Reaction path and free energy calculations of the transition between alternate conformations of HIV-1 protease

Proteins: Structure, Function and Genetics

Volumn 32, Issue 1, 1998, Pages 7-16

  Rick, Steven W ^a   Erickson, John W ^a   Burt, Stanley K ^a  

^a SAIC FREDERICK INC   (United States)

Author keywords

Conformational change; Free energy calculations; HIV protease; Molecular dynamics simulations; Protein structure

Indexed keywords

PROTEINASE; VIRUS PROTEIN;

ARTICLE; BINDING SITE; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; ENTROPY; ENZYME CONFORMATION; ENZYME STRUCTURE; HUMAN IMMUNODEFICIENCY VIRUS 1; MOLECULAR DYNAMICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN STRUCTURE; X RAY CRYSTALLOGRAPHY;

CRYSTALLOGRAPHY, X-RAY; ENERGY TRANSFER; HIV PROTEASE; HUMANS; MATHEMATICAL COMPUTING; PROTEIN CONFORMATION;

HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 0032127391     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19980701)32:1<7::AID-PROT3>3.0.CO;2-K     Document Type: Article

References (44)

1. Wlodawer, A., Erickson, J.W. Structure-based inhibitors of HIV-1 protease. Annu. Rev. Biochem. 62:543-585, 1993.
2. Miller, M., Schneider, J., Sathyanarayana, B.K. et al. Structure of complex of synthetic HIV-1 protease with a substrate-based inhibitor at 2.3 Å resolution. Science 246: 1149-1152, 1989.
3. Navia, M.A., Fitzgerald, P.M.D., McKeeve, B.M. et al. Three-dimensional structure of aspartyl protease from human immunodeficiency virus HIV-1. Nature (London) 337:615-620, 1989.
4. Wlodawer A., Miller, M., Jaskolski, M. et al. Conserved folding in retroviral proteases: Crystal structure of a synthetic HIV-1 proteinase. Science 245:616-621, 1989.
5. Spinelli, S., Liu, Q.Z., Alzari, P.M., Hirel, P.H., Poljak, R.J. The three dimensional structure of the aspartyl protease from the HIV-1 isolate BRU. Biochimie 73:1391-1396, 1991.
6. Wilderspin, A.F., Sugrue, R.J. Alternate native flap conformation revealed by 2.3 Å resolution structure of SIV protease. J. Mol. Biol. 239:97-103, 1994.
7. Chen, Z., Li, Y., Chen, E. et al. Crystal structure at 1.9-Å resolution of human immunodeficiency virus (HIV) II protease completed with L-735,524, an orally bioavailable inhibitor of the HIV proteases. J. Biol. Chem. 42:26344-26348, 1994.
8. Bhat, T.N., Erickson, J.W., private communication.
9. Miller, M., Jaskolski, M., Rao, J.K., Leis, J., Wlodawer, A. Crystal structure of a retroviral protease proves relationship to aspartic acid family. Nature (London) 337:576-579, 1989.
10. Schulz, G.E. Domain motions in proteins. Curr. Opin. Struct. Biol. 1:883-888, 1991.
11. Schiffer, M., Ainsworth, C., Xu, Z.-B. et al. Structure of a second crystal form of Bence-Jones protein loc: Strikingly different domain associations in two crystal forms of a single protein. Biochemistry 28:4066-4072, 1989.
12. Eigenbrot, C., Randal, M., Kossiakoff, A.A. Structural effects induced by mutagenesis affected by crystal packing factors: The structure of a 30-51 disulfide mutant of basic pancreatic trypsin inhibitor. Proteins 14:75-87, 1992.
13. McCammon, J.A., Harvey, S.C. "Dynamics of Proteins and Nucleic Acids." Cambridge, UK: Cambridge University Press, 1987.
14. Northrup, S.H., Pear, M.R., Lee, C.-H., McCammon, J.A., Karplus, M. Dynamical theory of activated processes in globular proteins. Proc. Natl. Acad. Sci. USA 79:4035-40397 1982.
15. 10-Helix transitions in α-methylalanine homopeptides: Conformational transition pathway and potential of mean force. Biopolymers 34:75-90, 1994.
16. Boczko, E.M., Brooks, C.L. First-principles calculation of the folding free energy of a three-helix bundle protein. Science 269:393-396, 1995.
17. Pratt, L. A statistical method for identifying transition states in high dimensional problems. J. Chem. Phys. 85:5045-5048, 1986.
18. Elber, R., Karplus, M. A method for determining reaction paths in large molecules: Application to myoglobin. Chem. Phys. Lett. 139:375-380, 1987.
19. Czerminski, R., Elber, R. Self-avoiding walk between two fixed points as a tool to calculate reaction paths in large molecular systems. Int. J. Quant. Chem. 24:167-1867 1990.
