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1

Selenium-bridged diiron hexacarbonyl complexes as biomimetic models for the active site of Fe-Fe hydrogenases.  

PubMed

Three N-substituted selenium-bridged diiron complexes [{(mu-SeCH2)2NC6H4R}Fe2(CO)6] (R = 4-NO2, 7; R = H, 8; R = 4-CH3, 9) were firstly prepared as biomimetic models for the Fe-Fe hydrogenases active site. Models could be generated by the convergent reaction of [(mu-HSe)2Fe2(CO)6] (6) with N,N-bis(hydroxymethyl)-4-nitroaniline (1), N,N-bis(hydroxymethyl)aniline (2), and N,N-bis(hydroxymethyl)-4-methylaniline (3) in 46-52% yields. All the new complexes were characterized by IR, 1H and 13C NMR and HRMS spectra and their molecular structures were determined by single-crystal X-ray analysis. The redox properties of and their dithiolate analogues [{(mu-SCH2)2NC6H4R}Fe2(CO)6] (R = 4-NO2, 7s; R = H, 8s; R = 4-CH3, 9s ) were evaluated by cyclic voltammograms. The electrochemical proton reduction by and were investigated in the presence of p-toluenesulfonic acid (HOTs) to evaluate the influence of changing the coordinating S atoms of the bridging ligands to Se atoms on the electrocatalytic activity for proton reduction. PMID:18398538

Gao, Shang; Fan, Jiangli; Sun, Shiguo; Peng, Xiaojun; Zhao, Xing; Hou, Jun

2008-04-28

2

[FeFe] hydrogenases and their evolution: a genomic perspective  

Microsoft Academic Search

.  Most hydrogenases (H2ases), the enzymes that produce or oxidize dihydrogen, possess dimetallic active sites and belong to either one of two phylogenetically\\u000a distinct classes, the [NiFe] and the [FeFe] H2ases. These families of H2ases share a number of similarities regarding active site structure and reaction mechanism, as a result of convergent evolution.\\u000a They are otherwise alien to each other, in

J. Meyer

2007-01-01

3

How oxygen attacks [FeFe] hydrogenases from photosynthetic organisms  

PubMed Central

Green algae such as Chlamydomonas reinhardtii synthesize an [FeFe] hydrogenase that is highly active in hydrogen evolution. However, the extreme sensitivity of [FeFe] hydrogenases to oxygen presents a major challenge for exploiting these organisms to achieve sustainable photosynthetic hydrogen production. In this study, the mechanism of oxygen inactivation of the [FeFe] hydrogenase CrHydA1 from C. reinhardtii has been investigated. X-ray absorption spectroscopy shows that reaction with oxygen results in destruction of the [4Fe-4S] domain of the active site H-cluster while leaving the di-iron domain (2FeH) essentially intact. By protein film electrochemistry we were able to determine the order of events leading up to this destruction. Carbon monoxide, a competitive inhibitor of CrHydA1 which binds to an Fe atom of the 2FeH domain and is otherwise not known to attack FeS clusters in proteins, reacts nearly two orders of magnitude faster than oxygen and protects the enzyme against oxygen damage. These results therefore show that destruction of the [4Fe-4S] cluster is initiated by binding and reduction of oxygen at the di-iron domain—a key step that is blocked by carbon monoxide. The relatively slow attack by oxygen compared to carbon monoxide suggests that a very high level of discrimination can be achieved by subtle factors such as electronic effects (specific orbital overlap requirements) and steric constraints at the active site.

Stripp, Sven T.; Goldet, Gabrielle; Brandmayr, Caterina; Sanganas, Oliver; Vincent, Kylie A.; Haumann, Michael; Armstrong, Fraser A.; Happe, Thomas

2009-01-01

4

New Insights into [FeFe] Hydrogenase Activation and Maturase Function  

PubMed Central

[FeFe] hydrogenases catalyze H2 production using the H-cluster, an iron-sulfur cofactor that contains carbon monoxide (CO), cyanide (CN–), and a dithiolate bridging ligand. The HydE, HydF, and HydG maturases assist in assembling the H-cluster and maturing hydrogenases into their catalytically active form. Characterization of these maturases and in vitro hydrogenase activation methods have helped elucidate steps in the H-cluster biosynthetic pathway such as the HydG-catalyzed generation of the CO and CN– ligands from free tyrosine. We have refined our cell-free approach for H-cluster synthesis and hydrogenase maturation by using separately expressed and purified HydE, HydF, and HydG. In this report, we illustrate how substrates and protein constituents influence hydrogenase activation, and for the first time, we show that each maturase can function catalytically during the maturation process. With precise control over the biomolecular components, we also provide evidence for H-cluster synthesis in the absence of either HydE or HydF, and we further show that hydrogenase activation can occur without exogenous tyrosine. Given these findings, we suggest a new reaction sequence for the [FeFe] hydrogenase maturation pathway. In our model, HydG independently synthesizes an iron-based compound with CO and CN– ligands that is a precursor to the H-cluster [2Fe]H subunit, and which we have termed HydG-co. We further propose that HydF is a transferase that stabilizes HydG-co and also shuttles the complete [2Fe]H subcluster to the hydrogenase, a translocation process that may be catalyzed by HydE. In summary, this report describes the first example of reconstructing the [FeFe] hydrogenase maturation pathway using purified maturases and subsequently utilizing this in vitro system to better understand the roles of HydE, HydF, and HydG.

Kuchenreuther, Jon M.; Britt, R. David; Swartz, James R.

2012-01-01

5

Effect of cyanide ligands on the electronic structure of [FeFe] hydrogenase active-site model complexes with an azadithiolate cofactor.  

PubMed

A detailed characterization of a close synthetic model of the [2?Fe]H subcluster in the [FeFe] hydrogenase active site is presented. It contains the full primary coordination sphere of the CO-inhibited oxidized state of the enzyme including the CN(-) ligands and the azadithiolate (adt) bridge, [((?-S?CH2 )2 NR)Fe2 (CO)4 (CN)2 ](2-) , R=CH2 CH2 SCH3 . The electronic structure of the model complex in its Fe(I) Fe(II) state was investigated by means of density functional theory (DFT) calculations and Fourier transform infrared (FTIR) spectroscopy. By using a combination of continuous-wave (CW) electron paramagnetic resonance (EPR) and hyperfine sublevel correlation (HYSCORE) experiments as well as DFT calculations, it is shown that, for this complex, the spin density is delocalized over both iron atoms. Interestingly, we found that the nitrogen hyperfine coupling, which represents the interaction between the unpaired electron and the nitrogen at the dithiolate bridge, is slightly larger than that in the analogous complex in which the CN(-) ligands are replaced with PMe3 ligands. This reveals, first, that the CN(-) /PMe3 ligands coordinated to the iron core are electronically coupled to the amine in the adt bridge. Second, the CN(-) ligands in this complex are somewhat stronger ?-donor ligands than the PMe3 ligand, and thereby enable more spin density to be transferred from the Fe core to the adt unit, which might in turn affect the reactivity of the bridging amine. PMID:24038239

Erdem, Özlen F; Stein, Matthias; Kaur-Ghumaan, Sandeep; Reijerse, Edward J; Ott, Sascha; Lubitz, Wolfgang

2013-10-18

6

Bridging-hydride influence on the electronic structure of an [FeFe] hydrogenase active-site model complex revealed by XAES-DFT.  

PubMed

Two crystallized [FeFe] hydrogenase model complexes, 1 = (?-pdt)[Fe(CO)(2)(PMe(3))](2) (pdt = SC1H2C2H2C3H2S), and their bridging-hydride (Hy) derivative, [1Hy](+) = [(?-H)(?-pdt)[Fe(CO)(2) (PMe(3))](2)](+) (BF(4)(?)), were studied by Fe K-edge X-ray absorption and emission spectroscopy, supported by density functional theory. Structural changes in [1Hy](+) compared to 1 involved small bond elongations (<0.03 Å) and more octahedral Fe geometries; the Fe–H bond at Fe1 (closer to pdt-C2) was ~0.03 Å longer than that at Fe2. Analyses of (1) pre-edge absorption spectra (core-to-valence transitions), (2) K?(1,3), K?', and K?(2,5) emission spectra (valence-to-core transitions), and (3) resonant inelastic X-ray scattering data (valence-to-valence transitions) for resonant and non-resonant excitation and respective spectral simulations indicated the following: (1) the mean Fe oxidation state was similar in both complexes, due to electron density transfer from the ligands to Hy in [1Hy](+). Fe 1s?3d transitions remained at similar energies whereas delocalization of carbonyl AOs onto Fe and significant Hy-contributions to MOs caused an ~0.7 eV up-shift of Fe1s?(CO)s,p transitions in [1Hy](+). Fed-levels were delocalized over Fe1 and Fe2 and degeneracies biased to O(h)–Fe1 and C(4v)–Fe2 states for 1, but to O(h)–Fe1,2 states for [1Hy](+). (2) Electron-pairing of formal Fe(d(7)) ions in low-spin states in both complexes and a higher effective spin count for [1Hy](+) were suggested by comparison with iron reference compounds. Electronic decays from Fe d and ligand s,p MOs and spectral contributions from Hys,p?1s transitions even revealed limited site-selectivity for detection of Fe1 or Fe2 in [1Hy](+). The HOMO/LUMO energy gap for 1 was estimated as 3.0 ± 0.5 eV. (3) For [1Hy](+) compared to 1, increased Fed (x(2) ? y(2)) ? (z(2)) energy differences (~0.5 eV to ~0.9 eV) and Fed?d transition energies (~2.9 eV to ~3.7 eV) were assigned. These results reveal the specific impact of Hy-binding on the electronic structure of diiron compounds and provide guidelines for a directed search of hydride species in hydrogenases. PMID:23446996

Leidel, Nils; Hsieh, Chung-Hung; Chernev, Petko; Sigfridsson, Kajsa G V; Darensbourg, Marcetta Y; Haumann, Michael

2013-06-01

7

A Cell-Free Microtiter Plate Screen for Improved [FeFe] Hydrogenases  

PubMed Central

Background [FeFe] hydrogenase enzymes catalyze the production and dissociation of H2, a potential renewable fuel. Attempts to exploit these catalysts in engineered systems have been hindered by the biotechnologically inconvenient properties of the natural enzymes, including their extreme oxygen sensitivity. Directed evolution has been used to improve the characteristics of a range of natural catalysts, but has been largely unsuccessful for [FeFe] hydrogenases because of a lack of convenient screening platforms. Methodology/Principal Findings Here we describe an in vitro screening technology for oxygen-tolerant and highly active [FeFe] hydrogenases. Despite the complexity of the protocol, we demonstrate a level of reproducibility that allows moderately improved mutants to be isolated. We have used the platform to identify a mutant of the Chlamydomonas reinhardtii [FeFe] hydrogenase HydA1 with a specific activity ?4 times that of the wild-type enzyme. Conclusions/Significance Our results demonstrate the feasibility of using the screen presented here for large-scale efforts to identify improved biocatalysts for energy applications. The system is based on our ability to activate these complex enzymes in E. coli cell extracts, which allows unhindered access to the protein maturation and assay environment.

Stapleton, James A.; Swartz, James R.

2010-01-01

8

Proton transport in Clostridium pasteurianum [FeFe] hydrogenase I: a computational study.  

PubMed

To better understand the proton transport through the H2 production catalysts, the [FeFe] hydrogenases, we have undertaken a modeling and simulation study of the proton transfer processes mediated by amino acid side-chain residues in hydrogenase I from Clostridium pasteurianum. Free-energy calculation studies show that the side chains of two conserved glutamate residues, Glu-279 and Glu-282, each possess two stable conformations with energies that are sensitive to protonation state. Coordinated conformational changes of these residues can form a proton shuttle between the surface Glu-282 and Cys-299, which is the penultimate proton donor to the catalytic H-cluster. Calculated acid dissociation constants are consistent with a proton relay connecting the H-cluster to the bulk solution. The complete proton-transport process from the surface-disposed Glu-282 to Cys-299 is studied using coupled semiempirical quantum-mechanical/classical-mechanical dynamics. Two-dimensional free-energy maps show the mechanisms of proton transport, which involve Glu-279, Ser-319, and a short internal water relay to connect functionally Glu-282 with the H-cluster. The findings of conformational bistability, PT event coupling with pKa mismatch, and water participation have implications in the design of artificial water reduction or general electrocatalytic H2-production catalysts. PMID:24405487

Long, Hai; King, Paul W; Chang, Christopher H

2014-01-30

9

The oxidative inactivation of FeFe hydrogenase reveals the flexibility of the H-cluster  

NASA Astrophysics Data System (ADS)

Nature is a valuable source of inspiration in the design of catalysts, and various approaches are used to elucidate the mechanism of hydrogenases, the enzymes that oxidize or produce H2. In FeFe hydrogenases, H2 oxidation occurs at the H-cluster, and catalysis involves H2 binding on the vacant coordination site of an iron centre. Here, we show that the reversible oxidative inactivation of this enzyme results from the binding of H2 to coordination positions that are normally blocked by intrinsic CO ligands. This flexibility of the coordination sphere around the reactive iron centre confers on the enzyme the ability to avoid harmful reactions under oxidizing conditions, including exposure to O2. The versatile chemistry of the diiron cluster in the natural system might inspire the design of novel synthetic catalysts for H2 oxidation.

Fourmond, Vincent; Greco, Claudio; Sybirna, Kateryna; Baffert, Carole; Wang, Po-Hung; Ezanno, Pierre; Montefiori, Marco; Bruschi, Maurizio; Meynial-Salles, Isabelle; Soucaille, Philippe; Blumberger, Jochen; Bottin, Hervé; de Gioia, Luca; Léger, Christophe

2014-04-01

10

Development of an In Vitro Compartmentalization Screen for High-Throughput Directed Evolution of [FeFe] Hydrogenases  

PubMed Central

Background [FeFe] hydrogenase enzymes catalyze the formation and dissociation of molecular hydrogen with the help of a complex prosthetic group composed of common elements. The development of energy conversion technologies based on these renewable catalysts has been hindered by their extreme oxygen sensitivity. Attempts to improve the enzymes by directed evolution have failed for want of a screening platform capable of throughputs high enough to adequately sample heavily mutated DNA libraries. In vitro compartmentalization (IVC) is a powerful method capable of screening for multiple-turnover enzymatic activity at very high throughputs. Recent advances have allowed [FeFe] hydrogenases to be expressed and activated in the cell-free protein synthesis reactions on which IVC is based; however, IVC is a demanding technique with which many enzymes have proven incompatible. Methodology/Principal Findings Here we describe an extremely high-throughput IVC screen for oxygen-tolerant [FeFe] hydrogenases. We demonstrate that the [FeFe] hydrogenase CpI can be expressed and activated within emulsion droplets, and identify a fluorogenic substrate that links activity after oxygen exposure to the generation of a fluorescent signal. We present a screening protocol in which attachment of mutant genes and the proteins they encode to the surfaces of microbeads is followed by three separate emulsion steps for amplification, expression, and evaluation of hydrogenase mutants. We show that beads displaying active hydrogenase can be isolated by fluorescence-activated cell-sorting, and we use the method to enrich such beads from a mock library. Conclusions/Significance [FeFe] hydrogenases are the most complex enzymes to be produced by cell-free protein synthesis, and the most challenging targets to which IVC has yet been applied. The technique described here is an enabling step towards the development of biocatalysts for a biological hydrogen economy.

Stapleton, James A.; Swartz, James R.

2010-01-01

11

Steps along the path to dihydrogen activation at [FeFe] hydrogenase structural models: dependence of the core geometry on electrocatalytic proton reduction.  

PubMed

Differences in the rate of electrocatalytic proton reduction by Fe2(mu-PPh2)2(CO)6, DP, and the linked phosphido-bridged analogue Fe2(mu,mu-PPh(CH2)3PPh)(CO)6, 3P, suggest that dihydrogen elimination proceeds through a bridging hydride. The reaction path was examined using electrochemical, spectroscopic, and in silico studies where reduction of 3P gives a moderately stable monoanion [Kdisp(3P-) = 13] and a distorted dianion. The monomeric formulation of 3P- is supported by the form of the IR and EPR spectra. EXAFS analysis of solutions of 3P, 3P-, and 3P2- indicates a large increase in the Fe-Fe separation following reduction (from 2.63 to ca. 3.1-3.55 A). DFT calculations of the 3P, 3P-, 3P2- redox series satisfactorily reproduce the IR spectra in the nu(CO) region and the crystallographic (3P) and EXAFS-derived Fe-Fe distances. Digital simulation of the electrocatalytic response for proton reduction indicates a low rate of dihydrogen evolution from the two-electron, two-proton product of 3P (H23P), with more rapid dihydrogen evolution following further reduction of H23P. Because dihydrogen evolution is not observed upon formation of H2DP, dihydrogen evolution at the two-electron-reduced level does not involve protonation of a hydridic Fe-H ligand. The rates of dihydrogen elimination from H2DP, H23P, and H2Fe2(mu,mu-S(CH2)3S)(CO)6 (H23S) are related to the DFT-calculated H-H distances [H23S (1.880 A) < H23P (2.064 A) < H2DP (3.100 A)], and this suggests a common reaction path for the thiolato- and phosphido-bridged diiron carbonyl compounds. PMID:17256930

Cheah, Mun Hon; Borg, Stacey J; Best, Stephen P

2007-03-01

12

Shewanella oneidensis: a new and efficient System for Expression and Maturation of heterologous [Fe-Fe] Hydrogenase from Chlamydomonas reinhardtii  

PubMed Central

Background The eukaryotic green alga, Chlamydomonas reinhardtii, produces H2 under anaerobic conditions, in a reaction catalysed by a [Fe-Fe] hydrogenase HydA1. For further biochemical and biophysical studies a suitable expression system of this enzyme should be found to overcome its weak expression in the host organism. Two heterologous expression systems used up to now have several advantages. However they are not free from some drawbacks. In this work we use bacterium Shewanella oneidensis as a new and efficient system for expression and maturation of HydA1 from Chlamydomonas reinhardtii. Results Based on codon usage bias and hydrogenase maturation ability, the bacterium S. oneidensis, which possesses putative [Fe-Fe] and [Ni-Fe] hydrogenase operons, was selected as the best potential host for C. reinhardtii [Fe-Fe] hydrogenase expression. Hydrogen formation by S. oneidensis strain AS52 (?hydA?hyaB) transformed with a plasmid bearing CrHydA1 and grown in the presence of six different substrates for anaerobic respiration was determined. A significant increase in hydrogen evolution was observed for cells grown in the presence of trimethylamine oxide, dimethylsulfoxide and disodium thiosulfate, showing that the system of S. oneidensis is efficient for heterologous expression of algal [Fe-Fe] hydrogenase. Conclusion In the present work a new efficient system for heterologous expression and maturation of C. reinhardtii hydrogenase has been developed. HydA1 of C. reinhardtii was purified and shown to contain 6 Fe atoms/molecule of protein, as expected. Using DMSO, TMAO or thiosulfate as substrates for anaerobic respiration during the cell growth, 0.4 – 0.5 mg l-1(OD600 = 1) of catalytically active HydA1 was obtained with hydrogen evolution rate of ~700 ?mol H2 mg-1 min-1.

Sybirna, Kateryna; Antoine, Tatiana; Lindberg, Pia; Fourmond, Vincent; Rousset, Marc; Mejean, Vincent; Bottin, Herve

2008-01-01

13

Density Functional Theory Calculation of Bonding and Charge Parameters for Molecular Dynamics Studies of [FeFe] Hydrogenases  

SciTech Connect

We have developed and tested molecular mechanics parameters for [FeS] clusters found in known [FeFe] hydrogenases. Bond stretching, angle bending, dihedral and improper torsion parameters for models of the oxidized and reduced catalytic H-cluster, [4Fe4S]{sup +,2+}Cys{sub 4}, [4Fe4S]{sup +,2+}Cys{sub 3}His, and [2Fe2S]{sup +,2+}Cys{sub 4}, were calculated solely from Kohn-Sham density functional theory and Natural Population Analysis. Circumsphere analysis of the cubane clusters in the energy-minimized structure of the full Clostridium pasteurianum hydrogenase I showed the resulting metallocluster structures to be similar to known cubane structures. All clusters were additionally stable in molecular dynamics simulations over the course of 1.0 ns in the fully oxidized and fully reduced enzyme models. Normal modes calculated by quasiharmonic analysis from the dynamics data show unexpected couplings among internal coordinate motions, which may reflect the effects of the protein structure on metallocluster dynamics.

Chang, C. H.; Kim, K.

2009-04-01

14

Patterns of [FeFe] Hydrogenase Diversity in the Gut Microbial Communities of Lignocellulose-Feeding Higher Termites  

PubMed Central

Hydrogen is the central free intermediate in the degradation of wood by termite gut microbes and can reach concentrations exceeding those measured for any other biological system. Degenerate primers targeting the largest family of [FeFe] hydrogenases observed in a termite gut metagenome have been used to explore the evolution and representation of these enzymes in termites. Sequences were cloned from the guts of the higher termites Amitermes sp. strain Cost010, Amitermes sp. strain JT2, Gnathamitermes sp. strain JT5, Microcerotermes sp. strain Cost008, Nasutitermes sp. strain Cost003, and Rhyncotermes sp. strain Cost004. Each gut sample harbored a more rich and evenly distributed population of hydrogenase sequences than observed previously in the guts of lower termites and Cryptocercus punctulatus. This accentuates the physiological importance of hydrogen for higher termite gut ecosystems and may reflect an increased metabolic burden, or metabolic opportunity, created by a lack of gut protozoa. The sequences were phylogenetically distinct from previously sequenced [FeFe] hydrogenases. Phylogenetic and UniFrac comparisons revealed congruence between host phylogeny and hydrogenase sequence library clustering patterns. This may reflect the combined influences of the stable intimate relationship of gut microbes with their host and environmental alterations in the gut that have occurred over the course of termite evolution. These results accentuate the physiological importance of hydrogen to termite gut ecosystems.

Ballor, Nicholas R.

2012-01-01

15

H?-dependent azoreduction by Shewanella oneidensis MR-1: involvement of secreted flavins and both [Ni-Fe] and [Fe-Fe] hydrogenases.  

PubMed

In this paper, the hydrogen (H2)-dependent discoloration of azo dye amaranth by Shewanella oneidensis MR-1 was investigated. Experiments with hydrogenase-deficient strains demonstrated that periplasmic [Ni-Fe] hydrogenase (HyaB) and periplasmic [Fe-Fe] hydrogenase (HydA) are both respiratory hydrogenases of dissimilatory azoreduction in S. oneidensis MR-1. These findings suggest that HyaB and HydA can function as uptake hydrogenases that couple the oxidation of H2 to the reduction of amaranth to sustain cellular growth. This constitutes to our knowledge the first report of the involvement of [Fe-Fe] hydrogenase in a bacterial azoreduction process. Assays with respiratory inhibitors indicated that a menaquinone pool and different cytochromes were involved in the azoreduction process. High-performance liquid chromatography analysis revealed that flavin mononucleotide and riboflavin were secreted in culture supernatant by S. oneidensis MR-1 under H2-dependent conditions with concentration of 1.4 and 2.4 ?mol g protein(-1), respectively. These endogenous flavins were shown to significantly accelerate the reduction of amaranth at micromolar concentrations acting as electron shuttles between the cell surface and the extracellular azo dye. This work may facilitate a better understanding of the mechanisms of azoreduction by S. oneidensis MR-1 and may have practical applications for microbiological treatments of dye-polluted industrial effluents. PMID:24081321

Le Laz, Sébastien; Kpebe, Arlette; Lorquin, Jean; Brugna, Myriam; Rousset, Marc

2014-03-01

16

Cell-free H-cluster Synthesis and [FeFe] Hydrogenase Activation: All Five CO and CN? Ligands Derive from Tyrosine  

PubMed Central

[FeFe] hydrogenases are promising catalysts for producing hydrogen as a sustainable fuel and chemical feedstock, and they also serve as paradigms for biomimetic hydrogen-evolving compounds. Hydrogen formation is catalyzed by the H-cluster, a unique iron-based cofactor requiring three carbon monoxide (CO) and two cyanide (CN?) ligands as well as a dithiolate bridge. Three accessory proteins (HydE, HydF, and HydG) are presumably responsible for assembling and installing the H-cluster, yet their precise roles and the biosynthetic pathway have yet to be fully defined. In this report, we describe effective cell-free methods for investigating H-cluster synthesis and [FeFe] hydrogenase activation. Combining isotopic labeling with FTIR spectroscopy, we conclusively show that each of the CO and CN? ligands derive respectively from the carboxylate and amino substituents of tyrosine. Such in vitro systems with reconstituted pathways comprise a versatile approach for studying biosynthetic mechanisms, and this work marks a significant step towards an understanding of both the protein-protein interactions and complex reactions required for H-cluster assembly and hydrogenase maturation.

Kuchenreuther, Jon M.; George, Simon J.; Grady-Smith, Celestine S.; Cramer, Stephen P.; Swartz, James R.

2011-01-01

17

(14)N HYSCORE investigation of the H-cluster of [FeFe] hydrogenase: evidence for a nitrogen in the dithiol bridge.  

PubMed

Hydrogenases are enzymes catalyzing the reversible heterolytic splitting of molecular hydrogen. Despite extensive investigations of this class of enzymes its catalytic mechanism is not yet well understood. In this paper spectroscopic investigations of the active site of [FeFe] hydrogenase are presented. The so-called H-cluster consists of a bi-nuclear catalytically active subcluster connected to a [4Fe4S] ferredoxin-like unit via a Cys-thiol bridge. An important feature of the H-cluster is that both irons in the bi-nuclear subcluster are coordinated by CN and CO ligands. The bi-nuclear site also carries a dithiol bridge, whose central atom has not yet been identified. Nitrogen and oxygen are the most probable candidates from a mechanistic point of view. Here we present a study of the (14)N nuclear quadrupole and hyperfine interactions of the active oxidized state of the H-cluster using advanced EPR methods. In total three (14)N nuclei with quadrupole couplings of 0.95 MHz, 0.35 MHz and 1.23 MHz were detected using hyperfine sublevel correlation spectroscopy (HYSCORE). The assignment of the signals is based on their (14)N quadrupole couplings in combination with DFT calculations. One signal is assigned to the CN ligand of the distal iron, one to a Lys side chain nitrogen and one to the putative nitrogen of the dithiol bridge. Hence, these results provide the first experimental evidence for a di-(thiomethyl)amine ligand (-S-CH(2)-NH-CH(2)-S-) in the bi-nuclear subcluster. This finding is important for understanding the mechanism of [FeFe] hydrogenases, since the nitrogen is likely to act as an internal base facilitating the heterolytic splitting/formation of H(2). PMID:19639134

Silakov, Alexey; Wenk, Brian; Reijerse, Eduard; Lubitz, Wolfgang

2009-08-21

18

The exchange activities of [Fe] hydrogenase (iron–sulfur-cluster-free hydrogenase) from methanogenic archaea in comparison with the exchange activities of [FeFe] and [NiFe] hydrogenases  

Microsoft Academic Search

[Fe] hydrogenase (iron–sulfur-cluster-free hydrogenase) catalyzes the reversible reduction of methenyltetrahydromethanopterin\\u000a (methenyl-H4MPT+) with H2 to methylene-H4MPT, a reaction involved in methanogenesis from H2 and CO2 in many methanogenic archaea. The enzyme harbors an iron-containing cofactor, in which a low-spin iron is complexed by a\\u000a pyridone, two CO and a cysteine sulfur. [Fe] hydrogenase is thus similar to [NiFe] and [FeFe] hydrogenases, in which a

Sonja Vogt; Erica J. Lyon; Seigo Shima; Rudolf K. Thauer

2008-01-01

19

Vibrational Analysis of the Model Complex (?-edt)[Fe(CO)3]2 and Comparison to Iron-only Hydrogenase: The Activation Scale of Hydrogenase Model Systems  

PubMed Central

Research on simple [FeFe] hydrogenase model systems of type (?-S2R)[Fe(CO)3]2 (R = ethane, propane) which have been shown to function as robust electrocatalysts for proton reduction, provides a reference to understand the electronic and vibrational properties of the active site of [FeFe] hydrogenases and of more sophisticated model systems. In this study, the solution and solid Raman spectra of (?-S2R)[Fe(CO)3]2 (R = ethane) and of the corresponding 13CO-labeled complex are presented and analyzed in detail, with focus on the ?(C=O) and ?(Fe-CO)/?(Fe-C=O) vibrational regions. These regions are specifically important as vibrations involving CO ligands serve as probes for the ‘electron richness’ of low-valent transition metal centers and the geometric structures of the complexes. The obtained vibrational spectra have been completely assigned in terms of the ?(C=O), ?(Fe-CO) and ?(Fe-C=O) modes, and the force constants of the important C=O and Fe-CO bonds have been determined using our Quantum Chemistry Centered Normal Coordinate Analysis (QCC-NCA). In the 400–650 cm?1 region, 15 mixed ?(Fe-CO)/?(Fe-C=O) modes have been identified. The most prominent Raman peaks at 454, 456 and 483 cm?1 correspond to a combination of ?(Fe-CO) stretching and ?(Fe-C=O) linear bending modes. The less intense peaks at 416 cm?1 and 419 cm?1 correspond to pure ?(Fe-C=O) linear bends. In the ?(C=O) region, the ?(C=O) normal modes at lower energy (1968 and 1964 cm?1) are almost pure equatorial (eq) ?(C=O)eq stretching vibrations, whereas the remaining four ?(C=O) normal modes show dominant (C=O)eq (2070 and 1961 cm?1) and (C=O)ax (2005 and 1979 cm?1; ax = axial) contributions. Importantly, an inverse correlation between the f(C=O)ax/eq and f(Fe-CO)ax/eq force constants is obtained, in agreement with the idea that the Fe(I)-CO bond in these types of complexes is dominated by ? backdonation. Compared to the reduced form of [FeFe] hydrogenase (Hred), the ?(C=O) vibrational frequencies of (?-edt)[Fe(CO)3]2 are higher in energy, indicating that the dinuclear iron core in (?-edt)[Fe(CO)3]2 is less electron rich compared to Hred in the actual enzyme. Finally, quantum yields for the photodecomposition of (?-edt)[Fe(CO)3]2 have been determined.

Galinato, Mary Grace I.; Whaley, C. Matthew; Lehnert, Nicolai

2010-01-01

20

Coordination and conformational isomers in mononuclear iron complexes with pertinence to the [FeFe] hydrogenase active site.  

PubMed

A series of six mononuclear iron complexes of the type [Fe(X-bdt)(P(R)2N(Ph)2)(CO)] (P(R)2N(Ph)2 = 1,5-diaza-3,7-diphosphaoctane, bdt = benzenedithiolate with X = H, Cl2 or Me and R = Ph, Bn, Cyc or tert-Bu) was prepared. This new class of penta-coordinate iron complexes contains a free coordination site and a pendant base as essential structural features of the [FeFe]-hydrogenase active site. The bidentate nature of the P(R)2N(Ph)2 ligands was found to be crucial for the preferential formation of coordinatively unsaturated penta-coordinate complexes, which is supported by first principle calculations. IR-spectroscopic data suggest the presence of coordination isomers around the metal center, as well as multiple possible conformers of the P(R)2N(Ph)2 ligand. This finding is further corroborated by X-ray crystallographic and computational studies. (31)P{(1)H}-NMR- and IR-spectroscopic as well as electrochemical measurements show that the electronic properties of the complexes are strongly, and independently, influenced by the P-substituents at the P(R)2N(Ph)2 ligand as well as by modifications of the bdt bridge. These results illustrate the advantages of this modular platform, which allows independent and selective tuning through site specific modifications. Potential catalytic intermediates, namely singly reduced and protonated complexes, have been further investigated by spectroscopic methods and exhibit remarkable stability. Finally, their general capacity for electro-catalytic reduction of protons to molecular hydrogen was verified. PMID:24457903

Orthaber, Andreas; Karnahl, Michael; Tschierlei, Stefanie; Streich, Daniel; Stein, Matthias; Ott, Sascha

2014-03-21

21

Time-resolved vibrational spectroscopy of [FeFe]-hydrogenase model compounds.  

PubMed

Model compounds have been found to structurally mimic the catalytic hydrogen-producing active site of Fe-Fe hydrogenases and are being explored as functional models. The time-dependent behavior of Fe(2)(?-S(2)C(3)H(6))(CO)(6) and Fe(2)(?-S(2)C(2)H(4))(CO)(6) is reviewed and new ultrafast UV- and visible-excitation/IR-probe measurements of the carbonyl stretching region are presented. Ground-state and excited-state electronic and vibrational properties of Fe(2)(?-S(2)C(3)H(6))(CO)(6) were studied with density functional theory (DFT) calculations. For Fe(2)(?-S(2)C(3)H(6))(CO)(6) excited with 266 nm, long-lived signals (? = 3.7 ± 0.26 ?s) are assigned to loss of a CO ligand. For 355 and 532 nm excitation, short-lived (? = 150 ± 17 ps) bands are observed in addition to CO-loss product. Short-lived transient absorption intensities are smaller for 355 nm and much larger for 532 nm excitation and are assigned to a short-lived photoproduct resulting from excited electronic state structural reorganization of the Fe-Fe bond. Because these molecules are tethered by bridging disulfur ligands, this extended di-iron bond relaxes during the excited state decay. Interestingly, and perhaps fortuitously, the time-dependent DFT-optimized exited-state geometry of Fe(2)(?-S(2)C(3)H(6))(CO)(6) with a semibridging CO is reminiscent of the geometry of the Fe(2)S(2) subcluster of the active site observed in Fe-Fe hydrogenase X-ray crystal structures. We suggest these wavelength-dependent excitation dynamics could significantly alter potential mechanisms for light-driven catalysis. PMID:22612846

Bingaman, Jamie L; Kohnhorst, Casey L; Van Meter, Glenn A; McElroy, Brent A; Rakowski, Elizabeth A; Caplins, Benjamin W; Gutowski, Tiffany A; Stromberg, Christopher J; Webster, Charles Edwin; Heilweil, Edwin J

2012-07-12

22

Atomic Resolution Modeling of the Ferredoxin:[FeFe] Hydrogenase Complex from Chlamydomonas reinhardtii  

PubMed Central

The [FeFe] hydrogenases HydA1 and HydA2 in the green alga Chlamydomonas reinhardtii catalyze the final reaction in a remarkable metabolic pathway allowing this photosynthetic organism to produce H2 from water in the chloroplast. A [2Fe-2S] ferredoxin is a critical branch point in electron flow from Photosystem I toward a variety of metabolic fates, including proton reduction by hydrogenases. To better understand the binding determinants involved in ferredoxin:hydrogenase interactions, we have modeled Chlamydomonas PetF1 and HydA2 based on amino-acid sequence homology, and produced two promising electron-transfer model complexes by computational docking. To characterize these models, quantitative free energy calculations at atomic resolution were carried out, and detailed analysis of the interprotein interactions undertaken. The protein complex model we propose for ferredoxin:HydA2 interaction is energetically favored over the alternative candidate by 20 kcal/mol. This proposed model of the electron-transfer complex between PetF1 and HydA2 permits a more detailed view of the molecular events leading up to H2 evolution, and suggests potential mutagenic strategies to modulate electron flow to HydA2.

Chang, Christopher H.; King, Paul W.; Ghirardi, Maria L.; Kim, Kwiseon

2007-01-01

23

Atomic Resolution Modeling of the Ferredoxin:[FeFe] Hydrogenase Complex from Chlamydomonas reinhardtii  

SciTech Connect

The [FeFe] hydrogenases HydA1 and HydA2 in the green alga Chlamydomonas reinhardtii catalyze the final reaction in a remarkable metabolic pathway allowing this photosynthetic organism to produce H2 from water in the chloroplast. A [2Fe-2S] ferredoxin is a critical branch point in electron flow from Photosystem I toward a variety of metabolic fates, including proton reduction by hydrogenases. To better understand the binding determinants involved in ferredoxin:hydrogenase interactions, we have modeled Chlamydomonas PetF1 and HydA2 based on amino-acid sequence homology, and produced two promising electron-transfer model complexes by computational docking. To characterize these models, quantitative free energy calculations at atomic resolution were carried out, and detailed analysis of the interprotein interactions undertaken. The protein complex model we propose for ferredoxin:HydA2 interaction is energetically favored over the alternative candidate by 20kcal/mol. This proposed model of the electron-transfer complex between PetF1 and HydA2 permits a more detailed view of the molecular events leading up to H2 evolution, and suggests potential mutagenic strategies to modulate electron flow to HydA2.

Chang, C. H.; King, P. W.; Ghirardi, M. L.; Kim, K.

2007-11-01

24

Spin distribution of the H-cluster in the H(ox)-CO state of the [FeFe] hydrogenase from Desulfovibrio desulfuricans: HYSCORE and ENDOR study of (14)N and (13)C nuclear interactions.  

PubMed

Hydrogenases are enzymes which catalyze the reversible cleavage of molecular hydrogen into protons and electrons. In [FeFe] hydrogenases the active center is a 6Fe6S cluster, referred to as the "H-cluster." It consists of the redox-active binuclear subcluster ([2Fe](H)) coordinated by CN(-) and CO ligands and the cubane-like [4Fe-4S](H) subcluster which is connected to the protein via Cys ligands. One of these Cys ligands bridges to the [2Fe](H) subcluster. The CO-inhibited form of [FeFe] hydrogenase isolated from Desulfovibrio desulfuricans was studied using advanced EPR methods. In the H(ox)-CO state the open coordination site at the [2Fe](H) subcluster is blocked by extrinsic CO, giving rise to an EPR-active S = 1/2 species. The CO inhibited state was prepared with (13)CO and illuminated under white light at 273 K. In this case scrambling of the CO ligands occurs. Three (13)C hyperfine couplings of 17.1, 7.4, and 3.8 MHz (isotropic part) were observed and assigned to (13)CO at the extrinsic, the bridging, and the terminal CO-ligand positions of the distal iron, respectively. No (13)CO exchange of the CO ligand to the proximal iron was observed. The hyperfine interactions detected indicate a rather large distribution of the spin density over the terminal and bridging CO ligands attached to the distal iron. Furthermore, (14)N nuclear spin interactions were measured. On the basis of the observed (14)N hyperfine couplings, which result from the CN(-) ligands of the [2Fe](H) subcluster, it has been concluded that there is very little unpaired spin density on the cyanides of the binuclear subcluster. PMID:19011912

Silakov, Alexey; Wenk, Brian; Reijerse, Eduard; Albracht, Simon P J; Lubitz, Wolfgang

2009-02-01

25

Genomic Analysis Reveals Multiple [FeFe] Hydrogenases and Hydrogen Sensors Encoded by Treponemes from the H 2 Rich Termite Gut  

Microsoft Academic Search

We have completed a bioinformatic analysis of the hydrogenases encoded in the genomes of three termite gut treponeme isolates:\\u000a hydrogenotrophic, homoacetogenic Treponema primitia strains ZAS-1 and ZAS-2, and the hydrogen-producing, sugar-fermenting Treponema azotonutricium ZAS-9. H2 is an important free intermediate in the breakdown of wood by termite gut microbial communities, reaching concentrations\\u000a in some species exceeding those measured for any

Nicholas R. Ballor; Ian Paulsen; Jared R. Leadbetter

26

Artificial Hydrogenases  

PubMed Central

Decades of biophysical study on the hydrogenase (H2ase) enzymes have yielded sufficient information to guide the synthesis of analogues of their active sites. Three families of enzymes serve as inspiration for this work: the [FeFe]-, [NiFe]-, and [Fe]-H2ases, all of which feature iron centers bound to both CO and thiolate. Artificial H2ases effect the oxidation of H2 of H2 and the reverse reaction, the reduction of protons. These reactions occur via the intermediacy of metal hydrides. The inclusion of amine bases within the catalysts is an important design feature that is emulated in related bioinspired catalysts. Continuing challenges are the low reactivity of H2 towards biomimetic H2ases.

Barton, Bryan E.; Olsen, Matthew T.; Rauchfuss, Thomas B.

2010-01-01

27

Heterolytic cleavage of hydrogen by an iron hydrogenase model: an Fe-H???H-N dihydrogen bond characterized by neutron diffraction.  

PubMed

Hydrogenase enzymes in nature use hydrogen as a fuel, but the heterolytic cleavage of H-H bonds cannot be readily observed in enzymes. Here we show that an iron complex with pendant amines in the diphosphine ligand cleaves hydrogen heterolytically. The product has a strong Fe-H???H-N dihydrogen bond. The structure was determined by single-crystal neutron diffraction, and has a remarkably short H???H distance of 1.489(10)?Å between the protic N-H(?+) and hydridic Fe-H(?-) part. The structural data for [Cp(C5F4N)FeH(P(tBu)2N(tBu)2H)](+) provide a glimpse of how the H-H bond is oxidized or generated in hydrogenase enzymes. These results now provide a full picture for the first time, illustrating structures and reactivity of the dihydrogen complex and the product of the heterolytic cleavage of H2 in a functional model of the active site of the [FeFe] hydrogenase enzyme. PMID:24757087

Liu, Tianbiao; Wang, Xiaoping; Hoffmann, Christina; DuBois, Daniel L; Bullock, R Morris

2014-05-19

28

Model study of CO inhibition of [NiFe]hydrogenase.  

PubMed

We propose a modified mechanism for the inhibition of [NiFe]hydrogenase ([NiFe]H(2)ase) by CO. We present a model study, using a NiRu H(2)ase mimic, that demonstrates that (i) CO completely inhibits the catalytic cycle of the model compound, (ii) CO prefers to coordinate to the Ru(II) center rather than taking an axial position on the Ni(II) center, and (iii) CO is unable to displace a hydrido ligand from the NiRu center. We combine these studies with a reevaluation of previous studies to propose that, under normal circumstances, CO inhibits [NiFe]H(2)ase by complexing to the Fe(II) center. PMID:21853978

Matsumoto, Takahiro; Kabe, Ryota; Nonaka, Kyoshiro; Ando, Tatsuya; Yoon, Ki-Seok; Nakai, Hidetaka; Ogo, Seiji

2011-09-19

29

Synthesis and reactivity of mononuclear iron models of [Fe]-hydrogenase that contain an acylmethylpyridinol ligand.  

PubMed

[Fe]-hydrogenase has a single iron-containing active site that features an acylmethylpyridinol ligand. This unique ligand environment had yet to be reproduced in synthetic models; however the synthesis and reactivity of a new class of small molecule mimics of [Fe]-hydrogenase in which a mono-iron center is ligated by an acylmethylpyridinol ligand has now been achieved. Key to the preparation of these model compounds is the successful C-O cleavage of an alkyl ether moiety to form the desired pyridinol ligand. Reaction of solvated complex [(2-CH2CO-6-HOC5H3N)Fe(CO)2(CH3CN)2](+)(BF4)(-) with thiols or thiophenols in the presence of NEt3 yielded 5-coordinate iron thiolate complexes. Further derivation produced complexes [(2-CH2CO-6-HOC5H3N)Fe(CO)2(SCH2CH2OH)] and [(2-CH2CO-6-HOC5H3N)Fe(CO)2(CH3COO)], which can be regarded as models of FeGP cofactors of [Fe]-hydrogenase extracted by 2-mercaptoethanol and acetic acid, respectively. When the derivative complexes were treated with HBF4 ?Et2O, the solvated complex was regenerated by protonation of the thiolate ligands. The reactivity of several models with CO, isocyanide, cyanide, and H2 was also investigated. PMID:24402840

Hu, Bowen; Chen, Dafa; Hu, Xile

2014-02-01

30

Roles of HynAB and Ech, the only two hydrogenases found in the model sulfate reducer Desulfovibrio gigas.  

PubMed

Sulfate-reducing bacteria are characterized by a high number of hydrogenases, which have been proposed to contribute to the overall energy metabolism of the cell, but exactly in what role is not clear. Desulfovibrio spp. can produce or consume H2 when growing on organic or inorganic substrates in the presence or absence of sulfate. Because of the presence of only two hydrogenases encoded in its genome, the periplasmic HynAB and cytoplasmic Ech hydrogenases, Desulfovibrio gigas is an excellent model organism for investigation of the specific function of each of these enzymes during growth. In this study, we analyzed the physiological response to the deletion of the genes that encode the two hydrogenases in D. gigas, through the generation of ?echBC and ?hynAB single mutant strains. These strains were analyzed for the ability to grow on different substrates, such as lactate, pyruvate, and hydrogen, under respiratory and fermentative conditions. Furthermore, the expression of both hydrogenase genes in the three strains studied was assessed through quantitative reverse transcription-PCR. The results demonstrate that neither hydrogenase is essential for growth on lactate-sulfate, indicating that hydrogen cycling is not indispensable. In addition, the periplasmic HynAB enzyme has a bifunctional activity and is required for growth on H2 or by fermentation of pyruvate. Therefore, this enzyme seems to play a dominant role in D. gigas hydrogen metabolism. PMID:23974026

Morais-Silva, Fabio O; Santos, Catia I; Rodrigues, Rute; Pereira, Inês A C; Rodrigues-Pousada, Claudina

2013-10-01

31

Synthesis, structure and reactivity of Ni site models of [NiFeSe] hydrogenases.  

PubMed

A series of structural models of the Ni centre in [NiFeSe] hydrogenases has been developed which exhibits key structural features of the Ni site in the H2 cycling enzyme. Specifically, two complexes with a hydrogenase-analogous four-coordinate 'NiS3Se' primary coordination sphere and complexes with a 'NiS2Se2' and a 'NiS4' core are reported. The reactivity of the complexes towards oxygen and protons shows some relevance to the chemistry of [NiFeSe] hydrogenases. Exposure of a 'NiS3Se' complex to atmospheric oxygen results in the oxidation of the selenolate group in the complex to a diselenide, which is released from the nickel site. Oxidation of the selenolate ligand on Ni occurs approximately four times faster than oxidation with the analogous sulfur complex. Reaction of the complexes with one equivalent of HBF4 results in protonation of the monodentate chalcogenolate and the release of this ligand from the metal centre as a thiol or selenol. Unrelated to their biomimetic nature, the complexes serve also as molecular precursors to modify electrodes with Ni-S-Se containing particles by electrochemical deposition. The activated electrodes evolve H2 in pH neutral water with an electrocatalytic onset potential of -0.6 V and a current density of 15 ?A cm(-2) at -0.75 V vs. NHE. PMID:24366040

Wombwell, Claire; Reisner, Erwin

2014-03-21

32

Diferrous cyanides as models for the Fe-only hydrogenases.  

PubMed

The first systematic study of diferrous dicyano dithiolates is described. Oxidation of [Fe2(S2C2H4)(CN)2(CO)4](2-) in the presence of cyanide and tertiary phosphines and of Fe2(S2C2H4)(CO)4(PMe3)2 in the presence of cyanide affords a series of diferrous cyanide derivatives that bear a stoichiometric, structural, and electronic relationship to the H(ox)(air) state of the Fe-only hydrogenases. With PPh3 as the trapping ligand, we obtained an unsymmetrical isomer of Fe2(S2C2H4)(mu-CO)(CN)2(PPh3)2(CO)2, as confirmed crystallographically. This diferrous cyanide features the semibridging CO-ligand, with Fe-muC bond lengths of 2.15 and 1.85 A. Four isomers of Fe2(S2C2H4)(mu-CO)(CN)2(PMe3)2(CO)2 were observed, the initial product again being unsymmetrical but more stable isomers being symmetrical. DFT calculations confirm that the most stable isomers of Fe2(S2C2H4)(mu-CO)(CN)2(PMe3)2(CO)2 have cyanide trans to mu-CO. Oxidative decarbonylation also afforded the new tetracyanide [Fe2(S2C2H4)(mu-CO)(CN)4(CO)2]2-. Insights into the oxidative decarbonylation mechanism of these syntheses come from the spectroscopic characterization of the tetracarbonyl [Fe2(S2C2H4)(mu-CO)(CN)3(CO)3](-). This species reacts with PEt3 to produce the stable adduct [Fe2(S2C2H4)(mu-CO)(CN)3(CO)2(PEt3)](-). PMID:16076208

Boyke, Christine A; van der Vlugt, Jarl Ivar; Rauchfuss, Thomas B; Wilson, Scott R; Zampella, Giuseppe; De Gioia, Luca

2005-08-10

33

O2 migration rates in [NiFe] hydrogenases. A joint approach combining free-energy calculations and kinetic modeling.  

PubMed

Hydrogenases are promising candidates for the catalytic production of green energy by means of biological ways. The major impediment to such a production is rooted in their inhibition under aerobic conditions. In this work, we model dioxygen migration rates in mutants of a hydrogenase of Desulfovibrio fructusovorans. The approach relies on the calculation of the whole potential of mean force for O2 migration within the wild-type as well as in V74M, V74F, and V74Q mutant channels. The three free-energy barriers along the entire migration pathway are converted into chemical rates through modeling based on Transition State Theory. The use of such a model recovers the trend of O2 migration rates among the series. PMID:24377375

Topin, Jérémie; Diharce, Julien; Fiorucci, Sébastien; Antonczak, Serge; Golebiowski, Jérôme

2014-01-23

34

Reactions of [FeFe]-hydrogenase models involving the formation of hydrides related to proton reduction and hydrogen oxidation.  

PubMed

[FeFe]-hydrogenases are enzymes in nature that catalyze the reduction of protons and the oxidation of H2 at neutral pH with remarkably high activities and incredibly low overpotential. Structural and functional biomimicking of the active site of [FeFe]-hydrogenases can provide helpful hints for elucidating the mechanism of H2 evolution and uptake at the [FeFe]-hydrogenase active site and for designing bioinspired catalysts to replace the expensive noble metal catalysts for H2 generation and uptake. This perspective focuses on the recent progress in the formation and reactivity of iron hydrides closely related to the processes of proton reduction and hydrogen oxidation mediated by diiron dithiolate complexes. The second section surveys the bridging and terminal hydride species formed from various diiron complexes as well as the intramolecular proton transfer. The very recent progress in H2 activation by diiron dithiolate models are reviewed in the third section. In the concluding remarks and outlook, the differences in structure and catalytic mechanism between the synthetic models and the native [FeFe]-H2ase active site are compared and analyzed, which may cause the need for a significantly larger driving force and may lead to lower activities of synthetic models than the [FeFe]-H2ases for H2 generation and uptake. PMID:23846321

Wang, Ning; Wang, Mei; Chen, Lin; Sun, Licheng

2013-09-14

35

Time-resolved infrared studies of a trimethylphosphine model derivative of [FeFe]-hydrogenase.  

PubMed

Model compounds that structurally mimic the hydrogen-producing active site of [FeFe]-hydrogenases have been studied to explore potential ground-state electronic structure effects on reaction mechanisms compared to hexacarbonyl derivatives. The time-dependent behavior of Fe2(?-S2C3H6)(CO)4(PMe)2 (A) in room temperature n-heptane and acetonitrile solutions was examined using various ultrafast UV and visible excitation pulses with broadband IR-probe spectroscopy of the carbonyl (CO) stretching region. Ground- and excited-state electronic and CO-stretching mode vibrational properties of the possible isomers of A were also examined using density functional theory (DFT) computations. In n-heptane, 355 and 532 nm excitation resulted in short-lived (135 ± 74 ps) bands assigned to excited-state, CO-loss photoproducts. These bands decay away, forming new long-lived absorptions that are likely a mixture of isomers of both three-CO and four-CO ground-state isomers. These new bands grow in with a time scale of 214 ± 119 ps and persist for more than 100 ns. In acetonitrile, similar results are seen with a 532 nm pump, but the 355 nm data lack evidence of the longer-lived bands. In either solvent, the 266 nm pump data seem to also lack longer-lived bands, but the intensities are significantly lower in this data, making firm conclusions more difficult. We suggest that these wavelength-dependent excitation dynamics significantly alter potential mechanisms and efficiencies for light-driven catalysis. PMID:24083980

Johnson, Melissa; Thuman, James; Letterman, Roger G; Stromberg, Christopher J; Webster, Charles Edwin; Heilweil, Edwin J

2013-12-12

36

Interaction of [FeFe]-Hydrogenases with Single-walled Carbon Nanotubes  

SciTech Connect

Single-walled carbon nanotubes (SWNT) are promising candidates for use in energy conversion devices as an active photo-collecting elements, for dissociation of bound excitons and charge-transfer from photo-excited chromophores, or as molecular wires to transport charge. Hydrogenases are enzymes that efficiently catalyze the reduction of protons from a variety of electron donors to produce molecular hydrogen. Hydrogenases together with SWNT suggest a novel biohybrid material for direct conversion of sunlight into H{sub 2}. Here, we report changes in SWNT optical properties upon addition of recombinant [FeFe] hydrogenases from Clostridium acetobutylicum and Chlamydomonas reinhardtii. We find evidence that novel and stable charge-transfer complexes are formed under conditions of the hydrogenase catalytic turnover, providing spectroscopic handles for further study and application of this hybrid system.

Chang, D. S.; McDonald, T. J.; Kim, Y.-H.; Blackburn, J. L.; Heben, M. J.; King, P. W.

2007-01-01

37

Characterization of a HoxEFUYH type of [NiFe] hydrogenase from Allochromatium vinosum and some EPR and IR properties of the hydrogenase module.  

PubMed

A soluble hydrogenase from Allochromatium vinosum was purified. It consisted of a large (M (r) = 52 kDa) and a small (M (r) = 23 kDa) subunit. The genes encoding for both subunits were identified. They belong to an open reading frame where they are preceded by three more genes. A DNA fragment containing all five genes was cloned and sequenced. The deduced amino acid sequences of the products characterized the complex as a member of the HoxEFUYH type of [NiFe] hydrogenases. Detailed sequence analyses revealed binding sites for eight Fe-S clusters, three [2Fe-2S] clusters and five [4Fe-4S] clusters, six of which are also present in homologous subunits of [FeFe] hydrogenases and NADH:ubiquione oxidoreductases (complex I). This makes the HoxEFUYH type of hydrogenases the one that is evolutionary closest to complex I. The relative positions of six of the potential Fe-S clusters are predicted on the basis of the X-ray structures of the Clostridium pasteurianum [FeFe] hydrogenase I and the hydrophilic domain of complex I from Thermus thermophilus. Although the HoxF subunit contains binding sites for flavin mononucleotide and NAD(H), cell-free extracts of A. vinosum did not catalyse a H(2)-dependent reduction of NAD(+). Only the hydrogenase module (HoxYH) could be purified. Its electron paramagnetic resonance (EPR) and IR spectral properties showed the presence of a Ni-Fe active site and a [4Fe-4S] cluster. Its activity was sensitive to carbon monoxide. No EPR signals from a light-sensitive Ni(a)-C* state could be observed. This study presents the first IR spectroscopic data on the HoxYH module of a HoxEFUYH type of [NiFe] hydrogenase. PMID:16969669

Long, Minnan; Liu, Jingjing; Chen, Zhifeng; Bleijlevens, Boris; Roseboom, Winfried; Albracht, Simon P J

2007-01-01

38

Photoelectron spectroscopy of dithiolatodiironhexacarbonyl models for the active site of [Fe Fe] hydrogenases: Insight into the reorganization energy of the “rotated” structure in the enzyme  

NASA Astrophysics Data System (ADS)

Synthetic analogs, ?-(RS) 2Fe 2(CO) 6, of the active site of [Fe-Fe] hydrogenases do not have the semi-bridged CO and "rotated" structure found in the enzyme. However, recent studies have shown that cations of dithiolatodiiron complexes adopt this rotated structure. This paper reports the use of photoelectron spectroscopy in combination with density functional theory calculations to show that two previously reported complexes: ?-(1,2-benzenedithiolato)Fe 2(CO) 6 and ?-(1,3-propanedithiolato)Fe 2(CO) 6 and two new complexes: ?-(2,3-pyridinodithiolato)Fe 2(CO) 6 and ?-(norbornane-2-exo,3-exo-dithiolato)Fe 2(CO) 6 favor the "rotated" structure in their corresponding cations. Furthermore, these methods provide a measure of the reorganization energy between the "rotated" and "unrotated" structures in the gas phase. The results provide insight on the entatic state of the dithiolatodiiron site in the enzyme, in which the protein controls the structure of the active site. This structure influences the redox energy and reorganization energy enabling fast electron transfer.

Petro, Benjamin J.; Vannucci, Aaron K.; Lockett, L. Tori; Mebi, Charles; Kottani, Rudresha; Gruhn, Nadine E.; Nichol, Gary S.; Goodyer, Paul A. J.; Evans, Dennis H.; Glass, Richard S.; Lichtenberger, Dennis L.

