Physical properties of the HIV-1 capsid from all-atom molecular dynamics simulations

Perilla, Juan R.; Schulten, Klaus

doi:10.1038/ncomms15959

Physical properties of the HIV-1 capsid from all-atom molecular dynamics simulations

Journal Article · Wed Jul 19 00:00:00 EDT 2017 · Nature Communications

DOI:https://doi.org/10.1038/ncomms15959· OSTI ID:1393179

^[1]; Schulten, Klaus ^[2]

Univ. of Illinois, Urbana-Champaign, IL (United States). Dept. of Physics and Beckman Inst.; Univ. of Delaware, Newark, DE (United States). Dept. of Chemistry and Biochemistry; University of Illinois at Urbana-Champaign, Urbana, Illinois
Univ. of Illinois, Urbana-Champaign, IL (United States). Dept. of Physics and Beckman Inst.

Human immunodeficiency virus type 1 (HIV-1) infection is highly dependent on its capsid. The capsid is a large container, made of B 1,300 proteins with altogether 4 million atoms. Though the capsid proteins are all identical, they nevertheless arrange themselves into a largely asymmetric structure made of hexamers and pentamers. The large number of degrees of freedom and lack of symmetry pose a challenge to studying the chemical details of the HIV capsid. Simulations of over 64 million atoms for over 1 μs allow us to conduct a comprehensive study of the chemical–physical properties of an empty HIV-1 capsid, including its electrostatics, vibrational and acoustic properties, and the effects of solvent (ions and water) on the capsid. Furthermore, the simulations reveal critical details about the capsid with implications to biological function.

View Accepted Manuscript (DOE)

Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States). Oak Ridge Leadership Computing Facility (OLCF); UT-Battelle, LLC, Oak Ridge, TN (United States)

Sponsoring Organization:: Oak Ridge Leadership Computing Facility; Oak Ridge National Laboratory (ORNL); USDOE Office of Science (SC); National Institutes of Health (NIH)

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 1393179

Journal Information:: Nature Communications, Journal Name: Nature Communications Vol. 8; ISSN 2041-1723

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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