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Updated: Feb 12, 2026

Structure of HIV-1 Capsid Assemblies by Cryo-electron Microscopy and Iterative Helical Real-space Reconstruction

Structure of HIV-1 Capsid Assemblies by Cryo-electron Microscopy and Iterative Helical Real-space Reconstruction

Published on: August 9, 2011

Molecular dynamics study of T = 3 capsid assembly.

¹Department of Physics, Bar-Ilan University, Ramat-Gan, 52900, Israel. rapaport@mail.biu.ac.il.

Journal of Biological Physics

|April 3, 2018

Summary

Molecular dynamics simulations successfully modeled virus capsid self-assembly using 180 trapezoidal particles. The study reveals key intermediate structures, aiding experimental interpretation of viral shell formation.

Keywords:

Capsid Self-assembly Simulation Virus

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Alternative In Vitro Methods for the Determination of Viral Capsid Structural Integrity

Alternative In Vitro Methods for the Determination of Viral Capsid Structural Integrity

Published on: November 16, 2017

Area of Science:

Computational biology
Biophysics
Structural biology

Background:

Virus capsid self-assembly is a complex process crucial for viral replication.
Understanding quasi-equivalence is key to modeling T=3 capsids.
Previous models often lack atomistic detail or explicit solvent effects.

Purpose of the Study:

To model the self-assembly of T=3 virus capsids using molecular dynamics.
To investigate the role of particle shape and quasi-equivalence in shell formation.
To reveal intermediate structures during the self-assembly pathway.

Main Methods:

Utilized molecular dynamics simulations.
Modeled self-assembly of 180 trapezoidal particles representing T=3 capsids.
Incorporated three slightly different particle shapes to account for quasi-equivalence.
Included reversible bond formation and explicit atomistic solvent.

Main Results:

Achieved formation of complete polyhedral shells under suitable conditions.
Observed majority of unused particles remaining as monomers.
Reported no significant formation of incorrect clusters or misassembled structures.
Identified and detailed intermediate structures along the assembly pathway.

Conclusions:

Molecular dynamics simulations can accurately model virus capsid self-assembly.
Quasi-equivalence plays a significant role in the formation of T=3 capsids.
The simulation provides valuable insights into the kinetics and intermediates of capsid formation, relevant for experimental validation.