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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 Networks02:26

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Covalently Linked Protein Regulators02:04

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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.
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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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Proteomics01:33

Proteomics

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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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Protein Modifications in the RER01:26

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Modification of secretory and transmembrane proteins entering the rough ER begins in the ER lumen. These modifications aid in protein folding and stabilize the acquired tertiary structure. Protein modifications in the rough ER co-occur at different stages of protein folding.
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Related Experiment Video

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Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization
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iPTMnet: Integrative Bioinformatics for Studying PTM Networks.

Karen E Ross1, Hongzhan Huang2, Jia Ren2

  • 1Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, 3300 Whitehaven Street NW, Suite 1200, Washington, DC, 20057, USA. ker25@georgetown.edu.

Methods in Molecular Biology (Clifton, N.J.)
|February 3, 2017
PubMed
Summary

Protein post-translational modifications (PTMs) are vital for cell regulation and implicated in disease. iPTMnet is a new bioinformatics resource that integrates PTM data, aiding in the analysis of PTMs and their functional impacts.

Keywords:
AcetylationDatabasePTM crosstalkPhosphorylationPost-translational modificationProtein ontologyProtein-protein interactionText mining

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Utilizing a Comprehensive Immunoprecipitation Enrichment System to Identify an Endogenous Post-translational Modification Profile for Target Proteins
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Area of Science:

  • Biochemistry
  • Bioinformatics
  • Molecular Biology

Background:

  • Protein post-translational modifications (PTMs) are crucial cellular regulatory mechanisms.
  • Dysregulation of PTMs is linked to various diseases, making them a significant research focus.
  • Existing scientific literature contains extensive PTM information, necessitating efficient retrieval and analysis tools.

Purpose of the Study:

  • To introduce iPTMnet, a user-friendly bioinformatics resource for PTM information.
  • To demonstrate how iPTMnet integrates data from text mining, curated databases, and ontologies.
  • To showcase iPTMnet's capabilities in analyzing PTM networks, crosstalk, and cross-species conservation.

Main Methods:

  • Utilizing text mining to extract PTM information from scientific literature.
  • Integrating data from established PTM databases and biological ontologies.
  • Developing visualization tools for exploring PTM networks and conservation.

Main Results:

  • iPTMnet successfully integrates diverse PTM data sources.
  • The resource provides visualization tools for PTM networks, crosstalk, and conservation.
  • Demonstrated the utility of iPTMnet in addressing specific PTM-related research queries.

Conclusions:

  • iPTMnet offers a valuable, user-friendly platform for PTM research.
  • The resource facilitates deeper understanding of PTMs, their functions, and disease implications.
  • iPTMnet supports comprehensive analysis of PTM data, advancing the field of molecular biology.