Substrate Specifity of Chymotrypsin. Study of Induced Strain by Molecular Mechanics

Abstract

Acylenzyme intermediates, produced by transfer of the acyl portions of selected natural substrates onto the catalytic serine hydroxyl of the serine protease chymotrypsin, were modeled with the AMBER force field. The obtained structures were used to calculate interaction and deformation energies. A set of 32 geometry variables were extracted out of each structure. They describe deformation effects specific for each substrate. It is shown by statistical analyses, that the interaction and deformation energies correspond to measured substrate reactivities. The extracted geometry variables are able to reproduce this dependency through multivariante statistical methods. These analyses suggest that there exist specific deformations of both the substrate and the enzyme portion, which are related to substrate reactivity. The geometry changes observed for high specific substrates are interpreted in terms of mechanistical requirements of the enzymatic reaction. The obtained model validates the hypothesis of induced strain as possible source of substrate specifity of chymotrypsin.