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The nature of folded states of globular proteins
Abstract
We suggest, using dynamical simulations of a simple heteropolymer modelling the α‐carbon sequence in a protein, that genetically the folded states of globular proteins correspond to statistically well‐defined metastable states. This hypothesis, called the metastability hypothesis, states that there are several free energy minima separated by barriers of various heights such that the folded conformations of a polypeptide chain in each of the minima have similar structural characteristics but have different energies from one another. The calculated structural characteristics, such as bond angle and dihedral angle distribution functions, are assumed to arise from only those configurations belonging to a given minimum. The validity of this hypothesis is illustrated by simulations of a continuum model of a heteropolymer whose low temperature state is a well‐defined β‐barrel structure. The simulations were done using a molecular dynamics algorithm (referred to as the “noisy” molecular dynamics method) containing both friction and noise terms. It is shown that for this model there are several distinct metastable minima in which the structural features are similar. Several new methods of analyzing fluctuations in structures belonging to two distinct minima are introduced. The most notable one is a dynamic measure of compactness that can in principle provide the time required for maximal compactness to be achieved. The analysis shows that for a given metastable state in which the protein has a well‐defined folded structure the transition to a state of higher compactness occurs very slowly, lending credence to the notion that the system encounters a late barrier in the process of folding to the most compact structure. The examination of the fluctuations in the structures near the unfolding → folding transition temperature indicates that the transition state for the unfolding to folding process occurs closer to the folded state.
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“Therefore, on the energy landscape, the protein native state is not a single structure but a collection of conformations fluctuating at the bottom of the funnel with comparable energy and small energy barriers.160–161”
From Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell (2016) · cites this paper as [161]
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Self-citation
Metadata
- Authors
- Honeycutt, J. D., & Thirumalai, D.
- Affiliations
- University of Maryland, College Park (US)
- ORCID
- Thirumalai, D.
- Venue
- Biopolymers
- Publisher
- Wiley
- Published
- 1992-06
- Volume
- 32
- Issue
- 6
- Pages
- 695-709
- ISSN
- 0006-3525 (ISSN-L)
- 1097-0282
- OpenAlex
- W2153333215
- Cited by
- 360
- References
- 71
- Citations by year
- 2026: 4 · 2025: 3 · 2024: 9 · 2023: 3 · 2022: 7 · 2021: 3 · 2020: 10 · 2019: 8 · 2018: 11 · 2017: 3 · 2016: 13 · 2015: 7 · 2014: 9 · 2013: 8 · 2012: 9
- FWCI
- 5.03
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Biopolymers (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Advanced Physical and Chemical Molecular Interactions
- Keywords
- protein folding, metastable states, free energy minima, beta-barrel, protein compactness, transition state, conformational fluctuations, dihedral angle distribution
- MeSH terms
- Algorithms, Mathematics, Models, Molecular, Models, Theoretical, Protein Conformation, Proteins, Thermodynamics
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