Auracyanin A from the thermophilic green gliding photosynthetic bacterium Chloroflexus aurantiacus represents an unusual class of small blue copper proteins.

The amino acid sequence of the small copper protein auracyanin A isolated from the thermophilic photosynthetic green bacterium Chloroflexus aurantiacus has been determined to be a polypeptide of 139 residues. His58, Cys123, His128, and Met132 are spaced in a way to be expected if they are the evolutionary conserved metal ligands as in the known small copper proteins plastocyanin and azurin. Secondary structure prediction also indicates that auracyanin has a general beta-barrel structure similar to that of azurin from Pseudomonas aeruginosa and plastocyanin from poplar leaves. However, auracyanin appears to have sequence characteristics of both small copper protein sequence classes. The overall similarity with a consensus sequence of azurin is roughly the same as that with a consensus sequence of plastocyanin, namely 30.5%. We suggest that auracyanin A, together with the B forms, is the first example of a new class of small copper proteins that may be descendants of an ancestral sequence to both the azurin proteins occurring in prokaryotic nonphotosynthetic bacteria and the plastocyanin proteins occurring in both prokaryotic cyanobacteria and eukaryotic algae and plants. The N-terminal sequence region 1-18 of auracyanin is remarkably rich in glycine and hydroxy amino acids, and required mass spectrometric analysis to be determined. The nature of the blocking group X is not yet known, although its mass has been determined to be 220 Da. The auracyanins are the first small blue copper proteins found and studied in anoxygenic photosynthetic bacteria and are likely to mediate electron transfer between the cytochrome bc1 complex and the photosynthetic reaction center.

Multiple-stage tandem mass spectrometry for structural characterization of saponins.

Nanoelectrospray ion trap multiple-stage tandem mass spectrometry was applied to characterize saponins present in HPLC fractions from Quil A, a commercially available bark extract. An analytical strategy was developed based on recognition of carbohydrate sequence ions as well as glycosidic ring-cross ions formed by gamma-hydrogen rearrangements and successive retro-Diels-Alder fragmentations. These ions could be used for the determination of several glycosidic linkages, ring sizes, and positions of acyl groups. The presence of an acyl group on a monosaccharide residue facilitated the determination of the substitution pattern, due to the induction of ring-cross fragmentation. Deuteriomethylation resulted in a more extended set of ring-cross ions, thus allowing determination of additional glycosidic linkages. An analysis typically consumed 200 ng of sample and a total of 1-4 h for measurement and interpretation. The applied method is attractive as a pre-NMR analysis, especially because it resulted rapidly in an overall idea of the structure even when starting from scratch. The multiple-stage tandem approach enabled structural determination of saponins to a more detailed level than achievable with current single-stage tandem mass spectrometry.

Analysis of 8-hydroxy-2'-deoxyguanosine in rat urine and liver DNA by stable isotope dilution gas chromatography/mass spectrometry.

A previously developed gas chromatographic/mass spectrometric method was applied to the measurement of 8-hydroxy-2'-deoxyguanosine (8-OHdG) in rat liver DNA and in rat urine. For DNA samples, the method included: (i) fortification of samples with [15N]DNA (internal standard), (ii) enzymatic hydrolysis of DNA to deoxynucleosides, (iii) degradation of native nucleosides by treatment with trifluoroacetic acid and hydrazine, (iv) purification by C18 solid-phase extraction (SPE), (v) derivatization (acetylation followed by pentafluorobenzylation, Ac-PFB), and (vi) GC/MS analysis of the derivatives. For urine, the following methodology was used: (i) fortification of the samples with 8-18OHdG, (ii) prepurification by C18/OH SPE, (iii) derivatization, (iv) high-performance liquid chromatography purification of the Ac-PFB derivatives, and (v) GC/MS analysis. The precision of the method was demonstrated by carrying out replicate analysis of several urine and DNA samples: within-run and between-run variability was less than 5 and 8%, respectively. The analytical approaches were sufficiently sensitive to quantitate the urinary excretion of 8-OHdG (490 +/- 70 pmol/kg/24 h; sample size, 600 microliters urine) and to measure the level of 8-OHdG in liver DNA (20 8-OHdG/10(6) deoxynucleosides; sample size, 30 micrograms DNA) of rats not deliberately exposed to oxidative stress. Major advantages over previous methods are increased precision due to the use of proper isotopically labeled internal standards, and increased sensitivity due to the optimization of cleanup procedures. The simultaneous analysis of standards of three different oxidized nucleosides, namely 8-OHdG, thymidine glycol, and 5-hydroxy-methyl-2'-deoxyuridine, is shown.

