Circular proteins in plants - Solution structure of a novel macrocyclic trypsin inhibitor from Momordica cochinchinensis

Much interest has been generated by recent reports on the discovery of circular (i.e. head-to-tail cyclized) proteins in plants. Here we report the three-dimensional structure of one of the newest such circular proteins, MCoTI-II, a novel trypsin inhibitor from Momordica cochinchinensis, a member of the Cucurbitaceae plant family. The structure consists of a small beta -sheet, several turns, and a cystine knot arrangement of the three disulfide bonds. Interestingly, the molecular topology is similar to that of the plant cyclotides (Craik, D. J., Daly, N. L., Bond, T., and Waine, C. (1999) J. Mol. Biol, 294, 1327-1336), which derive from the Rubiaceae and Violaceae plant families, have antimicrobial activities, and exemplify the cyclic cystine knot structural motif as part of their circular backbone. The sequence, biological activity, and plant family of MCoTI-II are all different from known cyclotides. However, given the structural similarity, cyclic backbone, and plant origin of MCoTI-II, we propose that MCoTI-II can be classified as a new member of the cyclotide class of proteins. The expansion of the cyclotides to include trypsin inhibitory activity and a new plant family highlights the importance and functional variability of circular proteins and the fact that they are more common than has previously been believed, Insights into the possible roles of backbone cyclization have been gained by a comparison of the structure of MCoTI-II with the homologous acyclic trypsin inhibitors CMTI-I and EETI-II from the Cucurbitaceae plant family.

In vivo protein cyclization promoted by a circularly permuted Synechocystis sp PCC6803 DnaB mini-intein

A synthetic Synechocystis sp. PCC6803 DnaB split mini-intein gene was constructed for the in vivo cyclization of recombinant proteins expressed in Escherichia coli. The system was used to cyclize the NH2-terminal domain of E. coli DnaB, the structure of which had been determined previously by NMR spectroscopy. Cyclization was found to proceed efficiently, with little accumulation of precursor, and the product was purified in high yield. The solution structure of cyclic DnaB-N is not significantly different from that of linear DnaB-N and it unfolds reversibly at temperatures similar to14 degreesC higher. Improved hydrogen bonding was observed in the first and last helices, and the length of the last helix was increased, while the 9-amino acid linker used to join the NH2 and COOH termini was found to be highly mobile. The measured thermodynamic stabilization of the structure (DeltaDeltaG approximate to 2 kcal/mol) agrees well with the value estimated from the reduced conformational entropy in the unfolded form. Simple polymer theory can be used to predict likely free energy changes resulting from protein cyclization and how the stabilization depends on the size of the protein and the length of the linker used to connect the termini.

Phoriospongin A and B: Two new nematocidal depsipeptides from the Australian marine sponges Phoriospongia sp and Callyspongia bilamellata

Bioassay-directed fractionation of two southern Australian sponges, Phoriospongia sp. and Callyspongia bilamellata, yielded two new nematocidal depsipeptides, identified as phoriospongins A (1) and B (2). The structures of the phoriospongins were determined by detailed spectroscopic analysis and comparison with the previously reported sponge depsipeptide cyclolithistide A (3), as well as ESIMS and HPLC analysis of acid hydrolysates. It is noteworthy that the unique and yet structurally related metabolites 1-3 are found in sponges spanning three taxonomic orders, Poescilosclerida, Haplosclerida, and Lithistida.

Conformations of platypus venom C-type natriuretic peptide in aqueous solution and sodium dodecyl sulfate micelles

