Metal-ion binding and limited proteolysis of betabellin 15D, a designed beta-sandwich protein.

Betabellin 15D is a 64-residue, disulfide-bridged homodimer. When folded into a beta structure, the protein is predicted to have two clusters of three histidine residues, each cluster able to bind a divalent metal ion. When the protein was incubated with Cu2+, Zn2+, Co2+, or Mn2+, metal complexes of betabellin 15D were observed by electrospray-ionization mass spectrometry. The relative abundances of the ionic complexes suggested an order of affinities of Cu2+ > Zn2+ > Co2+ > Mn2+, consistent with solution-phase affinities for nitrogen- or sulfur-containing ligands. Limited proteolysis of betabellin 15D by immobilized pepsin, as measured by nanoelectrospray-ionization mass spectrometry, showed that the Phe12-Ser13 peptide bond of betabellin 15D was cleaved more slowly in the presence of Cu2+ than in its absence. Because Cu2+ has little or no effect on the catalytic rate of pepsin, the slower cleavage of the Phe12-Ser13 peptide bond may be due to its decreased accessibility caused by Cu(2+)-induced folding of betabellin 15D.

Analysis of macromolecules using nanoelectrospray ionization mass spectrometry and low-energy collision activation.

The mass spectrometric analysis of several proteins using nanoelectrospray (nanoES) with elastic collisions showed an improvement in the sensitivity over nanoES without collisional activation. We believe this effect is due to a better declusterization/ionization process. Optimization of the collision parameters can be easily performed during the long experiment time allowed using the nanoES source. Moreover, an apparent shift in the charge-state distribution is observed, with lower charged ions becoming relatively more abundant with increasing either target gas pressure or kinetic energy of the precursor ions. Higher charge-state ions might be expected to have higher collision frequencies and correspondingly lose more kinetic energy than lower charge-state ions.

A multidimensional approach to protein characterization.

When mass spectrometry (MS) is used to study protein primary structure, it is used in a "static" mode. That is, the information is derived from a single MS or MS-MS spectrum. Information about more complex protein structure or protein interactions can also be gained via MS. If a series of mass spectra is collected as something else in the experiment is changing, we increase the "dimensionality" of the MS data. For example, measuring mass spectra as a function of time after exposure of a protein to deuterated solvents can provide information about protein structure. Likewise, by measuring mass spectra of a protein as the concentration of a binding ligand is changed, one can infer the stoichiometry of the complex. Another important, but fundamentally different way of increasing the dimensionality of mass spectral data is by coupling the mass spectrometer to a one- or two-dimensional separation technique.

Comprehensive on-line LC/LC/MS of proteins.

This is a description of a comprehensive two-dimensional liquid chromatography (LC) system for the separation of protein mixtures. This system uses cation-exchange chromatography followed by reversed-phase chromatography (RPLC). The two LC systems are coupled by an eight-port valve equipped with two storage loops and under computer control. The RPLC effluent is sampled by both a UV detector and an electrospray mass spectrometer. In this way, complex mixtures of large biomolecules can be rapidly separated, desalted, and analyzed for molecular weight in less than 2 h. The system's utility is demonstrated with a mixture of standards and an Escherichia coli cell lysate.

Activation of a novel calcium-dependent protein-tyrosine kinase. Correlation with c-Jun N-terminal kinase but not mitogen-activated protein kinase activation.

