Proteomic strategies for rapid characterization of micro-organisms

Bioinformatic considerations are offered to illustrate strengths and limitations of the characterization of Bacillus spores based on proteomic interpretation of matrix-assisted laser desorption/ionization spectra. In particular, species-specific biomarkers are evaluated in the context of both experimental access and uniqueness in silico.

Tandem mass spectrometry of intact proteins for characterization of biomarkers from Bacillus cereus T spores

Intact protein biomarkers from Bacillus cereus T spores have been analyzed by high-resolution tandem Fourier transform ion cyclotron resonance mass spectrometry. Two techniques have been applied for excitation of the isolated multiply charged precursor ion species: sustained off-resonance irradiation/collisionally activated dissociation and electron capture dissociation. Fragmentation-derived sequence tags and BLAST sequence similarity proteome database searches allow unequivocal identification of the major biomarker protein with unprecedented specificity. Sequence-specific fragmentation patterns further confirm protein identification. Moreover, methodology combining accurate mass measurements of intact proteins with additional information contained in a proteome database permits tentative assignment of several other protein biomarkers isolated from the B. cereus T spores. We argue that approaches involving tandem MS of protein biomarkers, combined with bioinformatics, can drastically improve the specificity of individual microorganism identification, particularly in complex environments.

Characterization of protein biomarkers desorbed by MALDI from whole fungal cells

In this publication, the use of ultraviolet (UV) matrix-assisted laser desorption/ionization (MALDI) time-of-fight (TOF) mass spectrometry (MS) for rapid identification and characterization of Saccharomyces cerevisiae, a fungus, is reported. S. cerevisiae is a unicellular eukaroyte that can serve as a model to study more complex organisms. We have determined that the best technique for cell wall lyses for MALDI involves the use of high concentrations of formic acid solutions. We also have shown that different fungal species exhibit different mass spectra, which can be used to distinguish them readily. Protein peaks from S. cerevisiae spectra have been tentatively identified using bioinformatics and are mainly assigned to ribosomal and mitochondrion-related proteins.

Factors contributing to peak broadening and mass accuracy in the characterization of intact spores using matrix-assisted laser desorption/ionization coupled with time-of-flight mass spectrometry

Factors contributing to peak broadening, accuracy and precision in mass assignment in the matrix-assisted laser desorption/ionization characterization of a lipopeptide desorbed from intact Bacillus spores were investigated. These spores were studied as an example of a thick, topologically irregular sample, which present a more difficult target than a pure peptide or protein. The type of matrix, matrix:sample ratio, laser fluence, and localized repetitive laser irradiation were all found to affect the full-width at half maximum of the biomarker. Both in-source and post-source phenomena were shown to contribute. Sample thickness had less effect. Precision and accuracy of mass assignment were also affected by matrix:sample ratio and laser fluence. In general, this sample was responsive to the same experimental variables as pure peptides, and the use of an internal standard produced significant improvements in precision and accuracy.

Characterization of intact microorganisms by MALDI mass spectrometry

The application of MALDI mass spectrometry to desorb protein biomarkers from intact viruses, bacteria, fungus, and spores is the focus of this review. Instrumentation, sample collection, sample preparation, and algorithms for data analysis are summarized. Optimally these analyses should be carried out in less than five minutes. Successful applications are discussed from biotechnology, cell biology, and the pharmaceutical industry.

Proteolytic 18O labeling for comparative proteomics: model studies with two serotypes of adenovirus

A new method for proteolytic stable isotope labeling is introduced to provide quantitative and concurrent comparisons between individual proteins from two entire proteome pools or their subfractions. Two 18O atoms are incorporated universally into the carboxyl termini of all tryptic peptides during the proteolytic cleavage of all proteins in the first pool. Proteins in the second pool are cleaved analogously with the carboxyl termini of the resulting peptides containing two 16O atoms (i.e., no labeling). The two peptide mixtures are pooled for fractionation and separation, and the masses and isotope ratios of each peptide pair (differing by 4 Da) are measured by high-resolution mass spectrometry. Short sequences and/or accurate mass measurements combined with proteomics software tools allow the peptides to be related to the precursor proteins from which they are derived. Relative signal intensities of paired peptides quantify the expression levels of their precursor proteins from proteome pools to be compared, using an equation described in the paper. Observation of individual (unpaired) peptides is mainly interpreted as differential modification or sequence variation for the protein from the respective proteome pool. The method is evaluated here in a comparison of virion proteins for two serotypes (Ad5 and Ad2) of adenovirus, taking advantage of information already available about protein sequences and concentrations. In general, proteolytic 18O labeling enables a shotgun approach for proteomic studies with quantitation capability and is proposed as a useful tool for comparative proteomic studies of very complex protein mixtures.

