Composition and organization of the pancreatic extracellular matrix by combined methods of immunohistochemistry, proteomics and scanning electron microscopy.

The epidemic expansion of diabetes is a major concern of public health. A promising treatment is the transplantation of islets of Langerhans isolated from the whole pancreas but the yields of islets isolation and the rates of successful engraftments still have to be improved to make this therapy effective. The extracellular matrix (ECM) of the pancreatic tissue is partially lost during the isolation process and a comprehensive knowledge of the pancreatic ECM composition and organization could identify targets to improve islets isolation and transplantation or highlight new therapeutics for pancreatic diseases. The organization, composition and three-dimensional architecture of the pancreatic ECM were analysed in mouse and pig by three different techniques. Laminin α-4 and ß-2 chains are localized by immunohistochemistry in the exocrine tissue and inside islets of mouse pancreas but not around islets that are surrounded by an ECM made of collagen type IV and type V. Collagen type I, III, and VI were identified by proteomics as specific constituents of the pig pancreatic ECM along with the low-abundance isoforms α3(IV) α4(IV) α5(IV) and α1(V) α2(V) α3(V) of collagen type IV and type V respectively. The three-dimensional ECM architecture is analysed on decellularized mouse pancreas by scanning electron microscopy and is organized in honeycomb structures made of thin ECM fibers assembled in thicker bundles. The combination of immunohistochemistry, proteomics and scanning electron microscopy gives complementary perspective on the pancreatic ECM composition and organization. It represents a valuable toolbox for deeper investigations of ECMs and proposes clues in tissue engineering of the pancreas.

Cytochromes c-552 from two strains of the hydrogenotrophic bacterium Alcaligenes eutrophus are sequence homologs of the cytochromes c8 from the denitrifying pseudomonads.

Soluble cytochromes c-552 were purified from two strains of the hydrogenothrophic species Alcaligenes eutrophus and their amino acid sequences determined. The two cytochromes were found to have 5 differences out of a total of 89 residues. The proteins are clearly related to the cytochromes c8 (formerly called Pseudomonas cytochromes c-551), but require a single residue insertion after the methionine sixth heme ligand relative to the Pseudomonas aeruginosa protein. The consensus residues Trp56 and Trp77, characteristic for the c8 family, are also present in the Alcaligenes proteins. Overall, the Alcaligenes cytochromes are only 43% identical to the Pseudomonas proteins which average 68% identity to one another. They are also only 45% identical to cytochrome c8 from Hydrogenobacter thermophilus, another hydrogenothrophic species, which indicates that the hydrogen utilizing bacteria are not more closely related to one another than they are to other species. The finding of cytochrome c8 in Alcaligenes eutrophus completes the recent characterization of a cytochrome cd1-nitrite reductase from this bacterial species and suggests the existence of the same denitrification pathway as in Pseudomonas where these two proteins are reaction partners.

Cytochrome c" from the obligate methylotroph Methylophilus methylotrophus, an unexpected homolog of sphaeroides heme protein from the phototroph Rhodobacter sphaeroides.

The complete primary structure of an unusual soluble cytochrome c isolated from the obligate methylotrophic bacterium Methylophilus methylotrophus has been determined to contain 124 amino acids and to have an average molecular mass of 14293.0 Da. The sequence has two unusual features: firstly, the location of the heme-binding cysteines is far downstream from the N-terminus, namely at positions 49 and 52; secondly, an extra pair of cysteine residues is present near the C-terminus. In both respects, cytochrome c" is similar to the oxygen-binding heme protein SHP from the purple phototrophic bacterium Rhodobacter sphaeroides. In contrast to SHP, cytochrome c" changes from low-spin to high-spin upon reduction, due to dissociation of a sixth heme ligand histidine which is identified as His-95 by analogy to the class I cytochromes c. The distance of His-95 from the heme (41 residues) and the presence of certain consensus residues suggests that cytochrome c" is the second example of a variant class I cytochrome c.

Cellobiohydrolase I from Trichoderma reesei: identification of an active-site nucleophile and additional information on sequence including the glycosylation pattern of the core protein.

