Catalytic Mechanisms

Chapter
First Online:

Abstract

The mechanisms of enzyme catalysis do not differ from those implicated in chemical catalysis. Enzymes however, due to the complexity of their three-dimensional structure, generally involve a greater number of efficiency factors than simple chemical catalysts. The principle of enzyme catalysis, like all catalysis, is to lower the energy barrier of a reaction, thereby increasing the rate of appearance of the products. There are two ways of lowering the energy barrier: either destabilising the initial state (1), or stabilising the transition state (2) in relation to the non-catalysed reaction (0), as is illustrated in Fig. 11.1. Catalysts can weaken strong substrate bonds or stabilise fractional bonds formed in activated complexes (transition states) in different manners: either by electrostatic interactions (polar effects), by covalent interaction with unpaired electrons, by creating distortions in the bond geometry, or by increasing resonance effects or internal inductive effects. In enzyme catalysis these diverse factors can intervene in the same reaction. The functional groups implicated in enzyme catalysis are of the same nature as those that are involved in chemical catalysis. They concern nucleophilic or electrophilic groups, acids or bases. It is important therefore to consider first the principles of chemical catalysis.

Keywords

Transition State Isotope Effect Enzyme Catalysis Nucleophilic Catalysis Catalytic Group 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
This is a preview of subscription content, log in to check access.

Bibliography

Books

  1. Bernhard S. –1968– Enzyme, struc-ture and function, Benjamin Inc., New York.Google Scholar
  2. Bruice T.C. & Benkovic S. –1966– Bioorganic mechanisms, Benjamin Inc., New York.Google Scholar
  3. Fersht A.N. –1984– Enzyme, struc-ture and mechanism 1rst ed. Freeman, New York.Google Scholar
  4. Fersht A.R. –1985– Enzyme, struc-ture and mechanism, 2nd ed., Freeman and Co, New York.Google Scholar
  5. Jencks W.P. –1969– Catalysis in chemistry and enzymology, Mc Graw Hill Book and Co, New York.Google Scholar
  6. Walsh C. –1979– Enzymatic reaction mechanisms, Freeman and Co, San Francisco.Google Scholar

General Reviews

  1. Bender M.L. –1960– Mechanisms of catalysis of nucleophilic reactions of carboxylic acid derivatives, in Chem. Rev. 60, 53–113.CrossRefGoogle Scholar
  2. Jencks W.P. –1975– Binding en-ergy, speci-ficity, and enzyme catalysis: the CIRCE effect, in Adv. Enzy-mol. 43, 219–410.Google Scholar

