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Find video protocols related to scientific articles indexed in Pubmed.
An integrative computational model for large-scale identification of metalloproteins in microbial genomes: a focus on iron-sulfur cluster proteins.
Metallomics
PUBLISHED: 08-13-2014
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Metalloproteins represent a ubiquitous group of molecules which are crucial to the survival of all living organisms. While several metal-binding motifs have been defined, it remains challenging to confidently identify metalloproteins from primary protein sequences using computational approaches alone. Here, we describe a comprehensive strategy based on a machine learning approach to design and assess a penalized generalized linear model. We used this strategy to detect members of the iron-sulfur cluster protein family. A new category of descriptors, whose profile is based on profile hidden Markov models, encoding structural information was combined with public descriptors into a linear model. The model was trained and tested on distinct datasets composed of well-characterized iron-sulfur protein sequences, and the resulting model provided higher sensitivity compared to a motif-based approach, while maintaining a good level of specificity. Analysis of this linear model allows us to detect and quantify the contribution of each descriptor, providing us with a better understanding of this complex protein family along with valuable indications for further experimental characterization. Two newly-identified proteins, YhcC and YdiJ, were functionally validated as genuine iron-sulfur proteins, confirming the prediction. The computational model was then applied to over 550 prokaryotic genomes to screen for iron-sulfur proteomes; the results are publicly available at: . This study represents a proof-of-concept for the application of a penalized linear model to identify metalloprotein superfamilies on a large-scale. The application employed here, screening for iron-sulfur proteomes, provides new candidates for further biochemical and structural analysis as well as new resources for an extensive exploration of iron-sulfuromes in the microbial world.
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Theoretical modeling of low-energy electronic absorption bands in reduced cobaloximes.
Chemphyschem
PUBLISHED: 08-11-2014
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The reduced Co(I) states of cobaloximes are powerful nucleophiles that play an important role in the hydrogen-evolving catalytic activity of these species. In this work we analyze the low-energy electronic absorption bands of two cobaloxime systems experimentally and use a variety of density functional theory and molecular orbital ab initio quantum chemical approaches. Overall we find a reasonable qualitative understanding of the electronic excitation spectra of these compounds but show that obtaining quantitative results remains a challenging task.
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Cobaloxime-based artificial hydrogenases.
Inorg Chem
PUBLISHED: 07-16-2014
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Cobaloximes are popular H2 evolution molecular catalysts but have so far mainly been studied in nonaqueous conditions. We show here that they are also valuable for the design of artificial hydrogenases for application in neutral aqueous solutions and report on the preparation of two well-defined biohybrid species via the binding of two cobaloxime moieties, {Co(dmgH)2} and {Co(dmgBF2)2} (dmgH2 = dimethylglyoxime), to apo Sperm-whale myoglobin (SwMb). All spectroscopic data confirm that the cobaloxime moieties are inserted within the binding pocket of the SwMb protein and are coordinated to a histidine residue in the axial position of the cobalt complex, resulting in thermodynamically stable complexes. Quantum chemical/molecular mechanical docking calculations indicated a coordination preference for His93 over the other histidine residue (His64) present in the vicinity. Interestingly, the redox activity of the cobalt centers is retained in both biohybrids, which provides them with the catalytic activity for H2 evolution in near-neutral aqueous conditions.
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TtcA a new tRNA-thioltransferase with an Fe-S cluster.
Nucleic Acids Res.
PUBLISHED: 06-09-2014
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TtcA catalyzes the post-transcriptional thiolation of cytosine 32 in some tRNAs. The enzyme from Escherichia coli was homologously overexpressed in E. coli. The purified enzyme is a dimer containing an iron-sulfur cluster and displays activity in in vitro assays. The type and properties of the cluster were investigated using a combination of UV-visible absorption, EPR and Mössbauer spectroscopy, as well as by site-directed mutagenesis. These studies demonstrated that the TtcA enzyme contains a redox-active and oxygen-sensitive [4Fe-4S] cluster, chelated by only three cysteine residues and absolutely essential for activity. TtcA is unique tRNA-thiolating enzyme using an iron-sulfur cluster for catalyzing a non-redox reaction.
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Terpyridine complexes of first row transition metals and electrochemical reduction of CO? to CO.
Phys Chem Chem Phys
PUBLISHED: 03-20-2014
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Homoleptic terpyridine complexes of first row transition metals are evaluated as catalysts for the electrocatalytic reduction of CO2. Ni and Co-based catalytic systems are shown to reduce CO2 to CO under the conditions tested. The Ni complex was found to exhibit selectivity for CO2 over proton reduction while the Co-based system generates mixtures of CO and H2 with CO?:?H2 ratios being tuneable through variation of the applied potential.
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Biosynthesis and physiology of coenzyme Q in bacteria.
Biochim. Biophys. Acta
PUBLISHED: 01-23-2014
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Ubiquinone, also called coenzyme Q, is a lipid subject to oxido-reduction cycles. It functions in the respiratory electron transport chain and plays a pivotal role in energy generating processes. In this review, we focus on the biosynthetic pathway and physiological role of ubiquinone in bacteria. We present the studies which, within a period of five decades, led to the identification and characterization of the genes named ubi and involved in ubiquinone production in Escherichia coli. When available, the structures of the corresponding enzymes are shown and their biological function is detailed. The phenotypes observed in mutants deficient in ubiquinone biosynthesis are presented, either in model bacteria or in pathogens. A particular attention is given to the role of ubiquinone in respiration, modulation of two-component activity and bacterial virulence. This article is part of a Special Issue entitled: 18th European Bioenergetic Conference.
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Activation of a Unique Flavin-Dependent tRNA-Methylating Agent.
Biochemistry
PUBLISHED: 11-20-2013
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TrmFO is a tRNA methyltransferase that uses methylenetetrahydrofolate (CH2THF) and flavin adenine dinucleotide hydroquinone as cofactors. We have recently shown that TrmFO from Bacillus subtilis stabilizes a TrmFO-CH2-FADH adduct and an ill-defined neutral flavin radical. The adduct contains a unique N-CH2-S moiety, with a methylene group bridging N(5) of the isoalloxazine ring and the sulfur of an active-site cysteine (Cys53). In the absence of tRNA substrate, this species is remarkably stable but becomes catalytically competent for tRNA methylation following tRNA addition using the methylene group as the source of methyl. Here, we demonstrate that this dormant methylating agent can be activated at low pH, and we propose that this process is triggered upon tRNA addition. The reaction proceeds via protonation of Cys53, cleavage of the C-S bond, and generation of a highly reactive [FADH(N(5))?CH2](+) iminium intermediate, which is proposed to be the actual tRNA-methylating agent. This mechanism is fully supported by DFT calculations. The radical present in TrmFO is characterized here by optical and EPR/ENDOR spectroscopy approaches together with DFT calculations and is shown to be the one-electron oxidized product of the TrmFO-CH2-FADH adduct. It is also relatively stable, and its decomposition is facilitated by high pH. These results provide new insights into the structure and reactivity of the unique flavin-dependent methylating agent used by this class of enzymes.
