Sequence signals for generation of antigenic peptides by the proteasome: Implications for proteasomal cleavage mechanism

Yael Altuvia, Hanah Margalit*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

51 Scopus citations


Proteasomal cleavage of proteins is the first step in the processing of most antigenic peptides that are presented to cytotoxic T cells. Still, its specificity and mechanism are not fully understood. To identify preferred sequence signals that are used for generation of antigenic peptides by the proteasome, we performed a rigorous analysis of the residues at the termini and flanking regions of naturally processed peptides eluted from MHC class I molecules. Our results show that both the C terminus (position P1 of the cleavage site) and its immediate flanking position (P1') possess significant signals. The N termini of the peptides show these signals only weakly, consistent with previous findings that antigenic peptides may be cleaved by the proteasome with N-terminal extensions. Nevertheless, we succeed to demonstrate indirectly that the N-terminal cleavage sites contain the same preferred signals at position P1'. This reinforces previous findings regarding the role of the P1' position of a cleavage site in determining the cleavage specificity, in addition to the well-known contribution of position P1. Our results apply to the generation of antigenic peptides and bare direct implications for the mechanism of proteasomal cleavage. We propose a model for proteasomal cleavage mechanism by which both ends of cleaved fragments are determined by the same cleavage signals, involving preferred residues at both P1 and P1' positions of a cleavage site. The compatibility of this model with experimental data on protein degradation products and generation of antigenic peptides is demonstrated. (C) 2000 Academic Press.

Original languageAmerican English
Pages (from-to)879-890
Number of pages12
JournalJournal of Molecular Biology
Issue number4
StatePublished - 28 Jan 2000

Bibliographical note

Funding Information:
We are grateful to Klaus Eichmann for valuable and inspiring discussions. We thank Norman Grover for statistical consultation, Jutta Bachmann for her help in the data organization, and Ora Schueler-Furman for helpful comments on the manuscript. This work has benefited from valuable discussions with Robert Huber, Wolfgang Baumeister, Robert Tampe, Michelle Groll, and Alfred Goldberg. The study was supported by grants from the US-Israel Binational Science Foundation, and from the Israel Cancer Research Fund, granted to H.M.


  • Antigenic peptides
  • Bioinformatics
  • Cleavage
  • Proteasome
  • Sequence signals


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