Hydrogen bonding between conserved heavy-chain cleft residues and the N- and C-termini of associated peptides typically limit their length to 8–13 residues (though exceptions abound [2]), and strictly dictate peptide directionality. Additionally, six defined

pockets (termed A–F) in the cleft confer specificity for peptide side chains oriented toward the groove [3]. Extensive polymorphism between the binding grooves of different MHC allomorphs (>7000 known alleles (and climbing) in human populations with up to six allomorphs expressed per person from the HLA-A, -B, and -C loci (http://hla.alleles.org/nomenclature/stats.html)), ensures that a wide spectrum of peptides is presented to the immune system, essentially preventing pathogen escape at the population level. Despite allelic preferences, common themes guide peptide/MHC (pMHC) binding. Pooled aa sequencing of peptides eluted from many different individual class I allomorphs revealed residues overrepresented Kinase Inhibitor Library mouse at each position [4, 5], though notably, these allele-specific peptide-binding motifs are also influenced by peptide liberation, transport, and trimming (reviewed in [6]). Most peptide pools exhibit highly dominant specific aas (or chemically similar aas) at or near their N- and C-termini [4, 5]. These “anchor” residues

greatly influence peptide-binding Sorafenib chemical structure affinity. The more N-terminal anchor is typically located at peptide position 2 or 3 (denoted as p2 and p3) and is accommodated by the B-pocket of the peptide-binding cleft, though it can be located up to p5 (C-pocket, as is the case for the mouse H-2Db allomorph [4]). The deep F-pocket cradles the C-terminal anchor, typically an aliphatic or aromatic residue for mouse class

I allomorphs (some human allomorphs also favor basic C-terminal anchors). Predictably, detailed peptide mapping [7] and high-throughput mass spectrometry [8] identify numerous high-affinity peptides that break these simple rules, increasing both the size of the immunopeptidome and the difficulty of in silico peptide-binding prediction. Class I molecules present tens of thousands of different self-peptides among approximately 105 pMHC complexes on the surface Tryptophan synthase of each cell [9], consistent with their role in tumor immunosurveillance. How does the cell supply this diverse array of pMHCs? Most MHC class I peptides arise from rapidly degraded polypeptides, ensuring representation among the translatome independently of protein stability and minimizing the time to detect viral translation [10]. To enhance immunosurveillance of tumor-associated Ags (TAAs), ribosome subpopulation sampling [11, 12] likely enables surveillance of low abundance bona fide and defective mRNAs [13, 14]. TAA–peptide abundance is critical, since many TAAs derive from nonmutated genes and are thus recognized by low-affinity T cells that escape self-tolerance [15]. The affinity of peptides for MHC governs the stability of complexes and hence levels of cell surface expression [16].