Cited by 262Protein Structure and DynamicsAdvanced Physical and Chemical Molecular InteractionsRNA and protein synthesis mechanisms

Stability and dynamics of virus capsids described by coarse-grained modeling

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Arkhipov, Anton, Freddolino, Lydia, Schulten, Klaus·2006·Structure

Abstract

We report a study of the structural dynamics of viral capsids, simulated on a microsecond timescale, by employing a coarse-graining molecular dynamics method. The method was calibrated against an all-atom simulation of one complete virus. Among the studied capsids, some collapsed rapidly, while others were found to be stable. Interlocking between coat proteins is found to be a key factor determining the stability of the capsids.

Integrity signals

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Crossref · 10.1016/j.str.2006.10.003

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67 of 67 references verified0 citation errors · 0 not checkable

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  • Traditional molecular modeling methods usually provide reliable simulation results but require heavy computational resources, limiting their applicability.

    “The methods in the first category, such as coarse-grained molecular dynamics simulations [9, 10], usually provide reliable simulation results but require heavy computational resources, which limits their applicability [11].”

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Authors
Arkhipov, A., Freddolino, L., & Schulten, K.
Affiliations
University of Illinois Urbana-Champaign (US)
Corresponding author
Schulten, Klaus
Venue
Structure
Publisher
Elsevier BV
Published
2006-12
Volume
14
Issue
12
Pages
1767-1777
ISSN
0969-2126 (ISSN-L)
OpenAlex
W1984909504
Cited by
262
References
67
Citations by year
2026: 4 · 2025: 8 · 2024: 12 · 2023: 13 · 2022: 10 · 2021: 14 · 2020: 8 · 2019: 14 · 2018: 12 · 2017: 11 · 2016: 15 · 2015: 11 · 2014: 13 · 2013: 19 · 2012: 24
FWCI
5.72
Type
journal article
Language
en
Open access
Locations
  • Structure (publishedVersion)
  • PubMed (publishedVersion)
Funders
  • National Institutes of Health
  • National Center for Research Resources (5P41 RR 05969, P41RR005969)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Advanced Physical and Chemical Molecular Interactions
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Keywords
viral capsid, capsid stability, structural dynamics, coarse-grained molecular dynamics
MeSH terms
Biochemistry, Calibration, Capsid, Computer Simulation, Computers, Models, Molecular, Molecular Conformation, Protein Binding, Protein Conformation, Time Factors, User-Computer Interface, Viral Proteins, Models, Statistical, Computational Biology

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