Many G protein-coupled receptors (e.g. that of angiotensin II) activate phospholipase Cbeta, initially increasing intracellular calcium and activating protein kinase C. In the WB and GN4 rat liver epithelial cell lines, agonist-induced calcium signals also stimulate tyrosine phosphorylation and subsequently increase the activity of c-Jun N-terminal kinase (JNK). We have now purified the major calcium-dependent tyrosine kinase (CADTK), and by peptide and nucleic acid sequencing identified it as a rat homologue of human PYK2. CADTK/PYK2 is most closely related to p125(FAK) and both enzymes are expressed in WB and GN4 cells. Angiotensin II, which only slightly increases p125(FAK) tyrosine phosphorylation in GN4 cells, substantially increased CADTK tyrosine autophosphorylation and kinase activity. Agonists for other G protein-coupled receptors (e.g. LPA), or those increasing intracellular calcium (thapsigargin), also stimulated CADTK. In comparing the two rat liver cell lines, GN4 cells exhibited approximately 5-fold greater angiotensin II- and thapsigargin-dependent CADTK activation than WB cells. Although maximal JNK activation by stress-dependent pathways (e.g. UV and anisomycin) was equivalent in the two cell lines, calcium-dependent JNK activation was 5-fold greater in GN4, correlating with CADTK activation. In contrast to JNK, the thapsigargin-dependent calcium signal did not activate mitogen-activated protein kinase and Ang II-dependent mitogen-activated protein kinase activation was not correlated with CADTK activation. Finally, while some stress-dependent activators of the JNK pathway (NaCl and sorbitol) stimulated CADTK, others (anisomycin, UV, and TNFalpha) did not. In summary, cells expressing CADTK/PYK2 appear to have two alternative JNK activation pathways: one stress-activated and the other calcium-dependent.

DNA adduct formation in B6C3F1 mice and Fischer-344 rats exposed to 1,2,3-trichloropropane.

1,2,3-Trichloropropane (TCP) is a multispecies, multisite carcinogen which has been found to be an environmental contaminant. In this study, we have characterized and measured DNA adducts formed in vivo following exposure to TCP. [14C]TCP was administered to male B6C3F1 mice and Fischer-344 rats by gavage at doses used in the NTP carcinogenesis bioassay. Both target and nontarget organs were examined for the formation of DNA adducts. Adducts were hydrolyzed from DNA by neutral thermal or mild acid hydrolysis, isolated by HPLC, and detected and quantitated by measurement of radioactivity. The HPLC elution profile of radioactivity suggested that one major DNA adduct was formed. To characterize this adduct, larger yields were induced in rats by intraperitoneal administration of TCP (300 mg/kg). The DNA adduct was isolated by HPLC based on coelution with the radiolabeled adduct, and compared to previously identified adducts. The isolated adduct coeluted with S-[1-(hydroxymethyl)-2-(N7-guanyl)-ethyl]glutathione, an adduct derived from the structurally related carcinogen 1,2-dibromo-3-chloropropane (DBCP). Analysis by electrospray mass spectrometry suggested that the TCP-induced adduct and the DBCP-derived adduct were identical. The 14C-labeled DNA adduct was distributed widely among the organs examined. Adduct levels varied depending on species, organ, and dose. In rat organs, adduct concentrations for the low dose ranged from 0.8 to 6.6 mumol per mol guanine and from 7.1 to 47.6 mumol per mol guanine for the high dose. In the mouse, adduct yields ranged from 0.32 to 28.1 mumol per mol guanine for the low dose and from 12.2 to 208.1 mumol per mol guanine for the high dose. The relationship between DNA adduct formation and organ-specific tumorigenesis was unclear. Although relatively high concentrations of DNA adducts were detected in target organs, several nontarget sites also contained high adduct levels. Our data suggest that factors in addition to adduct formation may be important in TCP-induced carcinogenesis.

Specific and nonspecific dimer formation in the electrospray ionization mass spectrometry of oligonucleotides.

Specific and nonspecific noncovalent dimer ions of oligonucleotides (ODNs) were observed when mixtures of complementary or noncomplementary strands were analyzed via negative ion electrospray ionization mass spectrometry. Dimer formation was concentration dependent and nearly always occurred when the concentration of ODN exceeded 100 µM. Dimers were observed even for short-length ODNs for which the melting temperature (T m) was well below the experimental temperature and which, therefore, would not be expected to form stable solution duplexes. The abundance of the heterodimer ions seems to correlate with the number of expected hydrogen bonds from Watson-Crick base pairing. As the energy of the incoming ion beam (orifice potential) was increased, the absolute and relative abundance of the dimer ions unexpectedly increased.

Deuterium exchange of alpha-helices and beta-sheets as monitored by electrospray ionization mass spectrometry.

