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Class I major histocompatibility complex (MHC) molecules assemble in the endoplasmic reticulum (ER) from three components: a 44-kD transmembrane glycoprotein, encoded by one of a number of MHC-linked genes; the soluble 12-kD protein β2-microglobulin (β2m); and a small peptide of eight to ten amino acids. The trimeric complex so formed contains the peptide embedded in a binding cleft consisting of two parallel α helices overlaying a platform of eight β strands, contributed by the amino-terminal two domains of the glycoprotein (Bjorkman et al. 1987). Amino acid substitutions in the α helices and β strands encoded by different class I alleles generate variability in the binding site and consequent variability in the peptides bound. Sequence “motifs” in the spectrum of bound peptides are a discernible result of this binding-site polymorphism, with preferred amino acid residues found at two or three positions in the peptides associated with particular alleles (Rotzschke et al....
Click et al. (Wed,) studied this question.