Molecular mimicry mediated by MHC class Ib molecules after infection with gram-negative pathogens.

The development of many autoimmune diseases has been etiologically linked to exposure to infectious agents. For example, a subset of patients with a history of Salmonella infection develop reactive arthritis. The persistence of bacterial antigen in arthritic tissue and the isolation of Salmonella or Yersinia reactive CD8+ T cells from the joints of patients with reactive arthritis support the etiological link between Gram-negative bacterial infection and autoimmune disease. Models proposed to account for the link between infection and autoimmunity include inflammation-induced presentation of cryptic self-epitopes, antigen persistence and molecular mimicry. Several studies support molecular mimicry as a mechanism for the involvement of class II epitopes in infectious disease-induced self-reactivity. Here, we have identified an immunodominant epitope derived from the S. typhimurium GroEL molecule. This epitope is presented by the mouse H2-T23-encoded class Ib molecule Qa-1 and was recognized by CD8+ cytotoxic T lymphocytes induced after natural infection. S. typhimurium-stimulated cytotoxic T lymphocytes recognizing the GroEL epitope cross-reacted with a peptide derived from mouse heat shock protein 60 and recognized stressed macrophages. Our results indicate involvement of MHC class Ib molecules in infection-induced autoimmune recognition and indicate a mechanism for the etiological link between Gram-negative bacterial infection and autoimmunity.

Glycosylphosphatidylinositol anchors of Plasmodium falciparum: molecular characterization and naturally elicited antibody response that may provide immunity to malaria pathogenesis.

Induction of proinflammatory cytokine responses by glycosylphosphatidylinositols (GPIs) of intraerythrocytic Plasmodium falciparum is believed to contribute to malaria pathogenesis. In this study, we purified the GPIs of P. falciparum to homogeneity and determined their structures by biochemical degradations and mass spectrometry. The parasite GPIs differ from those of the host in that they contain palmitic (major) and myristic (minor) acids at C-2 of inositol, predominantly C18:0 and C18:1 at sn-1 and sn-2, respectively, and do not contain additional phosphoethanolamine substitution in their core glycan structures. The purified parasite GPIs can induce tumor necrosis factor alpha release from macrophages. We also report a new finding that adults who have resistance to clinical malaria contain high levels of persistent anti-GPI antibodies, whereas susceptible children lack or have low levels of short-lived antibody response. Individuals who were not exposed to the malaria parasite completely lack anti-GPI antibodies. Absence of a persistent anti-GPI antibody response correlated with malaria-specific anemia and fever, suggesting that anti-GPI antibodies provide protection against clinical malaria. The antibodies are mainly directed against the acylated phosphoinositol portion of GPIs. These results are likely to be valuable in studies aimed at the evaluation of chemically defined structures for toxicity versus immunogenicity with implications for the development of GPI-based therapies or vaccines.

Natural ligand of mouse CD1d1: cellular glycosylphosphatidylinositol.

Mouse CD1d1, a member of the CD1 family of evolutionarily conserved major histocompatibility antigen-like molecules, controls the differentiation and function of a T lymphocyte subset, NK1+ natural T cells, proposed to regulate immune responses. The CD1d1 crystal structure revealed a large hydrophobic binding site occupied by a ligand of unknown chemical nature. Mass spectrometry and metabolic radiolabeling were used to identify cellular glycosylphosphatidylinositol as a major natural ligand of CD1d1. CD1d1 bound glycosylphosphatidylinositol through its phosphatidylinositol aspect with high affinity. Glycosylphosphatidylinositol or another glycolipid could be a candidate natural ligand for CD1d1-restricted T cells.

A strategy for rapid and efficient DNA sequencing by mass spectrometry.

Two methods of solid-phase Sanger DNA sequencing followed by detection with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry are demonstrated. In one method, sequencing ladders generated on an immobilized synthetic template were resolved up to the 63-mer including the primer. Detection sensitivity and resolution were sufficient for sequence analysis in the given range. This approach is particularly suitable for comparative (diagnostic) DNA sequencing. A second method that has the potential for high throughput de novo DNA sequencing is also presented; it uses immobilized duplex probes with five-base single-stranded overhangs to capture an unknown DNA template serving as primers for Sanger DNA sequencing. The power of mass spectrometry is demonstrated not only by its very high speed, but also by its ability to identify sequences that are not readable using gel electrophoresis.

