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JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
Published on: October 19, 2021
Constructing structural networks of signaling pathways on the proteome scale
Guray Kuzu1, Ozlem Keskin, Attila Gursoy
1Center for Computational Biology and Bioinformatics and College of Engineering, Koc University Rumelifeneri Yolu, 34450 Sariyer Istanbul, Turkey.
Current Opinion in Structural Biology
|May 12, 2012
Summary
This study constructs a structural network for extracellular signal-regulated kinases (ERK) in the mitogen-activated protein kinase (MAPK) pathway. Understanding these protein interactions reveals how they function and aids in predicting drug side effects.
Area of Science:
- Molecular Biology
- Bioinformatics
- Systems Biology
Background:
- Protein interactions are crucial for cellular processes.
- Classical network representations lack structural detail on interaction mechanisms.
- Structural data is limited, hindering a comprehensive understanding of protein function.
Purpose of the Study:
- To construct a structural network of extracellular signal-regulated kinases (ERK) within the mitogen-activated protein kinase (MAPK) signaling pathway.
- To provide insights into the 'how' of protein interactions, not just the 'who'.
- To explore the potential of structural networks in predicting drug side effects.
Main Methods:
- Utilized the PRISM (Protein-protein Interaction Structural Modeling) tool for large-scale prediction of protein interactions.
- Employed a knowledge-based, motif-based approach combined with flexible refinement and energy scoring.
- Predicted interactions based on structural and evolutionary similarity to known protein interfaces.
Main Results:
- Successfully constructed a structural network for ERK proteins in the MAPK pathway.
- The generated network provides detailed information on protein-protein interfaces.
- Demonstrated the capability of PRISM for proteome-scale interaction prediction.
Conclusions:
- Structural networks offer a deeper understanding of protein interactions compared to traditional methods.
- This approach can reveal simultaneous vs. competitive binding, aiding in drug discovery and safety.
- The developed structural network provides a valuable resource for studying the MAPK pathway and related cellular functions.
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,...
01:30Assembly 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,...
Interaction domains in cell signaling
Interaction domains recognize exposed features of their binding partners containing post-translationally modified sequences,...
01:33Proteomics
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...
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...
01:19Interactions Between Signaling Pathways
Signaling cascades usually lack linearity. Multiple pathways interact and regulate one another, allowing cells to integrate and respond to diverse environmental stimuli.
Convergence and divergence, and cross-talk between signaling pathways
Two distinct signaling pathways can converge on a single functional unit, which may either be a single protein or a complex of proteins. The response is either functionally distinct or synergistic between the two pathways but different from the response...
Convergence and divergence, and cross-talk between signaling pathways
Two distinct signaling pathways can converge on a single functional unit, which may either be a single protein or a complex of proteins. The response is either functionally distinct or synergistic between the two pathways but different from the response...
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...