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ubiJ, a New Gene Required for Aerobic Growth and Proliferation in Macrophage, Is Involved in Coenzyme Q Biosynthesis in Escherichia coli and Salmonella enterica Serovar Typhimurium.
J. Bacteriol.
PUBLISHED: 10-18-2013
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Ubiquinone (coenzyme Q or Q8) is a redox active lipid which functions in the respiratory electron transport chain and plays a crucial role in energy-generating processes. In both Escherichia coli and Salmonella enterica serovar Typhimurium, the yigP gene is located between ubiE and ubiB, all three being likely to constitute an operon. In this work, we showed that the uncharacterized yigP gene was involved in Q8 biosynthesis in both strains, and we have renamed it ubiJ. Under aerobic conditions, an ubiJ mutant was found to be impaired for Q8 biosynthesis and for growth in rich medium but did not present any defect anaerobically. Surprisingly, the C-terminal 50 amino acids, predicted to interact with lipids, were sufficient to restore Q8 biosynthesis and growth of the ubiJ mutant. Salmonella ubiE and ubiB mutants were impaired in Q8 biosynthesis and in respiration using different electron acceptors. Moreover, ubiE, ubiJ, and ubiB mutants were all impaired for Salmonella intracellular proliferation in macrophages. Taken together, our data establish an important role for UbiJ in Q8 biosynthesis and reveal an unexpected link between Q8 and virulence. They also emphasize that Salmonella organisms in an intracellular lifestyle rely on aerobic respiration to survive and proliferate within macrophages.
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An EPR/HYSCORE, Mössbauer, and resonance Raman study of the hydrogenase maturation enzyme HydF: a model for N-coordination to [4Fe-4S] clusters.
J. Biol. Inorg. Chem.
PUBLISHED: 08-20-2013
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The biosynthesis of the organometallic H cluster of [Fe-Fe] hydrogenase requires three accessory proteins, two of which (HydE and HydG) belong to the radical S-adenosylmethionine enzyme superfamily. The third, HydF, is an Fe-S protein with GTPase activity. The [4Fe-4S] cluster of HydF is bound to the polypeptide chain through only the three, conserved, cysteine residues present in the binding sequence motif CysXHisX(46-53)HisCysXXCys. However, the involvement of the two highly conserved histidines as a fourth ligand for the cluster coordination is controversial. In this study, we set out to characterize further the [4Fe-4S] cluster of HydF using Mössbauer, EPR, hyperfine sublevel correlation (HYSCORE), and resonance Raman spectroscopy in order to investigate the influence of nitrogen ligands on the spectroscopic properties of [4Fe-4S](2+/+) clusters. Our results show that Mössbauer, resonance Raman, and EPR spectroscopy are not able to readily discriminate between the imidazole-coordinated [4Fe-4S] cluster and the non-imidazole-bound [4Fe-4S] cluster with an exchangeable fourth ligand that is present in wild-type HydF. HYSCORE spectroscopy, on the other hand, detects the presence of an imidazole/histidine ligand on the cluster on the basis of the appearance of a specific spectral pattern in the strongly coupled region, with a coupling constant of approximately 6 MHz. We also discovered that a His-tagged version of HydF, with a hexahistidine tag at the N-terminus, has a [4Fe-4S] cluster coordinated by one histidine from the tag. This observation strongly indicates that care has to be taken in the analysis of data obtained on tagged forms of metalloproteins.
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Engineering the optical response of the titanium-MIL-125 metal-organic framework through ligand functionalization.
J. Am. Chem. Soc.
PUBLISHED: 07-15-2013
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Herein we discuss band gap modification of MIL-125, a TiO2/1,4-benzenedicarboxylate (bdc) metal-organic framework (MOF). Through a combination of synthesis and computation, we elucidated the electronic structure of MIL-125 with aminated linkers. The band gap decrease observed when the monoaminated bdc-NH2 linker was used arises from donation of the N 2p electrons to the aromatic linking unit, resulting in a red-shifted band above the valence-band edge of MIL-125. We further explored in silico MIL-125 with the diaminated linker bdc-(NH2)2 and other functional groups (-OH, -CH3, -Cl) as alternative substitutions to control the optical response. The bdc-(NH2)2 linking unit was predicted to lower the band gap of MIL-125 to 1.28 eV, and this was confirmed through the targeted synthesis of the bdc-(NH2)2-based MIL-125. This study illustrates the possibility of tuning the optical response of MOFs through rational functionalization of the linking unit, and the strength of combined synthetic/computational approaches for targeting functionalized hybrid materials.
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ubiI, a new gene in Escherichia coli coenzyme Q biosynthesis, is involved in aerobic C5-hydroxylation.
J. Biol. Chem.
PUBLISHED: 05-24-2013
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Coenzyme Q (ubiquinone or Q) is a redox-active lipid found in organisms ranging from bacteria to mammals in which it plays a crucial role in energy-generating processes. Q biosynthesis is a complex pathway that involves multiple proteins. In this work, we show that the uncharacterized conserved visC gene is involved in Q biosynthesis in Escherichia coli, and we have renamed it ubiI. Based on genetic and biochemical experiments, we establish that the UbiI protein functions in the C5-hydroxylation reaction. A strain deficient in ubiI has a low level of Q and accumulates a compound derived from the Q biosynthetic pathway, which we purified and characterized. We also demonstrate that UbiI is only implicated in aerobic Q biosynthesis and that an alternative enzyme catalyzes the C5-hydroxylation reaction in the absence of oxygen. We have solved the crystal structure of a truncated form of UbiI. This structure shares many features with the canonical FAD-dependent para-hydroxybenzoate hydroxylase and represents the first structural characterization of a monooxygenase involved in Q biosynthesis. Site-directed mutagenesis confirms that residues of the flavin binding pocket of UbiI are important for activity. With our identification of UbiI, the three monooxygenases necessary for aerobic Q biosynthesis in E. coli are known.
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Spontaneous activation of [FeFe]-hydrogenases by an inorganic [2Fe] active site mimic.
Nat. Chem. Biol.
PUBLISHED: 05-22-2013
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Hydrogenases catalyze the formation of hydrogen. The cofactor (H-cluster) of [FeFe]-hydrogenases consists of a [4Fe-4S] cluster bridged to a unique [2Fe] subcluster whose biosynthesis in vivo requires hydrogenase-specific maturases. Here we show that a chemical mimic of the [2Fe] subcluster can reconstitute apo-hydrogenase to full activity, independent of helper proteins. The assembled H-cluster is virtually indistinguishable from the native cofactor. This procedure will be a powerful tool for developing new artificial H?-producing catalysts.
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A computational study of the mechanism of hydrogen evolution by cobalt(diimine-dioxime) catalysts.
Chemistry
PUBLISHED: 05-14-2013
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Cobalt(diimine-dioxime) complexes catalyze hydrogen evolution with low overpotentials and remarkable stability. In this study, DFT calculations were used to investigate their catalytic mechanism, to demonstrate that the initial active state was a Co(I) complex and that H2 was evolved in a heterolytic manner through the protonation of a Co(II)-hydride intermediate. In addition, these catalysts were shown to adjust their electrocatalytic potential for hydrogen evolution to the pH value of the solution and such a property was assigned to the presence of a H(+)-exchange site on the oxime bridge. It was possible to establish that protonation of the bridge was directly involved in the H2-evolution mechanism through proton-coupled electron-transfer steps. A consistent mechanistic scheme is proposed that fits the experimentally determined electrocatalytic and electrochemical potentials of cobalt(diimine-dioxime) complexes and reproduces the observed positive shift of the electrocatalytic potential with increasing acidity of the proton source.
