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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...
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Assembly of Signaling Complexes01:30

Assembly of Signaling Complexes

Multiprotein signaling complexes are formed in a dynamic process involving protein-protein interactions at the cytoplasmic domain of transmembrane receptors or enzymatic and non-enzymatic proteins associated with the receptor. These complexes ensure the activation and propagation of intracellular signals that regulate cell functions.
Interaction domains in cell signaling
Interaction domains recognize exposed features of their binding partners containing post-translationally modified sequences,...

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JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
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Global alignment of multiple protein interaction networks.

Rohit Singh1, Jinbo Xu, Bonnie Berger

  • 1Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, USA. rsingh@mit.edu

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
|January 31, 2008
PubMed
Summary
This summary is machine-generated.

We developed a novel algorithm for aligning protein-protein interaction (PPI) networks across species. This method identifies functional orthologs, improving upon sequence-based predictions, especially for disease-related proteins.

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Area of Science:

  • Computational biology
  • Bioinformatics
  • Network science

Background:

  • Protein-protein interaction (PPI) networks are crucial for understanding cellular mechanisms.
  • Aligning these networks across species aids in identifying conserved biological functions.
  • Existing methods often struggle with comprehensive cross-species network analysis.

Purpose of the Study:

  • To develop and present a novel algorithm for the global alignment of multiple protein-protein interaction networks.
  • To identify functional orthologs across five species by leveraging network topology.
  • To compare the performance of the new orthology predictions against existing sequence-based methods.

Main Methods:

  • An algorithm was designed to maximize overall network matches by considering neighboring protein interactions.
  • Eigenvalue problems were constructed for pairwise network comparisons.
  • K-partite matching was employed to derive the final global alignment across species.

Main Results:

  • The first known global alignment of protein-protein interaction networks from yeast, fly, worm, mouse, and human was computed.
  • This alignment yielded a comprehensive set of functional orthologs across all five species.
  • The identified functional orthologs demonstrated superior performance compared to sequence-only orthology prediction, particularly for human disease proteins.

Conclusions:

  • The developed algorithm provides a powerful new approach for cross-species PPI network alignment.
  • The resulting functional orthologs represent a significant advancement in comparative genomics and functional inference.
  • This method enhances the prediction of orthologs, with implications for understanding human diseases.