Effects of medium polarization and pre-existing field on activation energy of enzymatic charge-transfer reactions

Biochimica et Biophysica Acta - Bioenergetics

Volumn 1459, Issue 1, 2000, Pages 88-105

  Krishtalik, L I ^a   Topolev, V V ^a  

^a FRUMKIN INSTITUTE OF PHYSICAL CHEMISTRY AND ELECTROCHEMISTRY   (Russian Federation)

Author keywords

Dielectric model of enzyme; Globule optimum radius; Hydrolytic enzyme; Intraprotein charge transfer; Polarization of a protein globule

Indexed keywords

CHYMOTRYPSIN A; ENZYME; HYDROLASE; LYSOZYME; PROTEIN; RIBOZYME; SERINE CARBOXYPEPTIDASE; SUBTILISIN;

ARTICLE; DIELECTRIC CONSTANT; ENERGY; GEOMETRY; MODEL; POLARIZATION; PRIORITY JOURNAL;

CARBOXYPEPTIDASES; CATALYSIS; ELECTROMAGNETIC FIELDS; ELECTROSTATICS; ENERGY TRANSFER; ENZYME ACTIVATION; ENZYMES; MURAMIDASE; PAPAIN; PROTEINS; SOLUTIONS; SUBTILISIN;

EID: 0034691755     PISSN: 00052728     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0005-2728(00)00116-X     Document Type: Article

References (58)