Nuclear magnetic resonance spectroscopy was used to investigate the conformations of the platypus venom C-type natriuretic peptide A (OvCNPa) in aqueous solutions and in solutions containing sodium dodecyl sulfate (SDS) micelles. The chemically synthesized OvCNPa showed a substantial decrease in flexibility in aqueous solution at 10 degreesC, allowing the observation of medium- and long-range nuclear Overhauser enhancement (NOE) connectivities. Three-dimensional structures calculated using these data showed flexible and reasonably well-defined regions, the locations of which were similar in the two solvents. In aqueous solution, the linear part that spans residues 3-14 was basically an extended conformation while the cyclic portion, defined by residues 23-39, contained a series of beta-turns. The overall shape of the cyclic portion was similar to that observed for an atrial natriuretic peptide (ANP) variant in aqueous solution. OvCNPa adopted a different conformation in SDS micelles wherein the N-terminal region, defined by residues 2-10, was more compact, characterised by turns and a helix, while the cyclic region had turns and an overall shape that was fundamentally different from those structures observed in aqueous solution. The hydrophobic cluster, situated at the centre of the ring of the structure in aqueous solution, was absent in the structure in the presence of SDS micelles. Thus, OvCNPa interacts with SDS micelles and can possibly form ion-channels in cell membranes. (C) 2002 Elsevier Science Ltd. All rights reserved.

Tissue-specific expression of head-to-tail cyclized miniproteins in Violaceae and structure determination of the root cyclotide Viola hederacea root cyclotide1

The plant cyclotides are a family of 28 to 37 amino acid miniproteins characterized by their head-to-tail cyclized peptide backbone and six absolutely conserved Cys residues arranged in a cystine knot motif: two disulfide bonds and the connecting backbone segments form a loop that is penetrated by the third disulfide bond. This knotted disulfide arrangement, together with the cyclic peptide backbone, renders the cyclotides extremely stable against enzymatic digest as well as thermal degradation, making them interesting targets for both pharmaceutical and agrochemical applications. We have examined the expression patterns of these fascinating peptides in various Viola species (Violaceae). All tissue types examined contained complex mixtures of cyclotides, with individual profiles differing significantly. We provide evidence for at least 57 novel cyclotides present in a single Viola species (Viola hederacea). Furthermore, we have isolated one cyclotide expressed only in underground parts of V, hederacea and characterized its primary and three-dimensional structure. We propose that cyclotides constitute a new family of plant defense peptides, which might constitute an even larger and, in their biological function, more diverse family than the well-known plant defensins.

Non-ribosomal peptides produced by Brazilian cyanobacterial isolates with antimicrobial activity

Cyanobacterial strains isolated from terrestrial and freshwater habitats in Brazil were evaluated for their antimicrobial and siderophore activities. Metabolites of fifty isolates were extracted from the supernatant culture media and cells using ethyl acetate and methanol, respectively. The extracts of 24 isolates showed antimicrobial activity against several pathogenic bacteria and one yeast. These active extracts were characterized by Q-TOF/MS. The cyanobacterial strains Cylindrospermopsis raciborskii 339-T3, Synechococcus elongatus PCC7942, Microcystis aeruginosa NPCD-1, M. panniformis SCP702 and Fischerella sp. CENA19 provided the most active extracts. The 50 cyanobacterial strains were also screened for the presence of non-ribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) genes and microcystin production. Putative fragment genes coding for NRPS adenylation domains and PKS keto-synthase domains were successfully PCR amplified from 92% and 80% of cyanobacterial strains, respectively. The potential therapeutical compounds siderophores were detected in five cyanobacterial isolates. Microcystin production was detected by ELISA test in 26% of the isolates. Further a protease inhibitor substance was detected by LC-MS/MS in the M. aeruginosa NPLJ-4 extract and the presence of aeruginosin and cyanopeptolin was confirmed by PCR amplification using specific primers, and sequenced. This screening study showed that Brazilian cyanobacterial isolates are a rich source of natural products with potential for pharmacological and biotechnological applications. (C) 2010 Elsevier GmbH. All rights reserved.