Deuterium exchange was monitored by electrospray ionization mass spectrometry (ESI-MS) to study the slowly exchanging (hydrogen bonded) peptide hydrogens of several alpha-helical peptides and beta-sheet proteins. Polypeptides were synthetically engineered to have mainly disordered, alpha-helical, or beta-sheet structure. For 3 isomeric 31-residue alpha-helical peptides, the number of slowly exchanging hydrogens as measured by ESI-MS in 50% CF3CD2OD (pD 9.5) provided estimates of their alpha-helicities (26%, 40%, 94%) that agreed well with the values (17%, 34%, 98%) measured by circular dichroic spectroscopy in the same nondeuterated solvent. For 3 betabellins containing a pair of beta-sheets and a related disordered peptide, their order of structural stability (12D > 12S > 14D > 14S) shown by their deuterium exchange rates in 10% CD3OD/0.5% CD3CO2D (pD 3.8) as measured by ESI-MS was the same as their order of structural stability to unfolding with increasing temperature or guanidinium chloride concentration as measured by circular dichroic spectroscopy in water. Compared to monitoring deuterium exchange by proton NMR spectrometry, monitoring deuterium exchange by ESI-MS requires much less sample (1-50 micrograms), much shorter analysis time (10-90 min), and no chemical quenching of the exchange reaction.

Conformation of cytochrome c studied by deuterium exchange-electrospray ionization mass spectrometry.

Deuterium exchange of bovine cytochrome c has been monitored by electrospray ionization mass spectrometry. Different charge-state distributions in the mass spectrum appear to represent different protein conformations, but rapid interconversion of the conformations can lead to a coincidence of the deuterium exchange rates. When interconversion is blocked, the conformation corresponding to higher m/z (lower charge) exchanges more slowly, indicating a tightly folded state. Furthermore, the data suggest that at least two conformations can have identical charge-state distributions, but have different exchange rates. Thus, neither charge-state distribution nor deuterium exchange rate alone is a sufficient indicator of protein conformation.

Preliminary X-ray diffraction studies of recombinant 19 kDa human fibroblast collagenase.

Crystals of the catalytic domain of human fibroblast collagenase have been grown in the presence and absence of an inhibitor. Crystals of the inhibitor complex grew from 0.2 M ammonium sulfate and 15 to 30% PEG 8000 at 22 degrees C as bipyramids in the space group P6(2) or P6(4). Crystals of the unligated enzyme grew as rods in the space group P4(1)2(1)2 or P4(3)2(1)2 from 1.0 to 2.0 M sodium formate at 4 degrees C. Both crystal forms grew quite slowly over a period of months, but ultimately yielded crystals that diffracted beyond 2.5 A. The collagenase samples used in these studies were heterogeneous at the amino terminus. Three major species (full length, N-1 and N-2) were identified by mass spectrometry and Edman sequencing. Analysis of dissolved crystals revealed the native crystal form selectively crystallized as the N-2 species; however, no selectivity of N-terminal forms was observed for crystals of the inhibitor complex.

The mass spectrometry of helical unfolding in peptides.

Two model peptides, melittin and a growth hormone releasing factor (GRF) analog, have been studied by mass spectrometry and tandem mass spectrometry during the course of their deuterium exchange. Both peptides are known from previous work to form α-helices in solution. When the peptides are exposed to deuterated solvents, their masses increase as deuterium atoms replace protons in the exchangeable sites of the peptides. The mass spectrometry results clearly indicate multiple populations of exchangeable protons: Some exchange very fast, and are presumably on the surface and not involved in hydrogen bonding; others exchange much more slowly, indicating that they are probably participating in hydrogen bonding.Tandem mass spectrometric experiments were conducted, and the masses of the product (fragment) ions were used to determine where in the peptide the deuterium atoms were incorporated. The results agree very well with NMR studies of the same peptides. Melittin appears as two helical segments with a kink around Pro-14. The GRF analog contains a single long helix, spanning almost the entire length of the peptide. The dynamics of the unfolding of the helices can also be explored by observing how the exchange progresses with time.

Comparison of separation and detection techniques for human growth hormone releasing factor (hGRF) and the products derived from deamidation.

