mPPI: a database extension to visualize structural interactome in a one-to-many manner.
Yekai Zhou1,2, Hongjun Chen1, Sida Li1
1Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
Summary
mPPI is a new tool that visualizes protein-protein interactions (PPIs) and their multiple binding partners simultaneously. This advances structural interactome coverage for drug discovery and protein complex prediction.
Area of Science:
- Structural Biology
- Bioinformatics
- Computational Biology
Background:
- Protein-protein interactions (PPIs) are crucial for biological functions.
- Existing PPI databases often lack comprehensive structural information and primarily focus on binary interactions.
- Understanding multi-protein complex structures is vital for drug discovery and predicting biological mechanisms.
Purpose of the Study:
- To develop an extension, mPPI, for visualizing protein-protein interactions with structural information.
- To enable simultaneous visualization of a target protein and its multiple interactors.
- To enhance the coverage of structural interactomes beyond experimentally resolved complexes.
Main Methods:
- Development of mPPI, a database extension for PPI structural visualization.
- Integration of a protein-protein docking algorithm to extend structural interactome coverage.
- Demonstration of mPPI's application in a neurodegenerative disease-related PPI database.
Main Results:
- mPPI allows simultaneous visualization of a protein and its multiple interactors, unlike existing pairwise databases.
- The use of protein-protein docking significantly expands the scope of the structural interactome.
- mPPI serves as a customizable and convenient plugin for various PPI databases.
Conclusions:
- mPPI facilitates multi-target drug discovery and the prediction of protein macro-complex structures.
- The tool offers a novel approach to visualizing and analyzing complex PPI networks.
- mPPI has broad applicability for enhancing existing PPI databases and research in structural biology.
More Related Videos
Related Concept Videos
02:26Protein Networks
4.2K
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,...
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,...
4.2K
02:26Protein Networks
2.5K
2.5K
02:04Protein-protein Interfaces
14.1K
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...
14.1K
01:57Protein Complexes with Interchangeable Parts
2.7K
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...
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...
2.7K
01:57Protein Complexes with Interchangeable Parts
2.0K
2.0K
01:33Proteomics
8.7K
A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...
8.7K