The specificity of peptides bound to human histocompatibility leukocyte antigen (HLA)-B27 influences the prevalence of arthritis in HLA-B27 transgenic rats.

Human histocompatibility leukocyte antigen B27 is highly associated with the rheumatic diseases termed spondyloarthropathies, but the mechanism is not known. B27 transgenic rats develop a spontaneous disease resembling the human spondyloarthropathies that includes arthritis and colitis. To investigate whether this disease requires the binding of specific peptides to B27, we made a minigene construct in which a peptide from influenza nucleoprotein, NP383-391 (SRYWAIRTR), which binds B27 with high affinity, is targeted directly to the ER by the signal peptide of the adenovirus E3/gp19 protein. Rats transgenic for this minigene, NP1, were made and bred with B27 rats. The production of the NP383-391 peptide in B27(+)NP1(+) rats was confirmed immunologically and by mass spectrometry. The NP1 product displaced approximately 90% of the 3H-Arg-labeled endogenous peptide fraction in B27(+)NP1(+) spleen cells. Male B27(+)NP1(+) rats had a significantly reduced prevalence of arthritis, compared with B27(+)NP- males or B27(+) males with a control construct, NP2, whereas colitis was not significantly affected by the NP1 transgene. These findings support the hypothesis that B27-related arthritis requires binding of a specific peptide or set of peptides to B27, and they demonstrate a method for efficient transgenic targeting of peptides to the ER.

Targeting of HIF-alpha to the von Hippel-Lindau ubiquitylation complex by O2-regulated prolyl hydroxylation.

Hypoxia-inducible factor (HIF) is a transcriptional complex that plays a central role in the regulation of gene expression by oxygen. In oxygenated and iron replete cells, HIF-alpha subunits are rapidly destroyed by a mechanism that involves ubiquitylation by the von Hippel-Lindau tumor suppressor (pVHL) E3 ligase complex. This process is suppressed by hypoxia and iron chelation, allowing transcriptional activation. Here we show that the interaction between human pVHL and a specific domain of the HIF-1alpha subunit is regulated through hydroxylation of a proline residue (HIF-1alpha P564) by an enzyme we have termed HIF-alpha prolyl-hydroxylase (HIF-PH). An absolute requirement for dioxygen as a cosubstrate and iron as cofactor suggests that HIF-PH functions directly as a cellular oxygen sensor.

A proof-of-principle gel-free proteomics strategy for the identification of predictive biomarkers for the onset of pre-eclampsia.

OBJECTIVE: Progress in the prevention and treatment of women at risk of pre-eclampsia (PE) still remains hindered by the lack of clinical screening tools that can accurately predict which mothers are at risk. The identification and validation of predictive biomarkers is therefore seen as a critical milestone towards improved healthcare provision and the clinical testing of new therapeutic strategies. Gel-free proteomic technologies offer the capability of analysing hundreds of plasma proteins simultaneously, but as yet these methods have not been applied to pregnancy complications. To assess the feasibility of such an approach to plasma biomarker research in pregnancy we have applied the technique to samples from women with PE to gestation-matched controls. SAMPLE: Pooled plasma samples taken at time of disease from women with PE (n = 23) and gestation-matched controls (n = 23). METHODS: Proteomics strategy for relative quantification of proteins using mass spectrometry. RESULTS: We identified several differences, including elevated levels of endoglin, PAPP-A and PSG1 in PE plasma. Increased levels of endoglin were validated using immunoassay analysis of individual plasma samples. CONCLUSIONS: Although at a relatively early stage, this mass spectrometry-based approach shows promise as a tool to identify global protein changes in plasma. The application of these methods to pre-disease samples is the next step in the identification of clinically useful biomarkers.

Measurement of diethylstilbestrol in plasma from patients with cancer of the prostate.

