Nano-electrospray Tandem Mass Spectrometry Research Articles

Proteomics analysis of mature seed of four peanut cultivars using two-dimensional gel electrophoresis reveals distinct differential expression of storage, anti-nutritional, and allergenic proteins

Profiles of total seed proteins isolated from mature seeds of four peanut cultivars, New Mexico Valencia C (NM Valencia C), Tamspan 90, Georgia Green, and NC-7, were studied using two-dimensional gel electrophoresis coupled with nano-electrospray ionization liquid chromatography tandem mass spectrometry (nESI-LC–MS/MS). Two-dimensional gels stained with silver nitrate revealed a total of 457, 516, 556, and 530 protein spots in NM Valencia C, Tamspan 90, Georgia Green, and NC-7, respectively. Twenty abundant protein spots showing differences in relative abundance among these cultivars were analyzed by nESI-LC–MS/MS, resulting in identification of 14 non-redundant proteins. The majority of these proteins belonged to the globulin fraction consisting of arachin (glycinin and Arah3/4) and conarachin seed storage proteins as well as other allergen proteins. The expression of some of these identified protein spots was cultivar-specific. For example, allergen Arah3/Arah4 and conarachin protein spots were only detected in Tamspan 90 and NC-7, whereas the Gly1 protein spot was detected only in NM Valencia C and NC-7. Moreover, a galactose-binding lectin protein spot with anti-nutritive properties was only present in Tamspan 90. Other proteins showing differences in relative abundance among the four cultivars included 13-lipoxygenase, fructose-biphosphate aldolase, and glyceraldehyde 3-phosphate dehydrogenase. Together, these results suggest that identified proteins might serve as potential markers for cultivar differentiation and may be associated with underlying sensory and nutritional traits of peanut cultivars.

N-Terminal Acetylation of Two Major Latex Proteins from Arabidopsis thaliana Using Electrospray Ionization Tandem Mass Spectrometry

The primary structure of two proteins named major latex protein in Arabidopsis thaliana were characterized by matrix-assisted laser desorption/ionization time of flight mass spectrometer and Nano-electrospray ionization tandem mass spectrometry (nanoESI-MS/MS) after two-dimensional gel electrophoresis separation. We revealed that the two proteins with the same N termini and the N-terminal alanine were acetylated after methionine cleavage by fragmentation of three doubly charged peptides using a quadrupole-time of flight 2 tandem mass spectrometer. It was worth noting that one peptide with sodium addition and acetylation was sequenced. It is usually difficult to analyze the peptide sequence of sodium adduct due to the 22-Da increment. The two proteins are highly homologous, and both their N-terminal and C-terminal peptides were sequenced. Of the two proteins, gi|15236568 (spot A) appears only in the seeding stage and flower organ, but gi|15236566 (spot B) appears throughout the whole life of A. thaliana. The biological mechanism of the two proteins and the function of N-terminal acetylation remain to be elucidated. This study showed that ESI-MS/MS was a powerful tool for the characterization of N-terminal acetylation of proteins.

The Effect of 24S-Hydroxycholesterol on Cholesterol Homeostasis in Neurons: Quantitative Changes to the Cortical Neuron Proteome