Specialised Articles

  1. Bash P.A., Field M.J., Davenport R.C., Petsko G.A., Ringe D. & Karplus M. –1991– Biochemistry 30, 5826.PubMedCrossRefGoogle Scholar
  2. Bechet J.J. & Yon J. –1964– Biochim. Biophys. Acta 89, 117.PubMedGoogle Scholar
  3. Bell R.P. & Kuhn A.T. –1963– Trans. Farad. Soc. 59, 1789.CrossRefGoogle Scholar
  4. Bender M.L., Begue Cantor M.L., Blakeley R.L., Brubacher L.J., Feder J., Gunter C.R., Kezdy F.J., Killhefer J.V., Marshall T.L., Miller C.G., Roeske R.W. & Stoops J.K. –1966– J. Am. Chem. Soc. 88, 5890.PubMedCrossRefGoogle Scholar
  5. Bender M.L., Kezdy F.J. & Gunter C.R. –1964– J. Am. Chem. Soc. 86, 3714.CrossRefGoogle Scholar
  6. Bruice T.C. & Bradbury W.C. –1965– J. Am. Chem. Soc. 87, 4846.PubMedCrossRefGoogle Scholar
  7. Brünger A.T., Brooks C.L. & Karplus M. –1985– Proc. Natl Acad. Sci. USA 82, 8458.PubMedCrossRefGoogle Scholar
  8. Bunton C.A. & Shiner V.J. –1961– J. Am. Chem. Soc. 83, 42.CrossRefGoogle Scholar
  9. Cannon and Berkovic –1998– J. Biol. Chem. 273, 26257.PubMedCrossRefGoogle Scholar
  10. Cannon W.R., Singleton S.S. & Benkovic S.T. –1998– Nat. Struct. Biol. 3, 821.CrossRefGoogle Scholar
  11. Cannon W.R. & Benkovic S.T. –1998– J. Biol. Chem. 273, 26257.PubMedCrossRefGoogle Scholar
  12. Chevallier J. & Yon J.M. –1966– Biochim. Biophys. Acta. 122, 116.PubMedCrossRefGoogle Scholar
  13. Cleland W.W., Frey P.A. & Gertl J.A. –1998– J. Biol. Chem. 273, 25529.PubMedCrossRefGoogle Scholar
  14. Collins K.D. & Stark G.R.–1969– J. Biol. Chem. 244, 1869.PubMedGoogle Scholar
  15. Cui Q. & Karplus M. –2001– J. Am. Chem. Soc. 123, 2284.PubMedCrossRefGoogle Scholar
  16. Dewar M.J.S. & Storch D.M. –1985– Proc. Natl Acad. Sci. USA 82, 2225.PubMedCrossRefGoogle Scholar
  17. Fersht A.R. & Kirby A.J. –1967– J. Am. Chem. Soc. 89, 4853 and 4857.PubMedCrossRefGoogle Scholar
  18. Fersht A.R. & Kirby A.J. –1968– J. Am. Chem. Soc. 90, 5818, 5826 and 5833.PubMedCrossRefGoogle Scholar
  19. Fersht A.R., Leatherbarrow R.J. & Wells T.N.C. –1986– Nature 332, 284.CrossRefGoogle Scholar
  20. Fersht A.R., Shi J.P., Knill-Jones J., Lowe D.M., Wilkinson A.J., Blow D.M., Brick P., Carter P., Ywaye M.M. & Winter G. –1985– Nature 314, 235.PubMedCrossRefGoogle Scholar
  21. Foucault G., Seydoux F. & Yon J.M. –1974– Eur. J. Biochem. 47, 295.PubMedCrossRefGoogle Scholar
  22. Hol W.G.–1985– Adv. Bio-phys. 19, 133.CrossRefGoogle Scholar
  23. Jencks W. & Gilchrist M. –1968– J. Am. Chem. Soc. 90, 2622.CrossRefGoogle Scholar
  24. Koshland D.E. –1962– J. Theor. Biol. 2, 75.CrossRefGoogle Scholar
  25. Koshland D.E., Néméthy G., & Filmer D. –1966– Biochemistry 5, 365.PubMedCrossRefGoogle Scholar
  26. Latherbarrow R.J., Fersht A.R. & Winter G. –1985– Proc. Natl Acad. Sci. USA 82, 7840.PubMedCrossRefGoogle Scholar
  27. Lipscomb W.N., Hartsuck J.A., Quiocho F.A. & Reeke G.N. –1969– Proc. Natl Acad. Sci. USA 64, 28.PubMedCrossRefGoogle Scholar
  28. Loew G.H. & Thomas D.D.–1972– J. Theoret. Biol. 36, 89.CrossRefGoogle Scholar
  29. Lowe D.M., Fersht A.N. & Wilkinson A.J. –1985– Biochemistry 24, 5106.PubMedCrossRefGoogle Scholar
  30. Marx J.L. –1986– Sci. Res. News 234, 141.Google Scholar
  31. Monnot M., Weintraub H. & Yon J.M. –1966– Bull. Soc. Chim. Biol. 48, 959.PubMedGoogle Scholar
  32. Northrop D.B. –1975– Biochemistry 14, 2644.PubMedCrossRefGoogle Scholar
  33. O’Keefe S.J. & Knowles J.R. –1986– Biochemistry 25, 6077.PubMedCrossRefGoogle Scholar
  34. Page M.I. –1973– Chem. Soc. Rev. 2, 295.CrossRefGoogle Scholar
  35. Pollack S.J., Jacobs J.W. & Schultz P.G. –1986– Science 234, 1570.PubMedCrossRefGoogle Scholar
  36. Pompon D. & Lederer F. –1985– Eur. J. Biochem. 148, 145.PubMedCrossRefGoogle Scholar
  37. Seydoux F. & Yon J.M. –1971– Biochem. Biophys. Res. Commun. 44, 745.PubMedCrossRefGoogle Scholar
  38. Stearn A.E. –1938– Ergeb. Enzymfor-schung 7, 1.Google Scholar
  39. Storm D.R. & Koshland D.E. –1970– Proc. Natl Acad. Sci. USA 66, 445.PubMedCrossRefGoogle Scholar
  40. Storm D.R. & Koshland D.E. –1972– J. Am. Chem. Soc. 94, 5805.CrossRefGoogle Scholar
  41. Swain C.G. & Brown J.F. –1952– J. Am. Chem. Soc. 74, 2534.CrossRefGoogle Scholar
  42. Tapia O., Brándén C.I. & Armbruster A.M. –1982– in Quantum Theory of Chemical Reactions, Vol. III, R. Daudel, A. Pullman, L. Salem & A. Viellard eds, Reidel Pub. and Co, 97–123.Google Scholar
  43. Tapia O. & Eklund H. –1986– Enzyme 36, 101.PubMedGoogle Scholar
  44. Tramontano A., Jarda K.D. & Lerner R.M. –1986– Science 234, 1566.PubMedCrossRefGoogle Scholar
  45. Urban P., Alliel P.M. & Lederer F. –1983– Eur. J. Biochem. 134, 275.PubMedCrossRefGoogle Scholar
  46. Urban P. & Lederer F. –1986– J. Biol. Chem. 260, 11115.Google Scholar
  47. Warshel A. –1978– Proc. Natl Acad. Sci. USA 75, 5250.PubMedCrossRefGoogle Scholar
  48. Warshel A. –1981a– Accounts Chem. Res. 14, 284–290.Google Scholar
  49. Warshel A. –1981b– Biochemistry 20, 3167.Google Scholar
  50. Warshel A. –1998– J. Biol. Chem. 273, 27035.PubMedCrossRefGoogle Scholar
  51. Warshel A., Aqvist J. & Creighton S. –1989– Proc. Natl Acad. Sci. USA 86, 5820.PubMedCrossRefGoogle Scholar
  52. Warshel A. & Levitt M. –1976– J. Mol. Biol. 103, 227.PubMedCrossRefGoogle Scholar
  53. Warshel A. & Weiss R.M. –1980– J. Am. Chem. Soc. 102, 6218.CrossRefGoogle Scholar
  54. Wells T.N.C. & Fersht A.N. –1986– Biochemistry 25, 1881.PubMedCrossRefGoogle Scholar
  55. Winter G., Fersht A.N., Wilkinson A.J., Zoller M. & Sunth M. –1982– Nature 299, 756.PubMedCrossRefGoogle Scholar
  56. Yon J.M. –1976– Biochimie 58, 61.PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  1. 1.Université Paris-Sud XI, UMR CNRS, Inst. Biochimie, BiophysiqueOrsayFrance
  2. 2.Labo. Biochimie des SignauxUniversité Paris VI, CNRS UMR 7631ParisFrance

Personalised recommendations