A specific radioimmunoassay has been developed for diethylstilbestrol (DES), using an antiserum raised against DES monocarboxymethyl ether and a tritium-labeled radioligand. Prior to radioimmunoassay, a fraction enriched in DES is obtained from a dichloroethane extract of plasma using Sephadex LH-20. The specificity of the assay is good, and the sensitivity (130 pg/ml) is adequate for accurate determination of DES in plasma from prostatic cancer patients treated with the drug. The precision is satisfactory, with an interassay coefficient of variation of approximately 10% at concentrations of approximately 1 ng/ml, and the blank values are negligible. Excellent agreement (r = 0.96) is observed between data obtained by radioimmunoassay and those obtained by a procedure using gas chromatography-high-resolution mass spectrometry. DES concentrations in the plasma of six treated (1 mg DES three times daily) patients were in the range 0.15 to 6.0 ng/ml. Increases in plasma concentration were observed within 2 hr of administration, with secondary rises occurring 5 to 6 hr later. Plasma testosterone concentrations were low in four of the patients; in a single subject, relatively high levels of testosterone were further elevated following administration of luteinizing hormone-releasing hormone.

Proapoptotic Bid binds to monolysocardiolipin, a new molecular connection between mitochondrial membranes and cell death.

Recent evidence indicates that the mitochondrial lipid cardiolipin may be instrumental in the proapoptotic action of Bcl-2 family proteins on mitochondrial membranes, leading to the release of apoptogenic factors. However, contrasting evidence indicates that progressive loss of cardiolipin occurs during apoptosis. Here we show that Bid, a crucial proapoptotic protein that integrates the action of other Bcl-2 family members, exhibits discrete specificity for metabolites of cardiolipin, especially monolysocardiolipin (MCL). MCL, normally present in the remodelling of mitochondrial lipids, progressively increases in mitochondria during Fas-mediated apoptosis as a by-product of cardiolipin degradation, and also enhances Bid binding to membranes. MCL may thus play a crucial role in connecting lipid metabolism, relocation of Bid to mitochondria and integrated action of Bcl-2 proteins on mitochondrial membranes. We propose that Bid interaction with MCL 'primes' the mitochondrial outer membrane via segregation of lipid domains, facilitating membrane discontinuity and leakage of apoptogenic factors.

Advances in mass spectrometry for proteome analysis.

The most demanding problems in proteomics continue to challenge modern mass spectrometry. Recent developments in instrument design have led to lower limits of detection, while new ion activation techniques and improved understanding of gas-phase ion chemistry have enhanced the capabilities of tandem mass spectrometry for peptide and protein structure elucidation. Future developments must address the., understanding of protein-protein interactions and the characterisation of the dynamic proteome.

Effect of polymorphisms on ligand binding by mouse major urinary proteins.

Mouse urine contains an abundance of major urinary proteins, lipocalins, whose roles include slow release of semiochemicals. These proteins are highly polymorphic, with small sequence differences between individual members. In this study, we purified to homogeneity four of these proteins from two strains of inbred mice and characterized them by mass spectrometry. This analysis has led to the discovery of another variant in this group of proteins. Three of the polymorphic variants that map to the surface have no effect on the binding of a fluorescent probe in the binding cavity, but the fourth, characterized by a Phe to Val substitution in the cavity, shows a substantially lower affinity and fluorescence yield for the probe. These results are interpreted in light of the known crystal structure of the protein and molecular modeling calculations, which rationalize the experimental findings. This work raises the possibility that the calyx-binding site can show specificity for different ligands, the implications of which on pheromone binding and chemical communication are discussed.

Physicochemical consequences of the perdeuteriation of glutathione S-transferase from S. japonicum.

