Structural insight into a novel human CCR5-V130I variant associated with resistance to HIV-1 infection

References

• Alkhatib, G., Combadiere, C., Broder, C. C., Feng, Y., Kennedy, P. E., Murphy, M., & Berger, E. A. (1996). CC CKR5: A RANTES, MIP-1alpha, MIP-1beta receptor as a fusion cofactor for macrophage-tropic HIV-1. Science, 272, 1955–1958.
   PubMed Web of Science ®Google Scholar
• Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990). Basic local alignment search tool. Journal of Molecular Biology, 215, 403–410.
   PubMed Web of Science ®Google Scholar
• Baldwin, J. M., Schertler, G. F. X., & Unger, V. M. (1997). An alpha-carbon template for the transmembrane helices in the rhodopsin family of G-protein-coupled receptors. Journal of Molecular Biology, 272, 144–164.
   PubMed Web of Science ®Google Scholar
• Bargagna-Mohan, P., Hamza, A., Kim, Y. E., Ho, Y. K. A., Mor-Valknin, N., Wendschlag, N., … Mohan, R. (2007). The tumor inhibitor and antiangiogenic agent withaferin A targets the intermediate filament protein vimentin. Chemistry & Biology, 14, 623–634.
   PubMed Web of Science ®Google Scholar
• Benson, D. A., Boguski, M. S., Lipman, D. J., Ostell, J., Ouellette, B. F. F., Rapp, B. A., & Wheeler, D. L. (1999). GenBank. Nucleic Acids Research, 27, 12–17.
   PubMed Web of Science ®Google Scholar
• Benton, P. A., Lee, D. R., & Kennedy, R. C. (1998). Sequence comparisons of non-human primate HIV-1 coreceptor homologues. Molecular Immunology, 35, 95–101.
   PubMedGoogle Scholar
• Berendsen, H. J. C., Postma, J. P. M., Vangunsteren, 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
• Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., & Hermans, J. (1981). Interaction models for water in relation to protein hydration. In B. Pullman (Ed.), Intermolecular forces (pp. 331–342). Dordrecht: D. Reidel.
   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
• Blanpain, C., Lee, B., Tackoen, M., Puffer, B., Boom, A., Libert, F., … Parmentier, M. (2000). Multiple nonfunctional alleles of CCR5 are frequent in various human populations. Blood, 96, 1638–1645.
   PubMed Web of Science ®Google Scholar
• Capoulade-Metay, C., Ma, L., Truong, L. X., Dudoit, Y., Versmisse, P., Nguyen, N. V., … Theodorou, I. (2004). New CCR5 variants associated with reduced HIV coreceptor function in southeast Asia. Aids, 18, 2243–2252.
   PubMedGoogle Scholar
• Carrington, M., Dean, M., Martin, M. P., & O’Brien, S. J. (1999). Genetics of HIV-1 infection: Chemokine receptor CCR5 polymorphism and its consequences. Human Molecular Genetics, 8, 1939–1945.
   PubMed Web of Science ®Google Scholar
• Choa, H., Huang, L. Y., Hamza, A., Gao, D. Q., Zhan, C. G., & Tai, H. H. (2006). Role of glutamine 148 of human 15-hydroxyprostaglandin dehydrogenase in catalytic oxidation of prostaglandin E-2. Bioorganic & Medicinal Chemistry, 14, 6486–6491.
   PubMed Web of Science ®Google Scholar
• Choe, H., Farzan, M., Sun, Y., Sullivan, N., Rollins, B., Ponath, P. D., … Sodroski, J. (1996). The beta-chemokine receptors CCR3 and CCR5 facilitate infection by primary HIV-1 isolates. Cell, 85, 1135–1148.
   PubMed Web of Science ®Google Scholar
• Dean, M., Carrington, M., Winkler, C., Huttley, G. A., Smith, M. W., Allikmets, R., … O’Brien, S. J. (1996). Genetic restriction of HIV-1 infection and progression to AIDS by a deletion allele of the CKR5 structural gene. Hemophilia Growth and Development Study, Multicenter AIDS Cohort Study, Multicenter Hemophilia Cohort Study, San Francisco City Cohort. ALIVE Study. Science, 273, 1856–1862.
   Google Scholar
• Deng, K., Liu, R., Ellmeier, W., Choe, S., Unutmaz, D., Burkhart, M., … Landau, R. (1996). Identification of a major co-receptor for primary isolates of HIV-1. Nature, 381, 661–666.
   PubMed Web of Science ®Google Scholar
• Dong, H. F., Wigmore, K., Carrington, M. N., Dean, M., Turpin, J. A., & Howard, O. M. (2005). Variants of CCR5, which are permissive for HIV-1 infection, show distinct functional responses to CCL3, CCL4 and CCL5. Genes and Immunity, 6, 609–619.
   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, 8577–8593.
