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Identification of Inositol Phosphate or Phosphoinositide Interacting Proteins by Affinity Chromatography Coupled to Western Blot or Mass Spectrometry

Identification of Inositol Phosphate or Phosphoinositide Interacting Proteins by Affinity Chromatography Coupled to Western Blot or Mass Spectrometry

Published on: July 26, 2019

YPIBP: A repository for phosphoinositide-binding proteins in yeast

Jagat Rathod¹, Han-Chen Yen², Biqing Liang¹

¹Department of Earth Sciences, College of Sciences, National Cheng Kung University, Tainan 701, Taiwan.

Computational and Structural Biotechnology Journal

|July 21, 2021

Summary

Researchers created the Yeast Phosphoinositide-Binding Proteins (YPIBP) knowledgebase, consolidating 679 proteins and their domains. This resource aids in understanding yeast lipid-protein interactions and cellular functions.

Area of Science:

Cell Biology
Biochemistry
Bioinformatics

Background:

Phosphoinositides (PIs) regulate crucial cellular processes like signaling and membrane trafficking.
Yeast is a model organism for studying lipid-protein interactions, but existing data on PI-binding proteins is fragmented.
A comprehensive database linking PI-binding proteins, their domains, and interactions is lacking.

Purpose of the Study:

To develop the first comprehensive knowledgebase of yeast phosphoinositide-binding proteins (YPIBP).
To integrate protein domain information with PI-binding data.
To provide tools for exploring the PI-domain-protein interactome.

Main Methods:

Compiled data from high-throughput studies, QuickGO, and literature mining.
Collected information on 679 PI-binding proteins from yeast.
Included protein domain classifications (lipid-binding, lipid-related, other).

Main Results:

Established the YPIBP knowledgebase with 679 yeast PI-binding proteins.
Integrated diverse protein domain data.
Developed search, browse, and enrichment analysis functionalities.
Provided interactive visualization of the PI-domain-protein interactome.

Conclusions:

YPIBP consolidates scattered knowledge on yeast PI-binding proteins.
The database offers new insights into PI-binding protein networks.
YPIBP serves as a valuable resource for lipid-protein interaction research.

Keywords:

ANTH, AP180 N-terminal Homology BAR, Bin-Amphiphysin-Rvs CAFA, Critical Assessment of Functional Annotation CRAL-TRIO, cellular retinaldehyde-binding protein (CRALBP) and TRIO guanine exchange factor Cvt, Cytoplasm-to-vacuole targeting ENTH, Epsin N-terminal Homology FDR, False Discovery Rate FYVE, Fab 1 (yeast orthologue of PIKfyve), YOTB, Vac 1 (vesicle transport protein), and EEA1 GO, Gene Ontology ITC, Isothermal Titration Calorimetry LBD, Lipid-Binding Domain LMPD, LIPID MAPS Proteome Database LMSD, LIPID MAPS Structure Database LRD, Lipid-Related Domain Lipid-binding domain OMIM, Online Mendelian Inheritance in Man OSBP, Oxysterol-Binding Protein PH, Pleckstrin Homology PI(3,4)P2, phosphatidylinositol-3,4-bisphosphate PI(3,4,5)P3, phosphatidylinositol-3,4,5-trisphosphate PI(3,5)P2, phosphatidylinositol-3,5-bisphosphate PI(4,5)P2, phosphatidylinositol-4,5-bisphosphate PI-binding protein PI3P, phosphatidylinositol-3-phosphate PI4P, phosphatidylinositol-4-phosphate PI5P, phosphatidylinositol-5-phosphate PIs, Phosphoinositides PMID, PubMed ID PX, Phox Homology Phosphatidylinositol (PtdIns)Phosphoinositides (PIs)PtdIns, Phosphatidylinositol QCM, Quartz Crystal Microbalance S. cerevisiae SNX, Sorting Nexin SPR, Surface Plasmon Resonance YPIBP, Yeast Phosphoinositide-Binding Proteins Yeast

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