Analysis of viral glycoproteins by MALDI-TOF mass spectrometry

Membrane glycoproteins were shown to be useful biomarkers of enveloped viruses using on-target deglycosylation and matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS). Sindbis virus, the prototype alpha-virus, was used as a model system. The glycoproteins and the capsid protein of the Sindbis virus were successfully detected by MALDI-TOF MS using two solvent systems. One of them is 0.5% n-octyl glucoside/0.5% trifluoroacetic acid. The two components of this solvent acted synergistically on the virus to help release and solubilize the structural proteins. The other is 70% acetonitrile/30% formic acid. This solvent solubilized the integral membrane glycoproteins very effectively even after serious aggregation. On-target deglycosylation was performed to confirm the detection of the glycoprotein peak and to produce protein moieties that can be used as biomarkers. After a simple and fast incubation using peptide-N-glycosidase F on target, sequential mass shifts were observed, which proved that the proteins detected at 51 000 Da have N-linked carbohydrate moieties at two sites. Observation of this mass shift could provide confirmatory evidence for viral identification.

Lectin and carbohydrate affinity capture surfaces for mass spectrometric analysis of microorganisms

In a preliminary report (Bundy, J. L.; Fenselau, C. Anal. Chem 1999, 71, 1460-1463), we demonstrated the use of lectin-derivatized surfaces to capture and concentrate complex carbohydrates as well as microorganisms from sample matrixes unamenable to direct MALDI mass spectrometry. Here, we extend the work to include samples representative of a wider variety of microorganisms of importance to human health and of enveloped viruses. In this study, lectins were immobilized directly to a membrane surface via primary amines. A complementary approach was also explored, using immobilized carbohydrates to capture bacteria via microbial lectins expressed on their surfaces. The carbohydrate-based surfaces were constructed by first immobilizing streptavidin to the membrane, followed by attachment of a commercially produced biotin/carbohydrate polymer. Acid treatment of the sample prior to mass spectrometric analysis permits the observation of protein biomarkers from the captured microbial samples in the 5-20 kDa mass range. Bacteria samples were detected from physiological buffers, urine, milk, and processed chicken samples using the biocapture probes. Viral samples were detected from culture based on glycoprotein moieties desorbed directly from the surface. The carbohydrate-based system provided greater sensitivity than the lectin system, possibly due to the larger number of accessible saccharide ligands on the polymer.

Characterization of the protein subset desorbed by MALDI from whole bacterial cells

This study characterizes various features of the proteins that are detected in MALDI mass spectra when whole bacteria cells are analyzed, in an effort to understand why some proteins are successfully detected and many others are not. Forty peaks observed in the mass range 4,000-20,000 Da in the spectra of Escherichia coli K-12 and 11775 are tentatively assigned to proteins in a protein database, and these proteins are characterized by cell location, copy number, pI, and hydropathicity. Those detected originate in the cytosol and generally share the traits of high abundance within the cell, strong bacisity, and medium hydrophilicity.

Kurstakins: a new class of lipopeptides isolated from Bacillus thuringiensis

A novel class of lipopeptides was isolated from Bacillus thuringiensis kurstaki HD-1. Four compounds (1-4) were separated by high-performance liquid chromatography and their primary structures determined using a combination of chemical reactions and mass spectrometry. The four lipopeptides were found to have the same amino acid sequence, Thr-Gly-Ala-Ser-His-Gln-Gln, but different fatty acids. The fatty acyl chain is linked to the N-terminal amino acid residue via an amide bond. Each lipopeptide has a lactone linkage between the carboxyl terminal amino acid and the hydroxyl group in the side chain of the serine residue. Antifungal activity was demonstrated against Stachybotrys charatum.

Rapid characterization of spores of Bacillus cereus group bacteria by matrix-assisted laser desorption-ionization time-of-flight mass spectrometry

Matrix-assisted laser desorption-ionization (MALDI) time-of-flight mass spectrometry was used to characterize the spores of 14 microorganisms of the Bacillus cereus group. This group includes the four Bacillus species B. anthracis, B. cereus, B. mycoides, and B. thuringiensis. MALDI mass spectra obtained from whole bacterial spores showed many similarities between the species, except for B. mycoides. At the same time, unique mass spectra could be obtained for the different B. cereus and B. thuringiensis strains, allowing for differentiation at the strain level. To increase the number of detectable biomarkers in the usually peak-poor MALDI spectra of spores, the spores were treated by corona plasma discharge (CPD) or sonicated prior to MALDI analysis. Spectra of sonicated or CPD-treated spores displayed an ensemble of biomarkers common for B. cereus group bacteria. Based on the spectra available, these biomarkers differentiate B. cereus group spores from those of Bacillus subtilis and Bacillus globigii. The effect of growth medium on MALDI spectra of spores was also explored.

