Mechanism of polymorphism and curvature of HIV capsid assemblies probed by 3D simulations with a novel coarse grain model

Biochimica Et Biophysica Acta
Xin QiaoBo Chen

Abstract

During the maturation process, HIV capsid proteins self-assemble into polymorphic capsids. The strong polymorphism precludes high resolution structural characterization under in vivo conditions. In spite of the determination of structural models for various in vitro assemblies of HIV capsid proteins, the assembly mechanism is still not well-understood. We report 3D simulations of HIV capsid proteins by a novel coarse grain model that captures the backbone of the rigid segments in the protein accurately. The effects of protein dynamics on assembly are emulated by a static ensemble of subunits in conformations derived from molecular dynamics simulation. We show that HIV capsid proteins robustly assemble into hexameric lattices in a range of conditions where trimers of dimeric subunits are the dominant oligomeric intermediates. Variations of hexameric lattice curvatures are observed in simulations with subunits of variable inter-domain orientations mimicking the conformation distribution in solution. Simulations with subunits based on pentameric structural models lead to assembly of sharp curved structures resembling the tips of authentic HIV capsids, along a distinct pathway populated by tetramers and pentamers with the character...Continue Reading

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Citations

Mar 27, 2016·Current Opinion in Virology·Michael F Hagan, Roya Zandi
Apr 14, 2016·Biochemistry·Bo Chen
Oct 30, 2016·Progress in Biophysics and Molecular Biology·Roland G HuberPeter J Bond
Oct 5, 2016·Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences·S Kashif Sadiq
Jan 18, 2017·Journal of the American Chemical Society·Jaekyun JeonBo Chen
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Aug 4, 2019·International Journal of Molecular Sciences·Nidhi Singh, Wenjin Li
Feb 10, 2021·Viruses·Morganne Wilbourne, Peijun Zhang
Dec 7, 2018·Current Opinion in Structural Biology·Alexander J Pak, Gregory A Voth
Aug 11, 2021·The Journal of Physical Chemistry Letters·Tyrone ThamesBo Chen
Aug 15, 2019·Journal of Chemical Information and Modeling·Bo WangYinghao Wu
Jun 28, 2019·Journal of the American Chemical Society·Alexander J PakGregory A Voth

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