Normal adaptive immune responses operate under major histocompatibility complex (MHC) restriction by binding to specific, short antigenic peptides and presenting them to appropriate T-cell receptors (TcRs). Sequence-structure-function information is critical in understanding the principles governing peptide/MHC (pMHC) and TcR/pMHC recognition and binding. A new database for sequence-structure-function information on TcR/pMHC interactions, MHC-Peptide Interaction Database version T (MPID-T), is now available with the latest available Protein Data Bank (PDB) data and interaction parameters on TcR/pMHC complexes. MPID-T is a manually curated MySQL® database containing experimentally determined structures of 187 pMHC complexes and 16 TcR/pMHC complexes available in the PDB. Each structure is manually verified, classified, and analysed for intermolecular interactions (i) between the MHC and its corresponding bound peptide and (ii) between TcR and its bound pMHC complex where TcR structural information is available. The MPID-T database retrieval system has precomputed interaction parameters that include solvent accessibility, hydrogen bonds, gap volume and gap index. Structural visualisation of the TcR/pMHC complex, pMHC complex, MHC or the bound peptide can be performed using freely available graphics applications such as MDL® Chime or RasMol, while structural alignment (based on MHC class and peptide length) can be viewed using the Jmol molecular viewer or an MDL® Chime-compatible web browser client. MPID-T contains structural descriptors for in-depth characterisation of TcR/pMHC and pMHC interactions. The ultimate purpose of MPID-T is to enhance the understanding of the binding mechanism underlying TcR/pMHC and pMHC interactions by mapping the TcR footprint on the MHC and its bound peptide, as this eventually determines T-cell recognition and binding.
Major Histocompatibility Complex Protein Data Bank Major Histocompatibility Complex Allele Protein Data Bank Entry Major Histocompatibility Complex Binding
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Rammensee HG, Falk K, Rotzschke O. Peptides naturally presented by MHC class I molecules. Annu Rev Immunol 1993; 11: 213–44PubMedCrossRefGoogle Scholar
Lefranc MP, Lefranc G. The T cell receptor factsbook. London: Academic Press, 2001: 398Google Scholar
Kangueane P, Sakharkar MK, Kolatkar PR, et al. Towards the MHC-peptide combinatorics. Hum Immunol 2001; 62: 539–56PubMedCrossRefGoogle Scholar
Govindarajan KR, Kangueane P, Tan TW, et al. MPID: MHC-Peptide Interaction Database for sequence-structure-function information on peptides binding to MHC molecules. Bioinformatics 2003; 19: 309–10PubMedCrossRefGoogle Scholar
Kaas Q, Ruiz M, Lefranc MP. IMGT/3Dstructure-DB and IMGT/StructuralQuery, a database and a tool for immunoglobulin, T cell receptor and MHC structural data. Nucleic Acids Res 2004; 32: D208–10PubMedCrossRefGoogle Scholar
Robinson J, Waller MJ, Parham P, et al. IMGT/HLA Database: a sequence database for the human major histocompatibility complex. Nucleic Acids Res 2001; 29: 210–3PubMedCrossRefGoogle Scholar