The MHC peptidebinding groove

The molecules encoded in the MHC complex form a family of highly polymorphic glycoproteins. Of these MHC proteins, the best characterized are the class I (HLA-A, -B, -C in humans and H-2K, -D, -L in mice) and class II (HLA-DR, -DQ, -DP in humans and I-A, I-E in the mice) molecules which present peptides to CD8+ and CD4+ lymphocytes, respectively. Class I molecules are dimers of a membrane-inserted heavy chain and a soluble light chain, the (32-microglobulin. Class II molecules are a(3 dimers of similar size, both of which are transmembrane proteins. The three-dimensional structure of several class I and class II molecules has been determined by X-ray crystallography. The class I peptide-binding site is formed by the two membrane-distal domains of the heavy chain and is composed of a floor of eight 0 strands flanked by two a helical walls. The organization of the class II peptide binding site is similar to the class

I binding site, even though it is formed by the membrane-distal domains of both class II chains, to which each contribute one a helix and four (3 strands. The (3 sheet floors and helical walls define a groove of suitable dimension for occupancy by 8-10 peptide residues in both MHC classes.

Despite an overall similarity of the class I and class

II groove, detailed differences with major functional consequences have been identified. The class I cleft is blocked completely at both ends by bulky amino acid side-chains, while the class II cleft is open due to a replacement and/or a repositioning of these blocking side-chains. Consequently, the majority of class I binding sequences are short peptides in the range of 8-10 residues. In contrast, the open class II cleft allows peptides to extend out, enabling as a result, the binding of a broader range of peptide lengths, typically 12-24 residues.

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