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Catalytic hydrogen production by a Ni-Ru mimic of NiFe hydrogenases involves a proton-coupled electron transfer step.
Chem. Commun. (Camb.)
PUBLISHED: 04-23-2013
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A combined electrochemical and theoretical study suggests that hydrogen evolution from weak acids catalyzed by a structural mimic of the active site of NiFe hydrogenases [Ni(xbsms)Ru(C6Me6)Cl](+) proceeds through proton-coupled electron transfer steps.
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Two Fe-S clusters catalyze sulfur insertion by radical-SAM methylthiotransferases.
Nat. Chem. Biol.
PUBLISHED: 03-05-2013
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How living organisms create carbon-sulfur bonds during the biosynthesis of critical sulfur-containing compounds is still poorly understood. The methylthiotransferases MiaB and RimO catalyze sulfur insertion into tRNAs and ribosomal protein S12, respectively. Both belong to a subgroup of radical-S-adenosylmethionine (radical-SAM) enzymes that bear two [4Fe-4S] clusters. One cluster binds S-adenosylmethionine and generates an Ado• radical via a well-established mechanism. However, the precise role of the second cluster is unclear. For some sulfur-inserting radical-SAM enzymes, this cluster has been proposed to act as a sacrificial source of sulfur for the reaction. In this paper, we report parallel enzymological, spectroscopic and crystallographic investigations of RimO and MiaB, which provide what is to our knowledge the first evidence that these enzymes are true catalysts and support a new sulfation mechanism involving activation of an exogenous sulfur cosubstrate at an exchangeable coordination site on the second cluster, which remains intact during the reaction.
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In vivo [Fe-S] cluster acquisition by IscR and NsrR, two stress regulators in Escherichia coli.
Mol. Microbiol.
PUBLISHED: 01-16-2013
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The multi-proteins Isc and Suf systems catalyse the biogenesis of [Fe-S] proteins. Here we investigate how NsrR and IscR, transcriptional regulators that sense NO and [Fe-S] homeostasis, acquire their [Fe-S] clusters under both normal and iron limitation conditions. Clusters directed at the apo-NsrR and apo-IscR proteins are built on either of the two scaffolds, IscU or SufB. However, differences arise in [Fe-S] delivery steps. In the case of NsrR, scaffolds deliver clusters to either one of the two ATCs, IscA and SufA, and, subsequently, to the non-Isc non-Suf ATC, ErpA. Nevertheless, a high level of SufA can bypass the requirement for ErpA. In the case of IscR, several routes occur. One does not include assistance of any ATC. Others implicate ATCs IscA or ErpA, but, surprisingly, SufA was totally absent from any IscR maturation pathways. Both IscR and NsrR have the intrinsic capacity to sense iron limitation. However, NsrR appeared to be efficiently matured by Isc and Suf, thereby preventing NsrR to act as a physiologically relevant iron sensor. This work emphasizes that different maturation pathways arise as a function of the apo-target considered, possibly in relation with the type of cluster, [2Fe-2S] versus [4Fe-4S], it binds.
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The methylthiolation reaction mediated by the Radical-SAM enzymes.
Biochim. Biophys. Acta
PUBLISHED: 08-18-2011
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Over the past 10 years, considerable progress has been made in our understanding of the mechanistic enzymology of the Radical-SAM enzymes. It is now clear that these enzymes appear to be involved in a remarkably wide range of chemically challenging reactions. This review article highlights mechanistic and structural aspects of the methylthiotransferases (MTTases) sub-class of the Radical-SAM enzymes. The mechanism of methylthio insertion, now observed to be performed by three different enzymes is an exciting unsolved problem. This article is part of a Special Issue entitled: Radical SAM enzymes and Radical Enzymology.
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Artificial photosynthesis: from molecular catalysts for light-driven water splitting to photoelectrochemical cells.
Photochem. Photobiol.
PUBLISHED: 08-08-2011
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Photosynthesis has been for many years a fascinating source of inspiration for the development of model systems able to achieve efficient light-to-chemical energetic transduction. This field of research, called "artificial photosynthesis," is currently the subject of intense interest, driven by the aim of converting solar energy into the carbon-free fuel hydrogen through the light-driven water splitting. In this review, we highlight the recent achievements on light-driven water oxidation and hydrogen production by molecular catalysts and we shed light on the perspectives in terms of implementation into water splitting technological devices.
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Splitting water with cobalt.
Angew. Chem. Int. Ed. Engl.
PUBLISHED: 07-11-2011
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The future of energy supply depends on innovative breakthroughs regarding the design of cheap, sustainable, and efficient systems for the conversion and storage of renewable energy sources, such as solar energy. The production of hydrogen, a fuel with remarkable properties, through sunlight-driven water splitting appears to be a promising and appealing solution. While the active sites of enzymes involved in the overall water-splitting process in natural systems, namely hydrogenases and photosystem II, use iron, nickel, and manganese ions, cobalt has emerged in the past five years as the most versatile non-noble metal for the development of synthetic H(2)- and O(2)-evolving catalysts. Such catalysts can be further coupled with photosensitizers to generate photocatalytic systems for light-induced hydrogen evolution from water.
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Methylations: a radical mechanism.
Chem. Biol.
PUBLISHED: 05-26-2011
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On the basis of labeling experiments, Grove et al. (2011) have shown how an electrophilic carbon (from an RNA adenosine) can be methylated by S-adenosylmethionine-dependent methyltransferases though an original radical mechanism.
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Coenzyme Q biosynthesis: Coq6 is required for the C5-hydroxylation reaction and substrate analogs rescue Coq6 deficiency.
Chem. Biol.
PUBLISHED: 04-08-2011
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Coenzyme Q (Q), an essential component of eukaryotic cells, is synthesized by several enzymes from the precursor 4-hydroxybenzoic acid. Mutations in six of the Q biosynthesis genes cause diseases that can sometimes be ameliorated by oral Q supplementation. We establish here that Coq6, a predicted flavin-dependent monooxygenase, is involved exclusively in the C5-hydroxylation reaction. In an unusual way, the ferredoxin Yah1 and the ferredoxin reductase Arh1 may be the in vivo source of electrons for Coq6. We also show that hydroxylated analogs of 4-hydroxybenzoic acid, such as vanillic acid or 3,4-dihydroxybenzoic acid, restore Q biosynthesis and respiration in a Saccharomyces cerevisiae coq6 mutant. Our results demonstrate that appropriate analogs of 4-hydroxybenzoic acid can bypass a deficient Q biosynthetic enzyme and might be considered for the treatment of some primary Q deficiencies.
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Deficit of tRNA(Lys) modification by Cdkal1 causes the development of type 2 diabetes in mice.
