Atomic-level characterization of the structural dynamics of proteins
Abstract
Molecular dynamics (MD) simulations are widely used to study protein motions at an atomic level of detail, but they have been limited to time scales shorter than those of many biologically critical conformational changes. We examined two fundamental processes in protein dynamics--protein folding and conformational change within the folded state--by means of extremely long all-atom MD simulations conducted on a special-purpose machine. Equilibrium simulations of a WW protein domain captured multiple folding and unfolding events that consistently follow a well-defined folding pathway; separate simulations of the protein's constituent substructures shed light on possible determinants of this pathway. A 1-millisecond simulation of the folded protein BPTI reveals a small number of structurally distinct conformational states whose reversible interconversion is slower than local relaxations within those states by a factor of more than 1000.
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Dynamic interconversion between multiple conformations underpins the functions of integral membrane proteins in all domains of life.
“Dynamic interconversion between multiple conformations underpins the functions of integral membrane proteins in all domains of life (Campbell et al., 2016; Cournia et al., 2015; Shaw et al., 2010; Boehr et al., 2009).”
From Sampling alternative conformational states of transporters and receptors with AlphaFold2 (2022) · cites this paper as Shaw et al., 2010
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- Authors
- Shaw, D. E., Maragakis, P., Lindorff-Larsen, K., Piana, S., Dror, R. O., Eastwood, M. P., Bank, J. A., Jumper, J. M., Salmon, J. K., Shan, Y., & Wriggers, W.
- Affiliations
- D. E. Shaw Research (US)
- D. E. Shaw Research, 120 West 45th Street, New York, NY 10036, USA.
- Corresponding author
- Shaw, David E.
- Maragakis, Paul
- Piana, Stefano
- Venue
- Science
- Published
- 2010-10-15
- Volume
- 330
- Issue
- 6002
- Pages
- 341-346
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- OpenAlex
- W2075460992
- Cited by
- 1,923
- References
- 49
- Citations by year
- 2026: 116 · 2025: 103 · 2024: 89 · 2023: 85 · 2022: 80 · 2021: 81 · 2020: 79 · 2019: 88 · 2018: 110 · 2017: 148 · 2016: 121 · 2015: 161 · 2014: 164 · 2013: 167 · 2012: 178
- FWCI
- 64.45
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Science (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, protein conformational change, protein dynamics, folding pathways, WW domain, aprotinin, folding and unfolding, conformational states
- MeSH terms
- Computers, Aprotinin, Kinetics, Microfilament Proteins, Models, Molecular, Protein Conformation, Proteins, Solvents, Thermodynamics, Protein Structure, Tertiary, Protein Folding, Computational Biology, Amino Acid Substitution, Mutant Proteins, Molecular Dynamics Simulation
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