Testing the significance of microorganism identification by mass spectrometry and proteome database search

We derive and validate a simple statistical model that predicts the distribution of false matches between peaks in matrix-assisted laser desorption/ionization mass spectrometry data and proteins in proteome databases. The model allows us to calculate the significance of previously reported microorganism identification results. In particular, for deltam = +/-1.5 Da, we find that the computed significance levels are sufficient to demonstrate the ability to identify microorganisms, provided the number of candidate microorganisms is limited to roughly three Escherichia coli-like or roughly 10 Bacillus subtilis-like microorganisms (in the sense of having roughly the same number of proteins per unit-mass interval). We conclude that, given the cluttered and incomplete nature of the data, it is likely that neither simple ranking nor simple hypothesis testing will be sufficient for truly robust microorganism identification over a large number of candidate microorganisms.

Intracellular sequestration of anti-tumor drugs by metallothionein

Acquired drug resistance is one of the most important problems in cancer chemotherapy. One of the mechanisms proposed to contribute to this phenomenon is the sequestration of alkylating agents by metallothionein (MT) in vivo. In this study cadmium-induced human bladder tumor T24 cells were exposed to the therapeutic agents chlorambucil and melphalan. MT-2a, was shown by capillary electrophoresis to comprise 56% of the MT isoforms in induced cells, and drug adducts of MT-2a were isolated and characterized by HPLC and electrospray ionization mass spectrometry. One to four equivalents of drug were found to be covalently adducted. Major binding sites on metallothionein were located in the C-terminal domain by peptide mapping, consistent with previous studies in vitro.

Metastable decay of peptide ions on a Fourier transform mass spectrometer equipped with an external ion source

Metastable decay rates of two peptides, RPPGFSPF and PKPQQFFGLM, were determined from ions produced in an external matrix-assisted laser desorption/ionization source with a Fourier transform mass spectrometer. An isolation and subtraction method that gives difference spectra was employed to monitor the product formation and metastable decays. The dependence of metastable decay rates on laser fluences and matrixes was demonstrated.

Molecular dynamics simulation of metallothionein-drug complexes

The intermolecular interactions of metallothionein with nitrogen mustard drugs were studied by molecular dynamics simulations. Previous laboratory experiments have defined selective alkylation of two cysteine residues, and selective binding was proposed to precede alkylation. The present study provides information about accessibility to cysteines based on evaluating the intermolecular energies and distances in the first few ps of dynamics simulations. A series of dynamics simulations was performed with three drug molecules positioned at the eight most solvent accessible cysteine residues of the dimeric form of the protein. Sites proximal to the sulfhydryl groups of Cys-33 and Cys-48 were found to be the most favorable for complexing the aziridinium forms of chlorambucil, melphalan, and mechlorethamine. The sites for preferential binding are in qualitative agreement with the sites of selective alkylation defined experimentally.

Matrix-assisted laser desorption/ionization time-of-flight analysis of Bacillus spores using a 2.94 microm infrared laser

The performance of infrared (2.94 microm) and ultraviolet (337 nm) lasers were compared for analysis of purified spores of B. subtilis, B. cereus and B. globigii on a four-inch end-cap reflectron time-of-flight instrument. Infrared matrix-assisted laser desorption/ionization (IR-MALDI) mass spectra of these microorganisms displayed a larger number of biomarker peaks above m/z 4000, compared with UV-MALDI. Biomarker peaks were observed at higher m/z values with the IR laser.

Identification of Bacillus spores by matrix-assisted laser desorption ionization-mass spectrometry

Unique patterns of biomarkers were reproducibly characterized by matrix-assisted laser desorption ionization (MALDI)-mass spectrometry and were used to distinguish Bacillus species members from one another. Discrimination at the strain level was demonstrated for Bacillus cereus spores. Lipophilic biomarkers were invariant in Bacillus globigii spores produced in three different media and in B. globigii spores stored for more than 30 years. The sensitivity was less than 5,000 cells deposited for analysis. Protein biomarkers were also characterized by MALDI analysis by using spores treated briefly with corona plasma discharge. Protein biomarkers were readily desorbed following this treatment. The effect of corona plasma discharge on the spores was examined.

Microorganism identification by mass spectrometry and protein database searches

A method for rapid identification of microorganisms is presented, which exploits the wealth of information contained in prokaryotic genome and protein sequence databases. The method is based on determining the masses of a set of ions by MALDI TOF mass spectrometry of intact or treated cells. Subsequent correlation of each ion in the set to a protein, along with the organismic source of the protein, is performed by searching an Internet-accessible protein database. Convoluting the lists for all ions and ranking the organisms corresponding to matched ions results in the identification of the microorganism. The method has been successfully demonstrated on B. subtilis and E. coli, two organisms with completely sequenced genomes. The method has been also tested for identification from mass spectra of mixtures of microorganisms, from spectra of an organism at different growth stages, and from spectra originating at other laboratories. Experimental factors such as MALDI matrix preparation, spectral reproducibility, contaminants, mass range, and measurement accuracy on the database search procedure are addressed too. The proposed method has several advantages over other MS methods for microorganism identification.