In humans, the brain represents only about 2% of the body's mass but contains about one-quarter of the body's free cholesterol. Cholesterol is synthesized de novo in brain and removed by metabolism to oxysterols. 24S-Hydoxycholesterol represents the major metabolic product of cholesterol in brain, being formed via the cytochrome P450 (CYP) enzyme CYP46A1. CYP46A1 is expressed exclusively in brain, normally by neurons. In this study, we investigated the effect of 24S-hydroxycholesterol on the proteome of rat cortical neurons. With the use of two-dimensional liquid chromatography linked to nanoelectrospray tandem mass spectrometry, over 1040 proteins were identified including members of the cholesterol, isoprenoid and fatty acid synthesis pathways. With the use of stable isotope labeling technology, the protein expression patterns of enzymes in these pathways were investigated. 24S-Hydroxycholesterol was found to down-regulate the expression of members of the cholesterol/isoprenoid synthesis pathways including 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1 (EC 2.3.3.10), diphosphomevalonate decarboxylase (EC 4.1.1.33), isopentenyl-diphosphate delta isomerase (EC 5.3.3.2), farnesyl-diphosphate synthase (Geranyl trans transferase, EC 2.5.1.10), and dedicated sterol synthesis enzymes, farnesyl-diphosphate farnesyltransferase 1 (squalene synthase, EC 2.5.1.21) and methylsterol monooxygenase (EC 1.14.13.72). The expression of many enzymes in the cholesterol/isoprenoid and fatty acid synthesis pathways are regulated by the membrane-bound transcription factors named sterol regulatory element-binding proteins (SREBPs), which themselves are both transcriptionally and post-transcriptionally regulated. The current proteomic data indicates that 24S-hydroxycholesterol down-regulates cholesterol synthesis in neurons, possibly, in a post-transcriptional manner through SREBP-2. In contrast to cholesterol metabolism, enzymes responsible for the synthesis of fatty acids were not found to be down-regulated in neurons treated with 24S-hydroxycholesterol, while apolipoprotein E (apo E), a cholesterol trafficking protein, was found to be up-regulated. Taken together, this data leads to the hypothesis that, in times of cholesterol excess, 24S-hydroxycholesterols signals down-regulation of cholesterol synthesis enzymes through SREBP-2, but up-regulates apo E synthesis (through the liver X receptor) leading to cholesterol storage and restoration of cholesterol balance.

A Novel Secondary Acyl Chain in the Lipopolysaccharide of Bordetella pertussis Required for Efficient Infection of Human Macrophages

Lipopolysaccharide is one of the major constituents of the Gram-negative bacterial outer membrane and is a potent stimulator of the host innate immune response. The biosynthesis of the lipid A moiety of lipopolysaccharide is a complex process in which multiple gene products are involved. Two late lipid A acyl transferases, LpxL and LpxM, were first identified in Escherichia coli and shown to be responsible for the addition of secondary acyl chains to the 2' and 3' positions of lipid A, respectively. Here, we describe the identification of two lpxL homologues in the genome of Bordetella pertussis. We show that one of them, LpxL2, is responsible for the addition of the secondary myristate group that is normally present at the 2' position of B. pertussis lipid A, whereas the other one, LpxL1, mediates the addition of a previously unrecognized secondary 2-hydroxy laurate at the 2 position. Increased expression of lpxL1 results in the appearance of a hexa-acylated lipopolysaccharide form with strongly increased endotoxic activity. In addition, we show that an lpxL1-deficient mutant of B. pertussis displays a defect in the infection of human macrophages.

Cryptosporidium p30, a Galactose/N-Acetylgalactosamine-specific Lectin, Mediates Infection in Vitro

Cryptosporidium sp. cause human and animal diarrheal disease worldwide. The molecular mechanisms underlying Cryptosporidium attachment to, and invasion of, host cells are poorly understood. Previously, we described a surface-associated Gal/GalNAc-specific lectin activity in sporozoites of Cryptosporidium parvum. Here we describe p30, a 30-kDa Gal/GalNAc-specific lectin isolated from C. parvum and Cryptosporidium hominis sporozoites by Gal-affinity chromatography. p30 is encoded by a single copy gene containing a 906-bp open reading frame, the deduced amino acid sequence of which predicts a 302-amino acid, 31.8-kDa protein with a 22-amino acid N-terminal signal sequence. The p30 gene is expressed at 24-72 h after infection of intestinal epithelial cells. Antisera to recombinant p30 expressed in Escherichia coli react with an approximately 30-kDa protein in C. parvum and C. hominis. p30 is localized to the apical region of sporozoites and is predominantly intracellular in both sporozoites and intracellular stages of the parasite. p30 associates with gp900 and gp40, Gal/GalNAc-containing mucin-like glycoproteins that are also implicated in mediating infection. Native and recombinant p30 bind to Caco-2A cells in a dose-dependent, saturable, and Gal-inhibitable manner. Recombinant p30 inhibits C. parvum attachment to and infection of Caco-2A cells, whereas antisera to the recombinant protein also inhibit infection. Taken together, these findings suggest that p30 mediates C. parvum infection in vitro and raise the possibility that this protein may serve as a target for intervention.

