Cited by 1,923Protein Structure and DynamicsRNA and protein synthesis mechanismsAdvanced Physical and Chemical Molecular Interactions

Atomic-level characterization of the structural dynamics of proteins

Shaw, David E., Maragakis, Paul, Lindorff-Larsen, Kresten, Piana, Stefano, Dror, Ron O., Eastwood, Michael P., Bank, Joseph A., Jumper, John M. +3 more·2010·Science

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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Crossref · 10.1126/science.1187409

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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).”

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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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