Transporter associated with antigen processing preselection of peptides binding to the MHC: a bioinformatic evaluation

Irini Doytchinova, Shelley Hemsley, Darren R. Flower

Research output: Contribution to journalArticle

Abstract

TAP is responsible for the transit of peptides from the cytosol to the lumen of the endoplasmic reticulum. In an immunological context, this event is followed by the binding of peptides to MHC molecules before export to the cell surface and recognition by T cells. Because TAP transport precedes MHC binding, TAP preferences may make a significant contribution to epitope selection.
To assess the impact of this preselection, we have developed a scoring function for TAP affinity prediction using the additive method, have used it to analyze and extend the TAP binding motif, and have evaluated how well this model acts as a preselection step in predicting MHC binding peptides. To distinguish between MHC alleles that are exclusively dependent on TAP and those
exhibiting only a partial dependence on TAP, two sets of MHC binding peptides were examined: HLA-A*0201 was selected as a representative of partially TAP-dependent HLA alleles, and HLA-A*0301 represented fully TAP-dependent HLA alleles. TAP preselection has a greater impact on TAP-dependent alleles than on TAP-independent alleles. The reduction in the number of nonbinders varied from 10% (TAP-independent) to 33% (TAP-dependent), suggesting that TAP preselection is an important component in the successful in silico prediction of T cell epitopes.
Original languageEnglish
Pages (from-to)6813-6819
Number of pages7
JournalJournal of Immunology
Volume173
Issue number11
DOIs
Publication statusPublished - 1 Dec 2004

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Antigen Presentation
Computational Biology
Alleles
T-Lymphocyte Epitopes
HLA-A Antigens
Endoplasmic Reticulum
Computer Simulation
Cytosol
Epitopes
MHC binding peptide
T-Lymphocytes
Peptides

Cite this

Doytchinova, Irini ; Hemsley, Shelley ; Flower, Darren R. / Transporter associated with antigen processing preselection of peptides binding to the MHC : a bioinformatic evaluation. In: Journal of Immunology. 2004 ; Vol. 173, No. 11. pp. 6813-6819.
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Transporter associated with antigen processing preselection of peptides binding to the MHC : a bioinformatic evaluation. / Doytchinova, Irini; Hemsley, Shelley; Flower, Darren R.

In: Journal of Immunology, Vol. 173, No. 11, 01.12.2004, p. 6813-6819.

Research output: Contribution to journalArticle

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