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Coarse-grained simulation reveals key features of HIV-1 capsid self-assembly

Grime, John M. A. and Dama, James F. and Ganser-Pornillos, Barbie K. and Woodward, Cora L. and Jensen, Grant J. and Yeager, Mark J. and Voth, Gregory A. (2016) Coarse-grained simulation reveals key features of HIV-1 capsid self-assembly. Nature Communications, 7 . Art. No. 11568. ISSN 2041-1723. PMCID PMC4869257. http://resolver.caltech.edu/CaltechAUTHORS:20160516-083514191

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Abstract

The maturation of HIV-1 viral particles is essential for viral infectivity. During maturation, many copies of the capsid protein (CA) self-assemble into a capsid shell to enclose the viral RNA. The mechanistic details of the initiation and early stages of capsid assembly remain to be delineated. We present coarse-grained simulations of capsid assembly under various conditions, considering not only capsid lattice self-assembly but also the potential disassembly of capsid upon delivery to the cytoplasm of a target cell. The effects of CA concentration, molecular crowding, and the conformational variability of CA are described, with results indicating that capsid nucleation and growth is a multi-stage process requiring well-defined metastable intermediates. Generation of the mature capsid lattice is sensitive to local conditions, with relatively subtle changes in CA concentration and molecular crowding influencing self-assembly and the ensemble of structural morphologies.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1038/ncomms11568DOIArticle
http://www.nature.com/ncomms/2016/160513/ncomms11568/full/ncomms11568.htmlPublisherArticle
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4869257/PubMed CentralArticle
http://www.nature.com/ncomms/2016/160513/ncomms11568/extref/ncomms11568-s1.pdfPublisherSupplementary Information
https://doi.org/10.1101/040741DOIDiscussion Paper
ORCID:
AuthorORCID
Jensen, Grant J.0000-0003-1556-4864
Additional Information:© 2016 Macmillan Publishers Limited. This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ Received 20 July 2015; Accepted 07 April 2016; Published 13 May 2016. This research was supported by National Institutes of Health grants P50 GM082545 (G.A.V. and M.Y.) and R01 GM066087 (M.Y.). The computations in this work are part of the Blue Waters sustained-petascale computing project, which is supported by the National Science Foundation (awards OCI-0725070 and ACI-1238993) and the state of Illinois. Blue Waters is a joint effort of the University of Illinois at Urbana-Champaign and its National Center for Supercomputing Applications. This work is also part of the ‘Ultra-Coarse-Grained Simulations of Biomolecular Processes at the Petascale’ Petascale Computing Resource Allocation (PRAC) support by the National Science Foundation (award number OCI-1440027). Author contributions: J.M.A.G., J.F.D. and G.A.V. conceived the study, designed the simulations and wrote the manuscript. J.M.A.G. performed the simulations. Additional experimental data were provided by C.L.W. Data analysis was performed by J.M.A.G., J.F.D., B.K.G.-P., G.J.J., M.J.Y. and G.A.V. The authors declare no competing financial interests.
Funders:
Funding AgencyGrant Number
NIHP50 GM082545
NIHR01 GM066087
NSFOCI‐0725070
NSFACI‐1238993
State of IllinoisUNSPECIFIED
NSFOCI‐1440027
PubMed Central ID:PMC4869257
Record Number:CaltechAUTHORS:20160516-083514191
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:20160516-083514191
Official Citation:Grime, J. M. A. et al. Coarse-grained simulation reveals key features of HIV-1 capsid self-assembly. Nat. Commun. 7:11568 doi: 10.1038/ncomms11568 (2016).
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:67098
Collection:CaltechAUTHORS
Deposited By: Ruth Sustaita
Deposited On:16 May 2016 18:48
Last Modified:26 Oct 2018 23:56

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