Hydrophobic core flexibility modulates enzyme activity in HIV-1 protease

Journal of the American Chemical Society

Volumn 134, Issue 9, 2012, Pages 4163-4168

  Mittal, Seema ^a   Cai, Yufeng ^a   Nalam, Madhavi N L ^a   Bolon, Daniel N A ^a   Schiffer, Celia A ^a  

^a UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVE SITE; DISULFIDE BOND FORMATION; DRUG RESISTANCE; HIV-1 PROTEASE; HUMAN IMMUNODEFICIENCY VIRUS TYPE-1; HYDROPHOBIC CORE; MOLECULAR DYNAMICS SIMULATIONS; PROTEASE ACTIVITIES; VIRAL MATURATION;

AMINO ACIDS; COVALENT BONDS; DYNAMICS; MASS SPECTROMETRY; MOLECULAR DYNAMICS; VIRUSES;

HYDROPHOBICITY;

CYSTEINE; HUMAN IMMUNODEFICIENCY VIRUS PROTEINASE;

ARTICLE; BINDING KINETICS; CATALYSIS; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; DISULFIDE BOND; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME SUBSTRATE; HUMAN IMMUNODEFICIENCY VIRUS 1; HYDROPHOBICITY; MASS SPECTROMETRY; MOLECULAR DYNAMICS; MUTATIONAL ANALYSIS; NONHUMAN; OXIDATION; PROTEIN CONFORMATION; PROTEIN CROSS LINKING; PROTEIN METABOLISM; STRUCTURE ACTIVITY RELATION;

CRYSTALLOGRAPHY, X-RAY; ENZYME ACTIVATION; HIV PROTEASE; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; MUTATION; PROTEIN CONFORMATION;

EID: 84857804736     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja2095766     Document Type: Article

References (30)

1. Kohl, N. E.; Emini, E. A.; Schleif, W. A.; Davis, L. J.; Heimbach, J. C.; Dixon, R. A.; Scolnick, E. M.; Sigal, I. S. Proc. Natl. Acad. Sci. U. S. A. 1988, 85, 4686-4690.
2. Kramer, R. A.; Schaber, M. D.; Skalka, A. M.; Ganguly, K.; Wong- Staal, F.; Reddy, E. P. Science 1986, 231, 1580-4.
3. Muzammil, S.; Ross, P.; Freire, E. Biochemistry 2003, 42, 631-8.
4. Ohtaka, H.; Schon, A.; Freire, E. Biochemistry 2003, 42, 13659-66.
5. Clemente, J. C.; Moose, R. E.; Hemrajani, R.; Whitford, L. R.; Govindasamy, L.; Reutzel, R.; McKenna, R.; Agbandje-McKenna, M.; Goodenow, M. M.; Dunn, B. M. Biochemistry 2004, 43, 12141-12151.
6. Ishima, R.; Freedberg, D. I.; Wang, Y. X.; Louis, J. M.; Torchia, D. A. Structure 1999, 7, 1047-55.
7. Freedberg, D. I.; Ishima, R.; Jacob, J.; Wang, Y. X.; Kustanovich, I.; Louis, J. M.; Torchia, D. A. Protein Sci. 2002, 11, 221-32.
8. Ishima, R.; Louis, J. M. Proteins 2008, 70, 1408-15.
9. Perryman, A. L.; Lin, J. H.; McCammon, J. A. Protein Sci. 2004, 13, 1108-23.
10. Perryman, A. L.; Lin, J. H.; McCammon, J. A. Biopolymers 2006, 82, 272-84.
11. Galiano, L.; Bonora, M.; Fanucci, G. E. J. Am. Chem. Soc. 2007, 129, 11004-5.
12. Foulkes-Murzycki, J. E.; Scott, W. R.; Schiffer, C. A. Structure 2007, 15, 225-33.
13. Seeger, M. A.; von Ballmoos, C.; Eicher, T.; Brandstatter, L.; Verrey, F.; Diederichs, K.; Pos, K. M. Nat. Struct. Mol. Biol. 2008, 15, 199-205.
14. Witkowski, W. A.; Hardy, J. A. Protein Sci. 2009, 18, 1459-68.
15. Busenlehner, L. S.; Armstrong, R. N. Arch. Biochem. Biophys. 2005, 433, 34-46.
16. Palmer, A. G. 3rd Annu. Rev. Biophys. Biomol. Struct. 2001, 30, 129-55.
17. Parak, F. G. Curr. Opin. Struct. Biol. 2003, 13, 552-7.
18. Blackburn, M. E.; Veloro, A. M.; Fanucci, G. E. Biochemistry 2009, 48, 8765-7.
19. Schmidt, B.; Ho, L.; Hogg, P. J. Biochemistry 2006, 45, 7429-33.
20. Brandes, N.; Schmitt, S.; Jakob, U. Antioxid. Redox Signaling 2009, 11, 997-1014.
21. Thornton, J. M. J. Mol. Biol. 1981, 151, 261-87.
22. Spadaro, D.; Yun, B. W.; Spoel, S. H.; Chu, C.; Wang, Y. Q.; Loake, G. J. Physiol. Plant 2010, 138, 360-71.
23. Lazear, E.; Carfi, A.; Whitbeck, J. C.; Cairns, T. M.; Krummenacher, C.; Cohen, G. H.; Eisenberg, R. J. J. Virol. 2008, 82, 700-9.
24. Bass, R. B.; Butler, S. L.; Chervitz, S. A.; Gloor, S. L.; Falke, J. J. Methods Enzymol. 2007, 423, 25-51.
25. Rose, R. B.; Craik, C. S.; Stroud, R. M. Biochemistry 1998, 37, 2607-21.
26. Galiano, L.; Ding, F.; Veloro, A. M.; Blackburn, M. E.; Simmerling, C.; Fanucci, G. E. J. Am. Chem. Soc. 2009, 131, 430-1.
27. Hazes, B.; Dijkstra, B. W. Protein Eng. 1988, 2, 119-25.
28. Surleraux, D. L.; Tahri, A.; Verschueren, W. G.; Pille, G. M.; de Kock, H. A.; Jonckers, T. H.; Peeters, A.; De Meyer, S.; Azijn, H.; Pauwels, R.; de Bethune, M. P.; King, N. M.; Prabu-Jeyabalan, M.; Schiffer, C. A.; Wigerinck, P. B. J. Med. Chem. 2005, 48, 1813-1822.
29. Prabu-Jeyabalan, M.; Nalivaika, E. A.; Schiffer, C. A. Structure 2002, 10, 369-381.
30. Rhee, S. Y.; Taylor, J.; Fessel, W. J.; Kaufman, D.; Towner, W.; Troia, P.; Ruane, P.; Hellinger, J.; Shirvani, V.; Zolopa, A.; Shafer, R. W. Antimicrob. Agents Chemother. 2010, 54, 4253-61.