(R,S)-3,4-Epoxybutyl beta-cellobioside, but not the corresponding propyl and pentyl derivatives, inactivates specifically and irreversibly cellobiohydrolase I from Trichoderma reesei by covalent modification of Glu212, the putative active-site nucleophile. The position and identity of the modified amino acid residue were determined using a combination of comparative liquid chromatography coupled on-line to electrospray ionization mass spectrometry, tandem mass spectrometry and microsequencing. It was found that the core protein corresponds to the N-terminal sequence pyrGlu1-Gly434 (Gly435) of intact cellobiohydrolase I. In the particular enzyme samples investigated, the asparagine residues in positions 45, 270 and 384 are each linked to a single 2-acetamido-2-deoxy-D-glucopyranose residue.

Eosinophilia-myalgia syndrome case-associated contaminants in commercially available 5-hydroxytryptophan.

Recently, 5-hydroxy-L-tryptophan (5-OHTrp) has been promoted as an alternative to banned L-tryptophan as a dietary supplement. It has been claimed to help alleviate obesity, insomnia, depression, and headaches. However, eosinophilia-myalgia syndrome (EMS)-like symptoms have also been associated with ingestion or exposure to 5-OHTrp. HPLC-UV analysis of EMS-implicated 5-OHTrp revealed the presence of peak X, described as case-implicated. We show that peak X is actually a family of contaminants with the same molecular weight (234 Da) and similar HPLC retention times. We also demonstrate that all eight samples of commercially available 5-OHTrp analyzed by HPLC-MS contained three or more contaminants of the peak X family. The significance of these findings is discussed.

Structural characterization of contaminants in commercial preparations of melatonin by on-line HPLC-electrospray ionization-tandem mass spectrometry.

Three different commercially available melatonin preparations were analyzed by on-line HPLC-electrospray ionization-tandem mass spectrometry. All three samples contained the same impurities at the approximately 0.1-0.5% level of parent melatonin. Based on accurate mass-HPLC-MS and tandem mass spectrometric analyses, two contaminants (both MH+ = 249) were identified as hydroxylation products of melatonin. One compound (MH+ = 265) was determined to be a C-2 oxidation product of hydroxymelatonin and a group of four regioisomers (MH+ = 477) were identified as melatonin-formaldehyde condensation products. These latter contaminants are structural analogues of the case-associated peak "E" found in L-tryptophan implicated in onset of eosinophilia-myalgia syndrome. The significance of these findings is discussed.

Applications of plasma desorption mass spectrometry in peptide and protein chemistry.

Molecular weight determination by plasma desorption (PD) mass spectrometry has been used in the different stages of protein sequence determination. It has been found to be a very valuable addition to the traditional techniques. For analysis in biotechnological development and production PD mass spectrometry meets the requirements for speed, precision and mass range. The amount of information can be increased by combining 'wet' biochemical procedures with analysis by PD mass spectrometry.

Plasma-desorption mass spectrometry as an aid in protein sequence determination. Application of the method on a cuticular protein from the migratory locust (Locusta migratoria).

The complete amino acid sequence of a structural protein, protein 8, isolated from the pharate cuticle of the locust Locusta migratoria was determined. Protein 8 contains 148 amino acid residues and has an Mr of 15,224. By the extensive use of information obtained by plasma-desorption mass spectrometry (p.d.m.s.) it was possible to reduce the need for conventional sequence determination and to improve the reliability of the results. On the basis of the determined Mr of the intact protein all the peptides that constitute the complete sequence could be isolated from a time-course enzymic digestion. The isolated peptides were sequenced by using a combination of Edman degradation and carboxypeptidase digestion monitored by p.d.m.s. The alignment of the peptides was established from the time-course digestion and further verified by a second enzymic digestion. The primary structure of the protein consists of two hydrophilic and two hydrophobic regions. The hydrophobic regions are enriched in alanine, valine and proline and dominated by a repetitive sequence Ala-Ala-Pro-(Ala/Val). The sequence strengthens the view that the cuticle proteins belong to a unique family of structural proteins.

Analysis of recombinant Schistosoma mansoni antigen rSmp28 by on-line liquid chromatography-mass spectrometry combined with sodium dodecyl sulfate polyacrylamide gel electrophoresis.

A recombinant Schistosoma mansoni antigen produced in Saccharomyces cerevisiae and purified by glutathione-Sepharose affinity chromatography was analyzed by tryptic peptide mapping using on-line reversed-phase high-performance liquid chromatography pneumatically assisted electrospray mass spectrometry confirming the complete primary structure. Partial covalent modification of the single cysteine in the protein with glutathione as well as partial dimerization of the Cys-containing tryptic peptide was observed. Combining sodium dodecyl sulfate-polyacrylamide gel electrophoresis under reducing conditions and tryptic digestion of the monomeric protein in the gel slice revealed that dimerization was occurring during enzymatic digestion. Furthermore, part of the Cys-containing fragment was covalently modified with one moiety of beta-mercaptoethanol by the electrophoresis sample buffer and five of the seven methionine-containing peptide fragments were partially oxidized to the respective sulfoxides. The use of capillary columns provided a complete peptide map of rSmp28 on 7 pmol of tryptic digest after sodium dodecyl sulfate-polyacrylamide gel electrophoresis.

