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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.
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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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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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Related Experiment Video

Updated: Feb 18, 2026

Utilizing a Comprehensive Immunoprecipitation Enrichment System to Identify an Endogenous Post-translational Modification Profile for Target Proteins
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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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iPTMnet: an integrated resource for protein post-translational modification network discovery.

Hongzhan Huang1,2, Cecilia N Arighi1,2, Karen E Ross3

  • 1Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA.

Nucleic Acids Research
|November 18, 2017
PubMed
Summary

iPTMnet integrates bioinformatics approaches for protein post-translational modification (PTM) discovery. This PTM knowledgebase aids in understanding enzyme-substrate relationships and PTM conservation across species.

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Area of Science:

  • Biochemistry and Bioinformatics
  • Molecular and Cellular Biology

Background:

  • Protein post-translational modifications (PTMs) are crucial for regulating protein function and biological processes.
  • Understanding PTMs, including enzyme-substrate-site relationships and protein-protein interactions (PPIs), is vital for biological discovery.

Purpose of the Study:

  • To develop iPTMnet, an integrative bioinformatics platform for comprehensive PTM knowledge discovery.
  • To capture and represent PTM information, including enzyme-substrate-site relationships, PTM-specific PPIs, and cross-species PTM conservation.

Main Methods:

  • Utilized an integrative bioinformatics approach combining text mining, data mining, and ontological representation.
  • Employed PTM-focused text mining tools (RLIMS-P, eFIP) for extracting phosphorylation data from literature.
  • Integrated curated databases of experimentally observed PTMs and the Protein Ontology for PTM proteoform representation.

Main Results:

  • iPTMnet covers eight major PTM types and contains over 654,500 PTM sites in more than 62,100 proteins.
  • The knowledgebase includes over 1200 PTM enzymes and more than 24,300 PTM enzyme-substrate-site relations.
  • The platform supports online search, browsing, retrieval, and visual analysis for PTM data.

Conclusions:

  • iPTMnet serves as a valuable resource for PTM knowledge discovery and exploration.
  • The platform facilitates the functional interpretation of PTM data, enabling PTM discovery and hypothesis generation.
  • iPTMnet provides a gateway for systematic analysis of PTM networks and conservation across species.