Enzyme catalysis computer simulations

It is common to compute relative free energies in simulations of enzyme catalysis. Computed activation free energies are usually compared to experimental values derived from cat using Eyring transition state theory (6). Transition State Theory provides a connection between Acat and the free energy of activation, AGh... 

The previous chapters taught us how to ask questions about specific enzymatic reactions. In this chapter we will attempt to look for general trends in enzyme catalysis. In doing so we will examine various working hypotheses that attribute the catalytic power of enzymes to different factors. We will try to demonstrate that computer simulation approaches are extremely useful in such examinations, as they offer a way to dissect the total catalytic effect into its individual contributions. 

Warshel, A. (2003) Computer simulations of enzyme catalysis methods, progress, and insights. Anna. Rev. Biophys. Biomol. Struct., 32, 425. 

This work addressed the issue of enzyme catalysis focusing on the principle of physical organic chemistry and the power of computer simulation approaches. It was shown that when such concepts as reorganization energy and Marcus parabolas are formulated in a consistent microscopic way, they could be used to explore the origin of enzyme catalysis. It was also clarified that phenomenological applications of the Marcus formula or related expressions can lead to problematic conclusions. 

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