J. Clin. Invest.
PUBLISHED: 03-17-2011
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The worldwide prevalence of type 2 diabetes (T2D), which is caused by a combination of environmental and genetic factors, is increasing. With regard to genetic factors, variations in the gene encoding Cdk5 regulatory associated protein 1-like 1 (Cdkal1) have been associated with an impaired insulin response and increased risk of T2D across different ethnic populations, but the molecular function of this protein has not been characterized. Here, we show that Cdkal1 is a mammalian methylthiotransferase that biosynthesizes 2-methylthio-N6-threonylcarbamoyladenosine (ms2t6A) in tRNA(Lys)(UUU) and that it is required for the accurate translation of AAA and AAG codons. Mice with pancreatic ? cell-specific KO of Cdkal1 (referred to herein as ? cell KO mice) showed pancreatic islet hypertrophy, a decrease in insulin secretion, and impaired blood glucose control. In Cdkal1-deficient ? cells, misreading of Lys codon in proinsulin occurred, resulting in a reduction of glucose-stimulated proinsulin synthesis. Moreover, expression of ER stress-related genes was upregulated in these cells, and abnormally structured ER was observed. Further, the ? cell KO mice were hypersensitive to high fat diet-induced ER stress. These findings suggest that glucose-stimulated translation of proinsulin may require fully modified tRNA(Lys)(UUU), which could potentially explain the molecular pathogenesis of T2D in patients carrying cdkal1 risk alleles.
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H2 evolution and molecular electrocatalysts: determination of overpotentials and effect of homoconjugation.
Inorg Chem
PUBLISHED: 10-21-2010
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In an effort to standardize the determination of overpotential values for H(2)-evolving catalysts in non-aqueous solvents and allow a reliable comparison of catalysts prepared and assayed by different groups, we propose to adopt the half-wave potential as reference potential. We provide a simple method for measuring it from usual stationary cyclic voltammograms, and we derive the formulas to which the measured potential should be compared, taking into account the effect of homoconjugation. We also revisit tabulated values of the standard reduction potential of protons in nonaqueous solvents, E(H+/H(2))°.
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A structural and functional mimic of the active site of NiFe hydrogenases.
Chem. Commun. (Camb.)
PUBLISHED: 07-12-2010
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The structural mimic of the active site of NiFe hydrogenases, [Ni(xbsms)FeCp(CO)](BF(4)), is an electrocatalyst for hydrogen evolution from trifluoroacetic acid in DMF.
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S-Adenosylmethionine-dependent radical-based modification of biological macromolecules.
Curr. Opin. Struct. Biol.
PUBLISHED: 06-30-2010
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Proteins and RNA molecules enjoy a variety of chemically complex post-translational and post-transcriptional modifications. The chemistry at work in these reactions, which was considered to be exclusively ionic in nature has recently been shown to depend on radical mechanisms in some cases. The overwhelming majority of these radical-based reactions are catalyzed by Radical-SAM enzymes. This review article highlights mechanistic and structural aspects of this class of reactions and indicates important research directions to be addressed.
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Identification of eukaryotic and prokaryotic methylthiotransferase for biosynthesis of 2-methylthio-N6-threonylcarbamoyladenosine in tRNA.
J. Biol. Chem.
PUBLISHED: 06-28-2010
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Bacterial and eukaryotic transfer RNAs have been shown to contain hypermodified adenosine, 2-methylthio-N(6)-threonylcarbamoyladenosine, at position 37 (A(37)) adjacent to the 3-end of the anticodon, which is essential for efficient and highly accurate protein translation by the ribosome. Using a combination of bioinformatic sequence analysis and in vivo assay coupled to HPLC/MS technique, we have identified, from distinct sequence signatures, two methylthiotransferase (MTTase) subfamilies, designated as MtaB in bacterial cells and e-MtaB in eukaryotic and archaeal cells. Both subfamilies are responsible for the transformation of N(6)-threonylcarbamoyladenosine into 2-methylthio-N(6)-threonylcarbamoyladenosine. Recently, a variant within the human CDKAL1 gene belonging to the e-MtaB subfamily was shown to predispose for type 2 diabetes. CDKAL1 is thus the first eukaryotic MTTase identified so far. Using purified preparations of Bacillus subtilis MtaB (YqeV), a CDKAL1 bacterial homolog, we demonstrate that YqeV/CDKAL1 enzymes, as the previously studied MTTases MiaB and RimO, contain two [4Fe-4S] clusters. This work lays the foundation for elucidating the function of CDKAL1.
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A genetic analysis of the response of Escherichia coli to cobalt stress.
Environ. Microbiol.
PUBLISHED: 06-16-2010
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Cobalt can be toxic and the way cells adapt to its presence is largely unknown. Here we carried out a transcriptomic analysis of Escherichia coli exposed to cobalt. A limited number of genes were either up- or downregulated. Upregulated genes include the isc and the nfuA genes encoding Fe/S biogenesis assisting factors, and the rcnA gene encoding a cobalt efflux system. Downregulated genes are implicated in anaerobic metabolism (narK, nirB, hybO, grcA), metal transport (feoB, nikA), sulfate/thiosulfate import (cysP), and one is of unknown function (yeeE). Cobalt regulation of isc, nfuA, hybO, cysP and yeeE genes was found to involve IscR, a Fe/S transcriptional regulator. Previously, the Suf Fe/S biogenesis machinery was found to be important for cobalt stress adaptation, but suf genes did not show up in the microarray analysis. Therefore, we used qRT-PCR analysis and found that cobalt induced the suf operon expression. Moreover, kinetic analysis of the cobalt-mediated induction of the suf operon expression allowed us to propose that cobalt toxicity is caused first by impaired Fe/S biogenesis, followed by decreased iron bioavailability and eventually oxidative stress.
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Iron-sulfur (Fe-S) cluster assembly: the SufBCD complex is a new type of Fe-S scaffold with a flavin redox cofactor.
J. Biol. Chem.
PUBLISHED: 05-11-2010
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Assembly of iron-sulfur (Fe-S) clusters and maturation of Fe-S proteins in vivo require complex machineries. In Escherichia coli, under adverse stress conditions, this process is achieved by the SUF system that contains six proteins as follows: SufA, SufB, SufC, SufD, SufS, and SufE. Here, we provide a detailed characterization of the SufBCD complex whose function was so far unknown. Using biochemical and spectroscopic analyses, we demonstrate the following: (i) the complex as isolated exists mainly in a 1:2:1 (B:C:D) stoichiometry; (ii) the complex can assemble a [4Fe-4S] cluster in vitro and transfer it to target proteins; and (iii) the complex binds one molecule of flavin adenine nucleotide per SufBC(2)D complex, only in its reduced form (FADH(2)), which has the ability to reduce ferric iron. These results suggest that the SufBC(2)D complex functions as a novel type of scaffold protein that assembles an Fe-S cluster through the mobilization of sulfur from the SufSE cysteine desulfurase and the FADH(2)-dependent reductive mobilization of iron.
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Involvement of mitochondrial ferredoxin and para-aminobenzoic acid in yeast coenzyme Q biosynthesis.
Chem. Biol.