2008-11-01

39

Role of the azadithiolate cofactor in models for [FeFe]-hydrogenase: novel structures and catalytic implications.  

PubMed

This paper summarizes studies on the redox behavior of synthetic models for the [FeFe]-hydrogenases, consisting of diiron dithiolato carbonyl complexes bearing the amine cofactor and its N-benzyl derivative. Of specific interest are the causes of the low reactivity of oxidized models toward H(2), which contrasts with the high activity of these enzymes for H(2) oxidation. The redox and acid-base properties of the model complexes [Fe(2)[(SCH(2))(2)NR](CO)(3)(dppv)(PMe(3))](+) ([2](+) for R = H and [2'](+) for R = CH(2)C(6)H(5), dppv = cis-1,2-bis(diphenylphosphino)ethylene)) indicate that addition of H(2) followed by deprotonation are (i) endothermic for the mixed valence (Fe(II)Fe(I)) state and (ii) exothermic for the diferrous (Fe(II)Fe(II)) state. The diferrous state is shown to be unstable with respect to coordination of the amine to Fe, a derivative of which was characterized crystallographically. The redox and acid-base properties for the mixed valence models differ strongly for those containing the amine cofactor versus those derived from propanedithiolate. Protonation of [2'](+) induces disproportionation to a 1:1 mixture of the ammonium [H2'](+) (Fe(I)Fe(I)) and the dication [2'](2+) (Fe(II)Fe(II)). This effect is consistent with substantial enhancement of the basicity of the amine in the Fe(I)Fe(I) state vs the Fe(II)Fe(I) state. The Fe(I)Fe(I) ammonium compounds are rapid and efficient H-atom donors toward the nitroxyl compound TEMPO. The atom transfer is proposed to proceed via the hydride. Collectively, the results suggest that proton-coupled electron-transfer pathways should be considered for H(2) activation by the [FeFe]-hydrogenases. PMID:21114298

Olsen, Matthew T; Rauchfuss, Thomas B; Wilson, Scott R

2010-12-22

40

Cobaloximes as functional models for hydrogenases. 2. Proton electroreduction catalyzed by difluoroborylbis(dimethylglyoximato)cobalt(II) complexes in organic media.  

PubMed

Cobaloximes are effective electrocatalysts for hydrogen evolution and thus functional models for hydrogenases. Among them, difluoroboryl-bridged complexes appear both to mediate proton electroreduction with low overpotentials and to be quite stable in acidic conditions. We report here a mechanistic study of [Co(dmgBF2)2L] (dmg2- = dimethylglyoximato dianion; L = CH3CN or N,N-dimethylformamide) catalyzed proton electroreduction in organic solvents. Depending on the applied potential and the strength of the acid used, three different pathways for hydrogen production were identified and a unified mechanistic scheme involving cobalt(II) or cobalt(III) hydride species is proposed. As far as working potential and turnover frequency are concerned, [Co(dmgBF2)2(CH3CN)2], in the presence of p-cyanoanilinium cation in acetonitrile, is one of the best synthetic catalysts of the first-row transition-metal series for hydrogen evolution. PMID:17269760

Baffert, Carole; Artero, Vincent; Fontecave, Marc

2007-03-01

41

Homology modeling reveals the structural background of the striking difference in thermal stability between two related [NiFe]hydrogenases  

Microsoft Academic Search

Hydrogenases are redox metalloenzymes in bacteria that catalyze the uptake or production of molecular hydrogen. Two homologous nickel–iron hydrogenases, HupSL and HydSL from the photosynthetic purple sulfur bacterium Thiocapsa roseopersicina, differ substantially in their thermal stabilities despite the high sequence similarity between them. The optimum temperature of HydSL activity is estimated to be at least 50 °C higher than that of

András Szilágyi; Kornél L. Kovács; Gábor Rákhely; Péter Závodszky

2002-01-01

42

Studies on hydrogenase  

PubMed Central

Hydrogenases are microbial enzymes which catalyze uptake and production of H2. Hydrogenases are classified into 10 classes based on the electron carrier specificity, or into 3 families, [NiFe]-family (including [NiFeSe]-subfamily), [FeFe]-family and [Fe]-family, based on the metal composition of the active site. H2 is heterolytically cleaved on the enzyme (E) to produce EHaHb, where Ha and Hb have different rate constants for exchange with the medium hydron. X-ray crystallography unveiled the three-dimensional structures of hydrogenases. The simplest [NiFe]-hydrogenase is a heterodimer, in which the large subunit bears the Ni-Fe center buried deep in the protein, and the small subunit bears iron-sulfur clusters, which mediate electron transfer between the Ni-Fe center and the protein surface. Some hydrogenases have additional subunit(s) for interaction with their electron carriers. Various redox states of the enzyme were characterized by EPR, FTIR, etc. Based on the kinetic, structural and spectroscopic studies, the catalytic mechanism of [NiFe]-hydrogenase was proposed to explain H2-uptake, H2-production and isotopic exchange reactions.

YAGI, Tatsuhiko; HIGUCHI, Yoshiki

2013-01-01

43

Combining acid-base, redox and substrate binding functionalities to give a complete model for the [FeFe]-hydrogenase  

PubMed Central

Some enzymes function by coupling substrate turnover with electron transfer from a redox cofactor such as ferredoxin. In the [FeFe]-hydrogenases, nature’s fastest catalysts for the production and oxidation of H2, the one-electron redox by a ferredoxin complements the one-electron redox by the diiron active site. In this Article, we replicate the function of the ferredoxins with the redox-active ligand Cp*Fe(C5Me4CH2PEt2) (FcP*). FcP* oxidizes at mild potentials, in contrast to most ferrocene-based ligands, which suggests that it might be a useful mimic of ferredoxin cofactors. The specific model is Fe2[(SCH2)2NBn](CO)3(FcP*)(dppv) (1), which contains the three functional components of the active site: a reactive diiron centre, an amine as a proton relay and, for the first time, a one-electron redox module. By virtue of the synthetic redox cofactor, [1]2+ exhibits unique reactivity towards hydrogen and CO. In the presence of excess oxidant and base, H2 oxidation by [1]2+ is catalytic.

Camara, James M.; Rauchfuss, Thomas B.

2012-01-01

44

Time resolved infrared spectroscopy: kinetic studies of weakly binding ligands in an iron-iron hydrogenase model compound.  

PubMed

Solution photochemistry of (?-pdt)[Fe(CO)(3)](2) (pdt = ?(2)-S(CH(2))(3)S), a precursor model of the 2-Fe subsite of the H-cluster of the hydrogenase enzyme, has been studied using time-resolved infrared spectroscopy. Following the loss of CO, solvation of the Fe center by the weakly binding ligands cyclohexene, 3-hexyne, THF, and 2,3-dihydrofuran (DHF) occurred. Subsequent ligand substitution of these weakly bound ligands by pyridine or cyclooctene to afford a more stable complex was found to take place via a dissociative mechanism on a seconds time scale with activation parameters consistent with such a pathway. That is, the ?S(‡) values were positive and the ?H(‡) parameters closely agreed with bond dissociation enthalpies (BDEs) obtained from DFT calculations. For example, for cyclohexene replacement by pyridine, experimental ?H(‡) and ?S(‡) values were determined to be 19.7 ± 0.6 kcal/mol (versus a theoretical prediction of 19.8 kcal/mol) and 15 ± 2 eu, respectively. The ambidentate ligand 2,3-DHF was shown to initially bind to the iron center via its oxygen atom followed by an intramolecular rearrangement to the more stable ?(2)-olefin bound species. DFT calculations revealed a transition state structure with the iron atom almost equidistant from the oxygen and one edge of the olefinic bond. The computed ?H(‡) of 10.7 kcal/mol for this isomerization process was found to be in excellent agreement with the experimental value of 11.2 ± 0.3 kcal/mol. PMID:22680284

Muhammad, Sohail; Moncho, Salvador; Brothers, Edward N; Darensbourg, Marcetta Y; Darensbourg, Donald J; Bengali, Ashfaq A

2012-07-01

45

Mechanistic studies on proton transfer in a [FeFe] hydrogenase mimic complex.  

PubMed

Four different pathways for deprotonation of [(?-pdt){Fe(CO)3}{Fe(CO)(?(2)-Me2PCH2N(Me)CH2PMe2)}] (pdt = propane-1,3-dithiolate) [1H?](1+) were examined, including (1) the "Direct" deprotonation; (2) the "Indirect" deprotonation via the pendant amine N; (3) the "Indirect" deprotonation via the distal metal Fe; and (4) the "Indirect" deprotonation via the dithiolate S. Only deprotonation of the "Indirect" pathway via the pendant amine N is feasible at room temperature. The most favorable migration destination for the bridging hydride in [1H?](1+) is the pendant amine N (activation energy barrier 16.1 kcal mol(-1)). Migrations to the other two possible sites including the distal metal Fe (34.6 kcal mol(-1)) and the S in the dithiolate group (41.5 kcal mol(-1)) were hindered by high proton shuttling barriers. Once the migration barriers of those three "Indirect" pathways are overcome, the following deprotonations from all three positions including the distal atom Fe, the dithiolate S and the pendant amine N, are all feasible. The results also demonstrate a large difference for deprotonation of the hydride from the terminal and bridging sites. The low energy of the virtual orbital associated with the antibonding M-H interaction of [1HFe](1+) implies the high activity for the interaction with aniline. PMID:23563224

Wang, Ying; Ahlquist, Mårten S G

2013-06-01

46

Dynamic electrochemical experiments on hydrogenases  

Microsoft Academic Search

A powerful approach for studying hydrogenases, applying a suite of dynamic electrochemical techniques known as protein film\\u000a electrochemistry, is trailblazing fresh discoveries and providing a wealth of quantitative data on these complex enzymes.\\u000a The information now stemming from experiments on tiny quantities of hydrogenases ranges from their kinetics and catalytic\\u000a bias (a preference to operate in H2 oxidation vs. H2

Fraser A. Armstrong

2009-01-01

47

Fe@Fe2O3 core-shell nanowires enhanced Fenton oxidation by accelerating the Fe(III)/Fe(II) cycles.  

PubMed

In this study we demonstrate Fe@Fe2O3 core-shell nanowires can improve Fenton oxidation efficiency by two times with rhodamine B as a model pollutant at pH > 4. Active species trapping experiments revealed that the rhodamine B oxidation enhancement was attributed to molecular oxygen activation induced by Fe@Fe2O3 core-shell nanowires. The molecular oxygen activation process could generate superoxide radicals to assist iron core for the reduction of ferric ions to accelerate the Fe(III)/Fe(II) cycles, which favored the H2O2 decomposition to produce more hydroxyl radicals for the rhodamine B oxidation. The combination of Fe@Fe2O3 core-shell nanowires and ferrous ions (Fe@Fe2O3/Fe(2+)) offered a superior Fenton catalyst to decompose H2O2 for producing OH. We employed benzoic acid as a probe reagent to check the generation of OH and found the OH generation rate of Fe@Fe2O3/Fe(2+) was 2-4 orders of magnitude larger than those of commonly used iron based Fenton catalysts and 38 times that of Fe(2+). The reusability and the stability of Fe@Fe2O3 core-shell nanowires were studied. Total organic carbon and ion chromatography analyses revealed the mineralization of rhodamine B and the releasing of nitrate ions. Gas chromatograph-mass spectrometry was used to investigate the degradation intermediates to propose the possible rhodamine B Fenton oxidation pathway in the presence of Fe@Fe2O3 nanowires. This study not only provides a new Fenton oxidation system for pollutant control, but also widen the application of molecular oxygen activation induced by nanoscale zero valent iron. PMID:24793112

Shi, Jingu; Ai, Zhihui; Zhang, Lizhi

2014-08-01

48

[FeFe]-Hydrogenase Maturation.  

PubMed

Hydrogenases are metalloenzymes that catalyze the reversible reduction of protons at unusual metal centers. This Current Topic discusses recent advances in elucidating the steps involved in the biosynthesis of the complex metal cluster at the [FeFe]-hydrogenase (HydA) active site, known as the H-cluster. The H-cluster is composed of a 2Fe subcluster that is anchored within the active site by a bridging cysteine thiolate to a [4Fe-4S] cubane. The 2Fe subcluster contains carbon monoxide, cyanide, and bridging dithiolate ligands. H-cluster biosynthesis is now understood to occur stepwise; standard iron-sulfur cluster assembly machinery builds the [4Fe-4S] cubane of the H-cluster, while three specific maturase enzymes known as HydE, HydF, and HydG assemble the 2Fe subcluster. HydE and HydG are both radical S-adenosylmethionine enzymes that interact with an iron-sulfur cluster binding GTPase scaffold, HydF, during the construction of the 2Fe subcluster moiety. In an unprecedented biochemical reaction, HydG cleaves tyrosine and decomposes the resulting dehydroglycine into carbon monoxide and cyanide ligands. The role of HydE in the biosynthetic pathway remains undefined, although it is hypothesized to be critical for the synthesis of the bridging dithiolate. HydF is the site where the complete 2Fe subcluster is formed and ultimately delivered to the immature hydrogenase protein in the final step of [FeFe]-hydrogenase maturation. This work addresses the roles of and interactions among HydE, HydF, HydG, and HydA in the formation of the mature [FeFe]-hydrogenase. PMID:24878200

Shepard, Eric M; Mus, Florence; Betz, Jeremiah N; Byer, Amanda S; Duffus, Benjamin R; Peters, John W; Broderick, Joan B

2014-07-01

49

Diversity and transcription of proteases involved in the maturation of hydrogenases in Nostoc punctiforme ATCC 29133 and Nostoc sp. strain PCC 7120  

PubMed Central

Background The last step in the maturation process of the large subunit of [NiFe]-hydrogenases is a proteolytic cleavage of the C-terminal by a hydrogenase specific protease. Contrary to other accessory proteins these hydrogenase proteases are believed to be specific whereby one type of hydrogenases specific protease only cleaves one type of hydrogenase. In cyanobacteria this is achieved by the gene product of either hupW or hoxW, specific for the uptake or the bidirectional hydrogenase respectively. The filamentous cyanobacteria Nostoc punctiforme ATCC 29133 and Nostoc sp strain PCC 7120 may contain a single uptake hydrogenase or both an uptake and a bidirectional hydrogenase respectively. Results In order to examine these proteases in cyanobacteria, transcriptional analyses were performed of hupW in Nostoc punctiforme ATCC 29133 and hupW and hoxW in Nostoc sp. strain PCC 7120. These studies revealed numerous transcriptional start points together with putative binding sites for NtcA (hupW) and LexA (hoxW). In order to investigate the diversity and specificity among hydrogeanse specific proteases we constructed a phylogenetic tree which revealed several subgroups that showed a striking resemblance to the subgroups previously described for [NiFe]-hydrogenases. Additionally the proteases specificity was also addressed by amino acid sequence analysis and protein-protein docking experiments with 3D-models derived from bioinformatic studies. These studies revealed a so called "HOXBOX"; an amino acid sequence specific for protease of Hox-type which might be involved in docking with the large subunit of the hydrogenase. Conclusion Our findings suggest that the hydrogenase specific proteases are under similar regulatory control as the hydrogenases they cleave. The result from the phylogenetic study also indicates that the hydrogenase and the protease have co-evolved since ancient time and suggests that at least one major horizontal gene transfer has occurred. This co-evolution could be the result of a close interaction between the protease and the large subunit of the [NiFe]-hydrogenases, a theory supported by protein-protein docking experiments performed with 3D-models. Finally we present data that may explain the specificity seen among hydrogenase specific proteases, the so called "HOXBOX"; an amino acid sequence specific for proteases of Hox-type. This opens the door for more detailed studies of the specificity found among hydrogenase specific proteases and the structural properties behind it.

2009-01-01

50

Hydrogenases, accessory genes and the regulation of [NiFe] hydrogenase biosynthesis in Thiocapsa roseopersicina  

Microsoft Academic Search

The purple (Sulphur) phototrophic bacterium, Thiocapsa roseopersicina BBS contains several [NiFe] hydrogenases, of which two are membrane bound. Mutant T. roseopersicina cells, carrying deletions in both gene clusters showed hydrogenase activity. This activity was located in the cytoplasm. The structural gene cluster hoxEFUYH was identified and sequenced. In addition, genes homologous to hupUV\\/hoxBC, the hydrogen sensing hydrogenase have been identified

Kornél L. Kovács; Barna Fodor; Ákos T. Kovács; Gyula Csanádi; Gergely Maróti; Judit Balogh; Solmaz Arvani; Gábor Rákhely

2002-01-01

51

The [4Fe-4S]-cluster coordination of [FeFe]-hydrogenase maturation protein HydF as revealed by EPR and HYSCORE spectroscopies.  

PubMed

[FeFe] hydrogenases are key enzymes for bio(photo)production of molecular hydrogen, and several efforts are underway to understand how their complex active site is assembled. This site contains a [4Fe-4S]-2Fe cluster and three conserved maturation proteins are required for its biosynthesis. Among them, HydF has a double task of scaffold, in which the dinuclear iron precursor is chemically modified by the two other maturases, and carrier to transfer this unit to a hydrogenase containing a preformed [4Fe-4S]-cluster. This dual role is associated with the capability of HydF to bind and dissociate an iron-sulfur center, due to the presence of the conserved FeS-cluster binding sequence CxHx(46-53)HCxxC. The recently solved three-dimensional structure of HydF from Thermotoga neapolitana described the domain containing the three cysteines which are supposed to bind the FeS cluster, and identified the position of two conserved histidines which could provide the fourth iron ligand. The functional role of two of these cysteines in the activation of [FeFe]-hydrogenases has been confirmed by site-specific mutagenesis. On the other hand, the contribution of the three cysteines to the FeS cluster coordination sphere is still to be demonstrated. Furthermore, the potential role of the two histidines in [FeFe]-hydrogenase maturation has never been addressed, and their involvement as fourth ligand for the cluster coordination is controversial. In this work we combined site-specific mutagenesis with EPR (electron paramagnetic resonance) and HYSCORE (hyperfine sublevel correlation spectroscopy) to assign a role to these conserved residues, in both cluster coordination and hydrogenase maturation/activation, in HydF proteins from different microorganisms. PMID:22985598

Berto, Paola; Di Valentin, Marilena; Cendron, Laura; Vallese, Francesca; Albertini, Marco; Salvadori, Enrico; Giacometti, Giorgio M; Carbonera, Donatella; Costantini, Paola

2012-12-01

52

Site Saturation Mutagenesis Demonstrates a Central Role for Cysteine 298 as Proton Donor to the Catalytic Site in CaHydA [FeFe]-Hydrogenase  

PubMed Central

[FeFe]-hydrogenases reversibly catalyse molecular hydrogen evolution by reduction of two protons. Proton supply to the catalytic site (H-cluster) is essential for enzymatic activity. Cysteine 298 is a highly conserved residue in all [FeFe]-hydrogenases; moreover C298 is structurally very close to the H-cluster and it is important for hydrogenase activity. Here, the function of C298 in catalysis was investigated in detail by means of site saturation mutagenesis, simultaneously studying the effect of C298 replacement with all other 19 amino acids and selecting for mutants with high retained activity. We demonstrated that efficient enzymatic turnover was maintained only when C298 was replaced by aspartic acid, despite the structural diversity between the two residues. Purified CaHydA C298D does not show any significant structural difference in terms of secondary structure and iron incorporation, demonstrating that the mutation does not affect the overall protein fold. C298D retains the hydrogen evolution activity with a decrease of kcat only by 2-fold at pH 8.0 and it caused a shift of the optimum pH from 8.0 to 7.0. Moreover, the oxygen inactivation rate was not affected demonstrating that the mutation does not influence O2 diffusion to the active site or its reactivity with the H-cluster. Our results clearly demonstrate that, in order to maintain the catalytic efficiency and the high turnover number typical of [FeFe] hydrogenases, the highly conserved C298 can be replaced only by another ionisable residue with similar steric hindrance, giving evidence of its involvement in the catalytic function of [FeFe]-hydrogenases in agreement with an essential role in proton transfer to the active site.

Morra, Simone; Giraudo, Alberto; Di Nardo, Giovanna; King, Paul W.; Gilardi, Gianfranco; Valetti, Francesca

2012-01-01

53

Photocatalytic hydrogen evolution by a diiron hydrogenase model based on a peptide fragment of cytochrome c556 with an attached diiron carbonyl cluster and an attached ruthenium photosensitizer.  

PubMed

It is of particular interest to mimic the process of intramolecular electron relay at the active site of [FeFe]-hydrogenase in order to understand the mechanism of the catalytic activity of H(2) evolution. We have recently focused on using the native CXXCH peptide sequence of the C-terminal segment of cytochrome c(556) as a platform which holds a diiron carbonyl cluster via two cysteines and have attached a ruthenium photosensitizer via a histidine. The modified peptide with the two metal moieties is found to act as the photocatalyst for H(2) evolution with a turnover number of ~9 over 2h at pH 8.5 in the presence of ascorbate as a sacrificial reagent. PMID:22420928

Sano, Yohei; Onoda, Akira; Hayashi, Takashi

2012-03-01

54

A genetic region downstream of the hydrogenase structural genes of Bradyrhizobium japonicum that is required for hydrogenase processing.  

PubMed Central

Deletion of a 2.9-kb chromosomal EcoRI fragment of DNA located 2.2 kb downstream from the end of the hydrogenase structural genes resulted in the complete loss of hydrogenase activity. The normal 65- and 35-kDa hydrogenase subunits were absent in the deletion mutants. Instead, two peptides of 66.5 and 41 kDa were identified in the mutants by use of anti-hydrogenase subunit-specific antibody. A hydrogenase structural gene mutant did not synthesize either the normal hydrogenase subunits or the larger peptides. Hydrogenase activity in the deletion mutants was complemented to near wild-type levels by plasmid pCF1, containing a 6.5-kb BglII fragment, and the 65- and 35-kDa hydrogenase subunits were also recovered in the mutants containing pCF1. Images

Fu, C; Maier, R J

1993-01-01

55

[NiFe] hydrogenases: how close do structural and functional mimics approach the active site?  

PubMed

Hydrogen is being considered as a versatile alternative fuel with the ever increasing energy demand and oil prices. Hydrogenases (H2ases) found in bacteria, archaea and eukaryotes are very efficient catalysts for biological hydrogen production. An important and unique hydrogenase enzyme is the [NiFe] H2ase, with an unusual heterobimetallic site. Since the determination of its crystal structure, a variety of complexes have been synthesised and studied. Bioinspired and biomimetic complexes have been investigated as potential catalysts. So far, of all the reported complexes only a few of them have been found to be catalytically active. Moreover, most of the reports are on the reverse reaction, e.g. proton reduction rather than dihydrogen oxidation. This perspective article therefore reviews the structural and functional aspects of the very recently reported model complexes that mimic the [NiFe] hydrogenase active site either in structure or function or both. PMID:24846119

Kaur-Ghumaan, Sandeep; Stein, Matthias

2014-06-01

56

O2 Reactions at the Six-iron Active Site (H-cluster) in [FeFe]-Hydrogenase*  

PubMed Central

Irreversible inhibition by molecular oxygen (O2) complicates the use of [FeFe]-hydrogenases (HydA) for biotechnological hydrogen (H2) production. Modification by O2 of the active site six-iron complex denoted as the H-cluster ([4Fe4S]-2FeH) of HydA1 from the green alga Chlamydomonas reinhardtii was characterized by x-ray absorption spectroscopy at the iron K-edge. In a time-resolved approach, HydA1 protein samples were prepared after increasing O2 exposure periods at 0 °C. A kinetic analysis of changes in their x-ray absorption near edge structure and extended X-ray absorption fine structure spectra revealed three phases of O2 reactions. The first phase (?1 ? 4 s) is characterized by the formation of an increased number of Fe–O,C bonds, elongation of the Fe–Fe distance in the binuclear unit (2FeH), and oxidation of one iron ion. The second phase (?2 ? 15 s) causes a ?50% decrease of the number of ?2.7-? Fe–Fe distances in the [4Fe4S] subcluster and the oxidation of one more iron ion. The final phase (?3 ? 1000 s) leads to the disappearance of most Fe–Fe and Fe–S interactions and further iron oxidation. These results favor a reaction sequence, which involves 1) oxygenation at 2FeH+ leading to the formation of a reactive oxygen species-like superoxide (O2?), followed by 2) H-cluster inactivation and destabilization due to ROS attack on the [4Fe4S] cluster to convert it into an apparent [3Fe4S]+ unit, leading to 3) complete O2-induced degradation of the remainders of the H-cluster. This mechanism suggests that blocking of ROS diffusion paths and/or altering the redox potential of the [4Fe4S] cubane by genetic engineering may yield improved O2 tolerance in [FeFe]-hydrogenase.

Lambertz, Camilla; Leidel, Nils; Havelius, Kajsa G. V.; Noth, Jens; Chernev, Petko; Winkler, Martin; Happe, Thomas; Haumann, Michael

2011-01-01

57

Hydrogenases and H(+)-reduction in primary energy conservation.  

PubMed

Hydrogenases are metalloenzymes subdivided into two classes that contain iron-sulfur clusters and catalyze the reversible oxidation of hydrogen gas (H(2)[Symbol: see text]left arrow over right arrow[Symbol: see text]2H(+)[Symbol: see text]+[Symbol: see text]2e(-)). Two metal atoms are present at their active center: either a Ni and an Fe atom in the [NiFe]hydrogenases, or two Fe atoms in the [FeFe]hydrogenases. They are phylogenetically distinct classes of proteins. The catalytic core of [NiFe]hydrogenases is a heterodimeric protein associated with additional subunits in many of these enzymes. The catalytic core of [FeFe]hydrogenases is a domain of about 350 residues that accommodates the active site (H cluster). Many [FeFe]hydrogenases are monomeric but possess additional domains that contain redox centers, mostly Fe-S clusters. A third class of hydrogenase, characterized by a specific iron-containing cofactor and by the absence of Fe-S cluster, is found in some methanogenic archaea; this Hmd hydrogenase has catalytic properties different from those of [NiFe]- and [FeFe]hydrogenases. The [NiFe]hydrogenases can be subdivided into four subgroups: (1) the H(2) uptake [NiFe]hydrogenases (group 1); (2) the cyanobacterial uptake hydrogenases and the cytoplasmic H(2) sensors (group 2); (3) the bidirectional cytoplasmic hydrogenases able to bind soluble cofactors (group 3); and (4) the membrane-associated, energy-converting, H(2) evolving hydrogenases (group 4). Unlike the [NiFe]hydrogenases, the [FeFe]hydrogenases form a homogeneous group and are primarily involved in H(2) evolution. This review recapitulates the classification of hydrogenases based on phylogenetic analysis and the correlation with hydrogenase function of the different phylogenetic groupings, discusses the possible role of the [FeFe]hydrogenases in the genesis of the eukaryotic cell, and emphasizes the structural and functional relationships of hydrogenase subunits with those of complex I of the respiratory electron transport chain. PMID:18500479

Vignais, Paulette M

2008-01-01

58

HYDROGENASE OF COLEMAN'S SULFATE-REDUCING BACTERIUM  

PubMed Central

Buller, C. S. (University of Kansas, Lawrence), and J. M. Akagi. Hydrogenase of Coleman's sulfate-reducing bacterium. J. Bacteriol. 88:440–443. 1964.—The hydrogenase of the Coleman organism was found to be associated with the particulate fraction of cell-free extracts. This enzyme catalyzed the oxidation of molecular hydrogen in the presence of various electron acceptors. It was also able to evolve hydrogen from reduced methyl viologen and reduced ferredoxin isolated from Clostridium pasteurianum. Other electron donors such as pyruvate and formate were capable of furnishing electrons for hydrogen evolution when suitable carriers were incorporated. Images

Buller, C. S.; Akagi, J. M.

1964-01-01

59

Effects of metal ions on the reactivity and corrosion electrochemistry of Fe/FeS nanoparticles.  

PubMed

Nano-zerovalent iron (nZVI) formed under sulfidic conditions results in a biphasic material (Fe/FeS) that reduces trichloroethene (TCE) more rapidly than nZVI associated only with iron oxides (Fe/FeO). Exposing Fe/FeS to dissolved metals (Pd(2+), Cu(2+), Ni(2+), Co(2+), and Mn(2+)) results in their sequestration by coprecipitation as dopants into FeS and FeO and/or by electroless precipitation as zerovalent metals that are hydrogenation catalysts. Using TCE reduction rates to probe the effect of metal amendments on the reactivity of Fe/FeS, it was found that Mn(2+) and Cu(2+) decreased TCE reduction rates, while Pd(2+), Co(2+), and Ni(2+) increased them. Electrochemical characterization of metal-amended Fe/FeS showed that aging caused passivation by growth of FeO and FeS phases and poisoning of catalytic metal deposits by sulfide. Correlation of rate constants for TCE reduction (kobs) with electrochemical parameters (corrosion potentials and currents, Tafel slopes, and polarization resistance) and descriptors of hydrogen activation by metals (exchange current density for hydrogen reduction and enthalpy of solution into metals) showed the controlling process changed with aging. For fresh Fe/FeS, kobs was best described by the exchange current density for activation of hydrogen, whereas kobs for aged Fe/FeS correlated with electrochemical descriptors of electron transfer. PMID:24579799

Kim, Eun-Ju; Kim, Jae-Hwan; Chang, Yoon-Seok; Turcio-Ortega, David; Tratnyek, Paul G

2014-04-01

60

A model for the CO-inhibited form of [NiFe] hydrogenase: synthesis of (CO)3Fe(?-StBu)3Ni{SC6H3-2,6-(mesityl)2} and reversible CO addition at the Ni site  

PubMed Central

A [NiFe] hydrogenase model compound having a distorted trigonal-pyramidal nickel center, (CO)3Fe(?-StBu)3Ni(SDmp), 1 (Dmp = C6H3-2,6-(mesityl)2), was synthesized from the reaction of the tetranuclear Fe-Ni-Ni-Fe complex [(CO)3Fe(?-StBu)3Ni]2(?-Br)2, 2 with NaSDmp at -40 °C. The nickel site of complex 1 was found to add CO or CNtBu at -40 °C to give (CO)3Fe(StBu)(?-StBu)2Ni(CO)(SDmp), 3, or (CO)3Fe(StBu)(?-StBu)2Ni(CNtBu)(SDmp), 4, respectively. One of the CO bands of 3, appearing at 2055 cm-1 in the infrared spectrum, was assigned as the Ni-CO band, and this frequency is comparable to those observed for the CO-inhibited forms of [NiFe] hydrogenase. Like the CO-inhibited forms of [NiFe] hydrogenase, the coordination of CO at the nickel site of 1 is reversible, while the CNtBu adduct 4 is more robust.

Ohki, Yasuhiro; Yasumura, Kazunari; Ando, Masaru; Shimokata, Satoko; Tatsumi, Kazuyuki

2010-01-01

61

Analyses of the Large Subunit Histidine-Rich Motif Expose an Alternative Proton Transfer Pathway in [NiFe] Hydrogenases  

PubMed Central

A highly conserved histidine-rich region with unknown function was recognized in the large subunit of [NiFe] hydrogenases. The HxHxxHxxHxH sequence occurs in most membrane-bound hydrogenases, but only two of these histidines are present in the cytoplasmic ones. Site-directed mutagenesis of the His-rich region of the T. roseopersicina membrane-attached Hyn hydrogenase disclosed that the enzyme activity was significantly affected only by the replacement of the His104 residue. Computational analysis of the hydrogen bond network in the large subunits indicated that the second histidine of this motif might be a component of a proton transfer pathway including Arg487, Asp103, His104 and Glu436. Substitutions of the conserved amino acids of the presumed transfer route impaired the activity of the Hyn hydrogenase. Western hybridization was applied to demonstrate that the cellular level of the mutant hydrogenases was similar to that of the wild type. Mostly based on theoretical modeling, few proton transfer pathways have already been suggested for [NiFe] hydrogenases. Our results propose an alternative route for proton transfer between the [NiFe] active center and the surface of the protein. A novel feature of this model is that this proton pathway is located on the opposite side of the large subunit relative to the position of the small subunit. This is the first study presenting a systematic analysis of an in silico predicted proton translocation pathway in [NiFe] hydrogenases by site-directed mutagenesis.

Szori-Doroghazi, Emma; Maroti, Gergely; Szori, Milan; Nyilasi, Andrea; Rakhely, Gabor; Kovacs, Kornel L.

2012-01-01

62

Microstructure, mechanical property, biodegradation behavior, and biocompatibility of biodegradable Fe-Fe2 O3 composites.  

PubMed

In this study, the effects of Fe2 O3 (addition, 2, 5, 10, and 50 wt %) on the microstructure, mechanical properties, corrosion behaviors, and in vitro biocompatibility of Fe-Fe2 O3 composites fabricated by spark plasma sintering were systematically investigated as a novel-structure biodegradable metallic material. The results of X-ray diffraction analysis and optical microscopy indicated that Fe-Fe2 O3 composite is composed of ?-Fe and FeO instead of Fe2 O3 . Both eletrochemical measurements and immersion test showed a faster degradation rate of Fe-2Fe2 O3 and Fe-5Fe2 O3 composites than pure iron and Fe-5Fe2 O3 exhibited the fastest corrosion rate among these composites. Besides, the effect of Fe2 O3 on the corrosion behavior of Fe-Fe2 O3 composites was discussed. The extracts of Fe-Fe2 O3 composite exhibited no cytotoxicity to both ECV304 and L929 cells, whereas greatly reduced cell viabilities of vascular smooth muscle cells. In addition, good hemocompatibility of all Fe-Fe2 O3 composites and pure iron was obtained. To sum up, Fe-5Fe2 O3 composite is a promising alternative for biodegradable stent material with elevated corrosion rate, enhanced mechanical properties, as well as excellent biocompatibility. © 2013 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 102A: 2277-2287, 2014. PMID:23894098

Cheng, J; Huang, T; Zheng, Y F

2014-07-01

63

A broad survey reveals substitution tolerance of residues ligating FeS clusters in [NiFe] hydrogenase  

PubMed Central

Background In order to understand the effects of FeS cluster attachment in [NiFe] hydrogenase, we undertook a study to substitute all 12 amino acid positions normally ligating the three FeS clusters in the hydrogenase small subunit. Using the hydrogenase from Alteromonas macleodii “deep ecotype” as a model, we substituted one of four amino acids (Asp, His, Asn, Gln) at each of the 12 ligating positions because these amino acids are alternative coordinating residues in otherwise conserved-cysteine positions found in a broad survey of NiFe hydrogenase sequences. We also hoped to discover an enzyme with elevated hydrogen evolution activity relative to a previously reported “G1” (H230C/P285C) improved enzyme in which the medial FeS cluster Pro and the distal FeS cluster His were each substituted for Cys. Results Among all the substitutions screened, aspartic acid substitutions were generally well-tolerated, and examination suggests that the observed deficiency in enzyme activity may be largely due to misprocessing of the small subunit of the enzyme. Alignment of hydrogenase sequences from sequence databases revealed many rare substitutions; the five substitutions present in databases that we tested all exhibited measurable hydrogen evolution activity. Select substitutions were purified and tested, supporting the results of the screening assay. Analysis of these results confirms the importance of small subunit processing. Normalizing activity to quantity of mature small subunit, indicative of total enzyme maturation, weakly suggests an improvement over the “G1” enzyme. Conclusions We have comprehensively screened 48 amino acid substitutions of the hydrogenase from A. macleodii “deep ecotype”, to understand non-canonical ligations of amino acids to FeS clusters and to improve hydrogen evolution activity of this class of hydrogenase. Our studies show that non-canonical ligations can be functional and also suggests a new limiting factor in the production of active enzyme.

2014-01-01

64

Hydrogenases and H + Reduction in Primary Energy Conservation  

Microsoft Academic Search

Hydrogenases are metalloenzymes subdivided into two classes that contain iron-sulfur clusters and\\u000a catalyze the reversible oxidation of hydrogen gas (H2???2H+?+?2e?).\\u000a Two metal atoms are present at their active center: either a Ni and an Fe atom in the [NiFe]hydrogenases,\\u000a or two Fe atoms in the [FeFe]hydrogenases. They are phylogenetically distinct classes of proteins. The\\u000a catalytic core of [NiFe]hydrogenases is a heterodimeric protein

Paulette M. Vignais

65

Evidence for three distinct hydrogenase activities in Rhodospirillum rubrum.  

PubMed

Inducer, inhibitor, and mutant studies on three hydrogenase activities of Rhodospirillum rubrum indicate that they are mediated by three distinct hydrogenase enzymes. Uptake hydrogenase mediates H2 uptake to an unknown physiological acceptor or methylene blue and is maximally synthesized during autotrophic growth in light. Formate-linked hydrogenase is synthesized primarily during growth in darkness or when light becomes limiting, and links formate oxidation to H2 production. Carbon-monoxide-linked hydrogenase is induced whenever CO is present and couples CO oxidation to H2 evolution. The enzymes can be expressed singly or conjointly depending on growth conditions, and the inhibitor or inducer added. All three hydrogenases can use methyl viologen as the mediator for both the H2 evolution and H2 uptake reactions while displaying distinct pH optima, reversibility, and sensitivity to C2H2 gas. Yet, we present evidence that the CO-linked hydrogenase, unlike the uptake hydrogenase, does not link to methylene blue as the electron acceptor. These differences allow conditions to be established to quantitatively assay each hydrogenase independently of the others both in vivo and in vitro. PMID:11778889

Maness, P C; Weaver, P F

2001-12-01

66

Small molecule mimics of hydrogenases: hydrides and redox†  

PubMed Central

This tutorial review is aimed at chemical scientists interested in understanding and exploiting the remarkable catalytic behavior of the hydrogenases. The key structural features are analyzed for the active sites of the two most important hydrogenases. Reactivity is emphasized, focusing on mechanism and catalysis. Through this analysis, gaps are identified in the synthesis of functional replicas of these fascinating and potentially useful enzymes.

Gloaguen, Frederic; Rauchfuss, Thomas B.

2012-01-01

67

Mechanism of electrocatalytic hydrogen production by a di-iron model of iron-iron hydrogenase: a density functional theory study of proton dissociation constants and electrode reduction potentials.  

PubMed

Simple dinuclear iron dithiolates such as (mu-SCH2CH2CH2S)[Fe(CO)3]2, (1) and (mu-SCH2CH2S)[Fe(CO)3]2 (2) are functional models for diiron-hydrogenases, [FeFe]-H2ases, that catalyze the reduction of protons to H2. The mechanism of H2 production with 2 as the catalyst and with both toluenesulfonic (HOTs) and acetic (HOAc) acids as the H+ source in CH3CN solvent has been examined by density functional theory (DFT). Proton dissociation constants (pKa) and electrode reduction potentials (E(o)) are directly computed and compared to the measured pKa of HOTs and HOAc acids and the experimental reduction potentials. Computations show that when the strong acid, HOTs, is used as a proton source the one-electron reduced species 2- can be protonated to form a bridging hydride complex as the most stable structure. Then, this species can be reduced and protonated to form dihydrogen and regenerate 2. This cycle produces H2 via an ECEC process at an applied potential of -1.8 V vs. Fc/Fc+. A second faster process opens for this system when the species produced at the ECEC step above is further reduced and H2 release returns the system to 2- rather than 2, an E[CECE] process. On the other hand, when the weak acid, HOAc, is the proton source a more negative applied reduction potential (-2.2 V vs. Fc/Fc+) is necessary. At this potential two one-electron reductions yield the dianion 2(2-) before the first protonation, which in this case occurs on the thiolate. Subsequent reduction and protonation form dihydrogen and regenerate 2- through an E[ECEC] process. PMID:20221544

Surawatanawong, Panida; Tye, Jesse W; Darensbourg, Marcetta Y; Hall, Michael B

2010-03-28

68

Purification and Properties of a Hydrogenase from Desulfovibrio vulgaris1  

PubMed Central

The soluble hydrogenase of Desulfovibrio vulgaris was purified and some of its properties are described. The molecular weight was determined for the enzyme by sedimentation equilibrium (45,400) and amino acid analysis (44,800). The hydrogenase appears to be a loosely coiled molecule or to have a high axial ratio, which is reflected in an unusually low sedimentation coefficient (2.58S) and a low diffusion coefficient (D 5.85). The molecular weight of the hydrogenase (41,000), as calculated by the Svedberg equation, was in general agreement with the sedimentation equilibrium molecular weight. Amino acid analysis revealed the presence of six halfcystine residues per mole of enzyme and a total of 417 amino acid residues. The specificity of the hydrogenase and its capacity to reduce certain low potential dyes and cytochrome c3 was studied. Metal analysis of the hydrogenase indicated the presence of 1 mole of ferrous iron per mole of enzyme. Images

Haschke, Richard H.; Campbell, L. Leon

1971-01-01

69

Electron transfer between hydrogenase and 316L stainless steel: identification of a hydrogenase-catalyzed cathodic reaction in anaerobic mic  

Microsoft Academic Search

Electron transfer between the NAD-dependent hydrogenase from Ralstonia eutropha and AISI 316L stainless steel was studied with a view to identifying a possible role of hydrogenase in anaerobic microbially influenced corrosion (mic), as already suspected. A thin spectroelectrochemical cell was designed and qualified, taking great care to obtain a reproducible surface state of the stainless steel grid electrode. Successive electrolyses

S Da Silva; R Basséguy; A Bergel

2004-01-01

70

Production of biohydrogen by recombinant expression of [NiFe]-hydrogenase 1 in Escherichia coli  

Microsoft Academic Search

BACKGROUND: Hydrogenases catalyze reversible reaction between hydrogen (H2) and proton. Inactivation of hydrogenase by exposure to oxygen is a critical limitation in biohydrogen production since strict anaerobic conditions are required. While [FeFe]-hydrogenases are irreversibly inactivated by oxygen, it was known that [NiFe]-hydrogenases are generally more tolerant to oxygen. The physiological function of [NiFe]-hydrogenase 1 is still ambiguous. We herein investigated

Jaoon YH Kim; Byung Hoon Jo; Hyung Joon Cha

2010-01-01

71

Hydrogenase activity in the thermophile mastigocladus laminosus  

SciTech Connect

Hydrogenase activity in the thermophilic cyanobacterium, Mastigocladus laminosus was studied both in vivo and in vitro. In vivo hydrogen consumption required oxygen but not light, was about ten-fold higher than in mesophilic cyanobacteria, and was relatively insensitive to carbon monoxide. H/sub 2/-supported acetylene reduction in reductant-limited cultures was a light-dependent, but O/sub 2/-independent reaction. In vitro hydrogen evolution was unaffected by carbon monoxide, and this activity could be partially purified using a procedure developed for Anabaena cylindrica.

Benemann, J.R.; Miyamoto, K.; Hallenbeck, P.C.; Murry, M.A.

1982-06-30

72

Simple ligand effects switch a hydrogenase mimic between H2 and O2 activation.  

PubMed

Herein, we report a [NiRu] biomimetic system for O(2)-tolerant [NiFe]hydrogenases and demonstrate that electron donation to the [NiRu] center can switch the system between the activation of H(2) and O(2) through simple ligand effects by using hexamethylbenzene and pentamethylcyclopentadienyl ligands, respectively. Furthermore, we present the synthesis and direct observations of a [NiRu]-peroxo species, which was formed by the oxygenation of a Ni-SIa model [NiRu] complex, that we propose as a biomimetic analogue of O(2)-bound species (OBS) of O(2)-tolerant [NiFe]hydrogenases. The [NiRu]-peroxo complex was fully characterized by X-ray analysis, X-ray photoelectron spectroscopy (XPS), mass spectrometry, and (1)H NMR spectroscopy. The OBS analogue was capable of oxidizing p-hydroquinone and sodium borohydride to turn back into the Ni-SIa model complex. PMID:22383335

Kim, Kyoungmok; Matsumoto, Takahiro; Robertson, Andrew; Nakai, Hidetaka; Ogo, Seiji

2012-06-01

73

Force Field Development and Molecular Dynamics of [NiFe] Hydrogenase  

SciTech Connect

Classical molecular force-field parameters describing the structure and motion of metal clusters in [NiFe] hydrogenase enzymes can be used to compare the dynamics and thermodynamics of [NiFe] under different oxidation, protonation, and ligation circumstances. Using density functional theory (DFT) calculations of small model clusters representative of the active site and the proximal, medial, and distal Fe/S metal centers and their attached protein side chains, we have calculated classical force-field parameters for [NiFe] in reduced and oxidized states, including internal coordinates, force constants, and atom-centered charges. Derived force constants revealed that cysteinate ligands bound to the metal ions are more flexible in the Ni-B active site, which has a bridging hydroxide ligand, than in the Ni-C active site, which has a bridging hydride. Ten nanosecond all-atom, explicit-solvent MD simulations of [NiFe] hydrogenase in oxidized and reduced catalytic states established the stability of the derived force-field parameters in terms of C{alpha} and metal cluster fluctuations. Average active site structures from the protein MD simulations are consistent with [NiFe] structures from the Protein Data Bank, suggesting that the derived force-field parameters are transferrable to other hydrogenases beyond the structure used for testing. A comparison of experimental H{sub 2}-production rates demonstrated a relationship between cysteinate side chain rotation and activity, justifying the use of a fully dynamic model of [NiFe] metal cluster motion.

Smith, Dayle MA; Xiong, Yijia; Straatsma, TP; Rosso, Kevin M.; Squier, Thomas C.

2012-05-09

74

Jahn-Teller distortion, ferromagnetic coupling, and electron delocalization in a high-spin Fe–Fe bonded dimer  

Microsoft Academic Search

Fe2(N,N’-diphenylformamidinate)4, 1, first synthesized in 1994, is one of very few non-organometallic compounds with Fe–Fe distances, (2.46Å) suggestive of an Fe–Fe bond. The electronic structure of 1 has been unclear because of its distorted D2 geometry, as well as its reported S=4 ground state. Computational investigations using DFT methods have shown that the D2 geometry is the result of a

George H. Timmer; John F. Berry

75

The role of the bidirectional hydrogenase in cyanobacteria.  

PubMed

Cyanobacteria have tremendous potential to produce clean, renewable fuel in the form of hydrogen gas derived from solar energy and water. Of the two cyanobacterial enzymes capable of evolving hydrogen gas (nitrogenase and the bidirectional hydrogenase), the hox-encoded bidirectional Ni-Fe hydrogenase has a high theoretical potential. The physiological role of this hydrogenase is a highly debated topic and is poorly understood relative to that of the nitrogenase. Here the structure, assembly, and expression of this enzyme, as well as its probable roles in metabolism, are discussed and analyzed to gain perspective on its physiological role. It is concluded that the bidirectional hydrogenase in cyanobacteria primarily functions as a redox regulator for maintaining a proper oxidation/reduction state in the cell. Recommendations for future research to test this hypothesis are discussed. PMID:21514820

Carrieri, Damian; Wawrousek, Karen; Eckert, Carrie; Yu, Jianping; Maness, Pin-Ching

2011-09-01

76

Photosensitized Production of Hydrogen by Hydrogenase in Reversed Micelles  

NASA Astrophysics Data System (ADS)

Hydrogenase (hydrogen:ferricytochrome c3 oxidoreductase, EC 1.12.2.1) from Desulfovibrio vulgaris was encapsulated in reversed micelles with cetyltrimethylammonium bromide as surfactant and a chloroform/octane mixture as solvent. Reducing equivalents for hydrogenase-catalyzed hydrogen production were provided by vectorial photosensitized electron transfer from a donor (thiophenol) in the organic phase through a surfactant-Ru2+ sensitizer located in the interphase to methyl viologen concentrated in the aqueous core of the reversed micelle. The results show that reversed micelles provide a microenvironment that (i) stabilizes hydrogenase against inactivation and (ii) allows an efficient vectorial photosensitized electron and proton flow from the organic phase to hydrogenase in the aqueous phase.

Hilhorst, Riet; Laane, Colja; Veeger, Cees

1982-06-01

77

Localization of an Uptake Hydrogenase in Anabaena 1  

PubMed Central

Occurrence and localization of an uptake hydrogenase were examined in three strains of the blue-green alga, Anabaena. In vivo H2 uptake was detected (0.60-1.44 ?moles/[mg of chlorophyll a per hour]) in all three strains when grown with N2 as the sole source of nitrogen. H2 uptake (in vivo and in vitro) was severely suppressed in cultures grown on NH4+ and lacking heterocysts. H2 uptake in cell-free extracts could be readily measured with a methyl viologen-ferricyanide electron acceptor system. Solubilization kinetics during cavitation of aerobically grown Anabaena 7120 indicates that the uptake hydrogenase is localized solely in the heterocyst. When the same organism is grown on N2/CO2, vegetative cells may account for up to 21% of the total hydrogenase activity in the filaments. The results are discussed in terms of a proposed functional relationship between nitrogenase and hydrogenase.

Peterson, Richard B.; Wolk, C. Peter

1978-01-01

78

Homologous Expression of a Subcomplex of Pyrococcus furiosus Hydrogenase that Interacts with Pyruvate Ferredoxin Oxidoreductase  

PubMed Central

Hydrogen gas is an attractive alternative fuel as it is carbon neutral and has higher energy content per unit mass than fossil fuels. The biological enzyme responsible for utilizing molecular hydrogen is hydrogenase, a heteromeric metalloenzyme requiring a complex maturation process to assemble its O2-sensitive dinuclear-catalytic site containing nickel and iron atoms. To facilitate their utility in applied processes, it is essential that tools are available to engineer hydrogenases to tailor catalytic activity and electron carrier specificity, and decrease oxygen sensitivity using standard molecular biology techniques. As a model system we are using hydrogen-producing Pyrococcus furiosus, which grows optimally at 100°C. We have taken advantage of a recently developed genetic system that allows markerless chromosomal integrations via homologous recombination. We have combined a new gene marker system with a highly-expressed constitutive promoter to enable high-level homologous expression of an engineered form of the cytoplasmic NADP-dependent hydrogenase (SHI) of P. furiosus. In a step towards obtaining ‘minimal’ hydrogenases, we have successfully produced the heterodimeric form of SHI that contains only two of the four subunits found in the native heterotetrameric enzyme. The heterodimeric form is highly active (150 units mg?1 in H2 production using the artificial electron donor methyl viologen) and thermostable (t1/2 ?0.5 hour at 90°C). Moreover, the heterodimer does not use NADPH and instead can directly utilize reductant supplied by pyruvate ferredoxin oxidoreductase from P. furiosus. The SHI heterodimer and POR therefore represent a two-enzyme system that oxidizes pyruvate and produces H2 in vitro without the need for an intermediate electron carrier.

Jenney, Francis E.; Chandrayan, Sanjeev K.; McTernan, Patrick M.; Adams, Michael W. W.

2011-01-01

79

Homologous expression of a subcomplex of Pyrococcus furiosus hydrogenase that interacts with pyruvate ferredoxin oxidoreductase.  

PubMed

Hydrogen gas is an attractive alternative fuel as it is carbon neutral and has higher energy content per unit mass than fossil fuels. The biological enzyme responsible for utilizing molecular hydrogen is hydrogenase, a heteromeric metalloenzyme requiring a complex maturation process to assemble its O(2)-sensitive dinuclear-catalytic site containing nickel and iron atoms. To facilitate their utility in applied processes, it is essential that tools are available to engineer hydrogenases to tailor catalytic activity and electron carrier specificity, and decrease oxygen sensitivity using standard molecular biology techniques. As a model system we are using hydrogen-producing Pyrococcus furiosus, which grows optimally at 100°C. We have taken advantage of a recently developed genetic system that allows markerless chromosomal integrations via homologous recombination. We have combined a new gene marker system with a highly-expressed constitutive promoter to enable high-level homologous expression of an engineered form of the cytoplasmic NADP-dependent hydrogenase (SHI) of P. furiosus. In a step towards obtaining 'minimal' hydrogenases, we have successfully produced the heterodimeric form of SHI that contains only two of the four subunits found in the native heterotetrameric enzyme. The heterodimeric form is highly active (150 units mg(-1) in H(2) production using the artificial electron donor methyl viologen) and thermostable (t(1/2) ?0.5 hour at 90°C). Moreover, the heterodimer does not use NADPH and instead can directly utilize reductant supplied by pyruvate ferredoxin oxidoreductase from P. furiosus. The SHI heterodimer and POR therefore represent a two-enzyme system that oxidizes pyruvate and produces H(2) in vitro without the need for an intermediate electron carrier. PMID:22039508

Hopkins, R Christopher; Sun, Junsong; Jenney, Francis E; Chandrayan, Sanjeev K; McTernan, Patrick M; Adams, Michael W W

2011-01-01

80

Optimized Expression and Purification for High-Activity Preparations of Algal [FeFe]-Hydrogenase  

SciTech Connect

Recombinant expression and purification of metallo-enzymes, including hydrogenases, at high-yields is challenging due to complex, and enzyme specific, post-translational maturation processes. Low fidelities of maturation result in preparations containing a significant fraction of inactive, apo-protein that are not suitable for biophysical or crystallographic studies. We describe the construction, overexpression and high-yield purification of a fusion protein consisting of the algal [2Fe2S]-ferredoxin PetF (Fd) and [FeFe]-hydrogenase HydA1. The maturation of Fd-HydA1 was optimized through improvements in culture conditions and media components used for expression. We also demonstrated that fusion of Fd to the N-terminus of HydA1, in comparison to the C-terminus, led to increased expression levels that were 4-fold higher. Together, these improvements led to enhanced HydA1 activity and improved yield after purification. The strong binding-affinity of Fd for DEAE allowed for two-step purification by ion exchange and StrepTactin affinity chromatography. In addition, the incorporation of a TEV protease site in the Fd-HydA1 linker allowed for the proteolytic removal of Fd after DEAE step, and purification of HydA1 alone by StrepTactin. In combination, this process resulted in HydA1 purification yields of 5 mg L{sup -1} of culture from E. coli with specific activities of 1000 U (U = 1 {micro}mol hydrogen evolved mg{sup -1} min{sup -1}). The [FeFe]-hydrogenases are highly efficient enzymes and their catalytic sites provide model structures for synthetic efforts to develop robust hydrogen activation catalysts. In order to characterize their structure-function properties in greater detail, and to use hydrogenases for biotechnological applications, reliable methods for rapid, high-yield expression and purification are required.

Yacoby, I.; Tegler, L. T.; Pochekailov, S.; Zhang, S.; King, P. W.

2012-04-01

81

Biomimetic assembly and activation of [FeFe]-hydrogenases  

PubMed Central

Hydrogenases are the most active molecular catalysts for hydrogen production and uptake on earth1,2 and are thus extensively studied with respect to their technological exploitation as noble metal substitutes in (photo)electrolysers and fuel cells3-5. In [FeFe]-hydrogenases catalysis takes place at a unique diiron center (the [2Fe] subsite) featuring a bridging dithiolate ligand, as well as three CO and two CN? ligands (Figure 1)6,7. Through a complex and as yet poorly understood multienzymatic biosynthetic process, this [2Fe] subsite is first assembled onto a maturation enzyme, HydF. From there, it is delivered to the apo-hydrogenase for activation8. Synthetic chemistry has allowed the preparation of remarkably close mimics of that subsite1 but failed to reproduce the natural enzymatic activities so far. Here we show that three such synthetic mimics (with different bridging dithiolate ligands) can be loaded onto HydF and then transferred to apo-HydA1, one of the hydrogenases of Chlamydomonas reinhardtii. Remarkably, full activation of HydA1 was achieved exclusively using the HydF hybrid protein containing the mimic with an azadithiolate bridge, confirming the presence of this ligand in the active site of [FeFe]-hydrogenases9,10. This is the first example of controlled metalloenzyme activation using the combination of a specific protein scaffold and active site synthetic analogues. This simple methodology provides both new mechanistic and structural insight into hydrogenase maturation and a unique tool for producing recombinant wild-type and variant [FeFe]-hydrogenases, with no requirement for the complete maturation machinery. It opens the possibility to engineer the [FeFe]-hydrogenase active site through synthetic chemistry.

Berggren, G.; Esselborn, J.; Atta, M.; Gambarelli, S.; Mouesca, JM; Reijerse, E.; Lubitz, W.; Happe, T.; Artero, V.; Fontecave, M.

2013-01-01

82

Characterization of the active site of catalytically inactive forms of [NiFe] hydrogenases by density functional theory.  