Covalent sequestration of phosphoramide mustard by metallothionein--an in vitro study

Acquired drug resistance is one of the most important problems in cancer chemotherapy. One of the proposed mechanisms for these phenomena is the sequestration of alkylating agents by metallothionein in vivo. This research shows that metallothionein can covalently sequester phosphoramide mustard, the active form of cyclophosphamide in vitro. On-line electrospray mass spectrometry reveals that it is phosphoramide, not nornitrogen mustard that alkylates metallothionein, although the metallothionein/nornitrogen mustard adduct was isolated as the major adduct. Tandem mass spectrometric experiments were performed on an isolated drug-modified tryptic peptide. The alkylation occurred predominantly at Cys48 of metallothionein. These results provide further evidence that overexpression of metallothionein can detoxify the active form of the drugs.

Lectin-based affinity capture for MALDI-MS analysis of bacteria

Immobilized lectins have now been incorporated into affinity surfaces that can be used to isolate broad classes of samples for mass spectrometric analysis. A carbohydrate and a bacterial species that displays the carbohydrate binding motif were isolated and concentrated out of solutions containing salt, urea, buffers, and other contaminants that are deleterious to MALDI mass spectrometry. Concanavalin A was immobilized to a gold foil via a self-assembled monolayer. Samples in phosphate buffer or urine were applied to the capture surface and allowed to interact. The capture surface was then washed to remove salts and other unbound components and subjected to matrix-assisted laser desorption/ionization on a time-of-flight mass spectrometer. The lectin-derivatized surface allowed samples to be concentrated and readily characterized at relatively low levels.

Investigation of Zinc Chelation in Zinc-Finger Arrays by Electrospray Mass Spectrometry

The chelation of zinc by consensus zinc-finger arrays of the CCCC, CCHC, and CCHH type has been investigated by electrospray ionization mass spectrometry. Accurate mass measurements of the most abundant isotopic species have demonstrated that two protons are lost for each Zn(II) ion chelated. Methylation of zinc-finger peptides has revealed that two thiolate anions from cysteine side-chains are necessary to maintain chelation. The other cysteine(s) retain the thiol proton(s) and can be methylated without loss of chelating ability.

Characterization of allosteric insulin hexamers by electrospray ionization mass spectrometry

Electrospray mass spectrometry is used at pH 8.0 in combination with accurate mass measurements to confirm the multiplicity of insulin in stable noncovalent complexes with Zn(II) ions. Determination of the nature and number of ligands involved in Zn(II) chelation is in agreement with crystal and solution structures. Counting the number of ligands participating in each center allows deduction of the geometric configuration of the ligand field and gives indirect information about the conformational state of the insulin monomers in solution.

Corona plasma discharge for rapid analysis of microorganisms by mass spectrometry

Corona plasma discharge provides a rapid and reliable tool for release of biomarkers from gram negative and positive bacteria, spores and viruses for characterization by mass spectrometry.

Stability of secondary structural elements in a solvent-free environment. II: the beta-pleated sheets

The stability of single beta-strands and multistrand beta-pleated sheets as elements of secondary structure is examined in the absence of intermolecular interactions. Such experimental conditions (e.g., complete removal of solvent molecules and counterions) are achieved by placing the peptide ions in the gas phase. The metastable multiply- charged peptide ions produced by electrospray ionization undergo unimolecular dissociation. Intercharge repulsion within the precursor ions gives rise to the elevated kinetic energy of fragment ions, which is measured using Mass-analyzed Ion Kinetic Energy (MIKE) spectrometry. Intercharge distances calculated based on these measurements are compared to the numbers derived from molecular mechanics calculations with charge site assignments based on relative proton affinities. Evidence is presented suggesting that single beta-strands form collapsed structures in the absence of solvents, while multistrand beta-pleated sheets are likely to retain "native-like" secondary structures under the same conditions. These results indicate that intramolecular hydrogen bonds are the major factor determining the three-dimensional arrangements of polypeptides in the gas phase, compensating both long- and short-range electrostatic repulsions. This is in good agreement with our earlier findings (Proteins 27:165170, 1997) concerning stability of helical conformation of melittin in the absence of solvent.

