ArticleBiophysical journal2007
Allosteric transitions in the chaperonin GroEL are captured by a dominant normal mode that is most robust to sequence variations.
Article in Biophysical journal, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
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Who cites it
54 citing papers in PubMed.
- Genetic and structural insights into the functional importance of the conserved gly-met-rich C-terminal tails in bacterial chaperonins.Communications biology · 2025Article
- Insight into the Nucleotide Based Modulation of the Grp94 Molecular Chaperone Using Multiscale Dynamics.The journal of physical chemistry. B · 2023Article
- Predicting allosteric pockets in protein biological assemblages.Bioinformatics (Oxford, England) · 2023Article
- Predicting allosteric sites using fast conformational sampling as guided by coarse-grained normal modes.The Journal of chemical physics · 2023Article
- Interpretation of Single-Molecule Force Experiments on Proteins Using Normal Mode Analysis.Nanomaterials (Basel, Switzerland) · 2021Article
- Structural Communication between theInternational journal of molecular sciences · 2021Article
- Normal Mode Analysis as a Routine Part of a Structural Investigation.Molecules (Basel, Switzerland) · 2019Review
- FcαRI binding at the IgA1 CProceedings of the National Academy of Sciences of the United States of America · 2018Article
- Signalling networks and dynamics of allosteric transitions in bacterial chaperonin GroEL: implications for iterative annealing of misfolded proteins.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2018Review
- The 'allosteron' model for entropic allostery of self-assembly.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2018Article
- Conservation of Dynamics Associated with Biological Function in an Enzyme Superfamily.Structure (London, England : 1993) · 2018Article
- Patterns of coevolving amino acids unveil structural and dynamical domains.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Directional Force Originating from ATP Hydrolysis Drives the GroEL Conformational Change.Biophysical journal · 2017Article
- Protein Allostery and Conformational Dynamics.Chemical reviews · 2016Review
- Flexibility-rigidity index for protein-nucleic acid flexibility and fluctuation analysis.Journal of computational chemistry · 2016Article
- Correlated rigid modes in protein families.Physical biology · 2016Article
- Multiscale Gaussian network model (mGNM) and multiscale anisotropic network model (mANM).The Journal of chemical physics · 2015Article
- AlloPred: prediction of allosteric pockets on proteins using normal mode perturbation analysis.BMC bioinformatics · 2015Article
- The Role of Conformational Dynamics and Allostery in the Disease Development of Human Ferritin.Biophysical journal · 2015Article
- Conformational dynamics of nonsynonymous variants at protein interfaces reveals disease association.Proteins · 2015Article
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3 authors.
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Abstract
The Escherichia coli chaperonin GroEL, which helps proteins to fold, consists of two heptameric rings stacked back-to-back. During the reaction cycle GroEL undergoes a series of allosteric transitions triggered by ligand (substrate protein, ATP, and the cochaperonin GroES) binding. Based on an elastic network model of the bullet-shaped double-ring chaperonin GroEL-(ADP)(7)-GroES structure (R''T state), we perform a normal mode analysis to explore the energetically favorable collective motions encoded in the R''T structure. By comparing each normal mode with the observed conformational changes in the R''T --> TR'' transition, a single dominant normal mode provides a simple description of this highly intricate allosteric transition. A detailed analysis of this relatively high-frequency mode describes the structural and dynamic changes that underlie the positive intra-ring and negative inter-ring cooperativity. The dynamics embedded in the dominant mode entails highly concerted structural motions with approximate preservation of sevenfold symmetry within each ring and negatively correlated ones between the two rings. The dominant normal mode (in comparison with the other modes) is robust to parametric perturbations caused by sequence variations, which validates its functional importance. Response of the dominant mode to local changes that mimic mutations using the structural perturbation method technique leads to a wiring diagram that identifies a network of key residues that regulate the allosteric transitions. Many of these residues are located in intersubunit interfaces, and may therefore play a critical role in transmitting allosteric signals between subunits.
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