Separation of the deamidation products, Asp8 Leu27 hGRF(1-32)NH2 (MH+ = 3654) and isoAsp8 Leu27 hGRF(1-32)NH2 (MH+ = 3654), from the parent analogue Leu27 hGRF(1-32)NH2 (MH+ = 3653) was achieved by reversed-phase LC and CE, where the retention order was seen to change from tr isoAsp8 hGRF < tr Asn8 hGRF < tr Asp8 hGRF to tr Asn8 hGRF < tr Asp8 hGRF < tr isoAsp8 hGRF, respectively. Both reversed-phase LC and CE gave adequate separations, limits of detection and standard curves. However, CE was preferred due to shorter analysis time, better separation and a smaller demand for material. Packed capillary LC with ESI-MS was then compared with UV detection. On-line LC-MS was found to offer the most efficient approach to detection and identification of hGRF analogues within a single methodology. Identification of Asn8 hGRF from the isobaric deamidation products was achieved from analysis of the triply charged states, where the species were separated by 0.5 amu. LC-MS separation and identification of degradation products offers a viable alternative to fraction collection and subsequent sequencing or enzymatic identification methods. The method becomes increasingly useful for such cases as trace degradation product identification, minimal sample availability or instability of resulting degradation products.

Crystallization and preliminary X-ray diffraction studies of recombinant human interleukin-5.

Recombinant human interleukin-5 (rhIL-5) has been crystallized by the hanging drop vapor diffusion method using 0.1 M-Tris.HCl buffer (pH 8.5) containing 0.2 to 0.25 M-sodium acetate and 26 to 30% PEG 4000 at 22 degrees C. The parallel-piped crystals belong to the space group C2 with unit cell dimensions of a = 122.1 A, b = 36.11 A, c = 56.42 A, beta = 98.59 degrees. They diffract to at least 2.0 A resolution on a rotating anode X-ray source. The molecular mass weight of the protein and the volume of the unit cell suggest that the asymmetric unit contains one intermolecular disulfide-bonded homodimer.

Probing the helical content of growth hormone-releasing factor analogs using electrospray ionization mass spectrometry.

A series of growth hormone-releasing factor analogs have been studied by both circular dichroism and electrospray ionization mass spectrometry (ESI/MS). The peptides are 32 residues long and are known to adopt a random-coil structure in aqueous solution but become increasingly helical as the proportion of organic solvent is increased. Deuterium exchange was observed as an increase in mass of the peptide, as measured by ESI/MS. Rates of exchange were measured and half-lives calculated for analogs containing amino acid substitutions designed to promote or discourage helix formation. Exchange was slower in peptides that are helical (as shown by circular dichroism) than in randomly coiled peptides. Solution conditions that favor helix formation also produced slower exchange rates. These studies suggest that ESI/MS can provide date about the extent and stability of helix formation.

Identification and quantitation of tetrapeptide deamidation products by mass spectrometry.

A method to quantify asparagine (Asn), aspartate (Asp) and isoaspartate (isoAsp) residues in small peptides by fast atom bombardment mass spectrometry (FAB-MS) was developed. Discrimination of isoAsp from Asp residues was accomplished by selective derivatization of isoAsp residues in acetic anhydride, D2O and pyridine. Deuteration occurred at any carbon adjacent to a free alpha-carboxyl group, through a transient oxazalone intermediate, allowing the isoAsp side chain and the C-terminus to incorporate deuterium. Thus, isoAsp-containing peptides incorporate one more deuterium than peptides with Asp and two more than Asn peptides. FAB CID-MS spectra of the Asn tetrapeptide, Thr-Asn-Ser-Tyr, were used to confirm the position of deuteration to the C-terminal residue. FAB and FAB CID-MS spectra demonstrated that the 1 amu shift in mass was not caused by derivatization induced deamidation of the Asn residue. FAB-MS spectra of deuterated peptide standards and mixtures containing deamidation products were obtained over the molecular ion region and deconvoluted using non-deuterated control spectra. Deuterium incorporation values for the Asn, Asp and iosAsp containing peptide standards were 80% mono-deuterated peptide, 95% mono-deuterated peptide and 63% di-deuterated peptide, respectively. IsoAsp to Asp ratios in an unknown mixture were obtained by a least-squares minimization of the difference between the unknown deuterated mixture and the isotopic envelopes from the deuterated standards. The mixture was found to contain 85% isoAsp peptide by FAB-MS, which agreed well with 81% isoAsp peptide when assayed by reversed-phase LC.