A novel a-factor-related peptide of Saccharomyces cerevisiae that exits the cell by a Ste6p-independent mechanism.

Many secreted signaling molecules are synthesized as precursors that undergo multiple maturation steps to generate their mature forms. The Saccharomyces cerevisiae mating pheromone a-factor is a C-terminally isoprenylated and carboxylmethylated dodecapeptide that is initially synthesized as a larger precursor containing 36 or 38 amino acids. We have previously shown that the maturation of a-factor occurs by an ordered biogenesis pathway involving 1) three C-terminal modification steps, 2) two N-terminal proteolytic processing events, and 3) a nonclassical export mechanism mediated by the ATP-binding-cassette (ABC) transporter Ste6p. In the present study, we demonstrate that an unexpected and abundant a-factor-related peptide (AFRP) exists in the culture fluid of MATa cells and that its biogenesis is integrally related to that of mature a-factor itself. We show by purification followed by mass spectrometry that AFRP corresponds to the C-terminal 7 amino acids (VFWDPAC) of mature a-factor (YIIKGVFWDPAC), including both the farnesyl- and carboxylmethylcysteine modifications. The formation and export of AFRP displays three striking features. First, we show that AFRP is produced intracellularly and that mutants (ste24 and axl1) that cannot produce mature a-factor due to an N-terminal processing defect are nevertheless normal for AFRP production. Thus, AFRP is not derived from mature a-factor but, instead, from the P1 form of the a-factor precursor. Second, fusion constructs with foreign amino acids substituted for authentic a-factor residues still yield AFRP-sized molecules; however, the composition of these corresponds to the altered residues instead of to AFRP residues. Thus, AFRP may be generated by a sequence-dependent but length-specific proteolytic activity. Third, a-factor and AFRP use distinct cellular machinery for their secretion. Whereas a-factor export is Ste6p-dependent, AFRP is secreted normally even in a ste6 deletion mutant. Thus, AFRP may exit the cell by another ATP-binding-cassette transporter, a different type of transporter altogether, or possibly by diffusion. Taken together, these studies indicate that the biogenesis of AFRP involves novel mechanisms and machinery, distinct from those used to generate mature a-factor. Because AFRP neither stimulates nor inhibits mating or a-factor halo activity, its function remains an intriguing question.

DNA sequence analysis by hybridization with oligonucleotide microchips: MALDI mass spectrometry identification of 5mers contiguously stacked to microchip oligonucleotides.

Matrix-assisted laser desorption ionization mass spectrometry (MALDI MS) has been applied to increase the informational output from DNA sequence analysis. It has been used to analyze DNA by hybridization with microarrays of gel-immobilized oligonucleotides extended with stacked 5mers. In model experiments, a 28 nt long DNA fragment was hybridized with 10 immobilized, overlapping 8mers. Then, in a second round of hybridization DNA-8mer duplexes were hybridized with a mixture of 10 5mers. The stability of the 5mer complex with DNA was increased to raise the melting temperature of the duplex by 10-15 degrees C as a result of stacking interaction with 8mers. Contiguous 13 bp duplexes containing an internal break were formed. MALDI MS identified one or, in some cases, two 5mers contiguously stacked to each DNA-8mer duplex formed on the microchip. Incorporating a mass label into 5mers optimized MALDI MS monitoring. This procedure enabled us to reconstitute the sequence of a model DNA fragment and identify polymorphic nucleotides. The application of MALDI MS identification of contiguously stacked 5mers to increase the length of DNA for sequence analysis is discussed.

Molecular pharmacology of hepsulfam, NSC 3296801: identification of alkylated nucleosides, alkylation site, and site of DNA cross-linking.

We have determined that hepsulfam, in common with its structural homologue busulfan, alkylates both free guanosine and GMP in DNA at the 7 nitrogen. Mass spectral analysis of the products of the reaction of hepsulfam with guanosine has identified the mono- and bis-alkylated guanosine adducts. UV spectrophotometry and mass spectrometry were used to confirm that alkylation occurred at the 7 nitrogen by following the formation of the formamidopyrimidyl form of the hepsulfam-guanosine adduct at high pH. We have also isolated and identified 1-guanyl,7-hydroxyheptane, 1-guanyl,7-sulfamylheptane, and 1,7-bis(guanyl)heptane from in vitro reaction mixtures of hepsulfam and calf thymus DNA. We have isolated bis-(7-formamidopyrimidyldeoxyguanosinyl)-heptane from an enzymatic digest of DNA treated with hepsulfam. Finally, we have found that hepsulfam forms interstrand cross-links at 5'-GXC-3' sites in model oligonucleotides.