Study of interactions between arsenicals and thioredoxins (human and E. coli) using mass spectrometry

Thioredoxin (Trx) plays an important role in achieving redox balances in cells and protecting the cells from oxidative damage. However, little is known about how arsenic affects Trx chemically. It is conceivable that trivalent arsenicals may bind to Trx, which has a highly conserved -CysGlyProCys- sequence. The objective of this study is to characterize the binding of seven arsenic species with Trx from E. coli and humans, using two mass spectrometry techniques. The arsenic-Trx complexes and the free arsenicals were well separated by size-exclusion liquid chromatography (LC) and detected with inductively coupled plasma mass spectrometry (ICPMS). The LC/ICPMS analyses showed that the trivalent arsenic species were able to form complexes with both human and E. coli Trx. Determination of binding constants indicated that affinity to Trx was higher for monomethylarsonous acid (MMA(III)) and phenylarsine oxide (PhAs(III)) than inorganic arsenite (iAs(III)) and dimethylarsinous acid (DMA(III)), probably because MMA(III) and PhAs(III) were able to form stable complexes by binding to two vicinal cysteines in the -CysGlyProCys- region of the Trx. The complexes of arsenicals with both human and E. coli Trx were further characterized by nano-electrospray tandem mass spectrometry. Binding stoichiometries for different arsenic species were consistent with the available cysteine residues in the Trx. Mass spectral evidence also suggests that the pentavalent arsenicals could be reduced by Trx. This study provides the first detailed chemical characterization of the interactions between Trx and arsenic species.

The Chaotrope-soluble Glycoprotein GP2 Is a Precursor of the Insoluble Glycoprotein Framework of the Chlamydomonas Cell Wall

The cell wall of the unicellular green alga Chlamydomonas reinhardtii consists of an insoluble, hydroxyproline-rich glycoprotein framework and several chaotrope-soluble, hydroxyproline-containing glycoproteins. Up to now, there have been no data concerning the amino acid sequences of the hydroxyproline-containing polypeptides of the insoluble wall fraction. Matrix-assisted laser desorption ionization time-of-flight analyses of peptides released from the insoluble cell wall fraction by trypsin treatment revealed the presence of 14 peptide fragments that could be attributed to non-glycosylated domains of the chaotrope-soluble cell wall glycoprotein GP2. However, these peptides cover only 15% of the GP2 polypeptide backbone. Considerably more information concerning the presence of GP2 in the insoluble cell wall fraction was obtained by an immunochemical approach. For this purpose, 407 overlapping pentadecapeptides covering the whole known amino acid sequence of GP2 were chemically synthesized and probed with a polyclonal antibody raised against the deglycosylated, insoluble cell wall fraction. This particular antibody reacted with 297 of the 407 GP2-derived peptides. The peptides that were recognized by this antibody are distributed over the whole known GP2 sequence. The epitopes recognized by polyclonal antibodies raised against the 64- and 45-kDa constituents purified from the deglycosylation products of the insoluble cell wall fraction are also distributed over the whole GP2 backbone, although the corresponding antigens are considerably smaller than GP2. The significance of the latter results for the structure of the insoluble cell wall fraction is discussed.

Fragmentation Studies of Monensin A and B in Negative Electrospray and Nanospray Tandem Mass Spectrometry

This paper reports the first comparative study of the gas-phase fragmentation chemistry of monensin in negative ion mode electrospray and nanoelectrospray tandem mass spectrometry. The fragmentation was observed to occur at lower energies in nanoelectrospray than electrospray. The major product ions are proposed to be formed via an initial neutral elimination of methanol followed be subsequent fragmentation. The low-mass product ions were observed at the same m/z for both monensin A and B.

Investigating protein haptenation mechanisms of skin sensitisers using human serum albumin as a model protein

