The molecular mechanism of two coreceptor binding site antibodies X5 and 17b neutralizing HIV-1: Insights from molecular dynamics simulation

Chemical Biology and Drug Design

Volumn 92, Issue 1, 2018, Pages 1357-1365

  Zhang, Yan ^a,b,c   Guo, Jingjing ^d   Huang, Le ^a   Tian, Jiaqi ^a   Yao, Xiaojun ^c   Liu, Huanxiang ^a,c  

^a LANZHOU UNIVERSITY   (China)

^b GUIYANG COLLEGE OF TRADITIONAL CHINESE MEDICINE   (China)

^c LANZHOU UNIVERSITY   (China)

^d HENAN NORMAL UNIVERSITY   (China)

Author keywords

17b; gp120; HIV 1; molecular dynamics simulation; X5

Indexed keywords

17B ANTIBODY; CD4 ANTIBODY; GLYCOPROTEIN GP 120; HUMAN IMMUNODEFICIENCY VIRUS ANTIBODY; NEUTRALIZING ANTIBODY; UNCLASSIFIED DRUG; X5 ANTIBODY; CD4 ANTIGEN; PROTEIN BINDING;

AMINO TERMINAL SEQUENCE; ANTIBODY COMBINING SITE; ANTIBODY STRUCTURE; ANTIGEN ANTIBODY COMPLEX; ANTIGEN BINDING; ARTICLE; CONFORMATIONAL TRANSITION; HEAVY CHAIN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS 1 INFECTION; LIGHT CHAIN; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; NONHUMAN; PRIORITY JOURNAL; BINDING SITE; CHEMISTRY; HUMAN; IMMUNOLOGY; METABOLISM; PRINCIPAL COMPONENT ANALYSIS; PROTEIN TERTIARY STRUCTURE;

ANTIBODIES, NEUTRALIZING; BINDING SITES; CD4 ANTIGENS; HIV ENVELOPE PROTEIN GP120; HIV-1; HUMANS; MOLECULAR DYNAMICS SIMULATION; PRINCIPAL COMPONENT ANALYSIS; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY;

EID: 85047463449     PISSN: 17470277     EISSN: 17470285     Source Type: Journal    
DOI: 10.1111/cbdd.13201     Document Type: Article

References (46)