PUBLISHED: 02-11-2010
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Yeast ubiquinone or coenzyme Q(6) (Q(6)) is a redox active lipid that plays a crucial role in the mitochondrial electron transport chain. At least nine proteins (Coq1p-9p) participate in Q(6) biosynthesis from 4-hydroxybenzoate (4-HB). We now show that the mitochondrial ferredoxin Yah1p and the ferredoxin reductase Arh1p are required for Q(6) biosynthesis, probably for the first hydroxylation of the pathway. Conditional Gal-YAH1 and Gal-ARH1 mutants accumulate 3-hexaprenyl-4-hydroxyphenol and 3-hexaprenyl-4-aminophenol. Para-aminobenzoic acid (pABA) is shown to be the precursor of 3-hexaprenyl-4-aminophenol and to compete with 4-HB for the prenylation reaction catalyzed by Coq2p. Yeast cells convert U-((13)C)-pABA into (13)C ring-labeled Q(6), a result that identifies pABA as a new precursor of Q(6) and implies an additional NH(2)-to-OH conversion in Q(6) biosynthesis. Our study identifies pABA, Yah1p, and Arh1p as three actors in Q(6) biosynthesis.
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Mechanism of hydrogen evolution catalyzed by NiFe hydrogenases: insights from a Ni-Ru model compound.
Dalton Trans
PUBLISHED: 12-14-2009
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DFT modeling has been used to investigate a previously proposed mechanism of proton reduction catalyzed by [Ni(xbsms)Ru(CO)(2)Cl(2)] (H(2)xbsms = 1,2-bis(4-mercapto-3,3-dimethyl-2-thiabutyl)benzene), a bio-inspired mimic of NiFe hydrogenases based on a Ni-Ru framework. Protonation of the 2e(-)-reduced compound, from which a chloride anion has been eliminated, results in the formation of a semi-bridging hydride derivative with structural features comparable to those of the Ni-C state catalytic intermediate of native hydrogenases. The present study thus provides structural and functional insights into the enzymatic mechanism including the possible involvement of a bridging hydride derivative and heterolytic formation of a dihydrogen molecule on a {Ni(mu-S)(2)M} framework.
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Post-translational modification of ribosomal proteins: structural and functional characterization of RimO from Thermotoga maritima, a radical S-adenosylmethionine methylthiotransferase.
J. Biol. Chem.
PUBLISHED: 12-09-2009
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Post-translational modifications of ribosomal proteins are important for the accuracy of the decoding machinery. A recent in vivo study has shown that the rimO gene is involved in generation of the 3-methylthio derivative of residue Asp-89 in ribosomal protein S12 (Anton, B. P., Saleh, L., Benner, J. S., Raleigh, E. A., Kasif, S., and Roberts, R. J. (2008) Proc. Natl. Acad. Sci. U. S. A. 105, 1826-1831). This reaction is formally identical to that catalyzed by MiaB on the C2 of adenosine 37 near the anticodon of several tRNAs. We present spectroscopic evidence that Thermotoga maritima RimO, like MiaB, contains two [4Fe-4S] centers, one presumably bound to three invariant cysteines in the central radical S-adenosylmethionine (AdoMet) domain and the other to three invariant cysteines in the N-terminal UPF0004 domain. We demonstrate that holo-RimO can specifically methylthiolate the aspartate residue of a 20-mer peptide derived from S12, yielding a mixture of mono- and bismethylthio derivatives. Finally, we present the 2.0 A crystal structure of the central radical AdoMet and the C-terminal TRAM (tRNA methyltransferase 2 and MiaB) domains in apo-RimO. Although the core of the open triose-phosphate isomerase (TIM) barrel of the radical AdoMet domain was conserved, RimO showed differences in domain organization compared with other radical AdoMet enzymes. The unusually acidic TRAM domain, likely to bind the basic S12 protein, is located at the distal edge of the radical AdoMet domain. The basic S12 protein substrate is likely to bind RimO through interactions with both the TRAM domain and the concave surface of the incomplete TIM barrel. These biophysical results provide a foundation for understanding the mechanism of methylthioation by radical AdoMet enzymes in the MiaB/RimO family.
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From hydrogenases to noble metal-free catalytic nanomaterials for H2 production and uptake.
Science
PUBLISHED: 12-08-2009
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Interconversion of water and hydrogen in unitized regenerative fuel cells is a promising energy storage framework for smoothing out the temporal fluctuations of solar and wind power. However, replacement of presently available platinum catalysts by lower-cost and more abundant materials is a requisite for this technology to become economically viable. Here, we show that the covalent attachment of a nickel bisdiphosphine-based mimic of the active site of hydrogenase enzymes onto multiwalled carbon nanotubes results in a high-surface area cathode material with high catalytic activity under the strongly acidic conditions required in proton exchange membrane technology. Hydrogen evolves from aqueous sulfuric acid solution with very low overvoltages (20 millivolts), and the catalyst exhibits exceptional stability (more than 100,000 turnovers). The same catalyst is also very efficient for hydrogen oxidation in this environment, exhibiting current densities similar to those observed for hydrogenase-based materials.
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Cobalt and nickel diimine-dioxime complexes as molecular electrocatalysts for hydrogen evolution with low overvoltages.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 11-30-2009
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Hydrogen production through the reduction of water appears to be a convenient solution for the long-run storage of renewable energies. However, economically viable hydrogen production requests platinum-free catalysts, because this expensive and scarce (only 37 ppb in the Earths crust) metal is not a sustainable resource [Gordon RB, Bertram M, Graedel TE (2006) Proc Natl Acad Sci USA 103:1209-1214]. Here, we report on a new family of cobalt and nickel diimine-dioxime complexes as efficient and stable electrocatalysts for hydrogen evolution from acidic nonaqueous solutions with slightly lower overvoltages and much larger stabilities towards hydrolysis as compared to previously reported cobaloxime catalysts. A mechanistic study allowed us to determine that hydrogen evolution likely proceeds through a bimetallic homolytic pathway. The presence of a proton-exchanging site in the ligand, furthermore, provides an exquisite mechanism for tuning the electrocatalytic potential for hydrogen evolution of these compounds in response to variations of the acidity of the solution, a feature only reported for native hydrogenase enzymes so far.
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Cyclopentadienyl ruthenium-nickel catalysts for biomimetic hydrogen evolution: electrocatalytic properties and mechanistic DFT studies.
Chemistry
PUBLISHED: 08-12-2009
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The new dinuclear nickel-ruthenium complexes [Ni(xbsms)RuCp(L)][PF(6)] (H(2)xbsms = 1,2-bis(4-mercapto-3,3-dimethyl-2-thiabutyl)benzene; Cp(-) = cyclopentadienyl; L = DMSO, CO, PPh(3), and PCy(3)) are reported and are bioinspired mimics of NiFe hydrogenases. These compounds were characterized by X-ray diffraction techniques and display novel structural motifs. Interestingly, [Ni(xbsms)RuCpCO][PF(6)] is stereochemically nonrigid in solution and an isomerization mechanism was derived with the help of density functional theory (DFT) calculations. Because of an increased electron density on the metal centers [Eur. J. Inorg. Chem. 2007, 18, 2613-2626] with respect to the previously described [Ni(xbsms)Ru(CO)(2)Cl(2)] and [Ni(xbsms)Ru(p-cymene)Cl](+) complexes, [Ni(xbsms)RuCp(dmso)][PF(6)] catalyzes hydrogen evolution from Et(3)NH(+) in DMF with an overpotential reduced by 180 mV and thus represents the most efficient NiFe hydrogenase functional mimic. DFT calculations were carried out with several methods to investigate the catalytic cycle and, coupled with electrochemical measurements, allowed a mechanism to be proposed. A terminal or bridging hydride derivative was identified as the active intermediate, with the structure of the bridging form similar to that of the Ni-C active state of NiFe hydrogenases.
