ArticleBiochemistry2006
Loop motions of triosephosphate isomerase observed with elastic networks.
Article in Biochemistry, 2006. 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.
- A Computationally Efficient Method to Generate Plausible Conformers for Ensemble Docking and Binding Free Energy Calculations.Journal of chemical information and modeling · 2025Article
- Sequence-sensitive elastic network captures dynamical features necessary for miR-125a maturation.PLoS computational biology · 2022Article
- Sampling of Protein Conformational Space Using Hybrid Simulations: A Critical Assessment of Recent Methods.Frontiers in molecular biosciences · 2022Article
- Uncovering the Role of Key Active-Site Side Chains in Catalysis: An Extended Brønsted Relationship for Substrate Deprotonation Catalyzed by Wild-Type and Variants of Triosephosphate Isomerase.Journal of the American Chemical Society · 2019Article
- Article
- 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
- Bridging between NMA and Elastic Network Models: Preserving All-Atom Accuracy in Coarse-Grained Models.PLoS computational biology · 2015Article
- How an Inhibitor Bound to Subunit Interface Alters Triosephosphate Isomerase Dynamics.Biophysical journal · 2015Article
- A coarse-grained elastic network atom contact model and its use in the simulation of protein dynamics and the prediction of the effect of mutations.PLoS computational biology · 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
- The importance of slow motions for protein functional loops.Physical biology · 2012Article
- Coupling between catalytic loop motions and enzyme global dynamics.PLoS computational biology · 2012Article
- SwarmDock and the use of normal modes in protein-protein docking.International journal of molecular sciences · 2010Article
- Rationale for more diverse inhibitors in competition with substrates in HIV-1 protease.Biophysical journal · 2010Article
- Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins.Chemical reviews · 2010Review
- Focused functional dynamics of supramolecules by use of a mixed-resolution elastic network model.Biophysical journal · 2009Article
- Protein elastic network models and the ranges of cooperativity.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
- Probing the flexibility of large conformational changes in protein structures through local perturbations.PLoS computational biology · 2009Article
- Dealing with structural variability in molecular replacement and crystallographic refinement through normal-mode analysis.Acta crystallographica. Section D, Biological crystallography · 2008Article
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3 authors.
Funding
Abstract
The internal dynamics of triosephosphate isomerase have been investigated with elastic networks, with and without a substrate bound. The slowest modes of motion involve large domain motions but also a loop motion that conforms to the changes observed between the crystal structures and . Our computations confirm that the different motions of this loop are important in several of the computed slowest modes. We have shown that elastic network computations on this protein system can combine atoms for the functional parts of the structure with coarse-grained (cg) representations of the remainder of the structure in several different ways. Similar loop motions are seen with elastic network models for atomistic and mixed cg models. The loop motions are reproduced with an overlap of 0.75-0.79 by combining the four slowest modes of motion for the free and complex forms of the enzyme.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.