Applications of 1.06-micron IR laser desorption on a Fourier transform mass spectrometer

Various sugars, peptides, and lipids were analyzed on a Fourier transform mass spectrometer using laser desorption and ionization with and without the assistance of matrixes. A compact Nd:YAG laser with an output at 1.06 microns corresponding to fundamental frequency was employed. Gram-negative and Gram-positive bacteria were also subjected to laser desorption mass spectrometry. Characteristics ions of conjugated lipid, formed by attachment of alkali metal cations, endogenous to the cells, were observed. Particle/liquid matrixes (e.g., cobalt in glycerol) proved to be useful with the 1.06-micron laser. The particles absorb efficiently laser radiation in a broad wavelength range. The liquid provides the same advantages as in fast atom bombardment: increased signal-to-noise ratios and enhanced sample lifetimes. The effect of laser power on total ion current was shown to differ for samples with and without the particle/liquid matrix. The Fourier transform analyzer provides MS/MS capability for both positive and negative ions from complex mixtures. Ions desorbed externally are introduced into the cell via a quadrupole ion guide with a lower mass cutoff. Such a setup allows matrix ions to be excluded and thus provides excellent signal-to-noise ratios for lower mass range fragment ions formed inside the cell.

Monitoring metal ion flux in reactions of metallothionein and drug-modified metallothionein by electrospray mass spectrometry

The capabilities of electrospray ionization mass spectrometry are demonstrated for monitoring the flux of metal ions out of and into the metalloprotein rabbit liver metallothionein and, in one example, chlorambucil-alkylated metallothionein. Metal ion transfers may be followed as the reactions proceed in situ to provide kinetic information. More uniquely to this technique, metal ion stoichiometries may be determined for reaction intermediates and products. Partners used in these studies include EDTA, carbonic anhydrase, a zinc-bound hexamer of insulin, and the core domain of bacteriophage T4 gene 32 protein, a binding protein for single-stranded DNA.

Viral characterization by direct analysis of capsid proteins

Matrix-assisted laser desorption/ionization mass spectrometry has enabled viral coat proteins to be characterized directly from the virus. This analysis, demonstrated here with tobacco mosaic virus U2, a bacteriophage MS2, and equine encephalitis TRD, is achieved with a combination of organic acid, UV-absorbing matrix, and high-energy desorption with a nitrogen laser. The molecular weights of these proteins are determined with sufficient accuracy to allow differentiation among viral species and strains. The abundant hydrophobic MS2 coat protein was analyzed in aliquots of culture medium and of the tobacco mosaic virus coat protein in infected leaves. This method provides rapid detection of coat protein in the low-femtomole range, as estimated by titering plaque-forming units of MS2.

Covalent sequestration of the nitrogen mustard mechlorethamine by metallothionein

The research reported here demonstrates covalent binding to the metal-binding protein metallothionein (MT) by the therapeutic nitrogen mustard mechlorethamine. The most surprising aspect of this interaction is the selectivity of the alkylating agent for specific residues of MT. A combination of MS and proteolytic and enzymatic methods was used to deduce specific locations of mechlorethamine alkylation. These experiments indicated that alkylation occurs predominantly in the carboxyl domain of MT, with one molecule of mechlorethamine covalently cross-linking two cysteine residues. Electrospray MS revealed the retention of all seven metal ions in the cross-linked MT/mechlorethamine adducts, highlighting the uniqueness of this protein. Computerized docking experiments supported the hypothesis that selective binding precedes selective alkylation, and the structure of the drug indicates the minimal structural requirements for this binding. These results support the idea that MT overexpressed in tumor cells contributes to the inactivation of anticancer drugs.

Stability of secondary structural elements in a solvent-free environment: the alpha helix

The stability of the alpha helix as an element of secondary structure is examined in the absence of solvation, in the gas phase. Mass-analyzed ion kinetic energy (MIKE) spectrometry was applied to measure intercharge repulsion and intercharge distance in multiply protonated melittin, a polypeptide known to possess a stable helical structure in a number of different environments. The experimental results, interpreted in combination with molecular mechanics calculations, suggest that triply charged melittin retains its secondary structure in the gas phase. The stability if the alpha-helical conformation of the polypeptide in the absence of solvent molecules reflects the fact that a network of intrinsic helical hydrogen bonds is energetically more favorable than unfolded conformations.

