Electrostatic coupling to pH-titrating sites as a source of cooperativity in protein-ligand binding

Protein Science

Volumn 7, Issue 9, 1998, Pages 2012-2025

  Spassov, Velin ^a,b   Bashford, Donald ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

^b INSTITUTE OF BIOPHYSICS AND BIOMEDICAL ENGINEERING   (Bulgaria)

Author keywords

Allostery; Calbindin D(9k) cooperativity; Electrostatics; Linked equilibrium; Multisite titration; pH titration of proteins; pK(a) values in proteins

Indexed keywords

CALBINDIN; CALCIUM; LIGAND; PROTEIN;

ARTICLE; BINDING SITE; COOPERATION; ELECTRICITY; LIGAND BINDING; PH; PKA; PRIORITY JOURNAL; PROTEIN BINDING; PROTON TRANSPORT; TITRIMETRY;

EID: 0031659673     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1002/pro.5560070918     Document Type: Article

References (34)

1. Ackers GK, Shea MA, Smith FR. 1983. Free energy coupling within macromolecules: The chemical work of ligand binding at the individual sites in cooperative systems. J Mol Biol 170:233-242.
2. 2 binding pathway. J Mol Biol 252:102-121.
3. a values of ionizable groups in bacteriorhodopsin. J Mol Biol 224:473-486.
4. a's of ionizable groups in proteins: Atomic detail from a continuum electrostatic model. Biochemistry 29:10219-10225.
5. Bashford D, Karplus M. 1991. Multiple-site titration curves of proteins: An analysis of exact and approximate methods for their calculation. J Phys Chem 95:9556-9561.
6. Bernstein FC, Koetzle TF, Williams GJB, Meyer EF Jr, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M. 1977. The protein data bank: A computer-based archival file for macromolecular structures. J Mol Biol 112:535-542.
7. Beroza P, Fredkin DR, Okamura MY, Feher G. 1991. Protonation of interacting residues in a protein by Monte Carlo method: Application to lysozyme and the photosynthetic reaction center of Rhodobacter sphaeroides. Proc Natl Acad Sci USA 88:5804-5808.
8. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. 1983. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J Comp Chem 4:187-217.
9. Brünger AT, Karplus M. 1988. Polar hydrogen positions in proteins: Empirical energy placement and neutron diffraction comparison. Proteins 4:148-156.
10. 9k. J Mol Biol 231:415-430.
11. Di Cera E. 1995. Thermodynamic theory of site-specific binding processes in biological molecules. Cambridge, England and New York: Cambridge University Press.
12. Forsén S, Linse S. 1995. Cooperativity: Over the hill. TIBS 20:495-497.
13. Gilson MK. 1993. Multiple-site titration and molecular modeling: Two rapid methods for computing energies and forces for ionizable groups in proteins. Proteins 15:266-282.
14. Hill TL. 1985. Cooperativity theory in biochemistry. New York, Berlin, Heidelberg, Tokyo: Springer-Verlag.
15. Koshland DE, Nemethy G, Filmer D. 1966. Comparison of experimental binding data and theoretical models in proteins containing subunits. Biochemistry 5:365-385.
16. 9k. Biochemistry 26:6723-6735.
17. Linse S, Brodin P, Johansson C, Thulin E, Grundstrom T, Forsén S. 1988. The role of protein surface charges in ion binding. Nature 335:651-652.
18. 9k. Biochemistry 30:154-162.
19. MacKerell AD Jr, Wiorkiewicz-Kuczera J, Karplus M. 1995. An all-atom empirical energy function for the simulation of nucleic acids. J Am Chem Soc 48:11946-11975.
20. McQuarrie DA. 1976. Statistical mechanics. New York: Harper and Row.
21. Monod J, Wyman J, Changeaux JP. 1965. On the nature of allosteric transitions: A plausible model. J Mol Biol 12:88-118.
22. Sackett DL, Saroff HA. 1996. The multiple origins of cooperativity in binding to multi-site lattices. FEBS Lett 397:1-6.
23. Saroff HA. 1970. Model for the action of hemoglobin. Proc Nat Acad Sci USA 67:1662-1668.
24. Saroff HA. 1991. Ionization of clusters. IV. Cooperativity and allosterism derived from shared clusters in macromolecules. Biopolymers 31:1037-1047.
25. Saroff HA. 1993. Linked functions and the analysis of individual-site binding data. Anal Biochem 208:88-95.
26. Schellman JA. 1975. Macromolecular binding. Biopolymers 14:999-1018.
27. Spassov VZ, Karshikoff AD, Ladenstein R. 1994. Optimization of the electrostatic interactions in proteins of different functional and folding type. Protein Sci 3:1556-1569.
28. 9k observed by X-ray crystallography. J Mol Biol 223:601-606.
29. Tanford C, Kirkwood JG. 1957. Theory of protein titration curves. I. General equations for impenetrable spheres. J Am Chem Soc 79:5333-5339.
30. Tanford C, Roxby R. 1972. Interpretation of protein titration curves. Biochemistry 11:2192-2198.
31. Weber G. 1975. Energetics of ligand binding to proteins. Adv Prot Chem 29: 1-83.
32. Wyman J. 1964. Linked functions and reciprocal effects in hemoglobin. A second look. Adv Prot Chem 19:223-286.
33. as in proteins. Proteins 15:252-265.
34. You T, Bashford D. 1995. Conformation and hydrogen ion titration of proteins: A continuum electrostatic model with conformational flexibility. Biophys J 69:1721-1733.