Dynamic domains and geometrical properties of HIV-1 gp120 during conformational changes induced by CD4 binding

Journal of Molecular Modeling

Volumn 13, Issue 3, 2007, Pages 411-424

  Liu, Shu Qun ^a   Liu, Shi Xi ^a   Fu, Yun Xin ^a,b  

^a YUNNAN UNIVERSITY   (China)

^b UNIVERSITY OF TEXAS   (United States)

Author keywords

CD4; Dynamic domain; Geometrical property; HIV 1 gp120; Induced fit; Interaction

Indexed keywords

CD4 ANTIGEN; CHEMOKINE RECEPTOR CCR4; CHEMOKINE RECEPTOR CXCR4; GLYCOPROTEIN GP 120;

AMINO ACID SEQUENCE; ARTICLE; BINDING AFFINITY; BINDING SITE; CELL SURFACE; COMPARATIVE STUDY; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; HOST CELL; HUMAN IMMUNODEFICIENCY VIRUS 1; LIGAND BINDING; MOLECULAR DYNAMICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN INTERACTION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; SIMIAN IMMUNODEFICIENCY VIRUS; STRUCTURE ANALYSIS; VIRUS VIRULENCE;

ANTIGENS, CD4; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; HIV ENVELOPE PROTEIN GP120; HUMANS; MODELS, MOLECULAR; PROTEIN CONFORMATION; RECEPTORS, CHEMOKINE; RECEPTORS, CXCR4; VIRAL PROTEINS;

HUMAN IMMUNODEFICIENCY VIRUS 1; SIMIAN IMMUNODEFICIENCY VIRUS;

EID: 33947579112     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-006-0158-3     Document Type: Article

References (48)

