Molecular insights into the promiscuity of serine hydrolases. Towards a computationally guided protocol for the redesign of enzymes

Abstract

Two serine hydrolases, Candida antarctica Lipase B (CALB) and para-nitrobenzyl (Bs2) esterase from Bacillus subtilis, were used as a model to study enzyme promiscuity through QM/MM methods and experimental enzymes kinetics. Both, the catalytic and the substrate promiscuity were studied. The hydrolysis of amides and the epoxidation of alkenes catalyzed by CALB were explored. Moreover, a computational scheme for the redesign of the Bs2 was also proposed. The electrostatic environment around the active site was analyzed and a map of structural determinants in the vicinity of the active site pocket was done using 3D Convolutional Neural Networks. The proposed computationally guided protocol for the mutagenesis of enzymes based on the detailed analysis of the electrostatic environment of two structurally aligned trajectories using rotation quaternions was applied. A new mutant variant of the Bs2 was suggested as an improved catalytic variant by combining the best electrostatic features of both enzymes.