1. P. Piot, S. S. A. Karim, R. Hecht, H. Legido-Quigley, K. Buse, J. Stover, S. Resch, T. Ryckman, S. Møgedal, M. Dybul, The Lancet 2015, 386, 171.
2. G. Dalgleish, P. Beverley, P. R. Clapham, D. H. Crawford, M. F. Greaves, R. A. Weiss, Nature 1983, 312, 763.
3. N. T. Freund, J. A. Horwitz, L. Nogueira, S. A. Sievers, L. Scharf, J. F. Scheid, A. Gazumyan, C. Liu, K. Velinzon, A. Goldenthal, PLoS Pathog. 2015, 11, e1005238.
4. E. O. Freed, M. A. Martin, J. Biol. Chem. 1995, 270, 23883.
5. K. N. Kirschner, A. B. Yongye, S. M. Tschampel, J. González-Outeiriño, C. R. Daniels, B. L. Foley, R. J. Woods, J. Comput. Chem. 2008, 29, 622.
6. H. Choe, M. Farzan, Y. Sun, N. Sullivan, B. Rollins, P. D. Ponath, L. Wu, C. R. Mackay, G. LaRosa, W. Newman, Cell 1996, 85, 1135.
7. M. O. McClure, Q. J. Sattentau, P. C. Beverley, J. P. Hearn, A. K. Fitzgerald, A. J. Zuckerman, R. A. Weiss, Nature 1987, 330, 487.
8. B. Davis, I. Dikic, D. Unutmaz, C. M. Hill, J. Arthos, M. A. Siani, D. A. Thompson, J. Schlessinger, D. R. Littman, J. Exp. Med. 1997, 186, 1793.
9. R. A. Furuta, C. T. Wild, Y. Weng, C. D. Weiss, Nat. Struct. Mol. Biol. 1998, 5, 276.
10. A. Finzi, S.-H. Xiang, B. Pacheco, L. Wang, J. Haight, A. Kassa, B. Danek, M. Pancera, P. D. Kwong, J. Sodroski, Mol. Cell 2010, 37, 656.
11. G. K. Nikolopoulos, E.-G. Kostaki, D. Paraskevis, Infect. Genet. Evol. 2016, 46, 256.
12. M. E. Curlin, R. Zioni, S. E. Hawes, Y. Liu, W. Deng, G. S. Gottlieb, T. Zhu, J. I. Mullins, PLoS Pathog. 2010, 6, e1001228.
13. R. Wyatt, P. D. Kwong, E. Desjardins, R. W. Sweet, J. Robinson, W. A. Hendrickson, J. G. Sodroski, Nature 1998, 393, 705.
14. P. D. Kwong, R. Wyatt, J. Robinson, R. W. Sweet, J. Sodroski, W. A. Hendrickson, Nature 1998, 393, 648.
15. T. Zhou, I. Georgiev, X. Wu, Z. Y. Yang, K. Dai, A. Finzi, Y. Do Kwon, J. F. Scheid, W. Shi, L. Xu, Y. Yang, J. Zhu, M. C. Nussenzweig, J. Sodroski, L. Shapiro, G. J. Nabel, J. R. Mascola, P. D. Kwong, Science 2010, 329, 811.
16. R. Burton, P. Poignard, R. L. Stanfield, I. A. Wilson, Science 2012, 337, 183.
17. F. Klein, H. Mouquet, P. Dosenovic, J. F. Scheid, L. Scharf, M. C. Nussenzweig, Science 2013, 341, 1199.
18. J. R. Mascola, B. F. Haynes, Immunol. Rev. 2013, 254, 225.
19. X. Wu, X.-P. Kong, Curr. Opin. Immunol. 2016, 42, 56.
20. C.-C. Huang, M. Tang, M.-Y. Zhang, S. Majeed, E. Montabana, R. L. Stanfield, D. S. Dimitrov, B. Korber, J. Sodroski, I. A. Wilson, Science 1025, 2005, 310.
21. H. Tan, A. Rader, Proteins: Struct. Funct. Bioinform. 2009, 74, 881.
22. M.-Y. Zhang, A. R. Borges, R. G. Ptak, Y. Wang, A. S. Dimitrov, S. M. Alam, L. Wieczorek, P. Bouma, T. Fouts, S. Jiang, V. R. Polonis, B. F. Haynes, G. V. Quinnan, D. C. Montefiori, D. S. Dimitrov, mAbs. 2010, 2, 266.
23. T. Hou, R. Yu, J. Med. Chem. 2007, 50, 1177.
24. N. Li, R. I. Ainsworth, B. Ding, T. Hou, W. Wang, J. Chem. Inf. Model. 2015, 55, 1400.
25. W. Xue, X. Jin, L. Ning, M. Wang, H. Liu, X. Yao, J. Chem. Inf. Model. 2013, 53, 210.
26. W. Xue, H. Liu, X. Yao, J. Comput. Chem. 2012, 33, 527.
27. E. Kortkhonjia, R. Brandman, J. Z. Zhou, V. A. Voelz, I. Chorny, B. Kabakoff, T. W. Patapoff, K. A. Dill, T. E. Swartz, mAbs 2013, 5, 306.
28. V. Hornak, R. Abel, A. Okur, B. Strockbine, A. Roitberg, C. Simmerling, Proteins: Struct. Funct. Bioinform. 2006, 65, 712.
29. W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, M. L. Klein, J. Chem. Phys. 1983, 79, 926.
30. H. J. Berendsen, J. P. M. Postma, W. F. van Gunsteren, A. DiNola, J. Haak, J. Chem. Phys. 1984, 81, 3684.
31. J.-P. Ryckaert, G. Ciccotti, H. J. Berendsen, J. Comput. Phys. 1977, 23, 327.
32. U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee, L. G. Pedersen, J. Chem. Phys. 1995, 103, 8577.
33. A. Sethi, J. Eargle, A. A. Black, Z. Luthey-Schulten, Proc. Natl. Acad. Sci. U. S. A. 2009, 106, 6620.
34. J. Earqle, Z. Luthey-Schulten, Bioinformatics 2012, 28, 3000.
35. M. Guttman, M. Kahn, N. K. Garcia, S. L. Hu, K. K. Lee, J. Virol. 2012, 86, 8750.
36. R. Wyatt, J. Sodroski, Science 1998, 280, 1884.
37. T. Zhou, L. Xu, B. Dey, A. J. Hessell, D. Van Ryk, S.-H. Xiang, X. Yang, M.-Y. Zhang, M. B. Zwick, J. Arthos, Nature 2007, 445, 732.
38. D. G. Myszka, R. W. Sweet, P. Hensley, M. Brigham-Burke, P. D. Kwong, W. A. Hendrickson, R. Wyatt, J. Sodroski, M. L. Doyle, Proc. Natl Acad. Sci. 2000, 97, 9026.
39. S. S. Hwang, T. J. Boyle, Science 1991, 253, 71.
40. J. P. Moore, P. L. Nara, AIDS 1991, 5, 21.
41. C. D. Rizzuto, R. Wyatt, N. Hernández-Ramos, Y. Sun, P. D. Kwong, W. A. Hendrickson, J. Sodroski, Science 1998, 280, 1949.
42. C.-C. Huang, S. N. Lam, P. Acharya, M. Tang, S.-H. Xiang, S. S.-U. Hussan, R. L. Stanfield, J. Robinson, J. Sodroski, I. A. Wilson, Science 2007, 317, 1930.
43. A. L. DeVico, Curr. HIV Res. 2007, 5, 561.
44. H. Golding, D. S. Dimitrov, J. Manischewitz, C. C. Broder, J. Robinson, S. Fabian, D. R. Littman, C. K. Lapham, J. Virol. 1995, 69, 6140.
45. D. Schenten, L. Marcon, G. B. Karlsson, C. Parolin, T. Kodama, N. Gerard, J. Sodroski, J. Virol. 1999, 73, 5373.
46. C. K. Lapham, J. Ouyang, B. Chandrasekhar, N. Y. Nguyen, Science 1996, 274, 602.