Chemical properties of the ultimate metabolites of 2-amino-5-phenylpyridine (PHE-P-1) and its ortho-methyl derivative.

The reactivity of the N-acetoxy metabolite of 2-amino-5-phenylpyridine (Phe-P-1), a pyrolysis product of phenylalanine, towards 2'-deoxyguanosine (dG), 2'-deoxyguanosine-3'-monophosphate (dGMP) and DNA was studied and compared with that of the ortho-methyl derivative. Reaction of 2-acetoxyamino-5-phenylpyridine (N-OAc-APP) with dG resulted in substitution at the 8-position of this nucleoside by the ortho carbon of the amine. The major reaction, however, was acetylation of dG. In contrast, 2-acetoxyamino-3-methyl-5-phenyl-pyridine (N-OAc-MeAPP) mainly attacked the 8-position of dG by the exocyclic nitrogen and hardly any acetylation of the nucleoside occurred. The adducts were chromatographically isolated and characterized by their mass and NMR spectra. Upon reaction of N-acetoxy compounds with DNA and dGMP, formation of the same adducts was observed, besides the formation of minor amounts of unidentified compounds, as was established by 32P-postlabelling analysis. The amount of DNA-bound amine, formed by the interaction of N-OAc-APP with DNA, was approximately 15 times smaller than that observed after the reaction with the corresponding ortho-methyl derivative under the same conditions.

Glycosyl compositions and structural characteristics of the potential immuno-adjuvant active saponins in the Quillaja saponaria Molina extract quil A.

Fifty saponin components of Quil A, a commercially available extract from the bark of the South American tree Quillaja saponaria Molina, were partially structurally characterised. The molecular weights were determined by fast-atom bombardment mass spectrometry. The glycosyl and elemental composition of all the saponins was determined by applying our recently developed method, monomer mapping, consisting of a computer program and accurate mass measurements. Support for the presumed identity of the aglycone, i.e. quillaic acid, was found in the accurate mass determination, 1H NMR measurement and chemical reactions. The saponin composition of Quil A was shown to consist of pairs. Within the 3-O bound glycosyl moiety of a pair there was a structural difference: a pentose and rhamnose were interchanged. Structural differences between different pairs were located in the 28-O bound glycosyl moiety. A structural element, unknown to date and of which the elemental composition was deduced to be C8H12O5, was found in the 28-O bound glycosyl moiety of several saponins.

Protected peptide disulfides by oxidative detachment from a support.

A new and efficient procedure for the preparation of protected cyclized and protected symmetrical dimeric peptide disulfides is described. A thiol is immobilized onto a solid phase through coupling of the thiol function with a resin-linked trityl group. Following conventional peptide assembly using the Fmoc-strategy, detachment is performed by oxidation with iodine in a suitable organic solvent. When N,N-dimethylformamide is used as the solvent, and the peptide chain contains an acetamidomethylthio function, located N-terminally in a N alpha-(9-fluorenylmethyloxycarbonyl), or N alpha-tert-butyloxycarbonyl cysteinyl residue, or occurring in the chain, then the corresponding fully protected cyclic peptide disulfide will be obtained in high yield and purity. In other solvents (e.g. dioxane or chloroform-methanol 1:1, v/v), the iodine-mediated oxidation gave not only the cyclic product, but also substantial amounts of the parallel symmetrical dimeric peptide retaining Cys(Acm) at the two identical N-termini.

Simultaneous multiple synthesis and selective conjugation of cyclized peptides derived from a surface loop of a meningococcal class 1 outer membrane protein.

