Theoretical Calculations on an Enzyme Catalyzed Reaction Mechanism

  • Giuliano Alagona
  • Caterina Ghio
Part of the Progress in Mathematics book series (NSSA)


Because of the continuous expansion of genetic engineering techniques, the availability of a theoretical approach for predicting the effect of site-specific mutagenesis could be extremely useful. Therefore, we are interested in the application of theoretical methods, mainly ab initio, in order to elucidate the enzyme catalysis process. While most of the classical mechanical tools are presented elsewhere in this book, a discussion of the quantum mechanical ones falls outside its scope. Thus, we will focus more on the methodological aspects of our research, rather than on its results, these nonetheless are thoroughly discussed in the source papers [1–3].


Quantum Mechanical Proton Transfer Reaction Coordinate Catalytic Rate Dihydroxy Acetone Phosphate 
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  1. 1.
    G. Alagona, P. Desmeules, C. Ghio, and P. A. Kollman, Quantum Mechanical and Molecular Mechanical Studies on a Model for the Dihydroxyacetone Phosphate - Glyceraldehyde Phosphate Isomerization Catalized by Triose-phosphate Isomerase (TIM), J. Am. Chem. Soc. 106: 3623 (1984).CrossRefGoogle Scholar
  2. 2.
    G. Alagona, C. Ghio, and P. A. Kollman, Simple Model for the Effect of Glu 165 - Asp165 Mutation on the Rate of Catalysis in Triosephosphate Isomerase, J. Mol. Biol. 191: 23 (1986).PubMedCrossRefGoogle Scholar
  3. 3.
    G. Alagona, C. Ghio, and P. A. Kollman, Computational Approaches to the Study of Protein-Ligand Interactions, in: “Macromolecular Biorecognition”, I. Chaiken, E. Chiancone, A. Fontana, and P. Neri, eds., p. 13, The Humana Press, Clifton (1987).Google Scholar
  4. 4.
    U. Chandra Singh and P. A. Kollman, A Combined Ab lnitio Quantum Mechanical and Molecular Mechanical Method for Carrying out Simulations on Complex Molecular Systems: Applications to the CH3C +Cl− Exchange Reaction and Gas Phase Protonation of Polyethers, J. Comp. Chem. 7: 718 (1986).CrossRefGoogle Scholar
  5. 5.
    J. A. McCammon and S. C. Harvey, “Dynamics of Proteins and Nucleic Acids”, Cambridge University Press, Cambridge (1987).CrossRefGoogle Scholar
  6. 6.
    T. Alber and G. A. Petsko, private communication.Google Scholar
  7. 7.
    D. Straus, R. Raines, E. Kawashima, J. R. Knowles, and W. Gilbert, Active Site of Triosephosphate Isomerase: in Vitro Mutagenesis and Characterization of an Altered Enzyme, Proc. Natl. Acad. Sci. U.S.A. 82: 2272 (1985).PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 1989

Authors and Affiliations

  • Giuliano Alagona
    • 1
  • Caterina Ghio
    • 1
  1. 1.Istituto di Chimica Quantistica ed Energetica Molecolare, del C.N.R.PisaItaly

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