Structural dynamics of V3 loop with different electrostatics: Implications on co-receptor recognition: A molecular dynamics study of HIV gp120

Journal of Biomolecular Structure and Dynamics

Volumn 31, Issue 4, 2013, Pages 403-413

  Chandramouli, Balasubramanian ^a   Chillemi, Giovanni ^b   Giombini, Emanuela ^c   Capobianchi, Maria R ^c   Rozera, Gabriella ^c   Desideri, Alessandro ^a,b  

^a UNIVERSITY OF ROME TOR VERGATA   (Italy)

^b CASPUR   (Italy)

^c NATIONAL INSTITUTE FOR INFECTIOUS DISEASES L SPALLANZANI   (Italy)

Author keywords

CD4 binding; Gp120; Molecular dynamics; V3 loop

Indexed keywords

CD4 ANTIGEN; GLYCOPROTEIN GP 120;

ARTICLE; CLUSTER ANALYSIS; CORRELATION ANALYSIS; HUMAN IMMUNODEFICIENCY VIRUS; MOLECULAR DYNAMICS; MOLECULAR MODEL; MOLECULAR RECOGNITION; NONHUMAN; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN PROTEIN INTERACTION; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; STATIC ELECTRICITY; VIRUS STRAIN;

ANTIGENS, CD4; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; HIV ENVELOPE PROTEIN GP120; HIV INFECTIONS; HIV-1; HUMANS; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; RECEPTORS, CCR5; RECEPTORS, CXCR4; STATIC ELECTRICITY;

EID: 84879249367     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.2012.703068     Document Type: Article

References (53)

