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Related Concept Videos

Protein Networks02:26

Protein Networks

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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,...
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Protein-protein Interfaces02:04

Protein-protein Interfaces

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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...
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Protein Kinases and Phosphatases02:54

Protein Kinases and Phosphatases

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Proteins undergo chemical modifications that trigger changes in the charge, structure, and conformation of the proteins. Phosphorylation, acetylation, glycosylation, nitrosylation, ubiquitination, lipidation, methylation, and proteolysis are various protein modifications that regulate protein activity. Such modifications are usually enzyme-driven.
Protein kinases
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Proteomics01:33

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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.
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Related Experiment Video

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Identification of Kinase-substrate Pairs Using High Throughput Screening
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Quantitative phosphoproteomics-based molecular network description for high-resolution kinase-substrate interactome

Yuta Narushima1, Hiroko Kozuka-Hata1, Kouhei Tsumoto2

  • 1Medical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 108-8639, Japan.

Bioinformatics (Oxford, England)
|May 7, 2016
PubMed
Summary

We developed PTMapper, a platform for analyzing phosphorylation-dependent signaling networks. This tool integrates protein-protein interaction data with kinase-substrate information, aiding in the discovery of new drug targets for diseases.

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Area of Science:

  • Cellular signaling and molecular biology.
  • Bioinformatics and computational biology.

Background:

  • Phosphorylation is crucial for cellular processes like proliferation, differentiation, and apoptosis.
  • Mass spectrometry-based phosphoproteomics allows for network-wide signaling dynamics measurement.
  • Conventional protein-protein interaction (PPI) analysis is limited for phosphorylation site-dependent dynamics.

Purpose of the Study:

  • To develop a high-resolution platform for kinase-substrate interactome analysis.
  • To enable systematic analysis of phosphorylation site-dependent complex interaction dynamics.

Main Methods:

  • Developed a Cytoscape-based bioinformatical platform named 'Post Translational Modification mapper (PTMapper)'.
  • Integrated PPI data with publicly available kinase-substrate relations at the resolution of phosphorylated amino acid residues.
  • Applied PTMapper to phosphoproteome data of EGF-induced signaling in glioblastoma stem cells.

Main Results:

  • PTMapper enables high-resolution molecular network description for kinase-substrate interactome analysis.
  • Discovered phosphorylation-dependent signaling modulation in the p70S6K1-related pathway.
  • Demonstrated the platform's utility in analyzing EGF-induced signaling in glioblastoma stem cells.

Conclusions:

  • High-resolution network description of phosphorylation-site dependent signaling accelerates phosphoproteomics research.
  • PTMapper facilitates the exploration of novel drug targets in disease-related signaling pathways.