PubMed

The inactive forms, unready (Ni-A, Ni-SU) and ready (Ni-B), of NiFe hydrogenases are modeled by examining the possibility of hydroxo, oxo, hydroperoxo, peroxo, and sulfenate groups in active-site models and comparing predicted IR frequencies and g tensors with those of the enzyme. The best models for Ni-A and Ni-SU have hydroxo (mu-OH) bridges between Fe and Ni and a terminal sulfenate [Ni-S(=O)Cys] group, although a hydroperoxo model for Ni-A is also quite viable, whereas the best model for Ni-B has only a mu-OH bridge. In addition, a mechanism for the activation of unready hydrogenase is proposed on the basis of the relative stabilities of sulfenate models versus peroxide models. PMID:17440755

Pardo, Alejandro; De Lacey, Antonio L; Fernández, Víctor M; Fan, Yubo; Hall, Michael B

2007-08-01

83

Modeling the Active Site of [NiFe] Hydrogenases and the [NiFeu] Subsite of the C-Cluster of Carbon Monoxide Dehydrogenases: Low-Spin Iron(II) Versus High-Spin Iron(II).  

PubMed

A series of four [S2Ni(?-S)2FeCp*Cl] compounds with different tetradentate thiolate/thioether ligands bound to the Ni(II) ion is reported (Cp* = C5Me5). The {S2Ni(?-S)2Fe} core of these compounds resembles structural features of the active site of [NiFe] hydrogenases. Detailed analyses of the electronic structures of these compounds by Mössbauer and electron paramagnetic resonance spectroscopy, magnetic measurements, and density functional theory calculations reveal the oxidation states Ni(II) low spin and Fe(II) high spin for the metal ions. The same electronic configurations have been suggested for the Cred1 state of the C-cluster [NiFeu] subsite in carbon monoxide dehydrogenases (CODH). The Ni-Fe distance of ?3 Å excludes a metal-metal bond between nickel and iron, which is in agreement with the computational results. Electrochemical experiments show that iron is the redox active site in these complexes, performing a reversible one-electron oxidation. The four complexes are discussed with regard to their similarities and differences both to the [NiFe] hydrogenases and the C-cluster of Ni-containing CODH. PMID:24903610

Weber, Katharina; Erdem, Ozlen F; Bill, Eckhard; Weyhermüller, Thomas; Lubitz, Wolfgang

2014-06-16

84

The role of Hox hydrogenase in the H 2 metabolism of Thiocapsa roseopersicina  

Microsoft Academic Search

The purple sulfur phototrophic bacterium Thiocapsa roseopersicina BBS synthesizes at least three NiFe hydrogenases (Hox, Hup, Hyn). We characterized the physiological H2 consumption\\/evolution reactions in mutants having deletions of the structural genes of two hydrogenases in various combinations. This made possible the separation of the functionally distinct roles of the three hydrogenases. Data showed that Hox hydrogenase (unlike the Hup

Gábor Rákhely; Tatyana V. Laurinavichene; Anatoly A. Tsygankov; Kornél L. Kovács

2007-01-01

85

Bioaccumulation of palladium by Desulfovibrio fructosivorans wild-type and hydrogenase-deficient strains.  

PubMed

Wild-type Desulfovibrio fructosivorans and three hydrogenase-negative mutants reduced Pd(II) to Pd(0). The location of Pd(0) nanoparticles on the cytoplasmic membrane of the mutant retaining only cytoplasmic membrane-bound hydrogenase was strong evidence for the role of hydrogenases in Pd(0) deposition. Hydrogenase activity was retained at acidic pH, shown previously to favor Pd(0) deposition. PMID:18689514

Mikheenko, I P; Rousset, M; Dementin, S; Macaskie, L E

2008-10-01

86

Bioaccumulation of Palladium by Desulfovibrio fructosivorans Wild-Type and Hydrogenase-Deficient Strains?  

PubMed Central

Wild-type Desulfovibrio fructosivorans and three hydrogenase-negative mutants reduced Pd(II) to Pd(0). The location of Pd(0) nanoparticles on the cytoplasmic membrane of the mutant retaining only cytoplasmic membrane-bound hydrogenase was strong evidence for the role of hydrogenases in Pd(0) deposition. Hydrogenase activity was retained at acidic pH, shown previously to favor Pd(0) deposition.

Mikheenko, I. P.; Rousset, M.; Dementin, S.; Macaskie, L. E.

2008-01-01

87

Desulfovibrio vulgaris hydrogenase: a nonheme iron enzyme lacking nickel that exhibits anomalous EPR and Moessbauer spectra  

Microsoft Academic Search

A purification procedure for the periplasmic hydrogenase from Desulfovibrio vulgaris is reported. The purified hydrogenase has a specific activity of 4800 units per mg of protein. Plasma emission studies reveal that this highly active hydrogenase is free of nickel and contains 11 (+\\/-1) nonheme iron atoms per molecule. A combined EPR and Moessbauer study indicates that the majority of the

B. H. Huynh; M. H. Czechowski; H. J. Krueger; D. V. DerVartanian; H. D. Jr. Peck; J. LeGall

1984-01-01

88

Dissecting the roles of Escherichia coli hydrogenases in biohydrogen production.  

PubMed

Escherichia coli can perform at least two modes of anaerobic hydrogen metabolism and expresses at least two types of hydrogenase activity. Respiratory hydrogen oxidation is catalysed by two 'uptake' hydrogenase isoenzymes, hydrogenase -1 and -2 (Hyd-1 and -2), and fermentative hydrogen production is catalysed by Hyd-3. Harnessing and enhancing the metabolic capability of E. coli to perform anaerobic mixed-acid fermentation is therefore an attractive approach for bio-hydrogen production from sugars. In this work, the effects of genetic modification of the genes encoding the uptake hydrogenases, as well as the importance of preculture conditions, on hydrogen production and fermentation balance were examined. In suspensions of resting cells pregrown aerobically with formate, deletions in Hyd-3 abolished hydrogen production, whereas the deletion of both uptake hydrogenases improved hydrogen production by 37% over the parent strain. Under fermentative conditions, respiratory H2 uptake activity was absent in strains lacking Hyd-2. The effect of a deletion in hycA on H2 production was found to be dependent upon environmental conditions, but H2 uptake was not significantly affected by this mutation. PMID:17995952

Redwood, Mark D; Mikheenko, Iryna P; Sargent, Frank; Macaskie, Lynne E

2008-01-01

89

Physiological Reactions of the Reversible Hydrogenase from Anabaena 7120 1  

PubMed Central

The reversible hydrogenase from Anabaena 7120 appeared when O2 was continuously removed from a growing culture. Activity increased further when cells were incubated under argon in the dark or in the light plus 3-(3,4-dichlorophenyl)-1,1-dimethylurea. Hydrogenase existed in an inactive state during periods of O2 evolution. It could be reductively activated by exposure to reduced methyl viologen or by dark, anaerobic incubation. Hydrogenase-containing cells evolved H2 slowly during dark anaerobic incubations, and the rate of H2 evolution was increased by illumination with low intensity light. Light enhancement of H2 evolution was of short duration and was eliminated by the ferredoxin antagonist disalicylidene diaminopropane. Physiological acceptors that supported H2 uptake included NO3?, NO2?, and HSO3?, and light had a slight influence on the rate of H2 uptake with these acceptors. Low levels of O2 supported H2 uptake, but higher concentrations of O2 inactivated the hydrogenase. Hydrogen uptake with HCO3? as acceptor was the most rapid reaction measured, and it was strictly light-dependent. It occurred only at low light intensities, and higher light intensities restored normal O2-evolving photosynthesis. It is suggested that hydrogenase is present to capture exogenous H2 as a source of reducing equivalents during growth in anaerobic environments.

Houchins, Jeffrey P.; Burris, Robert H.

1981-01-01

90

Tuning exchange bias in Fe/?-Fe2O3 core-shell nanoparticles: Impacts of interface and surface spins  

NASA Astrophysics Data System (ADS)

A comparative study has been performed of the exchange bias (EB) effect in Fe/?-Fe2O3 core-shell nanoparticles with the same thickness of the ?-Fe2O3 shell (˜2 nm) and the diameter of the Fe core varying from 4 nm to 11 nm. Transmission electron microscopy (TEM) and high-resolution TEM confirmed the high quality of the core-shell nanostructures. A systematic analysis of magnetization versus magnetic field measurements under zero-field-cooled and field-cooled regimes using the Meiklejohn-Bean model and deconvoluting superparamagnetic and paramagnetic contribution to the total magnetic moment Langevin function shows that there exists a critical particle size (˜10 nm), above which the spins at the interface between Fe and ?-Fe2O3 contribute primarily to the EB, but below which the surface spin effect is dominant. Our finding yields deeper insight into the collective contributions of interface and surface spins to the EB in core-shell nanoparticle systems, knowledge of which is the key to manipulating EB in magnetic nanostructures for spintronics applications.

Khurshid, Hafsa; Phan, Manh-Huong; Mukherjee, Pritish; Srikanth, Hariharan

2014-02-01

91

Rhizobitoxine inhibition of hydrogenase synthesis in free-living Bradyrhizobium japonicum  

SciTech Connect

Rhizobitoxine produced by Bradyrhizobium species strongly prevented derepression of hydrogenase expression in free-living Bradyrhizobium japonicum, although the toxin had no effect on the activity of cells which had already synthesized hydrogenase protein. Dihydrorhizobitoxine, a structural analog of rhizobitoxine, proved to be a less potent inhibitor of hydrogenase derepression. Rhizobitoxine did not cause cell death at a concentration sufficient to eliminate hydrogenase expression. The large subunit of hydrogenase was not detectable with antibody after derepression in the presence of rhizobitoxine. The general pattern of proteins synthesized from {sup 14}C-labeled amino acids during derepression was not significantly different in the presence or absence of rhizobitoxine. These results indicated that rhizobitoxine inhibited hydrogenase synthesis in free-living B. japonicum. Cystathionine and methionine strongly prevented the inhibition of hydrogenase derepression by rhizobitoxine, suggesting that the inhibition involves the level of sulfur-containing amino acids in the cell.

Minamisawa, Kiwamu; Fukai, Kastuhiko; Asami, Teruo (Ibaraki Univ. (Japan))

1990-08-01

92

Gd13Fe10C13: indications of Fe-Fe multiple bonding emerging from chemical frustration.  

PubMed

We report the synthesis and crystal structure of the carbide Gd(13)Fe(10)C(13). This compound adopts a new structure type that is remarkable for its "H"-shaped C(2)FeFeC(2) units, which have some of the shortest Fe-Fe contacts known. A bonding analysis using DFT-calibrated Hückel calculations hints that Fe-Fe multiple bonding underlies these short distances. Gd(13)Fe(10)C(13) undergoes ferromagnetic ordering at ?55 K. PMID:22676209

Hadler, Amelia B; Fredrickson, Daniel C

2012-06-27

93

[NiFe] and [FeS] cofactors in the membrane-bound hydrogenase of Ralstonia eutropha investigated by X-ray absorption spectroscopy: insights into O(2)-tolerant H(2) cleavage.  

PubMed

Molecular features that allow certain [NiFe] hydrogenases to catalyze the conversion of molecular hydrogen (H(2)) in the presence of dioxygen (O(2)) were investigated. Using X-ray absorption spectroscopy (XAS), we compared the [NiFe] active site and FeS clusters in the O(2)-tolerant membrane-bound hydrogenase (MBH) of Ralstonia eutropha and the O(2)-sensitive periplasmic hydrogenase (PH) of Desulfovibrio gigas. Fe-XAS indicated an unusual complement of iron-sulfur centers in the MBH, likely based on a specific structure of the FeS cluster proximal to the active site. This cluster is a [4Fe4S] cubane in PH. For MBH, it comprises less than ~2.7 Å Fe-Fe distances and additional longer vectors of ?3.4 Å, consistent with an Fe trimer with a more isolated Fe ion. Ni-XAS indicated a similar architecture of the [NiFe] site in MBH and PH, featuring Ni coordination by four thiolates of conserved cysteines, i.e., in the fully reduced state (Ni-SR). For oxidized states, short Ni-?O bonds due to Ni-Fe bridging oxygen species were detected in the Ni-B state of the MBH and in the Ni-A state of the PH. Furthermore, a bridging sulfenate (CysSO) is suggested for an inactive state (Ni(ia)-S) of the MBH. We propose that the O(2) tolerance of the MBH is mainly based on a dedicated electron donation from a modified proximal FeS cluster to the active site, which may favor formation of the rapidly reactivated Ni-B state instead of the slowly reactivated Ni-A state. Thereby, the catalytic activity of the MBH is facilitated in the presence of both H(2) and O(2). PMID:21618994

Fritsch, Johannes; Löscher, Simone; Sanganas, Oliver; Siebert, Elisabeth; Zebger, Ingo; Stein, Matthias; Ludwig, Marcus; De Lacey, Antonio L; Dau, Holger; Friedrich, Bärbel; Lenz, Oliver; Haumann, Michael

2011-07-01

94

The [NiFe]-hydrogenase of the cyanobacterium Synechocystis sp. PCC 6803 works bidirectionally with a bias to H2 production.  

PubMed

Protein film electrochemistry (PFE) was utilized to characterize the catalytic activity and oxidative inactivation of a bidirectional [NiFe]-hydrogenase (HoxEFUYH) from the cyanobacterium Synechocystis sp. PCC 6803. PFE provides precise control of the redox potential of the adsorbed enzyme so that its activity can be monitored under changing experimental conditions as current. The properties of HoxEFUYH are different from those of both the standard uptake and the "oxygen-tolerant" [NiFe]-hydrogenases. First, HoxEFUYH is biased toward proton reduction as opposed to hydrogen oxidation. Second, despite being expressed under aerobic conditions in vivo, HoxEFUYH is clearly not oxygen-tolerant. Aerobic inactivation of catalytic hydrogen oxidation by HoxEFUYH is total and nearly instantaneous, producing two inactive states. However, unlike the Ni-A and Ni-B inactive states of standard [NiFe]-hydrogenases, both of these states are quickly (<90 s) reactivated by removal of oxygen and exposure to reducing conditions. Third, proton reduction continues at 25-50% of the maximal rate in the presence of 1% oxygen. Whereas most previously characterized [NiFe]-hydrogenases seem to be preferential hydrogen oxidizing catalysts, the cyanobacterial enzyme works effectively in both directions. This unusual catalytic bias as well as the ability to be quickly reactivated may be essential to fulfilling the physiological role in cyanobacteria, organisms expected to experience swings in cellular reduction potential as they switch between aerobic conditions in the light and dark anaerobic conditions. Our results suggest that the uptake [NiFe]-hydrogenases alone are not representative of the catalytic diversity of [NiFe]-hydrogenases, and the bidirectional heteromultimeric enzymes may serve as valuable models to understand the diverse mechanisms of tuning the reactivity of the hydrogen activating site. PMID:21675712

McIntosh, Chelsea L; Germer, Frauke; Schulz, Rüdiger; Appel, Jens; Jones, Anne K

2011-07-27

95

Structure and intermixing in Fe/Fe(110) and Fe/Ag/Fe(110) multilayers  

NASA Astrophysics Data System (ADS)

We have previously shown, in UHV-SEM studies of Ag/Fe(110), that Ag(111) islands grow on top of two intermediate monolayers of Ag in the Stranski-Krastanov (SK) mode. In the present work, Fe was deposited on samples consisting of (1-5 ML) annealed Ag layers on Fe(110). Growth, structure and intermixing were monitored by biased secondary electron imaging (b-SEI), reflection electron diffraction (RHEED) and Auger electron spectroscopy (AES). At room temperature (RT), Fe islands grow in a (110) orientation on (1-2 ML) Ag(111)/Fe(110). Due to kinetic limitations, these islands form facets similar to those obtained in the Fe/Fe(110) system. These limitations are overcome in the Fe/Fe(110) system by depositing at 250°C. All three orientations in the Nishiyama-Wassermann relationship are observed for Fe islands grown on thicker, but not on thinner, Ag layers. Quantitative AES indicates that there is intermixing at the monolayer level between the deposited Fe atoms and underlying Ag layers even at RT. During annealing, or for deposition at 250°C, Ag atoms undergo long range diffusion towards the top of the deposit, but kinetic limitations are not completely overcome for 5 ML Ag layers; for thinner layers, the Fe islands flatten forming additional substrate layers at the Ag/Fe(110) interface.

Persaud, R.; Noro, H.; Venables, J. A.

1998-05-01

96

The crystal structure of an oxygen-tolerant hydrogenase uncovers a novel iron-sulphur centre.  

PubMed

Hydrogenases are abundant enzymes that catalyse the reversible interconversion of H(2) into protons and electrons at high rates. Those hydrogenases maintaining their activity in the presence of O(2) are considered to be central to H(2)-based technologies, such as enzymatic fuel cells and for light-driven H(2) production. Despite comprehensive genetic, biochemical, electrochemical and spectroscopic investigations, the molecular background allowing a structural interpretation of how the catalytic centre is protected from irreversible inactivation by O(2) has remained unclear. Here we present the crystal structure of an O(2)-tolerant [NiFe]-hydrogenase from the aerobic H(2) oxidizer Ralstonia eutropha H16 at 1.5?Å resolution. The heterodimeric enzyme consists of a large subunit harbouring the catalytic centre in the H(2)-reduced state and a small subunit containing an electron relay consisting of three different iron-sulphur clusters. The cluster proximal to the active site displays an unprecedented [4Fe-3S] structure and is coordinated by six cysteines. According to the current model, this cofactor operates as an electronic switch depending on the nature of the gas molecule approaching the active site. It serves as an electron acceptor in the course of H(2) oxidation and as an electron-delivering device upon O(2) attack at the active site. This dual function is supported by the capability of the novel iron-sulphur cluster to adopt three redox states at physiological redox potentials. The second structural feature is a network of extended water cavities that may act as a channel facilitating the removal of water produced at the [NiFe] active site. These discoveries will have an impact on the design of biological and chemical H(2)-converting catalysts that are capable of cycling H(2) in air. PMID:22002606

Fritsch, Johannes; Scheerer, Patrick; Frielingsdorf, Stefan; Kroschinsky, Sebastian; Friedrich, Bärbel; Lenz, Oliver; Spahn, Christian M T

2011-11-10

97

High-Pressure Iron-Sulfur Compound, Fe3S2, and Melting Relations in the Fe-FeS System  

PubMed

An iron-sulfur compound (Fe3S2) was synthesized at pressures greater than 14 gigapascals in the system Fe-FeS. The formation of Fe3S2 changed the melting relations from a simple binary eutectic system to a binary system with an intermediate compound that melted incongruently. The eutectic temperature in the system at 14 gigapascals was about 400°C lower than that extrapolated from Usselman's data, implying that previous thermal models of Fe-rich planetary cores could overestimate core temperature. If it is found in a meteorite, the Fe3S2 phase could also be used to infer the minimum size of a parent body. PMID:9054351

Fei; Bertka; Finger

1997-03-14

98

Development of Fe/Fe3O4 core-shell nanocubes as a promising magnetic resonance imaging contrast agent.  

PubMed

Here, we report the synthesis, characterization, and properties of Fe/Fe3O4 core-shell nanocubes prepared via a simple route. It includes NaBH4 reduction of FeCl3 in an ethylene glycol solution in the presence of 2-mercaptopropionic acid (surfactant) and trisodium citrate (cosurfactant) followed by surface oxidation with trimethylamine N-oxide. The morphology and structure of Fe/Fe3O4 core-shell nanocubes were characterized using transmission electron microscopy (TEM), high-resolution TEM, selected area electron diffraction, X-ray powder diffraction, and X-ray photoelectron spectroscopy. All of the methods confirm a Fe/Fe3O4 core-shell structure of nanocubes. Magnetic measurements revealed that the Fe/Fe3O4 core/shell nanocubes are superparamagnetic at 300 K with a saturation magnetization of 129 emu/g. The T2 weighted imaging and the T2 relaxation time showed high MRI contrast and sensitivity, making these nanocubes viable candidates as enhanced MRI contrast agents. PMID:24079275

Mahmoud, Waleed E; Bronstein, Lyudmila M; Al-Hazmi, Faten; Al-Noaiser, Fowzia; Al-Ghamdi, A A

2013-10-22

99

Switchable transport strategy to deposit active Fe/Fe3C cores into hollow microporous carbons for efficient chromium removal.  

PubMed

Magnetic hollow structures with microporous shell and highly dispersed active cores (Fe/Fe3 C nanoparticles) are rationally designed and fabricated by solution-phase switchable transport of active iron species combined with a solid-state thermolysis technique, thus allowing selective encapsulation of functional Fe/Fe3 C nanoparticles in the interior cavity. These engineered functional materials show high loading (?54 wt%) of Fe, excellent chromium removal capability (100 mg g(-1)), fast adsorption rate (8766 mL mg(-1) h(-1)), and easy magnetic separation property (63.25 emu g(-1)). During the adsorption process, the internal highly dispersed Fe/Fe3 C nanoparticles supply a driving force for facilitating Cr(VI) diffusion inward, thus improving the adsorption rate and the adsorption capacity. At the same time, the external microporous carbon shell can also efficiently trap guest Cr(VI) ions and protect Fe/Fe3 C nanoparticles from corrosion and subsequent leaching problems. PMID:23749637

Liu, Dong-Hai; Guo, Yue; Zhang, Lu-Hua; Li, Wen-Cui; Sun, Tao; Lu, An-Hui

2013-11-25

100

Requirements for Heterologous Production of a Complex Metalloenzyme: the Membrane-Bound [NiFe] Hydrogenase  

PubMed Central

By taking advantage of the tightly clustered genes for the membrane-bound [NiFe] hydrogenase of Ralstonia eutropha H16, broad-host-range recombinant plasmids were constructed carrying the entire membrane-bound hydrogenase (MBH) operon encompassing 21 genes. We demonstrate that the complex MBH biosynthetic apparatus is actively produced in hydrogenase-free hosts yielding fully assembled and functional MBH protein.

Lenz, Oliver; Gleiche, Andrea; Strack, Angelika; Friedrich, Barbel

2005-01-01

101

Thermal Equations of State in the Fe-FeS, Fe-FeO, and Ammonia-Water Systems  

NASA Astrophysics Data System (ADS)

With the maturing of laser heating systems for the diamond anvil coupled to 3rd generation synchrotron radiation sources, studies at high pressures are moving from end member to binary and even more complex systems. Interesting discoveries are being made, for instance the addition of Si to pure Fe stabilizes the bcc phase to exceptionally high pressures [Lin, et al., 2002, Science]. More recently Ni has been found to also stabilize the bcc structure of iron at pressures in excess of 200 GPa [Dubrovinsky, et al., 2007, Science]. Thus minor elements can significantly change the topology of phase diagrams. The observations of Lin et. al. sparked the interests of theorticians who modeled the effects of impurities [Vocadlo, et al., 2003, Nature]. Various compositions in the binary system Fe-FeS have been studied to 160 GPa and in the Fe-FeO system to 100 GPa. In addition to thermal equation of state data we have also collected melting data and subsolidus phase relations. This data provide information on how these candidate minerals would behave at the elevated temperatures and pressures, and thus have implications for the current state of the interior of terrestrial planets and their thermal evolution. On a lighter note (in terms of atomic weight, and icy planets), the addition of ammonia to water affects the phase diagram of pure water in unexpected ways. For example at high ammonia concentrations, (>25 wt. %) Ice IV, a metastable phase in the pure water phase diagram is the first phase to crystallize. On further compression Ice IV transforms directly to Ice VII with a staggering 13 % density increase. The equation of state of Ice VI has also been studied, and has an impressively low bulk modulus of only 6 GPa. Pressure, temperature, volume and composition data in conjunction with the associated phase equilibria provide strong constraints for quantum mechanical calculations.

Heinz, D. L.; Seagle, C. T.; Campbell, A. J.; Miller, N.; Prakapenka, V. B.; Shen, G.

2007-12-01

102

Crystal Structure of HydF Scaffold Protein Provides Insights into [FeFe]-Hydrogenase Maturation*  

PubMed Central

[FeFe]-hydrogenases catalyze the reversible production of H2 in some bacteria and unicellular eukaryotes. These enzymes require ancillary proteins to assemble the unique active site H-cluster, a complex structure composed of a 2Fe center bridged to a [4Fe-4S] cubane. The first crystal structure of a key factor in the maturation process, HydF, has been determined at 3 ? resolution. The protein monomer present in the asymmetric unit of the crystal comprises three domains: a GTP-binding domain, a dimerization domain, and a metal cluster-binding domain, all characterized by similar folding motifs. Two monomers dimerize, giving rise to a stable dimer, held together mainly by the formation of a continuous ?-sheet comprising eight ?-strands from two monomers. Moreover, in the structure presented, two dimers aggregate to form a supramolecular organization that represents an inactivated form of the HydF maturase. The crystal structure of the latter furnishes several clues about the events necessary for cluster generation/transfer and provides an excellent model to begin elucidating the structure/function of HydF in [FeFe]-hydrogenase maturation.

Cendron, Laura; Berto, Paola; D'Adamo, Sarah; Vallese, Francesca; Govoni, Chiara; Posewitz, Matthew C.; Giacometti, Giorgio M.; Costantini, Paola; Zanotti, Giuseppe

2011-01-01

103

Role of nickel in membrane-bound hydrogenase and nickel metabolism in Rhizobium japonicum  

SciTech Connect

The membrane-bound hydrogenase of Rhizobium japonicum requires nickel for activity. Radioactive /sup 63/Ni co-migrates with hydrogenase activity in native gel systems and co-elutes with purified hydrogenase form an affinity matrix column. A simplified scheme for the purification of hydrogenase has been developed and constitutes the first report of the aerobic purification of this enzyme from R. japonicum. The aerobic purification utilizes the general affinity matrix. Reactive Red 120-agarose and results in higher specific activity and yield of enzyme than previously reported. The stability of aerobically purified hydrogenase to oxygen is substantially greater than that reported for anaerobically isolated enzyme. Reduction of the aerobically purified enzyme in the presence of oxygen, however, results in the rapid loss of activity. R. japonicum cells accumulate nickel during heterotrophic growth and as non-growing cells. The hydrogenase constitutive mutant SR470 accumulates substantially greater amounts of nickel under both conditions. Kinetic studies indicate that the nickel uptake system in the hydrogenase constitutive mutant SR470 is upregulated relative to SRwt cells. The uptake system is specific for nickel, although a 10-fold excess (relative to nickel) of copper or zinc inhibits nickel uptake. The nickel uptake system appears to require energy. Under nickel-free conditions hydrogenase protein is not synthesized as determined by cross-reactivity with antibodies directed against hydrogenase, indicating that nickel regulates the formation of the enzyme as well as being a constituent of the active protein.

Stults, L.W.

1986-01-01

104

Spontaneous activation of [FeFe]-hydrogenases by an inorganic [2Fe] active site mimic  

PubMed Central

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 novel artificial H2-producing catalysts.

Esselborn, Julian; Berggren, Gustav; Noth, Jens; Siebel, Judith; Hemschemeier, Anja; Artero, Vincent; Reijerse, Edward; Fontecave, Marc; Lubitz, Wolfgang; Happe, Thomas

2013-01-01

105

Oxygen-resistant hydrogenases and methods for designing and making same  

DOEpatents

The invention provides oxygen- resistant iron-hydrogenases ([Fe]-hydrogenases) for use in the production of H2. Methods used in the design and engineering of the oxygen-resistant [Fe]-hydrogenases are disclosed, as are the methods of transforming and culturing appropriate host cells with the oxygen-resistant [Fe]-hydrogenases. Finally, the invention provides methods for utilizing the transformed, oxygen insensitive, host cells in the bulk production of H.sub.2 in a light catalyzed reaction having water as the reactant.

King, Paul (Golden, CO); Ghirardi, Maria L (Lakewood, CO); Seibert, Michael (Lakewood, CO)

2009-03-10

106

An EPR/HYSCORE, Mössbauer, and resonance Raman study of the hydrogenase maturation enzyme HydF: a model for N-coordination to [4Fe-4S] clusters.  

PubMed

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. PMID:24240692

Berggren, Gustav; Garcia-Serres, Ricardo; Brazzolotto, Xavier; Clemancey, Martin; Gambarelli, Serge; Atta, Mohamed; Latour, Jean-Marc; Hernández, Heather L; Subramanian, Sowmya; Johnson, Michael K; Fontecave, Marc

2014-01-01

107

Reduction of the amount of periplasmic hydrogenase in Desulfovibrio vulgaris (Hildenborough) with antisense RNA: direct evidence for an important role of this hydrogenase in lactate metabolism.  

PubMed Central

To establish the function of the periplasmic Fe-only hydrogenase in the anaerobic sulfate reducer Desulfovibrio vulgaris (Hildenborough), derivatives with a reduced content of this enzyme were constructed by introduction of a plasmid that directs the synthesis of antisense RNA complementary to hydrogenase mRNA. It was demonstrated that the antisense RNA technique allowed specific suppression of the synthesis of this hydrogenase in D. vulgaris by decreasing the amount of hydrogenase mRNA but did not result in the complete elimination of the enzyme, as is usual with most conventional mutagenesis techniques. The hydrogenase content in these antisense RNA-producing D. vulgaris clones was two- to threefold lower than in the parental strain when the strains were grown in batch cultures with lactate as a substrate and sulfate as a terminal electron acceptor. Under these conditions, several differences in growth parameters were measured between the hydrogenase-suppressed clones and wild-type D. vulgaris: growth rates of the clones decreased two- to threefold, and at excess lactate, growth yields were reduced by 20%. Furthermore, the amount of hydrogen measured in the culture headspaces was reduced three- to fivefold for the clones. These observations indicate that this hydrogenase has an important function during growth on lactate and is involved in hydrogen production from protons and electrons originating from at least one of the two oxidation reactions in the conversion of lactate to acetate. The implications for the energy metabolism of D. vulgaris are discussed. Images

van den Berg, W A; van Dongen, W M; Veeger, C

1991-01-01

108

Cyanobacterial-Type, Heteropentameric, NAD+Reducing NiFe Hydrogenase in the Purple Sulfur Photosynthetic Bacterium Thiocapsa roseopersicina  

Microsoft Academic Search

Structural genes coding for two membrane-associated NiFe hydrogenases in the phototrophic purple sulfur bacterium Thiocapsa roseopersicina (hupSL and hynSL) have recently been isolated and characterized. Deletion of both hydrogenase structural genes did not eliminate hydrogenase activity in the cells, and considerable hydrogenase activity was detected in the soluble fraction. The enzyme responsible for this activity was partially purified, and the

Gabor Rakhely; Akos T. Kovacs; Gergely Maroti; Barna D. Fodor; Gyula Csanadi; Dora Latinovics; Kornel L. Kovacs

2004-01-01

109

Production of biohydrogen by heterologous expression of oxygen-tolerant Hydrogenovibrio marinus [NiFe]-hydrogenase in Escherichia coli  

Microsoft Academic Search

Oxygen sensitivity of hydrogenase is a critical issue in efficient biological hydrogen production. In the present study, oxygen-tolerant [NiFe]-hydrogenase from the marine bacterium, Hydrogenovibrio marinus, was heterologously expressed in Escherichia coli, for the first time. Recombinant E. coli BL21 expressing H. marinus [NiFe]-hydrogenase actively produced hydrogen, but the parent strain did not. Recombinant H. marinus hydrogenase required both nickel and

Jaoon Y. H. Kim; Byung Hoon Jo; Hyung Joon Cha

2011-01-01

110

A Novel Endo-Hydrogenase Activity Recycles Hydrogen Produced by Nitrogen Fixation  

PubMed Central

Background Nitrogen (N2) fixation also yields hydrogen (H2) at 1?1 stoichiometric amounts. In aerobic diazotrophic (able to grow on N2 as sole N-source) bacteria, orthodox respiratory hupSL-encoded hydrogenase activity, associated with the cell membrane but facing the periplasm (exo-hydrogenase), has nevertheless been presumed responsible for recycling such endogenous hydrogen. Methods and Findings As shown here, for Azorhizobium caulinodans diazotrophic cultures open to the atmosphere, exo-hydrogenase activity is of no consequence to hydrogen recycling. In a bioinformatic analysis, a novel seven-gene A. caulinodans hyq cluster encoding an integral-membrane, group-4, Ni,Fe-hydrogenase with homology to respiratory complex I (NADH : quinone dehydrogenase) was identified. By analogy, Hyq hydrogenase is also integral to the cell membrane, but its active site faces the cytoplasm (endo-hydrogenase). An A. caulinodans in-frame hyq operon deletion mutant, constructed by “crossover PCR”, showed markedly decreased growth rates in diazotrophic cultures; normal growth was restored with added ammonium—as expected of an H2-recycling mutant phenotype. Using A. caulinodans hyq merodiploid strains expressing ?-glucuronidase as promoter-reporter, the hyq operon proved strongly and specifically induced in diazotrophic culture; as well, hyq operon induction required the NIFA transcriptional activator. Therefore, the hyq operon is constituent of the nif regulon. Conclusions Representative of aerobic N2-fixing and H2-recycling ?-proteobacteria, A. caulinodans possesses two respiratory Ni,Fe-hydrogenases: HupSL exo-hydrogenase activity drives exogenous H2 respiration, and Hyq endo-hydrogenase activity recycles endogenous H2, specifically that produced by N2 fixation. To benefit human civilization, H2 has generated considerable interest as potential renewable energy source as its makings are ubiquitous and its combustion yields no greenhouse gases. As such, the reversible, group-4 Ni,Fe-hydrogenases, such as the A. caulinodans Hyq endo-hydrogenase, offer promise as biocatalytic agents for H2 production and/or consumption.

Park, Angela S.; Zenad, Lounis; Ludwig, Robert A.

2009-01-01

111

Distribution Analysis of Hydrogenases in Surface Waters of Marine and Freshwater Environments  

PubMed Central

Background Surface waters of aquatic environments have been shown to both evolve and consume hydrogen and the ocean is estimated to be the principal natural source. In some marine habitats, H2 evolution and uptake are clearly due to biological activity, while contributions of abiotic sources must be considered in others. Until now the only known biological process involved in H2 metabolism in marine environments is nitrogen fixation. Principal Findings We analyzed marine and freshwater environments for the presence and distribution of genes of all known hydrogenases, the enzymes involved in biological hydrogen turnover. The total genomes and the available marine metagenome datasets were searched for hydrogenase sequences. Furthermore, we isolated DNA from samples from the North Atlantic, Mediterranean Sea, North Sea, Baltic Sea, and two fresh water lakes and amplified and sequenced part of the gene encoding the bidirectional NAD(P)-linked hydrogenase. In 21% of all marine heterotrophic bacterial genomes from surface waters, one or several hydrogenase genes were found, with the membrane-bound H2 uptake hydrogenase being the most widespread. A clear bias of hydrogenases to environments with terrestrial influence was found. This is exemplified by the cyanobacterial bidirectional NAD(P)-linked hydrogenase that was found in freshwater and coastal areas but not in the open ocean. Significance This study shows that hydrogenases are surprisingly abundant in marine environments. Due to its ecological distribution the primary function of the bidirectional NAD(P)-linked hydrogenase seems to be fermentative hydrogen evolution. Moreover, our data suggests that marine surface waters could be an interesting source of oxygen-resistant uptake hydrogenases. The respective genes occur in coastal as well as open ocean habitats and we presume that they are used as additional energy scavenging devices in otherwise nutrient limited environments. The membrane-bound H2-evolving hydrogenases might be useful as marker for bacteria living inside of marine snow particles.

Barz, Martin; Beimgraben, Christian; Staller, Torsten; Germer, Frauke; Opitz, Friederike; Marquardt, Claudia; Schwarz, Christoph; Gutekunst, Kirstin; Vanselow, Klaus Heinrich; Schmitz, Ruth; LaRoche, Julie; Schulz, Rudiger; Appel, Jens

2010-01-01

112

Melting relationships in the Fe-Fe3S system based on X-ray diffraction up to 180 GPa  

NASA Astrophysics Data System (ADS)

The Earth's core is considered to be composed of Fe alloy with light element(s) based on cosmochemical constraints and seismic observation. Sulfur in particular has been considered as one of the most plausible light elements based on the solar abundances and high pressure partitioning experiments. It is important to investigate the Fe-FeS system up to the core conditions to discuss its chemical and physical properties. Nevertheless, there are not previous works under the core conditions. Therefore, we have investigated the melting relationships in the Fe-Fe3S system up to 190 GPa using a double-sided laser-heated diamond anvil cell (LHDAC) combined with the synchrotron X-ray. Some recovered samples were observed by using FE-SEM. The compositions of starting materials were Fe86.8S13.2. A sample foil was sandwiched between NaCl pellets. The sample was heated using fiber lasers. The shape of a fiver laser beam was changed to a flat-top using a beam shaping system at the BL10XU, SPring-8. The melting detection was based on disappearance of the X-ray diffraction (XRD) peaks derived from Fe3S. Disappearance of XRD from Fe3S was observed up to 182 GPa. The recovered samples from 122 GPa were observed by using FE-SEM and dendritic texture was observed in each sample. The melting temperatures of the present results in the Fe- Fe3S system are consistent with previous works up to around 70 GPa (e.g., Campbell et al., 2007; Morard et al., 2008). However, the slope of the melting temperature in the Fe-Fe3S system is slightly gentle above 100 GPa compared to the extrapolated melting curves of previous studies. The present results were fitted to the Kraut-Kennedy law in order to extrapolate the melting temperature of the Fe-Fe3S system up to the ICB condition. The eutectic temperature of the Fe-Fe3S system at the pressures relevant to the CMB and ICB conditions are 2990(100) and 4420(190) K, respectively. If S is the only light element in the core and the Fe-Fe3S system shows the eutectic system, the eutectic temperature of 4420 K at ICB condition suggests the lower bound of TICB. The upper bound of TICB which corresponds to the temperature of the total melting temperature of the Fe-Fe3S system estimated to be 5060 K by assuming that an ideal solution of Fe-S melt in the Fe-Fe3S system . The present ICB temperature is about 800 K below the temperature estimated by Ma et al. (2004). Campbell et al. (2007) estimated the temperature at ICB conditions to be at least 4500 K by assuming that the depression of melting temperature due to sulfur was 800 K. The present result is consistent with the lower bound of ICB temperature estimated by Campbell et al. (2007).

Kamada, S.; Ohtani, E.; Terasaki, H.; Sakai, T.; Ohishi, Y.; Hirao, N.; Miyahara, M.

2011-12-01

113

Salttolerant and high-pH-resistant hydrogenase from the haloalkaliphilic, sulfate-reducing bacterium Desulfonatronum thiodismutans  

Microsoft Academic Search

Hydrogenase is the key enzyme of energetic metabolism in cells, catalyzing the converse reaction of hydrogen oxidation and responsible for the consumption and excretion of hydrogen in bacteria. Hydrogenases are proteins, most of which contain either nickel and iron or iron alone in their active center. Hydrogenases have been found in many microorganisms, such as methanogenic, acetogenic, nitrogen-fixing, sulfate-reducing, photosynthetic

Ekaterina N. Detkova; Elena V. Pikuta; Richard B. Hoover

2004-01-01

114

Interaction between hydrogenase maturation factors HypA and HypB is required for [NiFe]-hydrogenase maturation.  

PubMed

The active site of [NiFe]-hydrogenase contains nickel and iron coordinated by cysteine residues, cyanide and carbon monoxide. Metal chaperone proteins HypA and HypB are required for the nickel insertion step of [NiFe]-hydrogenase maturation. How HypA and HypB work together to deliver nickel to the catalytic core remains elusive. Here we demonstrated that HypA and HypB from Archaeoglobus fulgidus form 1:1 heterodimer in solution and HypA does not interact with HypB dimer preloaded with GMPPNP and Ni. Based on the crystal structure of A. fulgidus HypB, mutants were designed to map the HypA binding site on HypB. Our results showed that two conserved residues, Tyr-4 and Leu-6, of A. fulgidus HypB are required for the interaction with HypA. Consistent with this observation, we demonstrated that the corresponding residues, Leu-78 and Val-80, located at the N-terminus of the GTPase domain of Escherichia coli HypB were required for HypA/HypB interaction. We further showed that L78A and V80A mutants of HypB failed to reactivate hydrogenase in an E. coli ?hypB strain. Our results suggest that the formation of the HypA/HypB complex is essential to the maturation process of hydrogenase. The HypA binding site is in proximity to the metal binding site of HypB, suggesting that the HypA/HypB interaction may facilitate nickel transfer between the two proteins. PMID:22384275

Chan, Kwok-Ho; Lee, Ka-Man; Wong, Kam-Bo

2012-01-01

115

Heterologous Expression of Alteromonas macleodii and Thiocapsa roseopersicina [NiFe] Hydrogenases in Synechococcus elongatus  

PubMed Central

Oxygen-tolerant [NiFe] hydrogenases may be used in future photobiological hydrogen production systems once the enzymes can be heterologously expressed in host organisms of interest. To achieve heterologous expression of [NiFe] hydrogenases in cyanobacteria, the two hydrogenase structural genes from Alteromonas macleodii Deep ecotype (AltDE), hynS and hynL, along with the surrounding genes in the gene operon of HynSL were cloned in a vector with an IPTG-inducible promoter and introduced into Synechococcus elongatus PCC7942. The hydrogenase protein was expressed at the correct size upon induction with IPTG. The heterologously-expressed HynSL hydrogenase was active when tested by in vitro H2 evolution assay, indicating the correct assembly of the catalytic center in the cyanobacterial host. Using a similar expression system, the hydrogenase structural genes from Thiocapsa roseopersicina (hynSL) and the entire set of known accessory genes were transferred to S. elongatus. A protein of the correct size was expressed but had no activity. However, when the 11 accessory genes from AltDE were co-expressed with hynSL, the T. roseopersicina hydrogenase was found to be active by in vitro assay. This is the first report of active, heterologously-expressed [NiFe] hydrogenases in cyanobacteria.

Weyman, Philip D.; Vargas, Walter A.; Tong, Yingkai; Yu, Jianping; Maness, Pin-Ching; Smith, Hamilton O.; Xu, Qing

2011-01-01

116

Immobilization of hydrogenase in nylon gel containing electron mediator and application to an artificial photosystem  

SciTech Connect

Hydrogenase of Desulfovibrio vulgaris was immobilized in nylon gel containing an electron mediator. With the immobilization, the stability for storage and repeated use increased and the optimal pH was shifted to the acidic side. Photoinduced hydrogen production was observed in an artificial photosystem consisting of the hydrogenase gel, metal porphyrin, and mercaptethanol.

Nosaka, Y.; Kuwabara, A.; Kobayashi, T.; Miyama, H.

1986-01-01

117

Production of biohydrogen by recombinant expression of [NiFe]-hydrogenase 1 in Escherichia coli  

PubMed Central

Background Hydrogenases catalyze reversible reaction between hydrogen (H2) and proton. Inactivation of hydrogenase by exposure to oxygen is a critical limitation in biohydrogen production since strict anaerobic conditions are required. While [FeFe]-hydrogenases are irreversibly inactivated by oxygen, it was known that [NiFe]-hydrogenases are generally more tolerant to oxygen. The physiological function of [NiFe]-hydrogenase 1 is still ambiguous. We herein investigated the H2 production potential of [NiFe]-hydrogenase 1 of Escherichia coli in vivo and in vitro. The hyaA and hyaB genes corresponding to the small and large subunits of [NiFe]-hydrogenase 1 core enzyme, respectively, were expressed in BL21, an E. coli strain without H2 producing ability. Results Recombinant BL21 expressing [NiFe]-hydrogenase 1 actively produced H2 (12.5 mL H2/(h·L) in 400 mL glucose minimal medium under micro-aerobic condition, whereas the wild type BL21 did not produce H2 even when formate was added as substrate for formate hydrogenlyase (FHL) pathway. The majority of recombinant protein was produced as an insoluble form, with translocation of a small fraction to the membrane. However, the membrane fraction displayed high activity (~65% of total cell fraction), based on unit protein mass. Supplement of nickel and iron to media showed these metals contribute essentially to the function of [NiFe]-hydrogenase 1 as components of catalytic site. In addition, purified E. coli [NiFe]-hydrogenase 1 using his6-tag displayed oxygen-tolerant activity of ~12 nmol H2/(min·mg protein) under a normal aeration environment, compared to [FeFe]-hydrogenase, which remains inactive under this condition. Conclusions This is the first report on physiological function of E. coli [NiFe]-hydrogenase 1 for H2 production. We found that [NiFe]-hydrogenase 1 has H2 production ability even under the existence of oxygen. This oxygen-tolerant property is a significant advantage because it is not necessary to protect the H2 production process from oxygen. Therefore, we propose that [NiFe]-hydrogenase can be successfully applied as an efficient biohydrogen production tool under micro-aerobic conditions.

2010-01-01

118

Energy harvesting based on FE-FE transition in ferroelectric single crystals.  

PubMed

The pyroelectric properties of Pb(Zn(1/3)Nb(2/3))(0955)Ti(0.045)O(3) single crystals versus an electric field have been studied for energy harvesting in this paper. Two thermodynamic cycles (Stirling and Ericsson) were used for this purpose. By applying an electric field, a FE-FE transition was induced, abruptly increasing the polarization. This transition minimized the supplied energy and improved the harvested energy. By discharging the single crystal at a higher temperature, a gain of 1100% was obtained with the Stirling cycle at 1 kV/mm (gain is defined as harvested energy divided by supplied energy). The study revealed that Stirling cycles are more interesting for low electric fields. Based on experimental results, simulations were carried out to estimate energy harvesting in high electric fields to evaluate the performances of thin samples (single crystals or oriented thin films). At high electric fields, both cycles gave almost the same energy harvesting, but Ericsson cycles were more appropriate to control the voltage on the sample. The simulation led to a harvested energy of 500 mJ/g for an applied electric field equal to 50 kV/mm. The efficiency with respect to Carnot was raised 20%. PMID:18334334

Guyomar, Daniel; Pruvost, Sebastien; Sebald, Gael

2008-02-01

119

A hidden reservoir of Fe/FeS in interstellar silicates?  

NASA Astrophysics Data System (ADS)

Context. The depletion of iron and sulphur into dust in the interstellar medium and the exact nature of interstellar amorphous silicate grains is still an open question. Aims: We study the incorporation of iron and sulphur into amorphous silicates of olivine- and pyroxene-types and their effects on the dust spectroscopy and thermal emission. Methods: We used the Maxwell-Garnett effective-medium theory to construct the optical constants for a mixture of silicates, metallic iron, and iron sulphide. We also studied the effects of iron and iron sulphide in aggregate grains. Results: Iron sulphide inclusions within amorphous silicates that contain iron metal inclusions show no strong differences in the optical properties of the grains. A mix of amorphous olivine- and pyroxene-type silicate broadens the silicate features. An amorphous carbon mantle with a thickness of 10 nm on the silicate grains leads to an increase in absorption on the short-wavelength side of the 10 ?m silicate band. Conclusions: The assumption of amorphous olivine-type and pyroxene-type silicates and a 10 nm thick amorphous carbon mantle better matches the interstellar silicate band profiles. Including iron nano-particles leads to an increase in the mid-IR extinction, while up to 5 ppm of sulphur can be incorporated as Fe/FeS nano inclusions into silicate grains without leaving a significant trace of its presence.

Köhler, M.; Jones, A.; Ysard, N.

2014-05-01

120

Investigation of Fe-FeS phase diagram and liquid structure at high pressure and high temperature  

NASA Astrophysics Data System (ADS)

Sulfur is believed to be an alloying light element in iron-rich planetary cores such as those of the Earth and Mars 1, 2. Recent studies have suggested that Mars, like the Earth, could have a liquid metallic outer core together with a solid inner core 3. Hence, it is important to investigate the evolution of the Fe-FeS phase diagram and of the structural properties of the liquid Fe-FeS alloys in respect to pressure, temperature and sulphur content. A new cell assembly has been developed to heat samples to more than 1300 K at 17 GPa using the Paris Edinburgh Press4. This allows us to conduct detailed structural investigations of the Fe-FeS eutectic liquid by in situ X-ray diffraction5 . Analysis of these data highlights an increase of the liquid compacity with increasing pressure. We also show that the eutectic liquid structure is closer to that of FeSi, explaining the closure of the miscibility gap in the Fe-S-Si system 6. The evolution of the Fe-FeS eutectic liquid structure at high pressure could have significant effect on extrapolated wave speed of metallic Fe-FeS alloy at core pressures. We have used a double-sided laser-heated diamond-anvil cell 7 to study the Fe-FeS phase diagram up to 65 GPa and 2500 K8. We used laser heated diamond anvil cell coupled with synchrotron radiation and confirm a S- solubility below 4 at% (2.3 %wt) up to 65 GPa. The eutectic temperatures present a uniform increase, with a rate of ~15K/GPa, up to 65 GPa and 2200 K. Finally, we present new constraints on the phase diagram evolution to very high pressures which provide unambiguous evidence for an upper limit of 4-8 %wt for the inner core S- content. Therefore, sulphur is not favoured to be the major light element in the Earth's core. 1. Allegre, C. J., Poirier, J. P., Humler, E. & Hofmann, A. W. The chemical composition of the Earth. Earth Planet. Sc. Lett. 134, 515-526 (1995). 2. Sohl, F. & Spohn, T. The interior structure of Mars : Implications from SNC meteorites. J. Geophys. Res. 102, 1613-1635 (1997). 3. Yoder, C. F., Konopliv, A. S., Yuan, D. N., Standish, E. M. & Folkner, W. M. Fluid core size of Mars from detection of the solar tide. Science 300, 299-303 (2003). 4. Morard, G. et al. Optimization of Paris Edinburgh cell assemblies for in situ monochromatic X-ray diffraction and X-ray absorption. High Press. Res. 27, 1-11 (2007). 5. Morard, G. et al. Structure of eutectic Fe-FeS melts up to 17 GPa: Implications for planetary cores. Earth Planet. Sc. Lett. in press (2007). 6. Sanloup, C. & Fei, Y. Closure of the Fe-S-Si liquid miscibility gap at high pressure. Phys. Earth Plan. Int. 147, 57 (2004). 7. Mezouar, M. et al. Development of a new state-of-the-art beamline optimized for monochromatic single crystal and powder X-ray diffraction under extreme conditions at the ESRF. J. Synch. Rad. 12, 659-664 (2005). 8. Morard, G. et al. Experimental constraints on the Earth's core sulphur content. Nature (Submitted).

Morard, G.; Sanloup, C.; Fiquet, G.; Mezouar, M.; Andrault, D.; Guignot, N.

2007-12-01

121

Production of biohydrogen by heterologous expression of oxygen-tolerant Hydrogenovibrio marinus [NiFe]-hydrogenase in Escherichia coli.  

PubMed

Oxygen sensitivity of hydrogenase is a critical issue in efficient biological hydrogen production. In the present study, oxygen-tolerant [NiFe]-hydrogenase from the marine bacterium, Hydrogenovibrio marinus, was heterologously expressed in Escherichia coli, for the first time. Recombinant E. coli BL21 expressing H. marinus [NiFe]-hydrogenase actively produced hydrogen, but the parent strain did not. Recombinant H. marinus hydrogenase required both nickel and iron for biological activity. Compared to the recombinant E. coli [NiFe]-hydrogenase 1 described in our previous report, recombinant H. marinus [NiFe]-hydrogenase displayed 1.6- to 1.7-fold higher hydrogen production activity in vitro. Importantly, H. marinus [NiFe]-hydrogenase exhibited relatively good oxygen tolerance in analyses involving changes of surface aeration and oxygen proportion within a gas mixture. Specifically, recombinant H. marinus [NiFe]-hydrogenase produced ?7- to 9-fold more hydrogen than did E. coli [NiFe]-hydrogenase 1 in a gaseous environment containing 5-10% (v/v) oxygen. In addition, purified H. marinus [NiFe]-hydrogenase displayed a hydrogen evolution activity of ?28.8 nmol H?/(minmg protein) under normal aerobic purification conditions. Based on these results, we suggest that oxygen-tolerant H. marinus [NiFe]-hydrogenase can be employed for in vivo and in vitro biohydrogen production without requirement for strictly anaerobic facilities. PMID:21794837

Kim, Jaoon Y H; Jo, Byung Hoon; Cha, Hyung Joon

2011-09-20

122

Ferracyclic carbamoyl complexes related to the active site of [Fe]-hydrogenase.  

PubMed

The active site of the [Fe]-hydrogenase features an iron(II) centre bearing cis carbonyl groups and a chelating pyridine-acyl ligand. Reproducing these unusual features in synthetic models is an intriguing challenge, which will allow both better understanding of the enzymatic system and more fundamental insight into the coordination modes of iron. By using the carbamoyl group as a surrogate for acyl, we have been able to synthesize a range of ferracyclic complexes. Initial reaction of Fe(CO)4Br2 with 2-aminopyridine yields a complex bearing a labile solvent molecule, which can be replaced by stronger donors bearing phosphorus atoms to produce a number of derivatives. Introduction of a hydroxy group using this method is unsuccessful both with a free OH group and when this is silyl-protected. In contrast, the analogous reactions starting from 2,6-diaminopyridine does allow synthesis of complexes bearing a pendant basic group. PMID:23595606

Turrell, Peter J; Hill, Amanda D; Ibrahim, Saad K; Wright, Joseph A; Pickett, Christopher J

2013-06-14

123

H2 and o2 activation-a remarkable insight into hydrogenase.  

PubMed

This article summarizes the development of a range of organometallic, biomimetic analogues of [NiFe]hydrogenases and their employment in a new generation of H2 -O2 fuel cells. It begins with a summary of O2 -sensitive and O2 -tolerant enzyme chemistry before detailing the properties and functionality of our biomimetic complexes, including: the first ever fully functional model, selective H2 and O2 activation, and the first catalyst using only common metals. These systems are centered on Ni-Fe, Ni-Ru, Ir-Ir, and Rh-Rh cores and use a range of ligands that all follow a set of design principles described herein. PMID:24890792

Ogo, Seiji

2014-06-01

124

Structure prediction and molecular simulation of gases diffusion pathways in hydrogenase  

PubMed Central

Although hydrogen is considered to be one of the most promising future energy sources and the technical aspects involved in using it have advanced considerably, the future supply of hydrogen from renewable sources is still unsolved. The [Fe]- hydrogenase enzymes are highly efficient H2 catalysts found in ecologically and phylogenetically diverse microorganisms, including the photosynthetic green alga, Chlamydomonas reinhardtii. While these enzymes can occur in several forms, H2 catalysis takes place at a unique [FeS] prosthetic group or H-cluster, located at the active site. 3D structure of the protein hydA1 hydrogenase from Chlamydomonas reinhardtti was predicted using the MODELER 8v2 software. Conserved region was depicted from the NCBI CDD Search. Template selection was done on the basis NCBI BLAST results. For single template 1FEH was used and for multiple templates 1FEH and 1HFE were used. The result of the Homology modeling was verified by uploading the file to SAVS server. On the basis of the SAVS result 3D structure predicted using single template was chosen for performing molecular simulation. For performing molecular simulation three strategies were used. First the molecular simulation of the protein was performed in solvated box containing bulk water. Then 100 H2 molecules were randomly inserted in the solvated box and two simulations of 50 and 100 ps were performed. Similarly 100 O2 molecules were randomly placed in the solvated box and again 50 and 100 ps simulation were performed. Energy minimization was performed before each simulation was performed. Conformations were saved after each simulation. Analysis of the gas diffusion was done on the basis of RMSD, Radius of Gyration and no. of gas molecule/ps plot.

Sundaram, Shanthy; Tripathi, Ashutosh; Gupta, Vipul

2010-01-01

125

Structure and magnetic properties of irradiated Fe/Fe oxide core-shell nanoclusters  

SciTech Connect

A cluster deposition method was used to produce a film of loosely aggregated particles of Fe-Fe3O4 core-shell nanoclusters with an 8 nm iron core size and 2 nm oxide shell thickness. The film of particles on a silicon substrate was irradiated with 5.5 MeV Si2+ ions to a fluence of 1016 cm-2 near room temperature, and computer simulations based on the SRIM (Stopping and Range of Ions in Matter) code show that the implanted Si species stops near the film-substrate interface. The ion irradiation creates a structural change in the film with corresponding chemical and magnetic changes. X-ray diffraction shows that the core size and chemistry stay the same but the shell becomes FeO that grows to a thickness of 17 nm. Helium ion microscopy shows that the previously separate particles have densified into a nearly continuous film. Major loop magnetic hysteresis measurements show a decrease in saturation magnetization that we attribute to the presence of the antiferromagnetic (AFM) FeO shell. First-order reversal curve measurements on the irradiated film performed with a vibrating sample magnetometer show that the AFM shell prevents the particles from interacting magnetically, leading to low coercivity from the iron core and little bias field from the core interactions. These results, and others reported previously on different compositions (Fe3O4 or FeO+Fe3N nanoclusters), show that the ion irradiation behavior of nanocluster films such as these depends strongly on the initial nanostructure and chemistry.

