Towards a cheminformatic design for quantum mechanical enzyme models: the case of catechol-O-methyltransferase

21 December 2020, Version 2
This content is a preprint and has not undergone peer review at the time of posting.

Abstract

The efficiency, accuracy, and replicability of enzyme simulations is often hampered by ad hoc model design. To address this problem, we have developed the Residue Interaction Network ResidUe Selector (RINRUS) toolkit. RINRUS utilizes residue contact networks to automate construction of rational quantum mechanical cluster models. This work examines this problem by computing the reaction kinetics and thermodynamics for 508 models of the active site of catechol-o-methyltransferase, an enzyme which catalyzes the methyl transfer from S-adenosyl methionine cofactor to catechol substrates. Our results demonstrate using RINRUS to rationally design small and accurate active site models.

Keywords

QM-only
QM-cluster
COMT
enzyme
mechanism
residue interaction networks
DFT
protein
computational chemistry
clustering

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