Patterns of phenolic compounds in leafy galls of tobacco.

The chemical composition of ethanolic and aqueous extracts from leafy galls produced after infection of Nicotiana tabacum L. plants with Rhodococcus fascians was drastically changed compared to uninfected controls. Chlorogenic acid was abundant both in uninfected and infected plants, but caffeic acid and another cinnamoyl analogue were new in leafy galls. The most pronounced product induced in leafy galls was identified as 7-O-methyl-6-O-beta-D-glucopyranosyl coumarin (7-methyl esculin). This is the first report of the presence of this coumarin derivative in tobacco. Interestingly, 7-methyl esculin did not accumulate in the presence of avirulent R. fascians strains nor was it found in leafy galls on other plant species. However, it did appear in crown galls induced by Agrobacterium tumefaciens on tobacco plants. Intriguingly, none of the phenolics known to accumulate in Solanaceae under pathogen attack were found in leafy galls. 7-Methyl esculin barely affected growth of R. fascians nor was it catabolized. Microscopical analysis showed that autofluorescent compounds were located mainly in the abundant meristematic regions of the leafy galls. We postulate that 7-methyl esculin might locally influence plant cell division.

Analysis of the primary structure and post-translational modifications of the Schistosoma mansoni antigen Smp28 by electrospray mass spectrometry.

The Schistosoma mansoni glutathione-S-transferase with an apparent molecular mass of 28 kDa, Smp28, has a blocked N-terminus which has been elucidated with the aid of the cDNA sequence combined with mass spectrometry and amino acid composition analysis of the N-terminal tryptic peptide. The blocked N-terminal tryptic peptide (m/z 695.8) contained an equimolar ratio of E, G, H, A, I and K3 upon amino acid composition analysis in agreement with its expected sequence AGEHIK, and showed a delta m = +41.7 Da compared to the predicted mass, which is consistent with the N-terminal alanine being acetylated (delta m = +42.0 Da). The mass of the complete molecule (23,744.5 +/- 3.3 Da) determined by electrospray mass spectrometry showed a further mass increase of 14 Da with respect to Smp28 containing an N-acetylated alanine. This result is consistent with one of the seven methionines being present as a methionine sulfoxide in ca. 90% of the Smp28 molecules in this preparation. Tryptic mapping of Smp28 showed five of the seven methionines to be partially oxidized by mass spectrometry. This is indicative of the ease with which this modification occurs. Two minor components were detected along with the intact molecule, corresponding to modified forms of the molecule, originating from reaction of the only cysteine residue either with itself forming a covalent dimer or with glutathione. On-line liquid chromatography-mass spectrometry has been compared with the off-line complete tryptic map of Smp28 confirming 97% of the primary structure in less than 2 h.

Epoxyalkyl glycosides of D-xylose and xylo-oligosaccharides are active-site markers of xylanases from glycoside hydrolase family 11, not from family 10.

A series of omega-epoxyalkyl glycosides of D-xylopyranose, xylobiose and xylotriose were tested as potential active-site-directed inhibitors of xylanases from glycoside hydrolase families10 and 11. Whereas family-10 enzymes (Thermoascus aurantiacus Xyn and Clostridium thermocellum Xyn Z) are resistant toelectrophilic attack of active-site carboxyl residues, glycosidehydrolases of family 11 (Thermomyces lanuginosus Xyn and Trichoderma reesei Xyn II) are irreversibly inhibited. Theapparent inactivation and association constants (k(i), 1/K(i)) are one order of magnitude higher for thexylobiose and xylotriose derivatives. The effects of the aglycone chainlength can clearly be described. Xylobiose and n-alkyl beta-D-xylopyranosides are competitive ligands and provide protectionagainst inactivation. MS measurements showed 1:1 stoichiometries inmost labelling experiments. Electrospray ionization MS/MS analysisrevealed the nucleophile Glu(86) as the modified residue inthe T. lanuginosus xylanase when 2,3-epoxypropyl beta-D-xylopyranoside was used, whereas the acid/base catalyst Glu(178) was modified by the 3,4-epoxybutyl derivative. The active-site residues Glu(86) and Glu(177) in T. reesei Xyn II are similarly modified, confirming earlier X-raycrystallographic data [Havukainen, Törrönen, Laitinen and Rouvinen (1996)Biochemistry 35, 9617-9624]. The inability of the omega-epoxyalkyl xylo(oligo)saccharide derivatives to inactivate family-10enzymes is discussed in terms of different ligand-subsiteinteractions.

