ArticleBiophysical journal2013
Effects of interactions with the GroEL cavity on protein folding rates.
Article in Biophysical journal, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 37 citations in OpenAlex.
- An outmoded in vitro-inferred mechanism for chaperonin-accelerated protein refolding is confirmed in cells by cryo-electron tomography.Cell stress & chaperones · 2024Article
- Electromechanical Photophysics of GFP Packed Inside Viral Protein Cages Probed by Force-Fluorescence Hybrid Single-Molecule Microscopy.Small (Weinheim an der Bergstrasse, Germany) · 2022Article
- Chaperonin facilitates protein folding by avoiding initial polypeptide collapse.Journal of biochemistry · 2018Article
- From chaperonins to Rubisco assembly and metabolic repair.Protein science : a publication of the Protein Society · 2017Review
- Chaperone-client interactions: Non-specificity engenders multifunctionality.The Journal of biological chemistry · 2017Review
- Predicting Protein-protein Association Rates using Coarse-grained Simulation and Machine Learning.Scientific reports · 2017Article
- Markov state models of protein misfolding.The Journal of chemical physics · 2016Article
- How do chaperonins fold protein?Biophysics (Nagoya-shi, Japan) · 2015Review
- Knotted proteins: A tangled tale of Structural Biology.Computational and structural biotechnology journal · 2015Review
- Role of denatured-state properties in chaperonin action probed by single-molecule spectroscopy.Biophysical journal · 2014Article
- GroEL/ES chaperonin modulates the mechanism and accelerates the rate of TIM-barrel domain folding.Cell · 2014Article
- Effect of interactions with the chaperonin cavity on protein folding and misfolding.Physical chemistry chemical physics : PCCP · 2014Article
- Comparing a simple theoretical model for protein folding with all-atom molecular dynamics simulations.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- How well does a funneled energy landscape capture the folding mechanism of spectrin domains?The journal of physical chemistry. B · 2013Article
- A sticky cage can slow down folding.Biophysical journal · 2013Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Encapsulation of proteins in chaperonins is an important mechanism by which the cell prevents the accumulation of misfolded species in the cytosol. However, results from theory and simulation for repulsive cavities appear to be inconsistent with recent experimental results showing, if anything, a slowdown in folding rate for encapsulated Rhodanese. We study the folding of Rhodanese in GroEL, using coarse-grained molecular simulations of the complete system including chaperonin and substrate protein. We find that, by approximating the substrate:GroEL interactions as repulsive, we obtain a strong acceleration in rate of between one and two orders of magnitude; a similar result is obtained by representing the chaperonin as a simple spherical cavity. Remarkably, however, we find that using a carefully parameterized, sequence-based potential to capture specific residue-residue interactions between Rhodanese and the GroEL cavity walls induces a very strong reduction of the folding rates. The effect of the interactions is large enough to completely offset the effects of confinement, such that folding in some cases can be even slower than that of the unconfined protein. The origin of the slowdown appears to be stabilization--relative to repulsive confinement--of the unfolded state through binding to the cavity walls, rather than a reduction of the diffusion coefficient along the folding coordinate.
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