Primary sequence information from intact proteins by electrospray ionization tandem mass spectrometry.

Tandem mass spectrometry has been used to obtain information related to portions of the primary sequence for an intact protein, bovine ribonuclease A. Multiply charged molecular ions, generated by electrospray ionization, were collisionally dissociated at low energies in a triple quadrupole mass spectrometer to yield singly and multiply charged fragment ions that can be assigned to the known sequence of the protein. Dissociation of the highly charged molecular ions resulted in pairs of complementary product ions. The higher order (gas-phase) protein structure affects the dissociation processes, as observed in comparisons of tandem mass spectra of the native and disulfide-reduced forms of ribonuclease A.

Structural analysis of wild-type and mutant yeast calmodulins by limited proteolysis and electrospray ionization mass spectrometry.

Calmodulin from Saccharomyces cerevisiae was expressed in Escherichia coli and purified. The purified protein was structurally characterized using limited proteolysis followed by ESI mass spectrometry to identify the fragments. In the presence of Ca2+, yeast calmodulin is sequentially cleaved at arginine 126, then lysine 115, and finally at lysine 77. The rapid cleavage at Arg-126 suggests that the fourth Ca(2+)-binding loop does not bind Ca2+. In the presence of EGTA, yeast calmodulin is more susceptible to proteolysis and is preferentially cleaved at Lys-106. In addition, mutant proteins carrying I100N, E104V or both mutations, which together confer temperature sensitivity to yeast, were characterized. The mutant proteins are more susceptible than wild-type calmodulin to proteolysis, suggesting that each mutation disrupts the structure of calmodulin. Furthermore, whereas wild-type calmodulin is cut at Lys-106 only in the presence of EGTA, this cleavage site is accessible in the mutants in the presence of Ca2+ as well. In these ways, the structural consequence of each mutation mimics the loss of a calcium ion in the third loop. In addition, although wild-type calmodulin binds to four proteins in a yeast crude extract in the presence of Ca2+, the mutants bind only to a subset of these. Thus, the inability to adopt the stable Ca(2+)-bound conformation in the third Ca(2+)-binding loop alters the ability of calmodulin to interact with yeast proteins in a Ca(2+)-dependent manner.

Identification of 12-keto-5,8,10-heptadecatrienoic acid as an arachidonic acid metabolite produced by human HL-60 leukemia cells.

An unusual cyclooxygenase-derived metabolite of arachidonic acid has been shown to be produced by N,N-dimethylformamide (DMF)-induced, terminally differentiated human HL-60 promyelocytic leukemia cells and to a much lesser extent by untreated cells. Biochemical evidence in conjunction with gas chromatography/mass spectrometry and liquid chromatography/thermospray mass spectrometry analyses indicates that the product is 12-keto-5,8,10-heptadecatrienoic acid (KHT). Both KHT and 12-hydroxy-5,8,10-heptadecatrienoic acid (HHT) were produced when arachidonic acid was incubated with cell lysates obtained from differentiated HL-60 granulocytes. Indomethacin and the thromboxane synthetase inhibitor UK-38485 inhibited the production of both metabolites, whereas ethacrynic acid inhibited only the production of KHT. In 100,000 g supernatant fractions, obtained from either untreated or differentiated cells, KHT was produced when HHT was used as substrate. The addition of exogenous NAD, but not NADP, to incubations caused a significant increase in the production of KHT coincident with a decrease in the level of HHT. These data suggest that, in both differentiated and undifferentiated HL-60 cells, an NAD-dependent enzyme, apparently 15-prostaglandin dehydrogenase (15-PGDH), is expressed and catalyzes the conversion of HHT to KHT. In differentiated HL-60 cells, this metabolite is produced from arachidonic acid through a multi-enzymatic process involving the activities of cyclooxygenase, thromboxane synthetase and 15-PGDH. The production of KHT from arachidonic acid in undifferentiated HL-60 cells is probably limited, therefore, by the virtual absence of cyclooxygenase activity in these cells.

Collisional activation and collision-activated dissociation of large multiply charged polypeptides and proteins produced by electrospray ionization.

