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Related Concept Videos

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-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 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 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...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...

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Resolving Affinity Purified Protein Complexes by Blue Native PAGE and Protein Correlation Profiling
09:35

Resolving Affinity Purified Protein Complexes by Blue Native PAGE and Protein Correlation Profiling

Published on: April 1, 2017

Predicting physical interactions between protein complexes.

Trevor Clancy1, Einar Andreas Rødland, Ståle Nygard

  • 1Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital and Oslo University Hospital, Oslo, Norway. trevor.clancy@rr-research.no

Molecular & Cellular Proteomics : MCP
|February 27, 2013
PubMed
Summary
This summary is machine-generated.

This study introduces a computational method to predict physical interactions between protein complexes. The novel approach successfully identifies complex-complex interactions, aiding the discovery of cellular relationships.

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Area of Science:

  • Cellular Biology
  • Biochemistry
  • Computational Biology

Background:

  • Protein complexes perform essential biochemical functions within cells.
  • Transient physical interactions between protein complexes are common but challenging to detect genome-wide.
  • Understanding these interactions is crucial for deciphering cellular processes.

Purpose of the Study:

  • To develop and apply a computational method for predicting physical interactions between protein complexes.
  • To identify pairs of protein complexes that physically interact based on integrated network data.
  • To explore the biological organization of these predicted complex-complex interactions.

Main Methods:

  • Integrated manually curated protein complex data with physical protein interaction networks.
  • Developed a statistical method to identify significant protein-protein interaction patterns indicative of complex-complex physical association.
  • Applied the method to human and yeast proteomes.

Main Results:

  • The computational method successfully predicted physical interactions between protein complexes.
  • An evaluation in yeast showed that 50% of known physical complex-complex interactions could be predicted.
  • Network analysis of high-scoring predicted interactions revealed biologically meaningful organization.

Conclusions:

  • The developed computational approach is effective for predicting physical protein complex interactions.
  • This method can uncover novel functional relationships and guide further experimental research.
  • Proteome-wide analysis of complex-complex interactions offers insights into cellular organization and function.