Starting from the alpha-(2,4-dimethoxybenzyl) ester of N-(9-fluorenylmethoxycarbonyl)aspartic acid [Fmoc-Asp-ODmb], side-chain-protected resin-bound Fmoc-peptides containing an N epsilon-1-(4,4-dimethyl-2,6-dioxocyclohexylidene)ethyl lysyl [Lys(Dde)] residue were prepared. The C-terminal dimethoxybenzyl esters of aspartic acid were removed with 1% trifluoroacetic acid and 10% anisole in dichloromethane, followed by Fmoc-cleavage in the usual manner. The resin-bound peptides were then cyclized using 1-benzotriazolyloxy-tris-[N-pyrrolidino]phosphonium hexafluorophosphate (PyBOP) in the presence of N-methylmorpholine. The (dimethyldioxocyclohexylidene)ethyl groups of lysine were removed with 1% hydrazine hydrate in N,N-dimethylacetamide, and the liberated side-chain amino functions were modified by reaction with pentafluorophenyl S-acetylmercaptoacetate (SAMA-OPfp). Finally, the peptides were side-chain deprotected, with exception of the Lys(SAMA) residue, and cleaved from the solid support with trifluoroacetic acid/anisole/water, 95/2.5/2.5. Cyclic peptides comprising 7-14 amino acid residues were obtained employing this procedure. As a model conjugation, cyclo[Thr-Asn-Asn-Asn-Leu-Lys(SAMA)-Thr-Lys-Asp] was coupled with bromoacetamide. The same peptide was also coupled with a bromoacetylpeptide to give a well defined peptide/peptide conjugate. All peptides were conjugated to bromoacetylated tetanus toxoid for immunization purposes.

Method for the analysis of oxidized nucleosides by gas chromatography/mass spectrometry.

A method for sensitive analysis of the oxidatively modified nucleosides 8-hydroxy-2'-deoxyguanosine (8-OHdG) and 5-hydroxymethyl-2'-deoxyuridine (HMdU) is described. The method combines acetylation and pentafluorobenzylation of the nucleosides followed by analysis by gas chromatography/electron capture negative ion chemical ionization-mass spectrometry. The detection limits of the method for aqueous standards of HMdU and 8-OHdG were 12 and 18 fmol of starting material (signal-to-noise ratio, 3:1), respectively. The method was linear for 8-hydroxy-2'-deoxyguanosine over five orders of magnitude and gave satisfactory reproducibilities (intraassay RSD < or = 5%) for the analysis of 8-OHdG in both aqueous standards and urine fortified at the level of 35 nM. The limit of detection for the analysis of 8-OHdG in urine was 1.8 pmol, corresponding to a level of 8-OHdG in urine of 35 nM (10 micrograms/liter) at a urine sample volume of 50 microliters. Besides urine the method was applied to the analysis of 5-hydroxy-methyl-2'-deoxyuridine isolated from genomic DNA of Bacillus subtilis bacteriophage H1. Results obtained indicate that the method is potentially suitable for the determination of oxidized nucleosides in biological samples. The selectivity of the method should be enhanced in order to lower the limit of detection in biological samples.

The identification of hydroxymethyluracil in DNA of Trypanosoma brucei.

We have previously reported the detection of two unusual nucleotides, pdJ and pdV, in the DNA of Trypanosoma brucei (Gommers-Ampt et al., 1991). pdJ was found to be a novel nucleotide and is possibly involved in the regulation of variant specific surface antigen gene expression in trypanosomes. Recent evidence suggests that V could be a precursor of J, making V a key compound in the study of the biosynthesis and function of J. We have therefore determined the structure of V and here we present proof that V is HOMeU. The identity is based on a detailed comparison of dV(p) with authentic HOMedU(p), showing: I) co-migration in three different liquid chromatography analyses II) identical UV absorbance characteristics III) identical behavior in acetyl-pentafluorobenzyl derivatization and subsequent Gas chromatography/Mass spectrometry (GC/MS). The GC/MS technique has not been used before to analyse HOMedU purified from biological material. Because of its high sensitivity, it may also be useful for the detection of the low amounts of HOMedU resulting from oxidative damage of DNA.

The primary structure of cytochrome c from the nematode Caenorhabditis elegans.

The complete amino acid sequence of cytochrome c from the nematode Caenorhabditis elegans was determined. The native protein displays the same spectral properties in the oxidized and reduced states as horse heart cytochrome c. The apoprotein consists of 110 amino acid residues and differs from human cytochrome c by 44 substitutions, one internal deletion, five N-terminal additions and two C-terminal additions. One of the substitutions is the replacement of an 'invariant' phenylalanine residue at position 15 by tyrosine. The N-terminal sequence extension contains a short peptide motif, which is highly homologous with a peptide fragment present at the N-terminus of annelid and insect cytochrome c sequences. From the number of amino acid changes and the evolutionary rate of cytochrome c it would appear that nematodes diverged from a line leading to man about 1.4 billion years ago. When similar data based on the amino acid sequences of the histones H1, H2A, H2B and H3 are taken into account, the average estimate is 1.1 +/- 0.1 billion years.