A Computational Methodology to Screen Activities of Enzyme Variants

TL;DR

This paper introduces a rapid computational approach for screening enzyme variants by estimating mutation effects on reaction barrier heights within 24 hours, enabling high-throughput analysis of hundreds of mutants.

Contribution

The methodology combines PM6 and MOZYME in MOPAC2009 to efficiently predict enzyme mutation effects, achieving near-quantitative accuracy with automation for large-scale screening.

Findings

Barrier heights estimated within 3 kcal/mol of high-level calculations.

Reliable results require strict convergence and long NDDO cutoff distances.

Automated setup allows screening of hundreds of mutants in weeks.

Abstract

We present a fast computational method to efficiently screen enzyme activity. In the presented method, the effect of mutations on the barrier height of an enzyme-catalysed reaction can be computed within 24 hours on roughly 10 processors. The methodology is based on the PM6 and MOZYME methods as implemented in MOPAC2009, and is tested on the first step of the amide hydrolysis reaction catalyzed by Candida Antarctica lipase B (CalB) enzyme. The barrier heights are estimated using adiabatic mapping and are shown to give barrier heights to within 3kcal/mol of B3LYP/6-31G(d)//RHF/3-21G results for a small model system. Relatively strict convergence criteria (0.5kcal/(mol{\AA})), long NDDO cutoff distances within the MOZYME method (15{\AA}) and single point evaluations using conventional PM6 are needed for reliable results. The generation of mutant structure and subsequent setup of the semiempirical calculations are automated so that the effect on barrier heights can be estimated for hundreds of mutants in a matter of weeks using high performance computing.