Dynamics of preferential substrate recognition in HIV-1 protease: Redefining the substrate envelope

Journal of Molecular Biology

Volumn 410, Issue 4, 2011, Pages 726-744

  Özen, Ayşegül ^a   Haliloǧlu, Türkan ^b   Schiffer, Celia A ^a  

^a UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

^b BOGAZICI UNIVERSITY   (Turkey)

Author keywords

Computational modeling; HIV 1 protease inhibitors; Protein dynamics; Structure based drug design; Substrate envelope hypothesis

Indexed keywords

PROTEINASE;

AMINO ACID SEQUENCE; ARTICLE; ENZYME CONFORMATION; ENZYME SUBSTRATE; ENZYME SUBSTRATE COMPLEX; HUMAN IMMUNODEFICIENCY VIRUS 1; MOLECULAR DYNAMICS; MOLECULAR RECOGNITION; PRIORITY JOURNAL; PROTEIN CLEAVAGE; PROTEIN PROTEIN INTERACTION;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 80051739212     PISSN: 00222836     EISSN: 10898638     Source Type: Journal    
DOI: 10.1016/j.jmb.2011.03.053     Document Type: Article

References (23)

1. Prabu-Jeyabalan, M., Nalivaika, E. & Schiffer, C. A. (2000). How does a symmetric dimer recognize an asymmetric substrate? A substrate complex of HIV-1 protease. J. Mol. Biol. 301, 1207-1220.
2. Prabu-Jeyabalan, M., Nalivaika, E. & Schiffer, C. A. (2002). Substrate shape determines specificity of recognition for HIV-1 protease: analysis of crystal structures of six substrate complexes. Structure, 10, 369-381. (Pubitemid 34230624)
3. King, N. M., Melnick, L., Prabu-Jeyabalan, M., Nalivaika, E. A., Yang, S. S., Gao, Y. et al. (2002). Lack of synergy for inhibitors targeting a multi-drug-resistant HIV-1 protease. Protein Sci. 11, 418-429. (Pubitemid 34075805)
4. Nalam, M. N. & Schiffer, C. A. (2008). New approaches to HIV protease inhibitor drug design II: testing the substrate envelope hypothesis to avoid drug resistance and discover robust inhibitors. Curr. Opin. HIV AIDS, 3, 642-646.
5. Nalam, M. N., Ali, A., Altman, M. D., Reddy, G. S., Chellappan, S., Kairys, V. et al. (2010). Evaluating the substrate-envelope hypothesis: structural analysis of novel HIV-1 protease inhibitors designed to be robust against drug resistance. J. Virol. 84, 5368-5378.
6. Chellappan, S., Kiran Kumar Reddy, G. S., Ali, A., Nalam, M. N., Anjum, S. G., Cao, H. et al. (2007). Design of mutation-resistant HIV protease inhibitors with the substrate envelope hypothesis. Chem. Biol. Drug Des. 69, 298-313. (Pubitemid 46817456)
7. Altman, M. D., Ali, A., Reddy, G. S., Nalam, M. N., Anjum, S. G., Cao, H. et al. (2008). HIV-1 protease inhibitors from inverse design in the substrate envelope exhibit subnanomolar binding to drug-resistant variants. J. Am. Chem. Soc. 130, 6099-6113. (Pubitemid 351657286)
8. Prabu-Jeyabalan, M., Nalivaika, E. A., King, N. M. & Schiffer, C. A. (2004). Structural basis for coevolution of a human immunodeficiency virus type 1 nucleocapsid-p1 cleavage site with a V82A drug-resistant mutation in viral protease. J. Virol. 78, 12446-12454. (Pubitemid 39458763)
9. Kolli, M., Lastere, S. & Schiffer, C. A. (2006). Co-evolution of nelfinavir-resistant HIV-1 protease and the p1-p6 substrate. Virology, 347, 405-409.
10. Tozser, J., Blaha, I., Copeland, T. D., Wondrak, E. M. & Oroszlan, S. (1991). Comparison of the HIV-1 and HIV-2 proteinases using oligopeptide substrates representing cleavage sites in Gag and Gag-Pol polyproteins. FEBS Lett. 281, 77-80.
11. Rhee, S. Y., Gonzales, M. J., Kantor, R., Betts, B. J., Ravela, J. & Shafer, R. W. (2003). Human immunodeficiency virus reverse transcriptase and protease sequence database. Nucleic Acids Res. 31, 298-303. (Pubitemid 36150389)
12. Choudhury, S., Everitt, L., Pettit, S. C. & Kaplan, A. H. (2003). Mutagenesis of the dimer interface residues of tethered and untethered HIV-1 protease result in differential activity and suggest multiple mechanisms of compensation. Virology, 307, 204-212. (Pubitemid 36344156)
13. King, N. M., Prabu-Jeyabalan, M., Nalivaika, E. A. & Schiffer, C. A. (2004). Combating susceptibility to drug resistance: lessons from HIV-1 protease. Chem. Biol. 11, 1333-1338. (Pubitemid 39351371)
14. Pettit, S. C., Clemente, J. C., Jeung, J. A., Dunn, B. M. & Kaplan, A. H. (2005). Ordered processing of the human immunodeficiency virus type 1 GagPol precursor is influenced by the context of the embedded viral protease. J. Virol. 79, 10601-10607. (Pubitemid 41098599)
15. Olson, A. J. & Goodsell, D. S. (1998). Automated docking and the search for HIV protease inhibitors. SAR QSAR Environ. Res. 8, 273-285.
16. Case, D. A., Darden, T. A., Cheatham, T. E., III, Simmerling, C. L., Wang, J., Duke, R. E. et al. (2004). AMBER 8. University of California, San Francisco.
17. Case, D. A., Cheatham, T. E., III, Darden, T., Gohlke, H., Luo, R., Merz, K. M., Jr. et al. (2005). The Amber biomolecular simulation programs. J. Comput. Chem. 26, 1668-1688. (Pubitemid 43076180)
18. Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W. & Klein, M. L. (1983). Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79, 926-935.
19. Ryckaert, J. P., Ciccotti, G. & Berendsen, H. J. C. (1977). Numerical-integration of Cartesian equations of motion of a system with constraints-molecular-dynamics of n-alkanes. J. Comput. Phys. 23, 327-341.
20. Berendsen, H. J. C., Postma, J. P. M., Vangunsteren, W. F., Dinola, A. & Haak, J. R. (1984). Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81, 3684-3690.
21. Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H. & Pedersen, L. G. (1995). A smooth particle mesh Ewald method. J. Chem. Phys. 103, 8577-8593.
22. Chellappan, S., Kairys, V., Fernandes, M. X., Schiffer, C. & Gilson, M. K. (2007). Evaluation of the substrate envelope hypothesis for inhibitors of HIV-1 protease. Proteins; Struct. Funct. Bioinformatics, 68, 561-567. (Pubitemid 46981948)
23. Humphrey, W., Dalke, A. & Schulten, K. (1996). VMD: visual molecular dynamics.J. Mol. Graph. 14, 33-38; 27-38. (Pubitemid 26152973)