Molecular dynamics simulations of large macromolecular complexes

Perilla, Juan R.; Goh, Boon Chong; Cassidy, C. Keith; Liu, Bo; Bernardi, Rafael C.; Rudack, Till; Yu, Hang; Wu, Zhe; Schulten, Klaus

doi:10.1016/j.sbi.2015.03.007

Molecular dynamics simulations of large macromolecular complexes

Journal Article · Sat Apr 04 00:00:00 EDT 2015 · Current Opinion in Structural Biology

DOI:https://doi.org/10.1016/j.sbi.2015.03.007· OSTI ID:1565310

^[1]; Goh, Boon Chong ^[1]; Cassidy, C. Keith ^[1]; Liu, Bo ^[2]; Bernardi, Rafael C. ^[3]; Rudack, Till ^[4]; ^[2]; Wu, Zhe ^[5]; Schulten, Klaus ^[6]

Univ. of Illinois at Urbana-Champaign, Urbana, IL (United States). Beckman Inst., and Dept. of Physics
Univ. of Illinois at Urbana-Champaign, Urbana, IL (United States). Beckman Inst., and Center for Biophysics and Computational Biology
Univ. of Illinois at Urbana-Champaign, Urbana, IL (United States). Beckman Inst., and Energy Biosciences Inst.
Univ. of Illinois at Urbana-Champaign, Urbana, IL (United States). Beckman Inst.
Univ. of Illinois at Urbana-Champaign, Urbana, IL (United States). Beckman Inst., and Center for Physics of Living Cells
Univ. of Illinois at Urbana-Champaign, Urbana, IL (United States). Beckman Inst., Dept. of Physics, Energy Biosciences Inst., Center for the Physics of Living Cells, and Center for Biophysics and Computational Biology

Connecting dynamics to structural data from diverse experimental sources, molecular dynamics simulations permit the exploration of biological phenomena in unparalleled detail. Advances in simulations are moving the atomic resolution descriptions of biological systems into the million-to-billion atom regime, in which numerous cell functions reside. In this opinion, we review the progress, driven by large-scale molecular dynamics simulations, in the study of viruses, ribosomes, bioenergetic systems, and other diverse applications. Finally, these examples highlight the utility of molecular dynamics simulations in the critical task of relating atomic detail to the function of supramolecular complexes, a task that cannot be achieved by smaller-scale simulations or existing experimental approaches alone.

View Accepted Manuscript (DOE)

Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States). Oak Ridge Leadership Computing Facility (OLCF)

Sponsoring Organization:: USDOE Office of Science (SC)

OSTI ID:: 1565310

Journal Information:: Current Opinion in Structural Biology, Journal Name: Current Opinion in Structural Biology Vol. 31; ISSN 0959-440X

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

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Mechanisms of Nanonewton Mechanostability in a Protein Complex Revealed by Molecular Dynamics Simulations and Single-Molecule Force Spectroscopy C., Bernardi, Rafael; Ellis, Durner,; Constantin, Schoeler, American Chemical Society https://doi.org/10.5451/unibas-ep72178	text	January 2019
CryoEM and computer simulations reveal a novel kinase conformational switch in bacterial chemotaxis signaling Cassidy, C. Keith; Himes, Benjamin A.; Alvarez, Frances J. eLife, Vol. 4 https://doi.org/10.7554/elife.08419	journal	November 2015
All-atom molecular dynamics of the HBV capsid reveals insights into biological function and cryo-EM resolution limits Hadden, Jodi A.; Perilla, Juan R.; Schlicksup, Christopher John eLife, Vol. 7 https://doi.org/10.7554/elife.32478	journal	April 2018

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