The Prominence of the Ligand Peptide Carboxyl Terminus in the MHC Class I Molecules Stability and Affinity

Abstract

Major histocompatibility class I complex (MHC) proteins are intracellular receptors that bind peptides of eight to ten amino acids to present them to the immune system. The stability of the interaction between MHC class I and peptide is governed by length and sequence of the peptide. The carboxyl and amino termini of the peptide make a significant contribution to binding energy by forming networks of hydrogen bonds. In addition, the carboxy terminal side chain of the peptid serves as an anchor residue in all the known MHC class I alleles, i.e., it binds into a pocket at the bottom of the binding site.We show here that the binding of the carboxyl terminus of the peptide has a strong influence on the dynamics, binding energy, folding, peptide affinity and stability on the cell surface of two MHC class I mouse allotypes. Molecular Mechanic/ Poisson-Boltzmann Surface Area (MM-PBSA) and potential mean force (PMF) analysis demonstrate that binding of the the carboxy terminus causes a decrease in the peptide free binding energy to MHC class I. This is verified in vitro by thermal denaturation by tryptophan fluorescence (TDTF) and Fluorescence anisotropy (FA) assays, which show a considerable decrease in the thermal stability and peptide binding affinity of C-terminally truncated peptides to class I. Such truncated peptides are also much less efficient in stabilizing MHC class I at the cell surface.