Computational Prediction of ω-Transaminase Specificity by a Combination of Docking and Molecular Dynamics Simulations

w-Transaminases (omega-TAs) catalyze the conversion of ketones to chiral amines, often with high enantioselectivity and specificity, which makes them attractive for industrial production of chiral amines. Tailoring omega-TAs to accept non-natural substrates is necessary because of their limited substrate range. We present a computational protocol for predicting the enantioselectivity and catalytic selectivity of an omega-TA from Vibrio fluvialis with different substrates and benchmark it against 62 compounds gathered from the literature. Rosetta-generated complexes containing an external aldimine intermediate of the transamination reaction are used as starting conformations for multiple short independent molecular dynamics (MD) simulations. The combination of molecular docking and MD simulations ensures sufficient and accurate sampling of the relevant conformational space. Based on the frequency of near-attack conformations observed during the MD trajectories, enantioselectivities can be quantitatively predicted. The predicted enantioselectivities are in agreement with a benchmark dataset of experimentally determined ee% values. The substraterange predictions can be based on the docking score of the external aldimine intermediate. The low computational cost required to run the presented framework makes it feasible for use in enzyme design to screen thousands of enzyme variants.

Automated summary

A computational protocol for predicting the enantioselectivity and catalytic selectivity of an omega-TA from Vibrio fluvialis with different substrates has been presented and benchmarked against 62 compounds. The protocol combines molecular docking and MD simulations, ensuring accurate sampling of conformational space for predicting enantioselectivities. The framework has low computational cost and is feasible for enzyme design to screen thousands of enzyme variants.