A solution NMR study of the binding kinetics and the internal dynamics of an HIV-1 protease-substrate complex

Protein Science

Volumn 12, Issue 7, 2003, Pages 1376-1385

  Katoh, Etsuko ^a   Louis, John M ^b   Yamazaki, Toshimasa ^a   Gronenborn, Angela M ^b   Torchia, Dennis A ^c   Ishima, Rieko ^c  

^a NATIONAL INSTITUTE OF AGROBIOLOGICAL SCIENCES   (Japan)

^b NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES   (United States)

^c NATIONAL INSTITUTE OF DENTAL AND CRANIOFACIAL RESEARCH   (United States)

Author keywords

AIDS; Aspartic protease; Enzyme; Protein; Relaxation; Slow exchange

Indexed keywords

CHROMOGENIC SUBSTRATE; NITROGEN 15; PROTEINASE; VIRUS PROTEIN;

ARTICLE; BINDING KINETICS; DISSOCIATION CONSTANT; DYNAMICS; ENZYME ACTIVE SITE; ENZYME BINDING; ENZYME CONFORMATION; ENZYME INHIBITOR COMPLEX; ENZYME SUBSTRATE COMPLEX; HUMAN IMMUNODEFICIENCY VIRUS 1; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; PH; PRIORITY JOURNAL; TIME;

HIV PROTEASE; KINETICS; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN CONFORMATION; SOLUTIONS; SUBSTRATE SPECIFICITY;

HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1; RNA VIRUSES;

EID: 0037634016     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.0300703     Document Type: Article

References (32)

