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Related Concept Videos

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...
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 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.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
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.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...

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Related Experiment Video

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Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling
11:19

Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling

Published on: November 17, 2019

Cost-effective strategies for completing the interactome.

Ariel S Schwartz1, Jingkai Yu, Kyle R Gardenour

  • 1Department of Bioengineering, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.

Nature Methods
|December 17, 2008
PubMed
Summary

Mapping protein interactions is costly. This study models experimental designs to significantly reduce the time and resources needed for accurate protein-interaction maps, improving efficiency in biological research.

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Published on: October 3, 2018

Area of Science:

  • Proteomics
  • Systems Biology
  • Bioinformatics

Background:

  • Large-scale protein-interaction mapping projects are essential for understanding cellular mechanisms.
  • Accurate and complete protein-interaction maps require significant time, cost, and personnel.
  • Estimating these resource requirements is crucial for project feasibility.

Purpose of the Study:

  • To model the cost-effectiveness of various experimental designs for protein-interaction map completion.
  • To identify strategies for substantially reducing the cost and time of interaction mapping.
  • To provide a framework for assessing and improving the efficiency of these projects.

Main Methods:

  • Computational modeling of experimental designs for protein-interaction mapping.
  • Exploration of cost-reduction strategies including protein pair prioritization, probability thresholding, and interaction prediction.
  • Validation of optimized designs in a real-world project using Drosophila melanogaster.

Main Results:

  • Current protein-interaction mapping efforts may require up to 20 tests per protein pair for completion.
  • Optimized experimental designs can reduce overall costs by fourfold and early-stage costs by over 100-fold.
  • A validated strategy successfully mapped 450 high-confidence interactions using only 47 microtiter plates.

Conclusions:

  • Efficient experimental designs are critical for the feasibility of comprehensive protein-interaction mapping.
  • Prioritization, thresholding, and prediction significantly enhance the cost-effectiveness of mapping projects.
  • This framework enables better planning and execution of future large-scale protein interaction studies.