Abstract
Two methods for computer simulation of enzymatic reactions are described. The first method allows one to estimate activation-free energies of enzymatic reactions by using available X-ray structures of enzyme-substrate complexes. This method is based on the empirical valence bond (EVB) approach which correlates reaction rates with the difference in electrostatic stabilization of the relevant resonance structures in the enzyme and in solution. The second method is based on a molecular dynamics extension of the EVB approach. This method allows one to study fundamental aspects of enzymatic reactions, including analysis of the role of structural fluctuations and estimates of entropic effects. The dynamical method is used here for examination of the relationship between reaction free energies (ΔGo) and activation free energies (Δg≠) in enzyme catalysis. The preliminary results presented here indicate that the rates of proton transfer reactions in enzymes might be correlated in a simple way with the corresponding pKa differences.
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© 1984 Pontificia Academia Scientiarum — Città del Vaticano
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Warshel, A. (1984). Simulating the Energetics and Dynamics of Enzymatic Reactions. In: Chagas, C., Pullman, B. (eds) Specificity in Biological Interactions. Springer, Dordrecht. https://doi.org/10.1007/978-94-009-6457-0_4
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DOI: https://doi.org/10.1007/978-94-009-6457-0_4
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