Antigen-presenting molecules, encoded by the major histocompatibility complex (MHC) and CD1 family, bind peptide- and lipid-based antigens, respectively, for recognition by T cells. Mucosal-associated invariant T (MAIT) cells are an abundant population of innate-like T cells in humans that are activated by an antigen(s) bound to the MHC class I-like molecule MR1. Although the identity of MR1-restricted antigen(s) is unknown, it is present in numerous bacteria and yeast. Here we show that the structure and chemistry within the antigen-binding cleft of MR1 is distinct from the MHC and CD1 families. MR1 is ideally suited to bind ligands originating from vitamin metabolites. The structure of MR1 in complex with 6-formyl pterin, a folic acid (vitamin B9) metabolite, shows the pterin ring sequestered within MR1. Furthermore, we characterize related MR1-restricted vitamin derivatives, originating from the bacterial riboflavin (vitamin B2) biosynthetic pathway, which specifically and potently activate MAIT cells. Accordingly, we show that metabolites of vitamin B represent a class of antigen that are presented by MR1 for MAIT-cell immunosurveillance. As many vitamin biosynthetic pathways are unique to bacteria and yeast, our data suggest that MAIT cells use these metabolites to detect microbial infection.

A database of 5500 unique peptide tandem mass spectra acquired in an ion trap mass spectrometer was assembled for peptides derived from proteins digested with trypsin. Peptides were identified initially from their tandem mass spectra by the SEQUEST algorithm and subsequently validated manually. Two different statistical methods were used to identify sequence-dependent fragmentation patterns that could be used to improve fragmentation models incorporated into current peptide sequencing and database search algorithms. The currently accepted "mobile proton" model was expanded to derive a new classification scheme for peptide mass spectra, the "relative proton mobility" scale, which considers peptide ion charge state and amino acid composition to categorize peptide mass spectra into peptide ions containing "nonmobile", "partially mobile", or "mobile" protons. Quantitation of amide bond fragmentation, both N- and C-terminal to any given amino acid, as well as the positional effect of an amino acid in a peptide and peptide length on such fragmentation, has been determined. Peptide bond cleavage propensities, both positive (i.e., enhanced) and negative (i.e., suppressed), were determined and ranked in order of their cleavage preferences as primary, secondary, or tertiary cleavage effects. For example, primary positive cleavage effects were observed for Xaa-Pro and Asp-Xaa bond cleavage for mobile and nonmobile peptide ion categories, respectively. We also report specific pairwise interactions (e.g., Asn-Gly) that result in enhanced amide bond cleavages analogous to those observed in solution-phase chemistry. Peptides classified as nonmobile gave low or insignificant scores, below reported MS/MS score thresholds (cutoff filters), indicating that incorporation of the relative proton mobility scale classification would lead to improvements in current MS/MS scoring functions.

Two gas-phase catalytic cycles for the two-electron oxidation of primary and secondary alcohols were detected by multistage mass spectrometry experiments. A binuclear dimolybdate center [Mo(2)O(6)(OCHR(2))](-) acts as the catalyst in both these cycles. The first cycle proceeds via three steps: (1) reaction of [Mo(2)O(6)(OH)](-) with alcohol R(2)HCOH and elimination of water to form [Mo(2)O(6)(OCHR(2))](-); (2) oxidation of the alkoxo ligand and its elimination as aldehyde or ketone in the rate-determining step; and (3) regeneration of the catalyst via oxidation by nitromethane. Step 2 does not occur at room temperature and requires the use of collisional activation to proceed. The second cycle is similar but differs in the order of reaction with alcohol and nitromethane. The nature of each of these reactions was probed by kinetic measurements and by variation of the substrate alcohols (structure and isotope labeling). The role of the binuclear molybdenum center was assessed by examination of the relative reactivities of the mononuclear [MO(3)(OH)](-) and binuclear [M(2)O(6)(OH)](-) ions (M = Cr, Mo, W). The molybdenum and tungsten binuclear centers [M(2)O(6)(OH)](-) (M = Mo, W) were reactive toward alcohol but the chromium center [Cr(2)O(6)(OH)](-) was not. This is consistent with the expected order of basicity of the hydroxo ligand in these species. The chromium and molybdenum centers [M(2)O(6)(OCHR(2))](-) (M = Cr, Mo) oxidized the alkoxo ligand to aldehyde, while the tungsten center [W(2)O(6)(OCHR(2))](-) did not, instead preferring the non-redox elimination of alkene. This is consistent with the expected order of oxidizing power of the anions. Each of the mononuclear anions [MO(3)(OH)](-) (M = Cr, Mo, W) was inert to reaction with methanol, highlighting the importance of the second MoO(3) unit in these catalytic cycles. Only the dimolybdate center has the mix of properties that allow it to participate in each of the three steps of the two catalytic cycles. The three reactions of these cycles are equivalent to the three essential steps proposed to occur in the industrial oxidation of gaseous methanol to formaldehyde at 300-400 degrees C over solid-state catalysts based upon molybdenum(VI)-trioxide. The new gas-phase catalytic data is compared with those for the heterogeneous process.

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The collision-induced dissociation (CID) of a series of gas-phase complexes [M(III)(salen)(P)](+) [where M = Cr, Mn, Fe, and Co; P = hexapeptides YGGFLR, WGGFLR, and GGGFLR; and salen = N,N'-ethylenebis(salicylideneaminato)] has been examined with respect to the ability of the complexes to form the corresponding cationic peptide radical ions, P(+)(*), by homolytic cleavage of the metal peptide bond. This is the first example of the use of gas-phase ternary metal peptide complexes to produce the corresponding cationic peptide radical for a metal other than copper(II). The fragmentation reactions competing with radical formation are highly dependent on the metal ion used. In addition, examination of modified complexes in which the periphery of the salen was substituted allowed evaluation of electronic effects on the CID process, presumably without significant change in the geometry surrounding the metal. This substitution demonstrates that the ligand can be used to tune the dissociation chemistry to favor radical formation and suppress unwanted further fragmentation of the peptide radical that is typically observed immediately following its dissociation from the complex.

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This account describes the experimental tools (multi-stage mass spectrometric experiments, isotopic and structural labelling, kinetics and theoretical modelling) and physical organic concepts (influence of charge, the intermediacy of ion-molecule complexes, etc.) that can be used to unravel the mechanisms of gas-phase unimolecular and bimolecular ionic reactions of peptides. The role that nucleophile-electrophile interactions play in charge-directed reactions is highlighted for both unimolecular fragmentations (examples are illustrated for protonated sulfur-containing amino acids and peptides) and bimolecular ion-molecule reactions which cleave peptide bonds.