Glutathione S:-transferase (GST) from Schistosoma japonicum has been prepared in both normal protiated (pGST) and fully deuteriated (dGST) form by recombinant DNA technology. Electrospray mass spectrometry showed that the level of deuteriation in dGST was 96% and was homogeneous across the sample. This result is attributed to the use of a deuterium-tolerant host Escherichia coli strain in the preparation of the protein. 10 heteroatom-bound deuteriums (in addition to the carbon-bound deuteriums) were resistant to exchange when dGST was incubated in protiated buffer. The physicochemical and biological properties of the two proteins were compared. dGST was relatively less stable to heat denaturation and to proteolytic cleavage than was pGST. The midpoint transition temperature for pGST was 54.9 degrees C, whereas that for dGST was 51.0 degrees C. Static light-scattering measurements revealed that the association behavior of dGST is also different from that of pGST. The perdeuteriated enzyme shows a tendency to associate into dimers of the fundamental dimer. This is in contrast with results that have been obtained for other perdeuteriated proteins in which perdeuteriation has been shown to promote dissociation of aggregates. dGST showed a similar K(m) to pGST; similar results had been obtained previously with bacterial alkaline phosphatase. However, whereas the alkaline phosphatase showed a reduced rate of catalysis on deuteriation, dGST exhibited a slightly higher rate of catalysis than pGST. It is clear that the bulk substitution of deuterium for protium has significant effects on the properties of proteins. Until many more examples have been studied, it will be difficult to predict these effects for any given protein. Nevertheless, deuteriation represents an intriguing method of preparing functional analogs of recombinant proteins.

Tissue androgen concentrations in golden hamsters with benign prostatic tumours.

Using gas chromatography-high resolution mass spectrometry with selected ion detection, the concentrations of testosterone, 5alpha-dihydrotestosterone, androsterone, 5alpha-androstane-3alpha,17beta-diol, 5alpha-androstane-3beta,17alpha-diol and 5alpha-androstane-3beta,17beta-diol were measured in the dorsal and ventral prostates of two strains of golden hamster (Mesocricetus auratus) at various ages from 60 to 250 days. The tissue concentrations from a control strain were compared with those of the BIO 87.2 strain of hamster, the latter developing benign hyperplasia of the prostate between 90 and 120 days of age. Marked increases in the concentration of total 5alpha-androstanediols in both prostatic lobes of the BIO 87.2 strain were detected, with the highest level of over 345 nmol/g protein being found at 200 days of age. In comparison, the control strain showed a less pronounced increase in concentration at 150 days. Increases in total 5alpha-androstanediols were mainly associated with increases in the concentration of 5alpha-androstane-3alpha,17beta-diol. Concentrations of testosterone in prostatic tissue were also found to increase in the BIO 87.2 animals with peak values being seen at 200 days. Increases in concentration of androsterone were observed by 150 days and these levels were maintained up to 250 days of age. Control animals showed no comparable increases in testosterone and androsterone during the time-course studied. Surprisingly, no significant variation in 5alpha-dihydrotestosterone concentration was detected in either strain from 60 to 250 days although levels were slightly but consistently higher in the BIO 87.2 strain. There were no significant fluctuations in any of the androgens assayed either before or during tumour development. The increases in 5alpha-androstane-3alpha,17beta-diol, testosterone and androsterone were detected only after tumours had become established.

Determination of tamoxifen and an hydroxylated metabolite in plasma from patients with advanced breast cancer using gas chromatography-mass spectrometry.

An assay has been established for the selective measurement of tamoxifen and its monohydroxy derivative, metabolite B, in human plasma. The assay was used to examine the concentrations of these compounds, relative to oestradiol-17 beta, in the plasma of patients undergoing tamoxifen therapy for advanced breast cancer. Oral administration of the drug (20 mg twice a day) raised the level of tamoxifen in plasma to approximately 200 ng/ml 20 days after the commencement of treatment. This level was 3000-fold higher than the corresponding concentration of oestradiol which remained within the range for post-menopausal women. Metabolite B was present in plasma at a much lower concentration than tamoxifen although in considerable excess over oestradiol. The overall results are discussed in relation to the possible mechanism of action of the drug.

Origin of the tailing signal on the low-energy side of the main beam in mass-analyzed ion kinetic energy spectra.