Collisional activation (CA) and collision-activated dissociation (CAD) of multiply protonated molecular ions produced by electrospray ionization using an atmospheric pressure source are described. A TAGA 6000E triple-quadrupole mass spectrometer, in both unmodified and differentially pumped inlet arrangements, was used to investigate CA and CAD during transfer through the atmosphere-vacuum interface and subsequent CAD in the tandem instrument. Melittin, which has a molecular weight (M r ) of 2846, is efficiently dissociated in the interface at higher nozzle-skimmer voltages, yielding fragmentation that can be assigned to the various charge states. Selection of such product ions formed in the interface for subsequent tandem mass spectrometry allows confirmation of earlier sequence assignments and extends the utility of these methods. Various charge states of larger polypeptides, such as human parathyroid hormone (1-44) (M r 5064), can be efficiently collisionally dissociated in the second (rf-only) quadrupole. However, for molecular ions of this size, the low-energy collisions used for CAD yield only partial sequence information. For large molecules such as horse heart myoglobin (M r 16,951), the effects of nozzle-skimmer bias are explored, and it is shown that higher charge states (at ≤ m/z 1400) can be effectively dissociated in the interface. Initial results for both metastable (unimolecular) and CAD for myoglobin are reported. The potential and limitations of CAD for large biomolecular ions are discussed. The feasibility of fingerprinting for proteins is illustrated by the CAD spectra of cytochrome c from nine species.

Analysis of mutagens from cooked foods by directly combined liquid chromatography-mass spectrometry.

Directly combined high performance liquid chromatography-mass spectrometry (LC/MS) has been studied as a method of analysis of heterocyclic aromatic mutagens in cooked foods, in the parts per billion concentration range. Identification and semiquantitative estimation of mutagens is based on accurate measurement of chromatographic retention (k') and molecular weight-selective detection of mutagens, which are protonated during passage of the chromatographic eluant into a thermospray interface of a quadrupole mass spectrometer. Standard chromatographic retention (k') values in two reversed-phase systems and data from thermospray mass spectra from nine mutagens are reported. An isolation scheme employing CH3OH extraction, acid-base partition, cellulose-trisulfo-Cu-phthalocyanine adsorption, and normal-phase HPLC was used prior to LC/MS analysis. Initial applications have been demonstrated in the analysis of 2-amino-3-methylimidazo[4,5-f]quinoline (IQ) and 2-amino-3,4-dimethylimidazo[4,5-f]quinoline (MeIQ) in broiled salmon flesh. Levels measured were estimated to be in the range 0.2 to 0.4 microgram/kg IQ and 0.4 to 0.9 microgram/kg MeIQ. The method is judged to be generally applicable with minimal sample prefractionation to detection of mutagens at the parts per billion level in cooked foods.

Characterization of radiation-induced thymine-tyrosine crosslinks by electrospray ionization mass spectrometry.

Exposure to ionizing radiation leads to formation of covalent crosslinks between DNA and proteins. The nature, extent and site of the modifications are not well understood due to the difficulty in assessing free radical-induced damage in biopolymers. Electrospray ionization mass spectrometry (ESI-MS) permits direct analyses of intact oligopeptides, permitting characterization of the radiation-induced DNA-protein covalently crosslinked constituents. Our first application of this methodology to free radical-induced damage was in a model system where angiotensin, a small 10-amino acid peptide, is irradiated at various doses in the presence of excess thymine. The relative yield of crosslinks, which ranged from 0.1 to 15%, was linearly related to radiation dose for doses from 0.1 to 100 Gy. Detection of thymine-tyrosine moieties in this model system was possible at doses as low as 0.1 Gy with a signal-to-noise ratio of 4 to 1. ESI-MS revealed that the site of crosslink was located exclusively on the tyrosine residue as expected.

Stable isotope dilution quantification of mutagens in cooked foods by combined liquid chromatography-thermospray mass spectrometry.

