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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.
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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

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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...

Protein Complexes with Interchangeable Parts

Protein Complexes with Interchangeable Parts

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Related Experiment Video

Updated: Apr 20, 2026

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

Published on: October 19, 2021

Community structure detection for overlapping modules through mathematical programming in protein interaction

Laura Bennett¹, Aristotelis Kittas², Songsong Liu¹

¹Centre for Process Systems Engineering, Department of Chemical Engineering, UCL (University College London), Torrington Place, WC1E 7JE, London, United Kingdom.

|November 21, 2014

Summary

This summary is machine-generated.

This study introduces OverMod, a novel method to identify overlapping communities in complex networks. It distinguishes between inter-connector and intra-connector proteins, revealing proteins with multiple distinct biological roles.

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Last Updated: Apr 20, 2026

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

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

Published on: July 14, 2015

Area of Science:

Network analysis
Systems biology
Bioinformatics

Background:

Community structure detection is crucial for understanding complex networks.
Existing methods often assume disjoint communities, limiting realistic interaction modeling.
Overlapping community structures offer a more nuanced representation of biological systems.

Purpose of the Study:

To develop a method for detecting overlapping communities in biological networks.
To analyze the topological and functional properties of proteins connecting different communities.
To differentiate between proteins with multiple distinct roles and simple hub proteins.

Main Methods:

A two-step procedure involving initial hard partition detection.
Application of a novel mixed integer non-linear programming (MINLP) model named OverMod.
Evaluation on protein-protein interaction (PPI) networks from rat, E. coli, yeast, and human.

Main Results:

Connector nodes in hard partitions show potential for multiple module membership.
OverMod identifies two types of connector nodes: inter-connectors and intra-connectors.
Inter-connector proteins are conserved, involved in essential cellular processes, and exhibit distinct roles compared to intra-connectors and hubs.

Conclusions:

The OverMod model effectively transforms disjoint communities into overlapping ones.
Connector proteins, particularly inter-connectors, play significant roles in network organization and possess multiple distinct biological functions.
This approach distinguishes multifunctional proteins from simple hubs in biological networks.