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The CsdA cysteine desulphurase promotes Fe/S biogenesis by recruiting Suf components and participates to a new sulphur transfer pathway by recruiting CsdL (ex-YgdL), a ubiquitin-modifying-like protein.
Mol. Microbiol.
PUBLISHED: 06-23-2009
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Cysteine desulphurases are primary sources of sulphur that can eventually be used for Fe/S biogenesis or thiolation of various cofactors and tRNA. Escherichia coli contains three such enzymes, IscS, SufS and CsdA. The importance of IscS and SufS in Fe/S biogenesis is well established. The physiological role of CsdA in contrast remains uncertain. We provide here additional evidences for a functional redundancy between the three cysteine desulphurases in vivo. In particular, we show that a deficiency in isoprenoid biosynthesis is the unique cause of the lethality of the iscS sufS mutant. Moreover, we show that CsdA is engaged in two separate sulphur transfer pathways. In one pathway, CsdA interacts functionally with SufE-SufBCD proteins to assist Fe/S biogenesis. In another pathway, CsdA interacts with CsdE and a newly discovered protein, which we called CsdL, resembling E1-like proteins found in ubiquitin-like modification systems. We propose this new pathway to allow synthesis of an as yet to be discovered thiolated compound.
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Snapshots of dynamics in synthesizing N(6)-isopentenyladenosine at the tRNA anticodon.
Biochemistry
PUBLISHED: 05-14-2009
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Bacterial and eukaryotic tRNAs that decode codons starting with uridine have a hydrophobically hypermodified adenosine at position 37 (A(37)) adjacent to the 3-end of the anticodon, which is essential for efficient and highly accurate protein translation by the ribosome. However, it remains unclear as to how the corresponding tRNAs are selected to be modified by alkylation at the correct position of the adenosine base. We have determined a series of crystal structures of bacterial tRNA isopentenyltransferase (MiaA) in apo- and tRNA-bound forms, which completely render snapshots of substrate selections during the modification of RNA. A compact evolutionary inserted domain (herein swinging domain) in MiaA that exhibits as a highly mobile entity moves around the catalytic domain as likely to reach and trap the tRNA substrate. Thereby, MiaA clamps the anticodon stem loop of the tRNA substrate between the catalytic and swinging domains, where the two conserved elongated residues from the swinging domain pinch the two flanking A(36) and A(38) together to squeeze out A(37) into the reaction tunnel. The site-specific isopentenylation of RNA is thus ensured by a characteristic pinch-and-flip mechanism and by a reaction tunnel to confine the substrate selection. Furthermore, combining information from soaking experiments with structural comparisons, we propose a mechanism for the ordered substrate binding of MiaA.
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Native Escherichia coli SufA, coexpressed with SufBCDSE, purifies as a [2Fe-2S] protein and acts as an Fe-S transporter to Fe-S target enzymes.
J. Am. Chem. Soc.
PUBLISHED: 04-16-2009
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Iron-sulfur (Fe-S) clusters are versatile biological cofactors that require biosynthetic systems in vivo to be assembled. In Escherichia coli, the Isc (iscRSUA-hscBA-fdx-iscX) and Suf (sufABCDSE) pathways fulfill this function. Despite extensive biochemical and genetic analysis of these two pathways, the physiological function of the A-type proteins of each pathway (IscA and SufA) is still unclear. Studies conducted in vitro suggest two possible functions for A-type proteins, as Fe-S scaffold/transfer proteins or as iron donors during cluster assembly. To resolve this issue, SufA was coexpressed in vivo with its cognate partner proteins from the suf operon, SufBCDSE. Native SufA purified anaerobically using this approach was unambiguously demonstrated to be a [2Fe-2S] protein by biochemical analysis and UV-vis, Mossbauer, resonance Raman, and EPR spectroscopy. Furthermore, native [2Fe-2S] SufA can transfer its Fe-S cluster to both [2Fe-2S] and [4Fe-4S] apoproteins. These results clearly show that A-type proteins form Fe-S clusters in vivo and are competent to function as Fe-S transfer proteins as purified. This study resolves the contradictory results from previous in vitro studies and demonstrates the critical importance of providing in vivo partner proteins during protein overexpression to allow correct biochemical maturation of metalloproteins.
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The Zn center of the anaerobic ribonucleotide reductase from E. coli.
J. Biol. Inorg. Chem.
PUBLISHED: 01-30-2009
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Strict and facultative anaerobes depend on a class III ribonucleotide reductase for their growth. These enzymes are the sole cellular catalysts for de novo biosynthesis of the deoxyribonucleotides needed for DNA chain elongation and repair. In its active form, the class III ribonucleotide reductase from Escherichia coli contains a free radical located on the G681 residue which is essential for the activation of the ribonucleotide substrate toward its reduction. The 3D structure of the homologous enzyme from bacteriophage T4 has revealed the presence of a metal center bound to four conserved cysteine residues. In this report we identify the metal of the E. coli enzyme as Zn. We show that the presence of Zn in this site protects the protein from proteolysis and prevents the formation of disulfide bridges within it. Finally, we show with the fully Zn-loaded reductase that thioredoxin or small thiols are dispensable for the formation of the glycyl radical. However, they are necessary for obtaining high turnover numbers, suggesting that they intervene in radical transfer steps subsequent to the formation of the glycyl radical.
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The role of the maturase HydG in [FeFe]-hydrogenase active site synthesis and assembly.
FEBS Lett.
PUBLISHED: 01-07-2009
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[FeFe]-hydrogenases catalyze the protons/hydrogen interconversion through a unique di-iron active site consisting of three CO and two CN ligands, and a non-protein SCH(2)XCH(2)S (X=N or O) dithiolate bridge. Site assembly requires two "Radical-S-adenosylmethionine (SAM or AdoMet)" iron-sulfur enzymes, HydE and HydG, and one GTPase, HydF. The sequence homology between HydG and ThiH, a Radical-SAM enzyme which cleaves tyrosine into p-cresol and dehydroglycine, and the finding of a similar cleavage reaction catalyzed by HydG suggests a mechanism for hydrogenase maturation. Here we propose that HydG is specifically involved in the synthesis of the dithiolate ligand, with two tyrosine-derived dehydroglycines as precursors along with an [FeS] cluster of HydG functioning both as electron shuttle and source of the sulfur atoms.
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Molecular engineering of a cobalt-based electrocatalytic nanomaterial for H? evolution under fully aqueous conditions.