McCloy, John S.; Jiang, Weilin; Sundararajan, Jennifer A.; Qiang, You; Burks, Edward; Liu, Kai

2013-04-25

126

Activities, Occurrence, and Localization of Hydrogenase in Free-Living and Symbiotic Frankia1  

PubMed Central

Symbiotic and free-living Frankia were investigated for correlation between hydrogenase activities (in vivo/in vitro assays) and for occurrence and localization of hydrogenase protein by Western blots and immuno-gold localization, respectively. Freshly prepared nodule homogenates from the symbiosis between Alnus incana and a local source of Frankia did not show any detectable in vivo or in vitro hydrogenase uptake activity, as also has been shown earlier. However, a free-living Frankia strain originally isolated from these nodules clearly showed both in vivo and in vitro hydrogenase activity, with the latter being approximately four times higher. Frankia strain Cpl1 showed hydrogen uptake activity both in symbiosis with Alnus incana and in a free-living state. Western blots on the different combinations of host plants and Frankia strains used in the present study revealed that all the Frankia sources contained a hydrogenase protein, even the local source where no in vivo or in vitro activity could be measured. The 72 kilodalton protein found in the symbiotic Frankia as well as in the free-living Frankia strains were immunologically related to the large subunit of a dimeric hydrogenase purified from Alcaligenes latus. Recognitions to polypeptides with molecular masses of about 41 and 19.5 kilodaltons were also observed in Frankia strain UGL011101 and in the local source of Frankia, respectively. Immunogold localization of the protein demonstrated that in both the symbiotic state and the free-living nitrogen-fixing Frankia, the protein is located in vesicles and in hyphae. The inability to measure any uptake hydrogenase activity is therefore not due to the absence of hydrogenase enzyme. However, the possibility of an inactive hydrogenase enzyme cannot be ruled out. Images Figure 1 Figure 2 Figure 3 Figure 4

Sellstedt, Anita; Lindblad, Peter

1990-01-01

127

Melting relations in the Fe-rich portion of the system FeFeS at 30 kb pressure  

USGS Publications Warehouse

The melting relations of FeFeS mixtures covering the composition range from Fe to Fe67S33 have been determined at 30 kb pressure. The phase relations are similar to those at low pressure. The eutectic has a composition of Fe72.9S27.1 and a temperature of 990??C. Solubility of S in Fe at elevated temperatures at 30 kb is of the same order of magnitude as at low pressure. Sulfur may have significantly lowered the melting point of iron in the upper mantle during the period of coalescence of metal prior to core formation in the primitive earth. ?? 1969.

Brett, R.; Bell, P. M.

1969-01-01

128

The hydrogenase structural operon in Rhodobacter capsulatus contains a third gene, hupM, necessary for the formation of a physiologically competent hydrogenase.  

PubMed

The hupM gene, previously called ORFX, found downstream from and contiguous with the structural hydrogenase genes hupS and hupL in Rhodobacter capsulatus, is shown here to form a single hupSLM transcription unit with the two other genes. The hupM gene was inactivated by interposon mutagenesis. The two selected mutants, BCX1 and BCX2, which contained the kanamycin-resistance gene in opposite orientation, still exhibited hydrogenase activity when assayed with the artificial electron acceptors benzylviologen and methylene blue. However, the hydrogenase was not physiologically active in these mutants, which could not grow autotrophically and were unable to recycle electrons to nitrogenase or to respire on H2. The hupM gene starts nine base pairs downstream from the TGA stop codon of hupL gene, which encodes the large subunit of the [NiFe]hydrogenase of Rhodobacter capsulatus. The three contiguous genes hupS, hupL and hupM were subcloned downstream from the promoter of hupSL, either with the promoter in the correct orientation (plasmid pBC8) or with the promoter in the opposite orientation (plasmid pBC9), then the constructs were introduced into the mutant strains. Only plasmid pBC8 could restore the formation of a competent hydrogenase in mutants BCX1 and BCX2, indicating that the hupM gene is expressed only from the hupSL promoter. PMID:1791762

Cauvin, B; Colbeau, A; Vignais, P M

1991-10-01

129

Effect of Hydrogenase and Mixed Sulfate-Reducing Bacterial Populations on the Corrosion of Steel  

PubMed Central

The importance of hydrogenase activity to corrosion of steel was assessed by using mixed populations of sulfate-reducing bacteria isolated from corroded and noncorroded oil pipelines. Biofilms which developed on the steel studs contained detectable numbers of sulfate-reducing bacteria (104 increasing to 107/0.5 cm2). However, the biofilm with active hydrogenase activity (i.e., corrosion pipeline organisms), as measured by a semiquantitative commercial kit, was associated with a significantly higher corrosion rate (7.79 mm/year) relative to noncorrosive biofilm (0.48 mm/year) with 105 sulfate-reducing bacteria per 0.5 cm2 but no measurable hydrogenase activity. The importance of hydrogenase and the microbial sulfate-reducing bacterial population making up the biofilm are discussed relative to biocorrosion. Images

Bryant, Richard D.; Jansen, Wayne; Boivin, Joe; Laishley, Edward J.; Costerton, J. William

1991-01-01

130

Engineering Oxidoreductases: Utilization of an Unnatural Amino Acid to Create Artificial Hydrogenases.  

National Technical Information Service (NTIS)

This report describes progress towards creating peptide-based artificial hydrogenases for interfacing with electrocatalytic applications. The goal of such catalysts is to create hydrogen production or oxidation systems. Basic research in two areas has bee...

A. K. Jones

2011-01-01

131

Photosynthetic electron partitioning between [FeFe]-hydrogenase and ferredoxin:NADP+-oxidoreductase (FNR) enzymes in vitro.  

PubMed

Photosynthetic water splitting, coupled to hydrogenase-catalyzed hydrogen production, is considered a promising clean, renewable source of energy. It is widely accepted that the oxygen sensitivity of hydrogen production, combined with competition between hydrogenases and NADPH-dependent carbon dioxide fixation are the main limitations for its commercialization. Here we provide evidence that, under the anaerobic conditions that support hydrogen production, there is a significant loss of photosynthetic electrons toward NADPH production in vitro. To elucidate the basis for competition, we bioengineered a ferredoxin-hydrogenase fusion and characterized hydrogen production kinetics in the presence of Fd, ferredoxin:NADP(+)-oxidoreductase (FNR), and NADP(+). Replacing the hydrogenase with a ferredoxin-hydrogenase fusion switched the bias of electron transfer from FNR to hydrogenase and resulted in an increased rate of hydrogen photoproduction. These results suggest a new direction for improvement of biohydrogen production and a means to further resolve the mechanisms that control partitioning of photosynthetic electron transport. PMID:21606330

Yacoby, Iftach; Pochekailov, Sergii; Toporik, Hila; Ghirardi, Maria L; King, Paul W; Zhang, Shuguang

2011-06-01

132

Photosynthetic electron partitioning between [FeFe]-hydrogenase and ferredoxin:NADP+-oxidoreductase (FNR) enzymes in vitro  

PubMed Central

Photosynthetic water splitting, coupled to hydrogenase-catalyzed hydrogen production, is considered a promising clean, renewable source of energy. It is widely accepted that the oxygen sensitivity of hydrogen production, combined with competition between hydrogenases and NADPH-dependent carbon dioxide fixation are the main limitations for its commercialization. Here we provide evidence that, under the anaerobic conditions that support hydrogen production, there is a significant loss of photosynthetic electrons toward NADPH production in vitro. To elucidate the basis for competition, we bioengineered a ferredoxin-hydrogenase fusion and characterized hydrogen production kinetics in the presence of Fd, ferredoxin:NADP+-oxidoreductase (FNR), and NADP+. Replacing the hydrogenase with a ferredoxin-hydrogenase fusion switched the bias of electron transfer from FNR to hydrogenase and resulted in an increased rate of hydrogen photoproduction. These results suggest a new direction for improvement of biohydrogen production and a means to further resolve the mechanisms that control partitioning of photosynthetic electron transport.

Yacoby, Iftach; Pochekailov, Sergii; Toporik, Hila; Ghirardi, Maria L.; King, Paul W.; Zhang, Shuguang

2011-01-01

133

(Catalytic mechanism of hydrogenase from aerobic N sub 2 -fixing microorganisms)  

SciTech Connect

The results of this DOE-sponsored project have contributed to our understanding of the catalytic mechanism of A. vinelandii hydrogenase. A group of inhibitors have been characterized. These provide information about the different types of redox clusters involved in catalysis and the roles of each. One group has already used acetylene in a study of three desulfovibrian hydrogenases and shown that only the NiFe hydrogenases are inhibited. We have characterized a number of spectral properties of A. vinelandii hydrogenase. The EPR signals associated with this hydrogenase in the reduced state are reminiscent of other NiFe dimeric hydrogenases such as A. eutrophus, but distinctly difference from others such as D. gigas and Chromatium vinosum. Thus, while the NiFe dimeric hydrogenases are now recognized as a large group of similar enzymes, there are differences in the spectral and catalytic properties which are not explained by their similar redox inventories, identical subunit structures, immunological cross reactivity and conserved sequences. The inhibitors we have characterized are also proving of value in the spectral characterizations. Surprisingly, we only see a significant EP signal attributable to Ni after the enzyme has been inactivated with O{sub 2} and then reduced (though not reactivated). No spectral perterbations (EPR or UV-V is) of active enzyme can be attributed to binding of H{sub 2}, even though H{sub 2} clearly binds to this form of the enzyme. Acetylene, which does not substantially perterb the EPR signal of active hydrogenase, does result in a new absorption envelope in the UV-V is spectrum. Overall, the results of this project have revealed the complex interactions of the redox clusters in catalysis through studies of inhibitor mechanisms and spectral properties. 14 refs., 9 figs.

Arp, D.J.

1991-01-01

134

Function of Periplasmic Hydrogenases in the Sulfate-Reducing Bacterium Desulfovibrio vulgaris Hildenborough? †  

PubMed Central

The sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough possesses four periplasmic hydrogenases to facilitate the oxidation of molecular hydrogen. These include an [Fe] hydrogenase, an [NiFeSe] hydrogenase, and two [NiFe] hydrogenases encoded by the hyd, hys, hyn1, and hyn2 genes, respectively. In order to understand their cellular functions, we have compared the growth rates of existing (hyd and hyn1) and newly constructed (hys and hyn-1 hyd) mutants to those of the wild type in defined media in which lactate or hydrogen at either 5 or 50% (vol/vol) was used as the sole electron donor for sulfate reduction. Only strains missing the [Fe] hydrogenase were significantly affected during growth with lactate or with 50% (vol/vol) hydrogen as the sole electron donor. When the cells were grown at low (5% [vol/vol]) hydrogen concentrations, those missing the [NiFeSe] hydrogenase suffered the greatest impairment. The growth rate data correlated strongly with gene expression results obtained from microarray hybridizations and real-time PCR using mRNA extracted from cells grown under the three conditions. Expression of the hys genes followed the order 5% hydrogen > 50% hydrogen > lactate, whereas expression of the hyd genes followed the reverse order. These results suggest that growth with lactate and 50% hydrogen is associated with high intracellular hydrogen concentrations, which are best captured by the higher activity, lower affinity [Fe] hydrogenase. In contrast, growth with 5% hydrogen is associated with a low intracellular hydrogen concentration, requiring the lower activity, higher affinity [NiFeSe] hydrogenase.

Caffrey, Sean M.; Park, Hyung-Soo; Voordouw, Johanna K.; He, Zhili; Zhou, Jizhong; Voordouw, Gerrit

2007-01-01

135

Hydrogen Production by a Hyperthermophilic Membrane-Bound Hydrogenase in Soluble Nanolipoprotein Particles  

Microsoft Academic Search

Hydrogenases constitute a promising class of enzymes for ex vivo hydrogen production. Implementation of such applications is currently hindered by oxygen sensitivity and, in the case of membrane-bound hydrogenases (MBH), poor water solubility. Nanolipoprotein particles (NLPs), formed from apolipoproteins and phospholipids, offer a novel means to incorporate MBH into in a well-defined water-soluble matrix that maintains the enzymatic activity and

S E Baker; R C Hopkins; C Blanchette; V Walsworth; R Sumbad; N Fischer; E Kuhn; M Coleman; B Chromy; S Letant; P Hoeprich; M W Adams; P T Henderson

2008-01-01

136

X-ray absorption spectroscopy of nickel in the hydrogenase from Desulfovibrio gigas  

Microsoft Academic Search

Results of preliminary X-ray absorption spectroscopic studies of the Desulfovibrio gigas enzyme indicate that the nickel is reduced from Ni(III) to Ni(II) upon Hâ reduction of the oxidized enzyme and that the ligands are bound to the nickel through the S atoms. Hydrogenase from Desulfovibrio gigas exhibited a single bond on disc acrylamide gel electrophoresis, and hydrogenase activity was determined

Robert A. Scott; Sten A. Wallin; Melvin Czechowski; D. V. DerVartanian; Jean LeGall; Harry D. Peck; Isabel Moura

1984-01-01

137

A proton-deuterium exchange study of three types of Desulfovibrio hydrogenases  

Microsoft Academic Search

Summary Hydrogenases are among the main enzymes involved in bacterial anaerobic corrosion of metals. The study of their mode of action is important for a full comprehension of this phenomenon. The three types ofDesulfovibrio hydrogenases [(Fe), (NiFe), (NiFeSe)] present different patterns in the pH dependence of their activity. The periplasmic enzyme fromDesulfovibrio salexigens and the cytoplasmic enzyme fromDesulfovibrio baculatus both

Guy D. Fauque; Yves M. Berlier; Melvin H. Czechowski; Bernard Dirnon; Paul A. Lespinat; Jean LeGall

1987-01-01

138

Bioelectrocatalytic hydrogen production using Thiocapsa roseopersicina hydrogenase in two-compartment fuel cells  

Microsoft Academic Search

Bioelectrocatalytic hydrogen (H2) production was studied using Thiocapsa roseopersicina hydrogenase in a two-compartment proton-exchange-membrane (PEM) fuel-cell system equipped with carbon–paper electrodes. Sodium dithionite (SD), as an electron donor, and hydrogenase, as a catalyst, were used in the anodic oxidation reaction and in the cathodic reduction reaction, respectively. Methyl viologen (MV) was added for the electron relays in both reactions. The

You-Kwan Oh; Yu-jin Lee; Eun-Hye Choi; Mi-Sun Kim

2008-01-01

139

Dramatically enhanced aerobic atrazine degradation with Fe@Fe2O3 core-shell nanowires by tetrapolyphosphate.  

PubMed

In this study, the effects of an inorganic ligand tetrapolyphosphate on the molecular oxygen activation and the subsequent aerobic atrazine degradation by Fe@Fe2O3 core-shell nanowires were investigated systematically at a circumneutral to alkaline pH range (pH 6.0-9.0). We interestingly found that the addition of tetrapolyphosphate could enhance the aerobic atrazine degradation rate 955 times, which was even 10 times that of the traditional organic ligand ethylenediamine tetraacetate. This tetrapolyphosphate induced dramatic aerobic atrazine degradation enhancement could be attributed to two factors. One was that the presence of tetrapolyphosphate strongly suppressed hydrogen evolution from the reduction of proton by Fe@Fe2O3 core-shell nanowires through proton confinement, leaving over more electrons for the reduction of Fe(III) to Fe(II) and the subsequent molecular oxygen activation. The other was that the complexation of tetrapolyphosphate with ferrous ions not only guaranteed enough soluble Fe(II) for Fenton reaction, but also provided another route to produce more •OH in the solution via the single-electron molecular oxygen reduction pathway. We employed gas chromatography-mass spectrometry and liquid chromatography-mass spectrometry to identify the atrazine degradation intermediates and proposed a possible aerobic atrazine degradation pathway. This study not only sheds light on the promotion effects of ligands on the molecular oxygen activation by nanoscale zerovalent iron, but also offers a facile and green iron-based method for the oxidative atrazine removal. PMID:24527762

Wang, Li; Cao, Menghua; Ai, Zhihui; Zhang, Lizhi

2014-03-18

140

Structural basis for GTP-dependent dimerization of hydrogenase maturation factor HypB.  

PubMed

Maturation of [NiFe]-hydrogenase requires the insertion of iron, cyanide and carbon monoxide, followed by nickel, to the catalytic core of the enzyme. Hydrogenase maturation factor HypB is a metal-binding GTPase that is essential for the nickel delivery to the hydrogenase. Here we report the crystal structure of Archeoglobus fulgidus HypB (AfHypB) in apo-form. We showed that AfHypB recognizes guanine nucleotide using Asp-194 on the G5 loop despite having a non-canonical NKxA G4-motif. Structural comparison with the GTP?S-bound Methanocaldococcus jannaschii HypB identifies conformational changes in the switch I region, which bring an invariant Asp-72 to form an intermolecular salt-bridge with another invariant residue Lys-148 upon GTP binding. Substitution of K148A abolished GTP-dependent dimerization of AfHypB, but had no significant effect on the guanine nucleotide binding and on the intrinsic GTPase activity. In vivo complementation study in Escherichia coli showed that the invariant lysine residue is required for in vivo maturation of hydrogenase. Taken together, our results suggest that GTP-dependent dimerization of HypB is essential for hydrogenase maturation. It is likely that a nickel ion is loaded to an extra metal binding site at the dimeric interface of GTP-bound HypB and transferred to the hydrogenase upon GTP hydrolysis. PMID:22276211

Chan, Kwok-Ho; Li, Ting; Wong, Ching-On; Wong, Kam-Bo

2012-01-01

141

Occurrence and localization of two distinct hydrogenases in the heterocystous cyanobacterium Anabaena sp. strain 7120.  

PubMed Central

Two distinct types of hydrogenase occur in Anabaena 7120 and are distinguishable in whole filaments by the application of selective assay methods. A reversible hydrogenase occurs both in heterocysts and vegetative cells and can be selectively assayed by measuring H2 evolution from reduced methyl viologen. Activities in aerobically grown filaments were low but could be increased by 2 to 3 orders of magnitude by growing cells microaerobically. The presence of the reversible hydrogenase was independent of the N2-fixing properties of the organism, and activity did not respond to added H2 in the culture. Illumination was necessary during derepression of the reversible hydrogenase, and addition of 3-(3',4'-dichlorophenyl)-1,1-dimethylurea increased the amount of enzyme that was synthesized. An uptake hydrogenase occurred only in heterocysts of aerobically grown filaments, but a small amount of activity also was present in the vegetative cells of filaments grown microaerobically with 20% H2. It was assayed selectively by measuring an oxyhydrogen reaction at atmospheric levels of O2. Additional uptake hydrogenase could be elicited by including H2 or by removing O2 from the sparging gas of a culture.

Houchins, J P; Burris, R H

1981-01-01

142

Analyses of the Large Subunit Histidine-Rich Motif Expose an Alternative Proton Transfer Pathway in [NiFe] Hydrogenases  

Microsoft Academic Search

A highly conserved histidine-rich region with unknown function was recognized in the large subunit of [NiFe] hydrogenases. The HxHxxHxxHxH sequence occurs in most membrane-bound hydrogenases, but only two of these histidines are present in the cytoplasmic ones. Site-directed mutagenesis of the His-rich region of the T. roseopersicina membrane-attached Hyn hydrogenase disclosed that the enzyme activity was significantly affected only by

Emma Sz?ri-Dorogházi; Gergely Maróti; Milán Sz?ri; Andrea Nyilasi; Gábor Rákhely; Kornél L. Kovács

2012-01-01

143

A unique iron-sulfur cluster is crucial for oxygen tolerance of a [NiFe]-hydrogenase  

Microsoft Academic Search

Hydrogenases are essential for H2 cycling in microbial metabolism and serve as valuable blueprints for H2-based biotechnological applications. However, most hydrogenases are extremely oxygen sensitive and prone to inactivation by even traces of O2. The O2-tolerant membrane-bound [NiFe]-hydrogenase of Ralstonia eutropha H16 is one of the few examples that can perform H2 uptake in the presence of ambient O2. Here

Tobias Goris; Annemarie F Wait; Miguel Saggu; Johannes Fritsch; Nina Heidary; Matthias Stein; Ingo Zebger; Friedhelm Lendzian; Fraser A Armstrong; Bärbel Friedrich; Oliver Lenz

2011-01-01

144

Identification of a locus within the hydrogenase gene cluster involved in intracellular nickel metabolism in Bradyrhizobium japonicum  

SciTech Connect

A 0.6-kb fragment of DNA involved in intracellular Ni metabolism was isolated and cloned from a cosmid containing 23.2 kb of hydrogenase-related genes of Bradyrhizobium japonicum. This locus is located 8.3 kb upstream of the hydrogenase structural genes. The hydrogenase activity of a mutant with a gene-directed mutation at this locus (strain JHK7) showed dependency on nickel provided during hydrogenase depression. The hydrogenase activity was only 20% of that in the wild-type strain, JH, at a concentration of 0.5 {mu}M NiCl{sub 2}. The hydrogenase activity in JH reached its maximum at 3 {mu}M NiCl{sub 2}, whereas the mutant (JHK7) reached wild-type levels of hydrogenase activity when derepressed in 50 {mu}M NiCl{sub 2}. Studies with the hup-lacZ transcriptional fusion plasmid pSY7 in JHK7 showed that the mutant JHK7 expressed less promoter activity under low-nickel conditions than did strain JH. The mutant accumulated less nickel during a 45-h hydrogenase under low-nickel conditions than did strain JH. The mutant accumulated less nickel during a 45-h hydrogenase derepression period than did the wild type. However, both JHK7 and the JH wild-type strain had the same short-term Ni transport rates, and the K{sub m}s for Ni of both strains were about 62 {mu}M. When incubated under non-hydrogenase-derepression conditions, the mutant accumulated Ni at the same rate as strain JH. However, this stored source of nickel was unable to restore hydrogenase expression ability of the mutant to wild-type levels during derepression without nickel. The results that the locus identified in B. japonicum is not involved in nickel-specific transport.

Changlin Fu; Maier, R.J. (John Hopkins Univ., Baltimore, MD (United States))

1991-12-01

145

Essential anaplerotic role for the energy-converting hydrogenase Eha in hydrogenotrophic methanogenesis  

PubMed Central

Despite decades of study, electron flow and energy conservation in methanogenic Archaea are still not thoroughly understood. For methanogens without cytochromes, flavin-based electron bifurcation has been proposed as an essential energy-conserving mechanism that couples exergonic and endergonic reactions of methanogenesis. However, an alternative hypothesis posits that the energy-converting hydrogenase Eha provides a chemiosmosis-driven electron input to the endergonic reaction. In vivo evidence for both hypotheses is incomplete. By genetically eliminating all nonessential pathways of H2 metabolism in the model methanogen Methanococcus maripaludis and using formate as an additional electron donor, we isolate electron flow for methanogenesis from flux through Eha. We find that Eha does not function stoichiometrically for methanogenesis, implying that electron bifurcation must operate in vivo. We show that Eha is nevertheless essential, and a substoichiometric requirement for H2 suggests that its role is anaplerotic. Indeed, H2 via Eha stimulates methanogenesis from formate when intermediates are not otherwise replenished. These results fit the model for electron bifurcation, which renders the methanogenic pathway cyclic, and as such requires the replenishment of intermediates. Defining a role for Eha and verifying electron bifurcation provide a complete model of methanogenesis where all necessary electron inputs are accounted for.

Lie, Thomas J.; Costa, Kyle C.; Lupa, Boguslaw; Korpole, Suresh; Whitman, William B.; Leigh, John A.

2012-01-01

146

Selenium increases hydrogenase expression is autotrophically cultured Bradyrhizobium japonicum and is a constituent of the purified enzyme  

SciTech Connect

The authors have investigated the effect of added selenite on autotrophic growth and the time course of hydrogen oxidation derepression in Bradyrhizobium japonicum 122DES cultured in a medium purified to remove selenium compounds. In addition, hydrogenase was purified to near homogeneity and examined for the specific incorporation of Se into the enzyme. The addition of Se at 0.1 {mu}M significantly increased total cell protein and hydrogenase specific activity of harvested cells. Also, the addition of SeO{sub 3}{sup 2{minus}} enhanced the time course of hydrogenase derepression by 133%, whereas VO{sub 3}, AsO{sub 2}{sup 2{minus}}, SO{sub 2}{sup 2{minus}}, and TeO{sub 3}{sup 2{minus}} failed to substantially affect hydrogenase derepression. During the final chromatographic purification of hydrogenase, a striking coincidence in peaks of protein content, Se radioactivity, and hydrogenase activity of fractions was obtained. The total Se content expressed per milligram of protein increased manyfold during the purification procedure. The mean Se content of the purified hydrogenase was 0.56 {plus minus} 0.13 mol of Se per mol of enzyme. These results indicate that Se is an important element in the H{sub 2} metabolism of B. japonicum and that hydrogenase from B. japonicum is a seleno protein.

Boursier, P.; Hanus, F.J.; Papen, H.; Becker, M.M.; Russell, S.A.; Evans, H.J. (Oregon State Univ., Corvallis (USA))

1988-12-01

147

Selenium increases hydrogenase expression in autotrophically cultured Bradyrhizobium japonicum and is a constituent of the purified enzyme.  

PubMed Central

We have investigated the effect of added selenite on autotrophic growth and the time course of hydrogen oxidation derepression in Bradyrhizobium japonicum 122DES cultured in a medium purified to remove selenium compounds. In addition, hydrogenase was purified to near homogeneity and examined for the specific incorporation of Se into the enzyme. The addition of Se at 0.1 microM significantly increased total cell protein and hydrogenase specific activity of harvested cells. Also, the addition of SeO3(2-) enhanced the time course of hydrogenase derepression by 133%, whereas VO3, AsO2(2-), SO2(2-), and TeO3(2-) failed to substantially affect hydrogenase derepression. During the final chromatographic purification of hydrogenase, a striking coincidence in peaks of protein content, Se radioactivity, and hydrogenase activity of fractions was obtained. The total Se content expressed per milligram of protein increased manyfold during the purification procedure. The mean Se content of the purified hydrogenase was 0.56 +/- 0.13 mol of Se per mol of enzyme. These results indicate that Se is an important element in the H2 metabolism of B. japonicum and that hydrogenase from B. japonicum is a seleno protein. Images

Boursier, P; Hanus, F J; Papen, H; Becker, M M; Russell, S A; Evans, H J

1988-01-01

148

Characterization of the oxygen tolerance of a hydrogenase linked to a carbon monoxide oxidation pathway in Rubrivivax gelatinosus.  

PubMed

A hydrogenase linked to the carbon monoxide oxidation pathway in Rubrivivax gelatinosus displays tolerance to O2. When either whole-cell or membrane-free partially purified hydrogenase was stirred in full air (21% O2, 79% N2), its H2 evolution activity exhibited a half-life of 20 or 6 h, respectively, as determined by an anaerobic assay using reduced methyl viologen. When the partially purified hydrogenase was stirred in an atmosphere containing either 3.3 or 13% O2 for 15 min and evaluated by a hydrogen-deuterium (H-D) exchange assay, nearly 80 or 60% of its isotopic exchange rate was retained, respectively. When this enzyme suspension was subsequently returned to an anaerobic atmosphere, more than 90% of the H-D exchange activity was recovered, reflecting the reversibility of this hydrogenase toward O2 inactivation. Like most hydrogenases, the CO-linked hydrogenase was extremely sensitive to CO, with 50% inhibition occurring at 3.9 microM dissolved CO. Hydrogen production from the CO-linked hydrogenase was detected when ferredoxins of a prokaryotic source were the immediate electron mediator, provided they were photoreduced by spinach thylakoid membranes containing active water-splitting activity. Based on its appreciable tolerance to O2, potential applications of this hydrogenase are discussed. PMID:12039713

Maness, Pin-Ching; Smolinski, Sharon; Dillon, Anne C; Heben, Michael J; Weaver, Paul F

2002-06-01

149

Molecular cloning of structural and regulatory hydrogenase (hox) genes of Alcaligenes eutrophus H16.  

PubMed

A gene bank of the 450-kilobase (kb) megaplasmid pHG1 from the hydrogen-oxidizing bacterium Alcaligenes eutrophus H16 was constructed in the broad-host-range mobilizable vector pSUP202 and maintained in Escherichia coli. hox DNA was identified by screening the E. coli gene bank for restoration of hydrogenase activity in A. eutrophus Hox mutants. Hybrid plasmids that contained an 11.6-kb EcoRI fragment restored soluble NAD-dependent hydrogenase activity when transferred by conjugation into one class of Hos- mutants. An insertion mutant impaired in particulate hydrogenase was partially restored in Hop activity by an 11-kb EcoRI fragment. A contiguous sequence of two EcoRI fragments of 8.6 and 2.0 kb generated Hox+ recombinants from mutants that were devoid of both hydrogenase proteins. hox DNA was subcloned into the vector pVK101. The resulting recombinant plasmids were used in complementation studies. The results indicate that we have cloned parts of the structural genes coding for Hos and Hop activity and a complete regulatory hox DNA sequence which encodes the thermosensitive, energy-dependent derepression signal of hydrogenase synthesis in A. eutrophus H16. PMID:3536856

Eberz, G; Hogrefe, C; Kortlüke, C; Kamienski, A; Friedrich, B

1986-11-01

150

Structural And Biological Analysis of the Metal Sites of Escherichia Coli Hydrogenase Accessory Protein  

SciTech Connect

The [NiFe]-hydrogenase protein produced by many types of bacteria contains a dinuclear metal center that is required for enzymatic activity. Assembly of this metal cluster involves the coordinated activity of a number of helper proteins including the accessory protein, HypB, which is necessary for Ni(II) incorporation into the hydrogenase proteins. The HypB protein from Escherichia coli has two metal-binding sites, a high-affinity Ni(II) site that includes ligands from the N-terminal domain and a low-affinity metal site located within the C-terminal GTPase domain. In order to determine the physiological relevance of the two separate sites, hydrogenase production was assessed in strains of E. coli expressing wild-type HypB, the isolated GTPase domain, or site-directed mutants of metal-binding residues. These experiments demonstrate that both metal sites of HypB are critical for the maturation of the hydrogenase enzymes in E. coli. X-ray absorption spectroscopy of purified proteins was used to examine the detailed coordination spheres of each nickel-loaded site. In addition, because the low-affinity metal site has a stronger preference for Zn(II) than Ni(II), the ligands and geometry for this metal were also resolved. The results from these experiments are discussed in the context of a mechanism for Ni(II) insertion into the hydrogenase protein.

Dias, A.V.; Mulvihill, C.M.; Leach, M.R.; Pickering, I.J.; George, G.N.; Zamble, D.B.

2009-05-12

151

Molecular dynamics and experimental investigation of H2 and O2 diffusion in [Fe]-hydrogenase  

PubMed Central

The [Fe]-hydrogenase enzymes are highly efficient H2 catalysts found in ecologically, and phylogenetically diverse microorganisms, including the photosynthetic green alga, Chlamydomonas reinhardtii. Although these enzymes can occur in several forms, H2 catalysis takes place at a unique [FeS] prosthetic group, or H-cluster, located at the active site. Significant to the function of hydrogenases is how the surrounding protein structure facilitates substrate-product transfer, and protects the active site H-cluster from inactivation. To elucidate the role of protein structure in O2 inactivation of [Fe]-hydrogenases, experimental and theoretical investigations have been performed. Molecular dynamics was used to comparatively investigate O2 and H2 diffusion in [Fe]-hydrogenase CpI. The results are compared to initial investigations of H2 diffusion in [NiFe]-hydrogenase [1]. Our preliminary results suggest that H2 diffuses more easily and freely than O2, which is restricted to a small number of allowed pathways to and from the active site. These O2 pathways are located in the conserved active site domain, shown experimentally to have an essential role in active site protection.

Cohen, Jordi; Kim, Kwiseon; Posewitz, Matthew; Ghirardi, Maria L.; Schulten, Klaus; Seibert, Michael; King, Paul

2008-01-01

152

Three different [NiFe] hydrogenases confer metabolic flexibility in the obligate aerobe Mycobacterium smegmatis.  

PubMed

Mycobacterium smegmatis is an obligate aerobe that harbours three predicted [NiFe] hydrogenases, Hyd1 (MSMEG_2262–2263), Hyd2 (MSMEG_2720-2719) and Hyd3 (MSMEG_3931-3928). We show here that these three enzymes differ in their phylogeny, regulation and catalytic activity. Phylogenetic analysis revealed that Hyd1 groups with hydrogenases that oxidize H2 produced by metabolic processes, and Hyd2 is homologous to a novel group of putative high-affinity hydrogenases. Hyd1 and Hyd2 respond to carbon and oxygen limitation, and, in the case of Hyd1, hydrogen supplementation. Hydrogen consumption measurements confirmed that both enzymes can oxidize hydrogen. In contrast, the phylogenetic analysis and activity measurements of Hyd3 are consistent with the enzyme evolving hydrogen. Hyd3 is controlled by DosR, a regulator that responds to hypoxic conditions. The strict dependence of hydrogen oxidation of Hyd1 and Hyd2 on oxygen suggests that the enzymes are oxygen tolerant and linked to the respiratory chain. This unique combination of hydrogenases allows M. smegmatis to oxidize hydrogen at high (Hyd1) and potentially tropospheric (Hyd2) concentrations, as well as recycle reduced equivalents by evolving hydrogen (Hyd3). The distribution of these hydrogenases throughout numerous soil and marine species of actinomycetes suggests that oxic hydrogen metabolism provides metabolic flexibility in environments with changing nutrient fluxes. PMID:24536093

Berney, Michael; Greening, Chris; Hards, Kiel; Collins, Desmond; Cook, Gregory M

2014-01-01

153

Temperature profile of the outer core based on X-ray diffraction of Fe-Fe3S and (Fe,Ni)-(Fe,Ni)3S system  

NASA Astrophysics Data System (ADS)

The Earth’s core is considered to be composed of Fe-Ni alloy with light element(s). Sulfur in particular has been considered as one of the most plausible light elements based on the solar abundances and high pressure partitioning experiments. Therefore, it is important to investigate the Fe-FeS system up to the core conditions to discuss its chemical and physical properties. Nevertheless, there are not previous works under the core conditions. Therefore, we have investigated the melting relationships in the Fe-Fe3S system up to 190 GPa, and those in the (Fe,Ni)-(Fe,Ni)3S system up to 100 GPa using a double-sided laser-heated diamond anvil cell (LHDAC) combined with the synchrotron X-ray. A foil of Fe86.8S13.2 or Fe75.0Ni10.0S15.0 was sandwiched between NaCl pellets. The sample was heated using fiber lasers. The shape of a fiver laser beam was changed to a flat-top using a beam shaping system at the BL10XU, SPring-8. The melting detection was based on disappearance of the X-ray diffraction (XRD) peaks derived from Fe3S or (Fe,Ni)3S. Disappearance of XRD from Fe3S was observed at 64.2, 78.0, 113.7, 136.3, and 181.6 GPa. That of XRD from (Fe,Ni)3S was observed at 74.5 and 104.6 GPa. The melting temperatures of the present results in the Fe-Fe3S system are consistent with previous works up to around 70 GPa (e.g., Campbell et al., 2007; Morard et al., 2008). However, the slope of the melting temperature in the Fe-Fe3S system is slightly gentle above 100 GPa compared to the extrapolated melting curves of previous studies. On the other hand, the melting temperatures in the (Fe,Ni)-(Fe,Ni)3S system are similar to those in the Fe-Fe3S system. This suggests that 10 at. % Ni does not affect on melting significantly. The present results were fitted to the Kraut-Kennedy law in order to extrapolate the melting temperature of the Fe-Fe3S system up to the ICB condition. The eutectic temperature of the Fe-Fe3S system at the pressures relevant to the CMB and ICB conditions are 3010(80) and 4440(140) K, respectively. If S is the only light element in the core, the eutectic temperature of 4440 K at ICB condition suggests the lower bound of TICB and the upper bound of TICB which corresponds to the temperature of the total melting temperature of the Fe-Fe3S system because the Fe-Fe3S system may show the eutectic system at the core conditions. The present ICB temperature is about 800 K below the temperature estimated by Ma et al. (2004). Campbell et al. (2007) estimated the temperature at ICB conditions to be at least 4500 K by assuming that the depression of melting temperature due to sulfur was 800 K. The present result is consistent with the lower bound of ICB temperature estimated by Campbell et al. (2007). If the adiabatic gradient through the whole outer core can be assumed, the temperature at the top of the outer core is calculated to be 3400 K assuming the temperature at ICB of 4440 K and ?th of 1.3 (Stacey, 1995). The estimated temperature at the CMB condition based on the adiabatic gradient is 390 K higher than the eutectic temperature at CMB conditions.

Kamada, S.; Ohtani, E.; Terasaki, H.; Sakai, T.; Ohishi, Y.; Hirao, N.; Sata, N.

2010-12-01

154

Identification of a locus within the hydrogenase gene cluster involved in intracellular nickel metabolism in Bradyrhizobium japonicum.  

PubMed Central

A 0.6-kb fragment of DNA involved in intracellular Ni metabolism was isolated and cloned from a cosmid containing 23.2 kb of hydrogenase-related genes of Bradyrhizobium japonicum. This locus is located 8.3 kb upstream of the hydrogenase structural genes. The hydrogenase activity of a mutant with a gene-directed mutation at this locus (strain JHK7) showed dependency on nickel provided during hydrogenase derepression. The hydrogenase activity was only 20% of that in the wild-type strain, JH, at a concentration of 0.5 microM NiCl2. The hydrogenase activity in JH reached its maximum at 3 microM NiCl2, whereas the mutant (JHK7) reached wild-type levels of hydrogenase activity when derepressed in 50 microM NiCl2. Studies with the hup-lacZ transcriptional fusion plasmid pSY7 in JHK7 showed that the mutant JHK7 expressed less promoter activity under low-nickel conditions than did strain JH. The mutant accumulated less nickel during a 45-h hydrogenase derepression period than did the wild type. However, both JHK7 and the JH wild-type strain had the same short-term Ni transport rates, and the KmS for Ni of both strains were about 62 microM. When incubated under non-hydrogenase-derepression conditions, the mutant accumulated Ni at the same rate as strain JH. However, this stored source of nickel was unable to restore hydrogenase expression ability of the mutant to wild-type levels during derepression without nickel. The results indicate that the locus identified in B. japonicum is not involved in nickel-specific transport; indeed, it was not at all homologous to the "nickel transporter" hoxN gene of Alcaligenes eutrophus.(ABSTRACT TRUNCATED AT 250 WORDS) Images

Fu, C L; Maier, R J

1991-01-01

155

Efficiency of Hydrogen Photoproduction by Chloroplast-Bacterial Hydrogenase Systems  

PubMed Central

A comparative study of H2 photoproduction by chloroplasts and solubilized chlorophyll was performed in the presence of hydrogenase preparations of Clostridium butyricum. The photoproduction of H2 by chloroplasts in the absence of exogenous electron donors, and with irreversibly oxidized dithiothreitol and cysteine, is thought to be limited by a cyclic transport of electrons wherein methylviologen short-circuits the electron transport in photosystem I. The efficiency of H2 photoproduction by chloroplasts with ascorbate and NADPH is limited by a back reaction between light-reduced methylviologen and the oxidized electron donors. The use of a combination of electron donors (dithiothreitol and ascorbate), providing anaerobiosis without damage to chloroplasts, makes it possible to avoid consumption of reduced methylviologen for the reduction of oxidized electron donors and to exclude the short-circuiting of electron transfer. Under these conditions, photoproduction of H2 was observed to occur with a rate of 350 to 400 micromoles H2 per milligram chlorophyll per hour. In this case, the full electron-transferring capability of photosystem I (measured by irreversible photoreduction of methyl red or O2) is used to produce H2.

Krasnovsky, A. A.; Van Ni, Chan; Nikandrov, V. V.; Brin, G. P.

1980-01-01

156

[Stability of the hydrogenase from Tetraselmis subcordiformis and its preliminary purification].  

PubMed

Tetraselmis subcordiformis, a marine green alga, can produce hydrogen by photobiologically hydrolyzing seawater with hydrogenase. In this study, the preliminary purification of the enzyme was explored by ammonium sulfate precipitation, and the impact of sodium dithionite, beta-mercaptoethanol and glycerol on the enzyme stability during the process was investigated. The experimental results illustrated that sodium dithionite provided significant protection on the hydrogenase by depleting oxygen, while glycerol, a protectant against the structure instability of the enzyme, also presented protection. Crude enzyme with specific activity of 0.557 U/mg protein was extracted using 60%-70% saturated ammonium sulfate solution supplemented with 200 mmol/L sodium dithionite and 5% glycerol, and the hydrogenase recovery yield was about 30%. PMID:20954403

Yan, Fei; Chen, Zhao'an; Cao, Xupeng; Lu, Hongbin; Xue, Song; Zhang, Wei

2010-07-01

157

Evolutionary and Biotechnological Implications of Robust Hydrogenase Activity in Halophilic Strains of Tetraselmis  

PubMed Central

Although significant advances in H2 photoproduction have recently been realized in fresh water algae (e.g. Chlamydomonas reinhardtii), relatively few studies have focused on H2 production and hydrogenase adaptations in marine or halophilic algae. Salt water organisms likely offer several advantages for biotechnological H2 production due to the global abundance of salt water, decreased H2 and O2 solubility in saline and hypersaline systems, and the ability of extracellular NaCl levels to influence metabolism. We screened unialgal isolates obtained from hypersaline ecosystems in the southwest United States and identified two distinct halophilic strains of the genus Tetraselmis (GSL1 and QNM1) that exhibit both robust fermentative and photo H2-production activities. The influence of salinity (3.5%, 5.5% and 7.0% w/v NaCl) on H2 production was examined during anoxic acclimation, with the greatest in vivo H2-production rates observed at 7.0% NaCl. These Tetraselmis strains maintain robust hydrogenase activity even after 24 h of anoxic acclimation and show increased hydrogenase activity relative to C. reinhardtii after extended anoxia. Transcriptional analysis of Tetraselmis GSL1 enabled sequencing of the cDNA encoding the FeFe-hydrogenase structural enzyme (HYDA) and its maturation proteins (HYDE, HYDEF and HYDG). In contrast to freshwater Chlorophyceae, the halophilic Tetraselmis GSL1 strain likely encodes a single HYDA and two copies of HYDE, one of which is fused to HYDF. Phylogenetic analyses of HYDA and concatenated HYDA, HYDE, HYDF and HYDG in Tetraselmis GSL1 fill existing knowledge gaps in the evolution of algal hydrogenases and indicate that the algal hydrogenases sequenced to date are derived from a common ancestor. This is consistent with recent hypotheses that suggest fermentative metabolism in the majority of eukaryotes is derived from a common base set of enzymes that emerged early in eukaryotic evolution with subsequent losses in some organisms.

D'Adamo, Sarah; Jinkerson, Robert E.; Boyd, Eric S.; Brown, Susan L.; Baxter, Bonnie K.; Peters, John W.; Posewitz, Matthew C.

2014-01-01

158

Evolutionary and biotechnological implications of robust hydrogenase activity in halophilic strains of tetraselmis.  

PubMed

Although significant advances in H2 photoproduction have recently been realized in fresh water algae (e.g. Chlamydomonas reinhardtii), relatively few studies have focused on H2 production and hydrogenase adaptations in marine or halophilic algae. Salt water organisms likely offer several advantages for biotechnological H2 production due to the global abundance of salt water, decreased H2 and O2 solubility in saline and hypersaline systems, and the ability of extracellular NaCl levels to influence metabolism. We screened unialgal isolates obtained from hypersaline ecosystems in the southwest United States and identified two distinct halophilic strains of the genus Tetraselmis (GSL1 and QNM1) that exhibit both robust fermentative and photo H2-production activities. The influence of salinity (3.5%, 5.5% and 7.0% w/v NaCl) on H2 production was examined during anoxic acclimation, with the greatest in vivo H2-production rates observed at 7.0% NaCl. These Tetraselmis strains maintain robust hydrogenase activity even after 24 h of anoxic acclimation and show increased hydrogenase activity relative to C. reinhardtii after extended anoxia. Transcriptional analysis of Tetraselmis GSL1 enabled sequencing of the cDNA encoding the FeFe-hydrogenase structural enzyme (HYDA) and its maturation proteins (HYDE, HYDEF and HYDG). In contrast to freshwater Chlorophyceae, the halophilic Tetraselmis GSL1 strain likely encodes a single HYDA and two copies of HYDE, one of which is fused to HYDF. Phylogenetic analyses of HYDA and concatenated HYDA, HYDE, HYDF and HYDG in Tetraselmis GSL1 fill existing knowledge gaps in the evolution of algal hydrogenases and indicate that the algal hydrogenases sequenced to date are derived from a common ancestor. This is consistent with recent hypotheses that suggest fermentative metabolism in the majority of eukaryotes is derived from a common base set of enzymes that emerged early in eukaryotic evolution with subsequent losses in some organisms. PMID:24465722

D'Adamo, Sarah; Jinkerson, Robert E; Boyd, Eric S; Brown, Susan L; Baxter, Bonnie K; Peters, John W; Posewitz, Matthew C

2014-01-01

159

A missing link between complex I and group 4 membrane-bound [NiFe] hydrogenases.  

PubMed

Complex I of respiratory chains is an energy transducing enzyme present in most bacteria, mitochondria and chloroplasts. It catalyzes the oxidation of NADH and the reduction of quinones, coupled to cation translocation across the membrane. The complex has a modular structure composed of several proteins most of which are identified in other complexes. Close relations between complex I and group 4 membrane-bound [NiFe] hydrogenases and some subunits of multiple resistance to pH (Mrp) Na(+)/H(+) antiporters have been observed before and the suggestion that complex I arose from the association of a soluble nicotinamide adenine dinucleotide (NAD(+)) reducing hydrogenase with a Mrp-like antiporter has been put forward. In this article we performed a thorough taxonomic profile of prokaryotic group 4 membrane-bound [NiFe] hydrogenases, complexes I and complex I-like enzymes. In addition we have investigated the different gene clustering organizations of such complexes. Our data show the presence of complexes related to hydrogenases but which do not contain the binding site of the catalytic centre. These complexes, named before as Ehr (energy-converting hydrogenases related complexes) are a missing link between complex I and group 4 membrane-bound [NiFe] hydrogenases. Based on our observations we put forward a different perspective for the relation between complex I and related complexes. In addition we discuss the evolutionary, functional and mechanistic implications of this new perspective. This article is part of a Special Issue entitled: The evolutionary aspects of bioenergetic systems. PMID:23000657

Marreiros, Bruno C; Batista, Ana P; Duarte, Afonso M S; Pereira, Manuela M

2013-02-01

160

Characterization of the hydrogen-deuterium exchange activities of the energy-transducing HupSL hydrogenase and H(2)-signaling HupUV hydrogenase in Rhodobacter capsulatus.  

PubMed

Rhodobacter capsulatus synthesizes two homologous protein complexes capable of activating molecular H(2), a membrane-bound [NiFe] hydrogenase (HupSL) linked to the respiratory chain, and an H(2) sensor encoded by the hupUV genes. The activities of hydrogen-deuterium (H-D) exchange catalyzed by the hupSL-encoded and the hupUV-encoded enzymes in the presence of D(2) and H(2)O were studied comparatively. Whereas HupSL is in the membranes, HupUV activity was localized in the soluble cytoplasmic fraction. Since the hydrogenase gene cluster of R. capsulatus contains a gene homologous to hoxH, which encodes the large subunit of NAD-linked tetrameric soluble hydrogenases, the chromosomal hoxH gene was inactivated and hoxH mutants were used to demonstrate the H-D exchange activity of the cytoplasmic HupUV protein complex. The H-D exchange reaction catalyzed by HupSL hydrogenase was maximal at pH 4. 5 and inhibited by acetylene and oxygen, whereas the H-D exchange catalyzed by the HupUV protein complex was insensitive to acetylene and oxygen and did not vary significantly between pH 4 and pH 11. Based on these properties, the product of the accessory hypD gene was shown to be necessary for the synthesis of active HupUV enzyme. The kinetics of HD and H(2) formed in exchange with D(2) by HupUV point to a restricted access of protons and gasses to the active site. Measurement of concentration changes in D(2), HD, and H(2) by mass spectrometry showed that, besides the H-D exchange reaction, HupUV oxidized H(2) with benzyl viologen, produced H(2) with reduced methyl viologen, and demonstrated true hydrogenase activity. Therefore, not only with respect to its H(2) signaling function in the cell, but also to its catalytic properties, the HupUV enzyme represents a distinct class of hydrogenases. PMID:11029418

Vignais, P M; Dimon, B; Zorin, N A; Tomiyama, M; Colbeau, A

2000-11-01

161

Hydrogen Production by a Hyperthermophilic Membrane-Bound Hydrogenase in Soluble Nanolipoprotein Particles  

SciTech Connect

Hydrogenases constitute a promising class of enzymes for ex vivo hydrogen production. Implementation of such applications is currently hindered by oxygen sensitivity and, in the case of membrane-bound hydrogenases (MBH), poor water solubility. Nanolipoprotein particles (NLPs), formed from apolipoproteins and phospholipids, offer a novel means to incorporate MBH into in a well-defined water-soluble matrix that maintains the enzymatic activity and is amenable to incorporation into more complex architectures. We report the synthesis, hydrogen-evolving activity and physical characterization of the first MBH-NLP assembly. This may ultimately lead to the development of biomimetic hydrogen production devices.

Baker, S E; Hopkins, R C; Blanchette, C; Walsworth, V; Sumbad, R; Fischer, N; Kuhn, E; Coleman, M; Chromy, B; Letant, S; Hoeprich, P; Adams, M W; Henderson, P T

2008-10-22

162

Structural aspects and immunolocalization of the F420-reducing and non-F420-reducing hydrogenases from Methanobacterium thermoautotrophicum Marburg.  

PubMed Central

The F420-reducing hydrogenase and the non-F420-reducing hydrogenase (EC 1.12.99.1.) were isolated from a crude extract of Methanobacterium thermoautotrophicum Marburg. Electron microscopy of the negatively stained F420-reducing hydrogenase revealed that the enzyme is a complex with a diameter of 15.6 nm. It consists of two ring-like, stacked, parallel layers each composed of three major protein masses arranged in rotational symmetry. Each of these masses appeared to be subdivided into smaller protein masses. Electron microscopy of negatively stained samples taken from intermediate steps of the purification process revealed the presence of enzyme particles bound to inside-out membrane vesicles. Linker particles of 10 to 20 kDa which mediate the attachment of the hydrogenase to the cytoplasmic membrane were seen. Immunogold labelling confirmed that the F420-reducing hydrogenase is a membrane-bound enzyme. Electron microscopy of the negatively stained purified non-F420-reducing hydrogenase revealed that the enzyme is composed of three subunits exhibiting different diameters (5, 4, and 2 to 3 nm). According to immunogold labelling experiments, approximately 70% of the non-F420-reducing hydrogenase protein molecules were located at the cell periphery; the remaining 30% were cytoplasmic. No linker particles were observed for this enzyme. Images

Braks, I J; Hoppert, M; Roge, S; Mayer, F

1994-01-01

163

The uptake hydrogenase in the unicellular diazotrophic cyanobacterium Cyanothece sp. strain PCC 7822 protects nitrogenase from oxygen toxicity.  

PubMed

Cyanothece sp. strain PCC 7822 is a unicellular, diazotrophic cyanobacterium that can produce large quantities of H2 when grown diazotrophically. This strain is also capable of genetic manipulations and can represent a good model for improving H2 production from cyanobacteria. To this end, a knockout mutation was made in the hupL gene (?hupL), and we determined how this would affect the amount of H2 produced. The ?hupL mutant demonstrated virtually no nitrogenase activity or H2 production when grown under N2-fixing conditions. To ensure that this mutation only affected the hupL gene, a complementation strain was constructed readily with wild-type properties; this indicated that the original insertion was only in hupL. The mutant had no uptake hydrogenase activity but had increased bidirectional hydrogenase (Hox) activity. Western blotting and immunocytochemistry under the electron microscope indicated that the mutant had neither HupL nor NifHDK, although the nif genes were transcribed. Interestingly, biochemical analysis demonstrated that both HupL and NifH could be membrane associated. The results indicated that the nif genes were transcribed but that NifHDK was either not translated or was translated but rapidly degraded. We hypothesized that the Nif proteins were made but were unusually susceptible to O2 damage. Thus, we grew the mutant cells under anaerobic conditions and found that they grew well under N2-fixing conditions. We conclude that in unicellular diazotrophs, like Cyanothece sp. strain PCC 7822, the HupLS complex helps remove oxygen from the nitrogenase, and that this is a more important function than merely oxidizing the H2 produced by the nitrogenase. PMID:24317398

Zhang, Xiaohui; Sherman, Debra M; Sherman, Louis A

2014-02-01

164

hypD as a Marker for [NiFe]-Hydrogenases in Microbial Communities of Surface Waters.  

PubMed

Hydrogen is an important trace gas in the atmosphere. Soil microorganisms are known to be an important part of the biogeochemical H2 cycle, contributing 80 to 90% of the annual hydrogen uptake. Different aquatic ecosystems act as either sources or sinks of hydrogen, but the contribution of their microbial communities is unknown. [NiFe]-hydrogenases are the best candidates for hydrogen turnover in these environments since they are able to cope with oxygen. As they lack sufficiently conserved sequence motifs, reliable markers for these enzymes are missing, and consequently, little is known about their environmental distribution. We analyzed the essential maturation genes of [NiFe]-hydrogenases, including their frequency of horizontal gene transfer, and found hypD to be an applicable marker for the detection of the different known hydrogenase groups. Investigation of two freshwater lakes showed that [NiFe]-hydrogenases occur in many prokaryotic orders. We found that the respective hypD genes cooccur with oxygen-tolerant [NiFe]-hydrogenases (groups 1 and 5) mainly of Actinobacteria, Acidobacteria, and Burkholderiales; cyanobacterial uptake hydrogenases (group 2a) of cyanobacteria; H2-sensing hydrogenases (group 2b) of Burkholderiales, Rhizobiales, and Rhodobacterales; and two groups of multimeric soluble hydrogenases (groups 3b and 3d) of Legionellales and cyanobacteria. These findings support and expand a previous analysis of metagenomic data (M. Barz et al., PLoS One 5:e13846, 2010, http://dx.doi.org/10.1371/journal.pone.0013846) and further identify [NiFe]-hydrogenases that could be involved in hydrogen cycling in aquatic surface waters. PMID:24727276

Beimgraben, Christian; Gutekunst, Kirstin; Opitz, Friederike; Appel, Jens

2014-06-15

165

The H2 Sensor of Ralstonia eutropha Is a Member of the Subclass of Regulatory [NiFe] Hydrogenases  

PubMed Central

Two energy-generating hydrogenases enable the aerobic hydrogen bacterium Ralstonia eutropha (formerly Alcaligenes eutrophus) to use molecular hydrogen as the sole energy source. The complex synthesis of the nickel-iron-containing enzymes has to be efficiently regulated in response to H2, which is available in low amounts in aerobic environments. H2 sensing in R. eutropha is achieved by a hydrogenase-like protein which controls the hydrogenase gene expression in concert with a two-component regulatory system. In this study we show that the H2 sensor of R. eutropha is a cytoplasmic protein. Although capable of H2 oxidation with redox dyes as electron acceptors, the protein did not support lithoautotrophic growth in the absence of the energy-generating hydrogenases. A specifically designed overexpression system for R. eutropha provided the basis for identifying the H2 sensor as a nickel-containing regulatory protein. The data support previous results which showed that the sensor has an active site similar to that of prototypic [NiFe] hydrogenases (A. J. Pierik, M. Schmelz, O. Lenz, B. Friedrich, and S. P. J. Albracht, FEBS Lett. 438:231–235, 1998). It is demonstrated that in addition to the enzymatic activity the regulatory function of the H2 sensor is nickel dependent. The results suggest that H2 sensing requires an active [NiFe] hydrogenase, leaving the question open whether only H2 binding or subsequent H2 oxidation and electron transfer processes are necessary for signaling. The regulatory role of the H2-sensing hydrogenase of R. eutropha, which has also been investigated in other hydrogen-oxidizing bacteria, is intimately correlated with a set of typical structural features. Thus, the family of H2 sensors represents a novel subclass of [NiFe] hydrogenases denoted as the “regulatory hydrogenases.”

