Contribution of the 80s loop of HIV-1 protease to the multidrug-resistance mechanism: Crystallographic study of MDR769 HIV-1 protease variants

Acta Crystallographica Section D: Biological Crystallography

Volumn 67, Issue 6, 2011, Pages 524-532

  Yedidi, Ravikiran S ^a,c   Proteasa, Georghe ^a   Martinez, Jorge L ^a,d   Vickrey, John F ^a   Martin, Philip D ^a   Wawrzak, Zdzislaw ^b   Liu, Zhigang ^a   Kovari, Iulia A ^a   Kovari, Ladislau C ^a  

^a WAYNE STATE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b NORTHWESTERN UNIVERSITY   (United States)

^c NATIONAL INSTITUTES OF HEALTH   (United States)

^d QUEEN S UNIVERSITY   (Canada)

Author keywords

80s loop; docking; expanded active site cavity; HIV 1 protease; multidrug resistance; proline switch; wide open flaps

Indexed keywords

HUMAN IMMUNODEFICIENCY VIRUS PROTEINASE; P16 PROTEASE, HUMAN IMMUNODEFICIENCY VIRUS 1;

AMINO ACID SEQUENCE; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; ENZYMOLOGY; GENETICS; HUMAN IMMUNODEFICIENCY VIRUS 1; MOLECULAR GENETICS; MULTIDRUG RESISTANCE; MUTATION; PROTEIN QUATERNARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; SEQUENCE ALIGNMENT; X RAY CRYSTALLOGRAPHY;

AMINO ACID SEQUENCE; CRYSTALLOGRAPHY, X-RAY; DRUG RESISTANCE, MULTIPLE, VIRAL; HIV PROTEASE; HIV-1; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTATION; PROTEIN STRUCTURE, QUATERNARY; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 79958020234     PISSN: 09074449     EISSN: 13990047     Source Type: Journal    
DOI: 10.1107/S0907444911011541     Document Type: Article

References (33)

1. Case, D. A. et al. (2004). AMBER8. University of California, San Francisco, USA.
2. Evans, P. (2006). Acta Cryst. D 62, 72-82.
3. Heaslet, H., Rosenfeld, R., Giffin, M., Lin, Y.-C., Tam, K., Torbett, B. E., Elder, J. H., McRee, D. E. & Stout, C. D. (2007). Acta Cryst. D 63, 866-875.
4. Ishima, R., Torchia, D. A., Lynch, S. M., Gronenborn, A. M. & Louis, J. M. (2003). J. Biol. Chem. 278, 43311-43319.
5. Kabsch, W. (1976). Acta Cryst. A 32, 922-923.
6. Kohl, N. E., Emini, E. A., Schleif, W. A., Davis, L. J., Heimbach, J. C., Dixon, R. A., Scolnick, E. M. & Sigal, I. S. (1988). Proc. Natl Acad. Sci. USA, 85, 4686-4690.
7. Kumar, M., Kannan, K. K., Hosur, M. V., Bhavesh, N. S., Chatterjee, A., Mittal, R. & Hosur, R. V. (2002). Biochem. Biophys. Res. Commun. 294, 395-401.
8. Lamzin, V. S. & Wilson, K. S. (1993). Acta Cryst. D 49, 129-147.
9. Lapatto, R., Blundell, T., Hemmings, A., Overington, J., Wilderspin, A., Wood, S., Merson, J. R., Whittle, P. J., Danley, D. E. & Geoghegan, K. F. (1989). Nature (London), 342, 299-302.
10. Laskowski, R. A., MacArthur, M. W., Moss, D. S. & Thornton, J. M. (1993). J. Appl. Cryst. 26, 283-291.
11. Layten, M., Hornak, V. & Simmerling, C. (2006). J. Am. Chem. Soc. 128, 13360-13361.
12. Lee, B. & Richards, F. M. (1971). J. Mol. Biol. 55, 379-400.
13. Leslie, A. G. W. (2006). Acta Cryst. D 62, 48-57.
14. Lexa, K. W., Damm, K. L., Quintero, J. J., Gestwicki, J. E. & Carlson, H. A. (2009). Proteins, 74, 872-880.
15. Liu, F., Kovalevsky, A. Y., Louis, J. M., Boross, P. I., Wang, Y.-F., Harrison, R. W. & Weber, I. T. (2006). J. Mol. Biol. 358, 1191-1199.
16. Logsdon, B. C., Vickrey, J. F., Martin, P., Proteasa, G., Koepke, J. I., Terlecky, S. R., Wawrzak, Z., Winters, M. A., Merigan, T. C. & Kovari, L. C. (2004). J. Virol. 78, 3123-3132.
17. Martin, P., Vickrey, J. F., Proteasa, G., Jimenez, Y. L., Wawrzak, Z., Winters, M. A., Merigan, T. C. & Kovari, L. C. (2005). Structure, 13, 1887-1895.
18. McRee, D. E. (1999). J. Struct. Biol. 125, 156-165.
19. Morris, A. L., MacArthur, M. W., Hutchinson, E. G. & Thornton, J. M. (1992). Proteins, 12, 345-364.
20. Murshudov, G. N., Skubák, P., Lebedev, A. A., Pannu, N. S., Steiner, R. A., Nicholls, R. A., Winn, M. D., Long, F. & Vagin, A. A. (2011). Acta Cryst. D 67, 355-367.
21. Navia, M. A., Fitzgerald, P. M., McKeever, B. M., Leu, C.-T., Heimbach, J. C., Herber, W. K., Sigal, I. S., Darke, P. L. & Springer, J. P. (1989). Nature (London), 337, 615-620.
22. Palmer, S., Shafer, R. W. & Merigan, T. C. (1999). AIDS, 13, 611-667.
23. Peng, C., Ho, B. K., Chang, T. W. & Chang, N. T. (1989). J. Virol. 63, 2550-2556.
24. Perrakis, A., Morris, R. & Lamzin, V. S. (1999). Nature Struct. Mol. Biol. 6, 458-463.
25. Pillai, B., Kannan, K. K. & Hosur, M. V. (2001). Proteins, 43, 57-64.
26. Potterton, E., Briggs, P., Turkenburg, M. & Dodson, E. (2003). Acta Cryst. D 59, 1131-1137.
27. Prabu-Jeyabalan, M., Nalivaika, E. & Schiffer, C. A. (2002). Structure, 10, 369-381.
28. Spinelli, S., Liu, Q. Z., Alzari, P. M., Hirel, P. H. & Poljak, R. J. (1991). Biochimie, 73, 1391-1396.
29. Trott, O. & Olson, A. J. (2010). J. Comput. Chem. 31, 455-461.
30. Vagin, A. & Teplyakov, A. (2010). Acta Cryst. D 66, 22-25.
31. Vickrey, J. F., Logsdon, B. C., Proteasa, G., Palmer, S., Winters, M. A., Merigan, T. C. & Kovari, L. C. (2003). Protein Expr. Purif. 28, 165-172.
32. Winn, M. D. et al. (2011). Acta Cryst. D 67, 235-242.
33. Wlodawer, A., Miller, M., Jaskólski, M., Sathyanarayana, B. K., Baldwin, E., Weber, I. T., Selk, L. M., Clawson, L., Schneider, J. & Kent, S. B. (1989). Science, 245, 616-621.