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SwissPalm: Protein Palmitoylation database.

Mathieu Blanc1, Fabrice David1,2, Laurence Abrami1

  • 1Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland.

F1000Research
|September 5, 2015
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Summary

Protein S-palmitoylation, a key biological regulator, is now more accessible via SwissPalm. This database centralizes over 5000 S-palmitoylated proteins, aiding research into this vital post-translational modification.

Keywords:
Acyl-RACAcyl-biotin exchangeS-palmitoylationdatabasepalmitoyl-proteomesproteomics

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Area of Science:

  • Biochemistry and Molecular Biology
  • Proteomics
  • Post-Translational Modifications

Background:

  • Protein S-palmitoylation is a reversible lipid modification crucial for biological processes, but its full scope and function remain largely unknown.
  • High-throughput chemical methods have generated extensive palmitoyl-proteome data across various species, necessitating data centralization.
  • Existing data require curation and comparison to advance the understanding of S-palmitoylation.

Purpose of the Study:

  • To establish SwissPalm, a comprehensive, manually curated, and open-access resource for studying protein S-palmitoylation.
  • To centralize and enable comparison of existing palmitoyl-proteome data.
  • To provide tools for analyzing and validating S-palmitoylation sites and their biological relevance.

Main Methods:

  • Development of the SwissPalm database (http://swisspalm.epfl.ch).
  • Manual curation of over 5000 S-palmitoylated protein entries from seven species, including over 500 specific S-palmitoylation sites.
  • Integration of confidence filters, S-palmitoylated cysteine prediction scores, orthologs, and isoform alignments.

Main Results:

  • SwissPalm currently contains over 5000 S-palmitoylated protein hits and over 500 specific S-palmitoylation sites.
  • Systems analysis suggests that 10% or more of the human proteome is susceptible to S-palmitoylation.
  • Ontology and pathway analyses reveal the involvement of S-palmitoylation in key biological functions, with significant crosstalk with other post-translational modifications.

Conclusions:

  • SwissPalm serves as a powerful, centralized resource for the scientific community to investigate protein S-palmitoylation.
  • The data indicate a broad involvement of S-palmitoylation in fundamental biological processes.
  • Further research using SwissPalm will help unravel the global significance of this reversible lipid modification.