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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-protein Interfaces02:04

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 polypeptide...
Protein Complexes with Interchangeable Parts01:57

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 Parts01:57

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...
Proteomics01:33

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...

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Updated: Jun 19, 2026

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
07:28

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

Published on: October 19, 2021

Determining protein complex connectivity using a probabilistic deletion network derived from quantitative proteomics.

Mihaela E Sardiu1, Joshua M Gilmore, Michael J Carrozza

  • 1Stowers Institute for Medical Research, Kansas City, Missouri, United States of America.

Plos One
|October 7, 2009
PubMed
Summary
This summary is machine-generated.

This study presents a new computational method to predict protein relationships within stable complexes. The approach maps protein interactions and interdependencies, revealing new insights into complex organization.

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Published on: August 21, 2019

Area of Science:

  • Molecular biology
  • Systems biology
  • Proteomics

Background:

  • Protein complexes are crucial for cellular functions.
  • Understanding protein connectivity within complexes is challenging despite available interaction data.

Purpose of the Study:

  • To develop and demonstrate a method for predicting protein relationships within stable protein complexes.
  • To reveal new protein-protein interactions and submodule relationships within complexes.

Main Methods:

  • Utilized a combination of computational approaches and quantitative proteomics data.
  • Built a quantitative deletion-interaction network map from wild-type and deletion strain purifications.
  • Converted network data into an interdependency-interaction model.

Main Results:

  • Successfully applied the method to Saccharomyces cerevisiae Rpd3 histone deacetylase complexes.
  • Revealed novel protein-protein interactions and submodule organization within the Rpd3 complex.
  • Provided new information for mapping the functional organization of protein complexes.

Conclusions:

  • The developed method effectively predicts protein relationships within stable complexes.
  • This approach enhances the understanding of complex functional organization.
  • Offers a valuable tool for dissecting molecular machinery.