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PlaPPISite: a comprehensive resource for plant protein-protein interaction sites

Xiaodi Yang¹, Shiping Yang¹, Huan Qi¹

¹State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.

BMC Plant Biology

|February 8, 2020

Summary

PlaPPISite is a new database detailing protein-protein interactions (PPIs) across 13 plant species. It offers structural and interaction site information for plant PPIs, aiding biological function exploration.

Area of Science:

Plant biology
Bioinformatics
Structural biology

Background:

Protein-protein interactions (PPIs) are crucial for diverse biological processes in plants.
Understanding plant PPIs requires detailed interaction site and 3D structural information.
Previous tools like AraPPISite were limited to a single plant species.

Purpose of the Study:

To develop a comprehensive, multi-species database for plant protein-protein interaction details.
To expand upon previous single-species PPI resources by including 13 plant interactomes.
To provide a user-friendly platform for exploring plant PPIs.

Main Methods:

Constructed 3D complex structures for experimental/predicted PPIs in 13 plant species.
Annotated interaction sites and inferred domain-domain/domain-motif interactions for unmodeled structures.
Integrated data including GO annotations, subcellular localizations, and gene expression similarities.
Developed visualization tools for protein complexes, interaction sites, and networks using JavaScript.
Created an online tool for homology modeling and PPI site annotation.

Main Results:

Established PlaPPISite, a high-coverage database for 13 plant interactomes.
Collected 121 experimentally verified protein complex structures.
Annotated interaction sites and inferred DDIs/DMIs for a large set of plant PPIs.
Provided reliability assessment data for predicted PPIs.

Conclusions:

PlaPPISite serves as a valuable, easy-to-use resource for plant researchers.
The database facilitates the search and analysis of detailed protein interaction information.
It supports further investigation into the biological functions of PPIs in multiple plant species.

Keywords:

3D structures of protein complexes Database Domain-domain interaction Domain-motif interaction Interolog Plant Protein-protein interaction site

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