A method of general applicability for the detection and quantification of mutagens in cooked foods at the ppb level is presented. A minimal sample prefractionation is employed and [Me-2H3]-labeled analogs of the compounds of interest are added for identification and quantification of mutagens by accurate measurement of chromatographic retention (K') in reverse-phase high-performance liquid chromatography (HPLC), and by measurement of the ratio of response of the protonated molecular ions of analyte and internal standard by directly coupled liquid chromatography-mass spectrometry (LC/MS). Initial application is demonstrated in the analysis of 2-amino-3-methylimidazo[4,5-f]quinoline (IQ) and 2-amino-3,4-dimethylimidazo[4,5-f]quinoline (MeIQ) in broiled salmon. Measured levels of IQ and MeIQ in broiled salmon flesh were 0.3-1.8 ppb and 0.6-2.8 ppb, respectively, and for the skin of broiled salmon 1.1-1.7 ppb and 1.5-3.1 ppb, respectively. Results on cooked beef and sardine are also reported.

Thermospray liquid chromatography-mass spectrometry of nucleosides and of enzymatic hydrolysates of nucleic acids.

Nucleosides dissolved in aqueous buffered solutions undergo ionization during direct introduction of the solution into a mass spectrometer using a thermospray interface. The principal ions formed represent the protonated molecule, the corresponding protonated free base, and sugar. In addition to potential utility for characterization of new nucleosides, the technique can be used to monitor nucleosides separated from enzymatic hydrolysates by liquid chromatography. The selectivity of chromatographic detection is significantly greater than with UV absorbance alone so that independent detection of components of unresolved chromatographic peaks is usually possible. Detection limits, with signal/noise greater than 10 for most nucleosides, are approximately 0.1-1 ng per component for selected ion monitoring and 10-50 ng for full-scan mass spectra. Examples are given from the detection of modified nucleosides in enzymatic hydrolysates of 0.05 A260 units (2.5 micrograms) of rabbit liver tRNAVal and of unfractionated H. volcanii tRNA.

Applications of boronate derivatives in the study of ceramides by gas-liquid chromatography-mass spectrometry.

Methaneboronate derivatives of ceramides possess excellent gas-liquid chromatographic properties and give informative mass spectra. Molecular ions, present at high abundance where an unsaturated acyl substituent is present, are accompanied in the electron impact mass spectra by fragment ions which denote the acyl group and long-chain base. In the gas-liquid chromatographic-mass spectrometric analyses of natural ceramides, as methaneboronate derivatives, the properties of open-tubular columns are exploited to give good separations in moderate analysis times. An application is made to the analysis of ceramides derived from sphingomyelin of human arterial tissue.

Complete amino acid sequence of the Glycera dibranchiata monomer hemoglobin component IV: structural implications.

The globin derived from the monomer Component IV hemoglobin of the marine amnelid, Glycera dibranchiata, has been completely sequenced, and the resulting information has been used to create a structural model of the protein. The most important result is that the consensus sequence of Component IV differs by 3 amino acids from a cDNA-predicted amino acid sequence thought earlier to encode the Component IV hemoglobin. This work reveals that the histidine (E7), typical of most heme-containing globins, is replaced by leucine in Component IV. Also significant is that this sequence is not identical to any of the previously reported Glycera dibranchiata monomer hemoglobin sequences, including the sequence from a previously reported crystal structure, but has high identity to all. A three-dimensional structural model for monomer Component IV hemoglobin was constructed using the published 1.5 A crystal structure of a monomer hemoglobin from Glycera dibranchiata as a template. The model shows several interesting features: (1) a Phe31 (B10) that is positioned in the active site; (2) a His39 occurs in an interhelical region occupied by Pro in 98.2% of reported globin sequences; and (3) a Met41 is found at a position that emerges from this work as a previously unrecognized heme contact.

Tandem mass spectrometry of very large molecules: serum albumin sequence information from multiply charged ions formed by electrospray ionization.

