Paper Citing NAMD - Abstract
Zhao, Yuan; Chen, Nanhao; Wang, Chaojie; Cao, Zexing
A Comprehensive Understanding of Enzymatic Catalysis by Hydroxynitrile Lyases with S Stereoselectivity from the alpha/beta-Hydrolase Superfamily: Revised Role of the Active-Site Lysine and Kinetic Behavior of Substrate Delivery and Sequential Product Release
ACS CATALYSIS, 6:2145-2157, APR 2016
The highly homologous hydroxynitrile lyases from Manihot esculent (MeHNL) and Hevea brasiliensis (HbHNL) both belong to the alpha/beta-hydrolase superfamily, and they convert cyanohydrins into the corresponding ketone (aldehyde) and hydrocyanic acid, which is important for biosynthesis for carbon carbon formation. On the basis of extensive MM and ab initio QM/MM MD simulations, one-dimensional and two-dimensional free energy profiles on the whole enzymatic catalysis by MeHNL have been explored, and the effects of key residues around the channel on the delivery of substrate and product have been discussed. The residue Trp128 plays an important gate-switching role to manipulate the substrate access to the active site and product release. In particular, the release of acetone and HCN has been first detected to follow a step-wise mechanism. The release of HCN is quite facile, while the escape of acetone experiences a barrier of similar to 10 kcal/mol. The chemical reaction is an endergonic process with a free energy barrier of similar to 17.1 kcal/mol, which dominates the entire enzymatic efficiency. Such energy costs can be compensated by the remarkable energy release during the initial substrate binding. Here the carbon carbon cleavage is the rate-determining step, which differs from that of HbHNL. The protonation state of Lys237 plays an important role in carbon carbon bond cleavage by restoring the Ser80Ala mutant system to the wild system, which explains the discrepancy between MeHNL and HbHNL at the molecular or atomic scale. The present results provide a basis for understanding the similarity and difference in the enzymatic catalysis by MeHNL and HbHNL.
