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

Protein Folding01:22

Protein Folding

123.7K
Overview
123.7K
Protein Folding01:25

Protein Folding

9.8K
Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
9.8K
Protein Organization01:24

Protein Organization

8.1K
Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....
8.1K
Protein Organization01:13

Protein Organization

150.9K
Overview
150.9K
Protein Networks02:26

Protein Networks

4.2K
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
4.2K
Protein Networks02:26

Protein Networks

2.5K
2.5K

You might also read

Related Articles

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

Sort by
Same author

Annotating Interchromosomal Interactions at Sub-Megabase Resolution Using Network Clustering Coefficients.

bioRxiv : the preprint server for biology·2026
Same author

TDTAC: a generalized time-dependent torsion angle correlation framework for resolving directional coordination in large biomolecular assemblies.

Frontiers in molecular biosciences·2026
Same author

Molecular Behavior of Human β Defensin Type 3 Embedded in Different Model Lipid Membranes.

Journal of chemical information and modeling·2026
Same author

Conformational transition of a polycationic hinge domain contributes to DNA binding.

Biophysical chemistry·2025
Same author

Integrating FRET and Molecular Dynamics Simulation for Single-Molecule Aptameric Detection of Staphylococcus aureus IsdA Surface Protein.

Biotechnology journal·2025
Same author

Hormone response elements for the thyroid receptor-α include specific distal 5'-flanking DNA.

Science advances·2024

Related Experiment Video

Updated: Oct 29, 2025

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

15.6K

Protein conformational switch discerned via network centrality properties.

David Foutch1, Bill Pham2, Tongye Shen2,3

  • 1Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA.

Computational and Structural Biotechnology Journal
|July 14, 2021
PubMed
Summary

Network analysis reveals eigenvector centrality can detect subtle protein conformational changes. A modified protein structure network (PSN*) improves sensitivity for structural biology research.

Keywords:
Conformational switchNetwork analysisNetwork centralityProtein structure network

More Related Videos

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

69.2K
Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

7.4K

Related Experiment Videos

Last Updated: Oct 29, 2025

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

15.6K
A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

69.2K
Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

7.4K

Area of Science:

  • Structural biology
  • Computational biology
  • Biophysics

Background:

  • Network analysis is a powerful tool for studying biomolecular structures.
  • Protein structure networks (PSNs) help identify functionally important amino acid residues.
  • The sensitivity of network properties to subtle conformational changes needs further investigation.

Purpose of the Study:

  • To assess the sensitivity of network centrality measures to conformational changes in proteins.
  • To compare the effectiveness of different centrality measures (betweenness, closeness, degree, eigenvector) in detecting structural variations.
  • To evaluate a modified PSN approach (PSN*) for enhanced sensitivity.

Main Methods:

  • Analysis of four network centrality measures (betweenness, closeness, degree, eigenvector) applied to protein structure networks.
  • Focus on conformational changes in a sensor protein (constitutive androstane receptor) and an allosteric enzyme (ribonucleotide reductase) upon ligand binding.
  • Development and application of an ensemble-informed, modified PSN (PSN*) by removing static edges.

Main Results:

  • Eigenvector centrality demonstrated sensitivity in distinguishing structural features between different protein conformational states.
  • Closeness centrality and other measures were found to be less sensitive and more generic.
  • The modified PSN* approach showed enhanced sensitivity in discerning structural changes compared to standard PSNs.

Conclusions:

  • Eigenvector centrality is a valuable metric for analyzing subtle conformational changes in proteins using network analysis.
  • The PSN* method offers improved sensitivity for detecting structural variations, aiding in the study of protein dynamics.
  • Network analysis, particularly with refined methods like PSN*, provides deeper insights into protein structure-function relationships.