Modeling catalytic mechanism of nitrile hydratase by semi-empirical quantum mechanical calculation

Abstract

Nitrile hydratase (NHase) is an important industrial enzyme capable of converting nitriles to corresponding amides. Utilizing the method of semi-empirical quantum mechanical (QM) calculation by TRITON, the bioconversion process of acrylonitrile to acrylamide catalyzed by NHase was successfully performed on a computer. Crystal structure of a Co-type NHase from Pseudonocardia thermophila JCM 3095 (PDB code 1IRE) was selected as the target for acrylonitrile autodock. In silico calculations were performed on the NHase–acrylonitrile complex to simulate the enzyme catalysis mechanism by quantitatively comparing energy changes of each reaction pathway. Simulation results showed that active site activation is the first step of NHase catalysis, in which the Co 2+ coordinated to a water molecule forms a Co–OH complex mediated by the oxidized α-CEA113. Then the oxygen atom in the Co–OH attacks the C atom in the –CN triple bond of acrylonitrile, forming a precursor of acrylamide. Consequently, proton rearrangement happens transforming the precursor into the final product of acrylamide, under the assistance of the hydrogen atom in the –OH group of α-SER112. Gibbs energy changes of three steps corresponding to the active center activation, nucleophilic attack and proton rearrangement are around −31, 23 and −12 kcal/mol, respectively.