Serum albumin proteins, Mr approximately 66 kDa, from 10 different species (bovine, human, rat, horse, sheep, goat, rabbit, dog, porcine, and guinea pig) have been studied by electrospray ionization mass spectrometry (ESI-MS) and tandem MS using a triple-quadrupole instrument. The effectiveness of collisional activation for the multiply charged albumin ions greatly exceeds that for singly charged ions, allowing an extension by a factor of at least 20 to the molecular mass range for obtaining sequence-specific product ions by tandem MS. Efficient dissociation is largely attributed to "preheating" in the interface Coulombic instability and the large number of collisions. Increasing the electric field in the intermediate pressure region, between the nozzle-skimmer elements of the atmospheric pressure/vacuum interface, allows fragmentation of the multiply protonated (to 96+) molecules produced by ESI. The most abundant dissociation product ions assigned have a low charge state (2+ to 5+) and are attributed to "bn" mode species from cleavage of the -CO-N- peptide backbone bonds. Particularly abundant dissociation products originate from regions near residues n = 20-25 from the NH2 terminus for parent ions of moderate charge (approximately 50+). Collisionally activated dissociation (CAD) mass spectra from porcine serum albumin, in contrast to the other albumins, also gave prominent singly charged "yn" fragments formed from cleavages near the COOH terminus. Tandem mass spectrometry (MS/MS) of the multiply charged molecular ions, and of fragment species produced by dissociation in the interface (i.e., effective MS/MS/MS), produced similar "bn" species and served to confirm spectral assignments. We also show that ESI mass spectra allow a qualitative assessment of protein microheterogeneity and, in some cases, resolution of major contributions. The physical and analytical implications of the results are discussed, including the identification of possible errors in previously published sequences.

Tandem mass spectrometry of very large molecules. 2. Dissociation of multiply charged proline-containing proteins from electrospray ionization.

Collisional dissociation tandem mass spectra have been obtained for multiply charged molecules produced by electrospray ionization for a variety of proline-containing proteins extending up to 22,000 molecular weight. Interpretation of limited m/z range, low-resolution tandem mass spectra from multiply charged precursors can present difficulties due to the possibility of multiply charged product ions and the lack of unambiguous charge-state information. Methods used to guide the spectral interpretation process under these circumstances are discussed. Proline is a unique amino acid constituent because its side chain is bonded to the tertiary nitrogen in a cyclic pyrrolidine ring. For large polypeptides containing proline residues, we have observed that fragmentation due to cleavage of the amide bond to proline is often dominant. Such proline-directed processes are often the only dissociation pathways observed for large proteins. This is attributed to the quasithermal nature of large molecule collisional activation/dissociation processes and the lower dissociation energies for peptide bonds near proline residues. The present results also suggest possible effects on the dissociation processes for large molecules due to charge location and perhaps protein conformation.

Structural features of Glycera dibranchiata monomer hemoglobins. Primary sequences of monomer hemoglobin components II and III.

Primary sequences for the remaining two members (GMH2, GMH3) of the group of three major monomeric hemoglobins from the marine annelid Glycera dibranchiata have been obtained. Full sequences of each 147-amino acid globin were achieved with a high degree of confidence using standard Edman technology in combination with molecular mass determinations of the intact globins and of the cyanogen bromide cleavage fragments using electrospray ionization mass spectrometry. When minor assumptions concerning Q/E identities are made these new results indicate the likely correspondence of GMG2 with the protein represented by the first Glycera dibranchiata monomer hemoglobin complete sequence [Imamura et al., (1972), J. Biol. Chem. 247, 2785-2797]. When these new sequences are combined with the previously determined primary sequence for the third major monomer hemoglobin, GMH4 [Alam et al., J. Protein Chem. (1994), 13, 151-164], it becomes clear that these three (GMG2-4) are truly distinct proteins, contrary to previous suggestions. Surprisingly, our results show that none of these three primary sequences is identical to the published sequence of the refined monomer hemoglobin crystal structure protein; however, there is a strong correspondence to the GMG2 sequence. The present sequencing results, in combination with the published GMH4 sequence, confirm the presence of a distal Leu in place of the more commonly encountered distal His in all three of the major monomer hemoglobins isolated in this laboratory and indicate that the unusual B10 Phe occurs only in GMH4. Analysis of the sequences presented here, along with comparison of amino acid content for Glycera dibranchiata monomer hemoglobins isolated from three different laboratories, and comparison of NMR results from two laboratories suggest further correspondence which unify disparate published isolations.

Vanadate catalyzes photocleavage of adenylate kinase at proline-17 in the phosphate-binding loop.

