The immunodominant region of Staphylococcal nuclease is represented by multiple peptide sequences.

Several published reports have lead to the characterization of naturally processed peptides that are presented in association with either class I or class II MHC molecules. Most peptides isolated from class II molecules are heterogeneous in length and exhibit ragged amino and carboxy termini. An intriguing finding was that one region of a molecule was often represented by many distinct peptides, rather than by a single dominant peptide species. Each of the peptides representing this dominant region exhibited a common core of amino acids, suggesting that this core may play a significant role in the binding of the peptide to class II and the recognition by peptide-specific T cells. Work from our laboratory has focused on the mechanisms involved in the immunodominance of antigenic determinants using the bacterial antigen Staphylococcal nuclease (Nase) as a model. Using truncated synthetic peptides, we have identified the immunodominant determinant of Nase to be located within the region 81-100 with a minimal antigenic core of 91-100 as determined. Addition of five residues to the carboxy terminus of this peptide had a negative effect on T cell recognition of this region. The present studies were undertaken in an effort to determine the sequence of the naturally processed immunodominant Nase determinant(s) presented in association with I-Ek class II. Our results indicate that the dominant region of the Nase molecule is represented by at least four distinct peptide species that are predicted to lie between residues 86 and 106 with a common core sequence of 91-96. These results indicate that the negative effects of flanking regions are dependent upon length and amino acid composition, and thus the use of truncated peptides to study minimal antigenic determinants may be misleading.

Interference with the binding of a naturally processed peptide to class II alters the immunodominance of T cell epitopes in vivo.

T lymphocytes elicited in response to an immunizing Ag usually recognize only one or a few immunodominant peptides. The mechanisms governing this process are poorly understood. This study examines the consequences of peptide competition on immunodominance. Immunization of B10.A mice with the native Staphylococcus aureus nuclease protein primes T cells to the dominant 86-100 peptide presented in association with I-Ek class II molecules. To render the 86-100 peptide incapable of binding to the class II molecule, single amino acid substitutions were introduced in the native Staphylococcus aureus nuclease protein within a putative I-Ek class II binding motif. Introduction of residue changes at positions 89 and 91 in the protein prevents 86-100-specific T cell clone recognition of the protein in vitro. Competition studies demonstrate that substitutions at residues 89 or 91 decreased the I-Ek binding affinity of the 86-100 peptide. Immunization of B10.A mice with the L89F or Y91S mutant proteins does not prime T cells to the dominant 86-100 peptide; T cells are primed instead to I-Ek-restricted subdominant peptide(s) encompassed by the residues 111-135. In vitro binding studies demonstrate that both the 111-130 and 116-135 synthetic peptides compete with a labeled I-Ek-binding peptide 20-fold less efficiently than the dominant 86-100 peptide, suggesting that these subdominant peptides may be of lower binding affinity than the dominant 86-100 peptide. These results support the hypothesis that dominance is dependent on peptide binding affinity for the appropriate class II molecule and the ability to compete with other peptides, derived from the same Ag, for class II binding.