Characterization of the conformational state and flexibility of HIV-1 glycoprotein gp120 core domain

Journal of Biological Chemistry

Volumn 279, Issue 29, 2004, Pages 30523-30530

  Pan, Yongping ^a   Ma, Buyong ^a   Keskin, Ozlem ^a,b   Nussinov, Ruth ^a,c  

^a NATIONAL CANCER INSTITUTE   (United States)

^b KOÇ UNIVERSITY   (Turkey)

^c TEL AVIV UNIVERSITY   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

CRYSTAL STRUCTURE; MUTAGENESIS; THERMODYNAMICS; VIRUSES;

BRIDGING SHEET; VIRAL CELL ENTRY;

PROTEINS;

CD4 ANTIGEN; GLYCOPROTEIN GP 120;

ANTIGEN BINDING; ARTICLE; BETA SHEET; BINDING SITE; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; ENTHALPY; ENTROPY; HUMAN IMMUNODEFICIENCY VIRUS 1; HYDROPHOBICITY; MOLECULAR DYNAMICS; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN TERTIARY STRUCTURE; THERMODYNAMICS; VIRUS ADSORPTION; VIRUS MUTANT;

AMINO ACID MOTIFS; ANTIGENS, CD4; BINDING SITES; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; DNA MUTATIONAL ANALYSIS; ENTROPY; HIV ENVELOPE PROTEIN GP120; KINETICS; MODELS, MOLECULAR; MUTATION; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; SOFTWARE; THERMODYNAMICS; TIME FACTORS;

HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 3142689719     PISSN: 00219258     EISSN: None     Source Type: Journal    
DOI: 10.1074/jbc.M404364200     Document Type: Article

References (42)