Characterization of a microcystin and detection of microcystin synthetase genes from a Brazilian isolate of Nostoc

A nostocalean nitrogen-fixing cyanobacterium isolated from an eutrophic freshwater reservoir located in Piracicaba, Sao Paulo, Brazil, was evaluated for the production of hepatotoxic cyclic heptapeptides, microcystins. Morphologically this new cyanobacterium strain appears closest to Nostoc, however, in the phylogenetic analysis of 165 rRNA gene it falls into a highly stable cluster distantly only related to the typical Nostoc cluster. Extracts of Nostoc sp. CENA88 cultured cells, investigated using ELISA assay, gave positive results and the microcystin profile revealed by ESI-Q-TOF/MS/MS analysis confirmed the production of [Dha(7)]MCYST-YR. Further, Nostoc sp. CENA88 genomic DNA was analyzed by PCR for sequences of mcyD, mcyE and mcyG genes of microcystin synthetase (mcy) cluster. The result revealed the presence of mcyD, mcyE and mcyG genes with similarities to those from mcy of Nostoc sp. strains 152 and IO-102-I and other cyanobacterial genera. The phylogenetic tree based on concatenated McyG, McyD and McyE amino acids clustered the sequences according to cyanobacterial genera, with exception of the Nostoc sp. CENA88 sequence, which was placed in a clade distantly related from other Nostoc strains, as previously observed also in the 165 rRNA phylogenetic analysis. The present study describes for the first time a Brazilian Nostoc microcystin producer and also the occurrence of demethyl MCYST-YR variant in this genus. The sequenced Nostoc genes involved in the microcystin synthesis can contribute to a better understanding of the toxigenicity and evolution of this cyanotoxin. (C) 2009 Elsevier Ltd. All rights reserved.

Activity of platinum-tin catalysts prepared by the Pechini-Adams method for the electrooxidation of ethanol

Pt-Sn electrocatalysts of different compositions were prepared and dispersed on carbon Vulcan XC-72 using the Pechini-Adams method. The catalysts were characterized by energy dispersive X-ray analysis and X-ray diffraction. The electrochemical properties of these electrode materials were also examined by cyclic voltammetry and chronoamperometric experiments in acid medium. The results showed that the presence of Sn greatly enhances the activity of Pt towards the electrooxidation of ethanol. Moreover, it contributes to reduce the amount of noble metal in the anode of direct alcohol fuel cells, which remains one of the challenges to make the technology of direct alcohol fuel cells possible. Electrolysis of ethanol solutions at 0.55 V vs. RHE allowed to determine by liquid chromatography acetaldehyde and acetic acid as the main reaction products. CO(2) was also analyzed after trapping it in a NaOH solution indicating that the cleavage of the C-C bond in the ethanol molecule did occur during the adsorption process. In situ IR reflectance spectroscopy helped to investigate in more details the reaction mechanism through the identification of the reaction products as well as the presence of some intermediate adsorbed species, such as linearly bonded carbon monoxide. (C) 2009 Elsevier B.V. All rights reserved.

Solid-phase microextraction using poly(pyrrole) film and liquid chromatography with UV detection for analysis of antidepressants in plasma samples

Poly(pyrrole) (PPY) coating was prepared on a stainless-steel (SS) wire for solid-phase microextraction (SPME) by electrochemical deposition (cyclic voltammetric). The PPY was evaluated by analyzing new-generation antidepressants (mirtazapine, citalopram, paroxetine, duloxetine, fluoxetine, and sertraline) in plasma sample by SPME and liquid chromatography with UV detection (LC-UV). The effect of electrolyte Solution (lithium perchlorate or tetrabutylammonium perchlorate) and the number of cycles (50, 100 or 200) applied during the polymerization process on the SPME performance was evaluated. Important factors in the optimization of SPME efficiency such as extraction time, temperature, pH, influence of plasma proteins on sorption mechanisms, and desorption conditions are discussed. The SPME-PPY/LC method showed to be linear in concentrations ranging from the limit of quantification (LOQ) to 1200 ng mL(-1). The LOQ values range from 16 to 25 ng mL-1. The inter-day precision of the SPME-PPY/LC method presented coefficient of variation (CV) lower than 15%. Based on analytical validation results, the SPME-PPY/LC methodology showed to be adequate for antidepressant analysis, from therapeutic to toxic levels. In order to evaluate the proposed method for clinical use, the SPME-PPY/LC method was applied to the analysis of plasma samples from elderly depressed patients. (c) 2009 Elsevier B.V. All rights reserved,

