Molecular dynamics and quantum chemical studies on the catalytic mechanism of Delta5-3-ketosteroid isomerase: the catalytic diad versus the cooperative hydrogen bond mechanism.

To further understand Delta(5)-3-ketosteroid isomerase (KSI) catalysis, we carried out molecular dynamics (MD) simulations of the KSI dimer ligated with a substrate and reaction intermediate analogue and high level ab initio calculations on relevant enzymatic reaction models. Simulation of the enzyme-substrate complex dimer systems showed asymmetric dynamics between the two monomers, in which the hydrogen bond pattern between the substrate and active site residues in the first and the second subunits supported the cooperative hydrogen bond (CH) and the catalytic diad (CD) mechanisms, respectively. On the other hand, only the CH mechanism was supported in the MD simulation of the enzyme-intermediate complex dimer. From MP2/6-31+G**//RHF/6-31G** calculations, we found the kinetic barriers for the two reaction mechanisms were similar. The CH route afforded a greater stabilization to the enolate intermediate than did the CD counterpart. Thus, the present computational studies indicate that the CH mechanism would be favored over the CD one in the catalytic action of KSI. However, the latter could not be ruled out conclusively because of the explicit appearance of a CD configuration in the MD trajectories of the enzyme-substrate complex and because of the similar intrinsic activation barrier for the CH and CD mechanisms. The appearance of configurations that favor the CD pathway is rationalized in terms of a model in which the KSI-substrate complex does not have a strong preference for one hydrogen bonding pattern over another, while the KSI-intermediate complex favors a cooperative hydrogen bond pattern in order to stabilize the reaction intermediate. This hypothesis is supported by the ab initio calculations which indicate that the CH intermediate is more stable than the CD one by approximately 6.3 kcal/mol.