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Updated: Feb 5, 2026
12:38
Structure of HIV-1 Capsid Assemblies by Cryo-electron Microscopy and Iterative Helical Real-space Reconstruction
Published on: August 9, 2011
17.8K
All-atom normal mode dynamics of HIV-1 capsid
Hyuntae Na1, Guang Song2,3
1Department of Computer Science, Penn State Harrisburg, Middletown, Pennsylvania, United States of America.
Plos Computational Biology
|September 19, 2018
Summary
We developed a new model to analyze the dynamics of the HIV-1 capsid. This method reveals how pentamers stabilize the capsid and suggests nucleotide transport occurs near pentamers.
Area of Science:
- Biophysics
- Structural Biology
- Computational Biology
Background:
- Understanding biomolecular assembly dynamics is crucial for function.
- Analyzing large systems like the HIV-1 capsid (5 million atoms) is computationally demanding.
Purpose of the Study:
- To perform a full all-atom normal mode analysis of the entire HIV-1 capsid.
- To investigate the dynamic role of capsid components in stability and function.
Main Methods:
- Developed the BOSE (Block of Selected Elasticity) model based on resonance principles.
- Efficiently computed capsid vibrations by projecting capsomere motions into a subspace.
- Validated BOSE modes against benchmark calculations using the Hessian matrix.
Main Results:
- Revealed the stabilizing role of pentamers in the HIV-1 capsid structure.
- Demonstrated agreement with experimental data on pentamer destabilization preceding capsid disassembly.
- Identified specific hexamer pores near pentamers as preferential sites for nucleotide transport.
Conclusions:
- The BOSE model enables efficient all-atom normal mode analysis of large biomolecular assemblies.
- Pentamer dynamics are critical for HIV-1 capsid stability and disassembly.
- Nucleotide transport likely occurs at hexamers adjacent to pentamers, particularly at the larger capsid end.
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