ArticlePLoS computational biology2012
Coupling between catalytic loop motions and enzyme global dynamics.
Article in PLoS computational biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Methods for the establishment of enzymatic mechanisms - from QM to ML.Chemical science · 2026Review
- Deep learning insights into β-lactamase dynamics and resistance evolution.The Biochemical journal · 2026Review
- Loop dynamics, allostery, and function in protein tyrosine phosphatases: insights from molecular simulations.Biochemical Society transactions · 2026Review
- A Computationally Efficient Method to Generate Plausible Conformers for Ensemble Docking and Binding Free Energy Calculations.Journal of chemical information and modeling · 2025Article
- Protein Catalysis Through Structural Dynamics: A Comprehensive Analysis of Energy Conversion in Enzymatic Systems and Its Computational Limitations.Pharmaceuticals (Basel, Switzerland) · 2025Review
- Mutexa: A Computational Ecosystem for Intelligent Protein Engineering.Journal of chemical theory and computation · 2023Review
- Statistical learning of protein elastic network from positional covariance matrix.Computational and structural biotechnology journal · 2023Article
- Structural alterations in the catalytic core of hSIRT2 enzyme predict therapeutic benefits ofRSC advances · 2021Article
- Identification of Thermal Conduits That Link the Protein-Water Interface to the Active Site Loop and Catalytic Base in Enolase.Journal of the American Chemical Society · 2021Article
- Protein Tyrosine Phosphatases: A new paradigm in an old signaling system?Advances in cancer research · 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
- Dynamics-function relationship in the catalytic domains of N-terminal acetyltransferases.Computational and structural biotechnology journal · 2020Article
- ClustENM: ENM-Based Sampling of Essential Conformational Space at Full Atomic Resolution.Journal of chemical theory and computation · 2016Article
- Similarity in Shape Dictates Signature Intrinsic Dynamics Despite No Functional Conservation in TIM Barrel Enzymes.PLoS computational biology · 2016Article
- Role of Loop-Clamping Side Chains in Catalysis by Triosephosphate Isomerase.Journal of the American Chemical Society · 2015Article
- How an Inhibitor Bound to Subunit Interface Alters Triosephosphate Isomerase Dynamics.Biophysical journal · 2015Article
- Aldolases Utilize Different Oligomeric States To Preserve Their Functional Dynamics.Biochemistry · 2015Article
- Computational investigation of cholesterol binding sites on mitochondrial VDAC.The journal of physical chemistry. B · 2014Article
- Probing the global and local dynamics of aminoacyl-tRNA synthetases using all-atom and coarse-grained simulations.Journal of molecular modeling · 2014Article
- The critical role of the loops of triosephosphate isomerase for its oligomerization, dynamics, and functionality.Protein science : a publication of the Protein Society · 2014Article
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5 authors.
Funding
Abstract
Catalytic loop motions facilitate substrate recognition and binding in many enzymes. While these motions appear to be highly flexible, their functional significance suggests that structure-encoded preferences may play a role in selecting particular mechanisms of motions. We performed an extensive study on a set of enzymes to assess whether the collective/global dynamics, as predicted by elastic network models (ENMs), facilitates or even defines the local motions undergone by functional loops. Our dataset includes a total of 117 crystal structures for ten enzymes of different sizes and oligomerization states. Each enzyme contains a specific functional/catalytic loop (10-21 residues long) that closes over the active site during catalysis. Principal component analysis (PCA) of the available crystal structures (including apo and ligand-bound forms) for each enzyme revealed the dominant conformational changes taking place in these loops upon substrate binding. These experimentally observed loop reconfigurations are shown to be predominantly driven by energetically favored modes of motion intrinsically accessible to the enzyme in the absence of its substrate. The analysis suggests that robust global modes cooperatively defined by the overall enzyme architecture also entail local components that assist in suitable opening/closure of the catalytic loop over the active site.
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