   Web of Science ®Google Scholar
• Guex, N., & Peitsch, M. C. (1997). Swiss-Model and the Swiss-PdbViewer: An environment for comparative protein modelling. Electrophoresis, 18, 2714–2723.
   PubMed Web of Science ®Google Scholar
• Hamza, A., Wei, N.-N., Hao, C., Xiu, Z. & Zhan, C.-G. (2012). A novel and efficient ligand-based virtual screening approach using the HWZ scoring function and an enhanced shape-density model. Journal of Biomolecular Structure and Dynamics, 1–15.
   Google Scholar
• Hamza, A., Wei, N.-N., Johnson-Scalise, T., Naftolin, F., Cho, H., & Zhan, C.-G. (2012). Unveiling the unfolding pathway of F5F8D disorder-associated D81H/V100D Mutant of MCFD2 via multiple molecular dynamics simulations. Journal of Biomolecular Structure & Dynamics, 29, 699–714.
   PubMed Web of Science ®Google Scholar
• Hamza, A., Wei, N. N., & Zhan, C. G. (2012). Ligand-based virtual screening approach using a new scoring function. Journal of Chemical Information and Modeling, 52, 963–974.
   PubMed Web of Science ®Google Scholar
• Hess, B., Bekker, H., Berendsen, H. J. C., & Fraaije, J. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18, 1463–1472.
   Web of Science ®Google Scholar
• Hoffman, T. L., MacGregor, R. R., Burger, H., Mick, R., Doms, R. W., & Collman, R. G. (1997). CCR5 genotypes in sexually active couples discordant for human immunodeficiency virus type 1 infection status. Journal of Infectious Diseases, 176, 1093–1096.
   PubMedGoogle Scholar
• Horuk, R. (1994). Molecular properties of the chemokine receptor family. Trends in Pharmacological Sciences, 15, 159–165.
   PubMed Web of Science ®Google Scholar
• Horuk, R. (1999). Chemokine receptors and HIV-1: The fusion of two major research fields. Immunology Today, 20, 89–94.
   PubMedGoogle Scholar
• Howard, O. M., Shirakawa, A. K., Turpin, J. A., Maynard, A., Tobin, G. J., … Dean, M. (1999). Naturally occurring CCR5 extracellular and transmembrane domain variants affect HIV-1 Co-receptor and ligand binding function. Journal of Biological Chemistry, 274, 16228–16234.
   PubMed Web of Science ®Google Scholar
• Huttenrauch, F., Nitzki, A., Lin, F. T., Honing, S., & Oppermann, M. (2002). Beta-arrestin binding to CC chemokine receptor 5 requires multiple C-terminal receptor phosphorylation sites and involves a conserved Asp-Arg-Tyr sequence motif. Journal of Biological Chemistry, 277, 30769–30777.
   PubMed Web of Science ®Google Scholar
• Jlizi, A., Edouard, J., Fadhlaoui-Zid, K., Frigi, S., Debre, P., Slim, A., … Carpentier, W. (2007). Identification of the CCR5-Delta32 HIV resistance allele and new mutations of the CCR5 gene in different Tunisian populations. Human Immunology, 68, 993–1000.
   PubMed Web of Science ®Google Scholar
• Lagane, B., Ballet, S., Planchenault, T., Balabanian, K., Le Poul, E., Blanpain, C., … Bachelerie, F. (2005). Mutation of the DRY motif reveals different structural requirements for the CC chemokine receptor 5-mediated signaling and receptor endocytosis. Molecular Pharmacology, 67, 1966–1976.
   PubMed Web of Science ®Google Scholar
• Lindahl, E., Hess, B., & van der Spoel, D. (2001). GROMACS 3.0: A package for molecular simulation and trajectory analysis. Journal of Molecular Modeling, 7, 306–317.
   Web of Science ®Google Scholar
• Ma, L., Dudoit, Y., Tran, T., Xing, H., Chen, J., Pancino, G., … Capoulade-Metay, C. (2005). Biochemical and HIV-1 coreceptor properties of K26R, a new CCR5 Variant in China’s Sichuan population. Journal of Acquired Immune Deficiency Syndromes, 39, 38–43.
   PubMed Web of Science ®Google Scholar
• Marmor, M., Sheppard, H. W., Donnell, D., Bozeman, S., Celum, C., Buchbinder, S., … Seage, G. R. (2001). Homozygous and heterozygous CCR5-Delta32 genotypes are associated with resistance to HIV infection. Journal of Acquired Immune Deficiency Syndromes, 27, 472–481.
   PubMed Web of Science ®Google Scholar
• Oppermann, M. (2004). Chemokine receptor CCR5: Insights into structure, function, and regulation. Cellular Signalling, 16, 1201–1210.
   PubMed Web of Science ®Google Scholar
• Palczewski, K., Kumasaka, T., Hori, T., Behnke, C. A., Motoshima, H., Fox, B. A., … Miyano, M. (2000). Crystal structure of rhodopsin: A G protein-coupled receptor. Science, 289, 739–745.
