Volume 252, 2024

Harnessing conformational dynamics in enzyme catalysis to achieve nature-like catalytic efficiencies: the shortest path map tool for computational enzyme redesign

Abstract

Enzymes exhibit diverse conformations, as represented in the free energy landscape (FEL). Such conformational diversity provides enzymes with 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 nanosecond timescale molecular dynamics (MD) simulations. We recently introduced a template based AlphaFold2 (tAF2) approach coupled with 10 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. The selected model system is the beta subunit of tryptophan synthase (TrpB). We compare how the SPM pathways differ when integrating tAF2 with different MD simulation lengths from as short as 10 ns until 50 ns and considering two distinct Amber forcefield and water models (ff14SB/TIP3P versus ff19SB/OPC). The new methodology can more effectively capture the distal mutations found in laboratory evolution, thus showcasing the efficacy of tAF2-MD-SPM in rapidly estimating enzyme dynamics and identifying the key conformationally relevant hotspots for computational enzyme engineering.

Graphical abstract: Harnessing conformational dynamics in enzyme catalysis to achieve nature-like catalytic efficiencies: the shortest path map tool for computational enzyme redesign

  • This article is part of the themed collection: Biocatalysis

Associated articles

Supplementary files

Article information

Article type
Paper
Submitted
24 Nov 2023
Accepted
18 Mar 2024
First published
18 Mar 2024
This article is Open Access
Creative Commons BY-NC license

Faraday Discuss., 2024,252, 306-322

Harnessing conformational dynamics in enzyme catalysis to achieve nature-like catalytic efficiencies: the shortest path map tool for computational enzyme redesign

C. Duran, G. Casadevall and S. Osuna, Faraday Discuss., 2024, 252, 306 DOI: 10.1039/D3FD00156C

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