Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Protein Networks

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 Networks

Protein Networks

Protein-protein Interfaces

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...

Protein-Protein Interfaces

Protein-Protein Interfaces

Protein Complexes with Interchangeable Parts

Protein Complexes with Interchangeable Parts

Protein Complexes with Interchangeable Parts

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order...

You might also read

Related Articles

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

Sort by

Same author

Single-cell profiling reveals epithelial and immune responses in BK polyomavirus-infected human kidney biopsies.

JCI insight·2026

Same author

Emerging approaches for characterizing spatial and temporal dynamics of pathogen-induced organelle remodeling.

Cell systems·2026

Same author

Exploring How Workflow Variations in Denaturation-Based Assays Impact Global Protein-Protein Interaction Predictions.

Molecular & cellular proteomics : MCP·2025

Same author

Sequestration of ribosome biogenesis factors in HSV-1 nuclear aggregates revealed by spatially resolved thermal profiling.

Science advances·2025

Same author

Multi-epitope immunocapture of huntingtin reveals striatum-selective molecular signatures.

Molecular systems biology·2025

Same author

DNA-PK and ATM drive phosphorylation signatures that antagonistically regulate cytokine responses to herpesvirus infection or DNA damage.

Cell systems·2024

Same journal

Social Drivers of Health in the Electronic Health Record.

Annual review of biomedical data science·2026

Same journal

Artificial Intelligence in Image-Based Cardiovascular Disease Analysis.

Annual review of biomedical data science·2026

Same journal

Reclaiming Data, Restoring Health: The Indigenous Biomedical Data Science Renaissance.

Annual review of biomedical data science·2026

Same journal

Modeling the Language of Codons with Artificial Intelligence.

Annual review of biomedical data science·2026

Same journal

Exploring Genetic Variations Associated with the Immune Response in Underrepresented Populations.

Annual review of biomedical data science·2026

Same journal

Sex and the Genome: Divergent Genetic Architecture Across the Human Lifespan.

Annual review of biomedical data science·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Apr 23, 2026

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay PCA in Living Cells

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay PCA in Living Cells

Published on: March 3, 2015

Methods for Mapping and Analyzing Context-Specific Protein-Protein Interaction Networks.

¹Princeton Precision Health, Princeton University, Princeton, New Jersey, USA;

Annual Review of Biomedical Data Science

|April 21, 2026

Summary

This summary is machine-generated.

Mapping context-specific protein-protein interactions (PPIs) is crucial for understanding cellular functions. This review covers computational and experimental methods for analyzing these dynamic networks and extracting biological insights.

More Related Videos

Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling

Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling

Published on: November 17, 2019

Mapping Dysfunctional Protein-Protein Interactions in Disease

Mapping Dysfunctional Protein-Protein Interactions in Disease

Published on: October 24, 2025

Related Experiment Videos

Last Updated: Apr 23, 2026

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay PCA in Living Cells

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay PCA in Living Cells

Published on: March 3, 2015

Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling

Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling

Published on: November 17, 2019

Mapping Dysfunctional Protein-Protein Interactions in Disease

Mapping Dysfunctional Protein-Protein Interactions in Disease

Published on: October 24, 2025

Area of Science:

Systems Biology
Molecular Biology
Bioinformatics

Background:

Protein-protein interactions (PPIs) form dynamic, context-specific networks essential for cellular organization and function.
Understanding these context-dependent interactomes is key to deciphering cellular processes.
Variations in PPI networks occur across different cell types and perturbation states.

Purpose of the Study:

To review computational and experimental approaches for mapping and analyzing context-specific PPI networks.
To discuss analytical frameworks for extracting biological insights from PPI networks.
To highlight future directions in the field.

Main Methods:

Computational methods: refining global interactomes using expression data, literature, or machine learning integration of omics datasets.
Experimental methods: crosslinking mass spectrometry, cofractionation mass spectrometry, and denaturation-based mass spectrometry to capture physical PPIs.
Analytical frameworks: protein complex detection, network embedding, differential analysis, functional module detection, and biomarker discovery.

Main Results:

Computational and experimental methods provide complementary strategies for mapping context-specific PPIs.
Various analytical frameworks enable the extraction of functional and mechanistic insights from PPI networks.
Integration of multi-omics data and AI-driven interpretation holds promise for deeper understanding.

Conclusions:

Context-specific PPI network analysis is vital for advancing our understanding of cellular biology.
Future research should focus on multi-omic integration and enhanced spatial-temporal resolution.
AI-driven interpretation will further enrich biological insights from PPI networks.