1. Barre-Sinoussi F, Chermann JC, Rey F, Nugeyre MT, Chamaret S, Gruest J, Dauguet C, Axler-Blin C, Vezinet-Brun F, Rouzioux C, Rozenbaum W, Montagnier L (1983) Science 220:868-871
2. Gallo RC, Salahuddin SZ, Popovic M, Shearer GM, Kaplan M, Haynes BF, Palker TJ, Redfield R, Oleske J, Safai B (1984) Science 224:500-503
3. Allan JS, Coligan JE, Barin F, McLane MF, Sodroski JG, Rosen CA, Haseltine WA, Lee TH, Essex M (1985) Science 228:1091-1094
4. Veronese FD, DeVico AL, Copeland TD, Oroszlan S, Gallo RC, Sarngadharan MG (1985) Science 229:1402-1405
5. Center RJ, Leapman RD, Lebowitz J, Arthur LO, Earl PL, Moss B (2002) J Virol 76:7863-7867
6. Dalgleish AG, Beverley PC, Clapham PR, Crawford DH, Greaves MF, Weiss RA (1984) Nature 312:763-767
7. Feng Y, Broder CC, Kennedy PE, Berger EA (1996) Science 272:872-877
8. Trkola A, Dragic T, Arthos J, Binley JM, Olson WC, Allaway GP, Cheng-Mayer C, Robinson J, Maddon PJ, Moore JP (1996) Nature 384:184-187
9. Wu L, Gerard NP, Wyatt R, Choe H, Parolin C, Ruffing N, Borsetti A, Cardoso AA, Desjardin E, Newman W, Gerard C, Sodroski J (1996) Nature 384:179-183
10. Rizzuto CD, Wyatt R, Hernandez-Ramos N, Sun Y, Kwong PD, Hendrickson WA, Sodroski J (1998) Science 280:1949-1953
11. Liu SQ, Fan SX, Sun ZR (2003) J Mol Mod 9:329-336
12. Liu SQ, Shi XF, Liu CQ, Sun ZR (2004) J Mol Struct (THEOCHEM) 673:133-143
13. Chan DC, Fass D, Berger JM, Kim PS (1997) Cell 89:263-273
14. Weissenhorn W, Dessen A, Harrison SC, Skehel JJ, Wiley DC (1997) Nature 387:426-430
15. Kwong PD, Wyatt R, Robinson J, Sweet RW, Sodroski J, Hendrickson WA (1998) Nature 393:648-659
16. Kwong PD, Wyatt R, Majeed S, Robinson J, Sweet RW, Sodroski J, Hendrickson WA (2000) Structure Fold Des 8:1329-1339
17. Wyatt R, Kwong PD, Desjardins E, Sweet RW, Robinson J, Hendrickson WA (1998) Nature 393:705-711
18. Chen B, Vogan EM, Gong H, Skehel JJ, Wiley DC, Harrison SC (2005) Nature 433:834-841
19. Kwong PD, Doyle ML, Casper DJ, Cicala C, Leavitt SA, Majeed S, Steenbeke TD, Venturi M, Chaiken I, Fung M, Katinger H, Parren PW, Robinson J, Van Ryk D, Wang L, Burton DR, Freire E, Wyatt R, Sodroski J, Hendrickson WA, Arthos J (2002) Nature 420:678-682
20. Myszka DG, Sweet RW, Hensley P, Brigham-Burke M, Kwong PD, Hendrickson WA, Wyatt R, Sodroski J, Doyle ML (2000) Proc Natl Acad Sci USA 97:9026-9031
21. Rusche JR, Javaherian K, McDanal C, Petro J, Lynn DL, Grimaila R, Langlois A, Gallo RC, Arthur LO, Fischinger PJ, Bolognesi DP, Putney SD, Matthews TJ (1988) Proc Natl Acad Sci USA 85:3198-3202
22. Berger EA, Murphy PM, Farber JM (1999) Annu Rev Immunol 17:657-700
23. Rini JM, Stanfield RL, Stura EA, Salinas PA, Profy AT, Wilson IA (1993) Proc Natl Acad Sci USA 90:6325-6329
24. Tugarinov V, Zvi A, Levy R, Hayek Y, Matsushita S, Anglister J (2000) Struct Fold Des 8:385-395
25. Sharon M, Kessler N, Levy R, Zolla-Pazner S, Gorlach M, Anglister J (2003) Structure 11:225-236
26. Huang CC, Tang M, Zhang MY, Majeed S, Montabana E, Stanfield RL, Dimitrov DS, Korber B, Sodroski J, Wilson IA, Wyatt R, Kwong PD (2005) Science 310:1025-1028
27. Bairoch A, Apweiler R, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O'Donovan C, Redaschi N, Yeh, LS (2005) Nucl Acids Res 33 (Database issue):D154-159
28. Deshpande N, Addess KJ, Bluhm WF, Merino-Ott JC, Townsend-Merino W, Zhang Q (2005) Nucl Acids Res 33 (Database issue):D233-237
29. Vranken WF, Budesinsky M, Fant F, Boulez K, Borremans FA (1995) FEBS Lett 374:117-121
30. Baker D, Sali A (2001) Science 294:93-96
31. Humphrey W, Dalke A, Schulten K (1996) J Mol Graph 14(33-38):27-28
32. Sali A, Blundell TL (1993) J Mol Biol 234:779-815
33. Hayward S, Kitao A, Berendsen HJ (1997) Proteins 27:425-437
34. Hayward S, Berendsen HJ (1998) Proteins 30:144-154
35. Van Der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJ (2005) J Comput Chem 26:1701-1718
36. Lindahl E, Hess B, Van Der Spoel D (2001) J Mol Mod 7:306-317
37. Kabsch W, Sander C (1983) Biopolymers 22:2577-2637
38. Laskowski RA, MacArthur M, Moss DS, Thornton JM (1993) J Appl Crystallogr 26:283-291
39. de Groot BL, Hayward S, Van Aalten DM, Amadei A, Berendsen HJ (1998) Proteins 31:116-127
40. Mello LV, De Groot BL, Li S, Jedrzejas MJ (2002) J Biol Chem 277:36678-36688
41. Pan Y, Ma B, Keskin O, Nussinov R (2004) J Biol Chem 279:30523-30530
42. Pan Y, Ma B, Nussinov R (2005) J Mol Biol 350:514-527
43. Hsu ST, Bonvin AM (2004) Proteins 55:582-593
44. Poignard P, Saphire EO, Parren P, Burton, DR (2001) Annu Rev Immunol 19:253-274
45. Kwong PD, Wyatt R, Sattentau QJ, Sodroski J, Hendrickson WA (2000) J Virol 74:1961-1972
46. Ramachandran GN, Ramakrishnan C, Sasisekharan V (1963) J Mol Biol 7:95-99
47. Kraulis PJ (1991) J Appl Cryst 24:946-950
48. Sayle RA, Milner-White EJ (1995) Trends Biochem Sci 20:374-376