1. Collins, J.R., Burt, S.K., and Erickson, J.W. 1995. Flap opening in HIV-1 protease simulated by "activated" molecular dynamics. Nat. Struct. Biol. 2: 334-338.
2. Condra, J.H. 1998. Resistance to HIV protease inhibitors. Haemophilia 4: 610-615.
3. Erickson, J.W. and Burt, S.K. 1996. Structural mechanisms of HIV drug resistance. Annu. Rev. Pharmacol. Toxicol. 36: 545-571.
4. Farrow, N.A., Zhang, O., Forman-Kay, J.D., and Kay, L.E. 1994. A heteronuclear correlation experiment for simultaneous determination of 15N longitudinal decay and chemical exchange rates of systems in slow equilibrium. J. Biomol. NMR 4: 727-734.
5. Fersht, A. 1999. Structure and mechanism in protein science, pp. 158-168. W.H. Freeman and Company, New York.
6. Freedberg, D.I., Wang, Y.X., Stahl, S.J., Kaufman, J.D., Wingfield, P.T., Kiso, Y., and Torchia, D.A. 1998. Flexibility and function in HIV protease Dynamics of the HIV-1 protease bound to the asymmetric inhibitor kynostatin 272 (KNI-272). J. Am. Chem. Soc. 120: 7916-7923.
7. Freedberg, D.I., Ishima, R., Jacob, J., Wang, Y.X., Kustanovich, I., Louis, J.M., and Torchia, D.A. 2002. Rapid structural fluctuations of the free HIV protease flaps in solution: Relationship to crystal structures and comparison with predictions of dynamics calculations. Protein Sci. 11: 221-232.
8. Furfine, E.S., D'Souza, E., Ingold, K.J., Leban, J.J., Spector, T., and Porter, D.J. 1992. Two-step binding mechanism for HIV protease inhibitors. Biochemistry 31: 7886-7891.
9. Ishima, R., Freedberg, D.I., Wang, Y.X., Louis, J.M., and Torchia, D.A. 1999. Flap opening and dimer-interface flexibility in the free and inhibitor bound HIV protease. Structure 7: 1047-1055.
10. Johnson, K.A. 1992. Transient-state kinetic analysis of enzyme reaction pathways. In The enzymes, Vol. 20, pp. 1-61. Academic Press, Orlando, FL.
11. Katoh, E., Yamazaki, T., Kiso, Y., Wingfield, P.T., Stahl, S.J., Kaufman, J.D., and Torchia, D.A. 1999. Determination of the rate of monomer interchange in a ligand-bound homodimeric protein from NOESY cross peaks: Application to the HIV protease/KNI-529 complex. J. Am. Chem. Soc. 121: 2607-2608.
12. Louis, J.M., Clore, G.M., and Gronenborn, A.M. 1999. Autoprocessing of HIV-1 protease is tightly coupled to protein folding. Nat. Struct. Biol. 6: 868-875.
13. Luque, I., Todd, M.J., Gomez, J., Semo, N., and Freire, E. 1998. Molecular basis of resistance to HIV-1 protease inhibition: A plausible hypothesis. Biochemistry 37: 5791-5797.
14. Nicholson, L.K., Yamazaki, T., Torchia. D.A., Grzesiek, S., Bax, A., Stahl, S.J., Kaufman, J.D., Wingfield, P.T., Lam, P.Y., and Jadhav, P.K. 1995. Flexibility and function in HIV-1 protease. Nat. Struct. Biol. 2: 274-280.
15. Ohtaka, H., Velazquez-Campoy, A., Xie, D., and Freire, E. 2002. Overcoming drug resistance in HIV-1 chemotherapy: The binding thermodynamics of Amprenavir and TMC-126 to wild-type and drug-resistant mutants of the HIV-1 protease. Protein Sci. 11: 1908-1916.
16. Oroszlan, S. and Luftig, R.B. 1990. Retroviral proteinases. Curr. Top. Microbiol. Immunol. 157: 153-185.
17. Parikh, U., Hammond, J., Calef, C., Larder, B., Schinazi, R., and Mellors, J.W. 2000. The 2000 HIV sequence compendium, reviews: Mutations in retroviral genes associated with drug resistance. Los Alamos, NM.
18. Prabu-Jeyabalan, M., Nalivaika. E., and 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.
19. Prabu-Jeyabalan, M., Nalivaika. E., and 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.
20. Rick, S.W., Erickson, J.W., and Burt, S.K. 1998. Reaction path and free energy calculations of the transition between alternate conformations of the HIV-1 protease. Proteins 32: 7-16.
21. Rodriguez, E.J., Debouck, C., Deckman, I.C., Abu-Soud, H., Raushel, F.M., and Meek, T.D. 1993. Inhibitor binding to the Phe53Trp mutant of HIV-1 protease promotes conformational changes detectable by spectrofluorometry. Biochemistry 32: 3557-3563.
22. Rose, R.B., Craik, C.S., Douglas, N.L., and Stroud, R.M. 1996. Three-dimensional structures of HIV-1 and SIV protease product complexes. Biochemistry 35: 12933-12944.
23. Scott, W.R.P. and Schiffer, C.A. 2000. Curling of flap tips in HIV-1 protease as a mechanism for substrate entry and tolerance of drug resistance. Structure Fold. Des. 8: 1259-1265.
24. Shafer, R.W., Jung, D.R., Betts, B.J., Xi, Y., and Gonzales, M.J. 2000. Human immunodeficiency virus reverse transcriptase and protease sequence database. Nucleic Acids Res. 28: 346-348.
25. Shao, W., Everitt, L., Manchester, M., Loeb, D.D., Hutchison 3rd, C.A., and Swanstrom, R. 1997. Sequence requirements of the HIV-1 protease flap region determined by saturation mutagenesis and kinetic analysis of flap mutants. Proc. Natl. Acad. Sci. 94: 2243-2248.
26. Tjandra, N., Wingfield, P., Stahl, S., and Bax, A. 1996. Anisotropic rotational diffusion of perdeuterated HIV protease from 15N NMR relaxation measurements at two magnetic fields. J. Biomol. NMR 8: 273-284.
27. Todd, M.J. and Freire, E. 1999. The effect of inhibitor binding on the structural stability and cooperativity of the HIV-1 protease. Proteins 36: 147-156.
28. Tozser, J., Yin, F.H., Cheng, Y.S., Bagossi, P., Weber, I.T., Harrison, R.W., and Oroszlan, S. 1997. Activity of tethered human immunodeficiency virus 1 protease containing mutations in the flap region of one subunit. FEBS Lett. 244: 235-241.
29. Velazquez-Campoy, A., Kiso, Y., and Freire, E. 2001. The binding energetics of first- and second-generation HIV-1 protease inhibitors: Implications for drug design. Arch. Biochem. Biophys. 390: 169-175.
30. Vondrasek, J., van Buskirk, C.P., and Wlodawer, A. 1997. Database of three-dimensional structures of HIV proteinases. Nat. Struct. Biol. 4: 8.
31. Wlodawer, A. and Erickson, J.W. 1993. Structure-based inhibitors of HIV-1 protease. Annu. Rev. Biochem. 62: 543-585.
32. Yang, D. and Kay, L.E, 1996. Contributions to conformational entropy arising from bond vector fluctuations measured from NMR-derived order parameters: Application to protein folding. J. Mol. Biol. 263: 369-382.