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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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Protein Networks02:26

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Protein-protein Interfaces02:04

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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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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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Tomato Analyzer: A Useful Software Application to Collect Accurate and Detailed Morphological and Colorimetric Data from Two-dimensional Objects
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PTIR: Predicted Tomato Interactome Resource.

Junyang Yue1, Wei Xu1, Rongjun Ban2

  • 1School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei 230009, China.

Scientific Reports
|April 29, 2016
PubMed
Summary
This summary is machine-generated.

We developed the Predicted Tomato Interactome Resource (PTIR), a database of 357,946 protein-protein interactions (PPIs) in tomatoes. This resource aids in understanding tomato molecular mechanisms and was validated experimentally.

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Area of Science:

  • Plant biology
  • Bioinformatics
  • Proteomics

Background:

  • Protein-protein interactions (PPIs) are crucial for biological processes and cellular functions.
  • Understanding PPIs is fundamental to elucidating molecular mechanisms in signal transduction and metabolic pathways.
  • Research on tomato PPIs is limited, hindering a comprehensive understanding of tomato molecular biology.

Purpose of the Study:

  • To develop a comprehensive resource for exploring protein-protein interactions in tomatoes.
  • To predict and characterize PPIs in the tomato proteome.
  • To provide a valuable tool for plant biologists studying tomato molecular mechanisms.

Main Methods:

  • Developed the Predicted Tomato Interactome Resource (PTIR) using orthologous interactions from six model organisms.
  • Evaluated PPI reliability using shared gene ontology (GO) terms, co-evolution, co-expression, co-localization, and domain-domain interactions (DDIs).
  • Validated ten selected PPIs using yeast two-hybrid (Y2H) screening and bimolecular fluorescence complementation (BiFC) assays.

Main Results:

  • The PTIR contains 357,946 non-redundant PPIs among 10,626 tomato proteins.
  • Interactions are categorized into high (12,291), medium (226,553), and low (119,102) confidence levels.
  • The PTIR covers approximately 30.6% of the tomato proteome and includes experimentally verified interactions.

Conclusions:

  • The PTIR is a valuable, publicly accessible database for tomato interactomics research.
  • This resource facilitates the investigation of molecular mechanisms underlying biological processes in tomatoes.
  • The PTIR provides a foundation for future studies on tomato PPI networks and functional genomics.