Simulating enzyme catalysis with electrostatically embedded machine learning potentials

To simulate enzyme reactions, multiscale quantum mechanics/molecular mechanics (QM/MM) approaches are well established and popular. However, accurately and efficiently estimating enzyme activity is a challenge, because in general, precise methods are too computationally expensive. Here, we demonstrate that enzyme catalysis can be captured by coupling efficient machine-learned potentials (MLPs) for a reaction to the wider enzyme environment using electrostatic machine-learning embedding (EMLE). Our EMLE model is first applied to the natural Diels-Alderase AbyU, showing that it correctly differentiates the catalytic action on different enzyme-substrate conformations. Then, we show that training a reaction-specific EMLE model allows us to accurately capture the enzyme catalytic effects of the conversion of chorismate to prephenate, a reaction with a highly polarizable and charged transition state. In both cases, in contrast to mechanical embedding approaches, EMLE embedding allows accurate and efficient predictions of enzyme activity, agreeing with high-level QM/MM reference calculations. This approach facilitates the use of gas phase-trained MLPs in MLP/molecular mechanics (ML/MM) simulations and should thus be highly beneficial for computational activity screening of enzyme biocatalysts.