Irradiation of adenylate kinase (AK) from chicken muscle with 300-400-nm light in the presence of 0.25 mM vanadate ion first inactivated the enzyme and then cleaved the polypeptide chain near the NH2 terminus. The addition of the multisubstrate analogue, P1,P5-bis(5'-adenosyl) pentaphosphate, prevented both effects. ATP, but not AMP, blocked both inactivation and cleavage in a saturable manner, suggesting that both effects were due to modification at the ATP-binding site. The polypeptide products of the photocleavage were isolated by HPLC and characterized by amino acid composition, peptide sequencing, and mass spectral analyses. The predominant (greater than 90%) small peptide fragment contained the first 16 amino acids from the amino terminus of the enzyme. The amino terminus of this peptide contained an acetylated serine, and the "carboxy" terminus was modified by a cyclized gamma-aminobutyric acid which originated from photooxidation and decarboxylation of proline-17 by vanadate. Edman sequencing indicated that the majority of the large peptide fragment (Mr approximately 19,500) was amino-terminal blocked, but a small portion was sequenceable starting at either glycine-18 (7%) or serine-19 (2%). These studies indicate that in the ATP-AK complex proline-17 is close to the phosphate chain of ATP but not AMP, consistent with the latest evaluation of nucleotide-binding sites on mitochondrial matrix AK by X-ray crystallography [Diederichs, K., & Schulz, G.E. (1991) J. Mol. Biol. 217, 541-549]. Furthermore, this is the first report that an amino acid other than serine can be involved in vanadate-promoted photocleavage reactions.

Mass spectrometric analysis of the structure of gamma II bovine lens crystallin.

The amino acid sequence of bovine gamma II-crystallin has been verified by a combination of electrospray and fast atom bombardment mass spectrometry. The molecular weight of gamma II, isolated by gel filtration and ion exchange chromatography, was determined to be 20,967 +/- 3 by electrospray mass spectrometry. Another aliquot of gamma II was completely digested by trypsin in a medium of 20% CH3CN and 0.1 M Tris, pH 8.2. The tryptic peptides were separated by reversed phase HPLC and identified by their molecular weights, as determined by fast atom bombardment mass spectrometry (FABMS). The identification of each peptide was confirmed by digesting the peptide further to give new peptides whose molecular weights were also determined by FABMS and related to the proposed amino acid sequences. The data from both types of mass spectrometric analyses were consistent with the sequence previously proposed by Hay et al. (J. Biol. Chem. 1987, 146, 332-338), including threonine at position 119. The FAB mass spectrum of one HPLC fraction suggested that disulfide bonding between Cys 18 and Cys 22 was present in at least half the protein preparation. Whether the Cys 18/Cys 22 disulfide bond was present in native gamma II or was produced during isolation or enzymic digestion could not be determined from these studies. Samples that had been stored for several weeks showed that several of the cysteines had become disulfide bonded. These studies illustrate the power of mass spectrometric techniques to accurately confirm the primary structure of proteins and to identify post-translational modifications.

Effect of reducing disulfide-containing proteins on electrospray ionization mass spectra.

Electrospray ionization produces multiply charged molecular ions for biomolecules with molecular weights in excess of 100,000. This allows mass spectrometers with limited mass-to-charge range to extend their molecular weight range by a factor equal to the number of charges. The maximum number of observed charges for peptides and smaller proteins correlates well with the number of basic amino acid residues (Arg, Lys, His), except for disulfide-containing molecules, such as lysozyme and bovine albumin. However, reduction of disulfide linkages with 1,4-dithiothreitol (Cleland's reagent) may allow the protein to be in an extended conformation and make "buried" basic residues available for protonation to yield higher charged molecular ions by the electrospray ionization process. For larger proteins reduction of disulfide bridges greatly increases the maximum charge state, but charging of basic amino acid residues remains less efficient than for smaller proteins.

Transfer RNA(5-methylaminomethyl-2-thiouridine)-methyltransferase from Escherichia coli K-12 has two enzymatic activities.

