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Protein Networks

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 Networks

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 Interfaces

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 Interfaces

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 Parts

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 Parts

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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

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

Published on: March 3, 2015

Functionally guided alignment of protein interaction networks for module detection.

Waqar Ali¹, Charlotte M Deane

¹Department of Statistics, University of Oxford, OX1 3TG, UK. ali@stats.ox.ac.uk

Bioinformatics (Oxford, England)

|October 3, 2009

Summary

This summary is machine-generated.

We introduce a novel protein network alignment method using functional similarity, improving accuracy and coverage of experimental data. This approach enhances functional module detection in protein interaction networks.

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Area of Science:

Computational biology
Bioinformatics
Systems biology

Background:

Protein interaction network analysis is crucial but challenging due to data sparsity and errors.
Existing network alignment methods primarily use protein sequence similarity for cross-species mapping.
Accurate functional module detection is vital for understanding cellular processes.

Purpose of the Study:

To develop and evaluate a novel network alignment approach using protein functional similarity.
To improve the accuracy and coverage of functional module detection in protein interaction networks.
To compare the performance of function-based alignment with sequence-based methods.

Main Methods:

Network alignment was performed using a protein functional similarity measure.
The approach integrated sequence and function-based alignment with graph clustering.
Performance was evaluated based on functional coherence and overlap with known protein complexes.

Main Results:

Functional similarity-based network alignment significantly improves functional coherence and overlap with experimental protein complexes.
Results from function-based alignment show minimal overlap (<15%) with sequence similarity-based alignment.
The combined approach achieved a 200% increase in coverage of experimental datasets with comparable accuracy.

Conclusions:

Protein functional similarity is a valuable metric for improving cross-species network alignment.
Integrating multiple alignment strategies enhances the detection and coverage of functional modules.
This method offers a more comprehensive understanding of protein interaction networks and their functional organization.