Catalytic mechanism side chain locations

The reaction path of the enzyme TIM was characterized by energy minimizations using the combined AMl/CHARMM potential.28 >285 in that study, the substrate and the catalytic side chains of His-95 and Glu-165 were treated quantum mechanically, and all other molecules in a stochastic boundary system (a 16-A sphere) were treated by the empirical CHARMM potential. The entire system consisted of 1250 protein atoms and 100 water molecules. An energy decomposition method was used to locate residues important in catalysis. In addition to the large energy contributions from conserved residues, other amino acids make smaller contributions, but their cumulative effect is significant. Interestingly, a number of residues far from the active site also have sizable effects on the enzyme s catalytic ability.284... 

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