Covalent modification of skin proteins by electrophiles is a key event in the induction of skin sensitisation but not skin irritation although the exact nature of the binding mechanisms has not been determined empirically for the vast majority of sensitisers. It is also unknown whether immunologically relevant protein targets exist in the skin contributing to effecting skin sensitisation. To determine the haptenation mechanism(s) and spectra of amino acid reactivity in an intact protein for two sensitisers expected to react by different mechanisms, human serum albumin (HSA) was chosen as a model protein. The aim of this work was also to verify for selected non-sensitisers and irritants that no protein haptenation occurs even under forcing conditions. HSA was incubated with chemicals and the resulting complexes were digested with trypsin and analysed deploying matrix-assisted laser desorption/ionization mass spectrometry, reverse phase high performance liquid chromatography and nano-electrospray tandem mass spectrometry. The data confirmed that different residues (lysine, cysteine, histidine and tyrosine) are covalently modified in a highly selective and differential manner by the sensitisers 2,4-dinitro-1-chlorobenzene and phenyl salicylate. Additionally, non-sensitisers 2,4-dichloro-1-nitrobenzene, butyl paraben and benzaldehyde and irritants benzalkonium chloride and sodium dodecyl sulphate did not covalently modify HSA under any conditions. The data indicate that covalent haptenation is a prerequisite of skin sensitisation but not irritation. The data also suggest that protein modifications are targeted to certain amino acids residing in chemical microenvironments conducive to reactivity within an intact protein. Deriving such information is relevant to our understanding of antigen formation in the immunobiology of skin sensitisation and in the development of in vitro protein haptenation assays.

A novel phospholipase from Trypanosoma brucei

Phospholipase A(1) activities have been detected in most cells where they have been sought and yet their characterization lags far behind that of the phospholipases A(2), C and D. The study presented here details the first cloning and characterization of a cytosolic PLA(1) that exhibits preference for phosphatidylcholine (GPCho) substrates. Trypanosoma brucei phospholipase A(1) (TbPLA(1)) is unique from previously identified eukaryotic PLA(1) because it is evolutionarily related to bacterial secreted PLA(1). A T. brucei ancestor most likely acquired the PLA(1) from a horizontal gene transfer of a PLA(1) from Sodalis glossinidius, a bacterial endosymbiont of tsetse flies. Nano-electrospray ionization tandem mass spectrometry analysis of TbPLA(1) mutants established that the enzyme functions in vivo to synthesize lysoGPCho metabolites containing long-chain mostly polyunsaturated and highly unsaturated fatty acids. Analysis of purified mutated recombinant forms of TbPLA(1) revealed that this enzyme is a serine hydrolase whose catalytic mechanism involves a triad consisting of the amino acid residues Ser-131, His-234 and Asp-183. The TbPLA(1) homozygous null mutants generated here constitute the only PLA(1) double knockouts from any organism.

Identification and Functional Characterization of the Hepatic Stellate Cell CD38 Cell Surface Molecule

The activation of hepatic stellate cells (HSCs) is a critical event in hepatic fibrosis, because these cells are the main producers of extracellular matrix proteins in the liver and contribute to the modulation of inflammatory responses via the secretion of several cytokines and the expression of adhesion molecules. The goal of the present study was to characterize cell surface proteins that regulate HSC activation. To this end, a panel of monoclonal antibodies (mAbs) was generated. mAb 14.27 recognized a protein of 45 kd that was highly expressed on HSCs. Affinity purification of this protein followed by sequencing revealed that protein to be CD38. We subsequently demonstrated that CD38 was constitutively expressed by HSCs and that its expression increased after in vitro and in vivo activation. mAb 14.27 induced an increase in cytosolic Ca2+ levels in HSCs, showing that it functions as an agonistic antibody. Moreover, the effects mediated by the CD38 mAb included induction of the proinflammatory cytokine interleukin-6 and up-regulation of the adhesion molecules intercellular adhesion molecule-1, vascular cell adhesion molecule-1, and neural cell adhesion molecule. Collectively, our data suggest that CD38 can act as a regulator of HSC activation and effector functions.

Mouse Homologue of Skin-specific Retroviral-like Aspartic Protease Involved in Wrinkle Formation

