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 Networks02:26

Protein Networks

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,...
Protein Networks02:26

Protein Networks

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,...
Protein Organization01:24

Protein Organization

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.
Protein Organization01:13

Protein Organization

Overview
Protein Organization01:24

Protein Organization

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.
Protein Organization01:13

Protein Organization

Overview

You might also read

Related Articles

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

Sort by
Same author

Osr1-expressing mesoderm contributes to lymphatic vessel assembly and complexity in the mammalian kidney.

Cell reports·2026
Same author

Low-input proteomics identifies vWF as a negative regulator of Tet2 mutant hematopoietic stem cell expansion.

Cell reports·2025
Same author

Using Total Network Dissimilarity to Analyze Protein Structures Across Homologs.

Methods in molecular biology (Clifton, N.J.)·2025
Same author

GraSp-PSN: A web server for graph spectra based analysis of protein structure networks.

Current research in structural biology·2024
Same author

Preleukemic single-cell landscapes reveal mutation-specific mechanisms and gene programs predictive of AML patient outcomes.

Cell genomics·2023
Same author

Comparison of structural networks across homologous proteins.

Proteins·2023

Related Experiment Video

Updated: Jul 2, 2026

Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

Insights into protein-DNA interactions through structure network analysis.

R Sathyapriya1, M S Vijayabaskar, Saraswathi Vishveshwara

  • 1Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.

Plos Computational Biology
|September 6, 2008
PubMed
Summary
This summary is machine-generated.

This study introduces a novel network-based approach to analyze protein-DNA interactions, offering a holistic view beyond pairwise analysis. This method reveals unique interface clusters and identifies key residues for understanding DNA recognition mechanisms.

More Related Videos

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

Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry
07:33

Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry

Published on: October 15, 2018

Related Experiment Videos

Last Updated: Jul 2, 2026

Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

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

Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry
07:33

Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry

Published on: October 15, 2018

Area of Science:

  • Structural Biology
  • Bioinformatics
  • Computational Biology

Background:

  • Protein-DNA interactions are fundamental to cellular processes.
  • Previous studies primarily used pairwise analysis, limiting a comprehensive understanding of interaction interfaces.
  • A holistic, network-based perspective is needed to capture the complexity of these interactions.

Purpose of the Study:

  • To develop and apply a novel network/graph-based methodology for analyzing protein-DNA interactions.
  • To integrate both protein-centric and DNA-centric viewpoints for a comprehensive analysis.
  • To identify key parameters and characteristics of protein-DNA interaction networks.

Main Methods:

  • Development of a graph/network representation for protein-DNA complexes.
  • Introduction of key parameters for network analysis.
  • Identification of interacting residue clusters and highly connected residues (hubs).

Main Results:

  • A network representation provides a holistic view of the interacting surface, presented here for the first time.
  • Distinct clusters of deoxyribose-amino acid interactions were identified in beta-sheet proteins.
  • Specific interface cluster patterns were observed in helix-turn-helix and zipper-type proteins, not discernible by conventional methods.
  • A classification scheme for protein-DNA complexes based on interface clusters was proposed.

Conclusions:

  • The graph-based method offers deeper insights into protein-DNA recognition mechanisms.
  • This approach elucidates the nature and specificity of protein-DNA interactions.
  • The findings provide a general understanding of how proteins interact with DNA components across different complexes.