1. Arnold, K., Bordoli, L., Kopp, J., & Schwede, T. (2006). The SWISS-MODEL workspace: a Web-based environment for protein structure homology modelling. Bioinformatics, 22 (2), 195-201.
2. Baker, N.A., Sept, D., Joseph, S., Holst, M.J., & McCammon, J.A. (2001). Electrostatics of nanosystems: Application to microtubules and the ribosome. Proceedings of the National Academy of Sciences of the United States of America, 98(18), 10037-10041.
3. Berger, E.A., Doms, R.W., Fenyo, E.-M., Korber, B.T.M., Littman, D.R., Moore, J.P., ...Weiss, R.A. (1998). A new classification for HIV-1. Nature, 391(6664), 240.
4. Becker, O.M., Mackerell, A.D.Jr., Roux, B., & Watanabe, M. (2001). Computational biochemistry and biophysics (1st ed.). New York, NY: CRC Press.
5. Briggs, D.R., Tuttle, D.L., Sleasman, J.W., & Goodenow, M.M. (2000). Envelope V3 amino acid sequence predicts HIV-1 phenotype (co-receptor usage and tropism for macrophages). AIDS, 14(18), 2937-2939.
6. Catasti, P., Fontenot, J.D., Bradbury, E.M., & Gupta, G. (1995). Local and global structural properties of the HIVMN V3 loop. The Journal of Biological Chemistry, 270(5), 2224-2232.
7. Caves, L.S., Evanseck, J.D., & Karplus, M. (1998). Locally accessible conformations of proteins: Multiple molecular dynamics simulations of crambin. Protein Science: A Publication of the Protein Society, 7(3), 649-666.
8. Chandramouli, B., Chillemi, G., Abbate, I., Capobianchi, M.R., Rozera, G., & Desideri, A. (2012). Importance of V3 loop flexibility and net charge in the context of co-receptor recognition. A molecular dynamics study on HIV gp120. Journal of Biomolecular Structure & Dynamics, 29(5), 879-891.
9. Chillemi, G., Fiorani, P., Benedetti, P., & Desideri, A. (2003). Protein concerted motions in the DNA-human topoisomerase I complex. Nucleic Acids Research, 31(5), 1525-1535.
10. 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(17), 8953-8957.
11. Darden, T., York, D., & Pedersen, L. (1993). Particle mesh Ewald: An N [center-dot] log(N) method for Ewald sums in large systems. The Journal of Chemical Physics, 98(12), 10089-10092.
12. 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(11), 6777-6780.
13. Diskin, R., Marcovecchio, P.M., & Bjorkman, P.J. (2010). Structure of a clade C HIV-1 gp120 bound to CD4 and CD4-induced antibody reveals anti-CD4 polyreactivity. Nature Structural & Molecular Biology, 17(5), 608-613. doi: 10.1038/nsmb.1796.
14. Dybowski, J.N., Heider, D., & Hoffmann, D. (2010). Prediction of co-receptor usage of HIV-1 from genotype. PLoS Computational Biology, 6(4), e1000743.
15. Falconi, M., Stroppolo, M.E., Cioni, P., Strambini, G., Sergi, A., Ferrario, M., & Desideri, A. (2001). Dynamics-function correlation in Cu, Zn superoxide dismutase: a spectroscopic and molecular dynamics simulation study. Biophysical Journal, 80(6), 2556-2567.
16. Feig, M., Karanicolas, J., & Brooks, C.L.3rd. (2004). MMTSB tool set: Enhanced sampling and multiscale modeling methods for applications in structural biology. Journal of Molecular Graphics & Modelling, 22(5), 377-395.
17. 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(5), 3183-3187.
18. Galanakis, P.A., Spyroulias, G.A., Rizos, A., Samolis, P., & Krambovitis, E. (2005). Conformational properties of HIV- 1 gp120/V3 immunogenic domains. Current Medicinal Chemistry, 12(13), 1551-1568.
19. Groenink, M., Fouchier, R.A., Broersen, S., Baker, C.H., Koot, M., van't Wout, A.B., ...Schuitemaker, H. (1993). Relation of phenotype evolution of HIV-1 to envelope V2 configuration. Science, 260(5113), 1513-1516.
20. Hornak, V., Abel, R., Okur, A., Strockbine, B., Roitberg, A., & Simmerling, C. (2006). Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins, 65(3), 712-725.
21. Hsu, S.-T.D., & Bonvin, A.M.J.J. (2004). Atomic insight into the CD4 binding-induced conformational changes in HIV-1 gp120. Proteins, 55(3), 582-593.
22. 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(2), 359-375.
23. Huang, X., Bowman, G.R., Bacallado, S., & Pande, V.S. (2009). Rapid equilibrium sampling initiated from nonequilibrium data. Proceedings of the National Academy of Sciences of the United States of America, 106(47), 19765-19769.
24. Huang, C.-C., Lam, S.N., Acharya, P., Tang, M., Xiang, S.-H., Hussan, S.S.-U., ...Kwong, P.D. (2007). Structures of the CCR5 N terminus and of a tyrosine-sulfated antibody with HIV-1 gp120 and CD4. Science, 317(5846), 1930-1934.
25. Huang, C., Tang, M., Zhang, M.-Y., Majeed, S., Montabana, E., Stanfield, R.L., ...Kwong, P.D. (2005). Structure of a V3-containing HIV-1 gp120 core. Science, 310(5750), 1025-1028.
26. Huang, C., Venturi, M., Majeed, S., Moore, M.J., Phogat, S., Zhang, M.-Y., ...Kwong, P.D. (2004). Structural basis of tyrosine sulfation and VH-gene usage in antibodies that recognize the HIV type 1 coreceptor-binding site on gp120. Proceedings of the National Academy of Sciences of the United States of America, 101(9), 2706-2711.
27. Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14(1), 27, 28, 33-38.
28. Hunter, J. (2007). Matplotlib: A 2D graphics environment. Computing in Science and Engineering, 9(3), 90-95.
