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Emergence of Glass-like Behavior in Markov State Models of Protein Folding Dynamics
Open accessAbstract
The extent to which glass-like kinetics govern dynamics in protein folding has been heavily debated. Here, we address the subject with an application of space-time perturbation theory to the dynamics of protein folding Markov state models. Borrowing techniques from the s-ensemble method, we argue that distinct active and inactive phases exist for protein folding dynamics, and that kinetics for specific systems can fall into either dynamical regime. We do not, however, observe a true glass transition in any system studied. We go on to discuss how these inactive and active phases might relate to general protein folding properties.
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MSMs have been used to examine the role of glassy dynamics in protein folding, finding that true glass transitions appear to be absent in atomistic models of solvated protein dynamics.
“MSMs have also been used to examine the role of glassy dynamics in protein folding, finding that true glass transitions appear to be absent in atomistic models of solvated protein dynamics [52].”
From Markov state models of biomolecular conformational dynamics (2014) · cites this paper as [52]
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Metadata
- Authors
- Weber, J. K., Jack, R. L., & Pande, V. S.
- Affiliations
- Stanford University (US)
- University of Bath (GB)
- Corresponding author
- Pande, Vijay S.
- Venue
- Journal of the American Chemical Society
- Publisher
- American Chemical Society (ACS)
- Published
- 2013-04-03
- Volume
- 135
- Issue
- 15
- Pages
- 5501-5504
- ISSN
- 0002-7863 (ISSN-L)
- 1520-5126
- PMC
- PMC3677858
- OpenAlex
- W2054592353
- Cited by
- 50
- References
- 20
- Citations by year
- 2026: 1 · 2024: 1 · 2022: 1 · 2021: 1 · 2020: 2 · 2019: 5 · 2018: 7 · 2017: 6 · 2016: 8 · 2015: 9 · 2014: 7 · 2013: 2
- FWCI
- 3.88
- Type
- journal article
- Language
- en
- Open access
- Licence
- other-oa
- Locations
- Journal of the American Chemical Society (publishedVersion)
- PubMed (publishedVersion)
- Pure (University of Bath) (publishedVersion, other-oa)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- The University of Bath Online Publications Store (The University of Bath) (submittedVersion)
- Funders
- Engineering and Physical Sciences Research Council (EP/I003797/1)
- National Institute of General Medical Sciences (R01GM062868)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Materials Science › Materials Chemistry › Material Dynamics and Properties
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Keywords
- protein folding, glass transition, Markov state models, folding kinetics, folding dynamics
- MeSH terms
- Glass, Markov Chains, Models, Molecular, Proteins, Protein Structure, Tertiary, Protein Folding
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