The tRNA(5-methylaminomethyl-2-thiouridine)-methyltransferase, which is involved in the biosynthesis of the modified nucleoside 5-methylaminomethyl-2-thiouridine (mnm5s2U) present in the wobble position of some tRNAs, was purified close to homogeneity (95% purity). The molecular mass of the enzyme is 79,000 daltons. The enzyme activity has a pH optimum of 8.0-8.5, is inhibited by magnesium ions, and stimulated by ammonium ions. Two different intermediates in the biosynthesis of mnm5s2U34 are present in tRNA from the mutants trmC1 and trmC2. Unexpectedly, the product present in tRNA from trmC1 cells was identified by mass spectrometric and chromatographic analyses as 5-carboxymethylaminomethyl-2-thiouridine (cmnm5s2U), i.e. a more complex derivative than the final product mnm5s2U. The product present in tRNA from trmC2 cells was identified as 5-aminomethyl-2-thiouridine (nm5s2U). In the presence of S-adenosylmethionine the most purified enzyme fraction converts both cmnm5s2U34 and nm5s2U34 into mnm5s2U34. In the absence of S-adenosylmethionine, however, cmnm5s2U34 is converted into nm5s2U by this enzyme fraction. We conclude that the purified polypeptide has two enzymatic activities; one actually demodifies cmnm5s2U to nm5s2U and the other catalyzes the transfer of a methyl group from S-adenosylmethionine to nm5s2U, thus forming mnm5s2U. The sequential order of the biosynthesis of mnm5s2U34 is suggested to be: (Formula: see text). The molecular activity of the methyltransferase activity (nm5s2U34----mnm5s2U34) is 74 min-1, and the steady state concentration of the enzyme is only 78 molecules/genome equivalent in cells growing at a specific growth rate of 1.0/h.

Structures of bacitracin A and isolated congeners: sequencing of cyclic peptides with blocked linear side chains by electrospray ionization mass spectrometry.

The bacitracin antibiotic complex consists principally of bacitracin A, a peptide antibiotic containing seven amino acid residues in a ring and five amino acid residues in a blocked side chain, together with a mixture of minor components presumably related but of unknown structures. A preparative high-performance liquid chromatographic method was developed for isolating the minor components A2, B1 and B2 which were then characterized by amino acid analysis, exact mass fast atom bombardment (FAB) mass spectrometry, FAB tandem mass spectrometry (MS/MS) and electrospray ionization (ESI) mass spectrometry. For bacitracins A (MW 1421), A2 (MW 1421), B1a (MW 1407), B1b (MW 1407), B2 (MW 1407) and F (MW 1419), the side chain sequences were determined by ESI MS/MS and ESI nozzle-skimmer collision-induced dissociation (CID) mass spectrometry and the ring sequences elucidated by ESI nozzle-skimmer CID MS/MS. Relative to bacitracin A, bacitracin A2a has the modified isoleucine residue at position 1 replaced by a modified allo-isoleucine residue, bacitracin B1a has the isoleucine residue at position 8 replaced by a valine residue, bacitracin B1b has the isoleucine residue at position 5 replaced by a valine residue and bacitracin B2 has the modified isoleucine residue at position 1 replaced by a modified valine residue. FAB tandem mass spectra were shown to be consistent with the above structural assignments for the isolated bacitracin components. Structures were also proposed for the trace bacitracin components C1 (MW 1393) and D1 (MW 1379) using ESI MS/MS data obtained from the analysis of the bacitracin complex without isolation.

Capillary zone electrophoresis and isotachophoresis-mass spectrometry of polypeptides and proteins based upon an electrospray ionization interface.

The special capabilities of the capillary electrophoresis electrospray ionization-mass spectrometer interface for the analysis of peptides and proteins with molecular weights extending to in excess of 100,000 are reviewed. The dynamic combinations of both capillary zone electrophoresis and capillary isotachophoresis with electrospray ionization are illustrated for mixtures of peptides and proteins. Myoglobin and cytochrome c detection limits were ca. 100 fmol. The potential extension of these methods for determination of the primary structure (sequence) of polypeptides using tandem mass spectrometry is shown to be facilitated by the high charge state of ions produced by the electrospray interface. The relevance of these results for advances in analytical biochemistry are discussed.