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Updated: May 22, 2026
10:50
Assessment of Immunologically Relevant Dynamic Tertiary Structural Features of the HIV-1 V3 Loop Crown R2 Sequence by ab initio Folding
Published on: September 15, 2010
Structural dynamics of HIV-1 envelope Gp120 outer domain with V3 loop
Masaru Yokoyama1, Satoshi Naganawa, Kazuhisa Yoshimura
1Laboratory of Viral Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashi Murayama-shi, Tokyo, Japan. yokoyama@nih.go.jp
Plos One
|May 25, 2012
Summary
The HIV-1 gp120 V3 loop
Area of Science:
- Virology
- Structural Biology
- Immunology
Background:
- The V3 loop of HIV-1 gp120 outer domain influences viral phenotype.
- Molecular mechanisms of V3 loop modulation are not fully understood.
Purpose of the Study:
- To investigate how V3 loop net charge affects the gp120 interaction surface phenotype.
- To elucidate the structural and functional consequences of V3 charge variations.
Main Methods:
- Combined computational (molecular dynamics simulations) and experimental (neutralization assays) approaches.
- Analyzed gp120 outer domain conformations and loop fluctuations.
- Assessed neutralization resistance of HIV-1 variants.
Main Results:
- V3 loop net charge (+3 or +7) induced global changes in gp120 conformation and loop fluctuations.
- HIV-1 with +3 V3 gp120 showed resistance to anti-CD4 binding site antibodies, unlike +7 V3.
- V3 loop charge influenced heterogeneity of the gp120 outer domain surface.
Conclusions:
- The HIV-1 gp120 V3 loop functions as an electrostatic modulator of the gp120 interaction surface.
- V3 mutations impact HIV-1 replication fitness through structural alterations.
- Findings offer a novel structural basis for understanding HIV-1 evolution.
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