Mercury in a commercial preparation of rat amylin.

The biological activity of amylin is reported to vary widely depending on the source and purity of the material. Three commercial samples of rat amylin were compared for structural differences. The samples were nearly identical using most of the available analytical measures--amino acid analysis, HPLC retention, even Edman sequencing data. When the samples were compared by ion spray ionization mass spectrometry, the molecular mass of one sample was 200 daltons higher than anticipated. Careful analysis of the sample, including atomic emission spectrometry, revealed that a mercury atom was associated with the polypeptide. The mercury presumably resulted from a deprotection step in the synthesis, involving the removal of an acetamidomethyl group from cysteine.

Structure of Saccharomyces cerevisiae mating hormone a-factor. Identification of S-farnesyl cysteine as a structural component.

Mating type a cells of the yeast Saccharomyces cerevisiae produce a mating hormone, the a-factor, that we have previously characterized as a very hydrophobic, modified dodecapeptide (Betz, R., Crabb, J. W., Meyer, H. E., Wittig, R., and Duntze, W. (1987) J. Biol. Chem. 262, 546-548). We have investigated the molecular structure in detail using mass spectrometry and proton NMR spectrometry of the intact hormone and authentic component molecules. Tandem mass spectrometry confirms the previously determined peptide sequence of the hormone and shows that it contains additional structural components with masses of 205 and 15 daltons. These were identified by proton NMR and mass spectrometry as a farnesyl (C15H25) residue and a terminal methyl ester group. The farnesyl moiety is attached to the sulfur atom of the carboxyl-terminal cysteine residue, as revealed by NMR of synthetic S-farnesyl cysteine methyl ester. The stereochemical configuration of the farnesyl moiety was determined to be trans,trans by comparison of gas chromatography retention times, mass spectra, and NMR spectra with those of standards. These results define the structure of a-factor as: (Sequence: see text). Replacement of the farnesyl by a methyl group leads to a partial reduction in specific biological activity of the a-factor, whereas hydrolysis of the carboxyl-terminal methyl ester causes a complete loss of activity.

Correction of the cDNA-derived protein sequence of prostatic spermine binding protein: pivotal role of tandem mass spectrometry in sequence analysis.

Spermine binding protein (SBP) is a rat ventral prostate protein that binds various polyamines, and the level of this protein and its mRNA is regulated by androgens. Previously, the cDNA for SBP was cloned and sequenced and an amino acid sequence deduced from the cDNA. Data from cloned and sequenced and an amino acid sequence deduced from the cDNA. Data from partial amino acid sequencing of the purified protein were consistent with the amino acid sequence deduced from the cDNA. However, the amino terminus of the protein was blocked, and therefore, direct protein sequence information confirming the cDNA reading frame of this region could not be obtained by Edman degradation. We have now employed an integrated approach using fast atom bombardment mass spectrometry, tandem mass spectrometry, and conventional sequencing methodologies to establish the amino-terminal sequence of the protein and to identify an amino acid sequence (35 residues) present in the purified protein but missing from the amino acid sequence deduced from cDNA clones for this protein. The missing piece of cDNA corresponds to an exon found in mouse genomic clones for a protein similar to rat SBP. Therefore, the cDNA clones for rat SBP may represent splicing variants that lack the sequence information of one exon. The blocked amino terminus of the protein was identified as 5-oxopyrrolidine-2-carboxylic acid. Mass spectrometry also provided evidence regarding glycosylation of the protein. The first of two potential glycosylation sites clearly carries carbohydrate; the second site is, at most, only partially glycosylated.

Isolation and identification of the principal siderophore of the dermatophyte Microsporum gypseum.

The dermatophyte Microsporum gypseum has been shown to produce two siderophores under conditions of low-iron stress. These compounds have been separated as Fe(III) complexes on silica gel, and the principal siderophore has been identified as ferricrocin using the methods of amino acid analysis, comparative thin-layer chromatography, partial sequencing by gas chromatography-mass spectrometry, ultraviolet spectroscopy, and proton nuclear magnetic resonance spectroscopy of the Al(III) complex.