Chemical cross-linking, mass spectrometry, and in silico modeling of proteasomal 20S core particles of the haloarchaeon Haloferax volcanii

A fast and accurate method is reported to generate distance constraints between juxtaposited amino acids and to validate molecular models of halophilic protein complexes. Proteasomal 20S core particles (CPs) from the haloarchaeon Haloferax volcanii were used to investigate the quaternary structure of halophilic proteins based on their symmetrical, yet distinct subunit composition. Proteasomal CPs are cylindrical barrel-like structures of four-stacked homoheptameric rings of α- and β-type subunits organized in α(7)β(7) β(7)α(7) stoichiometry. The CPs of H. volcanii are formed from a single type of β subunit associated with α1 and/or α2 subunits. Tandem affinity chromatography and new genetic constructs were used to separately isolate α1(7)β(7)β(7)α1(7) and α2(7)β(7)β(7)α2(7) CPs from H. volcanii. Chemically cross-linked peptides of the H. volcanii CPs were analyzed by high-performance mass spectrometry and an open modification search strategy to first generate and then to interpret the resulting tandem mass spectrometric data. Distance constraints obtained by chemical cross-linking mass spectrometry, together with the available structural data of nonhalophilic CPs, facilitated the selection of accurate models of H. volcanii proteasomal CPs composed of α1-, α2-, and β-homoheptameric rings from several different possible structures from Protein Data Bank.     

Androstenol – a Steroid Derived Odor Activates the Hypothalamus in Women

Background

Whether pheromone signaling exists in humans is still a matter of intense discussion. In the present study we tested if smelling of Androstenol, a steroid produced by the human body and reported to affect human behavior, may elicit cerebral activation. A further issue was to evaluate whether the pattern of activation resembles the pattern of common odors.

Methodology

PET measurements of regional cerebral blood flow (rCBF) were conducted in 16 healthy heterosexual women during passive smelling of Androstenol, four ordinary odors (OO), and odorless air (the base line condition).

Principal findings

Smelling Androstenol caused activation of a portion of the hypothalamus, which according to animal data mediates the pheromone triggered mating behavior. Smelling of OO, on the other hand, engaged only the classical olfactory regions (the piriform cortex, lateral amygdala, anterior insular and anterior cingulate cortex).

Conclusions

The observed pattern of activation is very similar to the pattern previously detected with 4,16-androstadien-3-one in heterosexual females. It suggests that several compounds released by human body may activate cerebral networks involved in human reproduction.     

QSAR and 3D-QSAR of phenothiazine type multidrug resistance modulators in P388/ADR cells

A series of 25 phenothiazines and structurally related compounds was investigated by QSAR (quantitative structure activity relationship) and 3D-QSAR methods with respect to their MDR (multidrug resistance) reversing activity in P388/ADR- murine leukemia cell line resistant to ADR (adriamycin). The objective was to outline structural properties important for the investigated activity. Different measures for MDR reversal were used and compared. Two 3D-QSAR approaches were applied-CoMFA (comparative molecular field analysis) and CoMSIA (comparative molecular similarity indices analysis). Both, neutral and protonated forms of the compounds were investigated. Molecular models with good predictive power were derived using a hydrophobic field alone and a combination of steric, hydrophobic, and hydrogen bond acceptor fields of the compounds. In the combined models highest contribution of the hydrogen bond acceptor field was noticed. Thus, the dominant role of the hydrophobic and hydrogen bond acceptor fields for MDR reversing activity of the investigated compounds was demonstrated. The structural regions responsible for the differences in anti-MDR activity were analyzed in respect to their hydrophobic, hydrogen bond acceptor and steric nature. The results may direct design of new phenothiazines and related compounds as MDR modulators.     

Non-enzymatic glycation of elastin

Non-enzymatic glycation of proteins is one of the key mechanisms in the pathogenesis of diabetic complications and may be significant in the age-related changes of tissues. We investigated thein vitro glycation of human aortic -elastin, and chose and adapted methods for evaluating the degree and kinetics of glycation. -Elastin was prepared from thoracic aortas of young accident victims and glycated by incubating with different glucose concentrations (25, 50, 75 and 100 mmol/l) in 0.2 M phosphate buffer, pH 7.8 for 30 days, at 37°C. The degree of glycation was measured by three colorimetric methods,i.e. Nitroblue tetrazolium, 2-thiobarbituric acid and hydrazine; by aminophenyl-boronate affinity chromatography which determines Amadori products; and by a fluorescence method which determines advanced glycosylation end products. The highest degree of glycation was found on day 3 after the beginning of incubation. Fluorescence, as an index of advanced glycation, consistently increased from days 5 to 24. Investigation of the properties of glycated elastin may help in understanding the importance of this long-lived protein for the age-related changes in tissues and for diabetic complications.     

Role of nitrogen sources and metal ions in urease synthesis byMicrococcus varians

Urease (urea amidohydrolase E.C.3.5.1.5) synthesis inMicrococcus varians U-9 was not affected by nitrogen source (peptone or glutamic acid) or its concentration: but depended on the ratio of peptone and urea in culture medium. WhenM. varians grew in culture medium with peptone at or above 0.48g/l and NH₄Cl as an additional nitrogen source, two maxima of urease synthesis occurred; one in the exponential growth phase and the second in the stationary growth phase. Though this bacterium could not utilize either urea or ammonia as the sole nitrogen source, urea caused only one maximum of urease synthesis to occur and shifted the maximum into late exponential phase, suggesting that urea acts as a regulatory factor in urease synthesis. Synthesis of urease was not induced either by urea or by nitrogen starvation and was not repressed by ammonia or by excess of complex nitrogen source. NI²⁺ (up to 0.1 mM) stimulated urease synthesis but decreased bacterial growth, while Co²⁺ only affected bacterial growth and at 0.1 mM Inhibited the growth.