   PubMed Web of Science ®Google Scholar
• Philpott, S., Weiser, B., Tarwater, P., Vermund, S. H., Kleeberger, C. A., Gange, S. J., … Burger, H. (2003). CC chemokine receptor 5 genotype and susceptibility to transmission of human immunodeficiency virus type 1 in women. Journal of Infectious Diseases, 187, 569–575.
   PubMedGoogle Scholar
• Regoes, R. R., & Bonhoeffer, S. (2005). The HIV coreceptor switch: A population dynamical perspective. Trends in Microbiology, 13, 269–277.
   PubMed Web of Science ®Google Scholar
• Rucker, J., Samson, M., Doranz, B. J., Libert, F., Berson, J. F., Yi, Y., … Parmentier, M. (1996). Regions in beta-chemokine receptors CCR5 and CCR2b that determine HIV-1 cofactor specificity. Cell, 87, 437–446.
   PubMed Web of Science ®Google Scholar
• Schuler, L. D., Daura, X., & Van Gunsteren, W. F. (2001). An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase. Journal of Computational Chemistry, 22, 1205–1218.
   Web of Science ®Google Scholar
• Schwede, T., Kopp, J., Guex, N., & Peitsch, M. C. (2003). SWISS-MODEL: An automated protein homology-modeling server. Nucleic Acids Research, 31, 3381–3385.
   PubMed Web of Science ®Google Scholar
• Shieh, B., Liau, Y. E., Yan, Y. P., Sun, H. S., Chen, M. Y., Liu, Y. C., … Li, C. (1999). Alleles that may influence HIV-1 pathogenesis in Chinese subjects. Aids, 13, 421–424.
   PubMed Web of Science ®Google Scholar
• Shioda, T., Nakayama, E. E., Tanaka, Y., Xin, X., Liu, H., Kawana-Tachikawa, A., … Iwamoto, A. (2001). Naturally occurring deletional mutation in the C-terminal cytoplasmic tail of CCR5 affects surface trafficking of CCR5. Journal of Virology, 75, 3462–3468.
   PubMed Web of Science ®Google Scholar
• Stambouli, N., Dridi, M., Wei, N.-N., Jlizi, A., Bouraoui, A., Hamza, A., & Ben Ammar Elgaaied, A. (2013). Structural insight into the binding complex: β-arrestin/CCR5. Journal of Biomolecular Structure & Dynamics. Available from: http://dx.doi.org/10.1080/07391102.2013.819297
   Google Scholar
• Wei, N.-N., Hamza, A., Hao, C., Johnson-Scalise, T., Xiu, Z., Naftolin, F., & Zhan, C.-G. (2012). Protein flexibility and conformational states of Leishmania antigen eIF-4A: Identification of a novel plausible protein adjuvant using comparative genomics and molecular modeling. Journal of Biomolecular Structure and Dynamics, 1–13.
   Google Scholar
• Zhang, T., Hamza, A., Cao, X. H., Wang, B., Yu, S. W., Zhan, C. G., & Sun, D. X. (2008). A novel Hsp90 inhibitor to disrupt Hsp90/Cdc37 complex against pancreatic cancer cells. Molecular Cancer Therapeutics, 7, 162–170.
   PubMed Web of Science ®Google Scholar
• Zhang, W., Sviripa, V., Chen, X., Shi, J., Yu, T., Hamza, A., … Liu, C. (2013). Fluorinated N,N-Dialkylaminostilbenes repress colon cancer by targeting methionine S-Adenosyltransferase 2A. ACS Chemical Biology, 8, 796–803.
   Google Scholar
• Zheng, B. J., Zhao, X. Y., Zhu, N. S., Chan, C. P., Wong, K. H., Chan, K. C., … Lee, S. S. (2002). Polymorphisms of CCR5 gene in a southern Chinese population and their effects on disease progression in HIV infections. Aids, 16, 2480–2482.
   PubMed Web of Science ®Google Scholar
• Zhou, M., Hamza, A., Zhan, C.-G., & Thorson, J. S. (2013). Assessing the regioselectivity of OleD-Catalyzed Glycosylation with a diverse set of acceptors. Journal of Natural Products, 76, 279–286.
   PubMed Web of Science ®Google Scholar
• Zhou, M., Hou, Y., Hamza, A., Zhan, C.-G., Bugni, T. S., & Thorson, J. S. (2012). Probing the regiospecificity of enzyme-catalyzed steroid glycosylation. Organic Letters, 14, 5424–5427.
   PubMed Web of Science ®Google Scholar
• Zhu, T., Mo, H., Wang, N., Nam, D. S., Cao, Y., Koup, R. A., & Ho, D. D. (1993). Genotypic and phenotypic characterization of HIV-1 patients with primary infection. Science, 261, 1179–1181.
   PubMed Web of Science ®Google Scholar