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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,...
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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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 Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
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Related Experiment Video

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Probing High-density Functional Protein Microarrays to Detect Protein-protein Interactions
08:07

Probing High-density Functional Protein Microarrays to Detect Protein-protein Interactions

Published on: August 2, 2015

Pushing structural information into the yeast interactome by high-throughput protein docking experiments.

Roberto Mosca1, Carles Pons, Juan Fernández-Recio

  • 1Institute for Research in Biomedicine, Barcelona, Spain.

Plos Computational Biology
|August 29, 2009
PubMed
Summary

This study presents the first high-throughput protein docking experiment in yeast, generating structural models for over 3,000 protein interactions. It also assesses the utility of homology models for expanding structural coverage of the yeast interactome.

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Area of Science:

  • Structural biology
  • Computational biology
  • Yeast proteomics

Background:

  • Over 10,000 protein-protein interactions identified in Saccharomyces cerevisiae.
  • High-resolution 3D structures available for less than 100 yeast protein interactions.
  • Significant gap in structural information for the yeast interactome.

Purpose of the Study:

  • Expand structural information for yeast protein interactions.
  • Perform the first high-throughput protein docking experiment.
  • Evaluate the use of homology models to increase structural coverage.

Main Methods:

  • Applied state-of-the-art docking methodologies.
  • Utilized 217 experimental structures and 1,023 homology models.
  • Assessed the impact of homology model quality on docking performance.

Main Results:

  • Generated putative structural models for over 3,000 yeast protein-protein interactions.
  • Demonstrated the feasibility of high-throughput docking.
  • Provided detailed analysis of specific protein complex models (SAM1-anthranilate synthase, MET30-RNA polymerase III).

Conclusions:

  • High-throughput docking, including homology models, significantly expands structural coverage of the yeast interactome.
  • The generated structural models are valuable resources for the scientific community.
  • Results will be integrated into the 3D-Repertoire pipeline for comprehensive yeast complex structure determination.