Paper Citing NAMD - Abstract
Stavrakoudis, Athanassios
Molecular dynamics study of the human insulin B peptide SHLVEALYLVCGERGG complexed with HLA-DQ8 reveals important hydrogen bond interactions
MOLECULAR SIMULATION, 37:837-845, 2011
The basis of proper recognition of pathogens and tumours is provided by adaptive immunity. This immunological reaction of the recognition function of T-cell receptors on T lymphocytes detects antigenic peptides bound to major histocompatibility complex (MHC) molecules. Structural insight into this process has few grown considerably in the last years. In some of the cases, antigens are self-protein fragments causing autoimmunity diseases. Type 1 diabetes is such a disease connected with the human leukocyte antigen-DQ8 molecule, a class II MHC glycoprotein. Its crystal structure, complexed with LVEALYLVCGERGG peptide (insulin B peptide), has been solved, and important information about the significance of P1, P4 and P9 binding pockets has been discovered. The complex structure also revealed an unusual large number of intermolecular hydrogen bonds between insulin B peptide and MHC molecule. To further investigate the dynamics of peptide/MHC interactions, we perform molecular dynamic simulations in explicit water. Analysis of the results provided useful information of the binding of the peptide antigen to MHC molecule, which is supported by numerous hydrogen bonds besides the electrostatic (P1 and P9 pockets) or hydrophobic interactions (P4). Results also allowed some implications to be drawn for the role of residues located outside of the binding groove.
