Crystal structures of HLA-A*0201 complexed with antigenic peptides with either the amino- or carboxyl-terminal group substituted by a methyl group

Abstract

The crystal structures of class I major histocompatibility complex (MHC) molecules complexed with antigenic peptides revealed a network of hydrogen bonds between the charged amino- and carboxyl-termini of the peptides and conserved MHC residues at both ends of the peptide binding site. These interactions were shown to contribute substantially to the stability of class I MHC/peptide complexes by thermal denaturation studies using synthetic peptides in which either the amino- or carboxyl-terminal group is substituted by a methyl group. Here we report crystal structures of HLA-A*0201 complexed with these terminally modified synthetic peptides showing that they adopt the same bound conformation as antigenic peptides. A number of variations in peptide conformation were observed for the terminally modified peptides, including in one case, a large conformational difference in four central peptide residues that is apparently caused by the lattice contact. This is reminiscent of the way binding a T-cell receptor changed the conformation of central residues of an MHC-bound peptide. The structures determined identify which conserved hydrogen bonds are eliminated in terminally substituted peptides and suggest an increased energetic importance of the interactions at the peptide termini for MHC-peptide stability.

Peptide Modulation of Class I Major Histocompatibility Complex Protein Molecular Flexibility and the Implications for Immune Recognition*

“…(Note that accurate K D values are difficult to measure for class I MHC proteins as the peptide-free molecule is unstable, rapidly aggregates, and cannot be directly purified. However, the half-life of the Tax⅐HLA-A2 complex is 8 h at 25°C with an estimated K D of 18 nM (19), and the T m values of the Tax and Flu M1 complexes measured by thermal denaturation are identical within error (24,27). Further, as indicated below, identical results were obtained with and without the presence of excess peptide in the exchange reactions.…”

Functional and Structural Characteristics of NY-ESO-1-related HLA A2-restricted Epitopes and the Design of a Novel Immunogenic Analogue

“…In fact, the majority of HLA A2 structures encompass complexes in which the peptide ligand terminates in valine or leucine. One structure with an alanine-terminating peptide (a P9 leucine to alanine-substituted influenza virus matrix peptide, GILGFVTFA) has been reported previously (44). The conformation of the HLA A2 heavy chain was conserved in all structures, and only small differences in peptide conformation were observed.…”

The Structure and Stability of an HLA-A*0201/Octameric Tax Peptide Complex with an Empty Conserved Peptide-N-Terminal Binding Site

“…In vitro, in the absence of bound peptides, ␤ 2 m dissociates and Hc aggregates (17,22,(25)(26)(27)(28)(29), whereas in vivo in the endoplasmic reticulum peptide-free class I molecules are stabilized by chaperonins and the peptide transport and loading proteins, TAP and Tapasin (30,31). Thermal denaturation studies of MHC/peptide complexes in which either the peptide N-terminal amino group or C-terminal carboxylate group was substituted by a methyl group showed a decrease in the T m of the MHC/peptide of 22°C, indicating a decrease in stability of ϳ4.6 kcal/mol, whereas substituting both peptide anchor residues with alanine showed a decrease of only 5.5°C or ϳ1.2 kcal/mol (28,32). These thermodynamic data support the suggestion that the conserved interactions between the N and C termini of bound peptides may dominate in the formation and stabilization of peptide/MHC complexes.…”