Scholar
• Goudsmit, J., Debouck, C., Meloen, R. H., Smit, L., Bakker, M., Asher, D. M., … Gajdusek, D. C. (1988). Human immunodeficiency virus type 1 neutralization epitope with conserved architecture elicits early type-specific antibodies in experimentally infected chimpanzees. Proceedings of the National Academy of Sciences USA, 85, 4478–4482.
   PubMed Web of Science ®Google Scholar
• Gray, E. S., Madiga, M. C., Hermanus, T., Moore, P. L., Wibmer, C. K., Tumba, N. L., … CAPRISA002 Study Team (2011). HIV-1 neutralization breadth develops incrementally over 4 years and is associated with CD4+ T cell decline and high viral load during acute infection. Journal of Virology, 85, 4828–4840.
   PubMed Web of Science ®Google Scholar
• Grimaila, R. J., Fuller, B. A., Rennert, P. D., Nelson, M. B., Hammarskjöld, M. L., Potts, B., … Gray, G. (1992). Mutations in the principal neutralization determinant of human immunodeficiency virus type 1 affect syncytium formation, virus infectivity, growth kinetics, and neutralization. Journal of Virology, 66, 1875–1883.
   PubMed Web of Science ®Google Scholar
• Hartley, O., Klasse, P. J., Sattentau, Q. J., & Moore, J. P. (2005). V3: HIV’s switch-hitter. AIDS Research and Human Retroviruses, 21, 171–189.
   PubMed Web of Science ®Google Scholar
• Hioe, C. E., Wrin, T., Seaman, M. S., Yu, X., Wood, B., Self, S., … Zolla-Pazner, S. (2010). Anti-V3 monoclonal antibodies display broad neutralizing activities against multiple HIV-1 subtypes. PLoS ONE, 5, e10254.
   PubMed Web of Science ®Google Scholar
• Hoffman, T. L., LaBranche, C. C., Zhang, W., Canziani, G., Robinson, J., Chaiken, I., … Doms, R. W. (1999). Stable exposure of the coreceptor-binding site in a CD4-independent HIV-1 envelope protein. Proceedings of the National Academy of Sciences USA, 96, 6359–6364.
   PubMed Web of Science ®Google Scholar
• Hoxie, J. A. (2010). Toward an antibody-based HIV-1. The Annual Review of Medicine, 61, 135–152.
   PubMed Web of Science ®Google Scholar
• Hu, Q., Trent, J. O., Tomaras, G. D., Wang, Z., Murray, J. L., Conolly, S. M., … Peiper, S. C. (2000). Identification of Env determinants in V3 that influence the molecular anatomy of CCR5 utilization. Journal of Molecular Biology, 302, 359–375.
   PubMed Web of Science ®Google Scholar
• Huang, C. C., Lam, S. N., Acharya, P., Tang, M., Xiang, S. H., Hussan, S. S., Stanfield, R. L., … Kwong, P. D. (2007). Structures of the CCR5 N terminus and of a tyrosine-sulfated antibody with HIV-1 gp120 and CD4. Science, 317, 1930–1934.
   PubMed Web of Science ®Google Scholar
• Hwang, S. S., Boyle, T. J., Lyerly, H. K., & Cullen, B. R. (1992). Identification of envelope V3 loop as the major determinant of CD4 neutralization sensitivity of HIV-1. Science, 257, 535–537.
   Google Scholar
• Ivanoff, L. A., Dubay, J. W., Morris, J. F., Roberts, S. J., Gutshall, L., Sternberg, E. J., … Petteway, S. R., Jr. (1992). V3 loop region of the HIV-1 gp120 envelope protein is essential for virus infectivity. Virology, 187, 423–432.
   PubMed Web of Science ®Google Scholar
• Ivanoff, L. A., Looney, D. J., McDanal, C., Morris, J. F., Wong-Staal, F., Langlois, A. J., … Matthews, T. J. (1991). Alteration of HIV-1 infectivity and neutralization by a single amino acid replacement in the V3 loop domain. AIDS Research and Human Retroviruses, 7, 595–603.
   PubMed Web of Science ®Google Scholar
• Javaherian, K., Langlois, A. J., McDanal, C., Ross, K. L., Eckler, L. I., Jellis, C. L., … Putney, S. D. (1989). Principal neutralizing domain of the human immunodeficiency virus type 1 envelope protein. Proceedings of the National Academy of Sciences USA, 86, 6768–6772.