1. Perutz M.F. Concluding remarks [to discussion on the structure and function of lysozyme]. Proc. R. Soc. London, Ser. B. 167:1967;448-450.
2. L.I. Krishtalik, Charge Transfer Reactions in Electrochemical and Chemical Processes, Plenum, New York, 1986.
3. L.I. Krishtalik, Charge-medium interactions in biological charge transfer reactions, in: R.R. Dogonadze, E. Kálmán, A.A. Kornyshev, J. Ulstrup (Eds.), The Chemical Physics of Solvation, Part C, Elsevier, Amsterdam, 1988, pp. 707-739.
4. Krishtalik L.I. The specific features of enzyme as a polar medium and their role in the mechanism of the enzymatic process. Mol. Biol. (Moscow). 8:1974;91-99.
5. Dogonadze R.R., Kuznetsov A.M. Theory of charge transfer kinetics at solid-polar liquid interfaces. Prog. Surf. Sci. 6:1975;1-42.
6. Marcus R.A., Sutin N. Electron transfers in chemistry and biology. Biochim. Biophys. Acta. 811:1985;265-322.
7. A.M. Kuznetsov, J. Ulstrup, M.A. Vorotyntsev, Solvent effects in charge transfer processes, in: R.R. Dogonadze, E. Kálmán, A.A. Kornyshev, J. Ulstrup (Eds.), The Chemical Physics of Solvation, Elsevier, Amsterdam, 1988, pp. 163-273.
8. Krishtalik L.I. Globule size and the activation energy of an enzymatic process. Mol. Biol. (Moscow). 13:1979;577-581.
9. Krishtalik L.I. Catalytic acceleration of reactions by enzymes. Effect of screening of a polar medium by a protein globule. J. Theor. Biol. 86:1980;757-771.
10. Zhou H.-X. Effects of mutations and complex formation on the redox potentials of cytochrome c and cytochrome c peroxidase. J. Am. Chem. Soc. 116:1994;10362-10375.
11. Churg A.K., Weiss R.M., Warshel A., Takano T. On the action of cytochrome c: correlating geometry changes upon oxidation with activation energies of electron transfer. J. Phys. Chem. 87:1983;1683-1694.
12. Creighton S., Hwang J.K., Warshel A., Parson W.W., Norris J. Simulating the dynamics of the primary charge separation process in bacterial photosynthesis. Biochemistry. 27:1988;774-781.
13. Warshel A., Chu Z.T., Parson W.W. Dispersed polaron simulations of electron transfer in photosynthetic reaction centers. Science. 246:1989;112-116.
14. Parson W.W., Chu Z.-T., Warshel A. Electrostatic control of charge separation in bacterial photosynthesis. Biochim. Biophys. Acta. 1017:1990;251-272.
15. Schulten K., Tesch M. Coupling of protein motion to electron transfer molecular dynamics and stochastic quantum mechanics study of photosynthetic reaction center. Chem. Phys. 158:1991;421-446.
16. Zheng C., McCammon J.A., Wolynes P.G. Quantum simulation of conformation reorganization in the electron transfer reactions of tuna cytochrome c. Chem. Phys. 158:1991;261-270.
17. Yadav A., Jackson R.M., Holbrook J.J., Warshel A. Role of solvent reorganization energies in the catalytic activities of enzymes. J. Am. Chem. Soc. 113:1991;4800-4805.
18. Treutlein M., Schulten K., Brünger A.T., Karplus M., Deisenhofer J., Michel H. Chromophore-protein interactions and the function of the photosynthetic reaction center: A molecular dynamics study. Proc. Natl. Acad. Sci. USA. 89:1992;75-79.
19. Marchi M., Gehlen J.N., Chandler D., Newton M. Diabatic surfaces and the pathway for primary electron transfer in a photosynthetic reaction center. J. Am. Chem. Soc. 115:1993;4178-4190.
20. - interconversion step in human carbonic anhydrase I. J. Am. Chem. Soc. 115:1993;631-635.
21. Parson W.W., Chu Z.-T., Warshel A. Reorganization energy of the initial electron-transfer step in photosynthetic bacterial reaction centers. Biophysic. J. 74:1998;182-191.
22. L.I. Krishtalik, E.L. Mertz, V.V. Topolev, Proteins as specific media for charge transfer reactions, in A.A. Kornyshev, M. Tosi, J. Ulstrup (Eds.), Electron and Ion Transfer in Condensed Media (Proceedings of the Adriatico Research Conference at the Itnl. Centre for Theor. Phys.), World Scientific, Singapore, 1997, pp. 372-401.
23. Krishtalik L.I., Mertz E.L., Topolev V.V. Proteins as low-reorganization energy media for charge-transfer reactions. Biophys. J. 72:1997;A237.
24. L.I. Krishtalik, Specific effects of proteins as polar media on the intraprotein charge transfer reactions, in: Fourth European Biological Inorganic Chemistry Conference, Book of Abstracts, Seville, 1998, PL-3.
25. Krishtalik L.I., Kharkatz Yu.I. Medium reorganization energy in the charge transfer reactions in a protein globule. Biofizika. 29:1984;19-22.
26. Kharkatz Yu.I., Krishtalik L.I. Medium reorganization energy and enzymatic reaction activation energy. J. Theor. Biol. 112:1985;221-249.
27. Liu Y.-P., Newton M.D. Reorganization energy for electron transfer at film-modified electrode surfaces: a dielectric continuum model. J. Phys. Chem. 98:1994;7162-7169.
28. Marcus R.A. Free energy of nonequilibrium polarization systems. 4. A formalism based on the nonequilibrium dielectric displacement. J. Phys. Chem. 98:1994;7170-7174.
29. Medvedev I.G., Kuznetsov A.M. Activation free energy of the nonadiabatic process of electron transfer and the reorganization energy of the nonhomogeneous nonlocal medium. J. Phys. Chem. 100:1996;5721-5728.
30. J.A. Stratton, Electromagnetic Theory, McGraw-Hill, New York, 1941.
31. Krishtalik L.I. Intramembrane electron transfer: processes in photosynthetic reaction center. Biochim. Biophys. Acta. 1273:1996;139-149.
32. Krishtalik L.I. On the theory of charge transfer enzymatic reactions. Mol. Biol. (Moscow). 15:1981;290-297.