Nat Chem
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The viability of a hydrogen economy depends on the design of efficient catalytic systems based on earth-abundant elements. Innovative breakthroughs for hydrogen evolution based on molecular tetraimine cobalt compounds have appeared in the past decade. Here we show that such a diimine-dioxime cobalt catalyst can be grafted to the surface of a carbon nanotube electrode. The resulting electrocatalytic cathode material mediates H(2) generation (55,000 turnovers in seven hours) from fully aqueous solutions at low-to-medium overpotentials. This material is remarkably stable, which allows extensive cycling with preservation of the grafted molecular complex, as shown by electrochemical studies, X-ray photoelectron spectroscopy and scanning electron microscopy. This clearly indicates that grafting provides an increased stability to these cobalt catalysts, and suggests the possible application of these materials in the development of technological devices.
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Solar fuels generation and molecular systems: is it homogeneous or heterogeneous catalysis?
Chem Soc Rev
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Catalysis is a key enabling technology for solar fuel generation. A number of catalytic systems, either molecular/homogeneous or solid/heterogeneous, have been developed during the last few decades for both the reductive and oxidative multi-electron reactions required for fuel production from water or CO(2) as renewable raw materials. While allowing for a fine tuning of the catalytic properties through ligand design, molecular approaches are frequently criticized because of the inherent fragility of the resulting catalysts, when exposed to extreme redox potentials. In a number of cases, it has been clearly established that the true catalytic species is heterogeneous in nature, arising from the transformation of the initial molecular species, which should rather be considered as a pre-catalyst. Whether such a situation is general or not is a matter of debate in the community. In this review, covering water oxidation and reduction catalysts, involving noble and non-noble metal ions, we limit our discussion to the cases in which this issue has been directly and properly addressed as well as those requiring more confirmation. The methodologies proposed for discriminating homogeneous and heterogeneous catalysis are inspired in part by those previously discussed by Finke in the case of homogeneous hydrogenation reaction in organometallic chemistry [J. A. Widegren and R. G. Finke, J. Mol. Catal. A, 2003, 198, 317-341].
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FAD/folate-dependent tRNA methyltransferase: flavin as a new methyl-transfer agent.
J. Am. Chem. Soc.
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RNAs contain structurally and functionally important modified nucleosides. Methylation, the most frequent RNA modification in all living organisms, mostly relies on SAM (S-adenosylmethionine)-dependent methyltransferases. TrmFO was recently discovered as a unique tRNA methyltransferase using instead methylenetetrahydrofolate and reduced flavin adenine dinucleotide (FAD) as essential cofactors, but its mechanism has remained elusive. Here, we report that TrmFO carries an active tRNA-methylating agent and characterize it as an original enzyme-methylene-FAD covalent adduct by mass spectrometry and a combination of spectroscopic and biochemical methods. Our data support a novel tRNA methylating mechanism.
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Flavin conjugates for delivery of peptide nucleic acids.
Chembiochem
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Oligonucleotides and their analogues, such as peptide nucleic acids (PNAs), can be used in chemical strategies to artificially control gene expression. Inefficient cellular uptake and inappropriate cellular localization still remain obstacles in biological applications, however, especially for PNAs. Here we demonstrate that conjugation of PNAs to flavin resulted in efficient internalization into cells through an endocytic pathway. The flavin-PNAs exhibited antisense activity in the sub-micromolar range, in the context of a treatment facilitating endosomal escape. Increased endosomal release of flavin conjugates into the cytoplasm and/or nucleus was shown by chloroquine treatment and also--when the flavin-PNA was conjugated to rhodamine, a mild photosensitizer--upon light irradiation. In conclusion, an isoalloxazine moiety can be used as a carrier and attached to a cargo biomolecule, here a PNA, for internalization and functional cytoplasmic/nuclear delivery. Our findings could be useful for further design of PNAs and other oligonucleotide analogues as potent antisense agents.
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4-Demethylwyosine synthase from Pyrococcus abyssi is a radical-S-adenosyl-L-methionine enzyme with an additional [4Fe-4S](+2) cluster that interacts with the pyruvate co-substrate.
J. Biol. Chem.
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Wybutosine and its derivatives are found in position 37 of tRNA encoding Phe in eukaryotes and archaea. They are believed to play a key role in the decoding function of the ribosome. The second step in the biosynthesis of wybutosine is catalyzed by TYW1 protein, which is a member of the well established class of metalloenzymes called "Radical-SAM." These enzymes use a [4Fe-4S] cluster, chelated by three cysteines in a CX(3)CX(2)C motif, and S-adenosyl-L-methionine (SAM) to generate a 5-deoxyadenosyl radical that initiates various chemically challenging reactions. Sequence analysis of TYW1 proteins revealed, in the N-terminal half of the enzyme beside the Radical-SAM cysteine triad, an additional highly conserved cysteine motif. In this study we show by combining analytical and spectroscopic methods including UV-visible absorption, Mössbauer, EPR, and HYSCORE spectroscopies that these additional cysteines are involved in the coordination of a second [4Fe-4S] cluster displaying a free coordination site that interacts with pyruvate, the second substrate of the reaction. The presence of two distinct iron-sulfur clusters on TYW1 is reminiscent of MiaB, another tRNA-modifying metalloenzyme whose active form was shown to bind two iron-sulfur clusters. A possible role for the second [4Fe-4S] cluster in the enzyme activity is discussed.
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Molecular organization, biochemical function, cellular role and evolution of NfuA, an atypical Fe-S carrier.
Mol. Microbiol.
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Biosynthesis of iron-sulphur (Fe-S) proteins is catalysed by multi-protein systems, ISC and SUF. However, non-ISC, non-SUF Fe-S biosynthesis factors have been described, both in prokaryotes and eukaryotes. Here we report in vitro and in vivo investigations of such a non-ISC, non SUF component, the Nfu proteins. Phylogenomic analysis allowed us to define four subfamilies. Escherichia coli NfuA is within subfamily II. Most members of this subfamily have a Nfu domain fused to a degenerate A-type carrier domain (ATC*) lacking Fe-S cluster co-ordinating Cys ligands. The Nfu domain binds a [4Fe-4S] cluster while the ATC* domain interacts with NuoG (a complex I subunit) and aconitase B (AcnB). In vitro, holo-NfuA promotes maturation of AcnB. In vivo, NfuA is necessary for full activity of complex I under aerobic growth conditions, and of AcnB in the presence of superoxide. NfuA receives Fe-S clusters from IscU/HscBA and SufBCD scaffolds and eventually transfers them to the ATCs IscA and SufA. This study provides significant information on one of the Fe-S biogenesis factors that has been often used as a building block by ISC and/or SUF synthesizing organisms, including bacteria, plants and animals.
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Mesoporous ?-Fe2O3 thin films synthesized via the sol-gel process for light-driven water oxidation.