   PubMed Web of Science ®Google Scholar
• Jiang, X., Burke, V., Totrov, M., Williams, C., Cardozo, T., Gorny, M. K., … Kong, X. P. (2010). Conserved structural elements in the V3 crown of HIV-1 gp120. Nature Structural & Molecular Biology, 17, 955–961.
   PubMed Web of Science ®Google Scholar
• Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., & Klein, M. L. (1983). Comparison of simple potential functions for simulating liquid water. Journal of Chemical Physics, 79, 926–935.
   Web of Science ®Google Scholar
• Karnachi, P., & Kulkarni, A. (2006). In T. Langer, & R. D. Hoffmann (Eds.), Pharmacophores and pharmacophore searches. Weinheim: Wiley-VCH.
   Google Scholar
• Kato, K., Sato, H., & Takebe, Y. (1999). Role of naturally occurring basic amino acid substitutions in the human immunodeficiency virus type 1 subtype E envelope V3 loop on viral coreceptor usage and cell tropism. Journal of Virology, 73, 5520–5526.
   PubMed Web of Science ®Google Scholar
• Kirkpatrick, K. S., Gelatt, C. D., & Vecchi, M. P. (1983). Optimization by simulated annealing. Science, 220, 671–680.
   PubMed Web of Science ®Google Scholar
• Kwong, P. D., Mascola, J. R., & Nabel, G. J. (2011). Rational design of vaccines to elicit broadly neutralizing antibodies to HIV-1. Cold Spring Harbor Perspectives in Medicine, 1, a007278.
   PubMed Web of Science ®Google Scholar
• Kwong, P. D., Wyatt, R., Robinson, J., Sweet, R. W., Sodroski, J., & Hendrickson, W. A. (1998). Structure of an HIV gp120 envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody. Nature, 393, 648–659.
   PubMed Web of Science ®Google Scholar
• LaRosa, G. J., Davide, J. P., Weinhold, K., Waterbury, J. A., Profy, A. T., Lewis, J. A. … Putney, S. D. (1990). Conserved sequence and structural elements in the HIV-1 principal neutralizing determinant. Science, 249, 932–935.
   PubMed Web of Science ®Google Scholar
• Lindorff-Larsen, K., Piana, S., Palmo, K., Maragakis, P., Klepeis, J. L., Dror, R. O., & Shaw, D. E. (2010). Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins, 78, 1950–1958.
   PubMed Web of Science ®Google Scholar
• Liu, L., Cimbro, R., Lusso, P., & Berger, E. A. (2011). Intraprotomer masking of third variable loop (V3) epitopes by the first and second variable loops (V1V2) within the native HIV-1 envelope glycoprotein trimer. Proceedings of the National Academy of Sciences USA, 108, 20148–20153.
   PubMed Web of Science ®Google Scholar
• Lusso, P., Earl, P. L., Sironi, F., Santoro, F., Ripamonti, C., Scarlatti, G., … Burastero, S. E. (2005). Cryptic nature of a conserved, CD4-inducible V3 loop neutralization epitope in the native envelope glycoprotein oligomer of CCR5-restricted, but not CXCR4-using, primary human immunodeficiency virus type 1 strains. Journal of Virology, 79, 6957–6968.
   PubMed Web of Science ®Google Scholar
• Malenbaum, S. E., Yang, D., Cavacini, L., Posner, M., Robinson, J., & Cheng-Mayer, C. (2000). The N-terminal V3 loop glycan modulates the interaction of clade A and B human immunodeficiency virus type 1 envelopes with CD4 and chemokine receptors. Journal of Virology, 74, 11008–11013.
   PubMed Web of Science ®Google Scholar
• Masciocchi, J., Frau G., Fanton, M., Sturlese M., Floris, M., Pireddu, L., … Moro, S. (2009). MMsINC: A large-scale chemoinformatics database. Nucleic Acids Research, 37, D284–D290.
   PubMed Web of Science ®Google Scholar
• Mason, J. S., Morize, I., Menard, P. R., Cheney, D. L., Hulme, C., & Labaudiniere, R. F. (1999). New 4-point pharmacophore method for molecular similarity and diversity applications: overview of the method and applications, including a novel approach to the design of combinatorial libraries containing privileged substructures. Journal of Medicinal Chemistry, 42, 3251–3264.
   PubMed Web of Science ®Google Scholar
• Massova, I., & Kollman, P. A. (1999). Computational alanine scanning to probe protein-protein interactions: a novel approach to evaluate binding free energies. Journal of the American Chemical Society, 121, 8133–8143.
   Web of Science ®Google Scholar
• McCoy, L. E., & Weiss, R. A. (2013). Neutralizing antibodies to HIV-1 induced by immunization. The Journal of Experimental Medicine, 210, 209–223.
