Enzyme-inhibitor association thermodynamics: Explicit and continuum solvent studies

Biophysical Journal

Volumn 72, Issue 2 I, 1997, Pages 522-532

  Resat, Haluk ^a,b   Marrone, Tami J ^a   McCammon, J Andrew ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b KOÇ UNIVERSITY   (Turkey)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BINDING SITE; CRYSTAL STRUCTURE; ENZYME INHIBITOR COMPLEX; SIMULATION; SOLVATION; SYSTEM ANALYSIS; THERMODYNAMICS;

EID: 0031012579     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(97)78692-2     Document Type: Article

References (43)

1. Adams, D. J. 1975. Grand canonical ensemble (Monte Carlo) for a Lennard-Jones fluid. Mol. Phys. 29:307-311.
2. Antosiewicz, J., J. A. McCammon, and M. K. Gilson. 1994. Prediction of pH-dependent properties of proteins J. Mol. Biol. 238:415-436.
3. Beglov, D., and B. Roux. 1994. Finite representation of an infinite bulk system: solvent boundary potential for computer simulations. J. Chem. Phys. 100:9050-9063.
4. Bode, W., and P. Schwager. 1975. The refined crystal structure of bovine β-trypsin at 1.8 Å resolution. II. Crystallographic refinement, calcium binding site, benzamidine binding site and active site at pH 7.0. J. Mol. Biol. 98:693-717.
5. Bode, W., P. Schwager, and R. Huber. 1976. Structural studies of the pancreatic trypsin inhibitor-trypsin complex and its free components: structure and function relationship in serine protease inhibition and catalysis. In Proteolysis and Physiological Regulation, Miami Winter Symposia Series, Vol. 11. D. W. Ribbons and K. Brew, editors. Academic Press, New York. 43-76.
6. Bode, W., P, Schwager, and R. Huber. 1978. The transition of bovine trypsinogen to a trypsin-like state upon strong ligand binding. The refined crystal structures of the bovine trypsinogen-pancreatic trypsin inhibitor and of its ternary complex with Ile-Val at 1.9 Å resolution. J. Mol. Biol. 118:99-112.
7. Connolly, M. L. 1983. Analytical molecular surface calculation. J. Appl. Crystall. 16:548-558.
8. Davis, M. E., J. D. Madura, B. A. Luty, and J. A. McCammon. 1991. Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian dynamics program. Comput. Phys. Commun. 62:187-197.
9. Eisenberg, D., and A. D. McLachlan. 1986. Solvation energy in protein folding and binding. Nature. 319:199-203.
10. Finer-Moore, J. S., A. A. Kossiakoff, J. H. Hurley, T. Earnest, and R. M. Stroud. 1992. Solvent structure in crystals of trypsin determined by X-ray and neutron diffraction. Proteins Struct. Funct. Genet. 12:203-222.
11. Friedman, H. L. 1985. A Course in Statistical Mechanics. Prentice-Hall, Englewood Cliffs, NJ.
12. Frisch, M. J., G. W. Trucks, M. Head-Gordon, P. M. W. Gill, M. W. Wongand, J. B. Foresman, B. G. Johnson, H. B. Schlegel, M. A. Robb, E. S. Replogle, R. Gomperts, J. L. Andres, K. Raghavachari, J. S. Binkley, C. Gonzalez, R. L. Martin, D. J. Fox, D. J. Defrees, J. Baker, J. J. P. Stewart, and J. A. Pople. 1992. Baussian 92. Gaussian, Inc., Pittsburgh, PA.
13. Gilson, M. 1995. Theory of electrostatic interactions in macromolecules Curr. Opin. Struct. Biol. 5:216-223.
14. Honig, B., and A. Nicholls. 1995. Classical electrostatics in biology and chemistry. Science. 268:1144-1149.
15. Horvath, D., D. van Belle, G. Lippens, and S. J. Wodak. 1996-Development and parametrization of continuum solvent models. I. Models based on the boundary element method. J. Chem. Phys. 104:6679-6695.
16. Huber, R., D. Kukla, W. Bode, P. Schwager, K. Bartels, J. Deisenhofer, and W. Steigemann. 1974. Structure of the complex formed by bovine trypsin and bovine pancreatic trypsin inhibitor. II. Crystallographic refinement at 1.9 Å resolution. J. Mol. Biol. 89:73-101.
17. Jorgensen, W. L., J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein. 1983. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:926-935.
18. Jorgensen, W. L., and J. Tirado-Rives. 1988. The OPLS potential functions for proteins. Energy minimizations for crystals of cyclic peptides and crambin. J. Am. Chem. Soc. 110:1657-1666.
