OpenAlex ·
Quantum-accurate atomistic modeling of enzyme catalysis using a machine learned potential
- Published
- Source
- OpenAlex
- Published in
- arXiv (Cornell University)
- DOI
- 10.48550/arxiv.2609.09293
- Original
- Read it at the publisher
- Topics
Abstract
Electronic rearrangements associated with bond forming/breaking in catalytic enzymes require quantum mechanical (QM) treatment beyond classical molecular mechanics (MM). Hybrid QM/MM methods enable tractable simulations but require system-specific setup and are sensitive to the QM region choice and treatment of the QM/MM interface. We demonstrate quantum-accurate treatment of all-atom, complete enzymes in explicit solvent comprising up to 54k atoms and 1 microsecond of total simulation time using the machine-learned interatomic potential (MLIP) eSEN-omol. We reproduce experimental barrier trends for Claisen rearrangement in chorismate mutase, resolve critical intermediate states in PETase catalyzed polymer depolymerization, and distinguish mechanistic alternatives for metal-activated phosphoryl transfer in nucleoside diphosphate kinase. We realize 1000x speedups relative to typical QM/MM calculations without system-specific tuning. These results establish MLIPs as a practical route to QM-accurate simulations of enzyme catalysis.
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