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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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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

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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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Identifying novel protein interactions: Proteomic methods, optimisation approaches and data analysis pipelines.

Daniel Gonçalves Carneiro1, Thomas Clarke1, Clare C Davies1

  • 1College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.

Methods (San Diego, Calif.)
|September 1, 2015
PubMed
Summary
This summary is machine-generated.

This review explores advanced

Keywords:
Affinity purificationDNA–protein interactionsInteractomicsProtein–protein interactionRNA–protein interactionTAP-tagging

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Area of Science:

  • Cellular biology and molecular interactions.
  • Biochemistry and proteomics.
  • Bioinformatics and systems biology.

Background:

  • High-throughput 'omics' technologies have revolutionized cell biology.
  • Understanding protein interactions (interactomics) is crucial for basic and applied biological research.
  • Investigating complex networks involving proteins, RNA, and DNA is a key focus.

Purpose of the Study:

  • To review emerging and established techniques for interactomics analysis.
  • To highlight affinity-based purification systems and quantitative proteomics methods.
  • To discuss software resources and databases for interactomics data analysis.

Main Methods:

  • Tandem affinity purification (TAP) tagging.
  • Isolation of proteins on nascent DNA (IPOND).
  • RNA-protein immunoprecipitation in tandem (RIPiT).
  • Quantitative proteomics: Stable isotope labeling by amino acids in cell culture (SILAC), Localization of organelle proteins by isotope tagging (LOPIT), Proximity-dependent biotin identification (BioID).

Main Results:

  • A comprehensive overview of current interactomics methodologies.
  • Discussion on optimizing purification systems for enhanced specificity and stringency.
  • Introduction to software tools and open-access databases like Reactome and IntAct for data analysis and biological context.

Conclusions:

  • Interactomics is a cornerstone of modern biological science with broad applications.
  • Technological advancements continue to refine the study of molecular interactions.
  • Integrated approaches using diverse techniques and bioinformatics tools are essential for advancing interactomics research.