ArticleStructure (London, England : 1993)2005
Coupling between catalytic site and collective dynamics: a requirement for mechanochemical activity of enzymes.
Article in Structure (London, England : 1993), 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 112 papers.
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Who cites it
112 citing papers in PubMed.
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- Global hinge sites of proteins as target sites for drug binding.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
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- Influence of point mutations on PR65 conformational adaptability: Insights from molecular simulations and nanoaperture optical tweezers.Science advances · 2024Article
- Perspectives on Computational Enzyme Modeling: From Mechanisms to Design and Drug Development.ACS omega · 2024Review
- Allo-targeting of the kinase domain: Insights from in silico studies and comparison with experiments.Current opinion in structural biology · 2024Review
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- Mutually beneficial confluence of structure-based modeling of protein dynamics and machine learning methods.Current opinion in structural biology · 2023Review
- Statistical learning of protein elastic network from positional covariance matrix.Computational and structural biotechnology journal · 2023Article
- Conformational and mechanical stability of the isolated large subunit of membrane-bound [NiFe]-hydrogenase fromFrontiers in microbiology · 2022Article
- Sampling of Protein Conformational Space Using Hybrid Simulations: A Critical Assessment of Recent Methods.Frontiers in molecular biosciences · 2022Article
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- Normal Mode Analysis of KRas4B Reveals Partner Specific Dynamics.The journal of physical chemistry. B · 2021Article
- Energy Bilocalization Effect and the Emergence of Molecular Functions in Proteins.Frontiers in molecular biosciences · 2021Article
- Networks of Networks: An Essay on Multi-Level Biological Organization.Frontiers in genetics · 2021Review
- Exposing the distinctive modular behavior of β-strands and α-helices in folded proteins.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
52 more citing papers are in PubMed but not listed here.
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2 authors.
Funding
Abstract
Growing evidence supports the view that enzymatic activity results from a subtle interplay between chemical kinetics and molecular motions. A systematic analysis is performed here to delineate the type and level of coupling between catalysis and conformational mechanics. The dynamics of a set of 98 enzymes representative of different EC classes are analyzed with the Gaussian network model (GNM) and compared with experimental data. In more than 70% of the examined enzymes, the global hinge centers predicted by the GNM are found to be colocalized with the catalytic sites experimentally identified. Low translational mobility (< 7%) is observed for the catalytic residues, consistent with the fine-tuned design of enzymes to achieve precise mechanochemical activities. Ligand binding sites, while closely neighboring catalytic sites, enjoy a moderate flexibility to accommodate the ligand binding. These findings could serve as additional criteria for assessing drug binding residues and could lessen the computational burden of substrate docking searches.
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