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JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
Published on: October 19, 2021
Dynamic changes in protein functional linkage networks revealed by integration with gene expression data.
Shubhada R Hegde1, Palanisamy Manimaran, Shekhar C Mande
1Centre for DNA Fingerprinting and Diagnostics, Nacharam, Hyderabad, India.
Plos Computational Biology
|December 2, 2008
Summary
This study introduces a new method to analyze dynamic protein interactions in Escherichia coli under UV stress by combining gene expression and functional linkage data. The approach reveals subtle network changes crucial for understanding cellular responses to environmental challenges.
Area of Science:
- Systems Biology
- Molecular Biology
- Bioinformatics
Background:
- Cellular responses to environmental changes rely on complex biomolecular interactions.
- Understanding protein:protein interactions is key to deciphering cellular dynamics.
- Existing large-scale protein interaction datasets lack dynamic information.
Purpose of the Study:
- To develop a method for constructing conditional protein linkages to capture dynamic interaction changes.
- To analyze UV-induced cellular responses in Escherichia coli using this novel approach.
- To investigate systems-level cellular behavior by integrating functional linkages and gene expression data.
Main Methods:
- Integrated functional linkages and gene expression data to build conditional protein networks for Escherichia coli.
- Analyzed UV exposure effects on wild-type and SOS-deficient E. coli.
- Applied network analysis, including centrality measures, to identify changes in protein interactions.
- Examined topological properties and local network changes.
Main Results:
- Conditional networks showed similar global topological properties but distinct local changes.
- Observed alterations in carbohydrate metabolism pathways and reduced efficiency post-UV exposure.
- Identified increased importance of replication, repair, and stress proteins under UV treatment.
- Highlighted the significance of hub gene expression under specific conditions.
Conclusions:
- The developed approach effectively captures dynamic protein interaction changes.
- Subtle network alterations provide insights into cellular responses to environmental perturbations like UV radiation.
- Integrating genome-wide functional linkages and gene expression data offers a powerful systems-level view of organisms.
Related Concept Videos
02:26Protein 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,...
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,...
02:26Protein 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,...
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,...
02:04Protein-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...
02:04Covalently 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.
These groups modify specific amino acids in a protein.
02:04Covalently 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.
These groups modify specific amino acids in a protein.
00:49Ligand Binding and Linkage
Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked. In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...