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The Role of Electrostatics in Enzymes: Do Biomolecular Force Fields Reflect Protein Electric Fields?

preprint
submitted on 23.02.2020 and posted on 25.02.2020 by Richard T Bradshaw, Jacek Dziedzic, Chris-Kriton Skylaris, Jonathan W. Essex

Preorganization of large, directionally oriented, electric fields inside protein active sites has been proposed as a crucial contributor to catalytic mechanism in many enzymes, and may be efficiently investigated at the atomistic level with molecular dynamics simulations. Here we evaluate the ability of the AMOEBA polarizable force field, as well as the additive Amber ff14SB and Charmm C36m models, to describe the electric fields present inside the active site of the peptidyl-prolyl isomerase cyclophilin A. We compare the molecular mechanical electric fields to those calculated with a fully first principles quantum mechanical (QM) representation of the protein, solvent, and ions, and find that AMOEBA consistently shows far greater correlation with the QM electric fields than either of the additive force fields tested. Catalytically-relevant fields calculated with AMOEBA were typically smaller than those observed with additive potentials, but were generally consistent with an electrostatically-driven mechanism for catalysis. Our results highlight the accuracy and the potential advantages of using polarizable force fields in systems where accurate electrostatics may be crucial for providing mechanistic insights.

Funding

EP/K039156/1

History

Email Address of Submitting Author

R.T.Bradshaw@soton.ac.uk

Institution

University of Southampton

Country

United Kingdom

ORCID For Submitting Author

0000-0002-8652-4301

Declaration of Conflict of Interest

No conflict of interest

Licence

Exports