Addition of acetaldehyde to the N-terminus of a recombinant Schistosoma mansoni glutathione S-transferase upon high-level expression in Saccharomyces cerevisiae.

Intracellular expression of recombinant Schistosoma mansoni protein p28 (Smp28) in soluble form to a concentration of more than 6 g/l culture in Saccharomyces cerevisiae was accompanied by a post-translational modification, which occurred during the late stage of the culture. The modified protein, which had a reduced isoelectric point, was isolated by anion-exchange HPLC and characterized by tryptic mapping by means of on-line reversed-phase HPLC/electrospray mass spectrometry. Comparison with non-modified recombinant Smp28 allowed us to localize the modification to the N-terminal hexapeptide AGEHIK, which had an increased mass of 26 Da. Reversed-phase HPLC of the modified peptide with a shallow acetonitrile gradient revealed the presence of two components of identical mass and amino acid composition. Both peptides were inaccessible to N-terminal Edman sequencing, indicating that a rearrangement of the N-terminal region of recombinant Smp28 had taken place during tryptic digestion leading to two isomeric, N-terminally blocked peptides. Deuterium-exchange mass spectrometry showed that the modified peptides lacked two exchangeable protons, suggesting cyclic modifications implying the N-terminal amino group. Tandem mass spectrometry by means of the nano-electrospray technique and collision-induced dissociation allowed us to identify the modified sites as Ala1, His4 and Lys6 based on a characteristic modified a1 ion of Ala1 (70.0 Da), a modified immonium ion of His4 (136.0 Da) and a modified y1" ion (173.2 Da) of Lys6. Combination of all the above results led to the conclusion that recombinant Smp28 was initially modified at its N-terminus by addition of acetaldehyde to form an aldimine which rearranged during tryptic digestion to two different cyclic peptides.

The primary structure of soluble cytochrome c-551 from the phototrophic green sulfur bacterium Chlorobium limicola, strain Tassajara, reveals a novel c-type cytochrome.

Chlorobium limicola, strain Tassajara, cytochrome c-551 is a soluble dimeric protein containing identical subunits of about 30 kDa. The amino acid sequence was determined by a combination of automated Edman degradation and mass analysis. There are 258 residues with a single heme binding site located at cysteine positions 172 and 175. In addition, there is a disulfide bridge between Cys78 and Cys109, and a free cysteine at position 219 which was found to occur as cysteic acid. The only homologue of soluble cytochrome c-551 is the soxA protein which is part of the thiosulfate utilization operon of Paracoccus denitrificans. They are 32% identical with three small gaps. This is consistent with the observation that cytochrome c-551 is the electron acceptor for a thiosulfate-oxidizing enzyme. On the basis of the redox potential of 135 mV, the sixth heme ligand should be a methionine. Among the seven methionine residues that are present in c-551, only one is conserved, two residues ahead of the heme-binding site. The far-UV circular dichroism spectrum indicates 40% alpha helix and 25% beta secondary structure. No other known cytochrome c has such a mixed structure; they are either all helical or all beta. Thus, Chlorobium soluble cytochrome c-551 and soxA are likely to be representative of a new class of c-type cytochromes.

NodS is an S-adenosyl-L-methionine-dependent methyltransferase that methylates chitooligosaccharides deacetylated at the non-reducing end.