20. Gillilan, R.E., Wilson, K.R. Shadowing, rare events, and rubber bands. A varational Verlet algorithm for molecular dynamics. J. Chem. Phys. 97:1757-1772, 1992.
21. Cho, A.E., Doll, J.D., Freeman, D.L. The construction of double-ended classical trajectories. Chem. Phys. Lett. 229: 218-224, 1994.
22. Smart, O.S. A new method to calculate reaction paths tor conformational transitions of large molecules. Chem. Phys. Lett. 222:503-512, 1994.
23. Furfine, E.S., D'Souza, E., Ingold, K.J. et al. Two-step binding mechanism for HIV protease inhibitors. Biochemistry 31:7886-78911 1992.
24. Rodriguez, E.J., Deckman, C.D., Abu-Soud, H., Raushel, F. M., Meek, T.D. Inhibitor binding to the phe53trp mutant of HIV-1 protease promotes conformation changes detectable by spectroflourometry. Biochemistry 32:3557-3563, 1993.
25. Maschera, B., Palfi, G.D.G., Wright, L.L. et al. Human immunodeficiency virus. Mutations in the viral protease that confer resistance to saquinavir increase the dissociation rate constant of the protease-saquinavir complex. J. Biol. Chem. 271:33231-33235, 1996.
26. Nicholson, L.K., Yamazaki, T., Torchia, D.A. et al. Flexibility and function in HIV-1 protease. Struct. Biol. 2:274-280, 1995.
27. Collins, J.R., Burt, S.K., Erickson, J.W. Flap opening in HIV-1 protease simulated by "activated" molecular dynamics. Struct. Biol. 2:334-338, 1995.
28. Elber, R., Chen, D.P., Rojewska, D., Eisenberg, R. Sodium in gramicidin: An example of a permion. Biophys. J. 66:906-924, 1995.
29. Ferrenberg, A.M., Swendsen, R.H. Optimized Monte Carlo data analysis. Phys. Rev. Lett. 63:1195-1198, 1989.
30. Kumar, S., Bouzida, D., Swendsen, R.H., Kollman, P.A., Rosenberg, J.M. The weighted histrogram analysis method for free-energy calculations on biomolecules. I. The method. J. Comp. Chem. 13:1011-1021, 1992.
31. Elber, R., Roitberg, A., Simmerling, C. et al. "NATO Conference Proceeding on 'Statistical Mechanics and Protein Structure'." Doniach S. (ed.). New York: Plenum Press, 1994:165-191.
32. Pearlman, D.A., Case, D.A., Caldwell, J.W. "Amber 4.1." San Francisco: University of California, 1995.
33. Cornell, W.D., Cieplak, P., Bayly, C.I. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117:5179-5197, 1995.
34. York, D.M., Darden, T.A., Pedersen, L.G., Anderson, M.W. Molecular dynamics simulation of HW-1 protease in a crystalline environment and in solution. Biochemistry 32:1443-1453, 1993.
35. Jorgensen, W.L., Chandrasekhar, J., Madura, J.D., Impey, R.W., Klein, M.L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:926-9357 1983.
36. Allen, M.P., Tildesley, D.J. "Computer Simulation of Liquids." Oxford, UK: Oxford University Press, 1987.
37. York, D.M., Darden, T.A., Pedersen, L.G. The effect of long-range electrostatic interactions in simulations of macromolecular crystals: A comparison of the Ewald and truncated list methods. J. Chem. Phys. 99:8345-8348, 1993.
38. Berendsen, H.J.C., Postma, J.P.M., Gunsteren, W.F.V., DiNola, A., Haak, J.R. Molecular dynamics with coupling to to an external bath. J. Chem. Phys. 81:3684-36901 1984.
39. Harte, W.E., Jr., Swaminathan, S., Mansuri, M.M., Martin, J.C., Rosenberg, I.E., Beveridge, D.L. Domain communication in the dynamical structure of human immunodeficiency virus I protease. Proc. Natl. Acad. Sci. USA 87:8864-8868, 1990.
40. Jorgensen, W.L., Gao, J. Cis-trans energy difference for the peptide bond in the gas phase and in aqueous solution. J. Am. Chem. Soc. 110:4212-4216, 1988.
41. Cieplak, P., Kollman, P. On the use of electrostatic potential derived charges in molecular mechanics force fields. The relative salvation free energy of Cis- and Trans-N-methyl-acetamide. J. Comp. Chem. 12:1232,1991.
42. Rick, S.W., Berne, B.J. Dynamical fluctuating force fields: The aqueous salvation of amides. J. Am. Chem. Soc. 118:672-679, 1996.
43. Rutenber, E., Fauman, E.B., Keenan, R.J. Structure of a non-peptide inhibitor completed with HIV-1 protease. J. Biol. Chem. 268:15343-15346, 1993.
44. Kraulis, P.J. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J. Appl. Cryst. 24:946-950, 1991.