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Viruses are extraordinarily diverse in shape and size, but they all have several structural features in common. All viruses have a core that contains a DNA- or RNA-based genome. The core is surrounded by a protective coat of proteins called the capsid. The capsid is composed of subunits called capsomeres. The capsid and genome-containing core are together known as the nucleocapsid.
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Retroviruses have a single-stranded RNA genome that undergoes a special form of replication. Once the retrovirus has entered the host cell, an enzyme called reverse transcriptase synthesizes double-stranded DNA from the retroviral RNA genome. This DNA copy of the genome is then integrated into the host’s genome inside the nucleus via an enzyme called integrase. Consequently, the retroviral genome is transcribed into RNA whenever the host’s genome is transcribed, allowing the...
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Related Experiment Video

Updated: Mar 29, 2026

Structure of HIV-1 Capsid Assemblies by Cryo-electron Microscopy and Iterative Helical Real-space Reconstruction
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Modeling HIV-1 viral capsid nucleation by dynamical systems.

Farrah Sadre-Marandi1, Yuewu Liu2, Jiangguo Liu1

  • 1Department of Mathematics, Colorado State University, Fort Collins, CO 80523-1874, USA.

Mathematical Biosciences
|November 25, 2015
PubMed
Summary

This study models the nucleation stage of human immunodeficiency virus type 1 (HIV-1) capsid assembly. Mathematical models and simulations reveal the critical role of capsid protein (CA) trimer-of-dimers in viral assembly.

Keywords:
CapsidDimersDynamical systemsHIV-1HexamersSensitivity analysis

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Area of Science:

  • Virology
  • Biophysics
  • Computational Biology

Background:

  • Viral capsid assembly is crucial for viral replication, occurring in distinct nucleation and elongation stages.
  • Understanding the initial nucleation phase is key to deciphering viral self-assembly mechanisms.

Purpose of the Study:

  • To develop and validate mathematical models for human immunodeficiency virus type 1 (HIV-1) viral capsid nucleation.
  • To investigate the influence of association and dissociation rates on capsid protein (CA) multimer concentrations during nucleation.

Main Methods:

  • Development of a six-species dynamical system to model HIV-1 capsid nucleation.
  • Application of the Particle Swarm Optimization (PSO) algorithm for parameter fitting using experimental data.
  • Numerical simulations to analyze CA multimer concentrations and perform sensitivity analysis.

Main Results:

  • Simulated CA multimer concentrations showed strong agreement with experimental data.
  • Sensitivity analysis highlighted the significant impact of association and dissociation rates on nucleation dynamics.
  • Identified CA trimer-of-dimers as a critical component in the HIV-1 capsid nucleation stage.

Conclusions:

  • The developed mathematical models accurately represent HIV-1 capsid nucleation.
  • The study underscores the importance of specific CA multimer structures, like trimer-of-dimers, in initiating viral assembly.
  • Findings provide insights into the fundamental processes governing viral capsid formation.