A peptide filtering relation quantifies MHC class I peptide optimization
Dalchau, Neil, Phillips, Andrew, Goldstein, Leonard D., Howarth, Mark, Cardelli, Luca, Emmott, Stephen, Elliott, Tim and Werner, Joern M. (2011) A peptide filtering relation quantifies MHC class I peptide optimization. PLoS Computational Biology, 7, (10), e1002144-[14pp]. (doi:10.1371/journal.pcbi.1002144). (PMID:22022238).
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Major Histocompatibility Complex (MHC) class I molecules enable cytotoxic T lymphocytes to destroy virus-infected or cancerous cells, thereby preventing disease progression. MHC class I molecules provide a snapshot of the contents of a cell by binding to protein fragments arising from intracellular protein turnover and presenting these fragments at the cell surface. Competing fragments (peptides) are selected for cell-surface presentation on the basis of their ability to form a stable complex with MHC class I, by a process known as peptide optimization. A better understanding of the optimization process is important for our understanding of immunodominance, the predominance of some T lymphocyte specificities over others, which can determine the efficacy of an immune response, the danger of immune evasion, and the success of vaccination strategies. In this paper we present a dynamical systems model of peptide optimization by MHC class I. We incorporate the chaperone molecule tapasin, which has been shown to enhance peptide optimization to different extents for different MHC class I alleles. Using a combination of published and novel experimental data to parameterize the model, we arrive at a relation of peptide filtering, which quantifies peptide optimization as a function of peptide supply and peptide unbinding rates. From this relation, we find that tapasin enhances peptide unbinding to improve peptide optimization without significantly delaying the transit of MHC to the cell surface, and differences in peptide optimization across MHC class I alleles can be explained by allele-specific differences in peptide binding. Importantly, our filtering relation may be used to dynamically predict the cell surface abundance of any number of competing peptides by MHC class I alleles, providing a quantitative basis to investigate viral infection or disease at the cellular level. We exemplify this by simulating optimization of the distribution of peptides derived from Human Immunodeficiency Virus Gag-Pol polyprotein.
|Digital Object Identifier (DOI):||doi:10.1371/journal.pcbi.1002144|
|Subjects:||Q Science > QA Mathematics > QA76 Computer software
Q Science > QR Microbiology > QR180 Immunology
Q Science > QH Natural history > QH301 Biology
|Divisions:||Faculty of Medicine > Cancer Sciences
Faculty of Natural and Environmental Sciences > Biological Sciences
|Date Deposited:||24 Apr 2012 13:00|
|Last Modified:||15 Jul 2014 14:06|
|RDF:||RDF+N-Triples, RDF+N3, RDF+XML, Browse.|
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