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Résumé La synthèse d'uréase (urée-amidohydrolase E.C.3.5.1.5) chezMicrococcus varians n'est pas affectée par la source d'azote (peptone ou acide glutamique), ni par leurs concentrations, mais dépend du rapport de la peptone à l'urée dans le milieu de culture. QuandM. varians croît dans un milieu de culture contenant la peptone à la concentration égale ou supérieure à 0.48 g/l et le NH₄Cl comme source additionnelle d'azote, on observe deux maximum de synthèse d'uréase: la première dans la phase exponentielle de croissance, et la seconde dans la phase stationnaire de croissance. Blen que cette bactérie ne puisse utilliser ni l'urée ni l'ammoniac comme seule source d'azote, l'urée provoque un seul des maximum de synthèse d'uréase et déplace ce maximum vers la partie ultime de la phase exponentielle, suggérant que l'urée agit comme facteur de régulation dans la synthèse d'uréase. La synthèse d'uréase n'est induite ni par l'urée ni par la starvation d'azote et n'est réprimée ni par l'ammoniac ni par un excès de la source d'azote complexe. Le Ni²⁺ (jusqu'à 0.1 mM) stimule la synthèse d'uréase, mais diminue la croissance bactérienne, tandis que le Co²⁺ n'affecte que la croissance bactérienne et à 0.1 mM inhibe la croissance.

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This work was carried out at the Faculty of Food Technology and Biotechnology, University of Zagreb. Department of Biochemical Engineering, 41000 Zagreb, Pierottijeva 6/IV, Croatia, Yugoslavia.     

Influence of glycation on cis/trans isomerization and tautomerization in novel morphiceptin-related Amadori compounds

The influence of N-glycation of the N-terminus on amide bond stereochemistry and tautomeric distribution has been explored via the synthesis and NMR analysis of novel N-(1-deoxy-D-fructos-1-yl) derivatives (Amadori compounds) of the exogenous, milk derived, opioid tetrapeptide morphiceptin (H-Tyr-Pro-Phe-Pro-NH2). NMR analysis of the protected Amadori compounds revealed the presence of four configurational isomers in DMSO solution arising from cis/trans isomerization about Tyr1-Pro2 and Phe3-Pro4 peptide bonds. Comparison of the data obtained for protected Amadori compounds with those obtained for morphiceptin showed that equilibrium fraction of all-trans isomers in N-glycated peptide derivatives was smaller than in the parent peptide compound. Spectroscopic investigation of unprotected morphiceptin-related Amadori compound revealed the presence of multiple conformers in solution due to cis/trans isomerization of the peptide backbone and tautomerization of the sugar moiety. The equilibrium composition in DMSO is markedly shifted towards furanose forms, amounting to two-thirds of the mixture. The estimated equilibrium of the tautomeric forms in water solution revealed the -pyranose form as the major tautomer (66%).     

Identification and expression analysis of cDNAs encoding channel catfish type I interferons

Previously a cDNA encoding a putative interferon gene, designated CF IFN-1, was identified from a catfish EST library. However, its constitutive expression, absence of a signal peptide, and apparently low level of biological activity suggested that this cDNA likely encoded an expressed pseudogene. Since Southern blot analysis suggested the presence of two to three IFN genes, additional cDNAs were generated from catfish fibroblast and lymphoid cell lines using primers designed to conserved regions of zebrafish and catfish interferon. Using this approach, three novel CF IFN genes, two of which likely encode functional interferon molecules, were identified. At the amino acid level, similarity among CF IFNs ranged from 71% to 82%, whereas similarity to other fish IFNs ranged from 15% to 35%. Although CF IFN-3, like CF IFN-1, lacks a signal peptide, CF IFN-2 and -4 appear to encode full-length, signal sequence-bearing genes. Consistent with their putative identification as functional genes, CF IFN-2 and -4 were not expressed in unstimulated cell lines, and CF IFN-2 was rapidly upregulated in CCO cells in response to virus infection or treatment with dsRNA. Moreover, as with salmon, fugu, and zebrafish interferon genes, CF IFN-1 contained four introns whose locations were conserved not only with respect to other fish IFNs, but also with respect to mammalian IFN-lambda. While it is likely that CF IFNs represent Type I IFNs, several characteristics preclude assigning these cytokines to any particular subfamily.     

Molecular characterization of marine Cyanobacteria from the Indian subcontinent deduced from sequence analysis of the phycocyanin operon (cpcb-IGS-cpcA) and 16S-23S ITS region

Molecular characterization of ten marine cyanobacterial isolates belonging to the order Oscillatoriales was carried out using the phycocyanin locus (cpcBA-IGS) and the 16S-23S internally transcribed spacer region. DNA sequences from the phycocyanin operon discriminated ten genotypes, which corresponded to seven morphotypes identified by traditional microscopic analysis. The cpcB coding region revealed 17 % nucleotide variation, while cpcA exhibited 29 % variation across the studied species. Phylogenetic analyses support the conclusion that the Phormidium and Leptolyngbya genera are not monophyletic. The nucleotide variations were heterogeneously distributed with no or minimal informative nucleotides. Our results suggest that the discriminatory power of the phycocyanin region varies across the cyanobacterial species and strains. The DNA sequence analysis of the 16S-23S internally transcribed spacer region also supports the polyphyletic nature of the studied oscillatorian cyanobacteria. This study demonstrated that morphologically very similar strains might differ genotypically. Thus, molecular approaches comprising different gene regions in combination with morphological criteria may provide better taxonomical resolution of the order Oscillatoriales.