The tailing signal on the low-energy side of the precursor ion signal observed during fast atom bombardment (FAB) mass-analyzed ion kinetic energy spectrometric (MIKES) analyses is due largely to ions of higher m/z value than the chosen precursor. The majority of these ions are independent, unfragmented species that emerge from the ion source with less than the full amount of kinetic energy predicted by the source potential. The tailing precursor ion signal observed under helium collision-activated decomposition conditions is too short to account for the protracted MIKES tail (as judged from mass-to-charge ratio-deconvoluted MIKES analyses performed on a BEqQ hybrid instrument), and a tailing precursor signal is not observed under unimolecular decomposition conditions. Measurements of the mass-to-charge ratios of the ionic species comprising the MIKES tail demonstrated that ions higher in mass-to-charge ratio than the chosen precursor are present throughout the tail, with the mass-to-charge ratio increasing as kinetic energy decreases. These ions possess the same momentum as the chosen precursor, and thus were formed prior to the magnetic field. The existence of intact, source-formed [M + H](+) ions with reduced kinetic energy was demonstrated through several types of tandem mass spectrometric experiments. These [M + H](+) ions with reduced kinetic energy do not appear to have undergone collisional deceleration, because they do not possess increased internal energy (as judged by observation of their fragmentation patterns). The kinetic energy profiles of unfragmented FAB-desorbed ions were determined and found to exhibit a tailing character similar in appearance to that of the MIKES tail. The population of ions emerging from the source under FAB conditions thus incorporates the characteristics necessary to account for the MIKES tail, namely, the presence of ions of a mass-to-charge ratio higher than the chosen precursor (due to matrix and other background ions), which possess reduced kinetic energy such that their momentum is identical to that of the selected precursor. These ions may arise via desolvation and declustering processes in the acceleration region of the ion source, or via FAB or chemical ionization processes in regions removed from the FAB target.

Decompositions of cationized heterodimers of amino acids in relation to charge location in peptide ions.

The unimolecular decompositions of protonated heterodimers of native and derivatized amino acids to yield the protonated monomers were studied as a guide to charge location in peptide ions. Analyses using a hybrid instrument of BEqQ geometry demonstrated the advantages (with respect to mass resolution, sensitivityr reproducibility, and the elimination of extraneous signals) of the detection of product ions formed in the radiofrequency-only quadrupole region (q) rather than in the field-free region between Band E. Conversion of arginine to dimethylpyrimidylomithine (DMPO) reduced the proton affinity, as evidenced by the decomposition of the protonated arginine/DMPO heterodimer. Conversion of cysteine to pyridylethylcysteine enhanced the proton affinity. Application of these derivatization procedures to peptides resulted in changes in the observed fragmentations of the protonated precursors consistent with the predicted modifications in charge location. Unimolecular decomposition of the protonated dimer composed of glycine and N-acetylglycine yielded both protonated monomers with abundances differing by a factor of only 2; this suggests that in protonated peptides, the amide bonds are competitive with the N-terminal amino group as sites of protonation. It is clear that the propensities to proton' or metal-cation location at particular sites in peptides are influenced by both short- and long-range intraionic interactions. In peptides composed of amino acids of similar cation affinities, it may be postulated that the ion population is heterogeneous with respect to the site of charge, with consequent promotion of multiple low-energy fragmentation routes.

Dehydration of peptide [M + H](+) ions in the gas phase.

The loss of water from protonated peptides was studied using [(18)O]-labeling of the C-terminal carboxyl group. The structures (including the location of the isotopic label) of first-generation product ions were examined by sequential product ion scanning (MS(3) and MS(4)) using a hybrid sector/quadrupole mass spectrometer. Water loss may involve carboxylic acid groups, side-chain hydroxyls, or peptide backbone oxygens. Although one of these three pathways often predominates, more than one dehydration route can be operative for a single peptide structure. When peptide backbone oxygen is lost, the dehydration can occur at one or two primary sites along the backbone, with the location of the site(s) varying among peptides. When water loss involves the C-terminal carboxyl group, the resulting ion may undergo extensive intraionic oxygen isotope exchange. This evidence for complex intraionic interactions further emphasizes the significance of gas-phase conformation in determining the fragmentations of peptide ions.

Influence of cysteine to cysteic acid oxidation on the collision-activated decomposition of protonated peptides: Evidence for intraionic interactions.