Pt-RuO(2) electrodes prepared by thermal decomposition of polymeric precursors as catalysts for direct methanol fuel cell applications

The electrocatalytic activity of Pt and RuO(2) mixed electrodes of different compositions towards methanol oxidation was investigated. The catalysts were prepared by thermal decomposition of polymeric precursors and characterized by energy dispersive X-ray, scanning electronic microscopy, X-ray diffraction and cyclic voltammetry. This preparation method allowed obtaining uniform films with controlled stoichiometry and high surface area. Cyclic voltammetry experiments in the presence of methanol showed that mixed electrodes decreased the potential peak of methanol oxidation by approximately 100 mV (RHE) when compared to the electrode containing only Pt. In addition, voltammetric experiments indicated that the Pt(0.6)Ru(0.4)O(y) electrode led to higher oxidation current densities at lower potentials. Chronoamperometry experiments confirmed the contribution of RuO(2) to the catalytic activity as well as the better performance of the Pt(0.6)Ru(0.4)O(y) electrode composition. Formic acid and CO(2) were identified as being the reaction products formed in the electrolysis performed at 400 and 600 mV. The relative formation of CO(2) was favored in the electrolysis performed at 400 mV (RHE) with the Pt(0.6)Ru(0.4)O(y) electrode. The presence of RuO(2) in Pt-Ru-based electrodes is important for improving the catalytic activity towards methanol electrooxidation. Moreover, the thermal decomposition of polymeric precursors seems to be a promising route for the production of catalysts applicable to DMFC. (C) 2009 International Association for Hydrogen Energy. Published by Elsevier Ltd. All rights reserved.

Generation of Naphthoquinone Radical Anions by Electrospray Ionization: Solution, Gas-Phase, and Computational Chemistry Studies

Radical anions are present in several chemical processes, and understanding the reactivity of these species may be described by their thermodynamic properties. Over the last years, the formation of radical ions in the gas phase has been an important issue concerning electrospray ionization mass spectrometry studies. In this work, we report on the generation of radical anions of quinonoid compounds (Q) by electrospray ionization mass spectrometry. The balance between radical anion formation and the deprotonated molecule is also analyzed by influence of the experimental parameters (gas-phase acidity, electron affinity, and reduction potential) and solvent system employed. The gas-phase parameters for formation of radical species and deprotonated species were achieved on the basis of computational thermochemistry. The solution effects on the formation of radical anion (Q(center dot-)) and dianion (Q(2-)) were evaluated on the basis of cyclic voltammetry analysis and the reduction potentials compared with calculated electron affinities. The occurrence of unexpected ions [Q + 15](-) was described as being a reaction between the solvent system and the radical anion, Q(center dot-).The gas-phase chemistry of the electrosprayed radical anions was obtained by collisional-induced dissociation and compared to the relative energy calculations. These results are important for understanding the formation and reactivity of radical anions and to establish their correlation with the reducing properties by electrospray ionization analyses.

Impedance characteristics of the diamond/carbon fiber electrodes for electrical double-layer capacitor

The electrochemical performance of carbon fibers (CF) and boron-doped diamond electrodes grown on carbon fiber substrate (BDD/CF) was studied. CF substrates were obtained from polyacrylonitrile precursor heat treated at two different temperatures of 1000 and 2000 degrees C to produce the desirable CF carbon graphitization index. This graphitization process influenced the CF conductivity and its chemical surface, also analyzed from X-ray photoelectron spectroscopy measurements. These three-dimensional CF structures allowed a high incorporation of diamond films compared to other carbon substrates such as glass carbon or HOPG. The electrochemical responses, from these four classes of electrodes, were evaluated focusing their application as electrical double-layer capacitors using cyclic voltammetry and impedance measurements. Cyclic voltammetry results revealed that the electrode formed from BDD grown on CF-2000 presented a typical capacitor behavior with the best rectangular shape, compared to those electrodes of CF or BDD/CF-1000. Furthermore, the BDD/CF-2000 electrode presented the lowest impedance, associated to its significant capacitance value of 1940 mu F/cm(2) taking into account the BDD films. This behavior was attributed to the strong dependence between diamond coating texture and the CF graphitization temperature. The largest surface area of BDD/CF-2000 was promoted by its singular film growth mechanism associated to the substrate chemical surface. (c) 2008 Elsevier B.V. All rights reserved.

