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JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
Published on: October 19, 2021
Proteomic strategies to characterize signaling pathways
H C Harsha1, Sneha M Pinto, Akhilesh Pandey
1Institute of Bioinformatics, International Technology Park, Bangalore, India.
Methods in Molecular Biology (Clifton, N.J.)
|May 14, 2013
Summary
High-throughput proteomic strategies reveal cellular signaling pathways. Mass spectrometry uncovers known and novel signaling intermediates, aiding in understanding cell responses.
Area of Science:
- Cellular Biology
- Molecular Biology
- Biochemistry
Background:
- Cells transduce external signals via intracellular molecules, involving post-translational modifications like phosphorylation and ubiquitylation.
- Multi-protein complex formation is crucial in signal transduction cascades.
- Traditional methods for studying signaling pathways are often time-consuming.
Purpose of the Study:
- To discuss proteomic strategies for characterizing cellular signaling pathways.
- To provide protocols for phosphoproteomic analysis.
- To highlight the advancements in high-throughput technologies for probing signaling.
Main Methods:
- Utilizing advancements in biological mass spectrometry.
- Employing protein/peptide microarray technology.
- Applying high-throughput proteomic approaches.
Main Results:
- Mass spectrometry enables comprehensive analysis of signaling pathways.
- These methods can identify the majority of known signaling intermediates.
- Novel signaling intermediates can also be discovered.
Conclusions:
- Proteomic strategies significantly enhance the study of cellular signaling.
- High-throughput mass spectrometry is a powerful tool for pathway discovery.
- This work provides practical protocols for phosphoproteomic analysis.
Related Concept Videos
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...
02:26Protein 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,...
01:22Diversity in Cell Signaling Responses
The physiological function of a cell and cellular communication are outcomes of a range of extrinsic signals, intracellular signaling pathways, and cellular responses. No two cell types express the same repertoire of signaling components. Receptors are highly selective for their cognate ligands, but once activated, they can alter multiple cellular processes such as DNA transcription, protein synthesis, and metabolic activity.
Graded and Abrupt Responses
Some signaling systems generate...
Graded and Abrupt Responses
Some signaling systems generate...
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
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01:22Amplifying Signals via Enzymatic Cascade
When a ligand binds to a cell-surface receptor, the receptor's intracellular domain changes shape, which may either activate its enzyme function or allow its binding to other molecules. The initial signal is amplified by most signal transduction pathways. This means that a single ligand molecule can activate multiple molecules of a downstream target. Proteins that relay a signal are most commonly phosphorylated at one or more sites, activating or inactivating the protein. Kinases catalyze the...