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Examining asymmetric pairwise pre-reaction and transition states in enzymatic catalysis by molecular dynamics simulation and quantum mechanics/molecular mechanics calculation. | LitMetric

Examining asymmetric pairwise pre-reaction and transition states in enzymatic catalysis by molecular dynamics simulation and quantum mechanics/molecular mechanics calculation.

STAR Protoc

State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China. Electronic address:

Published: April 2023

AI Article Synopsis

Article Abstract

Here, we present a protocol to examine asymmetric pairwise pre-reaction and transition states in enzymatic catalysis. We describe steps to set up the calculated systems, run umbrella sampling molecular dynamics simulation, and conduct quantum mechanics/molecular mechanics calculations. We also provide analytical scripts to yield potential of mean force of pre-reaction states and reaction barriers. This protocol can generate quantum-mechanistic data for constructing pre-reaction state/transition state machine learning models. For complete details on the use and execution of this protocol, please refer to Luo et al. (2022)..

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Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10172999PMC
http://dx.doi.org/10.1016/j.xpro.2023.102263DOI Listing

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