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Comparative Study
. 2008 Dec;60(12):759-65.
doi: 10.1007/s00251-008-0330-2. Epub 2008 Sep 3.

MHC motif viewer

Nicolas Rapin  1 , Ilka Hoof, Ole Lund, Morten Nielsen
Affiliations
Comparative Study

MHC motif viewer

Nicolas Rapin et al. Immunogenetics. 2008 Dec.

Abstract

In vertebrates, the major histocompatibility complex (MHC) presents peptides to the immune system. In humans, MHCs are called human leukocyte antigens (HLAs), and some of the loci encoding them are the most polymorphic in the human genome. Different MHC molecules present different subsets of peptides, and knowledge of their binding specificities is important for understanding the differences in the immune response between individuals. Knowledge of motifs may be used to identify epitopes, to understand the MHC restriction of epitopes, and to compare the specificities of different MHC molecules. Algorithms that predict which peptides MHC molecules bind have recently been developed and cover many different alleles, but the utility of these algorithms is hampered by the lack of tools for browsing and comparing the specificity of these molecules. We have, therefore, developed a web server, MHC motif viewer, that allows the display of the likely binding motif for all human class I proteins of the loci HLA A, B, C, and E and for MHC class I molecules from chimpanzee (Pan troglodytes), rhesus monkey (Macaca mulatta), and mouse (Mus musculus). Furthermore, it covers all HLA-DR protein sequences. A special viewing feature, MHC fight, allows for display of the specificity of two different MHC molecules side by side. We show how the web server can be used to discover and display surprising similarities as well as differences between MHC molecules within and between different species. The MHC motif viewer is available at http://www.cbs.dtu.dk/biotools/MHCMotifViewer/ .

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Figures

Figure 1
Figure 1. MHC motif viewer interface
For MHC class I, the viewer includes binding motifs for HLA-A, HLA-B, HLA-C, and HLA-E alleles, as well as chimpanzee, rhesus monkey and mouse. For MHC class II, the human HLA-DR alleles are included.
Figure 2
Figure 2. MHC binding motifs for the HLA-A locus
The left panel displays a motif table, and the right panel displays an enlarged image of the predicted HLA-A*0265 binding motif. The Download and Matrix links in the upper left corner of the right panel allow for downloads of the binding motif image and PSSM matrix, respectively.
Figure 3
Figure 3. MHC fight viewer
Comparing the binding motif for the HLA-A*6801 and HLA-A*6802 molecules. The HLA-A*6801 has basic A3 supertype P9 preferences and HLA-A*6802 has hydrophobic A2 supertype P9 preferences.
Figure 4
Figure 4. MHC fight viewer
Comparing the binding motif for the HLA-A*2402 and chimpanzee Patr-A*0701 molecules.
Figure 5
Figure 5. Explaining MHC cross-reactivity
The EBV peptide AVLLHEESM cross-reacts to the HLA-A*31 and HLA-B*35 serotypes. Upper panel compares the motifs of HLA-A*3101 to HLA-B*3501. Lower panel compares the motifs of HLA-A*3108 to HLA-B*3510.
See this image and copyright information in PMC

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