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

Abstract

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.

Authors:
ORCiD logo [1];  [2]
  1. 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
  2. Univ. of Illinois, Urbana-Champaign, IL (United States). Dept. of Physics and Beckman Inst.
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Oak Ridge Leadership Computing Facility (OLCF); UT-Battelle, LLC, Oak Ridge, TN (United States)
Sponsoring Org.:
Oak Ridge Leadership Computing Facility; Oak Ridge National Laboratory (ORNL); USDOE Office of Science (SC); National Institutes of Health (NIH)
OSTI Identifier:
1393179
Grant/Contract Number:  
AC05-00OR22725; 9P41GM104601
Resource Type:
Accepted Manuscript
Journal Name:
Nature Communications
Additional Journal Information:
Journal Volume: 8; Journal ID: ISSN 2041-1723
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
60 APPLIED LIFE SCIENCES; 59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Perilla, Juan R., and Schulten, Klaus. Physical properties of the HIV-1 capsid from all-atom molecular dynamics simulations. United States: N. p., 2017. Web. doi:10.1038/ncomms15959.
Perilla, Juan R., & Schulten, Klaus. Physical properties of the HIV-1 capsid from all-atom molecular dynamics simulations. United States. doi:10.1038/ncomms15959.
Perilla, Juan R., and Schulten, Klaus. Wed . "Physical properties of the HIV-1 capsid from all-atom molecular dynamics simulations". United States. doi:10.1038/ncomms15959. https://www.osti.gov/servlets/purl/1393179.
@article{osti_1393179,
title = {Physical properties of the HIV-1 capsid from all-atom molecular dynamics simulations},
author = {Perilla, Juan R. and Schulten, Klaus},
abstractNote = {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.},
doi = {10.1038/ncomms15959},
journal = {Nature Communications},
number = ,
volume = 8,
place = {United States},
year = {2017},
month = {7}
}

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    Works referencing / citing this record:

    MS2 bacteriophage capsid studied using all-atom molecular dynamics
    journal, April 2019


    MS2 bacteriophage capsid studied using all-atom molecular dynamics
    journal, April 2019