Identification of a phosphorylation site in the hinge region of the human progesterone receptor and additional amino-terminal phosphorylation sites.

We have previously reported the identification of seven in vivo phosphorylation sites in the amino-terminal region of the human progesterone receptor (PR). From our previous in vivo studies, it was evident that several phosphopeptides remained unidentified. In particular, we wished to determine whether human PR contains a phosphorylation site in the hinge region, as do other steroid receptors including chicken PR, human androgen receptor, and mouse estrogen receptor. Previously, problematic trypsin cleavage sites hampered our ability to detect phosphorylation sites in large incomplete tryptic peptides. Using a combination of mass spectrometry and in vitro phosphorylation, we have identified six previously unidentified phosphorylation sites in human PR. Using nanoelectrospray ionization mass spectrometry, we have identified two new in vivo phosphorylation sites, Ser(20) and Ser(676), in baculovirus-expressed human PR. Ser(676) is analogous to the hinge site identified in other steroid receptors. Additionally, precursor ion scans identified another phosphopeptide that contains Ser(130)-Pro(131), a likely candidate for phosphorylation. In vitro phosphorylation of PR with Cdk2 has revealed five additional in vitro Cdk2 phosphorylation sites: Ser(25), Ser(213), Thr(430), Ser(554), and Ser(676). At least two of these, Ser(213) and Ser(676), are authentic in vivo sites. We confirmed the presence of the Cdk2-phosphorylated peptide containing Ser(213) in PR from in vivo labeled T47D cells, indicating that this is an in vivo site. Our combined studies indicate that most, if not all, of the Ser-Pro motifs in human PR are sites for phosphorylation. Taken together, these data indicate that the phosphorylation of PR is highly complex, with at least 14 phosphorylation sites.

Identification and characterization of the carboxyl-terminal region of rat dentin sialoprotein.

Two acidic proteins, dentin sialoprotein (DSP) and dentin phosphoprotein (DPP), are present in the extracellular matrix of dentin but not in bone. These two proteins are expressed in odontoblasts and preameloblasts as a single cDNA transcript coding a large precursor protein termed dentin sialophosphoprotein (DSPP). DSPP is specifically cleaved into two unique proteins, DSP and DPP. However, the cleavage site(s) of DSPP and the mechanisms for regulating the cleavages are unknown. To identify the specific site(s) of DSPP that are cleaved when the initial translation product is converted to DSP and DPP, we performed a detailed analysis (Edman degradation and mass spectrometry) on selected tryptic peptides of a size originating from the COOH-terminal region of rat DSP. After cleavage with trypsin, the DSP fragments were separated by a two-dimensional method (size-exclusion chromatography followed by reversed phase high performance liquid chromatography). We characterized 13 peptides from various regions of DSP. The analyses showed that peptide Ile(409)-Tyr(421) was the major COOH-terminal fragment, ending at Tyr(421) only 9 residues from the NH(2) terminus of DPP. Peptide Gln(385)-His(406) represented a second, minor COOH-terminal peptide that terminated at His(406). Both of these residues are well beyond the COOH terminus predicted previously by two independent studies estimating that rat DSP contained 360-370 amino acids. Careful studies on two peptides showed that, among 9 potential casein kinase II phosphorylation sites, 2 serines were phosphorylated. We found that rat DSP was heterogeneous with respect to phosphorylation, because this same peptide sequence eluted in two discrete peaks, one with 2 phosphoserines and the other having 1. The finding that 3 lysines just preceding the COOH termini were modified by a 43-Da substituent (possibly a carbamoyl substituent) suggests that the lysines in this region were particularly susceptible to attachment of this substituent.

A 21-kDa C-terminal fragment of protein-disulfide isomerase has isomerase, chaperone, and anti-chaperone activities.

