Predicting proteasomal cleavage sites: a comparison of available methods

Patricia Saxová; Søren Buus; Søren Brunak; Can Kesmir

Predicting proteasomal cleavage sites: a comparison of available methods

Patricia Saxová, Søren Buus, Søren Brunak, Can Kesmir

Department of Immunology and Microbiology

73 Citations (Scopus)

Abstract

The proteasome plays an essential role in the immune responses of vertebrates. By degrading intercellular proteins from self and non-self, the proteasome produces the majority of the peptides that are presented to cytotoxic T cells (CTL). There is accumulating evidence that the C-terminal, in particular, of CTL epitopes is cleaved precisely by the proteasome, whereas the N-terminal is produced with an extension, and later trimmed by peptidases in the cytoplasm and in the endoplasmic reticulum. Recently, three publicly available methods have been developed for prediction of the specificity of the proteasome. Here, we compare the performance of these methods on a large set of CTL epitopes. The best method, NetChop at www.cbs.dtu.dk/Services/NetChop, can capture approximately 70% of the C-termini correctly. This result suggests that the predictions can still be improved, particularly if more quantitative degradation data become available.

Original language	English
Journal	International Immunology
Volume	15
Issue number	7
Pages (from-to)	781-7
Number of pages	6
ISSN	0953-8178
Publication status	Published - 2003

Cite this

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title = "Predicting proteasomal cleavage sites: a comparison of available methods",

abstract = "The proteasome plays an essential role in the immune responses of vertebrates. By degrading intercellular proteins from self and non-self, the proteasome produces the majority of the peptides that are presented to cytotoxic T cells (CTL). There is accumulating evidence that the C-terminal, in particular, of CTL epitopes is cleaved precisely by the proteasome, whereas the N-terminal is produced with an extension, and later trimmed by peptidases in the cytoplasm and in the endoplasmic reticulum. Recently, three publicly available methods have been developed for prediction of the specificity of the proteasome. Here, we compare the performance of these methods on a large set of CTL epitopes. The best method, NetChop at www.cbs.dtu.dk/Services/NetChop, can capture approximately 70% of the C-termini correctly. This result suggests that the predictions can still be improved, particularly if more quantitative degradation data become available.",

author = "Patricia Saxov{\'a} and S{\o}ren Buus and S{\o}ren Brunak and Can Kesmir",

note = "Keywords: Algorithms; Amino Acid Sequence; Computational Biology; Computer Simulation; Cysteine Endopeptidases; Databases, Protein; Epitopes; HLA-A Antigens; HLA-B Antigens; Humans; Molecular Sequence Data; Multienzyme Complexes; Peptides; Proteasome Endopeptidase Complex; Proteins; Sequence Analysis, Protein",

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T1 - Predicting proteasomal cleavage sites: a comparison of available methods

AU - Saxová, Patricia

AU - Buus, Søren

AU - Brunak, Søren

AU - Kesmir, Can

N1 - Keywords: Algorithms; Amino Acid Sequence; Computational Biology; Computer Simulation; Cysteine Endopeptidases; Databases, Protein; Epitopes; HLA-A Antigens; HLA-B Antigens; Humans; Molecular Sequence Data; Multienzyme Complexes; Peptides; Proteasome Endopeptidase Complex; Proteins; Sequence Analysis, Protein

PY - 2003

Y1 - 2003

N2 - The proteasome plays an essential role in the immune responses of vertebrates. By degrading intercellular proteins from self and non-self, the proteasome produces the majority of the peptides that are presented to cytotoxic T cells (CTL). There is accumulating evidence that the C-terminal, in particular, of CTL epitopes is cleaved precisely by the proteasome, whereas the N-terminal is produced with an extension, and later trimmed by peptidases in the cytoplasm and in the endoplasmic reticulum. Recently, three publicly available methods have been developed for prediction of the specificity of the proteasome. Here, we compare the performance of these methods on a large set of CTL epitopes. The best method, NetChop at www.cbs.dtu.dk/Services/NetChop, can capture approximately 70% of the C-termini correctly. This result suggests that the predictions can still be improved, particularly if more quantitative degradation data become available.

AB - The proteasome plays an essential role in the immune responses of vertebrates. By degrading intercellular proteins from self and non-self, the proteasome produces the majority of the peptides that are presented to cytotoxic T cells (CTL). There is accumulating evidence that the C-terminal, in particular, of CTL epitopes is cleaved precisely by the proteasome, whereas the N-terminal is produced with an extension, and later trimmed by peptidases in the cytoplasm and in the endoplasmic reticulum. Recently, three publicly available methods have been developed for prediction of the specificity of the proteasome. Here, we compare the performance of these methods on a large set of CTL epitopes. The best method, NetChop at www.cbs.dtu.dk/Services/NetChop, can capture approximately 70% of the C-termini correctly. This result suggests that the predictions can still be improved, particularly if more quantitative degradation data become available.

M3 - Journal article

C2 - 12807816

SN - 0953-8178

VL - 15

SP - 781

EP - 787

JO - International Immunology

JF - International Immunology

IS - 7

ER -

Predicting proteasomal cleavage sites: a comparison of available methods

Abstract

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