Retroviral proteases are encoded in the retroviral genome and are responsible for maturation and assembly of infectious virus particles. A number of retroviral protease sequences with retroviral elements are integrated in every eukaryotic genome as endogenous retroviruses. Recently, retroviral-like aspartic proteases that were not embedded within endogenous retroviral elements were identified throughout the eukaryotic and prokaryotic genomes. However, the physiological role of this novel protease family, especially in mammals, is not known. During the high throughput in situ hybridization screening of mouse epidermis, as a granular layer-expressing clone, we identified a mouse homologue of SASPase (Skin ASpartic Protease), a recently identified retroviral-like aspartic protease. We detected and purified the endogenous 32-kDa (mSASP32) and 15-kDa (mSASP15) forms of mSASP from mouse stratum corneum extracts and determined their amino acid sequences. Next, we bacterially produced recombinant mSASP15 via autoprocessing of GST-mSASP32. Purified recombinant mSASP15 cleaved a quenched fluorogenic peptide substrate, designed from the autoprocessing site for mSASP32 maximally at pH 5.77, which is close to the pH of the epidermal surface. Finally, we generated mSASP-deficient mice that at 5 weeks of age showed fine wrinkles that ran parallel on the lateral trunk without apparent epidermal differentiation defects. These results indicate that the retroviral-like aspartic protease, SASPase, is involved in prevention of fine wrinkle formation via activation in a weakly acidic stratum corneum environment. This study provides the first evidence that retroviral-like aspartic protease is functionally important in mammalian tissue organization.

Analysis of human hippocampus gangliosides by fully-automated chip-based nanoelectrospray tandem mass spectrometry

Modern microfluidic devices are currently introduced in electrospray (ESI) mass spectrometry (MS), tending to substitute the classical capillary-based ESI infusion. Automated systems using the combination of robotized sample handling and chip-based ESI are significantly increasing the analysis reproducibility, precision, throughput, and efficiency. In the last couple of years our group developed the chip-based ESI–MS approach for glycomics in biomedical research and applied it for oligosaccharide, glycopeptide and ganglioside investigation. Here we report upon the optimization and application of this modern technique for the analysis of differential ganglioside expression patterns in human fetal and adult hippocampus. By this methodology, ganglioside species exhibiting high degree of heterogeneity in the ceramide motifs and biologically-relevant modifications could be identified in human hippocampus. The ultra-high reproducibility of the experiments uniquely provided by the chip-ESI approach allowed for a reliable MS-based ganglioside comparative assay. Moreover, the particular feature of chip ESI-tandem MS to provide structural information at high sensitivity was useful for detailed characterization of hippocampus-associated species. The experimental data presented in this study indicate the benefits of microfluidic/MS for determination of the topospecific brain ganglioside composition and development-related changes in their expression, which might be of high value in clinical investigation and for studies related to ganglioside-based therapy of central nervous system diseases.

Detection and Quantification of Endogenous Cyclic DNA Adducts Derived from trans-4-Hydroxy-2-nonenal in Human Brain Tissue by Isotope Dilution Capillary Liquid Chromatography Nanoelectrospray Tandem Mass Spectrometry

A sensitive and selective capillary liquid chromatography nanoelectrospray isotope dilution mass spectrometric method was developed to identify and quantify the endogenous cyclic DNA adducts derived from trans-4-hydroxy-2-nonenal with 2'-deoxyguanosine (HNE-dG) in human brain tissues. Authentic and 13C and 15N stable isotope-labeled HNE-dG were synthesized to serve as standards. The in vitro HNE-modified calf-thymus DNA as well as the DNA samples isolated from human brain tissues of normal and Alzheimer's disease subjects were enzymatically digested to nucleosides in vitro with the presence of internal standard (HNE-dG-13C10, 15N5). The enzymatic digests were cleaned up by solid phase extraction. Only 1-2 microg of DNA digests was loaded on a laboratory-constructed reversed phase capillary chromatography column, and the HNE-dG adducts were separated from intact nucleosides and quantified by a high capacity ion trap mass spectrometer in the MS/MS mode. This method was able to quantify an adduct level of approximately 40 lesions/10(9) normal DNA nucleosides. The detected level of HNE-dG adducts in hippocampus/parahippocampal gyrus and inferior parietal regions of postmortem brains from AD subjects were 556 +/- 379 and 238 +/- 72 adducts per 10(9) normal nucleosides, respectively. These results were consistent with the 32P postlabeling results, which detected 400-600 adducts per 10(9) normal nucleotides in the hippocampus.

