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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-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...

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Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay (PCA) in Living Cells
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Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay (PCA) in Living Cells

Published on: March 3, 2015

Protein interaction networks--more than mere modules.

Stefan Pinkert1, Jörg Schultz, Jörg Reichardt

  • 1Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany.

Plos Computational Biology
|February 4, 2010
PubMed
Summary
This summary is machine-generated.

This study introduces a new method to analyze protein-interaction networks (PINs) by grouping proteins into "functional roles" instead of just cohesive modules. This approach better captures network structure and experimental biases, improving function prediction.

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Quantification of Protein Interaction Network Dynamics using Multiplexed Co-Immunoprecipitation

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Area of Science:

  • Systems Biology
  • Bioinformatics
  • Network Science

Background:

  • Cellular functions are often thought to be modular, reflected in molecular networks.
  • Protein-interaction networks (PINs) are commonly analyzed for cohesive modules.
  • Existing algorithms focus on identifying densely connected protein groups.

Purpose of the Study:

  • To develop an alternative method for analyzing PINs beyond traditional cohesive modules.
  • To group proteins into 'functional roles' based on interaction patterns.
  • To better represent complex network structures and identify underlying biological insights.

Main Methods:

  • Developed a self-consistent approach to group proteins into functional roles.
  • Applied the method to the Human Protein Reference Database (HPRD) PIN.
  • Analyzed network structure by comparing functional role decomposition with cohesive module identification.
  • Mapped experimental methods to identified groups to detect data biases.

Main Results:

  • Cohesive module representation does not optimally capture global PIN structure.
  • Functional role decomposition better depicts network structure, including interdependencies and absence of interactions.
  • Transmembrane proteins, often not cohesive, can be identified within functional roles.
  • The method reveals profound differences in experimental method coverage across groups, highlighting experimental bias (e.g., yeast-two-hybrid data).

Conclusions:

  • PINs contain more complex structures than just cohesive modules.
  • Functional role analysis offers a more comprehensive representation of PINs.
  • This approach can significantly enhance automated protein function prediction algorithms.
  • The method effectively captures experimental biases present in interaction data.