29. Izaguirre, J.A., Catarello, D.P., Wozniak, J.M., & Skeel, R.D. (2001). Langevin stabilization of molecular dynamics. The Journal of Chemical Physics, 114(5), 2090-2098.
30. Jensen, M.A., Coetzer, M., van 't Wout, A.B., Morris, L., & Mullins, J. I. (2006). A reliable phenotype predictor for human immunodeficiency virus type 1 subtype C based on envelope V3 sequences. Journal of Virology, 80(10), 4698-4704.
31. Jorgensen, W.L., Chandrasekhar, J., Madura, J.D., Impey, R.W., & Klein, M.L. (1983). Comparison of simple potential functions for simulating liquid water. The Journal of Chemical Physics, 79(2), 926.
32. Kumar, S., & Nussinov, R. (2002). Close-range electrostatic interactions in proteins. Chembiochem: A European Journal of Chemical Biology, 3(7), 604-617.
33. Kwong, P.D., Wyatt, R., Majeed, S., Robinson, J., Sweet, R. W., Sodroski, J., & Hendrickson, W.A. (2000). Structures of HIV-1 gp120 envelope glycoproteins from laboratoryadapted and primary isolates. Structure, 8(12), 1329-1339.
34. 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 (6686), 648-659.
35. Myszka, D.G., Sweet, R.W., Hensley, P., Brigham-Burke, M., Kwong, P.D., Hendrickson, W.A., ...Doyle, M.L. (2000). Energetics of the HIV gp120-CD4 binding reaction. Proceedings of the National Academy of Sciences of the United States of America, 97(16), 9026-9031.
36. Olshevsky, U., Helseth, E., Furman, C., Li, J., Haseltine, W., & Sodroski, J. (1990). Identification of individual human immunodeficiency virus type 1 gp120 amino acids important for CD4 receptor binding. Journal of Virology, 64(12), 5701-5707.
37. Pan, Y., Ma, B., Keskin, O., & Nussinov, R. (2004). Characterization of the conformational state and flexibility of HIV-1 glycoprotein gp120 core domain. The Journal of Biological Chemistry, 279(29), 30523-30530.
38. Pettersen, E.F., Goddard, T.D., Huang, C.C., Couch, G.S., Greenblatt, D.M., Meng, E.C., & Ferrin, T.E. (2004). UCSF chimera - a visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605-1612.
39. Pillai, S., Good, B., Richman, D., & Corbeil, J. (2003). A new perspective on V3 phenotype prediction. AIDS Research and Human Retroviruses, 19(2), 145-149.
40. Princen, K., & Schols, D. (2005). HIV chemokine receptor inhibitors as novel anti-HIV drugs. Cytokine & Growth Factor Reviews, 16(6), 659-677.
41. Prosperi, M.C.F., Fanti, I., Ulivi, G., Micarelli, A., De Luca, A., & Zazzi, M. (2009). Robust supervised and unsupervised statistical learning for HIV type 1 coreceptor usage analysis. AIDS Research and Human Retroviruses, 25(3), 305-314.
42. Regoes, R.R., & Bonhoeffer, S. (2005). The HIV coreceptor switch: A population dynamical perspective. Trends in Microbiology, 13(6), 269-277.
43. Resch, W., Hoffman, N., & Swanstrom, R. (2001). Improved success of phenotype prediction of the human immunodeficiency virus type 1 from envelope variable loop 3 sequence using neural networks. Virology, 288(1), 51-62.
44. Rosen, O., Sharon, M., Quadt-Akabayov, S.R., & Anglister, J. (2006). Molecular switch for alternative conformations of the HIV-1 V3 region: Implications for phenotype conversion. Proceedings of the National Academy of Sciences of the United States of America, 103(38), 13950-13955.
45. Ryckaert, J., Ciccotti, G., & Berendsen, H. (1977). Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. Journal of Computational Physics, 23(3), 327-341.
46. Sander, O., Sing, T., Sommer, I., Low, A.J., Cheung, P.K., Harrigan, P.R., ...Domingues, F.S. (2007). Structural descriptors of gp120 V3 loop for the prediction of HIV-1 coreceptor usage. PLoS Computational Biology, 3(3), e58.
47. Saphire, E.O., Parren, P.W., Pantophlet, R., Zwick, M.B., Morris, G.M., Rudd, P.M., ...Wilson, I.A. (2001). Crystal structure of a neutralizing human IGG against HIV-1: A template for vaccine design. Science, 293(5532), 1155-1159.
48. Scheib, H., Sperisen, P., & Hartley, O. (2006). HIV-1 coreceptor selectivity: Structural analogy between HIV-1 V3 regions and chemokine beta-hairpins is not the explanation. Structure, 14(4), 645-647, discussion 649-651.
49. Sharon, M., Kessler, N., Levy, R., Zolla-Pazner, S., Görlach, M., & Anglister, J. (2003). Alternative conformations of HIV-1 V3 loops mimic beta hairpins in chemokines, suggesting a mechanism for coreceptor selectivity. Structure, 11(2), 225-236.
50. Shioda, T., Levy, J.A., & Cheng-Mayer, C. (1992). Small amino acid changes in the V3 hypervariable region of gp120 can affect the T-cell-line and macrophage tropism of human immunodeficiency virus type 1. Proceedings of the National Academy of Sciences of the United States of America, 89(20), 9434-9438.
51. Smith, L.J., Daura, X., & van Gunsteren, W.F. (2002). Assessing equilibration and convergence in biomolecular simulations. Proteins, 48(3), 487-496.
52. Wang, N., Zhu, T., & Ho, D.D. (1995). Sequence diversity of V1 and V2 domains of gp120 from human immunodeficiency virus type 1: Lack of correlation with viral phenotype. Journal of Virology, 69(4), 2708-2715.
53. Zhou, T., Xu, L., Dey, B., Hessell, A.J., Van Ryk, D., Xiang, S.-H., ...Kwong, P.D. (2007). Structural definition of a conserved neutralization epitope on HIV-1 gp120. Nature, 445(7129), 732-737.