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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.
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

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,...

Covalently Linked Protein Regulators

Covalently Linked Protein Regulators

Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
These groups modify specific amino acids in a protein.

Covalently Linked Protein Regulators

Covalently Linked Protein Regulators

Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
These groups modify specific amino acids in a protein.

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 to...

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 to...

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Related Experiment Video

Updated: Jun 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

The human protein coevolution network.

Elisabeth R M Tillier¹, Robert L Charlebois

¹Department of Medical Biophysics, University of Toronto, Ontario Cancer Institute, University Health Network, Canada. e.tillier@utoronto.ca

Genome Research

|August 22, 2009

Summary

This summary is machine-generated.

Detecting molecular coevolution reveals functional protein interactions. A new method, MatrixMatchMaker, identifies coevolving protein partners by analyzing evolutionary patterns, uncovering crucial cellular functions.

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Quantification of Protein Interaction Network Dynamics using Multiplexed Co-Immunoprecipitation

Quantification of Protein Interaction Network Dynamics using Multiplexed Co-Immunoprecipitation

Published on: August 21, 2019

Area of Science:

Evolutionary biology
Genomics
Bioinformatics

Background:

Coevolution, driven by reciprocal natural selection, maintains trait interactions.
Detecting molecular coevolution offers insights into functional molecular interactions, biological processes, and cellular networks.
Existing coevolution detection methods struggle with lineage-specific events and paralogous copies.

Purpose of the Study:

To develop a novel method for detecting coevolving protein partners.
To identify functional protein-protein interactions using evolutionary data.
To explore the human coevolution network and its implications for cellular function.

Main Methods:

Developed MatrixMatchMaker, a novel method for coevolution detection.
Identified coevolving protein partners by finding the largest common submatrix in distance matrices.
Applied MatrixMatchMaker to predict protein-protein interactions in the human genome.

Main Results:

MatrixMatchMaker successfully predicts protein-protein interactions, outperforming existing methods.
Physically interacting proteins exhibit stronger coevolutionary signals than proteins in the same pathway.
The human coevolution network is highly interconnected, suggesting numerous uncharacterized interactions.

Conclusions:

MatrixMatchMaker enables the detection of lineage-specific coevolution and multiple interaction partners.
The study reveals a highly connected human coevolution network, indicating extensive unannotated protein interactions.
Strongly coevolving proteins likely represent fundamental interactions crucial for cellular function over evolutionary time.