19. Lounnas, V., and B. M. Pettitt. 1994. A connected-cluster of hydration around myoglobin: correlation between molecular dynamics simulations and experiment. Proteins Struct. Funct. Genet. 18:133-147.
20. Luty, B. A., Z. R. Wasserman, P. F. W. Stouten, C. N. Hodge, M. Zacharias, and J. A. McCammon. 1995. A molecular mechanics/grid method for evaluation of ligand-receptor interactions. J. Comp. Chem. 16:454-464.
21. Lybrand, T. P. 1995. Ligand-protein docking and rational drug design. Curr. Opin. Struct. Biol. 5:224-228.
22. Madura, J. D., M. E. Davis, M. K. Gilson, R. C. Wade, B. A. Luty, and J. A. McCammon. 1994. Biological applications of electrostatic calculations and brownian dynamics simulations. Rev. Comp. Chem. 5:229-267.
23. Mares-Guia, M., D. L. Nelson, and E. Rogana. 1977. Electronic effects in the interaction of para-substituted benzamidines with trypsin: the involvement of the π-electronic density at the central atom of the substituent in binding. J. Am. Chem. Soc. 99:2331-2336.
24. Marquart, M., J. Walter, J. Deisenhofer, W. Bode, and R. Huber. 1983. The geometry of the reactive site and of the peptide groups in trypsin, trypsinogen and its complexes with inhibitors. Acta Crystallogr. B. 39:480-490.
25. Marrone, T. J., J. M. Briggs, and J. A. McCammon. 1997. Structure based drug design computational advances. Annu. Rev. Pharmacol. Toxicol. 37: in presss.
26. Mezei, M. 1987. Adaptive umbrella sampling: self-consistent determination of the non-Boltzmann bias. J. Comput. Phys. 68:237-248.
27. Mezei, M., and D. L. Beveridge. 1984. Generic solvent sites in a crystal. J. Comput. Chem. 5:523-527.
28. Mezei, M., and D. L. Beveridge. 1986. Free energy simulations. Ann. N.Y. Acad. Sci. 482:1-23.
29. Patey, G. N., and J. P. Valleau. 1975. A Monte Carlo method for obtaining the interionic potential of mean force inionic solution. J. Chem. Phys. 63:2334-2339.
30. Pettitt, B. M., M. Karplus, and P. J. Rossky. 1986. Integral equation model for aqueous solvation of polyatomic solutes: application to the determination of the free energy surface for the internal motion of biomolecules. J. Phys. Chem. 90:6335-6345.
31. Pratt, L. R., G. Hummer, and A. E. Garcia. 1994. Ion pair potentials of mean force in water. Biophys. Chem. 51:147-165.
32. Rashin, A. A. 1989. Electrostatics of ion-ion interactions in solution. J. Phys. Chem. 93:4664-4669.
33. Rashin, A. A., and K. Namboodiri. 1987. A simple method for the calculation of hydration enthalpies of polar molecules with arbitrary shapes. J. Phys. Chem. 91:6003-6012.
34. Resat, H., and M. Mezei. 1994. Grand canonical Monte Carlo simulation of water positions in crystal hydrates. J. Am. Chem. Soc. 116:7451-7452.
35. Resat, H., and M. Mezei. 1996. Grand canonical ensemble Monte Carlo simulation of the dCpG/proflavine crystal hydrate. Biophys. J. 71: 1179-1190.
36. Resat, H., M. Mezei, and J. A. McCammon. 1996. Use of the grand canonical ensemble in potential of mean force calculations. J. Phys. Chem. 100:1426-1433.
37. Simonson, T., and A. T. Brunger. 1994. Solvation free energies estimated from macroscopic continuum theory: an accuracy assessment. J. Phys. Chem. 98:4683-4694.
38. Sitkoff, D., K. A. Sharp, and B. Honig. 1994. Accurate calculation of hydration free energies using macroscopic solvent models. J. Phys. Chem. 98:1978-1988.
39. Soman, K., A.-S. Yang, B. Honig, and R. Fletterick. 1989. Electrical potentials in trypsin isozymes. Biochemistry. 28:9918-9926.
40. Straatsma, T. P., and J. A. McCammon. 1992. Computational alchemy. Annu. Rev. Phys. Chem. 43:407-35.
41. Walter, J., W. Steigemann, T. P. Singh, H. Bartunik, W. Bode, and R. Huber. 1982. On the disordered activation domain in trypsinogen. Chemical labelling and low-temperature crystallography. Acta Crystallogr., Sect. B. 38:1462.
42. Wong, C. F., and J. A. McCammon. 1986a. Computer simulation and the design of new biological molecules. Isr. J. Chem. 27:211-215.
43. Wong, C. F., and J. A. McCammon. 1986b. Dynamics and design of enzymes and inhibitors. J. Am. Chem. Soc. 108:3830-3832.