Mass spectrometric analysis of proteins.

The past year has seen greatly increased acceptance and application of the analytical capabilities of mass spectrometry by the biochemical community. The technique has been used to provide accurate mass determinations of non-covalently bound protein complexes, rapid mapping of molecular weights of altered peptides in protease digests, sequencing by collisional activation in tandem mass spectrometry, characterization of glycosylation and other modifications, and quantitation of peptides used in clinical diagnostics.

Isozyme-specific enzyme inhibitors. 11. L-homocysteine-ATP S-C5' covalent adducts as inhibitors of rat methionine adenosyltransferases.

The title compounds (14a,b) were 5' epimers of a derivative of a phosphonate isostere of ATP in which the CH2OP alpha system of ATP was replaced by CH(R)CH2P alpha [R = L-S(CH2)2CH(NH2)CO2H]. They resisted synthesis via attempted S-alkylation of the corresponding epimeric 5'-mercapto derivatives. A practicable route to 14a,b commenced with Michael condensation of L-homocysteine with the diphenyl ester of the 5',6'-vinyl phosphonate analogue of 2',3'-O-isopropylideneadenosine 5'-phosphate. The resulting epimeric 5' thioethers were separated by reverse-phase HPLC. The two phenyl groups were replaced by benzyl groups, after which the alpha-amino acid residue was protected as an N-Boc methyl ester. Both benzyl groups were removed by hydrogenolysis, and the resulting phosphonic acid was converted into its pyrophosphoryl derivative. Blocking groups were then removed under conditions that furnished 14a and 14b without racemization of their L-amino acid residues. Also synthesized were the P beta-NH-P gamma imido analogue (15a) of 14a and the sulfoxide derivative (16a) of 14a. The structures of 14a and 16a were verified by FAB mass spectra, which revealed the protonated molecular ions of their sodium salts. All adducts appeared to function as dual substrate site inhibitors (competitive to ATP and to methionine) of the rat normal tissue (MAT-2) form of methionine adenosyltransferase (MAT); 14a and 15a [KM(ATP)/Ki = 4 and 9, respectively] were the most effective. Adduct 15a was the most effective inhibitor [KM(ATP)/Ki = 13] of the MAT-T form from rat hepatoma tissue; the kinetic data indicated dual-site inhibition by 15a with apparently complete coverage of the ATP site and incomplete coverage of the methionine site. The inhibition properties of the adducts indicated little preference in the order in which the two MAT forms bound ATP and methionine.

Mass-correlated pulsed extraction: theoretical analysis and implementation with a linear matrix-assisted laser desorption/ionization time of flight mass spectrometer.

The pulsed extraction (PE) of ions produced by matrix-assisted laser desorption/ionization in time-of-flight mass spectrometers greatly improves mass resolution but, unfortunately, this method is mass dependent. Here we report an approach to expand the capabilities of the PE method so as to provide uniform focusing conditions over a wide mass range. Along with an extraction pulse, an additional pulse is applied to correct the mass dependency of the standard PE method. We describe the algorithm for derivation of this correction pulse waveform, where the first-order focusing conditions are valid all along the mass region of interest. Experimental verification of this method for correction of ion velocities demonstrated better mass resolution than standard PE over a wide mass range.

Ideal velocity focusing in a reflectron time-of-flight mass spectrometer.

A single-stage ion mirror in a time-of-flight (TOF) mass spectrometer (MS) can perform first order velocity focusing of ions initially located at a start focal plane while second order velocity focusing can be achieved using a double-stage reflectron. The situation is quite different when an ion source extraction field is taken into account. In this case which is common in any practical matrix-assisted laser desorption/ionization (MALDI) TOF-MS a single-stage reflectron, for example, cannot perform velocity focusing at all. In this paper an exact, analytic solution for an electric field inside a one-dimensional reflectron has been found to achieve universal temporal focusing of ions having an initial velocity distribution. The general solution is valid for arbitrary electric field distributions in the upstream (from the ion source to the reflectron) and downstream (from the reflectron to an ion detector) regions and in a decelerating part of the reflectron of a reflectron TOF mass spectrometer. The results obtained are especially useful for designing MALDI reflectron TOF mass spectrometers in which the initial velocity distribution of MALDI ions is the major limiting factor for achieving high mass resolution. Using analytical expressions obtained for an arbitrary case, convenient working formulas are derived for the case of a reflectron TOF-MS with a dual-stage extraction ion source. The special case of a MALDI reflectron TOF-MS with an ion source having a low acceleration voltage (or large extraction region) is considered. The formulas derived correct the effect of the acceleration regions in a MALDI ion source and after the reflectron before detecting ions.

