The effect of protein relaxation on charge-charge interactions and dielectric constants of proteins

Biophysical Journal

Volumn 74, Issue 4, 1998, Pages 1744-1753

  Sham, Yuk Yin ^a   Muegge, Ingo ^a,b   Warshel, Arieh ^a  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^b ABBOTT LABORATORIES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; DIELECTRIC CONSTANT; MATHEMATICAL ANALYSIS; MATHEMATICAL MODEL; NONHUMAN; PROTEIN ANALYSIS; RHODOBACTER SPHAEROIDES; THERMODYNAMICS; WATER TRANSPORT;

RHODOBACTER SPHAEROIDES; RHODOPSEUDOMONAS;

EID: 0010624785     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(98)77885-3     Document Type: Article

References (40)

1. Alden, R. G., W. W. Parson, Z. T. Chu, and A. Warshel. 1995. Calculations of electrostatic energies in photosynthetic reaction centers. J. Am. Chem. Soc. 117:12284-12298.
2. B in the reaction center. Biophys. J. 68:2233-2250.
3. Buono, G. S., F. E. Figueirido, and R. M. Levy. 1994. Intrinsic pKas of ionizable residues in proteins: an explicit solvent calculation for lysozyme. Proteins Struct. Funct. Genet. 20:85-97.
4. Cutler, R. L., A. M. Davies, S. Creighton, A. Warshel, G. R. Moore, M. Smith, and A. G. Mauk. 1989. Role of arginine-38 in regulation of the cytochrome c oxidation-reduction equilibrium. Biochemistry. 28: 3188-3197.
5. Demchuk, E., and R. C. Wade. 1996. Improving the continuum dielectric approach to calculating pKas of ionizable groups in proteins. J. Phys. Chem. 100:17373-17387.
6. Ennler, U., G. Fritzsch, S. K. Buchanan, and H. Michel. 1994. Structure of the photosynthetic reaction center from Rhodobacter sphaeroides at 2.65 angstrom resolution: cofactors and protein-cofactors interactions. Structure. 2:925-936.
7. Gilson, M. K. 1995. Theory of electrostatic interactions in macromolecules. Curr. Opin. Struct. Biol. 5:216-223.
8. Hwang, J. K., and A. Warshel. 1988. Why ion pair reversal by protein engineering is unlikely to succeed. Nature. 334:270-273.
9. King, G., F. S. Lee, and A. Warshel. 1991. Microscopic simulations of macroscopic dielectric constants of solvated proteins. J. Chem. Phys. 95:4366-4377.
10. King, G., and A. Warshel. 1989. A surface constrained all-atom solvent model for effective simulations of polar solutions. J. Chem. Phys. 91:3647-3661.
11. Lancaster, C. R. D., H. Michel, B. Honig, and M. R. Gunner. 1996. Calculated coupling of electron and proton transfer in the photosynthetic reaction center of Rhodopseudomonas viridis. Biophys. J. 70: 2469-2492.
12. 52→Ile mutation on the redox potential of yeast cytochrome c. J. Mol. Biol. 224:589-600.
13. Lee F. S., Z. T. Chu, M. B. Bolger, and A. Warshel. 1992. Calculations of antibody-antigen interactions: microscopic and semi-microscopic evaluation of the free energies of binding of phosphorylcholine analogs to McPC603. Protein Eng. 5:215-228.
14. Lee, F. S., Z. T. Chu, and A. Warshel. 1993. Microscopic and semimicroscopic calculations of electrostatic energies in proteins by the POLARIS and ENZYMIX programs. J. Comp. Chem. 14:161-185.
15. Lee, F. S., and A. Warshel. 1992. A local reaction field method for fast evaluation of long-range electrostatic interactions in molecular simulation. J. Chem. Phys. 97:3100-3107.
16. Matthew, J. B. 1985. Electrostatic effects in proteins. Annu. Rev. Biophys. Biophys. Chem. 14:387-417.
17. Mehler, E. L. 1996. Self-consistent, free-energy based approximation to calculate pH dependent electrostatic effects in proteins. J. Phys. Chem. 100:16006-16018.