Characterization of intermediates in the oxidation of zinc fingers in human immunodeficiency virus type 1 nucleocapsid protein P7

Oxidants targeted toward inactivation of the nucleocapsid zinc finger protein are under development as antiviral agents, especially for use against human immunodeficiency virus. In the present study, electrospray ionization-mass spectrometry is used to follow in situ the progress of the reactions of 2,2'-dithiodipyridine and disulfiram with recombinant nucleocapsid protein p7 (Ncp7) from human immunodeficiency virus-1 at pH 7.4. Both reagents react with the two zinc fingers in the protein, resulting in the ejection of two zinc ions and the formation of oxidized apo-Ncp7 with three intramolecular disulfide bonds. The ejection of zinc by 2,2'-dithiodipyridine occurs in two steps. Alkylation of unreacted cysteine residues with N-ethylmaleimide after a 2-min reaction with 2,2'-dithiodipyridine reveals that the carboxyl-terminal zinc finger is disrupted first. Cys-49, Cys-36, and, to a lesser extent, Cys-39 are all shown to be target residues for initial electrophilic attack. In the reaction of disulfiram with Ncp7, ejection of the two zinc ions also occurs in two steps; however, the fully oxidized apo-Ncp7 is formed more rapidly. Thus, after a 40-min reaction, 45% of native Ncp7 is oxidized by 2,2'-dithiodipyridine, whereas 75% is oxidized by disulfiram.

Cross-linking of human placenta pi class glutathione S-transferase dimer by chlorambucil

Interaction of chlorambucil and the glutathione-depleted human placenta pi class glutathione S-transferase (pi GST) results in the formation of a complex between the drug and the protein at physiological pH. This complex is not formed in the presence of glutathione or S-hexylglutathione. Molecular mass measurement of the reaction product using matrix-assisted laser desorption mass spectrometry indicates that one molecule of chlorambucil cross-links two subunits of the homodimeric protein. A combination of enzymic proteolysis, high performance liquid chromatography, and mass spectrometry reveals that chlorambucil alkylation occurs at cysteine 47 of one subunit and cysteine 101 of the second subunit. This result supports the idea that conformational changes occur in glutathione-depleted pi GST, which allow the bifunctional tether of chlorambucil to cross-link the two subunits of the protein.

Primary structure of bovine adenosine deaminase

Derivatized bovine adenosine deaminase is used in enzyme replacement therapy and as an adjunct to gene therapy against severe combined immunodeficiency syndrome. Although a gene sequence is known for human adenosine deaminase, the structure of the bovine enzyme has not been characterized. Structure studies using mass spectrometry are reported here that evaluate sequence, processing, post-translational modifications and the extent of homology between the human protein and its therapeutic surrogate.

A binding site for chlorambucil on metallothionein

It is of interest to test the hypothesis that induced metallothionein (MT) acts in acquired drug resistance by covalent sequestration. In this study MT was incubated in vitro with chlorambucil (CHB) under conditions where only 1:1 covalent adducts were formed. The proteolytic products of these adducts were analyzed by HPLC and mass spectrometry to reveal two major sites of modification. These were the sulfur atoms of cysteines 33 and 48, which cochelate the same metal atom in native MT. The time course of the reaction was followed using on-line electrospray ionization with a double-focusing mass spectrometer. These experiments showed that drug-modified MT binds seven metal ions, as does the unmodified protein. Molecular docking experiments showed that the selectively of drug binding is influenced by the presence of the aziridinium ion in the drug structure and complementary charge densities in the protein structure.

Specific disulfide formation in the oxidation of HIV-1 zinc finger protein nucleocapsid p7

In vitro oxidation of the HIV-1 nucleocapsid protein p7 by the C-nitroso compound 3-nitrosobenzamide (NOBA) has been investigated. When reconstituted p7 was incubated with NOBA, three disulfide bonds were formed per molecule of p7, Cys 15-Cys 18, Cys 28-Cys 36, and Cys 39-Cys 49. These were identified using the proteolytic enzyme endoproteinase Lys-C and mass spectrometry. When the denatured protein (Apo-p7) was incubated with NOBA, a more random pattern of multiple S-S linkages was found. Oxidation of reconstituted p7 also occurred on treatment with cupric ions (Cu2+), and the same three major disulfide bonds were formed as in the reaction with NOBA. These results suggest the interpretation that the oxidation reaction occurs at the zinc-binding centers while zinc cations are still bound and that the two zinc fingers are not identical in their chemical properties. This latter point is consistent with the independent biological roles reported previously for the two fingers in the viral infection cycle.

Covalent sequestration of melphalan by metallothionein and selective alkylation of cysteines

Rabbit liver metallothionein-2 is shown to form covalent bonds with the anticancer agent melphalan, in support of the hypothesis that covalent sequestration by metallothionein constitutes one mechanism for the cross-resistance acquired by cancer patients to therapeutic alkylating agents. Among 20 cysteines in the 2-domain protein, 89% of the first alkylation reaction occurs with 2 that cochelate a zinc cation in the carboxy domain. Computer-supported docking studies indicate a favorable binding site for melphalan near these cysteine sulfhydryl groups. Although folded metallothionein-2 is resistant to trypsin cleavage, alkylation by 1 mol of melphalan allows cleavage by trypsin between the two globular domains.