   PubMed Web of Science ®Google Scholar
• Milich, L., Margolin, B., & Swanstrom, R. (1993). V3 loop of the human immunodeficiency virus type 1 Env protein: interpreting sequence variability. Journal of Virology, 67, 5623–5634.
   PubMed Web of Science ®Google Scholar
• Milich, L., Margolin, B. H., & Swanstrom, R. (1997). Patterns of amino acid variability in NSI-like and SI-like V3 sequences and a linked change in the CD4-binding domain of the HIV-1 Env protein. Virology, 239, 108–118.
   PubMedGoogle Scholar
• Naganawa, S., Yokoyama, M., Shiino, T., Suzuki, T., Ishigatsubo, Y., Ueda, A., … Sato, H. (2008). Net positive charge of HIV-1 CRF01_AE V3 sequence regulates viral sensitivity to humoral immunity. PLoS One, 3, e3206.
   PubMed Web of Science ®Google Scholar
• Piantadosi, A., Panteleeff, D., Blish, C. A., Baeten, J. M., Jaoko, W., McClelland, R. S., & Overbaugh, J. (2009). HIV-1 neutralizing antibody breadth is affected by factors early in infection, but does not influence disease progression. Journal of Virology, 83, 10269–10274.
   PubMed Web of Science ®Google Scholar
• Ruche, F., Robinson, J. E., Morris, L., Shaw, G. M., Montefiori, D. C., & Mascola, J. R. (2008). Profiling the specificity of neutralizing antibodies in a large panel of plasmas from patients chronically infected with human immunodeficiency virus type 1 subtypes B and C. Journal of Virology, 82, 11651–11668.
   PubMed Web of Science ®Google Scholar
• Rusert, P., Krarup, A., Magnus, C., Brandenberg, O. F., Weber, J., Ehlert, A.-K., … Trkola, A. (2011). Interaction of the gp120 V1V2 loop with a neighboring gp120 unit shields the HIV envelope trimer against cross-neutralizing antibodies. The Journal of Experimental Medicine, 208, 1419–1433.
   PubMed Web of Science ®Google Scholar
• Ryckaert, J. P., Ciccotti, G., & Berendsen, H. J. C. (1977). Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. Journal of Computational Physics, 23, 327–341.
   Web of Science ®Google Scholar
• Sather, D. N., Armann, J., Ching, L. K., Mavrantoni, A., Sellhorn, G., Caldwell, Z., … Stamatatos, L. (2009). Factors associated with the development of cross-reactive neutralizing antibodies during human immunodeficiency virus type 1 infection. Journal of Virology, 83, 757–769.
   PubMed Web of Science ®Google Scholar
• Scheid, J. F., Mouquet, H., Feldhahn, N., Seaman, M. S., Velinzon, K., Pietzsch, J., … Nussenzweig, M. C. (2009). Broad diversity of neutralizing antibodies isolated from memory B cells in HIV-infected individuals. Nature, 458, 636–640.
   PubMed Web of Science ®Google Scholar
• Shimizu, N., Haraguchi, Y., Takeuchi, Y., Soda, Y., Kanbe, K., & Hoshino, H. (1999). Changes in and discrepancies between cell tropisms and coreceptor uses of human immunodeficiency virus type 1 induced by single point mutations at the V3 tip of the env protein. Virology, 259, 324–333.
   Google Scholar
• Shioda, T., Oka, S., Ida, S., Nokihara, K., Toriyoshi, H., Mori, S., … Nagai, Y. (1994). A naturally occurring single basic amino acid substitution in the V3 region of the human immunodeficiency virus type 1 env protein alters the cellular host range and antigenic structure of the virus. Journal of Virology, 68, 7689–7696.
   PubMed Web of Science ®Google Scholar
• Simek, M. D., Rida, W., Priddy, F. H., Pung, P., Carrow, E., Laufer, D. S., … Koff, W. C. (2009). Human immunodeficiency virus type 1 elite neutralizers: individuals with broad and potent neutralizing activity identified by using a high-throughput neutralization assay together with an analytical selection algorithm. Journal of Virology, 83(14), 7337–7348.
   PubMed Web of Science ®Google Scholar
• Sirois, S., Sing, T., & Chou, K. C. (2005). HIV-1 gp120 V3 loop for structure-based drug design. Current Protein & Peptide Science, 6, 413–422.