Phys Chem Chem Phys
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This work reports a facile and cost-effective method for synthesizing photoactive ?-Fe(2)O(3) films as well as their performances when used as photoanodes for water oxidation. Transparent ?-Fe(2)O(3) mesoporous films were fabricated by template-directed sol-gel chemistry coupled with the dip-coating approach, followed by annealing at various temperatures from 350 °C to 750 °C in air. ?-Fe(2)O(3) films were characterized by X-ray diffraction, XPS, FE-SEM and electrochemical measurements. The photoelectrochemical performance of ?-Fe(2)O(3) photoanodes was characterized and optimized through the deposition of Co-based co-catalysts via different methods (impregnation, electro-deposition and photo-electro-deposition). Interestingly, the resulting hematite films heat-treated at relatively low temperature (500 °C), and therefore devoid of any extrinsic dopant, achieve light-driven water oxidation under near-to-neutral (pH = 8) aqueous conditions after decoration with a Co catalyst. The onset potential is 0.75 V vs. the reversible hydrogen electrode (RHE), thus corresponding to 450 mV light-induced underpotential, although modest photocurrent density values (40 ?A cm(-2)) are obtained below 1.23 V vs. RHE. These new materials with a very large interfacial area in contact with the electrolyte and allowing for a high loading of water oxidation catalysts open new avenues for the optimization of photo-electrochemical water splitting.
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A Janus cobalt-based catalytic material for electro-splitting of water.
Nat Mater
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The future of energy supply depends on innovative breakthroughs regarding the design of cheap, sustainable and efficient systems for the conversion and storage of renewable energy sources. The production of hydrogen through water splitting seems a promising and appealing solution. We found that a robust nanoparticulate electrocatalytic material, H(2)-CoCat, can be electrochemically prepared from cobalt salts in a phosphate buffer. This material consists of metallic cobalt coated with a cobalt-oxo/hydroxo-phosphate layer in contact with the electrolyte and mediates H(2) evolution from neutral aqueous buffer at modest overpotentials. Remarkably, it can be converted on anodic equilibration into the previously described amorphous cobalt oxide film (O(2)-CoCat or CoPi) catalysing O(2) evolution. The switch between the two catalytic forms is fully reversible and corresponds to a local interconversion between two morphologies and compositions at the surface of the electrode. After deposition, the noble-metal-free coating thus functions as a robust, bifunctional and switchable catalyst.
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Combined experimental-theoretical characterization of the hydrido-cobaloxime [HCo(dmgH)2(PnBu3)].
Inorg Chem
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A combined theoretical and experimental approach has been employed to characterize the hydrido-cobaloxime [HCo(dmgH)(2)(PnBu(3))] compound. This complex was originally investigated by Schrauzer et al. [Schrauzer et al., J. Am. Chem. Soc. 1971, 93,1505] and has since been referred to as a key, stable analogue of the hydride intermediate involved in hydrogen evolution catalyzed by cobaloxime compounds [Artero, V. et al. Angew. Chem., Int. Ed. 2011, 50, 7238-7266]. We employed quantum chemical calculations, using density functional theory and correlated RI-SCS-MP2 methods, to characterize the structural and electronic properties of the compound and observed important differences between the calculated (1)H NMR spectrum and that reported in the original study by Schrauzer and Holland. To calibrate the theoretical model, the stable hydrido tetraamine cobalt(III) complex [HCo(tmen)(2)(OH(2))](2+) (tmen = 2,3-dimethyl-butane-2,3-diamine) [Rahman, A. F. M. M. et al. Chem. Commun. 2003, 2748-2749] was subjected to a similar analysis, and, in this case, the calculated results agreed well with those obtained experimentally. As a follow-up to the computational work, the title hydrido-cobaloxime compound was synthesized and recharacterized experimentally, together with the Co(I) derivative, giving results that were in agreement with the theoretical predictions.
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Evolution of Fe/S cluster biogenesis in the anaerobic parasite Blastocystis.
Proc. Natl. Acad. Sci. U.S.A.
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Iron/sulfur cluster (ISC)-containing proteins are essential components of cells. In most eukaryotes, Fe/S clusters are synthesized by the mitochondrial ISC machinery, the cytosolic iron/sulfur assembly system, and, in photosynthetic species, a plastid sulfur-mobilization (SUF) system. Here we show that the anaerobic human protozoan parasite Blastocystis, in addition to possessing ISC and iron/sulfur assembly systems, expresses a fused version of the SufC and SufB proteins of prokaryotes that it has acquired by lateral transfer from an archaeon related to the Methanomicrobiales, an important lineage represented in the human gastrointestinal tract microbiome. Although components of the Blastocystis ISC system function within its anaerobic mitochondrion-related organelles and can functionally replace homologues in Trypanosoma brucei, its SufCB protein has similar biochemical properties to its prokaryotic homologues, functions within the parasites cytosol, and is up-regulated under oxygen stress. Blastocystis is unique among eukaryotic pathogens in having adapted to its parasitic lifestyle by acquiring a SUF system from nonpathogenic Archaea to synthesize Fe/S clusters under oxygen stress.
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Overexpression of the Coq8 kinase in Saccharomyces cerevisiae coq null mutants allows for accumulation of diagnostic intermediates of the coenzyme Q6 biosynthetic pathway.
J. Biol. Chem.
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Most of the Coq proteins involved in coenzyme Q (ubiquinone or Q) biosynthesis are interdependent within a multiprotein complex in the yeast Saccharomyces cerevisiae. Lack of only one Coq polypeptide, as in ?coq strains, results in the degradation of several Coq proteins. Consequently, ?coq strains accumulate the same early intermediate of the Q(6) biosynthetic pathway; this intermediate is therefore not informative about the deficient biosynthetic step in a particular ?coq strain. In this work, we report that the overexpression of the protein Coq8 in ?coq strains restores steady state levels of the unstable Coq proteins. Coq8 has been proposed to be a kinase, and we provide evidence that the kinase activity is essential for the stabilizing effect of Coq8 in the ?coq strains. This stabilization results in the accumulation of several novel Q(6) biosynthetic intermediates. These Q intermediates identify chemical steps impaired in cells lacking Coq4 and Coq9 polypeptides, for which no function has been established to date. Several of the new intermediates contain a C4-amine and provide information on the deamination reaction that takes place when para-aminobenzoic acid is used as a ring precursor of Q(6). Finally, we used synthetic analogues of 4-hydroxybenzoic acid to bypass deficient biosynthetic steps, and we show here that 2,4-dihydroxybenzoic acid is able to restore Q(6) biosynthesis and respiratory growth in a ?coq7 strain overexpressing Coq8. The overexpression of Coq8 and the use of 4-hydroxybenzoic acid analogues represent innovative tools to elucidate the Q biosynthetic pathway.
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Phosphine coordination to a cobalt diimine-dioxime catalyst increases stability during light-driven H2 production.
Inorg Chem
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The combination of cobalt diimine-dioxime complexes with a cyclometalated iridium photosensitizer gives efficient systems for hydrogen generation under visible-light irradiation using triethylamine as a sacrificial electron donor. Interestingly, the addition of triphenylphosphine (PPh(3)) to the medium results in a significant improvement of the stability of the system, with up to ?700 turnovers achieved within 10 h. UV-visible spectroscopic monitoring of the reaction allows identification of a PPh(3)-coordinated Co(I) intermediate as the active species. Mechanistic issues regarding (i) the photogeneration of the Co(I) species, (ii) the nature of the active species, and (iii) the influence of PPh(3) on the H(2)-evolution mechanism are discussed.
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