A catalyst of disulfide formation and isomerization during protein folding, protein-disulfide isomerase (PDI) has two catalytic sites housed in two domains homologous to thioredoxin, one near the N terminus and the other near the C terminus. The thioredoxin domains, by themselves, can catalyze disulfide formation, but they are unable to catalyze disulfide isomerizations (Darby, N. J. and Creighton, T. E. (1995) Biochemistry 34, 11725-11735). A 21-kDa, C-terminal fragment of PDI (amino acids 308-491), termed weePDI, comprises the C-terminal third of the molecule. The kcat for ribonuclease oxidative folding by weePDI is 0.26 +/- 0.02 min-1, 3-fold lower than the wild-type enzyme but indistinguishable from the activity of a full-length mutant of PDI in which both active site cysteines of the N-terminal thioredoxin domain have been mutated to serine. Eliminating the ability of weePDI to escape easily from covalent complexes with substrate by mutating the active site cysteine nearer the C terminus to serine has a large effect on the isomerase activity of weePDI compared with its effect on the full-length enzyme. weePDI also displays chaperone and anti-chaperone activity characteristic of the full-length molecule. As isolated, weePDI is a disulfide-linked dimer in which the single cysteine (Cys-326) outside active site cross-links two weePDI monomers. The presence of the intermolecular disulfide decreases the activity by more than 2-fold. The results imply that the functions of the core thioredoxin domains of PDI and other members of the thioredoxin superfamily might be modified quite easily by the addition of relatively small accessory domains.

Species-dependent post-translational modification and position 2 allelism: effects on streptococcal superantigen SSA structure and V beta specificity.

Epidemiologic and molecular population genetic analyses support a role for superantigens (SAg) in the pathogenesis of severe staphylococcal and streptococcal infections. To investigate how variations in SAg structure influence immunomodulatory activity, we examined the biochemical and functional properties of two allelic variants of streptococcal SAg SSA that differ at position 2. Mass spectrometry revealed both recombinant (Escherichia coli) and native (Streptococcus pyogenes) SSA allelic variants to have significantly larger molecular masses than predicted by primary sequence alone and provided evidence that the proteins were modified by the addition of biochemical moieties, a phenomenon that has not been described for related SAg. Furthermore, the molecular masses of native and recombinant SSA were not the same; SSA was differentially post-translationally modified by the two bacterial genera. The substitution of E. coli-dependent processing for that of S. pyogenes altered both protease digestion and V beta specificity, suggesting that recombinant SAg from E. coli may not accurately represent the native toxin. In addition, the observation that SSA allelic variants differed in V beta specificity supports a role for position 2 in SSA-TCR interactions. That SSA position 2 contributes to V beta specificity could not have been predicted from functional or crystallographic studies of other SAg and suggests that SSA may adopt unique interactions with TCR and/or MHC class II molecules. Determining the structural basis for these differences should offer additional clues to the manner in which SAg exert their effects on the immune system during infection and may allow the designing of SAg mutants with specific quantitative and qualitative immunomodulatory properties.

Methyl-donor deficiency due to chemically induced glutathione depletion.

Dietary deficiency of methionine (Met) is known to deplete cellular Met and cause DNA hypomethylation, but depletion of Met and impairment in methylation due to chemically induced glutathione (GSH) depletion has escaped recognition. In this study, the effect of GSH depletion on the Met pool and methylation capability was examined after bromobenzene (BB), a model GSH-depleting hepatotoxin, was administered to the Syrian hamster. An i.p. dose of BB (800 mg/kg) caused a rapid and extensive depletion of liver GSH; approximately 68% of the initial concentration was depleted during the first hour. The lowest level of GSH, only 4% of the control, was detected at 5 h. GSH depletion was accompanied by a prompt increase in liver Met during the first hour. This initial increase was followed by an extensive depletion during the next 4 h. At 5 h after BB, liver Met was 12% below the control value, and it remained around this concentration throughout the 24-h experiment. To further confirm these results, the endogenous Met pool was labeled with deuterated Met. The administration of (L)- Met-methyl-d(3) to the Syrian hamster after GSH had been depleted by BB resulted in a significant protection of the liver against necrosis. The protection was accompanied by a marked incorporation of deuterated Met into the liver Met pool. The incorporation, which was determined by gas chromatography-mass spectrometry, shows BB dose dependence. Approximately 53% of the liver Met was labeled when a toxic BB dose (800 mg/kg) was used, while only 25% incorporation was found for the nontoxic dose (100 mg/kg). These results were different from the controls, where only 15% incorporation was found. The differences in the incorporation indicate that there are differences in the degree of utilization and/or depletion of Met in these hamsters, and these differences apparently are dependent upon the degree of toxicity and GSH depletion. The marked incorporation of deuterated Met in the high-dose group was accompanied with a striking increase in the methylation capability. Urinary excretion of the O- and S-methylated 4- and 5-bromo-2-hydroxythiophenols and S-methylated 4- and 5-bromo-2-hydroxy-1,2-dihydrobenzenethiols was significantly increased when compared with the BB treated alone. Approximately 40-45% of the methyl groups in these methylated BB metabolites were methyl-d(3). These results provide direct evidence that depletion of GSH leads to Met depletion and also injures the methylation processes.

