ArticlePLoS computational biology2009
Allosteric transitions of supramolecular systems explored by network models: application to chaperonin GroEL.
Article in PLoS computational biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.
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Who cites it
58 citing papers in PubMed.
- Generation of Pathway Signatures by Combining Normal Modes with Weighted Ensemble Simulations.bioRxiv : the preprint server for biology · 2026Article
- Efficient sampling of large-scale transition pathways and intermediate conformations in sub-mesoscopic protein complexes.Nature communications · 2026Article
- Uncovering the Role of Distal Regions in PDK1 Allosteric Activation.ACS bio & med chem Au · 2025Article
- Genetic and structural insights into the functional importance of the conserved gly-met-rich C-terminal tails in bacterial chaperonins.Communications biology · 2025Article
- Protein dynamics developments for the large scale and cryoEM: case study of ProDy 2.0.Acta crystallographica. Section D, Structural biology · 2022Review
- Article
- Novel cryo-EM structure of an ADP-bound GroEL-GroES complex.Scientific reports · 2021Article
- State-dependent sequential allostery exhibited by chaperonin TRiC/CCT revealed by network analysis of Cryo-EM maps.Progress in biophysics and molecular biology · 2021Article
- Towards gaining sight of multiscale events: utilizing network models and normal modes in hybrid methods.Current opinion in structural biology · 2020Review
- Intrinsic dynamics is evolutionarily optimized to enable allosteric behavior.Current opinion in structural biology · 2020Review
- Integrated Computational Approaches and Tools forAllosteric Drug Discovery.International journal of molecular sciences · 2020Review
- Simple mechanics of protein machines.Journal of the Royal Society, Interface · 2019Article
- Allosteric mechanism of the circadian protein Vivid resolved through Markov state model and machine learning analysis.PLoS computational biology · 2019Article
- Large-Scale Conformational Changes and Protein Function: Breaking theFrontiers in molecular biosciences · 2019Review
- Survey of the analysis of continuous conformational variability of biological macromolecules by electron microscopy.Acta crystallographica. Section F, Structural biology communications · 2019Review
- Designed Elastic Networks: Models of Complex Protein Machinery.International journal of molecular sciences · 2018Review
- Shared dynamics of LeuT superfamily members and allosteric differentiation by structural irregularities and multimerization.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2018Article
- Design of Elastic Networks with Evolutionary Optimized Long-Range Communication as Mechanical Models of Allosteric Proteins.Biophysical journal · 2017Article
- Directional Force Originating from ATP Hydrolysis Drives the GroEL Conformational Change.Biophysical journal · 2017Article
- Prediction and validation of protein intermediate states from structurally rich ensembles and coarse-grained simulations.Nature communications · 2016Article
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3 authors.
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Abstract
Identification of pathways involved in the structural transitions of biomolecular systems is often complicated by the transient nature of the conformations visited across energy barriers and the multiplicity of paths accessible in the multidimensional energy landscape. This task becomes even more challenging in exploring molecular systems on the order of megadaltons. Coarse-grained models that lend themselves to analytical solutions appear to be the only possible means of approaching such cases. Motivated by the utility of elastic network models for describing the collective dynamics of biomolecular systems and by the growing theoretical and experimental evidence in support of the intrinsic accessibility of functional substates, we introduce a new method, adaptive anisotropic network model (aANM), for exploring functional transitions. Application to bacterial chaperonin GroEL and comparisons with experimental data, results from action minimization algorithm, and previous simulations support the utility of aANM as a computationally efficient, yet physically plausible, tool for unraveling potential transition pathways sampled by large complexes/assemblies. An important outcome is the assessment of the critical inter-residue interactions formed/broken near the transition state(s), most of which involve conserved residues.
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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.