ArticleCatalysts (Basel, Switzerland)2016
Investigation of Structural Dynamics of Enzymes and Protonation States of Substrates Using Computational Tools.
Article in Catalysts (Basel, Switzerland), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Encapsulation of colistin using hyaluronic acid and PVA-PSS polymeric nanocarriers for enhanced drug delivery: a molecular dynamics simulation study.Scientific reports · 2026Article
- PKAD-R: curated, redesigned and expanded database of experimental pKa values in proteins.Journal of computational biophysics and chemistry · 2025Article
- Article
- FMO-guided design of darunavir analogs as HIV-1 protease inhibitors.Scientific reports · 2024Article
- Article
- Protein conformational switch discerned via network centrality properties.Computational and structural biotechnology journal · 2021Article
- Directed Evolution Mimics Allosteric Activation by Stepwise Tuning of the Conformational Ensemble.Journal of the American Chemical Society · 2018Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
This review discusses the use of molecular modeling tools, together with existing experimental findings, to provide a complete atomic-level description of enzyme dynamics and function. We focus on functionally relevant conformational dynamics of enzymes and the protonation states of substrates. The conformational fluctuations of enzymes usually play a crucial role in substrate recognition and catalysis. Protein dynamics can be altered by a tiny change in a molecular system such as different protonation states of various intermediates or by a significant perturbation such as a ligand association. Here we review recent advances in applying atomistic molecular dynamics (MD) simulations to investigate allosteric and network regulation of tryptophan synthase (TRPS) and protonation states of its intermediates and catalysis. In addition, we review studies using quantum mechanics/molecular mechanics (QM/MM) methods to investigate the protonation states of catalytic residues of β-Ketoacyl ACP synthase I (KasA). We also discuss modeling of large-scale protein motions for HIV-1 protease with coarse-grained Brownian dynamics (BD) simulations.
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Registered trials
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