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TurboID-Based Proximity Labeling for In Planta Identification of Protein-Protein Interaction Networks
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Using PlaPPISite to Predict and Analyze Plant Protein-Protein Interaction Sites
Jingyan Zheng1, Xiaodi Yang2, Ziding Zhang3
1State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, China.
Methods in Molecular Biology (Clifton, N.J.)
|July 14, 2023
Summary
PlaPPISite is a new database detailing plant protein-protein interactions (PPIs) and their 3D structures. This resource aids plant systems biology research by providing crucial interaction site information for understanding cellular machinery.
Area of Science:
- Plant Biology
- Structural Biology
- Bioinformatics
Background:
- Systematic characterization of protein-protein interactions (PPIs) is essential for understanding cellular functions.
- Existing plant PPI data lacks detailed three-dimensional (3D) structural information of interaction sites/interfaces.
- The demand for accessible 3D structural data of plant PPIs is growing, especially in the post-AlphaFold2 era.
Purpose of the Study:
- To develop and introduce PlaPPISite, a user-friendly database for plant PPIs.
- To provide detailed interaction site information, including 3D structural contexts, for 13 plant interactomes.
- To guide users on accessing and utilizing PPI data within the PlaPPISite database.
Main Methods:
- Development of the PlaPPISite database.
- Inclusion of data for 13 plant interactomes.
- Provision of a user guide detailing database navigation, input formats, and information retrieval.
Main Results:
- PlaPPISite offers a comprehensive resource for plant PPIs with detailed interaction site information.
- The database facilitates the visualization and analysis of 3D structural contexts of protein interactions.
- Examples demonstrate how to retrieve specific interaction site data relevant to biological questions.
Conclusions:
- PlaPPISite enhances the study of plant systems biology by providing crucial 3D interaction data.
- The database is a valuable tool for deciphering molecular mechanisms underlying biological processes in plants.
- Accessible 3D structural information of PPIs will accelerate research in plant biology.
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