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MPID-T: database for sequence-structure-function information on T-cell receptor/peptide/MHC interactions.

Joo Chuan Tong1, Lesheng Kong, Tin Wee Tan

  • 1Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore Institute for Infocomm Research, Singapore. jctong@i2r.a-star.edu.sg

Applied Bioinformatics
|May 26, 2006
PubMed
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A new database, MPID-T, offers critical sequence-structure-function data for T-cell receptor (TCR) and peptide/MHC interactions. This resource aids in understanding the molecular basis of adaptive immunity and T-cell recognition.

Area of Science:

  • Immunology and structural biology
  • Computational biology and bioinformatics

Background:

  • Adaptive immune responses rely on Major Histocompatibility Complex (MHC) restriction, where T-cell receptors (TcRs) bind specific antigenic peptides presented by MHC molecules.
  • Understanding the intricate sequence-structure-function relationships in peptide/MHC (pMHC) and TcR/pMHC interactions is crucial for deciphering T-cell recognition mechanisms.

Purpose of the Study:

  • To introduce the MHC-Peptide Interaction Database version T (MPID-T), a comprehensive resource for sequence-structure-function information on TcR/pMHC interactions.
  • To provide experimentally determined structural data and interaction parameters for pMHC and TcR/pMHC complexes to facilitate research.

Main Methods:

  • The MPID-T database was manually curated using data from the Protein Data Bank (PDB), including 187 pMHC and 16 TcR/pMHC complexes.

Related Experiment Videos

  • Structures were analyzed for intermolecular interactions between MHC-peptide and TcR-pMHC complexes.
  • Precomputed interaction parameters such as solvent accessibility, hydrogen bonds, gap volume, and gap index were incorporated into the retrieval system.

    • Main Results:

    • MPID-T contains manually verified and classified structures of pMHC and TcR/pMHC complexes.
    • The database provides detailed structural descriptors for characterizing these interactions.
    • Tools for structural visualization and alignment are available, enabling in-depth analysis.

    Conclusions:

    • MPID-T enhances the understanding of binding mechanisms in TcR/pMHC and pMHC interactions.
    • Mapping the TcR footprint on MHC and bound peptides is facilitated, crucial for T-cell recognition.
    • The database serves as a valuable resource for researchers in immunology and structural biology.