Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Temperature-dependent γ' kinetic evolution and elemental partitioning in a novel CoNi-based superalloy: an integrated CALPHAD, phase-field, and experimental study.

Materials horizons·2026
Same author

Biogeography and species diversity of freshwater <i>Savoryellomycetidae</i> (<i>Sordariomycetes</i>) fungi.

Mycology·2026
Same author

Allosteric Activation through Coordinated Energy Landscape Reweighting and Information Flow.

Computational and structural biotechnology journal·2026
Same author

A few-shot high-resolution remote sensing image semantic segmentation method.

Scientific reports·2026
Same author

Inhibition of Wnt Signaling Using Axin Peptidomimetics through Direct Targeting of β-Catenin.

Journal of medicinal chemistry·2026
Same author

Structure-informed machine learning for drug discovery: a task-centric perspective.

Briefings in bioinformatics·2026

Related Experiment Video

Updated: Oct 3, 2025

Conformational Evaluation of HIV-1 Trimeric Envelope Glycoproteins Using a Cell-based ELISA Assay
07:10

Conformational Evaluation of HIV-1 Trimeric Envelope Glycoproteins Using a Cell-based ELISA Assay

Published on: September 14, 2014

14.5K

Deciphering gp120 sequence variation and structural dynamics in HIV neutralization phenotype by molecular dynamics

Yi Li1, Yu-Chen Guo1, Hong-Han Cheng1

  • 1College of Mathematics and Computer Science, Dali University, Dali, Yunnan, China.

Proteins
|February 16, 2022
PubMed
Summary

Human immunodeficiency virus (HIV) uses gp120 variation to evade antibodies. Molecular dynamics and machine learning reveal how gp120

Keywords:
HIV neutralization phenotypeenvelope glycoprotein gp120graph machine learningmolecular dynamics simulationsequence-structure-dynamics of protein

More Related Videos

Assessment of Immunologically Relevant Dynamic Tertiary Structural Features of the HIV-1 V3 Loop Crown R2 Sequence by ab initio Folding
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

9.7K
Determination of Molecular Structures of HIV Envelope Glycoproteins using Cryo-Electron Tomography and Automated Sub-tomogram Averaging
07:29

Determination of Molecular Structures of HIV Envelope Glycoproteins using Cryo-Electron Tomography and Automated Sub-tomogram Averaging

Published on: December 1, 2011

41.7K

Related Experiment Videos

Last Updated: Oct 3, 2025

Conformational Evaluation of HIV-1 Trimeric Envelope Glycoproteins Using a Cell-based ELISA Assay
07:10

Conformational Evaluation of HIV-1 Trimeric Envelope Glycoproteins Using a Cell-based ELISA Assay

Published on: September 14, 2014

14.5K
Assessment of Immunologically Relevant Dynamic Tertiary Structural Features of the HIV-1 V3 Loop Crown R2 Sequence by ab initio Folding
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

9.7K
Determination of Molecular Structures of HIV Envelope Glycoproteins using Cryo-Electron Tomography and Automated Sub-tomogram Averaging
07:29

Determination of Molecular Structures of HIV Envelope Glycoproteins using Cryo-Electron Tomography and Automated Sub-tomogram Averaging

Published on: December 1, 2011

41.7K

Area of Science:

  • Structural biology
  • Virology
  • Computational biology

Background:

  • Human immunodeficiency virus (HIV) employs sequence and structural variability in its envelope glycoprotein gp120 to evade neutralizing antibodies.
  • Understanding the interplay between gp120 dynamics, sequence variation, and neutralization resistance is crucial for developing effective HIV therapies.

Purpose of the Study:

  • To investigate the relationship between gp120 structural dynamics, sequence variation, and HIV neutralization phenotypes.
  • To identify specific regions of gp120 that contribute to immune evasion.

Main Methods:

  • Homology modeling of 45 prefusion gp120 structures from different HIV strains.
  • Molecular dynamics (MD) simulations to analyze structural flexibility and dynamics.
  • Graph machine learning (ML) with attention mechanisms to classify neutralization phenotypes.

Main Results:

  • Structural deviations, population distribution, and conformational flexibility of gp120 correlate with HIV neutralization phenotype.
  • Highly flexible local regions, particularly in second structural elements, are implicated in determining the neutralization phenotype.
  • A graph ML model successfully linked gp120 sequence variation and structural dynamics to neutralization phenotype classification.

Conclusions:

  • HIV neutralization phenotype is influenced by gp120 sequence variation and structural dynamics.
  • Specific flexible regions within gp120 play a key role in immune evasion.
  • Integrating MD simulations and ML provides insights into protein sequence-structure-dynamics relationships for HIV neutralization.