In response to phenolic compounds exuded by the host plant, symbiotic Rhizobium bacteria produce signal molecules (Nod factors), consisting of lipochitooligosaccharides with strain-specific substitutions. In Azorhizobium caulinodans strain ORS571 these modifications are an O-arabinosyl group, an O-carbamoyl group, and an N-methyl group. Several lines of evidence indicate that the nodS gene located in the nodABCSUIJ operon is implicated in the methylation of Nod factors. Previously we have shown that NodS is an S-adenosyl-L-methionine (SAM)-binding protein, essential for the L-[3H-methyl]-methionine labelling of ORS571 Nod factors in vivo. Here, we present an in vitro assay showing that NodS from either A. caulinodans or Rhizobium species NGR234 methylates end-deacetylated chitooligosaccharides, using [3H-methyl]-SAM as a methyl donor. The enzymatic and SAM-binding activity were correlated with the nodS gene and localized within the soluble protein fraction. The A. caulinodans nodS gene was expressed in Escherichia coli and a glutathione-S-transferase-NodS fusion protein purified. This protein bound SAM and could methylate end-deacetylated chitooligosaccharides, but could not fully methylate acetylated chitooligosaccharides or unmethylated lipo-chitooligosaccharides. These data implicate that the methylation step in the biosynthesis pathway of ORS571 Nod factors occurs after deacetylation and prior to acylation of the chitooligosaccharides.

Cuttlefish sperm protamines. 2. Mass spectrometry of protamines and related peptides.

The sequence of very basic proteins such as protamines (more than 50% arginines) and related peptides has been determined using mass spectrometry in conjunction with Edman degradation. The capabilities of three mass spectrometric (MS) techniques [fast-atom-bombardment (FAB), 252Cf plasma desorption (252CFPD) and electrospray (ES)] have been evaluated on stallion protamine 1, cuttlefish protamine, and the corresponding cleavage peptides. In contrast to FAB-MS and 252Cf PD-MS, ES-MS made possible an easy determination of the molecular mass of the intact protamines (approximately 8 kDa). With ES-MS about 0.2 nmol was sufficient to yield a mass measurement with an accuracy of 0.05%. On peptides smaller than 3500 Da, both FAB-MS and 252Cf PD-MS allowed mass measurements with an accuracy of 0.1%. 252Cf PD-MS appeared more sensitive than FAB-MS by about a factor of 10. FAB-MS is nevertheless particularly interesting since in most cases it produced spectra with intense A-type fragmentation ions which provided reliable primary structure information.

Sequence of pig lens aldose reductase and electrospray mass spectrometry of non-covalent and covalent complexes.

The complete sequence of pig lens aldose reductase (EC 1.1.1.21), a member of the nicotinamide coenzyme-dependent aldo-keto reductase super family, was determined by the combined use of data obtained from Edman degradation, fast-atom-bombardment mass spectrometry and electrospray mass spectrometry. The N-terminal residue of human and pig aldose reductase was shown to be acetylated. The assignment of a disulfide bridge (Cys298-Cys303) was obtained by mass spectrometry. Electrospray mass spectrometry has been used for molecular mass measurement of human muscle (35758 +/- 7 Da) and pig lens (35778 +/- 3Da) aldose reductase; using mild ionization conditions, it has also been used to study the reversible interaction involved in a non-covalent complex with NADP+ (36527 +/- 4Da). An alkylating analog of NADP+ (3-chloroacetylpyridine-adenine dinucleotide phosphate) was used as an irreversible inhibitor to investigate the NADP binding site and the mass of the covalent complex was measured (36521 +/- 3 Da).

Ligand binding and covalent structure of an oxygen-binding heme protein from Rhodobacter sphaeroides, a representative of a new structural family of c-type cytochromes.

The amino acid sequence of an oxygen-binding heme protein (SHP) from Rhodobacter sphaeroides has been determined. The cysteines, which bind the single heme group in the 112-residue protein, are located at positions 43 and 46. SHP is similar in size to the large membrane-bound form of the class I cytochrome c5 of Azotobacter vinelandii (116 residues) and in the location of the heme binding site at positions 48 and 51. Two extra cysteines in SHP (residues 89 and 97) are located in positions similar to those of cytochrome c5 (residues 98 and 101) and form a disulfide bridge in both proteins. In total, four regions of alpha-helix are predicted, covering 46% of the protein, which is comparable to that in other small cytochromes. SHP is thus distantly related to small class I c-type cytochromes but is representative of a distinct family by virtue of its high-spin nature, the lack of a strong sixth ligand, and its capacity to bind oxygen. Potentially, the most important characteristic of SHP is its ability to transiently bind oxygen during autoxidation, which occurs with a half-life of 3 min with a 4-fold excess of O2. SHP also binds carbon monoxide, azide, and cyanide. The kinetics of reduction by free flavins indicate that SHP is less reactive than other class I cytochromes c and that the heme is less accessible to solvent. There is localized positive charge (+3) at the site of reduction of SHP, although the overall protein charge is -2. This may account in part for the ability of SHP to bind anions.