Interface for a four-sector mass spectrometer with a dual-purpose collision cell: High transmission at low to intermediate energies

A new interface system that consists of an ion decelerator, a floating collision cell-chemical ionization ion source, and an ion extractor was designed and installed in the third field-free region of a four-sector tandem mass spectrometer. Important features include the use of cylindrical deceleration lenses and an extraction lens assembly. This new design was found to provide enhancement of ion transmission at low to intermediate ion kinetic energies (3 eV to 1 keV) compared with the standard collision cell design. Collision-induced dissociation experiments from 3 eV to 10 keV and ion-molecule reactions of mass-selected ions can be performed conveniently. A second, grounded, collision cell is located after the extraction lenses, which allows MS(4) experiments to be carried out via the normal linked (B/E) scan function in MS2. Incorporation of chemical ionization capability into the electrically isolated collision cell makes it possible to carry out neutralization chemical-reionization mass spectrometry.

Simple interface for microbore LC and electrospray ionization mass spectrometry and analysis of melphalan-alkylation sites in metallothionein

A microbore high pressure liquid chromatograph has been interfaced to a Vestec electrospray ionization source retrofitted to a Hewlett-Packard quadrupole mass spectrometer. The chief features include the absence of a splitter, the use of a second, ballast column to provide a stable flow rate across the gradient, and an in-line UV detector. The system was evaluated for analysis of peptide mixtures and applied to identification of drug-modified peptides released by tryptic digestion of drug-alkylated metallothionein.

Identification of an N-acetylated microsomal glutathione S-transferase by mass spectrometry

Microsomal glutathione S-transferase (mGST) was purified to homogeneity from male Sprague-Dawley rat liver, as determined by SDS-PAGE. Removal of Triton X-100 and further separation by reversed phase HPLC revealed two proteins, mGST 1 and mGST 2, in a 1:3 ratio. Analysis of mGST 1 and mGST 2 by electrospray ionization mass spectrometry determined their molecular weights to be 17,354.2 +/- 6.6 and 17,397.9 +/- 6.6, respectively. mGST 1 was in close agreement with the calculated molecular weight of 17,348, as predicted by the previously reported cDNA sequence. Cyanogen bromide digestion and peptide mapping by fast atom bombardment mass spectrometry (FAB-MS) localized the mass increase to the N-terminal peptide, 1-7. FAB-tandem mass spectrometry of this peptide in conjunction with Edman reactions on the intact protein demonstrated the N-terminal alanine to be acetylated.

Sequencing electroblotted proteins by tandem mass spectrometry

Electroblotting proteins separated by gel electrophoresis provides a suitable support for further manipulations and analysis of small amounts of relatively pure samples. On-membrane digestion, peptide mapping by mass spectrometry, and database searching offer sensitive and fast tools to identify the analyte. By providing sequence information, tandem mass spectrometry can go a step further, confirming the database identification, solving problems connected with post-translational modifications and sequence variations, or supplying the stretches of internal sequence necessary to synthesize an oligonucleotide probe for gene isolation. The viability of this approach was successfully evaluated using different tandem mass spectrometric techniques: metastable decomposition in a matrix-assisted laser desorption/ionization (MALDI) time-of-flight instrument with a curved-field reflectron; low energy collision-induced dissociation in a MALDI quadrupole ion trap mass spectrometer; and high energy collision-induced dissociation in a high-performance four-sector mass spectrometer with massive cluster-impact ionization.

Characterization and formation of the glutathione conjugate of clofibric acid

The incubation of 1-O-clofibryl glucuronide (1-O-CAG), a metabolite of clofibrate, with glutathione (GSH) resulted in the appearance of a new peak when analyzed by HPLC. The use of HPLC coupled to electrospray-MS permitted the identification of the peak as S-(p-chlorophenoxy-2-methylpropanoyl)glutathione (CA-SG), formed by nucleophilic displacement of the glucuronide moiety from 1-O-CAG. Conjugate formation was enhanced 8-fold by rat liver glutathione S-transferases (GSTs). GSH was unreactive with isomers of 1-O-CAG formed by acyl migration, indicating that 1-O-CAG itself was the preferred substrate. Rearrangement of 1-O-CAG to its isomers in vitro, was found to be decreased in the presence of GSH. In vivo studies indicated that, following an intravenous infusion of clofibric acid to rats (75 mg/kg), the concentration of CA-SG excreted in bile over 4 hr, was approximately 0.1% of the concurrent CAG concentrations. Although these results indicate a minor role for GST-catalyzed reactions in clofibrate metabolism in vivo, they do define 1-O-acyl-linked glucuronides as a new class of substrates for GSTs.

