Natural ligand motifs of H-2E molecules are allele specific and illustrate homology to HLA-DR molecules

Abstract

Motifs of peptides naturally associated with H-2E k and E d molecules were determined by (I) pool sequencing of natural ligand mixtures and (II) sequencing of Individual natural ligands followed by their alignment to the basic motif suggested by pool sequencing. The data reveal nine amlno acid motifs with Interaction sites at relative positions P1, P4, P6 and P9, with specificities that are identical at some but different at other anchor positions between E d and E k motifs, Illustrating the different requirements for peptides to be presented by these two MHC molecules. The anchors with the most restricted specificity are P1 and P9.

Posttranslational Regulation ofI-Edby Affinity for CLIP

“…We found that substitutions at the P1, P4, and P9 residues of CLIP (in the context of full-length Ii) had the most significant effects. Our results are consistent with published peptide-binding motifs (32)(33)(34) and with predictions from sequence and structural similarities and differences between I-E d and I-E k (our molecular modeling and Refs. 16 and 34).…”

“…The P1 pockets of I-E d and I-E k differ only at ␤87; ␤87F in I-E k reduces the pocket volume, while ␤87S in I-E d leaves a pocket that accommodates large aromatic peptide anchors (Ref. 34, illustrated in Fig. 8A).…”

“…Mutations in murine Ii that were likely to increase the affinity of CLIP for I-E d were chosen based on predictions using crystal structures of I-E k (14,15) to model I-E d , and on published peptidebinding motifs (32)(33)(34). None of the wt CLIP anchors (M90, A93, P95, and M98) conformed to known I-E d -binding motifs.…”

A role for “self” in T-cell activation

“…We visualized endogenous peptides in the synapse using the approach of Irvine et al 10 where MHC are pulsed on APCs with peptides that have long D-amino acid extensions (to prevent proteolysis) outside of the MHC binding portion, terminating in a biotin that can be labeled with streptavidin-Cy3 and then visualized by a sensitive camera. The endogenous peptides tested in these experiments were a panel of I-E k -specific endogenous peptides that had been previously identified using acidic elution and mass-spectroscopy 16,17 from spleen and thymus cells from mice, as well as from an I-E k specific cell line 16,17 . As shown in Fig.…”

CD4+ T Cell Responses to Self- and Mutated p53 Determinants During Tumorigenesis in Mice

“…To address this question, the wt mouse p53 amino acid sequence was screened for the presence of peptides containing MHC class II (A d and E d ) peptide-binding motifs. An E d motif has been previously determined using sequences of synthetic peptides that bind with high affinity to the E d molecule and natural peptide ligands eluted from the E d binding groove (31). This motif contained multiple basic residues, and the following preferential anchor residues at positions P1, P4, P6, and P9: a bulky aromatic amino acid (P1), a positively charged amino acid (P4), an aliphatic amino acid or glycine (P6), and a basic amino acid (P9) (Fig.…”