Age-associated tyrosine nitration of rat skeletal muscle glycogen phosphorylase b: characterization by HPLC–nanoelectrospray–Tandem mass spectrometry

We identified age-dependent post-translational modifications of skeletal muscle glycogen phosphorylase b (Ph-b), isolated from F1 hybrids of Fisher 344×Brown Norway rats. Ph-b isolated from 34 months old rats showed a statistically significant decrease in specific activity compared to 6 months old animals: 13.8±0.7 vs. 20.6±0.8 Umg −1 protein, respectively. Western blot analysis of the purified Ph-b with anti-3-NT antibodies revealed an age-dependent accumulation of 3-nitrotyrosine (3-NT), quantified by reverse-phase HPLC–UV analysis to increase from 0.05±0.03 to 0.34±0.11 (mol 3-NT/mol Ph-b) for 6 vs. 34 months old rats, respectively. HPLC–nanoelectrospray ionization—tandem mass spectrometry revealed the accumulation of 3-NT on Tyr 113, Tyr 161 and Tyr 573. While nitration of Tyr 113 was detected for both young and old rats, 3-NT at positions 161 and 573 was identified only for Ph-b isolated from 34 months old rats. The sequence of the rat muscle Ph-b was corrected based on our protein sequence mapping and a custom rat PHS2 sequence containing 17 differently located amino acid residues was used instead of the database sequence. The in vitro reaction of peroxynitrite with Ph-b resulted in the nitration of multiple Tyr residues at positions 51, 52, 113, 155, 185, 203, 262, 280, 404, 473, 731, and 732. Thus, the in vitro nitration conditions only mimic the nitration of a single Tyr residue observed in vivo suggesting alternative pathways controlling the accumulation of 3-NT in vivo. Our data show a correlation of age-dependent 3-NT accumulation with Ph-b inactivation.

Enolase Activates Homotypic Vacuole Fusion and Protein Transport to the Vacuole in Yeast

Membrane fusion and protein trafficking to the vacuole are complex processes involving many proteins and lipids. Cytosol from Saccharomyces cerevisiae contains a high Mr activity, which stimulates the in vitro homotypic fusion of isolated yeast vacuoles. Here we purify this activity and identify it as enolase (Eno1p and Eno2p). Enolase is a cytosolic glycolytic enzyme, but a small portion of enolase is bound to vacuoles. Recombinant Eno1p or Eno2p stimulates in vitro vacuole fusion, as does a catalytically inactive mutant enolase, suggesting a role for enolase in fusion that is separate from its glycolytic function. Either deletion of the non-essential ENO1 gene or diminished expression of the essential ENO2 gene causes vacuole fragmentation in vivo, reflecting reduced fusion. Combining an ENO1 deletion with ENO2-deficient expression causes a more severe fragmentation phenotype. Vacuoles from enolase 1 and 2-deficient cells are unable to fuse in vitro. Immunoblots of vacuoles from wild type and mutant strains reveal that enolase deficiency also prevents normal protein sorting to the vacuole, exacerbating the fusion defect. Band 3 has been shown to bind glycolytic enzymes to membranes of mammalian erythrocytes. Bor1p, the yeast band 3 homolog, localizes to the vacuole. Its loss results in the mislocalization of enolase and other vacuole fusion proteins. These studies show that enolase stimulates vacuole fusion and that enolase and Bor1p regulate selective protein trafficking to the vacuole.

Identification and characterization of p63 (CKAP4/ERGIC-63/CLIMP-63), a surfactant protein A binding protein, on type II pneumocytes

Surfactant protein A (SP-A) binds to alveolar type II cells through a specific high-affinity cell membrane receptor, although the molecular nature of this receptor is unclear. In the present study, we have identified and characterized an SP-A cell surface binding protein by utilizing two chemical cross-linkers: profound sulfo-SBED protein-protein interaction reagent and dithiobis(succinimidylpropionate) (DSP). Sulfo-SBED-biotinylated SP-A was cross-linked to the plasma membranes isolated from rat type II cells, and the biotin label was transferred from SP-A to its receptor by reduction. The biotinylated SP-A-binding protein was identified on blots by using streptavidin-labeled horseradish peroxidase. By using DSP, we cross-linked SP-A to intact mouse type II cells and immunoprecipitated the SP-A-receptor complex using anti-SP-A antibody. Both of the cross-linking approaches showed a major band of 63 kDa under reduced conditions that was identified as the rat homolog of the human type II transmembrane protein p63 (CKAP4/ERGIC-63/CLIMP-63) by matrix-assisted laser desorption ionization and nanoelectrospray tandem mass spectrometry of tryptic fragments. Thereafter, we confirmed the presence of p63 protein in the cross-linked SP-A-receptor complex by immunoprobing with p63 antibody. Coimmunoprecipitation experiments and functional assays confirmed specific interaction between SP-A and p63. Antibody to p63 could block SP-A-mediated inhibition of ATP-stimulated phospholipid secretion. Both intracellular and membrane localized pools of p63 were detected on type II cells by immunofluorescence and immunobloting. p63 colocalized with SP-A in early endosomes. Thus p63 closely interacts with SP-A and may play a role in the trafficking or the biological function of the surfactant protein.

