Modeling of protein conformational fluctuations in pK(a) predictions

Journal of Molecular Biology

Volumn 267, Issue 4, 1997, Pages 1002-1011

  Zhou, Huan Xiang ^a   Vijayakumar, Muthusamy ^a  

^a HONG KONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Hong Kong)

Author keywords

Conformational fluctuations; Cytochrome c; Electrostatic interactions; pK(a); Titration

Indexed keywords

CYTOCHROME C; PROTEIN; PROTON;

ARTICLE; CALCULATION; MOLECULAR DYNAMICS; MOLECULAR MODEL; PH; PKA; PRIORITY JOURNAL; PROTEIN CONFORMATION; SIMULATION; YEAST;

EID: 0031564641     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1997.0895     Document Type: Article

References (25)

1. Antosiewicz J., McCammon J. A., Gilson M. K. Prediction of pH-dependent properties of proteins. J. Mol. Biol. 238:1994;415-436.
2. as in proteins. Biochemistry. 35:1996;7819-7833.
3. Barker P. D., Mauk M. R., Mauk A. G. Proton titration of yeast iso-1-ferricytochrome c. Electrostatic and conformational effects of point mutations. Biochemistry. 30:1991;2377-2383.
4. avalues of ionizable groups in bacteriorhodopsin. J. Mol. Biol. 224:1992;473-486.
5. as of ionizable groups in proteins: atomic detail from a continuum electrostatic model. Biochemistry. 29:1990;10219-10225.
6. avalues in myoglobin and comparison with NMR data for histidines. Biochemistry. 32:1993;8045-8056.
7. Berghuis A. M., Brayer G. D. Oxidation state-dependent conformational changes in cytochrome c. J. Mol. Biol. 223:1992;959-976.
8. Beroza P., Fredkin D. R., Okamura M. Y., Feher G. Protonation of interacting residues in a protein by a Monte Carlo method: application to lysozyme and the photosynthetic reaction centre of Rhodobacter sphaeroides. Proc. Natl Acad. Sci. USA. 88:1991;5804-5808.
9. B-in the reaction center. Biophys. J. 68:1995;2233-2250.
10. Cutler R. L., Davies A. M., Creighton S., Warshel A., Moore G. R., Smith M., Mauk A. G. Role of arginine-38 in regulation of the cytochrome c oxidation-reduction equilibrium. Biochemistry. 28:1989;3188-3197.
11. acalculations. Biophys. J. 71:1996;138-147.
12. Hill T. L. An Introduction to Statistical Thermodynamics. 1986;Dover Publications Inc. New York.
13. a. Biochemistry. 30:1991;7609-7614.
14. Margalit R., Schejter A. Cytochrome c: a thermodynamic study of the relationships among oxidation state, ion-binding and structural parameters. 2. Ion-binding linked to oxidation state. Eur. J. Biochem. 32:1973;500-505.
15. avalues of titratable groups of an antigen-antibody complex, HyHEL-5-hen egg lysozyme. Protein Eng. 8:1995;915-924.
16. Oberoi H., Allewell N. M. Multigrid solution of the nonlinear Poisson-Boltzmann equation and calculation of titration curves. Biophys. J. 65:1993;48-55.
17. Sharp K. A., Honig B. Electrostatic interactions in macromolecules: theory and applications. Annu. Rev. Biophys. Chem. 19:1990;301-332.
18. Tanford C. Protein denaturation, part C. Advan. Protein Chem. 25:1970;1-95.
19. Warshel A., Russell S. T., Churg A. K. Macroscopic models for studies of electrostatic interactions in proteins: limitations and applicability. Proc. Natl Acad. Sci. USA. 81:1984;4785-4789.
20. Wendoloski J. J., Matthew J. B. Molecular dynamics effects on protein electrostatics. Proteins: Struct. Funct. Genet. 5:1989;313-321.
21. Yang A. S., Honig B. On the pH dependence of protein stability. J. Mol. Biol. 231:1993;459-474.
22. as in proteins. Proteins: Struct. Funct. Genet. 15:1993;252-265.
23. You T. J., Bashford D. Conformation and hydrogen ion titration of proteins: a continuum electrostatic model with conformational flexibility. Biophys. J. 69:1995;1721-1733.
24. Zhou H.-X. Boundary element solution of macromolecular electrostatics: interaction energy between two proteins. Biophys. J. 65:1993;955-963.
25. Zhou H.-X. Calculation of translational friction and intrinsic viscosity. II. Application to globular proteins. Biophys. J. 69:1995;2298-2303.