18. Muegge, I., T. Schweins, R. Langen, and A. Warshel. 1996. Electrostatic control of GTP and GDP binding in the oncoprotein p21ras. Structure. 4:475-489.
19. Muegge, I., H. Tao, and A. Warshel. 1998. A fast estimate of electrostatic group contributions to the free energy of protein-inhibitor binding. Protein Eng. (in press).
20. Nakamura, H. 1996. Roles of electrostatic interaction in proteins. Q. Rev. Biophys. 29:1-90.
21. Perutz, M. F. 1978. Electrostatic effects in proteins. Science. 201: 1187-1191.
22. Rees, D. C. 1980. Experimenbtal evaluation of the effective dielectric constant of proteins. J. Mol. Biol. 141:323-326.
23. Russell, S. T., and A. Warshel. 1985. Calculations of electrostatic energies in proteins: the energetics of ionized groups in bovine pancreatic trypsin inhibitor. J. Mol. Biol. 185:389-404.
24. Sham, Y. Y., Z. T. Chu, and A. Warshel. 1997. Consistent calculations of pKa's of ionizable residues in proteins: semi-microscopic and microscopic approaches. J. Phys. Chem. B. 101:4458-4472.
25. Sharp, K. A., and B. Honig. 1990b. Electrostatic interactions in macromolecules: theory and applications. Annu. Rev. Biophys. Biophys. Chem. 19:301-332.
26. Simonson, T., and D. Perahia. 1995. Microscopic dielectric properties of cytochrome c from molecular dynamics simulations in aqueous solution. J. Am. Chem. Soc. 117:7987-8000.
27. Svensson, B., and B. Jönsson. 1995. An efficient simulation technique for electrostatic free energies with application to azurin. J. Comp. Chem 16:370-377.
28. Warshel, A. 1978. The energetics of enzyme catalysis. Proc. Natl. Acad. Sci. USA. 75:5250-5254.
29. Warshel, A. 1979. Conversion of light energy to electrostatic energy in the proton pump of Halobacterium halobium. Photochem. Photabiol. 30: 285-290.
30. a, proton transfer reactions, and general acid catalysis reactions in enzymes. Biochemistry. 20:3167-3177.
31. Warshel, A. 1981b. Electrostatic basis of structure-function correlation in proteins. Acc. Chem. Res. 14:284-290.
32. Warshel, A. 1986. Correlation between the structure and efficiency of light induced proton pumps. Methods Enzymol. 127:578-587.
33. Warshel, A., and J. Åqvist. 1991. Electrostatic energy and macromolecular function. Annu. Rev. Biophys. Biophys. Chem. 20:267-298.
34. Warshel, A., and M. Levitt. 1976. Theoretical studies of enzymatic reactions. I. Dielectric electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. J. Mol. Biol. 103:227-249.
35. Warshel, A., A. Papazyan, and I. Muegge. 1997. Microscopic and semimicroscopic redox calculation: what can and cannot be learned from continuum models. J. Biol. Inorg. Chem. 2:143-152.
36. Warshel, A., and S. T. Russell. 1984. Calculations of electrostatic interactions in biological systems and in solutions. Q. Rev. Biol. 17:283-422.
37. Warshel, A., and S. T. Russell. 1985. Simulating solvent and dielectric effects. In Molecular Dynamics and Protein Structure. Polycrystal Book Service, Western Springs, IL. 23.
38. Warshel, A., S. T. Russell, and A. K. Churg. 1984. Macroscopic models for studies of electrostatic interactions in proteins: limitations and applicability. Proc. Natl. Acad. Sci. USA. 81:4785-4789.
39. Warwicker, J., and H. C. Watson. 1982. Calculation of the electric potential in the active site cleft due to alpha-helix dipoles. J. Mol. Biol. 157: 671-679.
40. Yang, A. S., M. R. Gunner, R. Sampogna, K. Sharp, and B. Honig. 1993. On the calculation of pKas in proteins. Proteins Struct. Fund. Genet. 15:252-265.