PROTEOMIC INVESTIGATION OF PROTEOLYTIC SYSTEMS IN REGULATED SECRETORY VESICLES OF NEUROENDOCRINE CHROMAFFIN CELLS.

Proprotein processing within regulated secretory vesicles is required for the production of biologically active peptides. In this study, investigation of the proteome of regulated secretory vesicles was performed to identify new protease and protease inhibitor components of these vesicles. The approach utilized soluble and membrane fractions of chromaffin granules in 1D SDS-PAGE, with tryptic digestion of gel slices for peptide sequencing by LC-MS/MS using microcapillary reverse-phase HPLC nano-electrospray tandem mass spectrometry (μLC-MS/MS) on a Finnigan LCQ DECA XP Plus quadrapole ion trap mass spectrometer. MS/MS spectra were correlated with known sequences using the Sequest algorithm and programs developed by Harvard Microchemistry Facility. Bioinformatic analyses organized 156 unique proteins according to functional biochemical processes, using protein sequence consisting of Gene Ontology with GOA, ProtFun, and KEGG. Protein sequence signals, motifs, and binding regions were analyzed with Blocks and Pfam/TIGRfam. Resulting proteins were organized into relevant functional categories. Further analysis identified proteases and protease inhibitor proteins. Notably, a subgroup consisting of about 10% of the 156 unique proteins were found to undergo proteolysis, including proneuropeptides. The newly identified cathepsin B was further studied for its function in the production of β-amyloid, a neurotoxic peptide that accumulates in Alzheimer's disease. These proteomic studies may shed light on new proteolytic systems in the secretory vesicle organelle.

Top‐down characterization of proteins and drug‐protein complexes using nanoelectrospray tandem mass spectrometry

We report a 'top-down' approach for characterization of proteins, and identification of binding sites in protein-drug complexes using nanoelectrospray ionization hybrid quadrupole time-of-flight tandem mass spectrometry (nanoESI-MS/MS). The efficiency of direct fragmentation of intact protein ions and the feasibility of this method were initially demonstrated using several well-characterized proteins with different molecular weights including metallothionein (6126 Da), cytochrome c (horse, 12360 Da), myoglobin (horse, 16592 Da), and hemoglobin (human, 64453 Da). Simply varying collision energy without enzyme digestion and gel or LC separation generated a range of peptide fragments of these proteins. Over 80% of these peptide ions matched those in the SWISS-PROT database with mass accuracy of 8 to 32 ppm with external calibration. This technique was further applied to fragment a cisplatin-metallothionein complex to identify the binding sites, demonstrating a potential application in the study of drug-protein binding.

81 INVITED Towards a realistic and effective Quality Assurance paradigm for IMRT

To identify CAP3 and CAP4, components of the CD95 (Fas/APO-1) death-inducing signaling complex, we utilized nano-electrospray tandem mass spectrometry, a recently developed technique to sequence femtomole quantities of polyacrylamide gel–separated proteins. Interestingly, CAP4 encodes a novel 55 kDa protein, designated FLICE, which has homology to both FADD and the ICE/CED-3 family of cysteine proteases. FLICE binds to the death effector domain of FADD and upon overexpression induces apoptosis that is blocked by the ICE family inhibitors, CrmA and z-VAD-fmk. CAP3 was identified as the FLICE prodomain which likely remains bound to the receptor after proteolytic activation. Taken together, this is unique biochemical evidence to link a death receptor physically to the proapoptotic proteases of the ICE/CED-3 family.