Morphological and electrochemical investigation of RuO(2)-Ta(2)O(5) oxide films prepared by the Pechini-Adams method

Preparation methods can profoundly affect the structural and electrochemical properties of electrocatalytic coatings. In this investigation, RuO(2)-Ta(2)O(5) thin films containing between 10 and 90 at.% Ru were prepared by the Pechini-Adams method. These coatings were electrochemically and physically characterized by cyclic voltammetry, scanning electron microscopy (SEM), energy dispersive X-ray spectroscopy (EDX), X-ray photoelectron spectroscopy (XPS) and X-ray diffraction (XRD). The composition and morphology of the oxide were investigated before and after accelerated life tests (ALT) by EDX and SEM. SEM results indicate typical mud-flat-cracking morphology for the majority of the films. High resolution SEMs reveal that pure oxide phases exhibit nanoporosity while binary compositions display a very compact structure. EDX analyses reveal considerable amounts of Ru in the coating even after total deactivation. XRD indicated a rutile-type structure for RuO(2) and orthorhombic structure for Ta(2)O(5). XPS data demonstrate that the binding energy of Ta is affected by Ru addition in the thin films, but the binding energy of Ru is not likewise influenced by Ta. The stability of the electrodes was evaluated by ALT performed at 750 mA cm(-2) in 80 degrees C 0.5 mol dm(-3) H(2)SO(4). The performance of electrodes prepared by the Pechini-Adams method is 100% better than that of electrodes prepared by standard thermal decomposition.

Characterization of lipopeptides from Paenibacillus sp (IIRAC30) suppressing Rhizoctonia solani

The main aim was to identify the active compound against Rhizoctonia solani produced by the cassava endophyte Paenibacillus sp. IIRAC-30. The compounds produced were extracted with ethyl acetate and purified by Sephadex column prior to analysis by Q-TOF mass spectrometry. A C(15)-lipopeptide with an estimated molecular weight of 1036 Da and homologues were identified. The lipopeptide had a cyclic structure, which was deduced by interpreting the ESI-MS/MS spectra of main protonated homologues containing 15:0 FA, and the amino acid composition was Glu-Leu-Leu-Val-Asp-Leu-Leu. Therefore, the lipopeptides produced by isolate IIRAC-30 was characterized as a surfactin series. Thus, the main mechanism used by Paenibacillus sp. IIRAC-30 to suppress R. solani was elucidated. Furthermore, because lipopeptides active against phytopathogens generally show low toxicity to humans and the environment, the positive findings presented here suggest that the isolate IIRAC-30 could be a possible candidate for biocontrol of R. solani.

The effect of methanol on the stability of Pt/C and Pt-RuO(x)/C catalysts

The behavior of Pt/C and Pt-RuO(x)/C electrodes subjected to a larger number of potential scans and constant potential for prolonged time periods was investigated in the absence and presence of methanol. The structural changes were analyzed on the basis of the modifications observed in the X-ray diffraction pattern of the catalysts. Carbon monoxide stripping experiments were performed before and after the potential scans, thus enabling analysis of the behavior of the electrochemically active surface area. The resulting solutions were examined by inductively coupled plasma mass spectrometry (ICP-MS). There was reduction in the electrochemically active surface area, as well as increase in crystallite size and dissolution of catalyst components after the potential scan tests. Catalyst degradation was more pronounced in the presence of methanol, and cyclic potential conditions accelerate the degradation mechanisms. (C) 2010 Professor T. Nejat Veziroglu. Published by Elsevier Ltd. All rights reserved.