Oligopeptide fragmentation viewed as constant neutral loss.

Spectra were recorded of all fragment ions formed by elimination of 28-u neutral fragments in fast atom bombardment spectra of peptides in the mass range 1000-1800 u, This approach can provide less complex spectra than either conventionally scanned spectra or product ion scans from collisionaIly activated four-sector experiments, and spectra that contain information that is both overlapping and complementary to those from the other techniques. Constant neutral loss spectra may provide a reading frame for distinguishing sequence ion series in tandem or single analyzer spectra.

Endothermic ion molecule reactions.

Endothermic ion-molecule reactions in a tandem mass spectrometer have been used for a number of years for determining thermodynamic quantities, such as heats of formation and proton affinities, for gaseous ions. Recently, the reactive, endothermic collision has been exploited as an analytical technique for the structural analysis of peptides and other biomolecules. The technique is based upon the endothermic transfer of protons associated with amide bonds to ammonia. This reaction proceeds via a long-lived collision complex. When additional beam energy is supplied, other dissociation channels are opened up, leading to the production of sequence ions for the mass-selected, protonated analyte that are normally observed in high energy collision-induced dissociation spectra. The advantage, however, is that such spectra can be produced at very low beam energies. In this article, the rationale for developing this scheme, and its roots in previous ion-molecule studies, are explored.

Matrix-assisted laser desorption/ionization tandem reflectron time-of-flight mass spectrometry of fullerenes.

Atandem reflectron time-of-flight mass spectrometer developed in our laboratory provides a unique opportunity to investigate the collision-induced dissociation of fullerene ions formed by matrix-assisted laser desorption/ionization (MALDI). Specifically, this opportunity arises from the ability to utilize high energy collisional activation (normally available only on tandem sector instruments by using continuous ionization techniques) for ions formed by pulsed laser desorption, whereas most MALDI time-of-flight instruments record product ion mass spectra of ions formed by metastable or postsource decay. In this study we investigate the products of mass-selected and collisionally activated C 60 (+) and C 70 (+) ions by using different target gases over a range of target gas pressures. In general, heavier target gases produce more extensive fragmentation and improve the mass resolution of lower mass ionic products because a greater portion of these ions are formed by single collisions. Additionally, the tandem time-of-flight instrument utilizes a nonlinear (curved-field) reflectron in the second mass analyzer that enables high energy collision-induced dissociation spectra to be recorded without scanning or stepping the reflectron voltage.

Miniaturized EI/Q/oa TOF mass spectrometer.

A miniaturized orthogonal time-of-flight mass spectrometer with an electron impact ionization ion source and a rf quadrupole ion guide has been developed. A mass resolving power of m/deltam = 5500 has been obtained in a 0.4 m instrument. The addition of helium at pressures of about 4.0 mtorr into the ion source showed collisional focusing taking place in the rf quadrupole. An automated gas chromatograph designed for air monitoring applications has been coupled to the time-of-flight mass analyzer and tested for the detection of simulants of chemical-warfare agents.

Peptide sequence information derived by pronase digestion and ammonium sulfate in-source decay matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

We present the use of Pronase digestion and in-source decay in the presence of ammonium sulfate as complementary techniques to confirm the amino acid sequence of a peptide. Pronase, a commercial preparation from Streptomyces griseus, is a combination of proteolytic enzymes. It produces carboxypeptidase and aminopeptidase ladders using a single Pronase digestion and represents an inexpensive, nonspecific, and fast supplement to traditional sequencing enzymes. However, N-terminal peptidase activity appears dependent on the terminal amino acid residue. We also introduce the use of saturated ammonium sulfate as an "on-slide" sample additive to promote in-source fragmentation of peptides. Use of saturated ammonium sulfate resulted in a simple way to increase peptide backbone fragmentation and essentially produced either a cn or yn ion series. Together these techniques provide useful supplements to existing methods for peptide sequence information.