Kleihues, Laura; Lenz, Oliver; Bernhard, Michael; Buhrke, Thorsten; Friedrich, Barbel

2000-01-01

166

Involvement of hyp gene products in maturation of the H2-sensing [NiFe] hydrogenase of Ralstonia eutropha  

Microsoft Academic Search

The biosynthesis of (NiFe) hydrogenases is a complex process that requires the function of the Hyp proteins HypA, HypB, HypC, HypD, HypE, HypF, and HypX for assembly of the H2-activating (NiFe) site. In this study we examined the maturation of the regulatory hydrogenase (RH) of Ralstonia eutropha. The RH is a H2-sensing (NiFe) hydrogenase and is required as a constituent

THORSTEN BUHRKE; BORIS BLEIJLEVENS; SIMON P. J. ALBRACHT; BARBEL FRIEDRICH

2001-01-01

167

A 2.8 Å Fe-Fe separation in the Fe2(III/IV) intermediate, X, from Escherichia coli ribonucleotide reductase.  

PubMed

A class Ia ribonucleotide reductase (RNR) employs a ?-oxo-Fe2(III/III)/tyrosyl radical cofactor in its ? subunit to oxidize a cysteine residue ~35 Å away in its ? subunit; the resultant cysteine radical initiates substrate reduction. During self-assembly of the Escherichia coli RNR-? cofactor, reaction of the protein's Fe2(II/II) complex with O2 results in accumulation of an Fe2(III/IV) cluster, termed X, which oxidizes the adjacent tyrosine (Y122) to the radical (Y122(•)) as the cluster is converted to the ?-oxo-Fe2(III/III) product. As the first high-valent non-heme-iron enzyme complex to be identified and the key activating intermediate of class Ia RNRs, X has been the focus of intensive efforts to determine its structure. Initial characterization by extended X-ray absorption fine structure (EXAFS) spectroscopy yielded a Fe-Fe separation (d(Fe-Fe)) of 2.5 Å, which was interpreted to imply the presence of three single-atom bridges (O(2-), HO(-), and/or ?-1,1-carboxylates). This short distance has been irreconcilable with computational and synthetic models, which all have d(Fe-Fe) ? 2.7 Å. To resolve this conundrum, we revisited the EXAFS characterization of X. Assuming that samples containing increased concentrations of the intermediate would yield EXAFS data of improved quality, we applied our recently developed method of generating O2 in situ from chlorite using the enzyme chlorite dismutase to prepare X at ~2.0 mM, more than 2.5 times the concentration realized in the previous EXAFS study. The measured d(Fe-Fe) = 2.78 Å is fully consistent with computational models containing a (?-oxo)2-Fe2(III/IV) core. Correction of the d(Fe-Fe) brings the experimental data and computational models into full conformity and informs analysis of the mechanism by which X generates Y122(•). PMID:24094084

Dassama, Laura M K; Silakov, Alexey; Krest, Courtney M; Calixto, Julio C; Krebs, Carsten; Bollinger, J Martin; Green, Michael T

2013-11-13

168

Mechanism of Proton Transfer in [FeFe]-Hydrogenase from Clostridium pasteurianum*  

PubMed Central

[FeFe]-Hydrogenases are complex metalloproteins that catalyze the reversible reduction of protons to molecular hydrogen utilizing a unique diiron subcluster bridged to a [4Fe4S] subcluster. Extensive studies have concentrated on the nature and catalytic activity of the active site, yet relatively little information is available concerning the mechanism of proton transport that is required for this activity. Previously, structural characterization of [FeFe]-hydrogenase from Clostridium pasteurianum indicated a potential proton transport pathway involving four residues (Cys-299, Glu-279, Ser-319, and Glu-282) that connect the active site to the enzyme surface. Here, we demonstrate that substitution of any of these residues resulted in a drastic reduction in hydrogenase activity relative to the native enzyme, supporting the importance of these residues in catalysis. Inhibition studies of native and amino acid-substituted enzymes revealed that Zn2+ specifically blocked proton transfer by binding to Glu-282, confirming the role of this residue in the identified pathway. In addition, all four of these residues are strictly conserved, suggesting that they may form a proton transport pathway that is common to all [FeFe]-hydrogenases.

Cornish, Adam J.; Gartner, Katrin; Yang, Hui; Peters, John W.; Hegg, Eric L.

2011-01-01

169

Molecular dynamics and experimental investigation of H(2) and O(2) diffusion in [Fe]-hydrogenase.  

PubMed

The [Fe]-hydrogenase enzymes are highly efficient H(2) catalysts found in ecologically and phylogenetically diverse microorganisms, including the photosynthetic green alga, Chlamydomonas reinhardtii. Although these enzymes can occur in several forms, H(2) catalysis takes place at a unique [FeS] prosthetic group or H-cluster, located at the active site. Significant to the function of hydrogenases is how the surrounding protein structure facilitates substrate-product transfer, and protects the active site H-cluster from inactivation. To elucidate the role of protein structure in O(2) inactivation of [Fe]-hydrogenases, experimental and theoretical investigations have been performed. Molecular dynamics was used to comparatively investigate O(2) and H(2) diffusion in CpI ([Fe]-hydrogenase I from Clostridium pasteurianum). Our preliminary results suggest that H(2) diffuses more easily and freely than O(2), which is restricted to a small number of allowed pathways to and from the active site. These O(2) pathways are located in the conserved active site domain, shown experimentally to have an essential role in active site protection. PMID:15667271

Cohen, J; Kim, K; Posewitz, M; Ghirardi, M L; Schulten, K; Seibert, M; King, P

2005-02-01

170

Demonstration of hydrogenase in extracts of the homoacetate-fermenting bacterium Clostridium thermoaceticum.  

PubMed Central

Cell-free extracts of the homoacetate-fermenting bacterium Clostridium thermoaceticum were shown to catalyze the hydrogen-dependent reduction of various artificial electron acceptors. The activity of the hydrogenase was optimal at pH 8.5 to 9 and was extremely sensitive to aeration. EDTA did not significantly reduce the liability of the enzymic activity to oxidation (aeration). At 50 degrees C, when both methyl viologen and hydrogen were at saturating concentrations with respect to hydrogenase, the specific activity of cell-free extracts approximated 4 mumol of H2 oxidized per min per mg of protein; fourfold higher specific activities were obtained when benzyl viologen was utilized as an electron acceptor. Activity stains of polyacrylamide gels demonstrated the presence of a single hydrogenase band, suggesting that the catalytic activity in cell extracts was due to a single enzyme. The activity was stable for at least 32 min at 55 degrees C but was slowly inactivated at 70 degrees C. NAD, NADP, flavin adenine dinucleotide, flavin mononucleotide, and ferredoxin were not significantly reduced, but possible reduction of the particulate b-type cytochrome of C. thermoaceticum was observed. NaCl, sodium dodecyl sulfate, iodoacetamide, and CO were shown to inhibit catalysis. A kinetic study is presented, and the possible physiologic roles for hydrogenase in C. thermoaceticum ar discussed. Images

Drake, H L

1982-01-01

171

Hydrogenases in green algae: do they save the algae's life and solve our energy problems?  

Microsoft Academic Search

Green algae are the only known eukaryotes with both oxygenic photosynthesis and a hydrogen metabolism. Recent physiological and genetic discoveries indicate a close connection between these metabolic pathways. The anaerobically inducible hydA genes of algae encode a special type of highly active [Fe]-hydrogenase. Electrons from reducing equivalents generated during fermentation enter the photosynthetic electron transport chain via the plastoquinone pool.

Thomas Happe; Anja Hemschemeier; Martin Winkler; Annette Kaminski

2002-01-01

172

Theoretical 57Fe Mössbauer spectroscopy: isomer shifts of [Fe]-hydrogenase intermediates.  

PubMed

Mössbauer spectroscopy is an indispensable spectroscopic technique and analytical tool in iron coordination chemistry. The linear correlation between the electron density at the nucleus ("contact density") and experimental isomer shifts has been used to link calculated contact densities to experimental isomer shifts. Here we have investigated relativistic methods of systematically increasing sophistication, including the eXact 2-Component (X2C) Hamiltonian and a finite-nucleus model, for the calculation of isomer shifts of iron compounds. While being of similar accuracy as the full four-component treatment, X2C calculations are far more efficient. We find that effects of spin-orbit coupling can safely be neglected, leading to further speedup. Linear correlation plots using effective densities rather than contact densities versus experimental isomer shift lead to a correlation constant a = -0.294 a0(-3) mm s(-1) (PBE functional) which is close to an experimentally derived value. Isomer shifts of similar quality can thus be obtained both with and without fitting, which is not the case if one pursues a priori a non-relativistic model approach. As an application for a biologically relevant system, we have studied three recently proposed [Fe]-hydrogenase intermediates. The structures of these intermediates were extracted from QM/MM calculations using large QM regions surrounded by the full enzyme and a solvation shell of water molecules. We show that a comparison between calculated and experimentally observed isomer shifts can be used to discriminate between different intermediates, whereas calculated atomic charges do not necessarily correlate with Mössbauer isomer shifts. Detailed analysis reveals that the difference in isomer shifts between two intermediates is due to an overlap effect. PMID:24468665

Hedegård, Erik Donovan; Knecht, Stefan; Ryde, Ulf; Kongsted, Jacob; Saue, Trond

2014-03-14

173

Importance of the Protein Framework for Catalytic Activity of [FeFe]-Hydrogenases  

PubMed Central

The active center (H-cluster) of [FeFe]-hydrogenases is embedded into a hydrophobic pocket within the protein. We analyzed several amino acids, located in the vicinity of this niche, by site-directed mutagenesis of the [FeFe]-hydrogenases from Clostridium pasteurianum (CpI) and Chlamydomonas reinhardtii (CrHydA1). These amino acids are highly conserved and predicted to be involved in H-cluster coordination. Characterization of two hydrogenase variants confirmed this hypothesis. The exchange of residues CrHydA1Met415 and CrHydA1Lys228 resulted in inactive proteins, which, according to EPR and FTIR analyses, contain no intact H-cluster. However, [FeFe]-hydrogenases in which CpIMet353 (CrHydA1Met223) and CpICys299 (CrHydA1Cys169) were exchanged to leucine and serine, respectively, showed a structurally intact H-cluster with catalytic activity either absent (CpIC299S) or strongly diminished (CpIM353L). In the case of CrHydA1C169S, the H-cluster was trapped in an inactive state exhibiting g values and vibrational frequencies that resembled the Htrans state of DdH from Desulfovibrio desulfuricans. This cysteine residue, interacting with the bridge head nitrogen of the di(methyl)amine ligand, seems therefore to represent an essential contribution of the immediate protein environment to the reaction mechanism. Exchanging methionine CpIM353 (CrHydA1M223) to leucine led to a strong decrease in turnover without affecting the Km value of the electron donor. We suggest that this methionine constitutes a “fine-tuning” element of hydrogenase activity.

Knorzer, Philipp; Silakov, Alexey; Foster, Carina E.; Armstrong, Fraser A.; Lubitz, Wolfgang; Happe, Thomas

2012-01-01

174

Distribution of Hydrogenase Genes in Desulfovibrio spp. and Their Use in Identification of Species from the Oil Field Environment  

PubMed Central

The distribution of genes for [Fe], [NiFe], and [NiFeSe] hydrogenases was determined for 22 Desulfovibrio species. The genes for [NiFe] hydrogenase were present in all species, whereas those for the [Fe] and [NiFeSe] hydrogenases had a more limited distribution. Sulfate-reducing bacteria from 16S rRNA groups other than the genus Desulfovibrio (R. Devereux, M. Delaney, F. Widdel, and D. A. Stahl, J. Bacteriol. 171:6689-6695, 1989) did not react with the [NiFe] hydrogenase gene probe, which could be used to identify different Desulfovibrio species in oil field samples following growth on lactate-sulfate medium. Images

Voordouw, Gerrit; Niviere, Vincent; Ferris, F. Grant; Fedorak, Phillip M.; Westlake, Donald W. S.

1990-01-01

175

[FeFe]-hydrogenase in Yellowstone National Park: evidence for dispersal limitation and phylogenetic niche conservatism.  

PubMed

Hydrogen (H?) has an important role in the anaerobic degradation of organic carbon and is the basis for many syntrophic interactions that commonly occur in microbial communities. Little is known, however, with regard to the biotic and/or abiotic factors that control the distribution and phylogenetic diversity of organisms which produce H? in microbial communities. In this study, we examined the [FeFe]-hydrogenase gene (hydA) as a proxy for fermentative bacterial H? production along physical and chemical gradients in various geothermal springs in Yellowstone National Park (YNP), WY, USA. The distribution of hydA in YNP geothermal springs was constrained by pH to environments co-inhabited by oxygenic phototrophs and to environments predicted to have low inputs of abiotic H?. The individual HydA asssemblages from YNP springs were more closely related when compared with randomly assembled communities, which suggests ecological filtering. Model selection approaches revealed that geographic distance was the best explanatory variable to predict the phylogenetic relatedness of HydA communities. This evinces the dispersal limitation imposed by the geothermal spring environment on HydA phylogenetic diversity even at small spatial scales. pH differences between sites is the second highest ranked explanatory variable of HydA phylogenetic relatedness, which suggests that the ecology related to pH imposes strong phylogenetic niche conservatism. Collectively, these results indicate that pH has imposed strong niche conservatism on fermentative bacteria and that, within a narrow pH realm, YNP springs are dispersal limited with respect to fermentative bacterial communities. PMID:20535223

Boyd, Eric S; Hamilton, Trinity L; Spear, John R; Lavin, Matthew; Peters, John W

2010-12-01

176

A simplified method for assay of hydrogenase activities of H 2 evolution and uptake in Enterobacter aerogenes  

Microsoft Academic Search

Assay of hydrogenase activity pertaining to H2 production needs anaerobic conditions. To establish a simplified method for assay of hydrogenase activities by using intact cells of Enterobateraerogenes, different chemicals capable of enhancing the cell-wall permeability to electron mediators were examined. As a result, Triton X-100 and CTAB were found to be appropriate for H2 uptake and evolution activities of the

YunLi Ren; Xin Hui Xing; Chong Zhang; ZhongXuan Gou

2005-01-01

177

Light-driven hydrogen production by a hybrid complex of a [NiFe]-hydrogenase and the cyanobacterial photosystem I.  

PubMed

In order to generate renewable and clean fuels, increasing efforts are focused on the exploitation of photosynthetic microorganisms for the production of molecular hydrogen from water and light. In this study we engineered a 'hard-wired' protein complex consisting of a hydrogenase and photosystem I (hydrogenase-PSI complex) as a direct light-to-hydrogen conversion system. The key component was an artificial fusion protein composed of the membrane-bound [NiFe] hydrogenase from the beta-proteobacterium Ralstonia eutropha H16 and the peripheral PSI subunit PsaE of the cyanobacterium Thermosynechococcus elongatus. The resulting hydrogenase-PsaE fusion protein associated with PsaE-free PSI spontaneously, thereby forming a hydrogenase-PSI complex as confirmed by sucrose-gradient ultracentrifuge and immunoblot analysis. The hydrogenase-PSI complex displayed light-driven hydrogen production at a rate of 0.58 mumol H(2).mg chlorophyll(-1).h(-1). The complex maintained its accessibility to the native electron acceptor ferredoxin. This study provides the first example of a light-driven enzymatic reaction by an artificial complex between a redox enzyme and photosystem I and represents an important step on the way to design a photosynthetic organism that efficiently converts solar energy and water into hydrogen. PMID:16542111

Ihara, Masaki; Nishihara, Hirofumi; Yoon, Ki-Seok; Lenz, Oliver; Friedrich, Bärbel; Nakamoto, Hitoshi; Kojima, Kouji; Honma, Daisuke; Kamachi, Toshiaki; Okura, Ichiro

2006-01-01

178

The effect of sulfur compounds on H 2 evolution\\/consumption reactions, mediated by various hydrogenases, in the purple sulfur bacterium, Thiocapsa roseopersicina  

Microsoft Academic Search

The influence of reduced sulfur compounds (including stored S0) on H2 evolution\\/consumption reactions in the purple sulfur bacterium, Thiocapsa roseopersicina BBS, was studied using mutants containing only one of the three known [NiFe] hydrogenase enzymes: Hox, Hup or Hyn. The observed\\u000a effects depended on the kind of hydrogenase involved. The mutant harbouring Hox hydrogenase was able to use S2O32?, SO32?,

Tatyana V. Laurinavichene; Gábor Rákhely; Kornél L. Kovács; Anatoly A. Tsygankov

2007-01-01

179

Characterization of the Hydrogen-Deuterium Exchange Activities of the Energy-Transducing HupSL Hydrogenase and H2Signaling HupUV Hydrogenase in Rhodobacter capsulatus  

Microsoft Academic Search

Rhodobacter capsulatus synthesizes two homologous protein complexes capable of activating molecular H2 ,a membrane-bound (NiFe) hydrogenase (HupSL) linked to the respiratory chain, and an H2 sensor encoded by the hupUV genes. The activities of hydrogen-deuterium (H-D) exchange catalyzed by the hupSL-encoded and the hupUV-encoded enzymes in the presence of D2 and H2O were studied comparatively. Whereas HupSL is in the

PAULETTE M. VIGNAIS; BERNARD DIMON; NIKOLAY A. ZORIN; MASAMITSU TOMIYAMA; ANNETTE COLBEAU

2000-01-01

180

Isolation, purification and characterization of the hydrogen evolution promoting factor of hydrogenase of Spirulina platensis  

NASA Astrophysics Data System (ADS)

A component (s-factor) with obvious promoting effect on hydrogen evolution of hydrogenase has been isolated and extracted from a cell-free preparation of Spirulina platensis. The effect of the s-factor in the reaction system is similar to that of Na2S2O4, but is coupled with light. The s-factor has the maximum absorption peak at 620 nm in the oxidized state, at 590 nm in the reduced state. The partially purified s-factor showed two bands by SDS-PAGE and is distinctly different from phycocyanin, which has no change of oxidized state and reduced state absorption spectra, and also has no promoting effect on hydrogenase of Spirulina platensis under the light.

Gu, Tian-Qing; Zhang, Hui-Miao; Sun, Shi-Hua

1996-03-01

181

Improved hydrogen production by uptake hydrogenase deficient mutant strain of Rhodobacter sphaeroides O.U.001  

Microsoft Academic Search

Rhodobacter sphaeroides O.U.001 is a purple non-sulfur bacterium producing hydrogen under photoheterotrophic conditions. Hydrogen is produced by Mo-nitrogenase enzyme and substantial amount of H2 is reoxidized by a membrane-bound uptake hydrogenase in the wild type strain. To improve the hydrogen producing capacity of the cells, a suicide vector containing a gentamicin cassette in the hupSL genes was introduced into R.

Gökhan Kars; Ufuk Gündüz; Gabor Rakhely; Meral Yücel; ?nci Ero?lu; Kornel L. Kovacs

2008-01-01

182

An FNR-Type Regulator Controls the Anaerobic Expression of Hyn Hydrogenase in Thiocapsa roseopersicina  

Microsoft Academic Search

The purple sulfur photosynthetic bacterium Thiocapsa roseopersicina BBS contains a heat-stable membrane- associated hydrogenase encoded by the hyn operon. Expression from the hyn operon regulatory region is up-regulated under anaerobic conditions. cis elements were mapped between positions 602 and 514 upstream from the hynS gene. Within this region two sequences that resemble DNA sites for FNR were recognized. The gene

Akos T. Kovacs; Gabor Rakhely; Douglas F. Browning; Andras Fulop; Gergely Maroti; Stephen J. W. Busby; Kornel L. Kovacs

2005-01-01

183

Reversible Electrocatalytic Production and Oxidation of Hydrogen at Low Overpotentials by a Functional Hydrogenase Mimic  

SciTech Connect

A new bis(diphosphine) nickel(II) complex, [Ni(PPh2NR2)2](BF4)2, 1, (R = CH2CH2OCH3) is described. A {Delta}G{sup o} of 0.84 kcal/mol{sup -1} for hydrogen addition for this complex was calculated from the experimentally determined equilibrium constant. This complex displays reversible electrocatalytic activity for hydrogen production and oxidation at low overpotentials, a characteristic most commonly associated with hydrogenase enzymes.

Smith, Stuart E.; Yang, Jenny Y.; DuBois, Daniel L.; Bullock, Morris

2012-03-26

184

Studies on the Iron-Sulfur clusters of hydrogenase, sulfite reductase, nitrogenase and the prismane protein  

Microsoft Academic Search

Iron-sulfur clusters are present in a large number of proteins. Sofar structures of four types of protein-bound iron-sulfur clusters have been determined by X-ray diffraction: rubredoxin-like, [2Fe-2S], [3Fe-4S] and [4Fe-4S] centers. The presence of any of these clusters in a protein can be predicted by comparison of spectroscopic properties. However a number of multiple-electron transferring enzymes, like the Fe-only hydrogenase,

A. J. Pierik

1993-01-01

185

Salmonella enterica Serovar Typhimurium NiFe Uptake-Type Hydrogenases Are Differentially Expressed In Vivo  

Microsoft Academic Search

Salmonella enterica serovar Typhimurium, a common enteric pathogen, possesses three NiFe uptake-type hydro- genases. The results from mouse infection studies suggest that the H2 oxidation capacity provided by these hydrogenases is important for virulence. Since the three enzymes are similar in structure and function, it may be expected that they are utilized under different locations and times during an infection.

Andrea L. Zbell; Susan E. Maier; Robert J. Maier

2008-01-01

186

Two membrane anchors of Wolinella succinogenes hydrogenase and their function in fumarate and polysulfide respiration  

Microsoft Academic Search

Wolinella succinogenes can grow by anaerobic respiration with fumarate or polysulfide as the terminal electron acceptor, and H2 or formate as the electron donor. A ?hydABC mutant lacking the hydrogenase structural genes did not grow with H2 and either fumarate or polysulfide. In contrast to the wild-type strain, the mutant grown with fumarate and with formate\\u000a instead of H2 did

Roland Gross; Jörg Simon; Friedbert Theis; Achim Kröger

1998-01-01

187

Reversible [4Fe-3S] cluster morphing in an O(2)-tolerant [NiFe] hydrogenase.  

PubMed

Hydrogenases catalyze the reversible oxidation of H(2) into protons and electrons and are usually readily inactivated by O(2). However, a subgroup of the [NiFe] hydrogenases, including the membrane-bound [NiFe] hydrogenase from Ralstonia eutropha, has evolved remarkable tolerance toward O(2) that enables their host organisms to utilize H(2) as an energy source at high O(2). This feature is crucially based on a unique six cysteine-coordinated [4Fe-3S] cluster located close to the catalytic center, whose properties were investigated in this study using a multidisciplinary approach. The [4Fe-3S] cluster undergoes redox-dependent reversible transformations, namely iron swapping between a sulfide and a peptide amide N. Moreover, our investigations unraveled the redox-dependent and reversible occurence of an oxygen ligand located at a different iron. This ligand is hydrogen bonded to a conserved histidine that is essential for H(2) oxidation at high O(2). We propose that these transformations, reminiscent of those of the P-cluster of nitrogenase, enable the consecutive transfer of two electrons within a physiological potential range. PMID:24705592

Frielingsdorf, Stefan; Fritsch, Johannes; Schmidt, Andrea; Hammer, Mathias; Löwenstein, Julia; Siebert, Elisabeth; Pelmenschikov, Vladimir; Jaenicke, Tina; Kalms, Jacqueline; Rippers, Yvonne; Lendzian, Friedhelm; Zebger, Ingo; Teutloff, Christian; Kaupp, Martin; Bittl, Robert; Hildebrandt, Peter; Friedrich, Bärbel; Lenz, Oliver; Scheerer, Patrick

2014-05-01

188

Studies on thermophilic sulfate-reducing bacteria. II. Hydrogenase activity of Clostridium nigrificans.  

PubMed

Akagi, J. M. (Western Reserve University, Cleveland, Ohio) and L. Leon Campbell. Studies on thermophilic sulfate-reducing bacteria. II. Hydrogenase activity of Clostridium nigrificans. J. Bacteriol. 82:927-932. 1961.-The hydrogenase of Clostridium nigrificans has been found to be associated with the cell-free particulate fraction which can be sedimented at 105,000 x g in 1 hr. The specific activity of this fraction was increased 2 to 3 fold over that of the crude extract. It was not found possible to liberate the enzyme from the particulate fraction by methods of enzymatic digestion, chemical extraction, or physical disruption. The optimum temperature for H(2) utilization using benzyl viologen as an electron acceptor was found to be 55 C, and the optimum pH range was 7 to 8. Employing metal complexing agents it was found that the enzyme required Fe(++) ions for H(2) utilization. In contrast, Fe(++) ions were not required to catalyze the evolution of H(2) from reduced methyl viologen. The role of Fe(++) ions in the hydrogenase activity of this organism is discussed. PMID:13859876

AKAGI, J M; CAMPBELL, L L

1961-12-01

189

[NiFe] hydrogenase from Alteromonas macleodii with unusual stability in the presence of oxygen and high temperature.  

PubMed

Hydrogenases are enzymes involved in the bioproduction of hydrogen, a clean alternative energy source whose combustion generates water as the only end product. In this article we identified and characterized a [NiFe] hydrogenase from the marine bacterium Alteromonas macleodii "deep ecotype" with unusual stability toward oxygen and high temperature. The A. macleodii hydrogenase (HynSL) can catalyze both H(2) evolution and H(2) uptake reactions. HynSL was expressed in A. macleodii under aerobic conditions and reached the maximum activity when the cells entered the late exponential phase. The higher level of hydrogenase activity was accompanied by a greater abundance of the HynSL protein in the late-log or stationary phase. The addition of nickel to the growth medium significantly enhanced the hydrogenase activity. Ni treatment affected the level of the protein, but not the mRNA, indicating that the effect of Ni was exerted at the posttranscriptional level. Hydrogenase activity was distributed ?30% in the membrane fraction and ?70% in the cytoplasmic fraction. Thus, HynSL appears to be loosely membrane-bound. Partially purified A. macleodii hydrogenase demonstrated extraordinary stability. It retained 84% of its activity after exposure to 80°C for 2 h. After exposure to air for 45 days at 4°C, it retained nearly 100% of its activity when assayed under anaerobic conditions. Its catalytic activity in the presence of O(2) was evaluated by the hydrogen-deuterium (H-D) exchange assay. In 1% O(2), 20.4% of its H-D exchange activity was retained. The great stability of HynSL makes it a potential candidate for biotechnological applications. PMID:21257809

Vargas, Walter A; Weyman, Philip D; Tong, Yingkai; Smith, Hamilton O; Xu, Qing

2011-03-01

190

Inactivation of Hydrogenase in Cell-free Extracts and Whole Cells of Chlamydomonas reinhardi by Oxygen 1  

PubMed Central

O2 irreversibly inactivates hydrogenase from Chlamydomonas reinhardi. The mechanism for the inactivation involves the reaction of one molecule of hydrogenase with one molecule of O2 (or two oxygen atoms) in the transition complex of the rate-limiting step. The second order rate constant for this reaction is 190 atmospheres?1 minute?1 (1.4 × 105 molar?1 minute?1). At levels above 0.01 atmosphere O2, the increased numbers of O2 molecules may compete for the site of inactivation hindering the proper orientation for inactivation of any one O2 molecule and resulting in lowered rates of inactivation. CO is a reversible inhibitor of hydrogenase acting competitively against H2. The Ki for CO is 0.0010 atmosphere. CO antagonizes O2 inactivation. In a period when complete inactivation by O2 would usually occur, the presence of CO greatly reduces the inactivation rate. After 3 hours of adaptation in whole cells, the presence of H2 lowers the rate of deadaptation of hydrogenase. Inasmuch as H2 promotes increased O2 uptake the cellular concentration of O2 is likely to be lower. After 48 hours of adaptation O2 uptake is reduced even when H2 is present and the pattern of deadaptation under O2 with and without H2 and CO is qualitatively the same as observed for the inactivation of cell-free hydrogenase. The mechanism of inactivation of cell-free hydrogenase by O2 may be the same as the mechanism for loss of hydrogenase during deadaptation in whole algal cells.

Erbes, David L.; King, Dan; Gibbs, Martin

1979-01-01

191

Halotolerant and Resistant to High pH Hydrogenase from Haloalkaliphilic Sulfate-Reducing Bacterium Desulfonatronum thiodismutans  

NASA Technical Reports Server (NTRS)

Hydrogenase is the key enzyme of energetic metabolism in cells, it catalyzing the converse reaction of hydrogen oxidation and responsible for consumption and excretion of hydrogen in bacteria. Hydrogenases are proteins containing either Nickel and Iron, or the only Iron in theirs active center. Hydrogenases have been found in many microorganisms, such as Methanogenic, acetogenic, nitrogen-fixing, photosynthetic and sulfate-reducing bacteria that could utilize the hydrogen as energy source or use it as electron sink. Hydrogenases are subject for wide physiological, biochemical, physicochemical and genetic studies due to theirs abilities produce the molecular hydrogen as alternative source of pure energy. Notwithstanding on enough large quantity of works that deal with intracellular and extrasellular enzymes of halophilic bacteria, the data about hydrogenases and theirs functions of salts practically are absent. The study of hydrogenase in cell-free extracts of extremely halophilic eubacterium Acetohalobium mabaticum showed dramatic increasing activity of the enzyme at high concentrations of NaCl and KCI (close to saturated solution). Here we present the data of free-cells extracted hydrogenase from new haloalkaliphilic sulfate-reducing bacterium Desulfonatronum thiodismutans, which grow on highly miniralized carbonate-bicarbonate medium in salinity range 1 to 7 % and at pH 7.8 - 10.5. Studied enzyme was active in Concentration range from 0 to 4.3 M NaCl with optimum at 1.0 M NaCl. At 1.0 M NaCl the enzyme activity was increased on 20 %, but with changing concentration from 2.1 M to 3.4 M the activity decreased and was kept on constant level. NaHCO3 inhibited hydrogenase activity on more then 30 %. The maximum of enzyme activity was observed at pH 9.5 with limits 7.5 and 11.5 that practically equal to pH optimum of bacterial growth. Therefore the hydrogenase of Desulfanatronum thiodismutans is tolerant to high concentrations of sodium salts and it also resistant to high pH that make it the unique subject for different biochemical research and detects the possibility for biotechnological application.

Detkova, Ekaterina N.; Pikuta, Elena V.; Hoover, Richard B.

2004-01-01

192

Transmembrane pH of Clostridium acetobutylicum is inverted (more acidic inside) when the in vivo activity of hydrogenase is decreased.  

PubMed Central

Evidence is reported here that alkalinization of Clostridium acetobutylicum cytoplasm involves hydrogenase activity. A decrease of in vivo hydrogenase activity is accompanied by intracellular accumulation of protons leading to a negative (interior acidic) pH gradient. However, the organism is able to maintain a constant proton motive force by interconverting chemical and electrical potentials.

Girbal, L; Vasconcelos, I; Soucaille, P

1994-01-01

193

The Hydrogenase Chip: a tiling oligonucleotide DNA microarray technique for characterizing hydrogen-producing and -consuming microbes in microbial communities  

PubMed Central

We developed a broad-ranging method for identifying key hydrogen-producing and consuming microorganisms through analysis of hydrogenase gene content and expression in complex anaerobic microbial communities. The method is based on a tiling hydrogenase gene oligonucleotide DNA microarray (Hydrogenase Chip), which implements a high number of probes per gene by tiling probe sequences across genes of interest at 1.67 × –2 × coverage. This design favors the avoidance of false positive gene identification in samples of DNA or RNA extracted from complex microbial communities. We applied this technique to interrogate interspecies hydrogen transfer in complex communities in (i) lab-scale reductive dehalogenating microcosms enabling us to delineate key H2-consuming microorganisms, and (ii) hydrogen-generating microbial mats where we found evidence for significant H2 production by cyanobacteria. Independent quantitative PCR analysis on selected hydrogenase genes showed that this Hydrogenase Chip technique is semiquantitative. We also determined that as microbial community complexity increases, specificity must be traded for sensitivity in analyzing data from tiling DNA microarrays.

Marshall, Ian PG; Berggren, Dusty RV; Azizian, Mohammad F; Burow, Luke C; Semprini, Lewis; Spormann, Alfred M

2012-01-01

194

Genetic diversity and expression of the [NiFe] hydrogenase large-subunit gene of Desulfovibrio spp. in environmental samples.  

PubMed Central

The genetic diversity and expression of the [NiFe] hydrogenase large-subunit gene of Desulfovibrio spp. in environmental samples were determined in order to show in parallel the existing and active members of Desulfovibrio populations. DNA and total RNA were extracted from different anaerobic bioreactor samples; RNA was transcribed into cDNA. Subsequently, PCR was performed to amplify a ca.-440-bp fragment of the [NiFe] hydrogenase large-subunit gene and its mRNA. Denaturing gradient gel electrophoresis analysis was used to separate the PCR products according to their sequence and thereby to visualize the individual community members. Desulfovibrio strains corresponding to amplified [NiFe] hydrogenase transcripts were regarded as metabolically active, because in pure cultures transcripts were detectable in exponentially growing cells but not in cultures in the stationary phase. DNA sequencing and comparative sequence analysis were used to identify the detected organisms on the basis of their [NiFe] hydrogenase sequences. The genes of characterized Desulfovibrio spp. showed a considerable extent of divergence (ca. 30%), whereas sequences obtained from bacterial populations of the bioreactors showed a low level of variation and indicated the coexistence of closely related strains probably belonging to the species Desulfovibrio sulfodismutans. Under methanogenic conditions, all detected populations were active; under denitrifying conditions, no [NiFe] hydrogenase mRNA was visible. Changes in activity and composition of Desulfovibrio populations caused by changes in the environmental conditions could be monitored by using the approach described in this study.

Wawer, C; Jetten, M S; Muyzer, G

1997-01-01

195

Novel [NiFe]- and [FeFe]-Hydrogenase Gene Transcripts Indicative of Active Facultative Aerobes and Obligate Anaerobes in Earthworm Gut Contents?†  

PubMed Central

The concomitant occurrence of molecular hydrogen (H2) and organic acids along the alimentary canal of the earthworm is indicative of ongoing fermentation during gut passage. Fermentative H2 production is catalyzed by [FeFe]-hydrogenases and group 4 [NiFe]-hydrogenases in obligate anaerobes (e.g., Clostridiales) and facultative aerobes (e.g., Enterobacteriaceae), respectively, functional groups that might respond differently to contrasting redox conditions. Thus, the objectives of this study were to assess the redox potentials of the alimentary canal of Lumbricus terrestris and analyze the hydrogenase transcript diversities of H2 producers in glucose-supplemented gut content microcosms. Although redox potentials in the core of the alimentary canal were variable on an individual worm basis, average redox potentials were similar. The lowest redox potentials occurred in the foregut and midgut regions, averaging 40 and 110 mV, respectively. Correlation plots between hydrogenase amino acid sequences and 16S rRNA gene sequences indicated that closely related hydrogenases belonged to closely related taxa, whereas distantly related hydrogenases did not necessarily belong to distantly related taxa. Of 178 [FeFe]-hydrogenase gene transcripts, 177 clustered in 12 Clostridiales-affiliated operational taxonomic units, the majority of which were indicative of heretofore unknown hydrogenases. Of 86 group 4 [NiFe]-hydrogenase gene transcripts, 79% and 21% were affiliated with organisms in the Enterobacteriaceae and Aeromonadaceae, respectively. The collective results (i) suggest that fermenters must cope with variable and moderately oxidative redox conditions along the alimentary canal, (ii) demonstrate that heretofore undetected hydrogenases are present in the earthworm gut, and (iii) corroborate previous findings implicating Clostridiaceae and Enterobacteriaceae as active fermentative taxa in earthworm gut content.

Schmidt, Oliver; Wust, Pia K.; Hellmuth, Susanne; Borst, Katharina; Horn, Marcus A.; Drake, Harold L.

2011-01-01

196

Hydrogen Production by Termite Gut Protists: Characterization of Iron Hydrogenases of Parabasalian Symbionts of the Termite Coptotermes formosanus? †  

PubMed Central

Cellulolytic flagellated protists in the guts of termites produce molecular hydrogen (H2) that is emitted by the termites; however, little is known about the physiology and biochemistry of H2 production from cellulose in the gut symbiotic protists due to their formidable unculturability. In order to understand the molecular basis for H2 production, we here identified two genes encoding proteins homologous to iron-only hydrogenases (Fe hydrogenases) in Pseudotrichonympha grassii, a large cellulolytic symbiont in the phylum Parabasalia, in the gut of the termite Coptotermes formosanus. The two Fe hydrogenases were phylogenetically distinct and had different N-terminal accessory domains. The long-form protein represented a phylogenetic lineage unique among eukaryotic Fe hydrogenases, whereas the short form was monophyletic with those of other parabasalids. Active recombinant enzyme forms of these two Fe hydrogenases were successfully obtained without the specific auxiliary maturases. Although they differed in their extent of specific activity and optimal pH, both enzymes preferentially catalyzed H2 evolution rather than H2 uptake. H2 evolution, at least that associated with the short-form enzyme, was still active even under high hydrogen partial pressure. H2 evolution activity was detected in the hydrogenosomal fraction of P. grassii cells; however, the vigorous H2 uptake activity of the endosymbiotic bacteria compensated for the strong H2 evolution activity of the host protists. The results suggest that termite gut symbionts are a rich reservoir of novel Fe hydrogenases whose properties are adapted to the gut environment and that the potential of H2 production in termite guts has been largely underestimated.

Inoue, Jun-Ichi; Saita, Kanako; Kudo, Toshiaki; Ui, Sadaharu; Ohkuma, Moriya

2007-01-01

197

Hydrogen production by termite gut protists: characterization of iron hydrogenases of Parabasalian symbionts of the termite Coptotermes formosanus.  

PubMed

Cellulolytic flagellated protists in the guts of termites produce molecular hydrogen (H(2)) that is emitted by the termites; however, little is known about the physiology and biochemistry of H(2) production from cellulose in the gut symbiotic protists due to their formidable unculturability. In order to understand the molecular basis for H(2) production, we here identified two genes encoding proteins homologous to iron-only hydrogenases (Fe hydrogenases) in Pseudotrichonympha grassii, a large cellulolytic symbiont in the phylum Parabasalia, in the gut of the termite Coptotermes formosanus. The two Fe hydrogenases were phylogenetically distinct and had different N-terminal accessory domains. The long-form protein represented a phylogenetic lineage unique among eukaryotic Fe hydrogenases, whereas the short form was monophyletic with those of other parabasalids. Active recombinant enzyme forms of these two Fe hydrogenases were successfully obtained without the specific auxiliary maturases. Although they differed in their extent of specific activity and optimal pH, both enzymes preferentially catalyzed H(2) evolution rather than H(2) uptake. H(2) evolution, at least that associated with the short-form enzyme, was still active even under high hydrogen partial pressure. H(2) evolution activity was detected in the hydrogenosomal fraction of P. grassii cells; however, the vigorous H(2) uptake activity of the endosymbiotic bacteria compensated for the strong H(2) evolution activity of the host protists. The results suggest that termite gut symbionts are a rich reservoir of novel Fe hydrogenases whose properties are adapted to the gut environment and that the potential of H(2) production in termite guts has been largely underestimated. PMID:17766465

Inoue, Jun-Ichi; Saita, Kanako; Kudo, Toshiaki; Ui, Sadaharu; Ohkuma, Moriya

2007-10-01

198

Purification and properties of the membrane-bound by hydrogenase from Desulfovibrio desulfuricans.  

PubMed Central

The membrane-bound hydrogenase from the anaerobic sulphate-reducing bacterium Desulfovibrio desulfuricans (Norway strain) has been purified to homogeneity, with an overall 80-fold purification and a specific activity of 70 mumol of H2 evolved/min per mg of protein. The hydrogenase had a relative molecular mass of 58 000 as determined by gel filtration and was estimated to contain six iron atoms and six acid-labile sulphur groups per molecule. The absorption spectrum of the enzyme was characteristic of an iron-sulphur protein. The E400 and E280 were 28 500 and 109 000 M-1.cm-1 respectively. The e.s.r. of the oxidized protein indicated the presence of [4Fe-4S]3+ or [3Fe-3S]3+, and another paramagnetic centre, probably Ni(III). The hydrogenase was inhibited by heavy-metal salts, carbon monoxide and high ionic strength. However, it was resistant to inhibition by thiol-blocking and metal-complexing reagents. N-Bromosuccinimide totally inhibited the enzyme activity at low concentrations. The enzyme was stable to O2 over long periods and to high temperatures. It catalyses both H2-evolution and H2-uptake with a variety of artificial electron carriers. D. desulfuricans cytochrome C3, its natural electron carrier, had a high affinity for the enzyme (Km = 2 microns). Rate enhancement was observed when cytochrome C3 was added to Methyl Viologen in the H2-evolution assay. The pH optimum for H2-evolution was 6.5.

Lalla-Maharajh, W V; Hall, D O; Cammack, R; Rao, K K; Le Gall, J

1983-01-01

199

The mechanism of activation of a [NiFe]-hydrogenase by electrons, hydrogen, and carbon monoxide.  

PubMed

Activation of the oxidized inactive state (termed Unready or Ni(u)) of the [NiFe]-hydrogenase from Allochromatium vinosum requires removal of an unidentified oxidizing entity [O], produced by partial reduction of O(2). Dynamic electrochemical kinetic studies, subjecting enzyme molecules on an electrode to sequences of potential steps and gas injections, establish the order of events in an otherwise complex sequence of reactions that involves more than one intermediate retaining [O] or its redox equivalent; fast and reversible electron transfer precedes the rate-determining step which is followed by a reaction with H(2), or the inhibitor CO, that renders the reductive activation process irreversible. PMID:15869280

Lamle, Sophie E; Albracht, Simon P J; Armstrong, Fraser A

2005-05-11

200

Comprehensive Phylogenetic Diversity of [FeFe]-Hydrogenase Genes in Termite Gut Microbiota  

PubMed Central

Phylogenetic diversity of [FeFe]-hydrogenase (HydA) in termite guts was assessed by pyrosequencing PCR amplicons obtained using newly designed primers. Of 8,066 reads, 776 hydA phylotypes, defined with 97% nucleotide sequence identity, were recovered from the gut homogenates of three termite species, Hodotermopsis sjoestedti, Reticulitermes speratus, and Nasutitermes takasagoensis. The phylotype coverage was 92–98%, and the majority shared only low identity with database sequences. It was estimated that 194–745 hydA phylotypes existed in the gut of each termite species. Our results demonstrate that hydA gene diversity in the termite gut microbiota is much higher than previously estimated.

Zheng, Hao; Bodington, Dylan; Zhang, Chong; Miyanaga, Kazuhiko; Tanji, Yasunori; Hongoh, Yuichi; Xing, Xin-Hui

2013-01-01

201

Analysis of [FeFe]-hydrogenase genes for the elucidation of a hydrogen-producing bacterial community in paddy field soil.  

PubMed

Hydrogen (H2) is one of the most important intermediates in the anaerobic decomposition of organic matter. Although the microorganisms consuming H2 in anaerobic environments have been well documented, those producing H2 are not well known. In this study, we elucidated potential members of H2 -producing bacteria in a paddy field soil using clone library analysis of [FeFe]-hydrogenase genes. The [FeFe]-hydrogenase is an enzyme involved in H2 metabolism, especially in H2 production. A suitable primer set was selected based on the preliminary clone library analysis performed using three primer sets designed for the [FeFe]-hydrogenase genes. Soil collected in flooded and drained periods was used to examine the dominant [FeFe]-hydrogenase genes in the paddy soil bacteria. In total, 115 and 108 clones were analyzed from the flooded and drained paddy field soils, respectively. Homology and phylogenetic analysis of the clones showed the presence of diverse [FeFe]-hydrogenase genes mainly related to Firmicutes, Deltaproteobacteria, and Chloroflexi. Predominance of Deltaproteobacteria and Chloroflexi suggests that the distinct bacterial community possessed [FeFe]-hydrogenase genes in the paddy field soil. Our study revealed the potential members of H2 -producing bacteria in the paddy field soil based on their genetic diversity and the distinctiveness of the [FeFe]-hydrogenase genes. PMID:24261851

Baba, Ryuko; Kimura, Makoto; Asakawa, Susumu; Watanabe, Takeshi

2014-01-01

202

The AbrB2 Autorepressor, Expressed from an Atypical Promoter, Represses the Hydrogenase Operon To Regulate Hydrogen Production in Synechocystis Strain PCC6803  

PubMed Central

We have thoroughly investigated the abrB2 gene (sll0822) encoding an AbrB-like regulator in the wild-type strain of the model cyanobacterium Synechocystis strain PCC6803. We report that abrB2 is expressed from an active but atypical promoter that possesses an extended ?10 element (TGTAATAT) that compensates for the absence of a ?35 box. Strengthening the biological significance of these data, we found that the occurrence of an extended ?10 promoter box and the absence of a ?35 element are two well-conserved features in abrB2 genes from other cyanobacteria. We also show that AbrB2 is an autorepressor that is dispensable to cell growth under standard laboratory conditions. Furthermore, we demonstrate that AbrB2 also represses the hox operon, which encodes the Ni-Fe hydrogenase of biotechnological interest, and that the hox operon is weakly expressed even though it possesses the two sequences resembling canonical ?10 and ?35 promoter boxes. In both the AbrB2-repressed promoters of the abrB2 gene and the hox operon, we found a repeated DNA motif [TT-(N5)-AAC], which could be involved in AbrB2 repression. Supporting this hypothesis, we found that a TT-to-GG mutation of one of these elements increased the activity of the abrB2 promoter. We think that our abrB2-deleted mutant with increased expression of the hox operon and hydrogenase activity, together with the reporter plasmids we constructed to analyze the abrB2 gene and the hox operon, will serve as useful tools to decipher the function and the regulation of hydrogen production in Synechocystis.

Dutheil, Jeremy; Saenkham, Panatda; Sakr, Samer; Leplat, Christophe; Ortega-Ramos, Marcia; Bottin, Herve; Cournac, Laurent; Cassier-Chauvat, Corinne

2012-01-01

203

Anaerobic regulation of the hydrogenase 1 (hya) operon of Escherichia coli.  

PubMed Central

Using a transcriptional fusion to the lacZ gene, we have analyzed the anaerobic regulation of the hydrogenase 1 (hya) operon in response to different anaerobic growth conditions and to mutations in regulatory genes. We found that the transcription of the hya operon was induced when the growth condition was changed from aerobic to anaerobic and that this induction was independent of Fnr but dependent on regulators AppY and ArcA. Furthermore, we found that the transcription of the hya operon was not regulated by the cyclic AMP-cyclic AMP receptor protein complex. Investigation of the effects of different anaerobic growth conditions on the expression of the hya operon showed that expression was induced by formate and repressed by nitrate. Formate induction was not mediated by the fhlA gene product, and nitrate repression was not mediated by the narL gene product. We found a high level of anaerobic expression of the hya operon in glucose medium supplemented with formate and in glycerol medium supplemented with fumarate, suggesting that hydrogenase isoenzyme 1 has a function during both fermentative growth and anaerobic respiration.

Br?ndsted, L; Atlung, T

1994-01-01

204

HypF, a carbamoyl phosphate-converting enzyme involved in [NiFe] hydrogenase maturation.  

PubMed

HypF has been characterized as an auxiliary protein whose function is required for the synthesis of active [NiFe] hydrogenases in Escherichia coli and other bacteria. To approach the functional analysis, in particular the involvement in CO/CN ligand synthesis, HypF was purified from an overproducing strain to apparent homogeneity. The purified protein behaves as a monomer on size exclusion chromatography, and it is devoid of nickel or other cofactors. As indicated by the existence of a sequence motif also present in several O-carbamoyltransferases, HypF interacts with carbamoyl phosphate as a substrate and releases inorganic phosphate. In addition, HypF also possesses ATP cleavage activity that gives rise to AMP and pyrophosphate as products and that is dependent on the presence of carbamoyl phosphate. This and the fact that HypF catalyzes a carbamoyl phosphate-dependent pyrophosphate ATP exchange reaction suggest that the protein catalyzes activation of carbamoyl phosphate. Extensive mutagenesis of the putative functional motifs deduced from the derived amino acid sequence showed a full correlation of the resulting variants between their activity in hydrogenase maturation and the in vitro reactivity with carbamoyl phosphate. The results are discussed in terms of the involvement of HypF in the conversion of carbamoyl phosphate to the CN ligand. PMID:12377778

Paschos, Athanasios; Bauer, Anette; Zimmermann, Anja; Zehelein, Eva; Böck, August

2002-12-20

205

How oxygen reacts with oxygen-tolerant respiratory [NiFe]-hydrogenases.  

PubMed

An oxygen-tolerant respiratory [NiFe]-hydrogenase is proven to be a four-electron hydrogen/oxygen oxidoreductase, catalyzing the reaction 2 H2 + O2 = 2 H2O, equivalent to hydrogen combustion, over a sustained period without inactivating. At least 86% of the H2O produced by Escherichia coli hydrogenase-1 exposed to a mixture of 90% H2 and 10% O2 is accounted for by a direct four-electron pathway, whereas up to 14% arises from slower side reactions proceeding via superoxide and hydrogen peroxide. The direct pathway is assigned to O2 reduction at the [NiFe] active site, whereas the side reactions are an unavoidable consequence of the presence of low-potential relay centers that release electrons derived from H2 oxidation. The oxidase activity is too slow to be useful in removing O2 from the bacterial periplasm; instead, the four-electron reduction of molecular oxygen to harmless water ensures that the active site survives to catalyze sustained hydrogen oxidation. PMID:24715724

Wulff, Philip; Day, Christopher C; Sargent, Frank; Armstrong, Fraser A

2014-05-01

206

Applications of bacterial hydrogenases in waste decontamination, manufacture of novel bionanocatalysts and in sustainable energy.  

PubMed

Bacterial hydrogenases have been harnessed to the removal of heavy metals from solution by reduction to less soluble metal species. For Pd(II), its bioreduction results in the deposition of cell-bound Pd(0)-nanoparticles that are ferromagnetic and have a high catalytic activity. Hydrogenases can also be used synthetically in the production of hydrogen from sugary wastes through breakdown of formate produced by fermentation. The Bio-H(2) produced can be used to power an electrical device using a fuel cell to provide clean electricity. Production of hydrogen from confectionery wastes by one organism (Escherichia coli) can be used as the electron donor for the production of Bio-Pd(0) from soluble Pd(II) by a second organism. The resulting Bio-Pd(0) can then be used as a bioinorganic catalyst in the remediation of Cr(VI)-contaminated solutions or polychlorinated biphenyls at the expense of Bio-H(2), as a hydrogenation catalyst for industry or as a component of a fuel cell electrode. PMID:15667270

Macaskie, L E; Baxter-Plant, V S; Creamer, N J; Humphries, A C; Mikheenko, I P; Mikheenko, P M; Penfold, D W; Yong, P

2005-02-01

207

GOLLUM [FeFe]-hydrogenase-like proteins are essential for plant development in normoxic conditions and modulate energy metabolism.  

PubMed

[FeFe]-hydrogenase-like genes encode [Fe4 S4]-containing proteins that are ubiquitous in eukaryotic cells. In humans, iron-only hydrogenase-like protein 1 (IOP1) represses hypoxia inducible factor-1? subunit (HIF1-?) at normal atmospheric partial O2 pressure (normoxia, 21 kPa O2). In yeasts, the nar1 mutant cannot grow at 21 kPa O2, but can develop at a lower O2 pressure (2 kPa O2). We show here that plant [FeFe]-hydrogenase-like GOLLUM genes are essential for plant development and cell cycle progression. The mutant phenotypes of these plants are seen in normoxic conditions, but not under conditions of mild hypoxia (5 kPa O2). Transcriptomic and metabolomic experiments showed that the mutation enhances the expression of some hypoxia-induced genes under normal atmospheric O2 conditions and changes the cellular content of metabolites related to energy metabolism. In conclusion, [FeFe]-hydrogenase-like proteins play a central role in eukaryotes including the adaptation of plants to the ambient O2 partial pressure. PMID:23639116

Mondy, Samuel; Lenglet, Aurore; Cosson, Viviane; Pelletier, Sandra; Pateyron, Stéphanie; Gilard, Françoise; Scholte, Marije; Brocard, Lysiane; Couzigou, Jean-Malo; Tcherkez, Guillaume; Péan, Michel; Ratet, Pascal

2014-01-01

208

Expression of Shewanella oneidensis MR-1 [FeFe]-Hydrogenase Genes in Anabaena sp. Strain PCC 7120  

PubMed Central

H2 generated from renewable resources holds promise as an environmentally innocuous fuel that releases only energy and water when consumed. In biotechnology, photoautotrophic oxygenic diazotrophs could produce H2 from water and sunlight using the cells' endogenous nitrogenases. However, nitrogenases have low turnover numbers and require large amounts of ATP. [FeFe]-hydrogenases found in other organisms can have 1,000-fold higher turnover numbers and no specific requirement for ATP but are very O2 sensitive. Certain filamentous cyanobacteria protect nitrogenase from O2 by sequestering the enzyme within internally micro-oxic, differentiated cells called heterocysts. We heterologously expressed the [FeFe]-hydrogenase operon from Shewanella oneidensis MR-1 in Anabaena sp. strain PCC 7120 using the heterocyst-specific promoter PhetN. Active [FeFe]-hydrogenase was detected in and could be purified from aerobically grown Anabaena sp. strain PCC 7120, but only when the organism was grown under nitrate-depleted conditions that elicited heterocyst formation. These results suggest that the heterocysts protected the [FeFe]-hydrogenase against inactivation by O2.

Gartner, Katrin; Lechno-Yossef, Sigal; Cornish, Adam J.; Wolk, C. Peter

2012-01-01

209

Purification and characterization of putative alkaline [Ni-Fe] hydrogenase from unicellular marine green alga, Tetraselmis kochinensis NCIM 1605.  

PubMed

Hydrogenase enzyme from the unicellular marine green alga Tetraselmis kochinensis NCIM 1605 was purified 467 fold to homogeneity. The molecular weight was estimated to be approximately 89kDa by SDS-PAGE. This enzyme consists of two subunits with molecular masses of approximately 70 and approximately 19kDa. The hydrogenase was found to contain 10g atoms of Fe and 1g of atom of Ni per mole of protein. The specific activity of hydrogen evolution was 50micromol H(2)/mg/h of enzyme using reduced methyl viologen as an electron donor. This hydrogenase enzyme has pI value approximately 9.6 representing its alkaline nature. The absorption spectrum of the hydrogenase enzyme showed an absorption peak at 425nm indicating that the enzyme had iron-sulfur clusters. The total of 16 cysteine residues were found per mole of enzyme under the denaturing condition and 20 cysteine residues in reduced denatured enzyme indicating that it has two disulfide bridges. PMID:17321121

Bhosale, S H; Pant, A; Khan, M I

2009-01-01

210

Overexpression, Isolation, and Spectroscopic Characterization of the Bidirectional [NiFe] Hydrogenase from Synechocystis sp. PCC 6803*  

PubMed Central

The bidirectional [NiFe] hydrogenase of the cyanobacterium Synechocystis sp. PCC 6803 was purified to apparent homogeneity by a single affinity chromatography step using a Synechocystis mutant with a Strep-tag II fused to the C terminus of HoxF. To increase the yield of purified enzyme and to test its overexpression capacity in Synechocystis the psbAII promoter was inserted upstream of the hoxE gene. In addition, the accessory genes (hypF, C, D, E, A, and B) from Nostoc sp. PCC 7120 were expressed under control of the psbAII promoter. The respective strains show higher hydrogenase activities compared with the wild type. For the first time a Fourier transform infrared (FTIR) spectroscopic characterization of a [NiFe] hydrogenase from an oxygenic phototroph is presented, revealing that two cyanides and one carbon monoxide coordinate the iron of the active site. At least four different redox states of the active site were detected during the reversible activation/inactivation. Although these states appear similar to those observed in standard [NiFe] hydrogenases, no paramagnetic nickel state could be detected in the fully oxidized and reduced forms. Electron paramagnetic resonance spectroscopy confirms the presence of several iron-sulfur clusters after reductive activation. One [4Fe4S]+ and at least one [2Fe2S]+ cluster could be identified. Catalytic amounts of NADH or NADPH are sufficient to activate the reaction of this enzyme with hydrogen.

Germer, Frauke; Zebger, Ingo; Saggu, Miguel; Lendzian, Friedhelm; Schulz, Rudiger; Appel, Jens

2009-01-01

211

How the structure of the large subunit controls function in an oxygen-tolerant [NiFe]-hydrogenase.  