Oxidation of cysteine residues to cysteic acids in C-terminal arginine-eontaining peptides (such as those derived by tryptic digestion of proteins) strongly promotes the formation of multiple members of the Y- series of fragment ions following low energy collision-activated decomposition (CAD) of the protonated peptides, Removal of the arginine residue abolishes the effect, which is also attenuated by conversion of the arginine to dimethylpyrim-idylornithine. The data indicate the importance of an intraionic interaction between the cysteic acid and arginine side-chains. Low energy CAD of peptides which include cysteic acid and histidine residues, also provides evidence for intraionic interactions. It is proposed that these findings are consistent with the general hypothesis that an increased heterogeneity (with respect to location of charge) of the protonated peptide precursor ion population is beneficial to the generation of a high yield of product ions via several charge-directed, low energy fragmentation pathways. Furthermore, these data emphasize the significance of gas-phase conformations of protonated peptides in determining fragmentation pathways.

Epitope mapping of monoclonal antibodies by mass spectrometry: identification of protein antigens in complex biological systems.

We describe the application of immunoaffinity extraction and mass spectrometry to the analysis of Ty1 Gag protein in lysates of Saccharomyces cerevisiae. A magnetic bead-conjugated monoclonal antibody was used to achieve selective extraction, the specificity of which was established by matrix-assisted laser desorption/ionization mass spectrometric (MS) analysis of an extract of the lysate of cells overexpressing the Ty1 Gag protein. MS analysis of similar extracts of lysates following tryptic hydrolysis confirmed selective extraction of the epitope-containing peptide fragment. Sufficient sensitivity was achieved to allow the application of this approach to the analysis of lysates of wild-type cells. Furthermore, the sequence of the epitope-containing peptide was confirmed by electrospray-tandem MS. To our knowledge, this constitutes the first report of the application of immunoaffinity extraction and tandem MS analysis to the characterization of an antigen recovered from a complex cellular system.

Determination of high-energy fragmentation of protonated peptides using a beqq hybrid mass spectrometer.

A hybrid tandem instrument of BEqQ geometry was used to determine high-energy decomposition of protonated peptides, such as side-chain fragmentation yielding d n and w n ions. The transmission through both E and Q of such product ions, formed in the second field-free region, permits improved mass resolution and confident mass assignment. The experimental technique may involve synchronous scanning of E and Q, or, for the purpose of identification of specific products, limited-range scanning of either E or Q with the other analyzer fixed. These techniques are not equivalent, with respect to product ion transmission, to the double focusing of product ions achieved with four-sector instruments but nevertheless represent a critical improvement over conventional mass-analyzed ion kinetic energy spectrometry analyses. Fragmentation of protonated peptides occurring in the second field-free region inside and outside the collision cell were distinguished by floating the collision cell above ground potential. Mass filtering using Q confirmed the mass assignments. The data indicate that product ions resulting from spontaneous decomposition are in some instances quantitatively more significant than those resulting from high-energy collisional activation. Furthermore, the differentiation of the products of low- and high-energy processes should facilitate spectral interpretation.

Role of the site of protonation in the low-energy decompositions of gas-phase peptide ions.

The dissociation of singly or multiply protonated peptide ions by using low-energy collisional activation (CA) is highly dependent on the sites of protonation. The presence of strongly basic amino acid residues in the peptide primary structure dictates the sites of protonation, which generates a precursor ion population that is largely homogeneous with respect to charge sites. Attempts to dissociate this type of precursor ion population by low-energy CA result in poor fragmentation via few pathways. The work described here represents a systematic investigation of the effects of charge heterogeneity in the precursor ion population of a series of model peptides in low-energy CA experiments. Incorporation of acidic residues in the peptide RLC*IFSC*FR (where C* indicates a cysteic acid residue), for example, balances the charge on the basic arginine residues, which enables the ionizing protons to reside on a number of less basic sites along the peptide backbone. This results in a precursor ion population that is heterogeneous with respect to charge site. Low-energy CA of these ions results in diverse and efficient fragmentation. Molecular modeling has been utilized to demonstrate that energetically preferred conformations incorporate an intraionic interaction between arginine and cysteic acid residues.

Multiple scan modes in the hybrid tandem mass spectrometric screening and characterization of the glutathione conjugate of 2-furamide.

