Harnessing Conformational Dynamics in Enzyme Catalysis to achieve Nature-like catalytic efficiencies: The Shortest Path Map tool for computational enzyme design

Abstract

Enzymes exhibit diverse conformations, as represented in the so-called Free Energy Landscape (FEL). Such conformational diversity of enzymes provides them the ability to evolve towards novel functions. The challenge lies in identifying mutations that enhance specific conformational changes, especially if located in distal sites from the active site cavity. The Shortest Path Map (SPM) method, which we developed to address this challenge, constructs a graph based on the distances and correlated motions of residues observed in long nanosecond timescale molecular dynamics (MD) simulations. We recently introduced a template based AlphaFold2 (tAF2) approach coupled with short nanosecond MD simulations to quickly estimate the conformational landscape of enzymes and assess how the FEL is shifted after mutation. In this study, we evaluate the potential of SPM when coupled with tAF2-MD in estimating conformational heterogeneity and identifying key conformationally-relevant positions, showcasing their efficacy in understanding enzyme dynamics for computational enzyme design.