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HypDB: A functionally annotated web-based database of the proline hydroxylation proteome.

Yao Gong1,2, Gaurav Behera1, Luke Erber1

  • 1Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota at Twin Cities, Minneapolis, Minnesota, United States of America.

Plos Biology
|August 26, 2022
PubMed
Summary
This summary is machine-generated.

Proline hydroxylation (Hyp) is crucial for protein function and disease. We created HypDB, a database of human Hyp sites, revealing its role in protein interactions and identifying new cancer biomarkers.

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Area of Science:

  • Biochemistry
  • Proteomics
  • Bioinformatics

Background:

  • Proline hydroxylation (Hyp) is a vital post-translational modification impacting protein structure, stability, and interactions.
  • Hyp is implicated in numerous cellular pathways and various human diseases.

Purpose of the Study:

  • To comprehensively profile the human Hyp proteome and understand the functional significance of Hyp.
  • To develop HypDB, an integrated database and web server for exploring Hyp sites and their associated data.

Main Methods:

  • Integrated diverse data sources for deep proteome profiling.
  • Performed extensive Liquid Chromatography-Mass Spectrometry (LC-MS) analysis and literature mining.
  • Developed HypDB, a web server providing site-specific Hyp modification data.

Main Results:

  • Identified 14,413 nonredundant Hyp sites across 5,165 human proteins.
  • Revealed significant enrichment of Hyp in functional domains and tissue-specific patterns.
  • Demonstrated Hyp's role in protein-protein interactions and identified novel Hyp biomarkers in lung and kidney cancers using data-independent acquisition (DIA).

Conclusions:

  • The Hyp proteome exhibits functional diversity and plays a critical role in cellular processes and disease.
  • HypDB provides a valuable, publicly accessible resource for quantitative analysis of Hyp in biological pathways and clinical applications.