The gene encoding glyoxalase I from Pseudomonas putida: cloning, overexpression, and sequence comparisons with human glyoxalase I

The gene encoding glyoxalase I (GlxI) from Pseudomonas putida has been cloned into the high-expression plasmid pBTacI. In the presence of IPTG, JM109 cells transformed with this vector give expression levels of GlxI 4000-fold higher than wild-type Escherichia coli. Contrary to a previous report, the nucleotide sequence of the gene encodes a 173-amino-acid polypeptide. Edman analysis indicates that the predicted N-terminal methionine is lost post-translationally to yield a 19407-Da protein. Mass spectrometry of the intact protein, and of the peptides generated from treatment with CNBr, does not indicate any additional post-translational modifications of the enzyme. Contrary to previous conclusions, there are no major regions of dissimilarity between the human and bacterial enzymes.

Amino acid sequence analysis of the proteolytic cleavage products of the bovine immunodeficiency virus Gag precursor polypeptide

Bovine immunodeficiency virus Gag proteins were purified from virions, and their amino acid sequences and molecular masses were determined. The matrix, capsid, and nucleocapsid (MA, CA, and NC, respectively) and three smaller proteins (p2L, p3, and p2) were found to have molecular masses of 14.6, 24.6, and 7.3 and 2.5, 2.7, and 1.9 kDa, respectively. The order of these six proteins in the Gag precursor, Pr53gag, is NH2-MA-p2L-CA-p3-NC-p2-COOH. In contrast to other retroviral MA proteins, the bovine immunodeficiency virus MA retains its N-terminal methionine and is not modified by fatty acids. In addition, the bovine immunodeficiency virus NC migrates as a 13-kDa protein in denaturing gel electrophoresis; however, its molecular mass was determined to be 7.3 kDa.

Optimization by mass spectrometry of a tryptophan-specific protein cleavage reaction

Mass spectrometry has been used to define the reaction of BNPS-skatole (3-bromo-3-methyl-2-(o-nitrophenylsulfenyl)indolenine) with selected proteins and peptides, confirming the cleavage of the protein chain at tryptophan residues, characterizing the products, and identifying the side reactions. A short procedure for carrying out the cleavage reaction with minimal side reactions is presented.

Collision energy effects on the collision-induced dissociation of multiply charged melittin

The fragmentation of the melittin 4+ ion has been studied over a range of collision energies from 28 eV to 12 keV in a four-sector mass spectrometer. Patterns of fragmentation and energy conversion were found to be analogous to those observed for singly charged peptides. High numbers of collisions were not required for activation at low energies.

Excretion of 3-hydroxy-diflunisal as a monosulphate conjugate--identification using ESI-MS

Electrospray-ionization mass spectrometry was used to identify a novel, highly polar metabolite of diflunisal isolated from Gunn rat urine. Negative ion spectra were obtained of the sulphate conjugate of diflunisal and the new metabolite, which was identified as a sulphate conjugate of 3-hydroxydiflunisal.

A strategy for characterization of polyethylene glycol-derivatized proteins. A mass spectrometric analysis of the attachment sites in polyethylene glycol-derivatized superoxide dismutase

Base treatment of polyethylene glycol-derivatized superoxide dismutase in which the polyethylene glycol is linked to the protein via a succinyl bridge, removes the polyethylene glycol leaving a succinyl marker. Exhaustive succinylation with d4-succinic anhydride completes the derivatization in order to minimize fractionation in proteolysis, chromatography, and desorption in the mass spectrometer. Production of peptides from the derivatized protein for high resolution and high-resolution tandem MS allows identification of the site that had been derivatized by polyethylene glycol and the determination of the amount of polyethylene glycol originally at each site. The mass spectrometric strategy outlined herein can be applied to other proteins derivatized for therapeutic administration.

High-energy collision-induced dissociation of multiply charged polypeptides produced by electrospray

The recent commercial implementation of an electrospray source on a four-sector mass spectrometer has allowed the study of high-energy collisional activation of multiply charged cations. With this configuration, higher mass-to-charge ratios can be accommodated in both precursor ion selection and fragment ion detection. Good mass accuracy facilitates analysis of fragment ions and allows more reliable mechanistic correlation of these fragments. A convenient scheme was devised to permit the use of kilovolt potentials in both MS-I and MS-II, with precursors of varying charge states. Algorithms were devised to assign masses of different types of multiply charged fragment ions. Nine polypeptides were studied in the mass range 2000-5000 Da. Through this entire mass range, fragment ions were observed to be amply formed by cleavages in both the backbone and side chains, analogous to high-energy collisional activation of singly charged ions. This stands in sharp contrast to the patterns reported with low-energy, multiple collisions. Abundances of sequence ion series are influenced by the positions of basic residues. Analysis of charge distributions in fragment ions also indicates that the charges tend to be spread out across the peptides.