1. Leonard, C. K., Spellman, M. W., Riddle, L., Harris, R. J., Thomas, J. N., and Gregory, T. J. (1990) J. Biol. Chem. 265, 10373-10382
2. Wei, X., Decker, J. M., Wang, S., Hui, H., Kappes, J. C., Wu, X., Salazar-Gonzalez, J. F., Salazar, M. G., Kilby, J. M., Saag, M. S., Komarova, N. L., Nowak, M. A., Hahn, B. H., Kwong, P. D., and Shaw, G. M. (2003) Nature 422, 307-312
3. Arendrup, M., Nielsen, C., Hansen, J. E., Pedersen, C., Mathiesen, L., and Nielsen, J. O. (1992) J. Acquired Immune Defic. Syndr. 5, 303-307
4. Weiss, C. D., Levy, J. A., and White, J. M. (1990) J. Virol. 64, 5674-5677
5. Kwong, P. D., Wyatt, R., Sattentau, Q. J., Sodroski, J., and Hendrickson, W. A. (2000) J. Virol. 74, 1961-1972
6. Kwong, P. D., Wyatt, R., Robinson, J., Sweet, R. W., Sodroski, J., and Hendrickson, W. A. (1998) Nature 393, 648-659
7. Xiang, S. H., Kwong, P. D., Gupta, R., Rizzuto, C. D., Casper, D. J., Wyatt, R., Wang, L., Hendrickson, W. A., Doyle, M. L., and Sodroski, J. (2002) J. Virol. 76, 9888-9899
8. Starcich, B. R., Hahn, B. H., Shaw, G. M., McNeely, P. D., Modrow, S., Wolf, H., Parks, E. S., Parks, W. P., Josephs, S. F., Gallo, R. C., and Wong-Staal, F. (1986) Cell 45, 637-648R. C.
9. Modrow, S., Hahn, B. H., Shaw, G. M., Gallo, R. C., Wong-Staal, F., and Wolf, H. (1987) J. Virol. 61, 570-578
10. Dalgleish, A. G., Beverley, P. C., Clapham, P. R., Crawford, D. H., Greaves, M. F., and Weiss, R. A. (1984) Nature 312, 763-767
11. Katzmann, D., Champagne, E., Chamaret, S., Gruest, J., Guetard, D., Hercend, T., Gluckman, J. C., and Montagnier, L. (1984) Nature 312, 767-768
12. Morikita, T., Maeda, Y., Fujii, S., Matsushita, S., Obaru, K., and Takatsuki, K. (1997) AIDS Res. Hum. Retroviruses 13, 1291-1299
13. Rizzuto, C. D., Wyatt, R., Hernandez-Ramos, N., Sun, Y., Kwong, P. D., Hendrickson, W. A., and Sodroski, J. (1998) Science 280, 1949-1953
14. Wu, L., Gerard, N. P., Wyatt, R., Choe, H., Parolin, C., Ruffing, N., Borsetti, A., Cardoso, A. A., Desjardin, E., Newman, W., Gerard, C., and Sodroski, J. (1996) Nature 384, 179-183
15. Trkola, A., Dragic, T., Arthos, J., Binley, J. M., Olson, W. C., Allaway, G. P., Cheng-Mayer, C., Robinson, J., Maddon, P. J., and Moore, J. P. (1996) Nature 384, 184-187
16. Alkhatib, G., Combadiere, C., Broder, C. C., Feng, Y., Kennedy, P. E., Murphy, P. M., and Berger, E. A. (1996) Science 272, 1955-1958
17. Choe, H., Farzan, M., Sun, Y., Sullivan, N., Rollins, B., Ponath, P. D., Wu, L., Mackay, C. R., LaRosa, G., Newman, W., Gerard, N., Gerard, C., and Sodroski, J. (1996) Cell 85, 1135-1148
18. Deng, H., Liu, R., Ellmeier, W., Choe, S., Unutmaz, D., Burkhart, M., Di Marzio, P., Marmon, S., Sutton, R. E., Hill, C. M., Davis, C. B., Peiper, S. C., Schall, T. J., Littman, D. R., and Landau, N. R. (1996) Nature 381, 661-666
19. Doranz, B. J., Rucker, J., Yi, Y., Smyth, R. J., Samson, M., Peiper, S. C., Parmentier, M., Collman, R. G., and Doms, R. W. (1996) Cell 85, 1149-1158
20. Dragic, T., Litwin, V., Allaway, G. P., Martin, S. R., Huang, Y., Nagashima, K. A., Cayanan, C., Maddon, P. J., Koup, R. A., Moore, J. P., and Paxton, W. A. (1996) Nature 381, 667-673
21. Wyatt, R., Kwong, P. D., Desjardins, E., Sweet, R. W., Robinson, J., Hendrickson, W. A., and Sodroski, J. G. (1998) Nature 393, 705-711
22. McKnight, A., and Weiss, R. A. (2003) Proc. Natl. Acad. Sci. U. S. A. 100, 10581-10582
23. Lin, P. F., Blair, W., Wang, T., Spicer, T., Guo, Q., Zhou, N., Gong, Y. F., Wang, H. G., Rose, R., Yamanaka, G., Robinson, B., Li, C. B., Fridell, R., Deminie, C., Demers, G., Yang, Z., Zadjura, L., Meanwell, N., and Colonno, R. (2003) Proc. Natl. Acad. Sci. U. S. A. 100, 11013-11018
24. Boussard, C., Doyle, V. E., Mahmood, N., Klimkait, T., Pritchard, M., and Gilbert, I. H. (2002) Eur. J. Med. Chem. 37, 883-890
25. Myszka, D. G., Sweet, R. W., Hensley, P., Brigham-Burke, M., Kwong, P. D., Hendrickson, W. A., Wyatt, R., Sodroski, J., and Doyle, M. L. (2000) Proc. Natl. Acad. Sci. U. S. A. 97, 9026-9031
26. Arthos, J., Deen, K. C., Chaikin, M. A., Fornwald, J. A., Sathe, G., Sattentau, Q. J., Clapham, P. R., Weiss, R. A., McDougal, J. S., Pietropaolo, C., Axel, R., Truneh, A., Maddon, P. J., and Sweet, R. W. (1989) Cell 57, 469-481
27. Brodsky, M. H., Warton, M., Myers, R. M., and Littman, D. R. (1990) J. Immunol. 144, 3078-3086
28. Cordonnier, A., Montagnier, L., and Emerman, M. (1989) Nature 340, 571-574
29. Lasky, L. A., Nakamura, G., Smith, D. H., Fennie, C., Shimasaki, C., Patzer, E., Berman, P., Gregory, T., and Capon, D. J. (1987) Cell 50, 975-985
30. Moebius, U., Clayton, L. K., Abraham, S., Harrison, S. C., and Reinherz, E. L. (1992) J. Exp. Med. 176, 507-517
31. Olshevsky, U., Helseth, E., Furman, C., Li, J., Haseltine, W., and Sodroski, J. (1990) J. Virol. 64, 5701-5707
32. Peterson, A., and Seed, B. (1988) Cell 54, 65-72
33. Kwong, P. D., Wyatt, R., Majeed, S., Robinson, J., Sweet, R. W., Sodroski, J., and Hendrickson, W. A. (2000) Structure Fold. Des. 8, 1329-1339
34. Ryu, S. E., Kwong, P. D., Truneh, A., Porter, T. G., Arthos, J., Rosenberg, M., Dai, X. P., Xuong, N. H., Axel, R., Sweet, R. W., and Hendrickson, W. A. (1990) Nature 348, 419-426
35. Wang, J. H., Yan, Y. W., Garrett, T. P., Liu, J. H., Rodgers, D. W., Garlick, R. L., Tarr, G. E., Husain, Y., Reinherz, E. L., and Harrison, S. C. (1990) Nature 348, 411-418
36. Wu, H., Kwong, P. D., and Hendrickson, W. A. (1997) Nature 387, 527-530
37. Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S., and Karplus, M. (1983) J. Comput. Chem. 4, 187-217
38. MacKerell, A. D. Jr., Bashford, D., Bellott, M., Dunbrack, R. L. Jr., Evanseck, J. D., Field, M. J., Fischer, S., Gao, J., Guo, H., Ha, S., Joseph-McCarthy, D., Kuchnir, L., Kuczera, K., Lau, F. T. K., Mattos, C., Michnick, S., Ngo, T., Nguyen, D. T., Prodhom, B., Reiher, W. E., III, Roux, B., Schlenkrich, M., Smith, J. C., Stote, R., Straub, J., Watanabe, M., Wiorkiewicz-Kuczera, J., Yin, D., and Karplus, M. (1998) J. Phys. Chem. B. 102, 3586-3616
39. Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., and Klein, M. L. (1983) J. Chem. Phys. 79, 926-935
40. Keskin, O., Durell, S. R., Bahar, I., Jernigan, R. L., and Covell, D. G. (2002) Biophys. J. 83, 663-680
41. Thali, M., Furman, C., Ho, D. D., Robinson, J., Tilley, S., Pinter, A., and Sodroski, J. (1992) J. Virol. 66, 5635-5641
42. Biorn, A. C., Cocklin, S., Madani, N., Si, Z., Ivanovic, T., Samanen, J., Van Ryk, D. I., Pantophlet, R., Burton, D. R., Freire, E., Sodroski, J., and Chaiken, I. M. (2004) Biochemistry 43, 1928-1938