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.

Charge promotion of low-energy fragmentations of peptide ions.

We have examined the hypothesis that structural features which predispose to localization of charge at a strongly favored site are not conducive to the low-energy fragmentation of peptide ions via a multiplicity of pathways. Consistent with this proposal, it is demonstrated that the formation of N- or C-terminal pre-charged derivatives is detrimental to the formation of sequence-specific product ions following low-energy collisional activation. Protonation of pre-charged derivatives (yielding doubly charged ions) restores favorable fragmentation properties; the effect is attributed to the fragmentation-directing properties of the proton which may occupy one of several sites. Similarly, a doubly protonated peptide which incorporates a C-terminal arginine residue as a single strongly favored site of protonation exhibits favored low-energy fragmentations attributable to location of the second proton at one of several sites remote from the C-terminus.

Oligosaccharide sequence determination using B/E linked field scanning or tandem mass spectrometry of phosphatidylethanolamine derivatives.

Product ion mass spectral data of [M + H]+ ions of oligosaccharides, mainly tetra- and pentasaccharides, as their dipalmitoyl phosphatidylethanolamine derivatives were obtained using both liquid secondary ion mass spectrometry with B/E linked scanning and fast atom bombardment ionization with collision-induced dissociation/tandem mass spectrometry. Both methods give similar positive product ion spectra of equivalent high sensitivity (detection limits of approximately 50 pmol) that principally contain glycosidic cleavage ions retaining the reducing end of the molecule from which monosaccharide sequence can be deduced. A series of ions from fission of the phosphate ester bond together with glycosidic cleavage are present in the tandem mass spectra and B/E linked scan spectra when helium collision gas is used. Monosaccharide linkage position of isomeric molecules is reflected in the intensity of glycosidic fragmentation, without retention of the oxygen atom, with decreasing cleavage in the order 1-3 greater than 1-4 greater than 1-6 linkage. Fucose and N-acetylhexosamines show an increased degree of fragmentation over hexose sugars. The application of product ion spectra of derivatized oligosaccharides is demonstrated for characterizing mixed samples and also the acquisition of spectra directly from the silica surface of high-performance thin-layer chromatography plates.

Preparation and tandem mass spectrometric analyses of deuterium-labeled cysteine-containing leukotrienes.

Leukotrienes (LT) C4, E4 and N-acetyl-E4, their respective monomethyl esters and 14,15-2H2 analogs have been synthesized. The collisionally activated decompositions of the [M + H]+ and [M - H]- ions formed by fast atom bombardment (FAB) have been studied by tandem mass spectrometry using a hybrid sector/quadrupole instrument. Structurally informative product ion spectra were obtained for each analyte; the fragmentation pathways proposed are consistent with the parallel data obtained for labeled and derivatized species. Fragmentation of [M + H]+ ions occurs prominently via cleavage of the thioether linkage with charge retention on the cysteine-containing (predominant for LTC4) or lipid-derived (predominant for LTE4) moieties. More pronounced differences were observed between the fragmentations of [M - H]- ions derived from LTC4 and LTE4; the preference for charge retention, however, parallels that observed for the fragmentation of [M + H]+ ions. Selected ion monitoring during continuous-flow FAB mass spectrometric analysis of authentic LTC4 indicated a low-picogram detection limit.