ArticleProceedings of the National Academy of Sciences of the United States of America2008
Thermodynamics and kinetics of protein folding under confinement.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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Who cites it
49 citing papers in PubMed.
- FINCHES: A Computational Framework for Predicting Intermolecular Interactions in Intrinsically Disordered Proteins.International journal of molecular sciences · 2025Review
- Combined effect of confinement and dielectric exclusion on ion adsorption in slits, pores, and cavities.AIP advances · 2024Article
- Genetic Functionalization of Protein-Based Biomaterials via Protein Fusions.Biomacromolecules · 2024Review
- Probe capsid structure stability and dynamics of adeno-associated virus as an important viral vector for gene therapy by hydrogen-deuterium exchange-mass spectrometry.Protein science : a publication of the Protein Society · 2024Article
- How the ribosome shapes cotranslational protein folding.Current opinion in structural biology · 2024Review
- The role of water in reactions catalysed by hydrolases under conditions of molecular crowding.Biophysical reviews · 2023Review
- Review
- Effect of Secondary Structures on the Adsorption of Peptides onto Hydrophobic Solid Surfaces Revealed by SALDI-TOF and MD Simulations.ACS omega · 2022Article
- Effects of Different Gluten Proteins on Starch's Structural and Physicochemical Properties during Heating and Their Molecular Interactions.International journal of molecular sciences · 2022Article
- The ribosome modulates folding inside the ribosomal exit tunnel.Communications biology · 2021Article
- Effects of Ionic Liquids on Metalloproteins.Molecules (Basel, Switzerland) · 2021Review
- Salt-Dependent RNA Pseudoknot Stability: Effect of Spatial Confinement.Frontiers in molecular biosciences · 2021Article
- Confinement and Crowding Effects on Folding of a Multidomain Y-Family DNA Polymerase.Journal of chemical theory and computation · 2020Article
- A hybrid, bottom-up, structurally accurate, Go¯-like coarse-grained protein model.The Journal of chemical physics · 2019Article
- Folding up and Moving on-Nascent Protein Folding on the Ribosome.Journal of molecular biology · 2018Review
- Thermal stability and conformation of DNA and proteins under the confined condition in the matrix of hydrogels.Molecular biology reports · 2018Article
- Computational modeling highlights the role of the disordered Formin Homology 1 domain in profilin-actin transfer.FEBS letters · 2018Article
- The exclusive effects of chaperonin on the behavior of proteins with 52 knot.PLoS computational biology · 2018Article
- Confinement and Stabilization of Fyn SH3 Folding Intermediate Mimetics within the Cavity of the Chaperonin GroEL Demonstrated by Relaxation-Based NMR.Biochemistry · 2017Article
- Knotting and unknotting proteins in the chaperonin cage: Effects of the excluded volume.PloS one · 2017Article
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2 authors.
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Abstract
Understanding the effects of confinement on protein stability and folding kinetics is important for describing protein folding in the cellular environment. We have investigated the effects of confinement on two structurally distinct proteins as a function of the dimension d(c) and characteristic size R of the confining boundary. We find that the stabilization of the folded state relative to bulk conditions is quantitatively described by R(-gamma(c)), where the exponent gamma(c) is approximately 5/3 independent of the dimension of confinement d(c) (cylindrical, planar, or spherical). Moreover, we find that the logarithm of the folding rates also scale as R(-gamma(c)), with deviations only being seen for very small confining geometries, where folding is downhill; for both stability and kinetics, the dominant effect is the change in the free energy of the unfolded state. A secondary effect on the kinetics is a slight destabilization of the transition state by confinement, although the contacts present in the confined transition state are essentially identical to the bulk case. We investigate the effect of confinement on the position-dependent diffusion coefficients D(Q) for dynamics along the reaction coordinate Q (fraction of native contacts). The diffusion coefficients only change in the unfolded state basin, where they are increased because of compaction.
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