PubMed

Salmonella enterica is an opportunistic pathogen that produces a [NiFe]-hydrogenase under aerobic conditions. In the present study, genetic engineering approaches were used to facilitate isolation of this enzyme, termed Hyd-5. The crystal structure was determined to a resolution of 3.2 Å and the hydro-genase was observed to comprise associated large and small subunits. The structure indicated that His229 from the large subunit was close to the proximal [4Fe-3S] cluster in the small subunit. In addition, His229 was observed to lie close to a buried glutamic acid (Glu73), which is conserved in oxygen-tolerant hydrogenases. His229 and Glu73 of the Hyd-5 large subunit were found to be important in both hydrogen oxidation activity and the oxygen-tolerance mechanism. Substitution of His229 or Glu73 with alanine led to a loss in the ability of Hyd-5 to oxidize hydrogen in air. Furthermore, the H229A variant was found to have lost the overpotential requirement for activity that is always observed with oxygen-tolerant [NiFe]-hydrogenases. It is possible that His229 has a role in stabilizing the super-oxidized form of the proximal cluster in the presence of oxygen, and it is proposed that Glu73could play a supporting role in fine-tuning the chemistry of His229 to enable this function. PMID:24428762

Bowman, Lisa; Flanagan, Lindsey; Fyfe, Paul K; Parkin, Alison; Hunter, William N; Sargent, Frank

2014-03-15

212

O2-stable membrane-bound [NiFe]hydrogenase from a newly isolated Citrobacter sp. S-77.  

PubMed

Hydrogenases are of great interest due to their potential use in H(2)-based technology. However, most hydrogenases are highly sensitive to O(2), which have been the major bottleneck in hydrogenase studies. Here we report an O(2)-stable membrane-bound [NiFe]hydrogenase (MBH) purified from a newly isolated strain, S-77. According to the 16S rRNA gene sequence and phylogenetic analysis of the strain S-77, it belongs to the genus of Citrobacter. In vitro experiments using the cytoplasmic membrane of strain S-77 suggested that a cytochrome b acts as the physiological electron acceptor of the MBH. The purified MBH was composed of a dimer of heterodimers, consisting of two distinct subunits with the molecular weights of 58.5 and 38.5 kDa. The enzyme showed a specific activity for H(2)-oxidation of 661 U/mg, which is 35-fold greater than that for H(2)-production of 18.7 U/mg. Notably, the MBH showed a remarkable O(2)-stability, maintaining almost 95% of its original activity even after incubation for 30 h in air at 4°C. These results suggest that the O(2)-stable MBH may play an important role in the H(2)-metabolic pathway under the aerobic conditions of Citrobacter sp. S-77. This is the first report of the purification and biochemical characterization of an O(2)-stable MBH from the genus of Citrobacter. PMID:22721689

Eguchi, Shigenobu; Yoon, Ki-Seok; Ogo, Seiji

2012-11-01

213

Unusual Organization of the Genes Coding for HydSL, the Stable (NiFe)Hydrogenase in the Photosynthetic Bacterium Thiocapsa roseopersicina BBS  

Microsoft Academic Search

The characterization of a hyd gene cluster encoding the stable, bidirectional (NiFe)hydrogenase 1 enzyme in Thiocapsa roseopersicina BBS, a purple sulfur photosynthetic bacterium belonging to the family Chromatiaceae, is presented. The heterodimeric hydrogenase 1 had been purified to homogeneity and thoroughly characterized (K. L. Kovacs et al., J. Biol. Chem. 266:947-951, 1991; C. Bagyinka et al., J. Am. Chem. Soc.

GABOR RAKHELY; ANNETTE COLBEAU; JEROME GARIN; PAULETTE M. VIGNAIS; KORNEL L. KOVACS

1998-01-01

214

Genetics and biotechnology of the H(2)-uptake [NiFe] hydrogenase from Rhizobium leguminosarum bv. viciae, a legume endosymbiotic bacterium.  

PubMed

A limited number of strains belonging to several genera of Rhizobiaceae are capable of expressing a hydrogenase system that allows partial or full recycling of hydrogen evolved by nitrogenase, thus increasing the energy efficiency of the nitrogen fixation process. This review is focused on the genetics and biotechnology of the hydrogenase system from Rhizobium leguminosarum bv. viciae, a frequent inhabitant of European soils capable of establishing symbiotic association with peas, lentils, vetches and other legumes. PMID:15667275

Palacios, J M; Manyani, H; Martínez, M; Ureta, A C; Brito, B; Báscones, E; Rey, L; Imperial, J; Ruiz-Argüeso, T

2005-02-01

215

The bidirectional NiFe-hydrogenase in Synechocystis sp. PCC 6803 is reduced by flavodoxin and ferredoxin and is essential under mixotrophic, nitrate-limiting conditions.  

PubMed

Cyanobacteria are able to use solar energy for the production of hydrogen. It is generally accepted that cyanobacterial NiFe-hydrogenases are reduced by NAD(P)H. This is in conflict with thermodynamic considerations, as the midpoint potentials of NAD(P)H do not suffice to support the measured hydrogen production under physiological conditions. We show that flavodoxin and ferredoxin directly reduce the bidirectional NiFe-hydrogenase of Synechocystis sp. PCC 6803 in vitro. A merodiploid ferredoxin-NADP reductase mutant produced correspondingly more photohydrogen. We furthermore found that the hydrogenase receives its electrons via pyruvate:flavodoxin/ferredoxin oxidoreductase (PFOR)-flavodoxin/ferredoxin under fermentative conditions, enabling the cells to gain ATP. These results strongly support that the bidirectional NiFe-hydrogenases in cyanobacteria function as electron sinks for low potential electrons from photosystem I and as a redox balancing device under fermentative conditions. However, the selective advantage of this enzyme is not known. No strong phenotype of mutants lacking the hydrogenase has been found. Because bidirectional hydrogenases are widespread in aquatic nutrient-rich environments that are capable of triggering phytoplankton blooms, we mimicked those conditions by growing cells in the presence of increased amounts of dissolved organic carbon and dissolved organic nitrogen. Under these conditions the hydrogenase was found to be essential. As these conditions close the two most important sinks for reduced flavodoxin/ferredoxin (CO2-fixation and nitrate reduction), this discovery further substantiates the connection between flavodoxin/ferredoxin and the NiFe-hydrogenase. PMID:24311779

Gutekunst, Kirstin; Chen, Xi; Schreiber, Karoline; Kaspar, Ursula; Makam, Srinivas; Appel, Jens

2014-01-24

216

Density comparison between liquid and solid phases in the Fe-FeS system by the sink/float method: Implications for the structural evolution of the cores  

NASA Astrophysics Data System (ADS)

At the early stage of the differentiated planetary bodies, a metallic component separated from a silicate component and formed a metallic core at the center of bodies. Cooling the early molten cores would lead to partial solidification of the core. For a sulfur-bearing iron core, the partially solidified core would consist of Fe-S liquid coexisting with either solid Fe or FeS depending on the S concentration. The stratification of the solid and liquid core is largely controlled by the density contrast between the solid and liquid phases. Based on the previous high-pressure and high-temperature density data of Fe-S liquid, solid Fe, and solid FeS [Nishida et al., 2008, 2011; Balog et al., 2003; Sakamaki et al., 2009; Urakawa et al., 2004], the Fe-S liquid at the Fe-rich side is predictably less dense than the coexisting solid Fe along the liquidus temperatures, whereas the Fe-S liquid at the FeS-rich side is denser than the coexisting solid FeS except only much near FeS. Such density relation implies that a S-rich core would consist of an "outer solid" core and an "inner liquid" core, in contrast to the Earth's core. The predicted density contrast between liquid and solid is relatively small and it is derived from the previous density measurements of the individual phases with large uncertainties, particularly for the liquid phase. In order to directly compare the densities between the liquid and solid phases in the Fe-FeS system, we have performed sink/float experiments to precisely determine the density relationship at high pressure and temperature. High-pressure and high-temperature melting experiments in the Fe-FeS system were carried out using the multi-anvil apparatus at the Geophysical Laboratory. An Fe or FeS pellet was placed at the center in a MgO capsule and surrounded by an Fe-FeS powder mixture (20 wt% S or 28 wt% S, respectively). From the sink-float behavior of the centered pellet at high temperature, we determine whether the solid phase (Fe or FeS) is denser than the coexisting liquid phase or less dense. The experiment at 4 GPa and 1100 °C, using the Fe pellet and Fe-20 wt% S mixture (Fe-rich side) as the starting materials, showed that the solid Fe sank in the liquid with a composition of Fe-22.8 wt% S. Similar experiments in the FeS-rich side were performed and the results will be discussed in conjunction with the stratification and evolution of the cores.

Shibazaki, Y.; Fei, Y.

2012-12-01

217

Comparison of N2 Fixation and Yields in Cajanus cajan between Hydrogenase-Positive and Hydrogenase-Negative Rhizobia by In Situ Acetylene Reduction Assays and Direct 15N Partitioning 1  

PubMed Central

Pigeon peas [Cajanus cajan (L.) Millsp.] were grown in soil columns containing 15N-enriched organic matter. Seasonal N2 fixation activity was determined by periodically assaying plants for reduction of C2H2. N2 fixation rose sharply from the first assay period at 51 days after planting to a peak of activity between floral initiation and fruit set. N2 fixation (acetylene reduction) activity dropped concomitantly with pod maturation but recovered after pod harvests. Analysis of 15N content of plant shoots revealed that approximately 91 to 94% of plant N was derived from N2 fixation. The effect of inoculation with hydrogenase-positive and hydrogenase-negative rhizobia was examined. Pigeon peas inoculated with strain P132 (hydrogenase-positive) yielded significantly more total shoot N than other inoculated or uninoculated treatments. However, two other hydrogenase-positive strains did not yield significantly more total shoot N than a hydrogenase-negative strain. The extent of nodulation by inoculum strains compared to indigenous rhizobia was determined by typing nodules according to intrinsic antibiotic resistance of the inoculum strains. The inoculum strains were detected in almost all typed nodules of inoculated plants. Gas samples were taken from soil columns several times during the growth cycle of the plants. H2 was never detected, even in columns containing pigeon peas inoculated with hydrogenase-negative rhizobia. This was attributed to H2 consumption by soil bacteria. Estimation of N2 fixation by acetylene reduction activity was closest to the direct 15N method when ethylene concentrations in the gas headspace (between the column lid and soil surface) were extrapolated to include the soil pore space as opposed solely to measurement in the headspace. There was an 8-fold difference between the two acetylene reduction assay methods of estimation. Based on a planting density of 15,000 plants per hectare, the direct 15N fixation rates ranged from 67 (noninoculated) to 134 kilograms per hectare, while grain yields ranged from 540 to 825 kilograms per hectare. Grain yields were not increased with N fertilizer.

La Favre, Jeffrey S.; Focht, Dennis D.

1983-01-01

218

Improved production of biohydrogen in light-powered Escherichia coli by co-expression of proteorhodopsin and heterologous hydrogenase  

PubMed Central

Background Solar energy is the ultimate energy source on the Earth. The conversion of solar energy into fuels and energy sources can be an ideal solution to address energy problems. The recent discovery of proteorhodopsin in uncultured marine ?-proteobacteria has made it possible to construct recombinant Escherichia coli with the function of light-driven proton pumps. Protons that translocate across membranes by proteorhodopsin generate a proton motive force for ATP synthesis by ATPase. Excess protons can also be substrates for hydrogen (H2) production by hydrogenase in the periplasmic space. In the present work, we investigated the effect of the co-expression of proteorhodopsin and hydrogenase on H2 production yield under light conditions. Results Recombinant E. coli BL21(DE3) co-expressing proteorhodopsin and [NiFe]-hydrogenase from Hydrogenovibrio marinus produced ~1.3-fold more H2 in the presence of exogenous retinal than in the absence of retinal under light conditions (70 ?mole photon/(m2·s)). We also observed the synergistic effect of proteorhodopsin with endogenous retinal on H2 production (~1.3-fold more) with a dual plasmid system compared to the strain with a single plasmid for the sole expression of hydrogenase. The increase of light intensity from 70 to 130 ?mole photon/(m2·s) led to an increase (~1.8-fold) in H2 production from 287.3 to 525.7 mL H2/L-culture in the culture of recombinant E. coli co-expressing hydrogenase and proteorhodopsin in conjunction with endogenous retinal. The conversion efficiency of light energy to H2 achieved in this study was ~3.4%. Conclusion Here, we report for the first time the potential application of proteorhodopsin for the production of biohydrogen, a promising alternative fuel. We showed that H2 production was enhanced by the co-expression of proteorhodopsin and [NiFe]-hydrogenase in recombinant E. coli BL21(DE3) in a light intensity-dependent manner. These results demonstrate that E. coli can be applied as light-powered cell factories for biohydrogen production by introducing proteorhodopsin.

2012-01-01

219

Wiring an [FeFe]-hydrogenase with photosystem I for light-induced hydrogen production.  

PubMed

A molecular wire is used to connect two proteins through their physiologically relevant redox cofactors to facilitate direct electron transfer. Photosystem I (PS I) and an [FeFe]-hydrogenase (H(2)ase) serve as the test bed for this new technology. By tethering a photosensitizer with a hydrogen-evolving catalyst, attached by Fe-S coordination bonds between the F(B) iron-sulfur cluster of PS I and the distal iron-sulfur cluster of H(2)ase, we assayed electron transfer between the two components via light-induced hydrogen generation. These hydrogen-producing nanoconstructs self-assemble when the PS I variant, the H(2)ase variant, and the molecular wire are combined. PMID:21058656

Lubner, Carolyn E; Knörzer, Philipp; Silva, Paulo J N; Vincent, Kylie A; Happe, Thomas; Bryant, Donald A; Golbeck, John H

2010-12-01

220

Extracellular Iron Reduction Is Mediated in Part by Neutral Red and Hydrogenase in Escherichia coli  

PubMed Central

Both microbial iron reduction and microbial reduction of anodes in fuel cells can occur by way of soluble electron mediators. To test whether neutral red (NR) mediates iron reduction, as it does anode reduction, by Escherichia coli, ferrous iron levels were monitored in anaerobic cultures grown with amorphous iron oxide. Ferrous iron levels were 19.4 times higher in cultures fermenting pyruvate in the presence of NR than in the absence of NR. NR did not stimulate iron reduction in cultures respiring with nitrate. To explore the mechanism of NR-mediated iron reduction, cell extracts of E. coli were used. Cell extract-NADH-NR mixtures had an enzymatic iron reduction rate almost 15-fold higher than the chemical NR-mediated iron reduction rate observed in controls with no cell extract. Hydrogen was consumed during stationary phase (in which iron reduction was detectable) especially in cultures containing both NR and iron oxide. An E. coli hypE mutant, with no hydrogenase activity, was also impaired in NR-mediated iron reduction activity. NR-mediated iron reduction rates by cell extracts were 1.5 to 2 times higher with hydrogen or formate as the electron source than with NADH. Our findings suggest that hydrogenase donates electrons to NR for extracellular iron reduction. This process appears to be analogous to those of iron reduction by bacteria that use soluble electron mediators (e.g., humic acids and 2,6-anthraquinone disulfonate) and of anode reduction by bacteria using soluble mediators (e.g., NR and thionin) in microbial fuel cells.

McKinlay, James B.; Zeikus, J. Gregory

2004-01-01

221

Roles of H2 uptake hydrogenases in Shigella flexneri acid tolerance  

PubMed Central

Hydrogenases play many roles in bacterial physiology, and use of H2 by the uptake-type enzymes of animal pathogens is of particular interest. Hydrogenases have never been studied in the pathogen Shigella, so targeted mutant strains were individually generated in the two Shigella flexneri H2-uptake enzymes (Hya and Hyb) and in the H2-evolving enzyme (Hyc) to address their roles. Under anaerobic fermentative conditions, a Hya mutant strain (hya) was unable to oxidize H2, while a Hyb mutant strain oxidized H2 like the wild-type. A hyc strain oxidized more exogenously added hydrogen than the parent. Fluorescence ratio imaging with dye JC-1 (5,5?,6,6?-tetrachloro-1,1?,3,3?-tetraethylbenzimidazolylcarbocyanine iodide) showed that the parent strain generated a membrane potential 15 times greater than hya. The hya mutant was also by far the most acid-sensitive strain, being even more acid-sensitive than a mutant strain in the known acid-combating glutamate-dependent acid-resistance pathway (GDAR pathway). In severe acid-challenge experiments, the addition of glutamate to hya restored survivability, and this ability was attributed in part to the GDAR system (removes intracellular protons) by mutant strain (e.g. hya/gadBC double mutant) analyses. However, mutant strain phenotypes indicated that a larger portion of the glutamate-rescued acid tolerance was independent of GadBC. The acid tolerance of the hya strains was aided by adding chloride ions to the growth medium. The whole-cell Hya enzyme became more active upon acid exposure (20 min), based on assays of hyc. Indeed, the very high rates of Shigella H2 oxidation by Hya in acid can supply each cell with 2.4×108 protons min?1. Electrons generated from Hya-mediated H2 oxidation at the inner membrane likely counteract cytoplasmic positive charge stress, while abundant proton pools deposited periplasmically likely repel proton influx during severe acid stress.

McNorton, Mykeshia M.

2012-01-01

222

HybF, a Zinc-Containing Protein Involved in NiFe Hydrogenase Maturation  

PubMed Central

HypA and HypB are maturation proteins required for incorporation of nickel into the hydrogenase large subunit. To examine the functions of these proteins in nickel insertion, the hybF gene, which is a homolog of hypA essential for maturation of hydrogenases 1 and 2 from Escherichia coli, was overexpressed, and the product was purified. This protein behaves like a monomer in gel filtration and contains stoichiometric amounts of zinc but insignificant or undetectable amounts of nickel and iron. In filter binding assays radioactively labeled nickel binds to HybF with a KD of 1.87 ?M and in a stoichiometric ratio. To identify amino acid residues of HybF involved in nickel and/or zinc binding, variants in which conserved residues were replaced were studied. An H2Q replacement eliminated both in vivo activity and in vitro binding of nickel. The purified protein, however, contained zinc at the level characteristic of the wild-type protein. When E3 was replaced by Q, activity was retained, but an E3L exchange was detrimental. Replacement of each of the four conserved cysteine residues of a zinc finger motif reduced the cellular amount of HybF protein without a loss of in vivo activity, indicating that these residues play a purely structural role. A triple mutant deficient in the synthesis or activity of HypA, HybF, and HypB was constructed, and it exhibited the same responsiveness for phenotypic complementation by high nickel as mutants with a single lesion in one of the genes exhibited. The results are interpreted in terms of a concerted action of HypB and HybF in nickel insertion in which HybF (as well as its homolog, HypA) functions as a metallochaperone and HypB functions as a regulator that controls the interaction of HybF with the target protein.

Blokesch, Melanie; Rohrmoser, Michaela; Rode, Sabine; Bock, August

2004-01-01

223

Isolation and Characterization of the Small Subunit of the Uptake Hydrogenase from the Cyanobacterium Nostoc punctiforme*  

PubMed Central

In nitrogen-fixing cyanobacteria, hydrogen evolution is associated with hydrogenases and nitrogenase, making these enzymes interesting targets for genetic engineering aimed at increased hydrogen production. Nostoc punctiforme ATCC 29133 is a filamentous cyanobacterium that expresses the uptake hydrogenase HupSL in heterocysts under nitrogen-fixing conditions. Little is known about the structural and biophysical properties of HupSL. The small subunit, HupS, has been postulated to contain three iron-sulfur clusters, but the details regarding their nature have been unclear due to unusual cluster binding motifs in the amino acid sequence. We now report the cloning and heterologous expression of Nostoc punctiforme HupS as a fusion protein, f-HupS. We have characterized the anaerobically purified protein by UV-visible and EPR spectroscopies. Our results show that f-HupS contains three iron-sulfur clusters. UV-visible absorption of f-HupS has bands ?340 and 420 nm, typical for iron-sulfur clusters. The EPR spectrum of the oxidized f-HupS shows a narrow g = 2.023 resonance, characteristic of a low-spin (S = ½) [3Fe-4S] cluster. The reduced f-HupS presents complex EPR spectra with overlapping resonances centered on g = 1.94, g = 1.91, and g = 1.88, typical of low-spin (S = ½) [4Fe-4S] clusters. Analysis of the spectroscopic data allowed us to distinguish between two species attributable to two distinct [4Fe-4S] clusters, in addition to the [3Fe-4S] cluster. This indicates that f-HupS binds [4Fe-4S] clusters despite the presence of unusual coordinating amino acids. Furthermore, our expression and purification of what seems to be an intact HupS protein allows future studies on the significance of ligand nature on redox properties of the iron-sulfur clusters of HupS.

Raleiras, Patricia; Kellers, Petra; Lindblad, Peter; Styring, Stenbjorn; Magnuson, Ann

2013-01-01

224

Spin dynamics and criteria for onset of exchange bias in superspin glass Fe/?-Fe2O3 core-shell nanoparticles  

NASA Astrophysics Data System (ADS)

A detailed study is presented on Fe/?-Fe2O3 core-shell structured nanoparticles (mean size ˜10 nm) to understand the spin dynamics of the core and shell independently and their role in triggering exchange bias (EB) phenomena. The particle dynamics critically slow down at Tg ˜ 68 K, below which they exhibit memory effect in field-cooled and zero-field-cooled protocols associated with a superspin glass state. The field dependence of mean blocking temperature fits the de Almeida-Thouless line and shows two different linear responses in the low and high field regimes corresponding to the core and shell, respectively. We show that the energy barrier distribution estimated from the temperature decay of isothermal remanent magnetization shows two maxima that mark the freezing temperatures of the core (Tf-cr ˜ 48 K) and shell (Tf-sh ˜ 21 K). Last, hysteresis measurements after field cooling reveal strong EB indicated by a loop shift associated with unidirectional anisotropy. The onset of EB is at 35 K when the ferromagnetic core is frozen and the moments in the ferrimagnetic shell begin to block, resulting in enhanced exchange coupling.

Chandra, Sayan; Khurshid, H.; Li, Wanfeng; Hadjipanayis, G. C.; Phan, M. H.; Srikanth, H.

2012-07-01

225

Enhanced Oxygen-Tolerance of the Full Heterotrimeric Membrane-Bound [NiFe]-Hydrogenase of Ralstonia eutropha  

PubMed Central

Hydrogenases are oxygen-sensitive enzymes that catalyze the conversion between protons and hydrogen. Water-soluble subcomplexes of membrane-bound [NiFe]-hydrogenases (MBH) have been extensively studied for applications in hydrogen–oxygen fuel cells as they are relatively tolerant to oxygen, although even these catalysts are still inactivated in oxidative conditions. Here, the full heterotrimeric MBH of Ralstonia eutropha, including the membrane-integral cytochrome b subunit, was investigated electrochemically using electrodes modified with planar tethered bilayer lipid membranes (tBLM). Cyclic voltammetry and chronoamperometry experiments show that MBH, in equilibrium with the quinone pool in the tBLM, does not anaerobically inactivate under oxidative redox conditions. In aerobic environments, the MBH is reversibly inactivated by O2, but reactivation was found to be fast even under oxidative redox conditions. This enhanced resistance to inactivation is ascribed to the oligomeric state of MBH in the lipid membrane.

2014-01-01

226

Enhanced Oxygen-Tolerance of the Full Heterotrimeric Membrane-Bound [NiFe]-Hydrogenase of Ralstonia eutropha.  

PubMed

Hydrogenases are oxygen-sensitive enzymes that catalyze the conversion between protons and hydrogen. Water-soluble subcomplexes of membrane-bound [NiFe]-hydrogenases (MBH) have been extensively studied for applications in hydrogen-oxygen fuel cells as they are relatively tolerant to oxygen, although even these catalysts are still inactivated in oxidative conditions. Here, the full heterotrimeric MBH of Ralstonia eutropha, including the membrane-integral cytochrome b subunit, was investigated electrochemically using electrodes modified with planar tethered bilayer lipid membranes (tBLM). Cyclic voltammetry and chronoamperometry experiments show that MBH, in equilibrium with the quinone pool in the tBLM, does not anaerobically inactivate under oxidative redox conditions. In aerobic environments, the MBH is reversibly inactivated by O2, but reactivation was found to be fast even under oxidative redox conditions. This enhanced resistance to inactivation is ascribed to the oligomeric state of MBH in the lipid membrane. PMID:24866391

Radu, Valentin; Frielingsdorf, Stefan; Evans, Stephen D; Lenz, Oliver; Jeuken, Lars J C

2014-06-18

227

The activation of the [NiFe]-hydrogenase from Allochromatium vinosum . An infrared spectro-electrochemical study  

Microsoft Academic Search

The membrane-bound [NiFe]-hydrogenase from Allochromatium vinosum can occur in several inactive or active states. This study presents the first systematic infrared characterisation of the A. vinosum enzyme, with emphasis on the spectro-electrochemical properties of the inactive\\/active transition. This transition involves an energy barrier, which can be overcome at elevated temperatures. The reduced Ready enzyme can exist in two different inactive

Boris Bleijlevens; Fleur A. van Broekhuizen; Antonio L. De Lacey; Winfried Roseboom; Victor M. Fernandez; Simon P. J. Albracht

2004-01-01

228

Duplication of hyp genes involved in maturation of [NiFe] hydrogenases in Alcaligenes eutrophus H16  

Microsoft Academic Search

Alcaligenes eutrophus H16 harbors seven hyp genes (hypA, B, F, C, D, E, and X) as part of the hydrogenase gene cluster on megaplasmid pHG1. Here we demonstrate that three of the hyp genes (hypA, B, and F) are duplicated in A. eutrophus, which explains the lack of a phenotypic change in single-site mutants impaired in one of the two

Ingo Wolf; Thorsten Buhrke; Jens Dernedde; Anne Pohlmann; Bärbel Friedrich

1998-01-01

229

Synthesis and enzymatic photo-activity of an O2 tolerant hydrogenase-CdSe@CdS quantum rod bioconjugate.  

PubMed

This communication reports on the preparation of stable and photo-active nano-heterostructures composed of O2 tolerant [NiFe] hydrogenase extracted from the Aquifex aeolicus bacterium grafted onto hydrophilic CdSe/CdS quantum rods in view of the development of H2/O2 biofuel cells. The resulting complex is efficient towards H2 oxidation, displays good stability and new photosensitive properties. PMID:24468861

Hamon, C; Ciaccafava, A; Infossi, P; Puppo, R; Even-Hernandez, P; Lojou, E; Marchi, V

2014-04-17

230

Photosensitivity of the Ni-A state of [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F with visible light  

SciTech Connect

Highlights: Black-Right-Pointing-Pointer Ni-A state of [NiFe] hydrogenase showed light sensitivity. Black-Right-Pointing-Pointer New FT-IR bands were observed with light irradiation of the Ni-A state. Black-Right-Pointing-Pointer EPR g-values of the Ni-A state shifted upon light irradiation. Black-Right-Pointing-Pointer The light-induced state converted back to the Ni-A state under the dark condition. -- Abstract: [NiFe] hydrogenase catalyzes reversible oxidation of molecular hydrogen. Its active site is constructed of a hetero dinuclear Ni-Fe complex, and the oxidation state of the Ni ion changes according to the redox state of the enzyme. We found that the Ni-A state (an inactive unready, oxidized state) of [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F (DvMF) is light sensitive and forms a new state (Ni-AL) with irradiation of visible light. The Fourier transform infrared (FT-IR) bands at 1956, 2084 and 2094 cm{sup -1} of the Ni-A state shifted to 1971, 2086 and 2098 cm{sup -1} in the Ni-AL state. The g-values of g{sub x} = 2.30, g{sub y} = 2.23 and g{sub z} = 2.01 for the signals in the electron paramagnetic resonance (EPR) spectrum of the Ni-A state at room temperature varied for -0.009, +0.012 and +0.010, respectively, upon light irradiation. The light-induced Ni-AL state converted back immediately to the Ni-A state under dark condition at room temperature. These results show that the coordination structure of the Fe site of the Ni-A state of [NiFe] hydrogenase is perturbed significantly by light irradiation with relatively small coordination change at the Ni site.

Osuka, Hisao [Graduate School of Life Science, University of Hyogo, 3-2-1, Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297 (Japan) [Graduate School of Life Science, University of Hyogo, 3-2-1, Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297 (Japan); Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5, Takayama-cho, Ikoma-shi, Nara 630-0192 (Japan); Shomura, Yasuhito; Komori, Hirofumi; Shibata, Naoki [Graduate School of Life Science, University of Hyogo, 3-2-1, Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297 (Japan)] [Graduate School of Life Science, University of Hyogo, 3-2-1, Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297 (Japan); Nagao, Satoshi [Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5, Takayama-cho, Ikoma-shi, Nara 630-0192 (Japan)] [Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5, Takayama-cho, Ikoma-shi, Nara 630-0192 (Japan); Higuchi, Yoshiki, E-mail: hig@sci.u-hyogo.ac.jp [Graduate School of Life Science, University of Hyogo, 3-2-1, Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297 (Japan) [Graduate School of Life Science, University of Hyogo, 3-2-1, Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297 (Japan); CREST, JST, Gobancho, Chiyoda-ku, Tokyo 102-0076 (Japan); Hirota, Shun, E-mail: hirota@ms.naist.jp [Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5, Takayama-cho, Ikoma-shi, Nara 630-0192 (Japan) [Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5, Takayama-cho, Ikoma-shi, Nara 630-0192 (Japan); CREST, JST, Gobancho, Chiyoda-ku, Tokyo 102-0076 (Japan)

2013-01-04

231

Photosensitivity of the Ni-A state of [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F with visible light.  

PubMed

[NiFe] hydrogenase catalyzes reversible oxidation of molecular hydrogen. Its active site is constructed of a hetero dinuclear Ni-Fe complex, and the oxidation state of the Ni ion changes according to the redox state of the enzyme. We found that the Ni-A state (an inactive unready, oxidized state) of [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F (DvMF) is light sensitive and forms a new state (Ni-AL) with irradiation of visible light. The Fourier transform infrared (FT-IR) bands at 1956, 2084 and 2094 cm(-1) of the Ni-A state shifted to 1971, 2086 and 2098 cm(-1) in the Ni-AL state. The g-values of g(x)=2.30, g(y)=2.23 and g(z)=2.01 for the signals in the electron paramagnetic resonance (EPR) spectrum of the Ni-A state at room temperature varied for -0.009, +0.012 and +0.010, respectively, upon light irradiation. The light-induced Ni-AL state converted back immediately to the Ni-A state under dark condition at room temperature. These results show that the coordination structure of the Fe site of the Ni-A state of [NiFe] hydrogenase is perturbed significantly by light irradiation with relatively small coordination change at the Ni site. PMID:23159801

Osuka, Hisao; Shomura, Yasuhito; Komori, Hirofumi; Shibata, Naoki; Nagao, Satoshi; Higuchi, Yoshiki; Hirota, Shun

2013-01-01

232

A mutation in a Rhodobacter capsulatus gene encoding an integration host factor-like protein impairs in vivo hydrogenase expression.  

PubMed Central

A gene capable of encoding a protein sharing 45% identical amino acids with the alpha subunit of the integration host factor (IHF) of Escherichia coli was isolated from the photosynthetic bacterium Rhodobacter capsulatus strain B10 by complementation of a hydrogenase-deficient (Hup-) mutant, IR4. A DNA fragment of 274 base pairs containing an IHF binding consensus sequence, isolated from the promoter region of the hydrogenase structural genes (hupSL), was shown by gel retardation assays to bind the IHF protein from E. coli. The product of the R. capsulatus gene was shown to bind specifically to the 274-base-pair DNA fragment from the hupSL promoter. By analogy to the E. coli himA gene, which encodes the alpha subunit of IHF, the gene complementing the IR4 mutant was named himA of R. capsulatus. The wild-type himA gene, cloned in plasmid pBO2, was introduced into the IR4 strain and shown to restore, in trans, hydrogenase activity and autotrophic growth in the mutant. In IR4, a C----T transition mutation had replaced Arg-8 by Cys-8. Gel mobility shifts of the 274-base-pair DNA fragment, not observed with the himA gene product of IR4, were restored with extracts from IR4(pBO2) cells, containing the himA gene on the recombinant plasmid pBO2. Images

Toussaint, B; Bosc, C; Richaud, P; Colbeau, A; Vignais, P M

1991-01-01

233

Biochemical Analysis of the Interactions between the Proteins Involved in the [FeFe]-Hydrogenase Maturation Process*  

PubMed Central

[FeFe]-hydrogenases are iron-sulfur proteins characterized by a complex active site, the H-cluster, whose assembly requires three conserved maturases. HydE and HydG are radical S-adenosylmethionine enzymes that chemically modify a H-cluster precursor on HydF, a GTPase with a dual role of scaffold on which this precursor is synthesized, and carrier to transfer it to the hydrogenase. Coordinate structural and functional relationships between HydF and the two other maturases are crucial for the H-cluster assembly. However, to date only qualitative analysis of this protein network have been provided. In this work we showed that the interactions of HydE and HydG with HydF are distinct events, likely occurring in a precise functional order driven by different kinetic properties, independently of the HydF GTPase activity, which is instead involved in the dissociation of the maturases from the scaffold. We also found that HydF is able to interact with the hydrogenase only when co-expressed with the two other maturases, indicating that under these conditions it harbors per se all the structural elements needed to transfer the H-cluster precursor, thus completing the maturation process. These results open new working perspectives aimed at improving the knowledge of how these complex metalloenzymes are biosynthesized.

Vallese, Francesca; Berto, Paola; Ruzzene, Maria; Cendron, Laura; Sarno, Stefania; De Rosa, Edith; Giacometti, Giorgio M.; Costantini, Paola

2012-01-01

234

Using Gas Chromatography/Isotope Ratio Mass Spectrometry to Determine the Fractionation Factor for H2 Production by Hydrogenases  

SciTech Connect

Hydrogenases catalyze the reversible formation of H2, and they are key enzymes in the biological cycling of H2. H isotopes should be a very useful tool in quantifying proton trafficking in biological H2 production processes, but there are several obstacles that have thus far limited the use of this tool. In this manuscript, we describe a new method that overcomes some of these barriers and is specifically designed to measure isotopic fractionation during enzyme-catalyzed H2 evolution. A key feature of this technique is that purified hydrogenases are employed, allowing precise control over the reaction conditions and therefore a high level of precision. A custom-designed high-throughput gas chromatography-isotope ratio mass spectrometer is employed to measure the isotope ratio of the H2. Using this method, we determined that the fractionation factor of H2 production by the [NiFe]-hydrogenase from Desulfivibrio fructosovran is 0.27. This result indicates that, as expected, protons are highly favored over deuterons during H2 evolution. Potential applications of this new method are discussed.

Yang, Hui; Ghandi, H.; Shi, Liang; Kreuzer, Helen W.; Ostrom, Nathaniel; Hegg, Eric L.

2012-01-15

235

A unique iron-sulfur cluster is crucial for oxygen tolerance of a [NiFe]-hydrogenase.  

PubMed

Hydrogenases are essential for H(2) cycling in microbial metabolism and serve as valuable blueprints for H(2)-based biotechnological applications. However, most hydrogenases are extremely oxygen sensitive and prone to inactivation by even traces of O(2). The O(2)-tolerant membrane-bound [NiFe]-hydrogenase of Ralstonia eutropha H16 is one of the few examples that can perform H(2) uptake in the presence of ambient O(2). Here we show that O(2) tolerance is crucially related to a modification of the internal electron-transfer chain. The iron-sulfur cluster proximal to the active site is surrounded by six instead of four conserved coordinating cysteines. Removal of the two additional cysteines alters the electronic structure of the proximal iron-sulfur cluster and renders the catalytic activity sensitive to O(2) as shown by physiological, biochemical, spectroscopic and electrochemical studies. The data indicate that the mechanism of O(2) tolerance relies on the reductive removal of oxygenic species guided by the unique architecture of the electron relay rather than a restricted access of O(2) to the active site. PMID:21390036

Goris, Tobias; Wait, Annemarie F; Saggu, Miguel; Fritsch, Johannes; Heidary, Nina; Stein, Matthias; Zebger, Ingo; Lendzian, Friedhelm; Armstrong, Fraser A; Friedrich, Bärbel; Lenz, Oliver

2011-05-01

236

Involvement of hydrogenases in the formation of highly catalytic Pd(0) nanoparticles by bioreduction of Pd(II) using Escherichia coli mutant strains.  

PubMed

Escherichia coli produces at least three [NiFe] hydrogenases (Hyd-1, Hyd-2 and Hyd-3). Hyd-1 and Hyd-2 are membrane-bound respiratory isoenzymes with their catalytic subunits exposed to the periplasmic side of the membrane. Hyd-3 is part of the cytoplasmically oriented formate hydrogenlyase complex. In this work the involvement of each of these hydrogenases in Pd(II) reduction under acidic (pH 2.4) conditions was studied. While all three hydrogenases could contribute to Pd(II) reduction, the presence of either periplasmic hydrogenase (Hyd-1 or Hyd-2) was required to observe Pd(II) reduction rates comparable to the parent strain. An E. coli mutant strain genetically deprived of all hydrogenase activity showed negligible Pd(II) reduction. Electron microscopy suggested that the location of the resulting Pd(0) deposits was as expected from the subcellular localization of the particular hydrogenase involved in the reduction process. Membrane separation experiments established that Pd(II) reductase activity is membrane-bound and that hydrogenases are required to initiate Pd(II) reduction. The catalytic activity of the resulting Pd(0) nanoparticles in the reduction of Cr(VI) to Cr(III) varied according to the E. coli mutant strain used for the initial bioreduction of Pd(II). Optimum Cr(VI) reduction, comparable to that observed with a commercial Pd catalyst, was observed when the bio-Pd(0) catalytic particles were prepared from a strain containing an active Hyd-1. The results are discussed in the context of economic production of novel nanometallic catalysts. PMID:20542928

Deplanche, Kevin; Caldelari, Isabelle; Mikheenko, Iryna P; Sargent, Frank; Macaskie, Lynne E

2010-09-01

237

Electrochemical sensing the DNA damage in situ induced by a cathodic process based on Fe@Fe(2)O(3) core-shell nanonecklace and Au nanoparticles mimicking metal toxicity pathways in vivo.  

PubMed

Sensitive electrochemical sensing for the DNA damage in situ based on a cathodic process of Fe@Fe(2)O(3) core-shell nanonecklace and Au nanoparticles was performed by a novel biosensor, which was constructed via a glassy carbon electrode (GCE) modified with a multilayer film comprising of separate layers of poly(dimethyldiallylammonium chloride) (PDDA), the mixture of Fe@Fe(2)O(3) core-shell nanonecklace and Au nanoparticles, PDDA and double strand DNA (ds-DNA). Iron ions and H(2)O(2) (Fenton reagents) were generated continuously at a constant rate by the cathodic process. The two Fenton reagents reacted further to generate hydroxyl radicals in situ, which attacked ds-DNA in the film and caused severe damage of ds-DNA molecules. These courses of DNA damage were just like those happened in organism. It could be used to mimic metal toxicity pathways in vivo. Fe@Fe(2)O(3) core-shell nanonecklace and Au nanoparticles played considerable synergistic effects for DNA damage. Differential pulse voltammetry and cyclic voltammetry were applied to monitor the DNA damage. Different from the previously reported metal-mediated DNA damage sensor, the process of the ds-DNA damage was not achieved in the solution of metal ions and H(2)O(2), but merely in buffer solution, and the instable enzymes were not used in the whole course. The biosensor possesses the potential as a screening tool for rapid assessment of the genotoxicity of existing and new chemicals. PMID:19734034

Wang, Xueliang; Yang, Tao; Jiao, Kui

2009-12-15

238

Organization of the genes encoding [Fe] hydrogenase in Desulfovibrio vulgaris subsp. oxamicus Monticello.  

PubMed Central

The genes encoding the periplasmic [Fe] hydrogenase from Desulfovibrio vulgaris subsp. oxamicus Monticello were cloned by exploiting their homology with the hydAB genes from D. vulgaris subsp. vulgaris Hildenborough, in which this enzyme is present as a heterologous dimer of alpha and beta subunits. Nucleotide sequencing showed that the enzyme is encoded by an operon in which the gene for the 46-kilodalton (kDa) alpha subunit precedes that of the 13.5-kDa beta subunit, exactly as in the Hildenborough strain. The pairs of hydA and hydB genes are highly homologous; both alpha subunits (420 amino acid residues) share 79% sequence identity, while the unprocessed beta subunits (124 and 123 amino acid residues, respectively) share 71% sequence identity. In contrast, there appears to be no sequence homology outside these coding regions, with the exception of a possible promoter element, which was found approximately 90 base pairs upstream from the translational start of the hydA gene. The recently discovered hydC gene, which may code for a 65.8-kDa fusion protein (gamma) of the alpha and beta subunits and is present immediately downstream from the hydAB genes in the Hildenborough strain, was found to be absent from the Monticello strain. The implication of this result for the possible function of the hydC gene product in Desulfovibrio species is discussed. Images

Voordouw, G; Strang, J D; Wilson, F R

1989-01-01

239

Direct evidence of active site reduction and photo-driven catalysis in sensitized hydrogenase assemblies  

PubMed Central

We report photo-catalytic H2 production by hydrogenase (H2ase)-quantum dot (QD) hybrid assemblies. Quenching of the CdTe exciton emission is observed, consistent with electron transfer from quantum dot to H2ase. GC analysis shows light driven H2 production in the presence of a sacrificial electron donor with an efficiency of 4%, which is likely a lower limit to these hybrid systems. FTIR was employed for direct observation of active site reduction in unprecedented detail for photo-driven H2ase catalysis with sensitivity towards both H2ase and sacrificial electron donor. Photosensitization with Ru(bpy)32+ shows distinct FTIR photo- reduction properties generating all states along the steady-state catalytic cycle with minimal H2 production indicating slow, sequential one electron reduction steps. Comparing H2ase activity and FTIR results of both systems shows that QDs bind more efficiently for electron transfer and the final enzyme state is different for the two sensitizers. The possible origins of these differences and their implications for the enzymatic mechanism are discussed.

Greene, Brandon L.; Joseph, Crisjoe A.; Maroney, Michael J.; Dyer, R. Brian

2012-01-01

240

Hydrogen production by the naked active site of the di-iron hydrogenases in water.  

PubMed

We explored the reactivity of the active center of the [FeFe]-hydrogenases detached from the enzyme and immersed in acidified water by first-principles Car-Parrinello molecular-dynamics simulations. We focused on the identification of the structures that are stable and metastable in acidified water and on their activity for hydrogen production. Our calculations revealed that the naked active center could be an efficient catalyst provided that electrons are transferred to the cluster. We found that both bridging and terminal isomers are present at equilibrium and that the bridging configuration is essential for efficient hydrogen production. The formation of the hydrogen molecule occurs via sequential protonations of the distal iron and of the N-atom of the S-CH(2)-NH-CH(2)-S chelating group. H(2) desorption does not involve a significant energy barrier, making the process very efficient at room temperature. We established that the bottleneck in the reaction is the direct proton transfer from water to the vacant site of the distal iron. Moreover, we found that even if the terminal isomer is present at the equilibrium, its strong local hydrophobicity prevents poisoning of the cluster. PMID:19737003

Zipoli, Federico; Car, Roberto; Cohen, Morrel H; Selloni, Annabella

2009-10-01

241

Hydrogenase-Mediated Activities in Isolated Chloroplasts of Chlamydomonas reinhardii1  

PubMed Central

Isolated intact chloroplasts of Chlamydomonas reinhardii were found to catalyze photoreduction of CO2 in the presence of 3-(3,4-dichlorophenyl)-1,1-dimethylurea when adapted under an atmosphere of H2 demonstrating the association of a hydrogenase and anaerobic adaptation system with these plastids. The specific activity of photoreduction was approximately one third that detected in cells and protoplasts. Photoreduction was found to have a lower osmoticum optimum relative to aerobically maintained chloroplasts (50 millimolar versus 120 millimolar mannitol). 3-Phosphoglycerate (3-PGA) stimulated photoreduction up to a peak at 0.25 millimolar beyond which inhibition was observed. In the absence of 3-PGA, inorganic phosphate had no effect on photoreduction but in the presence of 3-PGA, inorganic phosphate also stimulated the reaction. Carbonyl cyanide-p-trifluoromethoxyphenylhydrazone and 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone inhibited photoreduction but inhibition by the former could be partially overcome by exogenously added ATP. The intact plastid can also catalyze photoevolution of H2 while lysed chloroplast extracts catalyzed the reduction of methyl viologen by H2. Both reactions occurred at rates approximately one-third of those found in cells. The oxyhydrogen reaction in the presence or absence of CO2 was not detected.

Maione, Theodore E.; Gibbs, Martin

1986-01-01

242

Characterization of a cyanobacterial-like uptake [NiFe] hydrogenase: EPR and FTIR spectroscopic studies of the enzyme from Acidithiobacillus ferrooxidans.  

PubMed

Electron paramagnetic resonance (EPR) and Fourier transform IR studies on the soluble hydrogenase from Acidithiobacillus ferrooxidans are presented. In addition, detailed sequence analyses of the two subunits of the enzyme have been performed. They show that the enzyme belongs to a group of uptake [NiFe] hydrogenases typical for Cyanobacteria. The sequences have also a close relationship to those of the H(2)-sensor proteins, but clearly differ from those of standard [NiFe] hydrogenases. It is concluded that the structure of the catalytic centre is similar, but not identical, to that of known [NiFe] hydrogenases. The active site in the majority of oxidized enzyme molecules, 97% in cells and more than 50% in the purified enzyme, is EPR-silent. Upon contact with H(2) these sites remain EPR-silent and show only a limited IR response. Oxidized enzyme molecules with an EPR-detectable active site show a Ni(r)*-like EPR signal which is light-sensitive at cryogenic temperatures. This is a novelty in the field of [NiFe] hydrogenases. Reaction with H(2) converts these active sites to the well-known Ni(a)-C* state. Illumination below 160 K transforms this state into the Ni(a)-L* state. The reversal, in the dark at 200 K, proceeds via an intermediate Ni EPR signal only observed with the H(2)-sensor protein from Ralstonia eutropha. The EPR-silent active sites in as-isolated and H(2)-treated enzyme are also light-sensitive as observed by IR spectra at cryogenic temperatures. The possible origin of the light sensitivity is discussed. This study represents the first spectral characterization of an enzyme of the group of cyanobacterial uptake hydrogenases. PMID:17082918

Schröder, Olga; Bleijlevens, Boris; de Jongh, Thyra E; Chen, Zhujun; Li, Tianshu; Fischer, Jörg; Förster, Jochen; Friedrich, Cornelius G; Bagley, Kimberly A; Albracht, Simon P J; Lubitz, Wolfgang

2007-02-01

243

The crystal structure of the [NiFe] hydrogenase from the photosynthetic bacterium Allochromatium vinosum: characterization of the oxidized enzyme (Ni-A state).  

PubMed

The crystal structure of the membrane-associated [NiFe] hydrogenase from Allochromatium vinosum has been determined to 2.1 Å resolution. Electron paramagnetic resonance (EPR) and Fourier transform infrared spectroscopy on dissolved crystals showed that it is present in the Ni-A state (>90%). The structure of the A. vinosum [NiFe] hydrogenase shows significant similarities with [NiFe] hydrogenase structures derived from Desulfovibrio species. The amino acid sequence identity is ? 50%. The bimetallic [NiFe] active site is located in the large subunit of the heterodimer and possesses three diatomic non-protein ligands coordinated to the Fe (two CN(-) , one CO). Ni is bound to the protein backbone via four cysteine thiolates; two of them also bridge the two metals. One of the bridging cysteines (Cys64) exhibits a modified thiolate in part of the sample. A mono-oxo bridging ligand was assigned between the metal ions of the catalytic center. This is in contrast to a proposal for Desulfovibrio sp. hydrogenases that show a di-oxo species in this position for the Ni-A state. The additional metal site located in the large subunit appears to be a Mg(2+) ion. Three iron-sulfur clusters were found in the small subunit that forms the electron transfer chain connecting the catalytic site with the molecular surface. The calculated anomalous Fourier map indicates a distorted proximal iron-sulfur cluster in part of the crystals. This altered proximal cluster is supposed to be paramagnetic and is exchange coupled to the Ni(3+) ion and the medial [Fe(3)S(4)](+) cluster that are both EPR active (S=1/2 species). This finding of a modified proximal cluster in the [NiFe] hydrogenase might explain the observation of split EPR signals that are occasionally detected in the oxidized state of membrane-bound [NiFe] hydrogenases as from A. vinosum. PMID:20673834

Ogata, Hideaki; Kellers, Petra; Lubitz, Wolfgang

2010-09-17

244

Biologically-assisted hydrogen production: attempts at optimizing the use of polymeric viologen mediators in a bioreactor based on the hydrogenase-catalyzed decomposition of dithionite  

SciTech Connect

A small scale hydrogen-producing bioreactor has been assembled. It is based on the hydrogenase-catalyzed decomposition of sodium dithionite as mediated by a polymeric viologen. Optimization of the conditions for producing a crude, cell-free extract of hydrogenase from Clostridium pasteurianum has been investigated. Using the results obtained, a larger laboratory-scale hydrogen generator has been assembled which was shown to yield sustained hydrogen production. Incorporation of a waste-removal system into the unit was also investigated. 8 refs.

Williams, R.W.; Toye, B.W.; Martin, S.M.

1981-01-01

245

Cloning and sequencing of the genes encoding the large and small subunits of the periplasmic (NiFeSe) hydrogenase of Desulfovibrio baculatus.  

PubMed Central

The genes coding for the large and small subunits of the periplasmic hydrogenase from Desulfovibrio baculatus have been cloned and sequenced. The genes are arranged in an operon with the small subunit gene preceding the large subunit gene. The small subunit gene codes for a 32 amino acid leader sequence supporting the periplasmic localization of the protein, however no ferredoxin-like or other characteristic iron-sulfur coordination sites were observed. The periplasmic hydrogenases from D. baculatus (an NiFeSe protein) and D. vulgaris (an Fe protein) exhibit no homology suggesting that they are structurally different, unrelated entities. Images

Menon, N K; Peck, H D; Gall, J L; Przybyla, A E

1987-01-01

246

Fractionation of sulfur isotopes by Desulfovibrio vulgaris mutants lacking hydrogenases or type I tetraheme cytochrome c 3.  

PubMed

The sulfur isotope effect produced by sulfate reducing microbes is commonly used to trace biogeochemical cycles of sulfur and carbon in aquatic and sedimentary environments. To test the contribution of intracellular coupling between carbon and sulfur metabolisms to the overall magnitude of the sulfur isotope effect, this study compared sulfur isotope fractionations by mutants of Desulfovibrio vulgaris Hildenborough. We tested mutant strains lacking one or two periplasmic (Hyd, Hyn-1, Hyn-2, and Hys) or cytoplasmic hydrogenases (Ech and CooL), and a mutant lacking type I tetraheme cytochrome (TpI-c 3). In batch culture, wild-type D. vulgaris and its hydrogenase mutants had comparable growth kinetics and produced the same sulfur isotope effects. This is consistent with the reported redundancy of hydrogenases in D. vulgaris. However, the TpI-c 3 mutant (?cycA) exhibited slower growth and sulfate reduction rates in batch culture, and produced more H2 and an approximately 50% larger sulfur isotope effect, compared to the wild type. The magnitude of sulfur isotope fractionation in the CycA deletion strain, thus, increased due to the disrupted coupling of the carbon oxidation and sulfate reduction pathways. In continuous culture, wild-type D. vulgaris and the CycA mutant produced similar sulfur isotope effects, underscoring the influence of environmental conditions on the relative contribution of hydrogen cycling to the electron transport. The large sulfur isotope effects associated with the non-ideal stoichiometry of sulfate reduction in this study imply that simultaneous fermentation and sulfate reduction may be responsible for some of the large naturally-occurring sulfur isotope effects. Overall, mutant strains provide a powerful tool to test the effect of specific redox proteins and pathways on sulfur isotope fractionation. PMID:23805134

Sim, Min Sub; Wang, David T; Zane, Grant M; Wall, Judy D; Bosak, Tanja; Ono, Shuhei

2013-01-01

247

Mutational analysis and characterization of the Escherichia coli hya operon, which encodes [NiFe] hydrogenase 1.  

PubMed Central

Deletion mutants of Escherichia coli specific for hydrogenase isoenzyme 1 (HYD1) have been constructed and characterized. The hya operon, which contains genes for the two HYD1 structural subunits and four additional genes, was mapped at 22 min on the E. coli chromosome. The total hydrogenase activities of the HYD1-negative mutant and wild-type strains were similar. However, the formate dehydrogenase activity associated with the formate hydrogen lyase pathway was lower in the mutant. The hya mutant (strain AP1), complemented with only the hydrogenase structural genes (hyaAB), produced antigenically identifiable but inactive HYD1 protein. The first five genes of hya (hyaA to hyaE) were required for the synthesis of active HYD1, but wild-type levels of HYD1 activity were restored only when mutant cells were transformed with all six genes of the operon. When AP1 was complemented with hya carried on a high-copy-number plasmid, the HYD1 structural subunits were overexpressed, but the excess protein was unprocessed and localized in the soluble fraction of the cell. The products of hyaDEF are postulated to be involved in the processing of nascent structural subunits (HYAA and HYAB). This processing takes place only after the subunits are inserted into the cell membrane. It is concluded that the biosynthesis of active HYD1 is a complex biochemical process involving the cellular localization and processing of nascent structural subunits, which are in turn dependent on the insertion of nickel into the nascent HYD1 large subunit. Images

Menon, N K; Robbins, J; Wendt, J C; Shanmugam, K T; Przybyla, A E

1991-01-01

248

Fractionation of sulfur isotopes by Desulfovibrio vulgaris mutants lacking hydrogenases or type I tetraheme cytochrome c3  

PubMed Central

The sulfur isotope effect produced by sulfate reducing microbes is commonly used to trace biogeochemical cycles of sulfur and carbon in aquatic and sedimentary environments. To test the contribution of intracellular coupling between carbon and sulfur metabolisms to the overall magnitude of the sulfur isotope effect, this study compared sulfur isotope fractionations by mutants of Desulfovibrio vulgaris Hildenborough. We tested mutant strains lacking one or two periplasmic (Hyd, Hyn-1, Hyn-2, and Hys) or cytoplasmic hydrogenases (Ech and CooL), and a mutant lacking type I tetraheme cytochrome (TpI-c3). In batch culture, wild-type D. vulgaris and its hydrogenase mutants had comparable growth kinetics and produced the same sulfur isotope effects. This is consistent with the reported redundancy of hydrogenases in D. vulgaris. However, the TpI-c3 mutant (?cycA) exhibited slower growth and sulfate reduction rates in batch culture, and produced more H2 and an approximately 50% larger sulfur isotope effect, compared to the wild type. The magnitude of sulfur isotope fractionation in the CycA deletion strain, thus, increased due to the disrupted coupling of the carbon oxidation and sulfate reduction pathways. In continuous culture, wild-type D. vulgaris and the CycA mutant produced similar sulfur isotope effects, underscoring the influence of environmental conditions on the relative contribution of hydrogen cycling to the electron transport. The large sulfur isotope effects associated with the non-ideal stoichiometry of sulfate reduction in this study imply that simultaneous fermentation and sulfate reduction may be responsible for some of the large naturally-occurring sulfur isotope effects. Overall, mutant strains provide a powerful tool to test the effect of specific redox proteins and pathways on sulfur isotope fractionation.

Sim, Min Sub; Wang, David T.; Zane, Grant M.; Wall, Judy D.; Bosak, Tanja; Ono, Shuhei

2013-01-01

249

Rubredoxin-related maturation factor guarantees metal cofactor integrity during aerobic biosynthesis of membrane-bound [NiFe] hydrogenase.  

PubMed

The membrane-bound [NiFe] hydrogenase (MBH) supports growth of Ralstonia eutropha H16 with H2 as the sole energy source. The enzyme undergoes a complex biosynthesis process that proceeds during cell growth even at ambient O2 levels and involves 14 specific maturation proteins. One of these is a rubredoxin-like protein, which is essential for biosynthesis of active MBH at high oxygen concentrations but dispensable under microaerobic growth conditions. To obtain insights into the function of HoxR, we investigated the MBH protein purified from the cytoplasmic membrane of hoxR mutant cells. Compared with wild-type MBH, the mutant enzyme displayed severely decreased hydrogenase activity. Electron paramagnetic resonance and infrared spectroscopic analyses revealed features resembling those of O2-sensitive [NiFe] hydrogenases and/or oxidatively damaged protein. The catalytic center resided partially in an inactive Niu-A-like state, and the electron transfer chain consisting of three different Fe-S clusters showed marked alterations compared with wild-type enzyme. Purification of HoxR protein from its original host, R. eutropha, revealed only low protein amounts. Therefore, recombinant HoxR protein was isolated from Escherichia coli. Unlike common rubredoxins, the HoxR protein was colorless, rather unstable, and essentially metal-free. Conversion of the atypical iron-binding motif into a canonical one through genetic engineering led to a stable reddish rubredoxin. Remarkably, the modified HoxR protein did not support MBH-dependent growth at high O2. Analysis of MBH-associated protein complexes points toward a specific interaction of HoxR with the Fe-S cluster-bearing small subunit. This supports the previously made notion that HoxR avoids oxidative damage of the metal centers of the MBH, in particular the unprecedented Cys6[4Fe-3S] cluster. PMID:24448806

Fritsch, Johannes; Siebert, Elisabeth; Priebe, Jacqueline; Zebger, Ingo; Lendzian, Friedhelm; Teutloff, Christian; Friedrich, Bärbel; Lenz, Oliver

2014-03-14

250

A dithiolate-bridged (CN)2(CO)Fe-Ni complex reproducing the IR bands of [NiFe] hydrogenase.  

