QM Cluster or QM/MM in Computational Enzymology: The Test Case of LigW-Decarboxylase

Frontiers in Chemistry
Mario PrejanòNino Russo

Abstract

The catalytic mechanism of the decarboxylation of 5-carboxyvanillate by LigW producing vanillic acid has been studied by using QM cluster and hybrid QM/MM methodologies. In the QM cluster model, the environment of a small QM model is treated with a bulky potential while two QM/MM models studies include partial and full protein with and without explicitly treated water solvent. The studied reaction involves two sequential steps: the protonation of the carbon of the 5-carboxy-vanillate substrate and the decarboxylation of the intermediate from which results deprotonated vanillic acid as product. The structures and energetics obtained by using three structural models and two density functionals are quite consistent to each other. This indicates that the small QM cluster model of the presently considered enzymatic reaction is appropriate enough and the reaction is mainly influenced by the active site.

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Citations

May 6, 2020·Chemistry : a European Journal·Mario PrejanòTiziana Marino
Nov 12, 2019·Organic & Biomolecular Chemistry·Shiqing Zhang, Yongjun Liu
Feb 20, 2021·Organic & Biomolecular Chemistry·Reynier SuardíazAdrian J Mulholland
Jun 19, 2021·Computational and Structural Biotechnology Journal·Xiang Sheng, Fahmi Himo
Apr 4, 2020·Journal of Chemical Theory and Computation·Rimsha Mehmood, Heather J Kulik

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Methods Mentioned

BETA
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Software Mentioned

Antechamber
Gaussian
NCIPLOT
AMBER16
Energetics

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