   PubMed Web of Science ®Google Scholar
• Sirois, S., Touaibia, M., Chou, K. C., & Roy, R. (2007). Glycosylation of HIV-1 gp120 V3 loop: towards the rational design of a synthetic carbohydrate vaccine. Current Medicinal Chemistry, 14, 3232–3242.
   PubMed Web of Science ®Google Scholar
• Speck, R. F., Wehrly, K., Platt, E. J., Atchison, R. E., Charo, I. F., Kabat, D., … Goldsmith, M. A. (1997). Selective employment of chemokine receptors as human immunodeficiency virus type 1 coreceptors determined by individual amino acids within the envelope V3 loop. Journal of Virology, 71, 7136–7139.
   PubMed Web of Science ®Google Scholar
• Swetnam, J., Shmelkov, E., Zolla-Pazner, S., & Cardozo, T. (2010). Comparative magnitude of cross-strain conservation of HIV variable loop neutralization epitopes. PLoS One, 5, e15994.
   PubMedGoogle Scholar
• Takeuchi, Y., Akutsu, M., Murayama, K., Shimizu, N., & Hoshino, H. (1991). Host range mutant of human immunodeficiency virus type 1: modification of cell tropism by a single point mutation at the neutralization epitope in the env gene. Journal of Virology, 65, 1710–1718.
   PubMed Web of Science ®Google Scholar
• Tian, H., Lan, C., & Chen, Y. H. (2002). Sequence variation and consensus sequence of V3 loop on HIV-1 gp120. Immunology Letters, 83, 231–233.
   PubMed Web of Science ®Google Scholar
• Trott, O., & Olson, A. J. (2010). AutoDock VINA: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading. Journal of Computational Chemistry, 31, 455–461.
   PubMed Web of Science ®Google Scholar
• Vogel, T., Kurth, R., & Norley, S. (1994). The majority of neutralizing Abs in HIV-1-infected patients recognize linear V3 loop sequences. Studies using HIV-1 MN multiple antigenic peptides. The Journal of Immunology, 153, 1895–1904.
   PubMed Web of Science ®Google Scholar
• Walker, L. M., & Burton, D. R. (2010). Rational antibody-based HIV-1 vaccine design: current approaches and future directions. Current Opinion in Immunology, 22, 358–366.
   PubMed Web of Science ®Google Scholar
• Wang, J., Wolf, R. M., Caldwell, J. W., Kollmann, P. A., & Case, D. A. (2004). Development and testing of a general amber force field. Journal of Computational Chemistry, 25, 1157–1174.
   PubMed Web of Science ®Google Scholar
• Willey, R. L., Martin, M. A., & Peden, K. W. (1994). Increase in soluble CD4 binding to and CD4-induced dissociation of gp120 from virions correlates with infectivity of human immunodeficiency virus type 1. Journal of Virology, 68, 1029–1039.
   PubMed Web of Science ®Google Scholar
• Willey, R. L., Theodore, T. S., & Martin, M. A. (1994). Amino acid substitutions in the human immunodeficiency virus type 1 gp120 V3 loop that change viral tropism also alter physical and functional properties of the virion envelope. Journal of Virology, 68, 4409–4419.
   PubMed Web of Science ®Google Scholar
• Wolk, T., & Schreiber, M. (2006). N-glycans in the gp120 V1/V2 domain of the HIV-1 strain NL4-3 are indispensable for viral infectivity and resistance against antibody neutralization. Medical Microbiology & Immunology, 195, 165–172.
   PubMed Web of Science ®Google Scholar
• Wu, L., Gerard, N. P., Wyatt, R., Choe, H., Parolin, C., Ruffing, N., … Sodroski, J. (1996). CD4-induced interaction of primary HIV-1 gp120 glycoproteins with the chemokine receptor CCR-5. Nature, 384, 179–183.
   PubMed Web of Science ®Google Scholar
• Wyatt, R., & Sodroski, J. (1998). The HIV-1 envelope glycoproteins: fusogens, antigens, and immunogens. Science, 280, 1884–1888.
   PubMed Web of Science ®Google Scholar
• Xiang, S.-H., Finzi, A., Pacheco, B., Alexander, K., Yuan, W., Rizzuto, C., … Sodroski, J. (2010). A V3 loop-dependent gp120 element disrupted by CD4 binding stabilizes the human immunodeficiency virus envelope glycoprotein trimer. Journal of Virology, 84, 3147–3161.
   Google Scholar
• Yokoyama, M., Naganawa, S., Yoshimura, K., Matsushita, S., & Sato, H. (2012). Structural dynamics of HIV1 envelope gp120 outer domain with V3 loop. PLoS One, 7, e37530.
   Google Scholar