PubMed

A dithiolate-bridged dinuclear Fe-Ni complex, which has the desired fac-(CN)(2)(CO) ligand set at iron, has been synthesized. Its CN/CO bands in the IR spectrum reproduce those of the Ni-A, Ni-B, and Ni-SU states, which indicate that these octahedral Fe(II) centers have similar electronic properties. This result verifies the assignment of a (CN)(2)(CO)Fe(II) moiety in the active site of [NiFe] hydrogenase. PMID:19222192

Tanino, Soichiro; Li, Zilong; Ohki, Yasuhiro; Tatsumi, Kazuyuki

2009-03-16

251

Proton Management as a Design Principle for Hydrogenase-inspired Catalysts  

SciTech Connect

The properties of the hydrogenase-inspired [Ni(PNP){sub 2}]{sup 2+} (PNP = Et{sub 2}PCH{sub 2}NMeCH{sub 2}PEt{sub 2}) catalyst for homogeneous hydrogen oxidation in acetonitrile solution are explored from a theoretical perspective for hydrogen production. The defining characteristic of this catalyst is the presence of pendent bases in the second coordination sphere that function as proton relays between the solution and the metal center. DFT calculations of the possible intermediates along proposed catalytic pathways are carried out and used to construct coupled Pourbaix diagrams of the redox processes and free-energy profiles along the reaction pathways. Analysis of the coupled Pourbaix diagrams reveals insights into the intermediate species and the mechanisms favored at different pH values of the solution. Consideration of the acid-base behavior of the metal hydride and H{sub 2} adduct species imposes additional constraints on the reaction mechanism, which can involve intramolecular as well as intermolecular proton-coupled electron-transfer steps. The efficacy of the catalyst is shown to depend critically on the pK{sub a} values of these potential intermediates, as they control both the species in solution at a given pH and the free-energy profile of reaction pathways. Optimal relationships among these pK{sub a} values can be identified, and it is demonstrated that 'proton management', i.e., the manipulation of these pK{sub a} values (e.g., through choice of metal or substituents on ligands), can serve as a design principle for improved catalytic behavior.

Muckerman, J.T.; Small, Y.A.; DuBois, D.L.; Fujita, E.

2011-08-01

252

Proton management as a design principle for hydrogenase-inspired catalysts  

SciTech Connect

The properties of the hydrogenase-inspired [Ni(PNP)2]2+ (PNP ¼ Et2PCH2NMeCH2PEt2) catalyst for homogeneous hydrogen oxidation in acetonitrile solution are explored from a theoretical perspective for hydrogen production. The defining characteristic of this catalyst is the presence of pendent bases in the second coordination sphere that function as proton relays between the solution and the metal center. DFT calculations of the possible intermediates along proposed catalytic pathways are carried out and used to construct coupled Pourbaix diagrams of the redox processes and free-energy profiles along the reaction pathways. Analysis of the coupled Pourbaix diagrams reveals insights into the intermediate species and the mechanisms favored at different pH values of the solution. Consideration of the acid-base behavior of the metal hydride and H2 adduct species imposes additional constraints on the reaction mechanism, which can involve intramolecular as well as intermolecular proton-coupled electron-transfer steps. The efficacy of the catalyst is shown to depend critically on the pKa values of these potential intermediates, as they control both the species in solution at a given pH and the freeenergy profile of reaction pathways. Optimal relationships among these pKa values can be identified, and it is demonstrated that ‘‘proton management’’, i.e., the manipulation of these pKa values (e.g., through choice of metal or substituents on ligands), can serve as a design principle for improved catalytic behavior. This material is based upon work supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the US Department of Energy, Office of Science, Office of Basic Energy Sciences.

Small, Yolanda A.; DuBois, Daniel L.; Fujita, Etsuko; Muckerman, J. T.

2011-06-01

253

Photochemical dihydrogen production using an analogue of the active site of [NiFe] hydrogenase.  

PubMed

Photoproduction of dihydrogen (H2) by a low molecular weight analogue of the active site of [NiFe] hydrogenase has been investigated by reduction of the [NiFe2] cluster, 1, by a photosensitier PS (PS = [ReCl(CO)3(bpy)] or [Ru(bpy)3][PF6]2). Reductive quenching of the (3)MLCT excited state of the photosensitizer by NEt3 or N(CH2CH2OH)3 (TEOA) generates PS(•-), and subsequent intermolecular electron transfer to 1 produces the reduced anionic form of 1. Time-resolved infrared spectroscopy (TRIR) has been used to probe the intermediates throughout the reduction of 1 and subsequent photocatalytic H2 production from [HTEOA][BF4], which was monitored by gas chromatography. Two structural isomers of the reduced form of 1 (1a(•-) and 1b(•-)) were detected by Fourier transform infrared spectroscopy (FTIR) in both CH3CN and DMF (dimethylformamide), while only 1a(•-) was detected in CH2Cl2. Structures for these intermediates are proposed from the results of density functional theory calculations and FTIR spectroscopy. 1a(•-) is assigned to a similar structure to 1 with six terminal carbonyl ligands, while calculations suggest that in 1b(•-) two of the carbonyl groups bridge the Fe centers, consistent with the peak observed at 1714 cm(-1) in the FTIR spectrum for 1b(•-) in CH3CN, assigned to a ?(CO) stretching vibration. Formation of 1a(•-) and 1b(•-) and production of H2 was studied in CH3CN, DMF, and CH2Cl2. Although the more catalytically active species (1a(•-) or 1b(•-)) could not be determined, photocatalysis was observed only in CH3CN and DMF. PMID:24749646

Summers, Peter A; Dawson, Joe; Ghiotto, Fabio; Hanson-Heine, Magnus W D; Vuong, Khuong Q; Davies, E Stephen; Sun, Xue-Z; Besley, Nicholas A; McMaster, Jonathan; George, Michael W; Schröder, Martin

2014-05-01

254

EPR/ENDOR, Mössbauer, and quantum-chemical investigations of diiron complexes mimicking the active oxidized state of [FeFe]hydrogenase.  

PubMed

Understanding the catalytic process of the heterolytic splitting and formation of molecular hydrogen is one of the key topics for the development of a future hydrogen economy. With an interest in elucidating the enzymatic mechanism of the [Fe(2)(S(2)C(2)H(4)NH)(CN)(2)(CO)(2)(?-CO)] active center uniquely found in [FeFe]hydrogenases, we present a detailed spectroscopic and theoretical analysis of its inorganic model [Fe(2)(S(2)X)(CO)(3)(dppv)(PMe(3))](+) [dppv = cis-1,2-bis(diphenylphosphino)ethylene] in two forms with S(2)X = ethanedithiolate (1edt) and azadithiolate (1adt). These complexes represent models for the oxidized mixed-valent Fe(I)Fe(II) state analogous to the active oxidized "H(ox)" state of the native H-cluster. For both complexes, the (31)P hyperfine interactions were determined by pulse electron paramagnetic resonance and electron nuclear double resonance (ENDOR) methods. For 1edt, the (57)Fe parameters were measured by electron spin-echo envelope modulation and Mössbauer spectroscopy, while for 1adt, (14)N and selected (1)H couplings could be obtained by ENDOR and hyperfine sublevel correlation spectroscopy. The spin density was found to be predominantly localized on the Fe(dppv) site. This spin distribution is different from that of the H-cluster, where both the spin and charge densities are delocalized over the two Fe centers. This difference is attributed to the influence of the "native" cubane subcluster that is lacking in the inorganic models. The degree and character of the unpaired spin delocalization was found to vary from 1edt, with an abiological dithiolate, to 1adt, which features the authentic cofactor. For 1adt, we find two (14)N signals, which are indicative for two possible isomers of the azadithiolate, demonstrating its high flexibility. All interaction parameters were also evaluated through density functional theory calculations at various levels. PMID:22800196

Silakov, Alexey; Olsen, Matthew T; Sproules, Stephen; Reijerse, Eduard J; Rauchfuss, Thomas B; Lubitz, Wolfgang

2012-08-01

255

Synthesis, structural characterization, and some properties of 2-acylmethyl-6-ester group-difunctionalized pyridine-containing iron complexes related to the active site of [Fe]-hydrogenase.  

PubMed

As biomimetic models for [Fe]-hydrogenase, the 2-acylmethyl-6-ester group-difunctionalized pyridine-containing iron(ii) complexes 1-4 have been successfully prepared via the following three separate steps. In the first step, the acylation or esterification of difunctionalized pyridine 2-(p-MeC6H4SO3CH2)-6-HOCH2C5H3N with acetyl chloride or benzoic acid gives the corresponding pyridine derivatives 2-(p-MeC6H4SO3CH2)-6-RCO2CH2C5H3N (A, R = Me; B, R = Ph). The second step involves reaction of A or B with Na2Fe(CO)4 followed by treatment of the intermediate Fe(0) complexes [Na(2-CH2-6-RCO2CH2C5H3N)Fe(CO)4] (M1, R = Me; M2, R = Ph) with iodine to afford 2-acylmethyl-6-acetoxymethyl or 6-benzoyloxymethyl-difunctionalized pyridine-containing Fe(ii) iodide complexes [2-C(O)CH2-6-RCO2CH2C5H3N]Fe(CO)2I (1, R = Me; 3, R = Ph). Finally, when 1 or 3 is treated with sodium 2-mercaptopyridinate, the corresponding difunctionalized pyridine-containing Fe(ii) mercaptopyridinate complexes [2-C(O)CH2-6-RCO2C5H3N]Fe(CO)2(2-SC5H4N) (2, R = Me; 4, R = Ph) are produced. While the structures of model complexes 1-4 are confirmed by X-ray crystallography, the electrochemical properties of 2 and 4 are compared with those of the two previously reported models. In addition, complexes 2 and 4 have been found to be catalysts for H2 production in the presence of TFA under CV conditions. PMID:24718303

Song, Li-Cheng; Hu, Fu-Qiang; Wang, Miao-Miao; Xie, Zhao-Jun; Xu, Kai-Kai; Song, Hai-Bin

2014-06-01

256

Radioassay for Hydrogenase Activity in Viable Cells and Documentation of Aerobic Hydrogen-Consuming Bacteria Living in Extreme Environments  

PubMed Central

An isotopic tracer assay based on the hydrogenase-dependent formation of tritiated water from tritium gas was developed for in life analysis of microbial hydrogen transformation. This method allowed detection of bacterial hydrogen metabolism in pure cultures or in natural samples obtained from aquatic ecosystems. A differentiation between chemical-biological and aerobic-anaerobic hydrogen metabolism was established by variation of the experimental incubation temperature or by addition of selective inhibitors. Hydrogenase activity was shown to be proportional to the consumption or production of hydrogen by cultures of Desulfovibrio vulgaris, Clostridium pasteurianum, and Methanosarcina barkeri. This method was applied, in connection with measurements of free hydrogen and most-probable-number enumerations, in aerobic natural source waters to establish the activity and document the ecology of hydrogen-consuming bacteria in extreme acid, thermal, or saline environments. The utility of the assay is based in part on the ability to quantify bacterial hydrogen transformation at natural hydrogen partial pressures, without the use of artificial electron acceptors.

Schink, Bernhard; Lupton, F. S.; Zeikus, J. G.

1983-01-01

257

The difference a Se makes? Oxygen-tolerant hydrogen production by the [NiFeSe]-hydrogenase from Desulfomicrobium baculatum.  

PubMed

Protein film voltammetry studies of the [NiFeSe]-hydrogenase from Desulfomicrobium baculatum show it to be a highly efficient H2 cycling catalyst. In the presence of 100% H2, the ratio of H2 production to H2 oxidation activity is higher than for any conventional [NiFe]-hydrogenases (lacking a selenocysteine ligand) that have been investigated to date. Although traces of O2 (< 1%) rapidly and completely remove H2 oxidation activity, the enzyme sustains partial activity for H2 production even in the presence of 1% O2 in the atmosphere. That H2 production should be partly allowed, whereas H2 oxidation is not, is explained because the inactive product of O2 attack is reductively reactivated very rapidly, but this requires a potential that is almost as negative as the thermodynamic potential for the 2H(+)/H2 couple. The study provides further encouragement and clues regarding the feasibility of microbial/enzymatic H2 production free from restrictions of anaerobicity. PMID:18781742

Parkin, Alison; Goldet, Gabrielle; Cavazza, Christine; Fontecilla-Camps, Juan C; Armstrong, Fraser A

2008-10-01

258

A Universal Scaffold for Synthesis of the Fe(CN)2(CO) Moiety of [NiFe] Hydrogenase*  

PubMed Central

Hydrogen-cycling [NiFe] hydrogenases harbor a dinuclear catalytic center composed of nickel and iron ions, which are coordinated by four cysteine residues. Three unusual diatomic ligands in the form of two cyanides (CN?) and one carbon monoxide (CO) are bound to the iron and apparently account for the complexity of the cofactor assembly process, which involves the function of at least six auxiliary proteins, designated HypA, -B, -C, -D, -E, and -F. It has been demonstrated previously that the HypC, -D, -E, and -F proteins participate in cyanide synthesis and transfer. Here, we show by infrared spectroscopic analysis that the purified HypCD complexes from Ralstonia eutropha and Escherichia coli carry in addition to both cyanides the CO ligand. We present experimental evidence that in vivo the attachment of the CN? ligands is a prerequisite for subsequent CO binding. With the aid of genetic engineering and subsequent mutant analysis, the functional role of conserved cysteine residues in HypD from R. eutropha was investigated. Our results demonstrate that the HypCD complex serves as a scaffold for the assembly of the Fe(CN)2(CO) entity of [NiFe] hydrogenase.

Burstel, Ingmar; Siebert, Elisabeth; Winter, Gordon; Hummel, Philipp; Zebger, Ingo; Friedrich, Barbel; Lenz, Oliver

2012-01-01

259

Observation of the Fe--CN and Fe--CO Vibrations in the Active Site of [NiFe] Hydrogenase by Nuclear Resonance Vibrational Spectroscopy**  

PubMed Central

Nuclear inelastic scattering of 57Fe labeled [NiFe] hydrogenase is shown to give information on different states of the enzyme. It was thus possible to detect and assign Fe–CO and Fe–CN bending and stretching vibrations of the active site outside the spectral range of the Fe–S cluster normal modes.

Kamali, Saeed; Wang, Hongxin; Mitra, Devrani; Ogata, Hideaki; Manor, Brian C.; Rauchfuss, Thomas B.; Byrne, Deborah; Bonnefoy, Violaine; Jenney, Francis E.; Adams, Michael W. W.; Yoda, Yoshitaka; Alp, Ercan; Zhao, Jiyong; Cramer, Stephen P.

2012-01-01

260

Sequence analysis and interposon mutagenesis of the hupT gene, which encodes a sensor protein involved in repression of hydrogenase synthesis in Rhodobacter capsulatus.  

PubMed Central

The hupT gene, which represses hydrogenase gene expression in the purple photosynthetic bacterium Rhodobacter capsulatus, has been identified and sequenced. The nucleotide sequence of hupT and of the contiguous downstream open reading frame, hupU, is reported. The HupT protein of 456 amino acids (48,414 Da) has sequence similarity with the FixL, DctB, NtrB, and ArcB proteins and is predicted to be a soluble sensor kinase. Insertional inactivation of the hupT gene led to deregulation of transcriptional control, so that the hydrogenase structural operon hupSLC became overexpressed in cells grown anaerobically or aerobically. The HupT- mutants were complemented in trans by a plasmid containing an intact copy of the hupT gene. The hupU open reading frame, capable of encoding a protein of 84,879 Da, shared identity with [NiFe]hydrogenase subunits; the strongest similarity was observed with the periplasmic hydrogenase of Desulfovibrio baculatus. Images

Elsen, S; Richaud, P; Colbeau, A; Vignais, P M

1993-01-01

261

QM/MM studies of Ni-Fe hydrogenases: the effect of enzyme environment on the structure and energies of the inactive and active states.  

PubMed

The catalytically active (Ni-SI and Ni-R) and inactive states (Ni-A and Ni-B) of Ni-Fe hydrogenases have been studied using density functional theory (DFT) methods. Both isolated clusters and clusters embedded in the enzyme have been used to model the Ni-A, Ni-B, Ni-SI and Ni-R states. The BP86 and B3LYP functionals were employed, and hybrid quantum mechanical (QM)/molecular mechanical (MM) methods were used for the embedded calculations. The QM/MM studies, rather than the isolated cluster calculations, were generally found to give structures which correlated better with X-ray data. The structure of the unready state (Ni-A), was correctly predicted by the QM/MM, but not by the isolated cluster calculation. Comparison with the observed crystal structure favoured the catalytically active state, Ni-SI, to be the protonated (Ni-SI(II)), rather than the unprotonated state (Ni-SI(I)). In the QM/MM studies, the binding of H(2) to Ni-SI(II) is preferred at the Ni (Ni-R(Ni)), rather than at the Fe centre (Ni-R(Fe)), in agreement with xenon binding studies, and in contrast to isolated cluster studies. These calculations cannot say with certainty which functional should be favoured, nor the preferred spin state of the catalytically active species. However, the lack of any predicted structure in which H(2) binds to the Fe centre, does favour a low spin state for Ni-SI(II), and the use of the BP86 functional. This is in agreement with recent high level ab initio calculations of a model of the Ni-SI(I) state. PMID:18633545

Jayapal, Prabha; Sundararajan, Mahesh; Hillier, Ian H; Burton, Neil A

2008-08-01

262

Nickel binding and [NiFe]-hydrogenase maturation by the metallochaperone SlyD with a single metal-binding site in Escherichia coli.  

PubMed

SlyD (sensitive to lysis D) is a nickel metallochaperone involved in the maturation of [NiFe]-hydrogenases in Escherichia coli (E. coli) and specifically contributes to the nickel delivery step during enzyme biosynthesis. This protein contains a C-terminal metal-binding domain that is rich in potential metal-binding residues that enable SlyD to bind multiple nickel ions with high affinity. The SlyD homolog from Thermus thermophilus does not contain the extended cysteine- and histidine-rich C-terminal tail of the E. coli protein, yet it binds a single Ni(II) ion tightly. To investigate whether a single metal-binding motif can functionally replace the full-length domain, we generated a truncation of E. coli SlyD, SlyD155. Ni(II) binding to SlyD155 was investigated by using isothermal titration calorimetry, NMR and electrospray ionization mass spectrometry measurements. This in vitro characterization revealed that SlyD155 contains a single metal-binding motif with high affinity for nickel. Structural characterization by X-ray absorption spectroscopy and NMR indicated that nickel was coordinated in an octahedral geometry with at least two histidines as ligands. Heterodimerization between SlyD and another hydrogenase accessory protein, HypB, is essential for optimal hydrogenase maturation and was confirmed for SlyD155 via cross-linking experiments and NMR titrations, as were conserved chaperone and peptidyl-prolyl isomerase activities. Although these properties of SlyD are preserved in the truncated version, it does not modulate nickel binding to HypB in vitro or contribute to the maturation of [NiFe]-hydrogenases in vivo, unlike the full-length protein. This study highlights the importance of the unusual metal-binding domain of E. coli SlyD in hydrogenase biogenesis. PMID:22310044

Kaluarachchi, Harini; Altenstein, Matthias; Sugumar, Sonia R; Balbach, Jochen; Zamble, Deborah B; Haupt, Caroline

2012-03-16

263

Reversible oxygen-tolerant hydrogenase carried by free-living N2-fixing bacteria isolated from the rhizospheres of rice, maize, and wheat  

PubMed Central

Hydrogen production by microorganisms is often described as a promising sustainable and clean energy source, but still faces several obstacles, which prevent practical application. Among them, oxygen sensitivity of hydrogenases represents one of the major limitations hampering the biotechnological implementation of photobiological production processes. Here, we describe a hierarchical biodiversity-based approach, including a chemochromic screening of hydrogenase activity of hundreds of bacterial strains collected from several ecosystems, followed by mass spectrometry measurements of hydrogenase activity of a selection of the H2-oxidizing bacterial strains identified during the screen. In all, 131 of 1266 strains, isolated from cereal rhizospheres and basins containing irradiating waste, were scored as H2-oxidizing bacteria, including Pseudomonas sp., Serratia sp., Stenotrophomonas sp., Enterobacter sp., Rahnella sp., Burkholderia sp., and Ralstonia sp. isolates. Four free-living N2-fixing bacteria harbored a high and oxygen-tolerant hydrogenase activity, which was not fully inhibited within entire cells up to 150–250 ?mol/L O2 concentration or within soluble protein extracts up to 25–30 ?mol/L. The only hydrogenase-related genes that we could reveal in these strains were of the hyc type (subunits of formate hydrogenlyase complex). The four free-living N2-fixing bacteria were closely related to Enterobacter radicincitans based on the sequences of four genes (16S rRNA, rpoB, hsp60, and hycE genes). These results should bring interesting prospects for microbial biohydrogen production and might have ecophysiological significance for bacterial adaptation to the oxic–anoxic interfaces in the rhizosphere.

Roumagnac, Philippe; Richaud, Pierre; Barakat, Mohamed; Ortet, Philippe; Roncato, Marie-Anne; Heulin, Thierry; Peltier, Gilles; Achouak, Wafa; Cournac, Laurent

2012-01-01

264

Purification and Characterization of the [NiFe]-Hydrogenase of Shewanella oneidensis MR-1 ?  

PubMed Central

Shewanella oneidensis MR-1 possesses a periplasmic [NiFe]-hydrogenase (MR-1 [NiFe]-H2ase) that has been implicated in H2 production and oxidation as well as technetium [Tc(VII)] reduction. To characterize the roles of MR-1 [NiFe]-H2ase in these proposed reactions, the genes encoding both subunits of MR-1 [NiFe]-H2ase were cloned and then expressed in an MR-1 mutant without hyaB and hydA genes. Expression of recombinant MR-1 [NiFe]-H2ase in trans restored the mutant's ability to produce H2 at 37% of that for the wild type. Following purification, MR-1 [NiFe]-H2ase coupled H2 oxidation to reduction of Tc(VII)O4? and methyl viologen. Change of the buffers used affected MR-1 [NiFe]-H2ase-mediated reduction of Tc(VII)O4? but not methyl viologen. Under the conditions tested, all Tc(VII)O4? used was reduced in Tris buffer, while in HEPES buffer, only 20% of Tc(VII)O4? was reduced. The reduced products were soluble in Tris buffer but insoluble in HEPES buffer. Transmission electron microscopy analysis revealed that Tc precipitates reduced in HEPES buffer were aggregates of crystallites with diameters of ?5 nm. Measurements with X-ray absorption near-edge spectroscopy revealed that the reduction products were a mixture of Tc(IV) and Tc(V) in Tris buffer but only Tc(IV) in HEPES buffer. Measurements with extended X-ray adsorption fine structure showed that while the Tc bonding environment in Tris buffer could not be determined, the Tc(IV) product in HEPES buffer was very similar to Tc(IV)O2·nH2O, which was also the product of Tc(VII)O4? reduction by MR-1 cells. These results shows for the first time that MR-1 [NiFe]-H2ase catalyzes Tc(VII)O4? reduction directly by coupling to H2 oxidation.

Shi, Liang; Belchik, Sara M.; Plymale, Andrew E.; Heald, Steve; Dohnalkova, Alice C.; Sybirna, Kateryna; Bottin, Herve; Squier, Thomas C.; Zachara, John M.; Fredrickson, James K.

2011-01-01

265

Iron Acyl Thiolato Carbonyls: Structural Models for the Active Site of the [Fe]-Hydrogenase (Hmd)  

PubMed Central

Phosphine-modified thioester derivatives are shown to serve as efficient precursors to phosphine-stabilized ferrous acyl thiolato carbonyls via the reaction of phosphine thioesters and sources of Fe(0). The reaction generates both Fe(SPh)(Ph2PC6H4CO)(CO)3 (1) and the diferrous diacyl Fe2(SPh)2(CO)3(Ph2PC6H4CO)2, which carbonylates to give 1. For the extremely bulky arylthioester Ph2PC6H4C(O)SC6H4-2,6-(2,4,6-trimethylphenyl)2, oxidative addition is arrested and the Fe(0) adduct of the phosphine is obtained. Complex 1 reacts with cyanide to give Et4N[Fe(SPh)(Ph2PC6H4CO)(CN)(CO)2] (Et4N[2]). 13C and 31P NMR spectra indicate that substitution is stereospecific and cis to P. The IR spectrum of [2]? in CH2Cl2 solution very closely matches that for HmdCN. XANES and EXAFS measurements also indicate close structural and electronic similarity of Et4N[2] to the active site of wild-type Hmd. Complex 1 also stereospecifically forms a derivative with TsCH2NC, but the adduct is more labile than Et4N[2]. Tricarbonyl 1 was found to reversibly protonate to give a thermally labile derivative, IR measurements of which indicate that the acyl and thiolate ligands are probably not protonated in Hmd.

Royer, Aaron M.; Salomone-Stagni, Marco

2012-01-01

266

Bimetallic carbonyl thiolates as functional models for Fe-only hydrogenases.  

PubMed

The anion [Fe(2)(S(2)C(3)H(6))(CN)(CO)(4)(PMe(3))](-) (2(-)) is protonated by sulfuric or toluenesulfonic acid to give HFe(2)(S(2)C(3)H(6))(CN)(CO)(4)(PMe(3)) (2H), the structure of which has the hydride bridging the Fe atoms with the PMe(3) and CN(-) trans to the same sulfur atom. (1)H, (13)C, and (31)P NMR spectroscopy revealed that HFe(2)(S(2)C(3)H(6))(CN)(CO)(4)(PMe(3)) is stereochemically rigid on the NMR time scale with four inequivalent carbonyl ligands. Treatment of 2(-) with (Me(3)O)BF(4) gave Fe(2)(S(2)C(3)H(6))(CNMe)(CO)(4)(PMe(3)) (2Me). The Et(4)NCN-induced reaction of Fe(2)(S(2)C(3)H(6))(CO)(6) with P(OMe)(3) gave [Fe(2)(S(2)C(3)H(6))(CN)(CO)(4)[P(OMe)(3)

Gloaguen, Frédéric; Lawrence, Joshua D; Rauchfuss, Thomas B; Bénard, Marc; Rohmer, Marie-Madeleine

2002-12-16

267

The Maturation Factors HoxR and HoxT Contribute to Oxygen Tolerance of Membrane-Bound [NiFe] Hydrogenase in Ralstonia eutropha H16 ? †  

PubMed Central

The membrane-bound [NiFe] hydrogenase (MBH) of Ralstonia eutropha H16 undergoes a complex maturation process comprising cofactor assembly and incorporation, subunit oligomerization, and finally twin-arginine-dependent membrane translocation. Due to its outstanding O2 and CO tolerance, the MBH is of biotechnological interest and serves as a molecular model for a robust hydrogen catalyst. Adaptation of the enzyme to oxygen exposure has to take into account not only the catalytic reaction but also biosynthesis of the intricate redox cofactors. Here, we report on the role of the MBH-specific accessory proteins HoxR and HoxT, which are key components in MBH maturation at ambient O2 levels. MBH-driven growth on H2 is inhibited or retarded at high O2 partial pressure (pO2) in mutants inactivated in the hoxR and hoxT genes. The ratio of mature and nonmature forms of the MBH small subunit is shifted toward the precursor form in extracts derived from the mutant cells grown at high pO2. Lack of hoxR and hoxT can phenotypically be restored by providing O2-limited growth conditions. Analysis of copurified maturation intermediates leads to the conclusion that the HoxR protein is a constituent of a large transient protein complex, whereas the HoxT protein appears to function at a final stage of MBH maturation. UV-visible spectroscopy of heterodimeric MBH purified from hoxR mutant cells points to alterations of the Fe-S cluster composition. Thus, HoxR may play a role in establishing a specific Fe-S cluster profile, whereas the HoxT protein seems to be beneficial for cofactor stability under aerobic conditions.

Fritsch, Johannes; Lenz, Oliver; Friedrich, Barbel

2011-01-01

268

Methanococcus voltae harbors four gene clusters potentially encoding two [NiFe] and two [NiFeSe] hydrogenases, each of the cofactor F 420 -reducing or F 420 -non-reducing types  

Microsoft Academic Search

Four gene clusters were identified inMethanococcus voltae which probably all encode hydrogenases of the [NiFe] type. One of these contains four genes, including those for the three subunits of the known [NiFeSe] hydrogenase capable of reducing the natural deazaflavin cofactor F420. In a second homologous cluster, the gene encoding the subunit corresponding to that which contains selenium in the know

Sabine Halboth; Albrecht Klein

1992-01-01

269

Accumulation of Ferrous Iron in Chlamydomonas reinhardtii. Influence of CO2 and Anaerobic Induction of the Reversible Hydrogenase1  

PubMed Central

The green alga, Chlamydomonas reinhardtii, can photoproduce molecular H2 via ferredoxin and the reversible [Fe]hydrogenase enzyme under anaerobic conditions. Recently, a novel approach for sustained H2 gas photoproduction was discovered in cell cultures subjected to S-deprived conditions (A. Melis, L. Zhang, M. Forestier, M.L. Ghirardi, M. Seibert [2000] Plant Physiol 122: 127–135). The close relationship between S and Fe in the H2-production process is of interest because Fe-S clusters are constituents of both ferredoxin and hydrogenase. In this study, we used Mössbauer spectroscopy to examine both the uptake of Fe by the alga at different CO2 concentrations during growth and the influence of anaerobiosis on the accumulation of Fe. Algal cells grown in media with 57Fe(III) at elevated (3%, v/v) CO2 concentration exhibit elevated levels of Fe and have two comparable pools of the ion: (a) Fe(III) with Mössbauer parameters of quadrupole splitting = 0.65 mm s?1 and isomeric shift = 0.46 mm s?1 and (b) Fe(II) with quadrupole splitting = 3.1 mm s?1 and isomeric shift = 1.36 mm s?1. Disruption of the cells and use of the specific Fe chelator, bathophenanthroline, have demonstrated that the Fe(II) pool is located inside the cell. The amount of Fe(III) in the cells increases with the age of the algal culture, whereas the amount of Fe(II) remains constant on a chlorophyll basis. Growing the algae under atmospheric CO2 (limiting) conditions, compared with 3% (v/v) CO2, resulted in a decrease in the intracellular Fe(II) content by a factor of 3. Incubating C. reinhardtii cells, grown at atmospheric CO2 for 3 h in the dark under anaerobic conditions, not only induced hydrogenase activity but also increased the Fe(II) content in the cells up to the saturation level observed in cells grown aerobically at high CO2. This result is novel and suggests a correlation between the amount of Fe(II) cations stored in the cells, the CO2 concentration, and anaerobiosis. A comparison of Fe-uptake results with a cyanobacterium, yeast, and algae suggests that the intracellular Fe(II) pool in C. reinhardtii may reside in the cell vacuole.

Semin, Boris K.; Davletshina, Lira N.; Novakova, Alla A.; Kiseleva, Tat'yana Y.; Lanchinskaya, Victoriya Y.; Aleksandrov, Anatolii Y.; Seifulina, Nora; Ivanov, Il'ya I.; Seibert, Michael; Rubin, Andrei B.

2003-01-01

270

The weak, fluctuating, dipole moment of membrane-bound hydrogenase from Aquifex aeolicus accounts for its adaptability to charged electrodes.  

PubMed

[NiFe] hydrogenases from Aquifex aeolicus (AaHase) and Desulfovibrio fructosovorans (DfHase) have been mainly studied to characterize physiological electron transfer processes, or to develop biotechnological devices such as biofuel cells. In this context, it remains difficult to control the orientation of AaHases on electrodes to achieve a fast interfacial electron transfer. Here, we study the electrostatic properties of these two proteins based on microsecond-long molecular dynamics simulations that we compare to voltammetry experiments. Our calculations show weak values and large fluctuations of the dipole direction in AaHase compared to DfHase, enabling the AaHase to absorb on both negatively and positively charged electrodes, with an orientation distribution that induces a spread in electron transfer rates. Moreover, we discuss the role of the transmembrane helix of AaHase and show that it does not substantially impact the general features of the dipole moment. PMID:24789038

Oteri, Francesco; Ciaccafava, Alexandre; Poulpiquet, Anne de; Baaden, Marc; Lojou, Elisabeth; Sacquin-Mora, Sophie

2014-05-21

271

Synthesis of the 2Fe subcluster of the [FeFe]-hydrogenase H cluster on the HydF scaffold  

PubMed Central

The organometallic H cluster at the active site of [FeFe]-hydrogenase consists of a 2Fe subcluster coordinated by cyanide, carbon monoxide, and a nonprotein dithiolate bridged to a [4Fe-4S] cluster via a cysteinate ligand. Biosynthesis of this cluster requires three accessory proteins, two of which (HydE and HydG) are radical S-adenosylmethionine enzymes. The third, HydF, is a GTPase. We present here spectroscopic and kinetic studies of HydF that afford fundamental new insights into the mechanism of H-cluster assembly. Electron paramagnetic spectroscopy reveals that HydF binds both [4Fe-4S] and [2Fe-2S] clusters; however, when HydF is expressed in the presence of HydE and HydG (HydFEG), only the [4Fe-4S] cluster is observed by EPR. Insight into the fate of the [2Fe-2S] cluster harbored by HydF is provided by FTIR, which shows the presence of carbon monoxide and cyanide ligands in HydFEG. The thorough kinetic characterization of the GTPase activity of HydF shows that activity can be gated by monovalent cations and further suggests that GTPase activity is associated with synthesis of the 2Fe subcluster precursor on HydF, rather than with transfer of the assembled precursor to hydrogenase. Interestingly, we show that whereas the GTPase activity is independent of the presence of the FeS clusters on HydF, GTP perturbs the EPR spectra of the clusters, suggesting communication between the GTP- and cluster-binding sites. Together, the results indicate that the 2Fe subcluster of the H cluster is synthesized on HydF from a [2Fe-2S] cluster framework in a process requiring HydE, HydG, and GTP.

Shepard, Eric M.; McGlynn, Shawn E.; Bueling, Alexandra L.; Grady-Smith, Celestine S.; George, Simon J.; Winslow, Mark A.; Cramer, Stephen P.; Peters, John W.; Broderick, Joan B.

2010-01-01

272

Crystal structures of the carbamoylated and cyanated forms of HypE for [NiFe] hydrogenase maturation  

PubMed Central

Hydrogenase pleiotropically acting protein (Hyp)E plays a role in biosynthesis of the cyano groups for the NiFe(CN)2CO center of [NiFe] hydrogenases by catalyzing the ATP-dependent dehydration of the carbamoylated C-terminal cysteine of HypE to thiocyanate. Although structures of HypE proteins have been determined, until now there has been no structural evidence to explain how HypE dehydrates thiocarboxamide into thiocyanate. Here, we report the crystal structures of the carbamoylated and cyanated forms of HypE from Thermococcus kodakarensis in complex with nucleotides at 1.53- and 1.64-Å resolution, respectively. Carbamoylation of the C-terminal cysteine (Cys338) of HypE by chemical modification is clearly observed in the present structures. In the presence of ATP, the thiocarboxamide of Cys338 is successfully dehydrated into the thiocyanate. In the carbamoylated state, the thiocarboxamide nitrogen atom of Cys338 is close to a conserved glutamate residue (Glu272), but the spatial position of Glu272 is less favorable for proton abstraction. On the other hand, the thiocarboxamide oxygen atom of Cys338 interacts with a conserved lysine residue (Lys134) through a water molecule. The close contact of Lys134 with an arginine residue lowers the pKa of Lys134, suggesting that Lys134 functions as a proton acceptor. These observations suggest that the dehydration of thiocarboxamide into thiocyanate is catalyzed by a two-step deprotonation process, in which Lys134 and Glu272 function as the first and second bases, respectively.

Tominaga, Taiga; Watanabe, Satoshi; Matsumi, Rie; Atomi, Haruyuki; Imanaka, Tadayuki; Miki, Kunio

2013-01-01

273

Crystal structures of the carbamoylated and cyanated forms of HypE for [NiFe] hydrogenase maturation.  

PubMed

Hydrogenase pleiotropically acting protein (Hyp)E plays a role in biosynthesis of the cyano groups for the NiFe(CN)2CO center of [NiFe] hydrogenases by catalyzing the ATP-dependent dehydration of the carbamoylated C-terminal cysteine of HypE to thiocyanate. Although structures of HypE proteins have been determined, until now there has been no structural evidence to explain how HypE dehydrates thiocarboxamide into thiocyanate. Here, we report the crystal structures of the carbamoylated and cyanated forms of HypE from Thermococcus kodakarensis in complex with nucleotides at 1.53- and 1.64-Å resolution, respectively. Carbamoylation of the C-terminal cysteine (Cys338) of HypE by chemical modification is clearly observed in the present structures. In the presence of ATP, the thiocarboxamide of Cys338 is successfully dehydrated into the thiocyanate. In the carbamoylated state, the thiocarboxamide nitrogen atom of Cys338 is close to a conserved glutamate residue (Glu272), but the spatial position of Glu272 is less favorable for proton abstraction. On the other hand, the thiocarboxamide oxygen atom of Cys338 interacts with a conserved lysine residue (Lys134) through a water molecule. The close contact of Lys134 with an arginine residue lowers the pKa of Lys134, suggesting that Lys134 functions as a proton acceptor. These observations suggest that the dehydration of thiocarboxamide into thiocyanate is catalyzed by a two-step deprotonation process, in which Lys134 and Glu272 function as the first and second bases, respectively. PMID:24297906

Tominaga, Taiga; Watanabe, Satoshi; Matsumi, Rie; Atomi, Haruyuki; Imanaka, Tadayuki; Miki, Kunio

2013-12-17

274

Delivery of Iron-Sulfur Clusters to the Hydrogen-Oxidizing [NiFe]-Hydrogenases in Escherichia coli Requires the A-Type Carrier Proteins ErpA and IscA  

PubMed Central

During anaerobic growth Escherichia coli synthesizes two membrane-associated hydrogen-oxidizing [NiFe]-hydrogenases, termed hydrogenase 1 and hydrogenase 2. Each enzyme comprises a catalytic subunit containing the [NiFe] cofactor, an electron-transferring small subunit with a particular complement of [Fe-S] (iron-sulfur) clusters and a membrane-anchor subunit. How the [Fe-S] clusters are delivered to the small subunit of these enzymes is unclear. A-type carrier (ATC) proteins of the Isc (iron-sulfur-cluster) and Suf (sulfur mobilization) [Fe-S] cluster biogenesis pathways are proposed to traffic pre-formed [Fe-S] clusters to apoprotein targets. Mutants that could not synthesize SufA had active hydrogenase 1 and hydrogenase 2 enzymes, thus demonstrating that the Suf machinery is not required for hydrogenase maturation. In contrast, mutants devoid of the IscA, ErpA or IscU proteins of the Isc machinery had no detectable hydrogenase 1 or 2 activities. Lack of activity of both enzymes correlated with the absence of the respective [Fe-S]-cluster-containing small subunit, which was apparently rapidly degraded. During biosynthesis the hydrogenase large subunits receive their [NiFe] cofactor from the Hyp maturation machinery. Subsequent to cofactor insertion a specific C-terminal processing step occurs before association of the large subunit with the small subunit. This processing step is independent of small subunit maturation. Using western blotting experiments it could be shown that although the amount of each hydrogenase large subunit was strongly reduced in the iscA and erpA mutants, some maturation of the large subunit still occurred. Moreover, in contrast to the situation in Isc-proficient strains, these processed large subunits were not membrane-associated. Taken together, our findings demonstrate that both IscA and ErpA are required for [Fe-S] cluster delivery to the small subunits of the hydrogen-oxidizing hydrogenases; however, delivery of the Fe atom to the active site might have different requirements.

Pinske, Constanze; Sawers, R. Gary

2012-01-01

275

Cloning of hydrogenase genes and fine structure analysis of an operon essential for H/sub 2/ metabolism in Escherichia coli  

SciTech Connect

Escherichia coli has two unlinked genes that code for hydrogenase synthesis and activity. The DNA fragments containing the two genes (hydA and hydB) were cloned into a plasmid vector, pBR322. The plasmids containing the hyd genes (pSE-290 and pSE-111 carrying the hydA and hydB genes, respectively) were used to genetically map a total of 51 mutant strains with defects in hydrogenase activity. A total of 37 mutants carried a mutation in the hydB gene, whereas the remaining 14 hyd were hydA. This complementation analysis also established the presence of two new genes, so far unidentified, one coding for formate dehydrogenase-2 (fdv) and another producing an electron transport protein (fhl) coupling formate dehydrogenase-2 to hydrogenase. Three of the four genes, hydB, fhl, and fdv, may constitute a single operon, and all three genes are carried by a 5.6-kilobase-pair chromosomal DNA insert in plasmid pSE-128. Plasmids carrying a part of this 5.6-kilobase-pair DNA (pSE-130) or fragments derived from this DNA in different orientations (pSE-126 and pSE-129) inhibited the production of active formate hydrogenlyase. This inhibition occurred even in a prototrophic E. coli, strain K-10, but only during an early induction period. These results, based on complementation analysis with cloned DNA fragments, show that both hydA and hydB genes are essential for the production of active hydrogenase. For the expression of active formate hydrogenlyase, two other gene products, fhl and fdv are also needed. All four genes map between 58 and 59 min in the E. coli chromosome.

Sankar, P.; Lee, J.H.; Shanmugam, K.T.

1985-04-01

276

An orientation-selected ENDOR and HYSCORE study of the NiC active state of Desulfovibrio vulgaris Miyazaki F hydrogenase  

Microsoft Academic Search

Electron nuclear double resonance (ENDOR) and hyperfine sublevel correlation spectroscopy (HYSCORE) are applied to study the active site of catalytic [NiFe]-hydrogenase from Desulfovibrio vulgaris Miyazaki F in the reduced Ni-C state. These techniques offer a powerful tool for detecting nearby magnetic nuclei, including a metal-bound substrate hydrogen, and for mapping the spin density distribution of the unpaired electron at the

Stefanie Foerster; Maurice van Gastel; Marc Brecht; Wolfgang Lubitz

2005-01-01

277

Hydrogenase activity in the foodborne pathogen Campylobacter jejuni depends upon a novel ABC-type nickel transporter (NikZYXWV) and is SlyD-independent.  

PubMed

Campylobacter jejuni is a human pathogen of worldwide significance. It is commensal in the gut of many birds and mammals, where hydrogen is a readily available electron donor. The bacterium possesses a single membrane-bound, periplasmic-facing NiFe uptake hydrogenase that depends on the acquisition of environmental nickel for activity. The periplasmic binding protein Cj1584 (NikZ) of the ATP binding cassette (ABC) transporter encoded by the cj1584c-cj1580c (nikZYXWV) operon in C. jejuni strain NCTC 11168 was found to be nickel-repressed and to bind free nickel ions with a submicromolar K(d) value, as measured by fluorescence spectroscopy. Unlike the Escherichia coli NikA protein, NikZ did not bind EDTA-chelated nickel and lacks key conserved residues implicated in metallophore interaction. A C. jejuni cj1584c null mutant strain showed an approximately 22-fold decrease in intracellular nickel content compared with the wild-type strain and a decreased rate of uptake of (63)NiCl(2). The inhibition of residual nickel uptake at higher nickel concentrations in this mutant by hexa-ammine cobalt (III) chloride or magnesium ions suggests that low-affinity uptake occurs partly through the CorA magnesium transporter. Hydrogenase activity was completely abolished in the cj1584c mutant after growth in unsupplemented media, but was fully restored after growth with 0.5 mM nickel chloride. Mutation of the putative metallochaperone gene slyD (cj0115) had no effect on either intracellular nickel accumulation or hydrogenase activity. Our data reveal a strict dependence of hydrogenase activity in C. jejuni on high-affinity nickel uptake through an ABC transporter that has distinct properties compared with the E. coli Nik system. PMID:22403188

Howlett, Robert M; Hughes, Bethan M; Hitchcock, Andrew; Kelly, David J

2012-06-01

278

Specificity and selectivity of HypC chaperonins and endopeptidases in the molecular assembly machinery of [NiFe] hydrogenases of Thiocapsa roseopersicina  

Microsoft Academic Search

The purple photosynthetic bacterium, Thiocapsa roseopersicina harbours at least three functional [NiFe] hydrogenases. Two of them are attached to the periplasmic membrane (HynSL, HupSL), while the third one is apparently localized in the cytoplasm (HoxEFUYH). Two hypC-type genes, coding for putative small maturation proteins, were found and their roles were studied by activity measurements performed with hypC mutants. Protein–protein interaction

Gergely Maróti; Gábor Rákhely; Judit Maróti; Emma Dorogházi; Eva Klement; Katalin F. Medzihradszky; Kornél L. Kovács

2010-01-01

279

Transposon Mutagenesis in Purple Sulfur Photosynthetic Bacteria: Identification of hypF, Encoding a Protein Capable of Processing [NiFe] Hydrogenases in  ,  , and   Subdivisions of the Proteobacteria  

Microsoft Academic Search

A random transposon-based mutagenesis system was optimized for the purple sulfur phototrophic bacte- rium Thiocapsa roseopersicina BBS. Screening for hydrogenase-deficient phenotypes resulted in the isolation of six independent mutants in a mini-Tn5 library. One of the mutations was in a gene showing high amino acid sequence similarity to HypF proteins in other organisms. Inactivation of hydrogen uptake activity in the

BARNA FODOR; GABOR RAKHELY; AKOS T. KOVACS; KORNEL L. KOVACS

2001-01-01

280

Molecular characterization and heterologous expression of hypCD , the first two [NiFe] hydrogenase accessory genes of Thermococcus litoralis  

Microsoft Academic Search

The hypCD genes, encoding the counterparts of mesophilic proteins involved in the maturation of [NiFe] hydrogenases, were isolated from the hyperthermophilic archaeon Thermococcus litoralis. The deduced gene products showed 30-40% identity to the corresponding mesophilic proteins. HypC and HypD were synthesized by the T7 expression system. Heterologous complementation experiments were done in Escherichia coli and Ralstonia eutropha strains lacking functionally

Mária Takács; Gábor Rákhely; Kornél L. Kovács

2001-01-01

281

Impact of amino acid substitutions near the catalytic site on the spectral properties of an O2-tolerant membrane-bound [NiFe] hydrogenase.  

PubMed

[NiFe] hydrogenases are widespread among microorganisms and catalyze the reversible cleavage of molecular hydrogen. However, only a few bacteria, such as Ralstonia eutropha H16 (Re), synthesize [NiFe] hydrogenases that perform H(2) cycling in the presence of O(2). These enzymes are of special interest for biotechnological applications. To gain further insight into the mechanism(s) responsible for the remarkable O(2) tolerance, we employ FTIR and EPR spectroscopy to study mutant variants of the membrane-bound hydrogenase (MBH) of Re-carrying substitutions of a particular cysteine residue in the vicinity of the [NiFe] active site that is characteristic of O(2)-tolerant membrane-bound [NiFe] hydrogenases. We demonstrate that these MBH variants, despite minor changes in the electronic structure and in the interaction behavior with the embedding protein matrix, display all relevant catalytic and noncatalytic states of the wild-type enzyme, as long as they are still located in the cytoplasmic membrane. Notably, in the oxidized Ni(r)-B state and the fully reduced forms, the CO stretching frequency increases with increasing polarity of the respective amino acid residue at the specific position of the cysteine residue. We purified the MBH mutant protein with a cysteine-to-alanine exchange to apparent homogeneity as dimeric enzyme after detergent solubilization from the membrane. This purified version displays increased oxygen sensitivity, which is reflected by detection of the oxygen-inhibited Ni(u)-A state, an irreversible inactive redox state, and the light-induced Ni(a)-L state even at room temperature. PMID:20376875

Saggu, Miguel; Ludwig, Marcus; Friedrich, Bärbel; Hildebrandt, Peter; Bittl, Robert; Lendzian, Friedhelm; Lenz, Oliver; Zebger, Ingo

2010-04-26

282

Investigation of the FeFe-hydrogenase gene diversity combined with phylogenetic microbial community analysis of an anaerobic domestic sewage sludge.  

PubMed

Biological hydrogen production through the anaerobic digestion is an environmental friendly alternative for satisfying future hydrogen demands. Microorganisms residing into waste water treatment plants are far from being exhaustively characterized and surveys on hydrogen production through FeFe-hydrogenase in such ecosystems are scarce. This study combined the analysis of 16S rRNA and [FeFe]-hydrogenase (hydA) genes with statistical tools to estimate richness and diversity of the microbial community of a domestic sewage treatment plant at the phylogenetic and functional levels. Archaeal groups were represented by 69 % of sequences assigned to Methanosarcinales and the remaining belonged to Methanomicrobiales. Within the bacterial library, 136 operational taxonomic units (OTUs) were distributed into 9 phyla, being 86 OTUs related to uncultivated bacteria. From these, 25 OTUs represented potential novel taxa within Synergistetes. Proteobacteria was the most predominant (36 % of the OTUs) and diversified phylogenetic group in the bacterial library, most of them assigned to the class Betaproteobacteria. Twenty-two putative hydA sequences were recovered into four distinct clusters and most of them were more closely related to each other than with sequences retrieved from databases, indicating they are hitherto undetected [Fe-Fe]-hydrogenase gene sequences. The richness estimates revealed that the number of sampled sequences was enough for full coverage of the archaeal diversity but not sufficient to cover both bacterial and hydA gene diversities. The results confirmed a great richness and diversity of bacterial and hydA sequences retrieved from the sewage sludge sample, suggesting such environment as a potential reservoir of new hydrogenase genes for biotechnological exploration. PMID:23632909

Tomazetto, Geizecler; Oliveira, Valéria M

2013-11-01

283

Cloning, sequence determination, and expression of the genes encoding the subunits of the nickel-containing 8-hydroxy-5-deazaflavin reducing hydrogenase from Methanobacterium thermoautotrophicum. Delta. H  

SciTech Connect

The genes frhA (1,217 bp), frhB (845 bp), and frhG (710 bp) encoding the three known subunits, {alpha}, {beta}, and {gamma}, of the 8-hydroxy-5-deazaflavin (F{sub 420}) reducing hydrogenase (FRH) from the thermophilic methanogen Methanobacterium thermoautotrophicum {Delta}H have been cloned, sequenced, and shown to be tightly linked, indicative of a single transcriptional unit. The DNA sequence contains a fourth open reading frame, designated frhD (476 bp), encoding a polypeptide ({delta}) that does not copurify with the active enzyme. Expression of the frh gene cluster in Escherichia coli shows that four polypeptides are synthesized. When analyzed by SDS-PAGE, the proteins migrate with mobilities consistent with their calculated molecular weights. In order to understand the mechanism of H{sub 2} oxidation by this enzyme, localization of redox cofactors (Ni, Fe/S, FAD) to specific subunits and information on their structure is needed. This has been hindered due to the refractory nature of the enzyme to denaturation methods needed in order to obtain individual subunits with cofactors intact. In this paper they discuss the possible localization of the redox cofactors as implicated from the DNA-derived protein sequences of the subunits. The amino acid sequences of the subunits of the FRH are compared with those of other Ni-containing hydrogenases, including the methyl viologen reducing hydrogenase (MVH) of M. thermoautotrophicum {Delta}H.

Alex, L.A. (Harvard Medical School, Boston, MA (USA) Massachusetts Institute of Technology, Cambridge (USA)); Reeve, J.N. (Ohio State Univ., Columbus (USA)); Orme-Johnson, W.H. (Massachusetts Institute of Technology, Cambridge (USA)); Walsh, C.T. (Harvard Medical School, Cambridge, MA (USA))

1990-08-07

284

Characterization of a unique [FeS] cluster in the electron transfer chain of the oxygen tolerant [NiFe] hydrogenase from Aquifex aeolicus  

PubMed Central

Iron-sulfur clusters are versatile electron transfer cofactors, ubiquitous in metalloenzymes such as hydrogenases. In the oxygen-tolerant Hydrogenase I from Aquifex aeolicus such electron “wires” form a relay to a diheme cytb, an integral part of a respiration pathway for the reduction of O2 to water. Amino acid sequence comparison with oxygen-sensitive hydrogenases showed conserved binding motifs for three iron-sulfur clusters, the nature and properties of which were unknown so far. Electron paramagnetic resonance spectra exhibited complex signals that disclose interesting features and spin-coupling patterns; by redox titrations three iron-sulfur clusters were identified in their usual redox states, a [3Fe4S] and two [4Fe4S], but also a unique high-potential (HP) state was found. On the basis of 57Fe Mössbauer spectroscopy we attribute this HP form to a superoxidized state of the [4Fe4S] center proximal to the [NiFe] site. The unique environment of this cluster, characterized by a surplus cysteine coordination, is able to tune the redox potentials and make it compliant with the [4Fe4S]3+ state. It is actually the first example of a biological [4Fe4S] center that physiologically switches between 3+, 2+, and 1+ oxidation states within a very small potential range. We suggest that the (1 + /2+) redox couple serves the classical electron transfer reaction, whereas the superoxidation step is associated with a redox switch against oxidative stress.

Pandelia, Maria-Eirini; Nitschke, Wolfgang; Infossi, Pascale; Giudici-Orticoni, Marie-Therese; Bill, Eckhard; Lubitz, Wolfgang

2011-01-01

285

Characterization of a unique [FeS] cluster in the electron transfer chain of the oxygen tolerant [NiFe] hydrogenase from Aquifex aeolicus.  

PubMed

Iron-sulfur clusters are versatile electron transfer cofactors, ubiquitous in metalloenzymes such as hydrogenases. In the oxygen-tolerant Hydrogenase I from Aquifex aeolicus such electron "wires" form a relay to a diheme cytb, an integral part of a respiration pathway for the reduction of O(2) to water. Amino acid sequence comparison with oxygen-sensitive hydrogenases showed conserved binding motifs for three iron-sulfur clusters, the nature and properties of which were unknown so far. Electron paramagnetic resonance spectra exhibited complex signals that disclose interesting features and spin-coupling patterns; by redox titrations three iron-sulfur clusters were identified in their usual redox states, a [3Fe4S] and two [4Fe4S], but also a unique high-potential (HP) state was found. On the basis of (57)Fe Mössbauer spectroscopy we attribute this HP form to a superoxidized state of the [4Fe4S] center proximal to the [NiFe] site. The unique environment of this cluster, characterized by a surplus cysteine coordination, is able to tune the redox potentials and make it compliant with the [4Fe4S](3+) state. It is actually the first example of a biological [4Fe4S] center that physiologically switches between 3+, 2+, and 1+ oxidation states within a very small potential range. We suggest that the (1 + /2+) redox couple serves the classical electron transfer reaction, whereas the superoxidation step is associated with a redox switch against oxidative stress. PMID:21444783

Pandelia, Maria-Eirini; Nitschke, Wolfgang; Infossi, Pascale; Giudici-Orticoni, Marie-Thérèse; Bill, Eckhard; Lubitz, Wolfgang

2011-04-12

286

Computational studies of the H-cluster of Fe-only hydrogenases: geometric, electronic, and magnetic properties and their dependence on the [Fe4S4] cubane.  

