ArticleFrontiers in chemistry2018
QM Cluster or QM/MM in Computational Enzymology: The Test Case of LigW-Decarboxylase.
Article in Frontiers in chemistry, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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9 citing papers in PubMed.
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- Fully Oxidized State of the Oxygen-Tolerant [NiFe] Hydrogenase fromInorganic chemistry · 2025Article
- Adaptive Restraints to Accelerate Geometry Optimizations of Large Biomolecular Systems.Journal of computational chemistry · 2025Article
- Perspective on the Current State-of-the-Art of Quantum Computing for Drug Discovery Applications.Journal of chemical theory and computation · 2022Review
- Two Sides of Quantum-Based Modeling of Enzyme-Catalyzed Reactions: Mechanistic and Electronic Structure Aspects of the Hydrolysis by Glutamate Carboxypeptidase.Molecules (Basel, Switzerland) · 2021Article
- Catalytic mechanism of the colistin resistance protein MCR-1.Organic & biomolecular chemistry · 2021Article
- Mechanisms of metal-dependent non-redox decarboxylases from quantum chemical calculations.Computational and structural biotechnology journal · 2021Review
- On the Catalytic Activity of the Engineered Coiled-Coil Heptamer Mimicking the Hydrolase Enzymes: Insights from a Computational Study.International journal of molecular sciences · 2020Article
- How the Destabilization of a Reaction Intermediate Affects Enzymatic Efficiency: The Case of Human Transketolase.ACS catalysis · 2020Article
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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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