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Related Concept Videos

Protein Networks02:26

Protein 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,...
Yeast Signaling01:28

Yeast Signaling

Yeasts are single-celled organisms, but unlike bacteria, they are eukaryotes (cells with a nucleus). Cell signaling in yeast is similar to signaling in other eukaryotic cells. A ligand, such as a protein or a small molecule released from a yeast cell, attaches to a receptor on the cell surface. The binding stimulates second-messenger kinases to activate or inactivate transcription factors that further regulate gene expression. Many of the yeast intracellular signaling cascades have similar...
Protein-protein Interfaces02:04

Protein-protein Interfaces

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 polypeptide...

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Related Experiment Video

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A Yeast 2-Hybrid Screen in Batch to Compare Protein Interactions
14:23

A Yeast 2-Hybrid Screen in Batch to Compare Protein Interactions

Published on: June 6, 2018

WI-PHI: a weighted yeast interactome enriched for direct physical interactions.

Lars Kiemer1, Stefano Costa, Marius Ueffing

  • 1Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome, Italy.

Proteomics
|February 8, 2007
PubMed
Summary

This study compiles a reliable yeast interactome by integrating diverse protein interaction data. WI-PHI offers a comprehensive, weighted network of yeast protein interactions for systems biology research.

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Area of Science:

  • Systems Biology
  • Proteomics
  • Bioinformatics

Background:

  • Understanding the yeast proteome's wiring is crucial for systems biology.
  • Existing protein interaction data from high-throughput experiments show discrepancies, hindering accurate analysis.
  • Previous efforts to create a reliable interactome were limited by data availability and integration challenges.

Purpose of the Study:

  • To develop a novel approach for compiling a yeast interactome based exclusively on physical interaction evidence.
  • To create an updated and more comprehensive yeast interactome network.
  • To provide a reliable resource for yeast systems biology research.

Main Methods:

  • Integrated heterogeneous data sources, including tandem affinity purification coupled to mass spectrometry (TAP-MS) and large-scale yeast two-hybrid studies.
  • Employed heuristic and probabilistic strategies for data analysis and network construction.
  • Leveraged results from small-scale experiments stored in dedicated databases.

Main Results:

  • Developed WI-PHI, a weighted network of yeast protein interactions.
  • The WI-PHI network encompasses a large majority of yeast proteins.
  • The approach successfully integrated newly available data, more than doubling the information on yeast proteome wiring.

Conclusions:

  • The compiled WI-PHI interactome provides a more reliable and comprehensive resource for studying yeast protein interactions.
  • This approach addresses the limitations of previous interactome studies by focusing on physical evidence.
  • WI-PHI serves as a valuable tool for advancing yeast systems biology research.