33. Krishtalik L.I., Kuznetsov A.M., Mertz E.L. Electrostatics of proteins: description in terms of two dielectric constants simultaneously. Proteins Struct. Funct. Genet. 28:1997;174-182.
34. Krishtalik L.I., Topolev V.V. The intraglobular electric field of an enzyme. I. The primary field set up by the polypeptide backbone, functional groups and ions of the α-chymotrypsin molecule. Mol. Biol. (Moscow). 17:1983;1034-1041.
35. Topolev V.V., Krishtalik L.I. The intraglobular electric field of an enzyme. II. The influence of polarization of surrounding medium. Mol. Biol. (Moscow). 17:1983;1177-1185.
36. Khoshtariya D.E., Topolev V.V., Krishtalik L.I. Study of proton transfer in enzymatic hydrolysis by the method of the temperature dependence of the kinetic isotope effect. I. α-chymotrypsin catalyzed hydrolysis of N-acetyl- and N-benzoyl-L-tyrosine ethyl esters. Bioorg. Khim. 4:1978;1341-1351.
37. Khoshtariya D.E. Study of proton transfer in enzymatic hydrolysis by the method of the temperature dependence of the kinetic isotope effect. II. Hydrolysis of Bz-Arg-OEt by β-trypsin. Bioorg. Khim. 4:1978;1673-1677.
38. Khoshtariya D.E., Topolev V.V., Krishtalik L.I., Reyzer I.L., Torchilin V.P. Study of proton transfer in enzymatic hydrolysis by the method of the temperature dependence of the kinetic isotope effect. III. Hydrolysis of N-acetyl- and N-benzoyl-L-tyrosine ethyl esters by α-chymotrypsin immobilized on soluble dextran. Bioorgan. Khim. 5:1979;1243-1247.
39. Kossiakoff A.A., Spencer S.A. Direct determination of the protonated states of aspartic acid-102 and histidine-57 in the tetrahedral intermediate of the serine proteases neutron structure of trypsin. Biochemistry. 20:1981;6462-6474.
40. Elrod J.P., Hogg J.L., Quinn D.M., Venkatasubban K.S., Schowen R.L. Protonic reorganization and substrate structure in catalysis by serine proteases. J. Am. Chem. Soc. 102:1980;3917-3922.
41. R.L. Schowen, Structural and energetic aspects of protolytic catalysis by enzymes: charge-relay catalysis in the function of serine proteases, in: J.F. Liebman, A. Greenberg (Eds.), Mechanistic Principles of Enzyme Activity, VCH, New York, 1988, pp. 119-168.
42. Fujinaga M., Sielecki A.R., Read R.J., Ardelt W., Laskowski M. Jr., James M.N.G. Crystal and molecular structures of the complex of alpha-chymotrypsin with its inhibitor turkey ovomucoid third domain at 1.8 Angstroms resolution. J. Mol. Biol. 195:1987;397-418.
43. Bode W., Papamokos E., Musil D. The high-resolution X-ray crystal structure of the complex formed between subtilisin Carlsberg and eglin-C, an elastase inhibitor from the leech Hirudo medicinalis. Structural analysis, subtilisin structure and interface geometry. Eur. J. Biochem. 166:1987;673-692.
44. Liao D.-I., Breddam K., Sweet R.M., Bullock T., Remington S.I. Refined atomic model of wheat serine carboxypeptidase II at 2.2-Angstrom resolution. Biochemistry. 31:1992;9796-9812.
45. A.C. Starer, R. Ménard, Catalytic mechanism in papain family of cysteine peptidases, in: A.J. Barrett (Ed.), Methods in Enzymology, Vol. 244, Proteolytic Enzymes: Serine and Cysteine Peptidases, Academic Press, San Diego, 1994, pp. 486-500.
46. Schröder E., Phillips C., Garman E., Harlos K., Crawford C. X-ray crystallographic structure of a papain-leupeptin complex. FEBS Lett. 315:1993;38-42.
47. G. Mooser, Glycosidases and glycosyltransferases, in: D.S. Sigman (Ed.), The Enzymes, Vol. 20, Mechanisms of Catalysis, 3rd Edn., Harcourt Brace Jovanovich, San Diego, 1992, pp. 187-233.
48. Cheetham J.C., Artymiuk P.J., Phillips D.C. Refinement of an enzyme complex with inhibitor bound at partial occupancy. Hen egg-white lysozyme and tri-N-acetylchitotriose at 1.75 Angstroms resolution. J. Mol. Biol. 224:1992;613-628.
49. N.D. Rawlings, A.J. Barrett, Families of serine peptidases, in: A.J. Barrett (Ed.), Methods in Enzymology, Vol. 244, Proteolytic Enzymes: Serine and Cysteine Peptidases, Academic Press, San Diego, 1994, pp. 19-60.
50. Krishtalik L.I. Effective activation energy of enzymatic and nonenzymatic reactions. Evolution-imposed requirements to enzyme structure. J. Theor. Biol. 112:1985;251-264.
51. Krishtalik L.I. Fast electron transfers in photosynthetic reaction centre: effect of the time-evolution of dielectric response. Biochim. Biophys. Acta. 1228:1995;58-66.
52. Honig B.H., Hubbell W.L., Flewelling R.F. Electrostatic interaction in membranes and proteins. Annu. Rev. Biophys. Biophys. Chem. 15:1986;163-194.
53. Harvey S.C. Treatment of electrostatic effects in macromolecular modeling. Proteins. 5:1989;78-92.
54. Davis M.E., McCammon J.A. Electrostatics in biomolecular structure and dynamics. Chem. Rev. 90:1990;509-521.
55. Sharp K.A., Honig B.H. Electrostatic interactions in macromolecules: theory and applications. Annu. Rev. Biophys. Biophys. Chem. 19:1990;301-332.
56. Warshel A., Åqvist J. Electrostatic energy and macromolecular function. Annu. Rev. Biophys. Biophys. Chem. 20:1991;267-298.
57. Cech T.R., Herschlag D., Piccirilli J.A., Pyle A.M. RNA catalysis by a group I rybozyme. Developing a model for transition state stabilization. J. Biol. Chem. 267:1992;17479-17482.
58. Cate J.H., Gooding A.R., Podell E., Zhou K., Golden B.L., Kundrot C.E., Cech T.R., Dounda J.A. Crystal structure of a group I ribozyme domain: principles of RNA packing. Science. 273:1996;1678-1685.