ArticlePLoS computational biology2011
Conformational sampling and nucleotide-dependent transitions of the GroEL subunit probed by unbiased molecular dynamics simulations.
Article in PLoS computational biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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12 citing papers in PubMed, 34 citations in OpenAlex.
- Seryl phosphorylation modulates chaperonin function of Mycobacterial chaperonin, Cpn60.1.Cell stress & chaperones · 2026Article
- The C-terminal tails of GroEL and its mitochondrial and chloroplastic homologs adopt polyproline II helices.Protein science : a publication of the Protein Society · 2025Article
- Mixed mechanism of conformational selection and induced fit as a molecular recognition process in the calreticulin family of proteins.PLoS computational biology · 2022Article
- Temperature Regulates Stability, Ligand Binding (MgJournal of the American Chemical Society · 2022Article
- Two zinc-binding domains in the transporter AdcA fromThe Journal of biological chemistry · 2018Article
- Maintaining and Enhancing Diversity of Sampled Protein Conformations in Robotics-Inspired Methods.Journal of computational biology : a journal of computational molecular cell biology · 2018Article
- Directional Force Originating from ATP Hydrolysis Drives the GroEL Conformational Change.Biophysical journal · 2017Article
- Cholesterol modulates the dimer interface of the β₂-adrenergic receptor via cholesterol occupancy sites.Biophysical journal · 2014Article
- Decipher the mechanisms of protein conformational changes induced by nucleotide binding through free-energy landscape analysis: ATP binding to Hsp70.PLoS computational biology · 2013Article
- Nucleotide-dependent conformations of FtsZ dimers and force generation observed through molecular dynamics simulations.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Molecular mechanism of allosteric communication in Hsp70 revealed by molecular dynamics simulations.PLoS computational biology · 2012Article
- Coherent conformational degrees of freedom as a structural basis for allosteric communication.PLoS computational biology · 2011Article
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Authors and funding
7 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
GroEL is an ATP dependent molecular chaperone that promotes the folding of a large number of substrate proteins in E. coli. Large-scale conformational transitions occurring during the reaction cycle have been characterized from extensive crystallographic studies. However, the link between the observed conformations and the mechanisms involved in the allosteric response to ATP and the nucleotide-driven reaction cycle are not completely established. Here we describe extensive (in total long) unbiased molecular dynamics (MD) simulations that probe the response of GroEL subunits to ATP binding. We observe nucleotide dependent conformational transitions, and show with multiple 100 ns long simulations that the ligand-induced shift in the conformational populations are intrinsically coded in the structure-dynamics relationship of the protein subunit. Thus, these simulations reveal a stabilization of the equatorial domain upon nucleotide binding and a concomitant "opening" of the subunit, which reaches a conformation close to that observed in the crystal structure of the subunits within the ADP-bound oligomer. Moreover, we identify changes in a set of unique intrasubunit interactions potentially important for the conformational transition.
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