ArticleJournal of the American Chemical Society2011
Simulation of chaperonin effect on protein folding: a shift from nucleation-condensation to framework mechanism.
Article in Journal of the American Chemical Society, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Protein-Protein Docking with Large-Scale Backbone Flexibility Using Coarse-Grained Monte-Carlo Simulations.International journal of molecular sciences · 2021Article
- Energy landscape remodeling mechanism of Hsp70-chaperone-accelerated protein folding.Biophysical journal · 2021Article
- Flexible docking of peptides to proteins using CABS-dock.Protein science : a publication of the Protein Society · 2020Article
- Antimicrobial Peptide Designing and Optimization Employing Large-Scale Flexibility Analysis of Protein-Peptide Fragments.ACS omega · 2019Article
- Structural Characterization of Open Reading Frame-Encoded Functional Genes from Tilapia Lake Virus (TiLV).Molecular biotechnology · 2019Article
- Recent Advances in Coarse-Grained Models for Biomolecules and Their Applications.International journal of molecular sciences · 2019Review
- Modeling of Disordered Protein Structures Using Monte Carlo Simulations and Knowledge-Based Statistical Force Fields.International journal of molecular sciences · 2019Review
- Modeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-Grained Simulations and Elastic Network Models.International journal of molecular sciences · 2018Review
- Protein-peptide molecular docking with large-scale conformational changes: the p53-MDM2 interaction.Scientific reports · 2016Article
- Hsp70 biases the folding pathways of client proteins.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site.Nucleic acids research · 2015Article
- CABS-flex predictions of protein flexibility compared with NMR ensembles.Bioinformatics (Oxford, England) · 2014Article
- Structure prediction of the second extracellular loop in G-protein-coupled receptors.Biophysical journal · 2014Article
- CABS-flex: Server for fast simulation of protein structure fluctuations.Nucleic acids research · 2013Article
- CABS-fold: Server for the de novo and consensus-based prediction of protein structure.Nucleic acids research · 2013Article
- Combining coarse-grained protein models with replica-exchange all-atom molecular dynamics.International journal of molecular sciences · 2013Article
- Article
- Macromolecule-assisted de novo protein folding.International journal of molecular sciences · 2012Review
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2 authors.
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Abstract
The iterative annealing mechanism (IAM) of chaperonin-assisted protein folding is explored in a framework of a well-established coarse-grained protein modeling tool, which enables the study of protein dynamics in a time-scale well beyond classical all-atom molecular mechanics. The chaperonin mechanism of action is simulated for two paradigm systems of protein folding, B domain of protein A (BdpA) and B1 domain of protein G (GB1), and compared to chaperonin-free simulations presented here for BdpA and recently published for GB1. The prediction of the BdpA transition state ensemble (TSE) is in perfect agreement with experimental findings. It is shown that periodic distortion of the polypeptide chains by hydrophobic chaperonin interactions can promote rapid folding and leads to a decrease in folding temperature. It is also demonstrated how chaperonin action prevents kinetically trapped conformations and modulates the observed folding mechanisms from nucleation-condensation to a more framework-like.
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