Injection of externally generated ions into an increasing trapping field of a quadrupole ion trap mass spectrometer.

Trapping ions injected into a quadrupole ion trap (QIT) by increasing the trapping r.f. voltage on a ring electrode is an effective and widely recognized method of interfacing an ion trap with pulsed ion sources such as matrix-assisted laser desorption/ionization (MALDI). In this paper, the problem of mass discrimination during the injection and trapping of ions by the increasing r.f. field was studied both experimentally and by numerical simulation using SIMION software. For a MALDI/QIT interface design with a remote external ion source described here, experiments with polyethylene glycol (PEG 1000 and PEG 1500) showed little mass discrimination for trapping ions in a wide mass range (500-2000 Dn) for a broad range of experimental conditions, which include kinetic energies of 5-40 eV for the injected ions and an r.f. voltage of 400-4000 Vo-p amplitude ramped at a rate of 30-140 Vo-p mus-1. In the numerical simulation, complex and sharp dependences of the trapping efficiency on the phase of the r.f. voltage and initial kinetic energy of ions were observed. However, after averaging over the r.f. phase and over a reasonable range of kinetic energy, the simulation resulted in relatively constant and high values for the trapping efficiency (normally 0.2-0.3) for any mass and kinetic energy considered, which are consistent with the weak sensitivity to injection parameters observed in the experiment. A simple model for the qualitative description of ion injection and trapping is suggested that relies on phase interaction of injected ions with the r.f. field rather than on collisions with the buffer gas molecules to decrease the ion kinetic energy.

A quadrupole ion trap/time-of-flight mass spectrometer with a parabolic reflectron.

A matrix-assisted laser desorption/ionization-quadrupole ion trap/reflectron time-of-flight (MALDI-QIT/reTOF) mass spectrometer design and its operation in both normal and tandem mass spectrometric modes are described. A parabolic reflectron was found to be capable of providing mass resolution of 5000 for an initial ion energy distribution ranging over a 50% energy interval of the entire reflectron energy range. The sensitivity, ion isolation and fragmentation efficiency in the MALDI-QIT/reTOF instrument were close to those observed in the MALDI/QIT mass spectrometer. The mass resolution was shown to depend on the extraction field potentials, the r.f. trapping voltage amplitude and the phase of shutting down the r.f. voltage before extraction. At values of qs < 0.3-0.4 the mass resolution does not depend on the ion mass, is in a range of 1000-1400 and is governed by the extraction voltages and the ion temperature before extraction, the latter shown to be in the range 1180-1690 K. The variation of the mass resolution for ions at values of qs > 0.4 is irregular but normally it is lower than that for ions having lower qs values. Mass spectral line positions shifted when the trapping voltage before extraction was varied. The line shifts were larger for lower mass ions and were comparable to the line widths in the case of very low masses.

Miniaturized time-of-flight mass spectrometer for peptide and oligonucleotide analysis.

A matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometer was developed which uses a novel reflectron composed of a grounded cylinder and an adjustable endcap electrode to provide high-order kinetic energy focusing for a miniaturized mass analyzer. The nearly quadratic potential form of the reflecting field focuses ions desorbed from a source of very small dimensions formed by placing the sample probe within the centered hole of the coaxial dual channel plate detector. At the same time, the depth of the reflectron can be adjusted to accommodate a short drift length between the source/detector and the reflectron. For larger drift lengths, in particular to allow the addition of an XY stage for the analysis of sample arrays, endcap reflectron focusing can be combined with time-delayed ion extraction to achieve good mass resolution. The instrument has been used for the analysis of peptides digested with trypsin or carboxypeptidase, and also small DNA oligomers.

Improving the sensitivity of the end-cap reflectron time-of-flight mass spectrometer.

A miniaturized time-of-flight (TOF) mass spectrometer utilizes an end-cap reflectron to achieve high kinetic energy focusing and improved mass resolution. However, the coaxial geometry gives rise to considerable losses in sensitivity resulting from reflected ion trajectories close to the center. These trajectories were modeled, using initial ion velocity distributions in the radial direction up to 300 m s(-1), and the portion of the active area of the detector that is utilized was evaluated experimentally using a variable diameter iris diaphragm. The sensitivity was improved by modification of the reflectron by tilting the end-cap electrode 4 degrees and redirecting the ions to a portion of the detector active area. Sensitivity was then measured as 3 fmol of the peptide substance P.