%0 Journal Article
%T Flanking p10 contribution and sequence bias in matrix based epitope prediction: revisiting the assumption of independent binding pockets
%A Christian S Parry
%J BMC Structural Biology
%D 2008
%I BioMed Central
%R 10.1186/1472-6807-8-44
%X One new matrix shows significant improvement over the base matrix; the other does not. The new matrices differ in the sequence of the peptide library.One of the extended quantitative matrices showed significant improvement in prediction over the original nine residue matrix and over the other extended matrix. Proline in the sequence of the peptide library of the better performing matrix presumably stabilizes the peptide conformation through neighbour interactions. Such interactions may influence epitope prediction in this test of quantitative matrices. This calls into question the assumption of the independent contribution of individual binding pockets.It is essential to understand the host immune response in order to boost or modulate the immune system in infectious diseases, autoimmune diseases, allergies or cancer. This requires knowledge of the peptides selected and presented by class II major histocompatibility complex (MHC) molecules and the rules governing their binding and presentation to CD4+ T cells. Molecules of the MHC are surface receptors on immune cells that bind and present selected antigen as short peptides or epitopes to T cells with matching receptors. The peptides are produced by the proteolytic machinery of the antigen presenting cell. Class I epitopes are generated from intracellular proteins [1] and class II epitopes are processed from vesicular, endocytosed and cytosolic proteins through the exogenous pathway [2]. Processed peptides are loaded in intracellular compartments and transported to the cell surface where they are displayed for recognition by T cells. The unique design of the peptide binding region of the MHC and the vast polymorphism, through duplication, gene conversion and other genetic mechanisms, combine to generate hundreds of molecular variants at class I HLA-A, -B, -C and class II HLA-D loci [3]. Through these mechanisms MHC molecules are able to recognize and bind a vast array of peptides with fine distinction. Each allele h
%U http://www.biomedcentral.com/1472-6807/8/44