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PCPS: A Web Server to Predict Proteasomal Cleavage Sites

  • Marta Gomez-Perosanz
  • Alvaro Ras-Carmona
  • Pedro A. RecheEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 2131)

Abstract

The proteasome complex is mainly responsible for proteolytic degradation of cytosolic proteins, generating the C-terminus of MHC I-restricted peptide ligands and CD8 T cell epitopes. Therefore, prediction of proteasomal cleavage sites is relevant for anticipating CD8 T-cell epitopes. There are two different proteasomes, the constitutive proteasome, expressed in all types of cells, and the immunoproteasome, constitutively expressed in dendritic cells. Although both proteasome forms generate peptides for presentation by MHC I molecules, the immunoproteasome is the main form involved in providing peptide fragments for priming CD8 T cells. On the contrary, the proteasome provides peptides for presentation by MHC I molecules that can be targeted by already primed CD8 T cells. Proteasome cleavage prediction server (PCPS) is a server for predicting cleavage sites generated by both the constitutive proteasome and the immunoproteasome. Here, we illustrate the usage of PCPS to predict proteasome and immunoproteasome cleavage sites and compare the results with those provided by NetChop, a related tool available online. PCPS is implemented for free public use available online at http://imed.med.ucm.es/Tools/pcps/.

Key words

Proteasome Immunoproteasome Prediction of cleavage sites PCPS 

Notes

Acknowledgments

We wish to thank the Spanish department of science at MINECO for supporting the research of the immunomedicine group through grants SAF2006:07879, SAF2009:08301 and BIO2014:54164-R to P.A.R.

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2020

Authors and Affiliations

  • Marta Gomez-Perosanz
    • 1
  • Alvaro Ras-Carmona
    • 1
  • Pedro A. Reche
    • 1
    Email author
  1. 1.Department of Immunology, School of MedicineComplutense University of MadridMadridSpain

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