The glutathione conjugate of 2-furamide has been screened for and structurally characterized by tandem mass spectrometry (MS(MS) by using a hybrid instrument of BEqQ design. Mass spectrometry experiments employed fast atom bombardment (FAB) ionization of a crude bile extract from a rat dosed with a 1:1 mixture of unlabeled and [ (13)C12-furamide. Initial screening for glutathione conjugates employed constant neutral loss scanning to detect the loss of 129 u, corresponding to the loss of the γ-glutamyl moiety of the conjugates. By direct comparison with control bile, [M + H] (+) ions of m/z 417 and 418 were readily identified as candidate ions corresponding to the glutathione conjugates of unlabeled and (13)C-labeled 2-furamide. Complementary screening information was generated by using a methylated bile extract, with constant neutral loss scanning to detect the loss of the methylated γ-glutamyl moiety (143 u). An alternative screening procedure employing parent ion scanning to detect the sodium adducts of methylated glutathione conjugates was also developed. Structural information was generated by frrst-generation product ion scanning of the protonated and sodium cationized forms of the candidate species, both native and derivatized. This provided a body of internally consistent evidence that the conjugate retains the pseudoaromatic furan ring system without ring hydroxylation. The utility of sequential mass spectrometry (MS(MS(MS) capability of the hybrid instrument in the analysis of complex biological mixtures was also demonstrated. Using the bile extract, first-generation product ions that formed in either the first or second field-free region of the double-focusing portion of the instrument were subsequently collisionally activated in the rf-only quadrupole followed by mass analysis of the second-generation product ions. Structural information so provided for the glutathione conjugate of 2-furamide further substantiated its retention of the pseudoaromatic furan ring system and facilitated plausible assignment of structures to ionic species generated through multiple decomposition events.

Noncovalent associations of glutathione S-transferase and ligands: a study using electrospray quadrupole/time-of-flight mass spectrometry.

Human glutathione S-transferase A1-1 was observed predominantly as dimeric ions (51 kDa) during electrospray mass spectrometric analysis from aqueous solution at pH 7.4, in keeping with the known dimeric structure in solution. When analyses were performed on solutions of the enzyme containing glutathione (GSH), noncovalent adducts of protein dimer and one or two ligand molecules were observed; each mass increment, which exceeded the mass of GSH alone, was provisionally interpreted to indicate concomitant association of two water molecules per bound GSH. Noncovalent adducts of ligand and protein dimer were similarly observed for oxidized glutathione and for two glutathione inhibitors, both incorporating substituted thiol structures. In these instances, the mass increments exactly matched the ligand masses, suggesting that the apparent concomitant binding of water was associated with the presence in the ligand of a free thiol group. Collisionally activated decomposition during tandem mass spectrometry analyses of noncovalent adducts incorporating protein dimer and ligands yielded initially the denuded dimer; at higher collision energies the monomer and a protein fragment were formed.

Tandem mass spectrometric characterization of a specific cysteic acid residue in oxidized human apoprotein B-100.

The oxidation of low density lipoprotein (LDL) in vivo may result in its unregulated uptake by macrophages, with the consequent accumulation of cholesterol that is characteristic of the development of atherosclerosis. This paper describes initial experiments to elucidate structural changes that occur in an in vitro model of LDL oxidation. LDL was isolated from human blood and oxidized in the presence of copper ion. Lipid was removed and the isolated apoprotein was subjected to tryptic hydrolysis. The hydrolysate was separated by high performance liquid chromatography and individual fractions were screened by amino acid analysis to detect cysteic acid residues. Appropriate fractions were analyzed by fast atom bombardment mass spectrometry and hybrid tandem mass spectrometry. In this manner a tryptic fragment was identified that corresponded to residues 4187-4195 (EELCTMFIR), in which the cysteine and methionine residues were oxidized to cysteic acid and methionine sulfoxide, respectively. Identical analysis of LDL not subjected to in vitro oxidation revealed no evidence for this oxidized peptide. Earlier work established a surface location for this cysteine residue (Cys24) on the LDL particle, which suggested that its modification may significantly affect the properties of LDL, such as the propensity to intermolecular interaction via disulfide bridges. The analytical protocol developed here (involving proteolysis, screening of peptide fragments, and tandem mass spectrometry analysis) constitutes a strategy of general applicability to the characterization of targeted modifications of large proteins via mass spectrometry.