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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...
Covalently Linked Protein Regulators02:04

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 Regulators02:04

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 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...

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Dissecting Multi-protein Signaling Complexes by Bimolecular Complementation Affinity Purification (BiCAP)
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Dissecting Multi-protein Signaling Complexes by Bimolecular Complementation Affinity Purification (BiCAP)

Published on: June 15, 2018

Discovering conditional co-regulated protein complexes by integrating diverse data sources.

Fei Luo1, Juan Liu, Jinyan Li

  • 1School of Computer, Wuhan University, Wuhan, Hubei, China. luofei@whu.edu.cn

BMC Systems Biology
|September 16, 2010
PubMed
Summary

This study introduces a new method to discover conditional co-regulated protein complexes by integrating transcription regulation, gene expression, and protein-protein interaction data. The findings reveal condition-specific protein interactions and predict novel transcriptional regulators.

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Area of Science:

  • Systems Biology
  • Molecular Biology
  • Genomics

Background:

  • Protein complexes are crucial for molecular functions but detecting them is costly.
  • Available protein-protein interaction (PPI) maps are condition-specific, necessitating context-aware discovery.
  • Understanding protein complex behavior requires specifying conditions under which they form.

Purpose of the Study:

  • To develop a framework for discovering conditional co-regulated protein complexes.
  • To integrate transcription regulation (TR), gene expression (GE), and PPI data for complex discovery.
  • To identify protein complexes with condition-specific functions.

Main Methods:

  • Integrated TR, GE, and PPI data at the systems biology level.
  • Proposed a framework for discovering conditional co-regulated protein complexes.
  • Tested the framework on Yeast datasets under various conditions (Cell Cycle, DNA Damage, Dauxic Shift).

Main Results:

  • Identified 29 conditional co-regulated protein complexes in Yeast.
  • Found 14 complexes with coding genes strongly associated with transcription factor (TF) activity.
  • Predicted and explained 39 novel TRs based on co-regulation, co-expression, and PPI relationships.

Conclusions:

  • Conditional co-regulated protein complexes exhibit condition-specific expression coherence and protein interactions.
  • TF activity influences the expression coherence and interactions of protein complexes.
  • The study successfully predicted novel transcriptional regulation interactions.