PubMed

The active sites of Fe-only hydrogenases (FeHases) feature an unusual polynuclear iron-sulfur cluster, known as the H-cluster, that consists of a [Fe4S4] cubane linked to a di-iron subunit (the [2Fe]H component) via a bridging cysteine ligand (SCys). While previous computational studies of FeHases employed H-cluster models that only included the [2Fe]H component, we have utilized density functional theory (DFT), in conjunction with the broken-symmetry (BS) approach, to explore the geometric, electronic, and magnetic properties of the entire H-cluster. These calculations have allowed us to evaluate, for the first time, the influence of the [Fe4S4] cubane on the [2Fe]H component of the H-cluster in its active (Hox) and CO-inhibited (Hox-CO) states, both of which are paramagnetic (S=1/2). Our results reveal that the presence of the cubane tunes both the position and the donor strength of the SCys ligand, which, in turn, modulates the internal geometric and electronic structures of the [2Fe]H subcluster. Importantly, the BS methodology provides an accurate description of the exchange interactions within the H-cluster, permitting insight into the electronic origin of the changes in magnetic properties observed experimentally upon conversion of Hox to Hox-CO. Specifically, while the unpaired spin density in the Hox state is localized on the distal Fe center, in the Hox-CO state, it is delocalized over the [2Fe]H component, such that the proximal Fe center acquires significant spin density (where distal and proximal refer to the positions of the Fe centers relative to the cubane). To validate our H-cluster models on the basis of experimental data, two DFT-based approaches and the semiempirical INDO/S method have been employed to compute electron paramagnetic resonance parameters for the H-cluster states. While most computations yield reasonably accurate g values and ligand hyperfine coupling constants (i.e., A values) for the Hox and Hox-CO states, they fail to reproduce the isotropic 57Fe A tensors found experimentally. Finally, extension of the computational methodology employed successfully for the Hox and Hox-CO states to the metastable Hoxphoto state, generated by irradiation of the Hox-CO state at cryogenic temperatures, has allowed us to discriminate between proposed structural models for this species. PMID:16323916

Fiedler, Adam T; Brunold, Thomas C

2005-12-12

287

Bis[1,2-bis-(eth-oxy-carbon-yl)ethene-1,2-dithiol-ato-?(2) S,S']bis-(?(5)-penta-methyl-cyclo-penta-dien-yl)tetra-?3-sulfido-diiron(IV)diiron(III)(3 Fe-Fe).  

PubMed

The title compound, [Fe4(C10H15)2(C8H10O4S2)2S4], contains a twisted Fe4S4 cubane-like core. A twofold rotation axis passes through the Fe4S4 core, completing the coordination of the four Fe atoms with two penta-methyl-cyclo-penta-dienyl ligands and two chelating dithiol-ate ligands. There are three short Fe-Fe and three long Fe?Fe contacts in the Fe4S4 core, suggesting bonding and non-bonding inter-actions, respectively. The Fe-S bonds in the Fe4S4 core range from 2.1523?(5) to 2.2667?(6)?Å and are somewhat longer than the Fe-S bonds involving the dithiol-ate ligand. PMID:23633986

Ito, Shohei; Hisamichi, Nozomu; Takase, Tsugiko; Inomata, Shinji

2013-04-01

288

Bis[1,2-bis-(eth-oxy-carbon-yl)ethene-1,2-dithiol-ato-?2 S,S?]bis-(?5-penta-methyl-cyclo-penta-dien-yl)tetra-?3-sulfido-diiron(IV)diiron(III)(3 Fe--Fe)  

PubMed Central

The title compound, [Fe4(C10H15)2(C8H10O4S2)2S4], contains a twisted Fe4S4 cubane-like core. A twofold rotation axis passes through the Fe4S4 core, completing the coordination of the four Fe atoms with two penta­methyl­cyclo­penta­dienyl ligands and two chelating dithiol­ate ligands. There are three short Fe—Fe and three long Fe?Fe contacts in the Fe4S4 core, suggesting bonding and non-bonding inter­actions, respectively. The Fe—S bonds in the Fe4S4 core range from 2.1523?(5) to 2.2667?(6)?Å and are somewhat longer than the Fe—S bonds involving the dithiol­ate ligand.

Ito, Shohei; Hisamichi, Nozomu; Takase, Tsugiko; Inomata, Shinji

2013-01-01

289

Direct Probing of Photoinduced Electron Transfer in a Self-Assembled Biomimetic [2Fe2S]-Hydrogenase Complex Using Ultrafast Vibrational Spectroscopy.  

PubMed

A pyridyl-functionalized diiron dithiolate complex, [?-(4-pyCH2-NMI-S2)Fe2(CO)6] (3, py = pyridine (ligand), NMI = naphthalene monoimide) was synthesized and fully characterized. In the presence of zinc tetraphenylporphyrin (ZnTPP), a self-assembled 3·ZnTPP complex was readily formed in CH2Cl2 by the coordination of the pyridyl nitrogen to the porphyrin zinc center. Ultrafast photoinduced electron transfer from excited ZnTPP to complex 3 in the supramolecular assembly was observed in real time by monitoring the ?(C?O) and ?(C?O)NMI spectral changes with femtosecond time-resolved infrared (TRIR) spectroscopy. We have confirmed that photoinduced charge separation produced the monoreduced species by comparing the time-resolved IR spectra with the conventional IR spectra of 3(•-) generated by reversible electrochemical reduction. The lifetimes for the charge separation and charge recombination processes were found to be ?CS = 40 ± 3 ps and ?CR = 205 ± 14 ps, respectively. The charge recombination is much slower than that in an analogous covalent complex, demonstrating the potential of a supramolecular approach to extend the lifetime of the charge-separated state in photocatalytic complexes. The observed vibrational frequency shifts provide a very sensitive probe of the delocalization of the electron-spin density over the different parts of the Fe2S2 complex. The TR and spectro-electrochemical IR spectra, electron paramagnetic resonance spectra, and density functional theory calculations all show that the spin density in 3(•-) is delocalized over the diiron core and the NMI bridge. This delocalization explains why the complex exhibits low catalytic dihydrogen production even though it features a very efficient photoinduced electron transfer. The ultrafast porphyrin-to-NMI-S2-Fe2(CO)6 photoinduced electron transfer is the first reported example of a supramolecular Fe2S2-hydrogenase model studied by femtosecond TRIR spectroscopy. Our results show that TRIR spectroscopy is a powerful tool to investigate photoinduced electron transfer in potential dihydrogen-producing catalytic complexes, and that way to optimize their performance by rational approaches. PMID:24766080

Li, Ping; Amirjalayer, Saeed; Hartl, František; Lutz, Martin; Bruin, Bas de; Becker, René; Woutersen, Sander; Reek, Joost N H

2014-05-19

290

New Nitrosyl Derivatives of Diiron Dithiolates Related to the Active Site of the [FeFe]-Hydrogenases  

PubMed Central

Nitrosyl derivatives of diiron dithiolato carbonyls have been prepared starting from the versatile precursor Fe2(S2CnH2n)(dppv)(CO)4 (dppv = cis-1,2-bis(diphenylphosphinoethylene). These studies expand the range of substituted diiron(I) dithiolato carbonyl complexes. From [Fe2(S2C2H4)(CO)3(dppv)(NO)]BF4 ([1(CO)3]BF4), the following compounds were prepared: [1(CO)2(PMe3)]BF4, [1(CO)(dppv)]BF4, NEt4[1(CO)(CN)2], and 1(CO)(CN)(PMe3). Some if not all of these substitution reactions occur via the addition of two equiv of the nucleophile followed by dissociation of one nucleophile and decarbonylation. Such a double adduct was characterized crystallographically in the case of [Fe2(S2C2H4)(CO)3(dppv)(NO)(PMe3)2]BF4. This result shows that the addition of two ligands causes scission of the Fe-Fe bond and one Fe-S bond. When cyanide is the nucleophile, nitrosyl migrates away from the Fe(dppv) site, yielding a Fe(CN)(NO)(CO) derivative. Compounds [1(CO)3]BF4, [1(CO)2(PMe3)]BF4, and [1(CO)(dppv)]BF4 were also prepared by the addition of NO+ to the di-, tri- and tetrasubstituted precursors. In these cases, the NO+ appears to form an initial 36e-adduct containing terminal Fe-NO, followed by decarbonylation. Several complexes were prepared by the addition of NO to the mixed-valence Fe(I)Fe(II) derivatives. The diiron nitrosyl complexes reduce at mild potentials and in certain cases form weak adducts with CO.

Olsen, Matthew T.; Justice, Aaron K.; Gloaguen, Frederic; Wilson, Scott R.

2008-01-01

291

Spin distribution of the H-cluster in the H ox –CO state of the [FeFe] hydrogenase from Desulfovibrio desulfuricans : HYSCORE and ENDOR study of 14 N and 13 C nuclear interactions  

Microsoft Academic Search

Hydrogenases are enzymes which catalyze the reversible cleavage of molecular hydrogen into protons and electrons. In [FeFe] hydrogenases\\u000a the active center is a 6Fe6S cluster, referred to as the “H-cluster.” It consists of the redox-active binuclear subcluster\\u000a ([2Fe]H) coordinated by CN? and CO ligands and the cubane-like [4Fe–4S]H subcluster which is connected to the protein via Cys ligands. One of these

Alexey Silakov; Brian Wenk; Eduard Reijerse; Simon P. J. Albracht; Wolfgang Lubitz

2009-01-01

292

Electrocatalytic hydrogen generation by a trithiolato-bridged dimanganese hexacarbonyl anion with a turnover frequency exceeding 40?000 s(-1.).  

PubMed

An unusual ionic manganese model complex [Mn(bpy)3](+)[(CO)3Mn(?-SPh)3Mn(CO)3](-)(bpy: 2,2'-bipyridine) has been synthesized, which bears some structural resemblance to the active site of [FeFe] hydrogenase. An overpotential of 0.61 V has been determined for the electrocatalytic proton reduction using this complex in CH3CN with CF3COOH as the proton source. A turnover frequency of 44?600 s(-1) is achieved at high scan rates and in the presence of a large amount of acid. PMID:24817512

Hou, Kaipeng; Poh, Hwa Tiong; Fan, Wai Yip

2014-05-27

293

Bias from H2 cleavage to production and coordination changes at the Ni-Fe active site in the NAD+-reducing hydrogenase from Ralstonia eutropha.  

PubMed

The soluble NAD+-reducing Ni-Fe hydrogenase (SH) from Ralstonia eutropha H16 is remarkable because it cleaves hydrogen in the presence of dioxygen at a unique Ni-Fe active site (Burgdorf et al. (2005) J. Am. Chem. Soc. 127, 576). By X-ray absorption (XAS), FTIR, and EPR spectroscopy, we monitored the structure and oxidation state of its metal centers during H2 turnover. In NADH-activated protein, a change occurred from the (CN)O2Ni(II)(mu-S)2Fe(II)(CN)3(CO) site dominant in the wild-type SH to a standard-like S2Ni(II)(mu-S)2Fe(II)(CN)2(CO) site as the prevailing species in a specific mutant protein, HoxH-H16L. The wild-type SH primarily was active in H2 cleavage. The nonstandard reaction mechanism does not involve stable EPR-detectable trivalent Ni oxidation states, namely, the Ni-A,B,C states as observed in standard hydrogenases. In the HoxH-mutant protein H16L, H2 oxidation was impaired, but H2 production occurred via a stable Ni-C state (Ni(III)-H(-)-Fe(II)), suggesting a reaction sequence similar to that of standard hydrogenases. It is proposed that reductive activation by NADH of both wild-type and H16L proteins causes the release of an oxygen species from Ni and is initiated by electron transfer from a [2Fe-2S] cluster in the HoxU subunit that at first becomes reduced by electrons from NADH. Electrons derived from H2 cleavage, on the other hand, are transferred to NAD+ via a different pathway involving a [4Fe-4S] cluster in HoxY, which is reducible only in wild-type SH but not in the H16L variant. PMID:16981725

Löscher, Simone; Burgdorf, Tanja; Zebger, Ingo; Hildebrandt, Peter; Dau, Holger; Friedrich, Bärbel; Haumann, Michael

2006-09-26

294

Structure of [NiFe] Hydrogenase Maturation Protein HypE from Escherichia coli and its Interaction with HypF  

SciTech Connect

Hydrogenases are enzymes involved in hydrogen metabolism, utilizing H2 as an electron source. [NiFe] hydrogenases are heterodimeric Fe-S proteins, with a large subunit containing the reaction center involving Fe and Ni metal ions and a small subunit containing one or more Fe-S clusters. Maturation of the [NiFe] hydrogenase involves assembly of nonproteinaceous ligands on the large subunit by accessory proteins encoded by the hyp operon. HypE is an essential accessory protein and participates in the synthesis of two cyano groups found in the large subunit. We report the crystal structure of Escherichia coli HypE at 2.0- Angstroms resolution. HypE exhibits a fold similar to that of PurM and ThiL and forms dimers. The C-terminal catalytically essential Cys336 is internalized at the dimer interface between the N- and C-terminal domains. A mechanism for dehydration of the thiocarbamate to the thiocyanate is proposed, involving Asp83 and Glu272. The interactions of HypE and HypF were characterized in detail by surface plasmon resonance and isothermal titration calorimetry, revealing a Kd (dissociation constant) of {approx}400 nM. The stoichiometry and molecular weights of the complex were verified by size exclusion chromatography and gel scanning densitometry. These experiments reveal that HypE and HypF associate to form a stoichiometric, hetero-oligomeric complex predominantly consisting of a [EF]2 heterotetramer which exists in a dynamic equilibrium with the EF heterodimer. The surface plasmon resonance results indicate that a conformational change occurs upon heterodimerization which facilitates formation of a productive complex as part of the carbamate transfer reaction.

Rangarajan,E.; Asinas, A.; Proteau, A.; Munger, C.; Baardsnes, j.; Iannuzzi, P.; Matte, A.; Cygler, m.

2008-01-01

295

Langmuir-Blodgett films of pyridyldithio-modified multiwalled carbon nanotubes as a support to immobilize hydrogenase.  

PubMed

Pyridylthio-modified multiwalled carbon nanotubes (pythio-MWNTs) have been prepared by a reaction of the oxidized MWNTs with S-(2-aminoethylthio)-2-thiopyridine hydrochloride. The obtained pythio-MWNTs nanocomposites formed stable floating monolayers at the air-water interface, which were transferred onto substrate surfaces by the Langmuir-Blodgett (LB) method. Compositions and morphologies of the LB films were characterized by absorption, Raman, X-ray photoelectron spectra as well as by scan electron microscopy and atomic force microscopy. These pythio-MWNTs LB films were then used as a support to immobilize hydrogenase (H(2)ase) to form bionanocomposite of pythio-MWNTs-H(2)ase. Cyclic voltammograms for indium tin oxide electrode covered with the pythio-MWNTs-H(2)ase films were investigated in both Ar and H(2) saturated 0.05 M KCl electrolyte solutions at pH from 4.0 to 9.0. A reversible redox couple of [4Fe-4S](2+/1+) clusters of H(2)ase was recorded when the pH value was 6.0 and 9.0, with reduction and oxidation potentials appearing at about -0.70 and -0.35 V vs Ag/AgCl, respectively. It was revealed that the H(2)ase was of high catalytic activity and strong stability in the LB films of pythio-MWNTs-H(2)ase. Hence, we suggested that the present bionanocomposites could be used as heterogeneous biocatalyst to catalyze reversible reaction between protons and H(2), resulting in potential applications in biohydrogen evolution and H(2) biofuel cells. PMID:20355722

Sun, Qing; Zorin, Nikolay A; Chen, Dan; Chen, Meng; Liu, Tian-Xi; Miyake, Jun; Qian, Dong-Jin

2010-06-15

296

Catalytic properties of the isolated diaphorase fragment of the NAD-reducing [NiFe]-hydrogenase from Ralstonia eutropha.  

PubMed

The NAD+-reducing soluble hydrogenase (SH) from Ralstonia eutropha H16 catalyzes the H?-driven reduction of NAD+, as well as reverse electron transfer from NADH to H+, in the presence of O?. It comprises six subunits, HoxHYFUI?, and incorporates a [NiFe] H+/H? cycling catalytic centre, two non-covalently bound flavin mononucleotide (FMN) groups and an iron-sulfur cluster relay for electron transfer. This study provides the first characterization of the diaphorase sub-complex made up of HoxF and HoxU. Sequence comparisons with the closely related peripheral subunits of Complex I in combination with UV/Vis spectroscopy and the quantification of the metal and FMN content revealed that HoxFU accommodates a [2Fe2S] cluster, FMN and a series of [4Fe4S] clusters. Protein film electrochemistry (PFE) experiments show clear electrocatalytic activity for both NAD+ reduction and NADH oxidation with minimal overpotential relative to the potential of the NAD+/NADH couple. Michaelis-Menten constants of 56 µM and 197 µM were determined for NADH and NAD+, respectively. Catalysis in both directions is product inhibited with K(I) values of around 0.2 mM. In PFE experiments, the electrocatalytic current was unaffected by O?, however in aerobic solution assays, a moderate superoxide production rate of 54 nmol per mg of protein was observed, meaning that the formation of reactive oxygen species (ROS) observed for the native SH can be attributed mainly to HoxFU. The results are discussed in terms of their implications for aerobic functioning of the SH and possible control mechanism for the direction of catalysis. PMID:22016788

Lauterbach, Lars; Idris, Zulkifli; Vincent, Kylie A; Lenz, Oliver

2011-01-01

297

Activation process of [NiFe] hydrogenase elucidated by high-resolution X-ray analyses: conversion of the ready to the unready state.  

PubMed

Hydrogenases catalyze oxidoreduction of molecular hydrogen and have potential applications for utilizing dihydrogen as an energy source. [NiFe] hydrogenase has two different oxidized states, Ni-A (unready, exhibits a lag phase in reductive activation) and Ni-B (ready). We have succeeded in converting Ni-B to Ni-A with the use of Na2S and O2 and determining the high-resolution crystal structures of both states. Ni-B possesses a monatomic nonprotein bridging ligand at the Ni-Fe active site, whereas Ni-A has a diatomic species. The terminal atom of the bridging species of Ni-A occupies a similar position as C of the exogenous CO in the CO complex (inhibited state). The common features of the enzyme structures at the unready (Ni-A) and inhibited (CO complex) states are proposed. These findings provide useful information on the design of new systems of biomimetic dihydrogen production and fuel cell devices. PMID:16271886

Ogata, Hideaki; Hirota, Shun; Nakahara, Asuka; Komori, Hirofumi; Shibata, Naoki; Kato, Tatsuhisa; Kano, Kenji; Higuchi, Yoshiki

2005-11-01

298

Effects of Metal on the Biochemical Properties of Helicobacter pylori HypB, a Maturation Factor of [NiFe]-Hydrogenase and Urease ? †  

PubMed Central

The biosyntheses of the [NiFe]-hydrogenase and urease enzymes in Helicobacter pylori require several accessory proteins for proper construction of the nickel-containing metallocenters. The hydrogenase accessory proteins HypA and HypB, a GTPase, have been implicated in the nickel delivery steps of both enzymes. In this study, the metal-binding properties of H. pylori HypB were characterized, and the effects of metal binding on the biochemical behavior of the protein were examined. The protein can bind stoichiometric amounts of Zn(II) or Ni(II), each with nanomolar affinity. Mutation of Cys106 and His107, which are located between two major GTPase motifs, results in undetectable Ni(II) binding, and the Zn(II) affinity is weakened by 2 orders of magnitude. These two residues are also required for the metal-dependent dimerization observed in the presence of Ni(II) but not Zn(II). The addition of metals to the protein has distinct impacts on GTPase activity, with zinc significantly reducing GTP hydrolysis to below detectable levels and nickel only slightly altering the kcat and Km of the reaction. The regulation of HypB activities by metal binding may contribute to the maturation of the nickel-containing enzymes.

Sydor, Andrew M.; Liu, Jenny; Zamble, Deborah B.

2011-01-01

299

Biochemical Characterization of HydF, a Scaffolding Enzyme, in the Synthesis of the Hydrogenase Active Site Metal Center: Implications Towards the Evolution of Biocatalysts from Mineral-based Components on Early Earth  

NASA Astrophysics Data System (ADS)

[FeFe]-hydrogenase active site biosynthesis utilizes radical chemistry on a scaffold protein whose ancestor may have been one of the earliest examples of a protein that couples the chemistry of an Fe-S peptide nest with a nucleotide binding nest.

Duffus, B. R.; Shepard, E. M.; McGlynn, S. E.; Bueling, A. L.; Winslow, M. A.; Peters, J. W.; Broderick, J. B.

2010-04-01

300

Genome Data Mining and Soil Survey for the Novel Group 5 [NiFe]-Hydrogenase To Explore the Diversity and Ecological Importance of Presumptive High-Affinity H2-Oxidizing Bacteria ?†  

PubMed Central

Streptomyces soil isolates exhibiting the unique ability to oxidize atmospheric H2 possess genes specifying a putative high-affinity [NiFe]-hydrogenase. This study was undertaken to explore the taxonomic diversity and the ecological importance of this novel functional group. We propose to designate the genes encoding the small and large subunits of the putative high-affinity hydrogenase hhyS and hhyL, respectively. Genome data mining revealed that the hhyL gene is unevenly distributed in the phyla Actinobacteria, Proteobacteria, Chloroflexi, and Acidobacteria. The hhyL gene sequences comprised a phylogenetically distinct group, namely, the group 5 [NiFe]-hydrogenase genes. The presumptive high-affinity H2-oxidizing bacteria constituting group 5 were shown to possess a hydrogenase gene cluster, including the genes encoding auxiliary and structural components of the enzyme and four additional open reading frames (ORFs) of unknown function. A soil survey confirmed that both high-affinity H2 oxidation activity and the hhyL gene are ubiquitous. A quantitative PCR assay revealed that soil contained 106 to 108 hhyL gene copies g (dry weight)?1. Assuming one hhyL gene copy per genome, the abundance of presumptive high-affinity H2-oxidizing bacteria was higher than the maximal population size for which maintenance energy requirements would be fully supplied through the H2 oxidation activity measured in soil. Our data indicate that the abundance of the hhyL gene should not be taken as a reliable proxy for the uptake of atmospheric H2 by soil, because high-affinity H2 oxidation is a facultatively mixotrophic metabolism, and microorganisms harboring a nonfunctional group 5 [NiFe]-hydrogenase may occur.

Constant, Philippe; Chowdhury, Soumitra Paul; Hesse, Laura; Pratscher, Jennifer; Conrad, Ralf

2011-01-01

301

Thiolate-bridged dinuclear iron(tris-carbonyl)-nickel complexes relevant to the active site of [NiFe] hydrogenase  

PubMed Central

The reaction of NiBr2(EtOH)4 with a 1:2–3 mixture of FeBr2(CO)4 and Na(SPh) generated a linear trinuclear Fe–Ni–Fe cluster (CO)3Fe(?-SPh)3Ni(?-SPh)3Fe(CO)3, 1, whereas the analogous reaction system FeBr2(CO)4/Na(StBu)/NiBr2(EtOH)4 (1:2–3:1) gave rise to a linear tetranuclear Fe–Ni–Ni–Fe cluster [(CO)3Fe(?-StBu)3Ni(?-Br)]2, 2. By using this tetranuclear cluster 2 as the precursor, we have developed a new synthetic route to a series of thiolate-bridged dinuclear Fe(CO)3–Ni complexes, the structures of which mimic [NiFe] hydrogenase active sites. The reactions of 2 with SC(NMe2)2 (tmtu), Na{S(CH2)2SMe} and ortho-NaS(C6H4)SR (R = Me, tBu) led to isolation of (CO)3Fe(?-StBu)3NiBr(tmtu), 3, (CO)3Fe(StBu)(?-StBu)2Ni{S(CH2)2SMe}, 4, and (CO)3Fe(StBu)(?-StBu)2Ni{S(C6H4)SR}, 5a (R = Me) and 5b (R = tBu), respectively. On the other hand, treatment of 2 with 2-methylthio-phenolate (ortho-O(C6H4)SMe) in methanol resulted in (CO)3Fe(?-StBu)3Ni(MeOH){O(C6H4)SMe}, 6a. The methanol molecule bound to Ni is labile and is readily released under reduced pressure to afford (CO)3Fe(StBu)(?-StBu)2Ni{O(C6H4)SMe}, 6b, and the coordination geometry of nickel changes from octahedral to square planar. Likewise, the reaction of 2 with NaOAc in methanol followed by crystallization from THF gave (CO)3Fe(?-StBu)3Ni(THF)(OAc), 7. The dinuclear complexes, 3-7, are thermally unstable, and a key to their successful isolation is to carry out the reactions and manipulations at ?40°C.

Ohki, Yasuhiro; Yasumura, Kazunari; Kuge, Katsuaki; Tanino, Soichiro; Ando, Masaru; Li, Zilong; Tatsumi, Kazuyuki

2008-01-01

302

Enzyme electrokinetics: electrochemical studies of the anaerobic interconversions between active and inactive states of Allochromatium vinosum [NiFe]-hydrogenase.  

PubMed

The cycling between active and inactive states of the catalytic center of [NiFe]-hydrogenase from Allochromatium vinosum has been investigated by dynamic electrochemical techniques. Adsorbed on a rotating disk pyrolytic graphite "edge" electrode, the enzyme is highly electroactive: this allows precise manipulations of the complex redox chemistry and facilitates quantitative measurements of the interconversions between active catalytic states and the inactive oxidized form Ni(r) (also called Ni-B or "ready") as functions of pH, H(2) partial pressure, temperature, and electrode potential. Cyclic voltammograms for catalytic H(2) oxidation (current is directly related to turnover rate) are highly asymmetric (except at pH > 8 and high temperature) due to inactivation being much slower than activation. Controlled potential-step experiments show that the rate of oxidative inactivation increases at high pH but is independent of potential, whereas the rate of reductive activation increases as the potential becomes more negative. Indeed, at 45 degrees C, activation takes just a few seconds at -288 mV. The cyclic asymmetry arises because interconversion is a two-stage reaction, as expected if the reduced inactive Ni(r)-S state is an intermediate. The rate of inactivation depends on a chemical process (rearrangement and uptake of a ligand) that is independent of potential, but sensitive to pH, while activation is driven by an electron-transfer process, Ni(III) to Ni(II), that responds directly to the driving force. The potentials at which fast activation occurs under different conditions have been analyzed to yield the potential-pH dependence and the corresponding entropies and enthalpies. The reduced (active) enzyme shows a pK of 7.6; thus, when a one-electron process is assumed, reductive activation at pH < 7 involves a net uptake of one proton (or release of one hydroxide), whereas, at pH > 8, there is no net exchange of protons with solvent. Activation is favored by a large positive entropy, consistent with the release of a ligand and/or relaxation of the structure around the active site. PMID:12848556

Jones, Anne K; Lamle, Sophie E; Pershad, Harsh R; Vincent, Kylie A; Albracht, Simon P J; Armstrong, Fraser A

2003-07-16

303

NADP-Specific Electron-Bifurcating [FeFe]-Hydrogenase in a Functional Complex with Formate Dehydrogenase in Clostridium autoethanogenum Grown on CO  

PubMed Central

Flavin-based electron bifurcation is a recently discovered mechanism of coupling endergonic to exergonic redox reactions in the cytoplasm of anaerobic bacteria and archaea. Among the five electron-bifurcating enzyme complexes characterized to date, one is a heteromeric ferredoxin- and NAD-dependent [FeFe]-hydrogenase. We report here a novel electron-bifurcating [FeFe]-hydrogenase that is NADP rather than NAD specific and forms a complex with a formate dehydrogenase. The complex was found in high concentrations (6% of the cytoplasmic proteins) in the acetogenic Clostridium autoethanogenum autotrophically grown on CO, which was fermented to acetate, ethanol, and 2,3-butanediol. The purified complex was composed of seven different subunits. As predicted from the sequence of the encoding clustered genes (fdhA/hytA-E) and from chemical analyses, the 78.8-kDa subunit (FdhA) is a selenocysteine- and tungsten-containing formate dehydrogenase, the 65.5-kDa subunit (HytB) is an iron-sulfur flavin mononucleotide protein harboring the NADP binding site, the 51.4-kDa subunit (HytA) is the [FeFe]-hydrogenase proper, and the 18.1-kDa (HytC), 28.6-kDa (HytD), 19.9-kDa (HytE1), and 20.1-kDa (HytE2) subunits are iron-sulfur proteins. The complex catalyzed both the reversible coupled reduction of ferredoxin and NADP+ with H2 or formate and the reversible formation of H2 and CO2 from formate. We propose the complex to have two functions in vivo, namely, to normally catalyze CO2 reduction to formate with NADPH and reduced ferredoxin in the Wood-Ljungdahl pathway and to catalyze H2 formation from NADPH and reduced ferredoxin when these redox mediators get too reduced during unbalanced growth of C. autoethanogenum on CO (E0? = ?520 mV).

Wang, Shuning; Huang, Haiyan; Kahnt, Jorg; Mueller, Alexander P.; Kopke, Michael

2013-01-01

304

Bis[1,2-bis-(meth-oxy-carbon-yl)ethene-1,2-dithiol-ato-?2 S,S?]bis-(?5-penta-methyl-cyclo-penta-dien-yl)tetra-?3-sulfido-tetra-iron(4 Fe-Fe) hexa-fluoridophosphate  

PubMed Central

The asymmetric unit of the title compound, [Fe4(C6H6O4S2)2(C10H15)2S4]PF6, contains two different complex cations and two PF6 ? anions. The two complex cations have similar conformations with the butterfly-like Fe4S4 core surrounded by two penta­methyl­cyclo­penta­dienyl ligands and the S atoms of two dithiol­ate ligands. In each Fe4S4 core, there are four short Fe—Fe and two long Fe?Fe contacts, suggesting bonding and non-bonding inter­actions, respectively. The Fe—S distances range from 2.1287?(13) to 2.2706?(16)?Å for one and from 2.1233?(13) to 2.2650?(16)?Å for the other Fe4S4 core. The Fe—S distances involving the dithiol­ate ligands are in a more narrow range [2.1764?(16)–2.1874?(13)?Å for one and 2.1743?(14)–2.1779?(16)?Å for the other cation]. There are no significant inter­actions between cations and anions.

Inomata, Shinji; Ito, Shohei; Takase, Tsugiko

2013-01-01

305

Oxygen limitation modulates pH regulation of catabolism and hydrogenases, multidrug transporters, and envelope composition in Escherichia coli K-12  

PubMed Central

Background In Escherichia coli, pH regulates genes for amino-acid and sugar catabolism, electron transport, oxidative stress, periplasmic and envelope proteins. Many pH-dependent genes are co-regulated by anaerobiosis, but the overall intersection of pH stress and oxygen limitation has not been investigated. Results The pH dependence of gene expression was analyzed in oxygen-limited cultures of E. coli K-12 strain W3110. E. coli K-12 strain W3110 was cultured in closed tubes containing LBK broth buffered at pH 5.7, pH 7.0, and pH 8.5. Affymetrix array hybridization revealed pH-dependent expression of 1,384 genes and 610 intergenic regions. A core group of 251 genes showed pH responses similar to those in a previous study of cultures grown with aeration. The highly acid-induced gene yagU was shown to be required for extreme-acid resistance (survival at pH 2). Acid also up-regulated fimbriae (fimAC), periplasmic chaperones (hdeAB), cyclopropane fatty acid synthase (cfa), and the "constitutive" Na+/H+ antiporter (nhaB). Base up-regulated core genes for maltodextrin transport (lamB, mal), ATP synthase (atp), and DNA repair (recA, mutL). Other genes showed opposite pH responses with or without aeration, for example ETS components (cyo,nuo, sdh) and hydrogenases (hya, hyb, hyc, hyf, hyp). A hypF strain lacking all hydrogenase activity showed loss of extreme-acid resistance. Under oxygen limitation only, acid down-regulated ribosome synthesis (rpl,rpm, rps). Acid up-regulated the catabolism of sugar derivatives whose fermentation minimized acid production (gnd, gnt, srl), and also a cluster of 13 genes in the gadA region. Acid up-regulated drug transporters (mdtEF, mdtL), but down-regulated penicillin-binding proteins (dacACD, mreBC). Intergenic regions containing regulatory sRNAs were up-regulated by acid (ryeA, csrB, gadY, rybC). Conclusion pH regulates a core set of genes independently of oxygen, including yagU, fimbriae, periplasmic chaperones, and nhaB. Under oxygen limitation, however, pH regulation is reversed for genes encoding electron transport components and hydrogenases. Extreme-acid resistance requires yagU and hydrogenase production. Ribosome synthesis is down-regulated at low pH under oxygen limitation, possibly due to the restricted energy yield of catabolism. Under oxygen limitation, pH regulates metabolism and transport so as to maximize alternative catabolic options while minimizing acidification or alkalinization of the cytoplasm.

Hayes, Everett T; Wilks, Jessica C; Sanfilippo, Piero; Yohannes, Elizabeth; Tate, Daniel P; Jones, Brian D; Radmacher, Michael D; BonDurant, Sandra S; Slonczewski, Joan L

2006-01-01

306

Transcriptional regulation of genes encoding the selenium-free [NiFe]-hydrogenases in the archaeon Methanococcus voltae involves positive and negative control elements.  

PubMed Central

Methanococcus voltae harbors genetic information for two pairs of homologous [NiFe]-hydrogenases. Two of the enzymes contain selenocysteine, while the other two gene groups encode apparent isoenzymes that carry cysteinyl residues in the homologous positions. The genes coding for the selenium-free enzymes, frc and vhc, are expressed only under selenium limitation. They are transcribed out of a common intergenic region. A series of deletions made in the intergenic region localized a common negative regulatory element for the vhc and frc promoters as well as two activator elements that are specific for each of the two transcription units. Repeated sequences, partially overlapping the frc promoter, were also detected. Mutations in these repeated heptanucleotide sequences led to a weak induction of a reporter gene under the control of the frc promoters in the presence of selenium. This result suggests that the heptamer repeats contribute to the negative regulation of the frc transcription unit.

Noll, I; Muller, S; Klein, A

1999-01-01

307

Helicobacter pylori hydrogenase accessory protein HypA and urease accessory protein UreG compete with each other for UreE recognition  

PubMed Central

Background The gastric pathogen Helicobacter pylori relies on nickel-containing urease and hydrogenase enzymes in order to colonize the host. Incorporation of Ni2+ into urease is essential for the function of the enzyme and requires the action of several accessory proteins, including the hydrogenase accessory proteins HypA and HypB and the urease accessory proteins UreE, UreF, UreG and UreH. Methods Optical biosensing methods (biolayer interferometry and plasmon surface resonance) were used to screen for interactions between HypA, HypB, UreE and UreG. Results Using both methods, affinity constants were found to be 5 nM and 13 nM for HypA–UreE and 8 µM and 14 µM for UreG-UreE. Neither Zn2+ nor Ni2+ had an effect on the kinetics or stability of the HypA–UreE complex. By contrast, addition of Zn2+, but not Ni2+, altered the kinetics and greatly increased the stability of the UreE–UreG complex, likely due in part to Zn2+-mediated oligomerization of UreE. Finally our results unambiguously show that HypA, UreE and UreG cannot form a heterotrimeric protein complex in vitro; instead, HypA and UreG compete with each other for UreE recognition. General significance Factors influencing the pathogen's nickel budget are important to understand pathogenesis and for future drug design.

Benoit, Stephane L.; McMurry, Jonathan L.; Hill, Stephanie A.; Maier, Robert J.

2014-01-01

308

Probing intermediates in the activation cycle of [NiFe] hydrogenase by infrared spectroscopy: the Ni-SIr state and its light sensitivity.  

PubMed

The [NiFe] hydrogenase from the sulphate-reducing bacterium Desulfovibrio vulgaris Miyazaki F is reversibly inhibited in the presence of molecular oxygen. A key intermediate in the reactivation process, Ni-SI(r), provides the link between fully oxidized (Ni-A, Ni-B) and active (Ni-SI(a), Ni-C and Ni-R) forms of hydrogenase. In this work Ni-SI(r) was found to be light-sensitive (T

Pandelia, Maria-Eirini; Ogata, Hideaki; Currell, Leslie J; Flores, Marco; Lubitz, Wolfgang

2009-11-01

309

Differential Expression of the Chlamydomonas [FeFe]-Hydrogenase-Encoding HYDA1 Gene Is Regulated by the COPPER RESPONSE REGULATOR11[C][W  

PubMed Central

The unicellular green alga Chlamydomonas reinhardtii adapts to anaerobic or hypoxic conditions by developing a complex fermentative metabolism including the production of molecular hydrogen by [FeFe]-hydrogenase isoform1 (HYDA1). HYDA1 transcript and hydrogenase protein accumulate in the absence of oxygen or copper (Cu). Factors regulating this differential gene expression have been unknown so far. In this study, we report on the isolation of a Chlamydomonas mutant strain impaired in HYDA1 gene expression by screening an insertional mutagenesis library for HYDA1 promoter activity using the arylsulfatase-encoding ARYLSULFATASE2 gene as a selection marker. The mutant strain has a deletion of the COPPER RESPONSE REGULATOR1 (CRR1) gene encoding for CRR1, indicating that this SQUAMOSA-PROMOTER BINDING PROTEIN (SBP) domain transcription factor is involved in the regulation of HYDA1 transcription. Treating the C. reinhardtii wild type with mercuric ions, which were shown to inhibit the binding of the SBP domain to DNA, prevented or deactivated HYDA1 gene expression. Reporter gene analyses of the HYDA1 promoter revealed that two GTAC motifs, which are known to be the cores of CRR1 binding sites, are necessary for full promoter activity in hypoxic conditions or upon Cu starvation. However, mutations of the GTAC sites had a much stronger impact on reporter gene expression in Cu-deficient cells. Electrophoretic mobility shift assays showed that the CRR1 SBP domain binds to one of the GTAC cores in vitro. These combined results prove that CRR1 is involved in HYDA1 promoter activation.

Pape, Miriam; Lambertz, Camilla; Happe, Thomas; Hemschemeier, Anja

2012-01-01

310

Borane-Protected Cyanides as Surrogates of H-Bonded Cyanides in [FeFe]-Hydrogenase Active Site Models.  

PubMed

Triarylborane Lewis acids bind [Fe2(pdt)(CO)4(CN)2](2-) [1](2-) (pdt(2-) = 1,3-propanedithiolate) and [Fe2(adt)(CO)4(CN)2](2-) [3](2-) (adt(2-) = 1,3-azadithiolate, HN(CH2S(-))2) to give the 2:1 adducts [Fe2(xdt)(CO)4(CNBAr3)2](2-). Attempts to prepare the 1:1 adducts [1(BAr3)](2-) (Ar = Ph, C6F5) were unsuccessful, but related 1:1 adducts were obtained using the bulky borane B(C6F4-o-C6F5)3 (BAr(F)*3). By virtue of the N-protection by the borane, salts of [Fe2(pdt)(CO)4(CNBAr3)2](2-) sustain protonation to give hydrides that are stable (in contrast to [H1](-)). The hydrides [H1(BAr3)2](-) are 2.5-5 pKa units more acidic than the parent [H1](-). The adducts [1(BAr3)2](2-) oxidize quasi-reversibly around -0.3 V versus Fc(0/+) in contrast to ca. -0.8 V observed for the [1](2-/-) couple. A simplified synthesis of [1](2-), [3](2-), and [Fe2(pdt)(CO)5(CN)](-) ([2](-)) was developed, entailing reaction of the diiron hexacarbonyl complexes with KCN in MeCN. PMID:24992155

Manor, Brian C; Ringenberg, Mark R; Rauchfuss, Thomas B

2014-07-21

311

Synthetic Models for the [FeFe]-Hydrogenase: Catalytic Proton Reduction and the Structure of the Doubly Protonated Intermediate  

PubMed Central

This report compares biomimetic HER catalysts with and without the amine cofactor (adtNH): Fe2(adtNH)(CO)2(dppv)2 (1NH) and Fe2(pdt)(CO)2(dppv)2 (2; (adtNH)2? = (HN(CH2S)22?, pdt2? = 1,3-(CH2)3S22?). These compounds are spectroscopically, structurally, and stereodynamically very similar but exhibit very different catalytic properties. Protonation of 1NH and 2 each give three isomeric hydrides beginning with the kinetically favored terminal hydride, which converts sequentially to sym and unsym isomers of the bridging hydrides. In the case of the amine, the corresponding ammonium-hydrides are also observed. In the case of the terminal amine hydride [t-H1NH]BF4, the ammonium/amine-hydride equilibrium is sensitive to counteranions and solvent. The species [t-H1NH2](BF4)2 represents the first example of a crystallographically characterized terminal hydride produced by protonation. The NH--HFe distance of 1.88(7) Å indicates dihydrogen bonding. The bridging hydrides [µ-H1NH]+ and [µ-H2]+ reduce near ?1.8 V, about 150 mV more negative than the reductions of the terminal hydride [t-H1NH]+ and [t-H2]+ at ?1.65 V. Reductions of the amine hydrides [t-H1NH]+ and [t-H1NH2]2+ are irreversible. For the pdt analog, the [t-H2]+/0 couple is unaffected by weak acids (pKaMeCN 15.3) but exhibits catalysis with HBF4•Et2O, albeit with a TOF around 4 s?1 and an overpotential greater than 1 V. The voltammetry of [t-H1NH]+ is strongly affected by relatively weak acids and proceeds at 5000 s?1 with an overpotential of 0.7 V. The ammonium-hydride [t-H1NH2]2+ is a faster catalyst with an estimated TOF of 58,000 s?1 and an overpotential of 0.5 V.

Carroll, Maria E.; Barton, Bryan E.; Rauchfuss, Thomas B.; Carroll, Patrick J.

2012-01-01

312

Enhanced co-production of hydrogen and poly-(R)-3-hydroxybutyrate by recombinant PHB producing E. coli over-expressing hydrogenase 3 and acetyl-CoA synthetase.  

PubMed

Recombinant Escherichia coli was constructed for co-production of hydrogen and polyhydroxybutyrate (PHB) due to its rapid growth and convenience of genetic manipulation. In particular, anaerobic metabolic pathways dedicated to co-production of hydrogen and PHB were established due to the advantages of directing fluxes away from toxic compounds such as formate and acetate to useful products. Here, recombinant E. coli expressing hydrogenase 3 and/or acetyl-CoA synthetase showed improved PHB and hydrogen production when grown with or without acetate as a carbon source. When hydrogenase 3 was over-expressed, hydrogen yield was increased from 14 to 153 mmol H(2)/mol glucose in a mineral salt (MS) medium with glucose as carbon source, accompanied by an increased PHB yield from 0.55 to 5.34 mg PHB/g glucose in MS medium with glucose and acetate as carbon source. PMID:22842473

Wang, Rui-Yan; Shi, Zhen-Yu; Chen, Jin-Chun; Wu, Qiong; Chen, Guo-Qiang

2012-09-01

313

Redirecting the electron flow towards the nitrogenase and bidirectional Hox-hydrogenase by using specific inhibitors results in enhanced H2 production in the cyanobacterium Anabaena siamensis TISTR 8012.  

PubMed

The inhibition of competitive metabolic pathways by various inhibitors in order to redirect electron flow towards nitrogenase and bidirectional Hox-hydrogenase was investigated in Anabaena siamensis TISTR 8012. Cells grown in BG11(0) supplemented with KCN, rotenone, DCMU, and DL-glyceraldehyde under light condition for 24 h showed enhanced H(2) production. Cells grown in BG11 medium showed only marginal H(2) production and its production was hardly increased by the inhibitors tested. H(2) production with either 20mM KCN or 50 ?M DCMU in BG11(0) medium was 22 ?mol H(2) mg chl a(-1) h(-1), threefold higher than the control. The increased H(2) production caused by inhibitors was consistent with the increase in the respective Hox-hydrogenase activities and nifD transcript levels, as well as the decrease in hupL transcript levels. The results suggested that interruption of metabolic pathways essential for growth could redirect electrons flow towards nitrogenase and bidirectional Hox-hydrogenase resulting in increased H(2) production. PMID:22705533

Khetkorn, Wanthanee; Baebprasert, Wipawee; Lindblad, Peter; Incharoensakdi, Aran

2012-08-01

314

Steady-state catalytic wave-shapes for 2-electron reversible electrocatalysts and enzymes.  

PubMed

Using direct electrochemistry to learn about the mechanism of electrocatalysts and redox enzymes requires that kinetic models be developed. Here we thoroughly discuss the interpretation of electrochemical signals obtained with adsorbed enzymes and molecular catalysts that can reversibly convert their substrate and product. We derive analytical relations between electrochemical observables (overpotentials for catalysis in each direction, positions, and magnitudes of the features of the catalytic wave) and the characteristics of the catalytic cycle (redox properties of the catalytic intermediates, kinetics of intramolecular and interfacial electron transfer, etc.). We discuss whether or not the position of the wave is determined by the redox potential of a redox relay when intramolecular electron transfer is slow. We demonstrate that there is no simple relation between the reduction potential of the active site and the catalytic bias of the enzyme, defined as the ratio of the oxidative and reductive limiting currents; this explains the recent experimental observation that the catalytic bias of NiFe hydrogenase depends on steps of the catalytic cycle that occur far from the active site [Abou Hamdan et al., J. Am. Chem. Soc. 2012, 134, 8368]. On the experimental side, we examine which models can best describe original data obtained with various NiFe and FeFe hydrogenases, and we illustrate how the presence of an intramolecular electron transfer chain affects the voltammetry by comparing the data obtained with the FeFe hydrogenases from Chlamydomonas reinhardtii and Clostridium acetobutylicum, only one of which has a chain of redox relays. The considerations herein will help the interpretation of electrochemical data previously obtained with various other bidirectional oxidoreductases, and, possibly, synthetic inorganic catalysts. PMID:23362993

Fourmond, Vincent; Baffert, Carole; Sybirna, Kateryna; Lautier, Thomas; Abou Hamdan, Abbas; Dementin, Sébastien; Soucaille, Philippe; Meynial-Salles, Isabelle; Bottin, Hervé; Léger, Christophe

2013-03-13

315

A single-crystal ENDOR and density functional theory study of the oxidized states of the [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F.  

PubMed

The catalytic center of the [NiFe] hydrogenase of Desulfovibrio vulgaris Miyazaki F in the oxidized states was investigated by electron paramagnetic resonance and electron-nuclear double resonance spectroscopy applied to single crystals of the enzyme. The experimental results were compared with density functional theory (DFT) calculations. For the Ni-B state, three hyperfine tensors could be determined. Two tensors have large isotropic hyperfine coupling constants and are assigned to the beta-CH2 protons of the Cys-549 that provides one of the bridging sulfur ligands between Ni and Fe in the active center. From a comparison of the orientation of the third hyperfine tensor with the tensor obtained from DFT calculations an OH- bridging ligand has been identified in the Ni-B state. For the Ni-A state broader signals were observed. The signals of the third proton, as observed for the "ready" state Ni-B, were not observed at the same spectral position for Ni-A, confirming a structural difference involving the bridging ligand in the "unready" state of the enzyme. PMID:16292669

van Gastel, Maurice; Stein, Matthias; Brecht, Marc; Schröder, Olga; Lendzian, Friedhelm; Bittl, Robert; Ogata, Hideaki; Higuchi, Yoshiki; Lubitz, Wolfgang

2006-01-01

316

How are the ready and unready states of nickel-iron hydrogenase activated by H2? A density functional theory study.  

PubMed

We have explored possible mechanisms for the formation of the catalytically active Ni(a)-S state of the enzyme, nickel iron hydrogenase, from the Ni*(r) (ready) or Ni*(u) (unready) state, by reaction with H(2), using density functional theory calculations with the BP86 functional in conjunction with a DZVP basis set. We find that for the reaction of the ready state, which is taken to have an -OH bridge, the rate determining step is the cleavage of H(2) at the Ni(3+) centre with a barrier of approximately 15 kcal mol(-1). We take the unready state to have a -OOH bridge, and find that reaction with H(2) to form the Ni(r)-S state can proceed by two possible routes. One such path has a number of steps involving electron transfer, which is consistent with experiment, as is the calculated barrier of approximately 19 kcal mol(-1). The alternative pathway, with a lower barrier, may not be rate determining. Overall, our predictions give barriers in line with experiment, and allow details of the mechanism to be explored which are inaccessible from experiment. PMID:17028697

Jayapal, Prabha; Sundararajan, Mahesh; Hillier, Ian H; Burton, Neil A

2006-09-21

317

Investigating the Role of the Outer-Coordination Sphere in [Ni(PPh2NPh-R2)2]2+ Hydrogenase Mimics  

SciTech Connect

A series of dipeptide nickel complexes with the general formula, [Ni(PPh2NNNA-amino acid/ester2)2](BF4)2, have been synthesized and characterized (P2N2= 1,5-diaza-3,7-diphosphacyclooctane, amino acid/esters = glutamic acid, alanine, lysine, and aspartic acid). Each of these complexes is an efficient electrocatalyst for H2 production. The contribution of the outer-coordination sphere, specifically the impact of sterics, the ability to protonate and the pKa of amino acid side chain on the hydrogen production activity of these complexes, was investigated. The rates of all of the catalysts ranged over an order of magnitude. The amino acid containing complexes display 2-3 times higher rates of hydrogen production than the corresponding ester complexes, suggesting the significance of protonated species (side chains/backbone of amino acids) in the outer-coordination sphere. The largest had the fastest rates suggesting that catalytic activity is not hindered by sterics. However, the shapes of catalytic waves are indicative of hindered electron transfer and may suggest a competing mechanism for catalysis than that observed for the unsubstituted parent complex. These studies demonstrate the significant contribution that the outer-coordination sphere can have in tuning the catalytic activity of small molecule hydrogenase mimics.

Jain, Avijita; Reback, Matthew L.; Lindstrom, Mary L.; Thogerson, Colleen E.; Helm, Monte L.; Appel, Aaron M.; Shaw, Wendy J.

2012-06-18

318

Nitrogen Fixation and Hydrogen Metabolism in Relation to the Dissolved Oxygen Tension in Chemostat Cultures of the Wild Type and a Hydrogenase-Negative Mutant of Azorhizobium caulinodans  

PubMed Central

Both the wild type and an isogenic hydrogenase-negative mutant of Azorhizobium caulinodans growing ex planta on N2 as the N source were studied in succinate-limited steady-state chemostat cultures under 0.2 to 3.0% dissolved O2 tension. Production or consumption of O2, H2, and CO2 was measured with an on-line-connected mass spectrometer. In the range of 0.2 to 3.0%, growth of both the wild type and the mutant was equally dependent on the dissolved O2 tension: the growth yield decreased, and the specific O2 consumption and CO2 production increased. A similar dependency on the dissolved O2 tension was found for the mutant with 2.5% H2 in the influent gas. The H2/N2 ratio (moles of H2 evolved per mole of N2 consumed via nitrogenase) of the mutant, growing with or without 2.5% H2, increased with increasing dissolved O2 tensions. This increase in the H2/N2 ratio was small but significant. The dependencies of the ATP/N2 ratio (moles of ATP consumed per mole of N2 fixed) and the ATP/2e- ratio [moles of ATP consumed per mole of electron pairs transferred from NAD(P)H to nitrogenase] on the dissolved O2 tension were estimated. These dependencies were interpreted in terms of the physiological concepts of respiratory protection and autoprotection.

Boogerd, Fred C.; Ferdinandy-van Vlerken, Marijke M. A.; Mawadza, Crispen; Pronk, Annemieke F.; Stouthamer, Adriaan H.; van Verseveld, Henk W.

1994-01-01

319

Roles of Coenzyme F420-Reducing Hydrogenases and Hydrogen- and F420-Dependent Methylenetetrahydromethanopterin Dehydrogenases in Reduction of F420 and Production of Hydrogen during Methanogenesis?  

PubMed Central

Reduced coenzyme F420 (F420H2) is an essential intermediate in methanogenesis from CO2. During methanogenesis from H2 and CO2, F420H2 is provided by the action of F420-reducing hydrogenases. However, an alternative pathway has been proposed, where H2-dependent methylenetetrahydromethanopterin dehydrogenase (Hmd) and F420H2-dependent methylenetetrahydromethanopterin dehydrogenase (Mtd) together reduce F420 with H2. Here we report the construction of mutants of Methanococcus maripaludis that are defective in each putative pathway. Their analysis demonstrates that either pathway supports growth on H2 and CO2. Furthermore, we show that during growth on formate instead of H2, where F420H2 is a direct product of formate oxidation, H2 production occurs. H2 presumably arises from the oxidation of F420H2, and the analysis of the mutants during growth on formate suggests that this too can occur by either pathway. We designate the alternative pathway for the interconversion of H2 and F420H2 the Hmd-Mtd cycle.

Hendrickson, Erik L.; Leigh, John A.

2008-01-01

320

The Relationship between H2 Evolution and Acetylene Reduction in Pisum sativum-Rhizobium leguminosarum Symbioses Differing in Uptake Hydrogenase Activity 1  

PubMed Central

Peas (Pisum sativum L.) were inoculated with strains of Rhizobium leguminosarum having different levels of uptake hydrogenase (Hup) activity and were grown in sterile Leonard jars under controlled conditions. Rates of H2 evolution and acetylene reduction were determined for intact nodulated roots at intervals after the onset of darkness or after removal of the shoots. Hup activity was estimated using treatment plants or equivalent plants from the growth chamber, by measuring the uptake of H2 or 3H2 in the presence of acetylene. In all cases, the rate of H2 evolution was a continuous function of the rate of acetylene reduction. In symbioses with no demonstrable Hup activity, H2 evolution increased in direct proportion to acetylene reduction and the slopes were similar with the Hup? strains NA502 and 128C79. Hup activity was similar in strains 128C30 and 128C52 but significantly lower in strain 128C54. With these strains, the slopes of the H2 evolution versus acetylene reduction curves initially increased with acetylene reduction, but became constant and similar to those for the Hup? strains at high rates of acetylene reduction. On these parallel portions of the curves, the decreases in H2 evolution by Hup+ strains were similar in magnitude to their H2-saturated rates of Hup activity. The curvilinear relationship between H2 evolution and acetylene reduction for a representative Hup+ strain (128C52) was the same, regardless of the experimental conditions used to vary the nitrogenase activity.

Mahon, John D.; Nelson, Louise M.

1986-01-01

321

Ferric iron reduction by Desulfovibrio vulgaris Hildenborough wild type and energy metabolism mutants  

Microsoft Academic Search

Desulfovibrio vulgaris Hildenborough wild type and its hyn1, hyd and hmc mutants, lacking genes for periplasmic [NiFe] hydrogenase-1, periplasmic [FeFe] hydrogenase or the transmembrane high molecular\\u000a weight cytochrome (Hmc) complex, respectively, were able to reduce Fe(III) chelated with nitrilotriacetic acid (NTA), but\\u000a not insoluble ferric oxide, with lactate as the electron donor. The rate and extent of Fe(III)-NTA reduction followed

Hyung Soo Park; Shiping Lin; Gerrit Voordouw

2008-01-01

322

Redox-dependent structural transformations of the [4Fe-3S] proximal cluster in O2-tolerant membrane-bound [NiFe]-hydrogenase: a DFT study.  

PubMed

Broken-symmetry density functional theory (BS-DFT) has been used to address the redox-dependent structural changes of the proximal [4Fe-3S] cluster, implicated in the O2-tolerance of membrane-bound [NiFe]-hydrogenase (MBH). The recently determined structures of the [4Fe-3S] cluster together with its protein ligands were studied at the reduced [4Fe-3S](3+), oxidized [4Fe-3S](4+), and superoxidized [4Fe-3S](5+) levels in context of their relative energies and protonation states. The observed proximal cluster conformational switch, concomitant with the proton transfer from the cysteine Cys20 backbone amide to the nearby glutamate Glu76 carboxylate, is found to be a single-step process requiring ~12-17 kcal/mol activation energy at the superoxidized [4Fe-3S](5+) level. At the more reduced [4Fe-3S](4+/3+) oxidation levels, this rearrangement has at least 5 kcal/mol higher activation barriers and prohibitively unfavorable product energies. The reverse transformation of the proximal cluster is a fast unidirectional process with ~8 kcal/mol activation energy, triggered by one-electron reduction of the superoxidized species. A previously discussed ambiguity of the Glu76 carboxylate and 'special' Fe4 iron positions in the superoxidized cluster is now rationalized as a superposition of two local minima, where Glu76-Fe4 coordination is either present or absent. The calculated 12.3-17.9 MHz (14)N hyperfine coupling (HFC) for the Fe4-bound Cys20 backbone nitrogen is in good agreement with the large 13.0/14.6 MHz (14)N couplings from the latest HYSCORE/ENDOR studies. PMID:23848168

Pelmenschikov, Vladimir; Kaupp, Martin

2013-08-14

323

Electronic Structure and Chemistry of Iron-Based Metal Oxide Nanostructured Materials: A NEXAFS Investigation of BiFeO3, Bi2Fe4O9, ?-Fe2O3, ?-Fe2O3, and Fe/Fe3O4  

SciTech Connect

We present a systematic and detailed near edge X-ray absorption fine structure (NEXAFS) experimental investigation of the electronic structure and chemistry of iron-based metal oxide nanostructured (FeMONS) materials including BiFeO3, Bi2Fe4O9, a-Fe2O3, ?-Fe2O3, and Fe/Fe3O4. Correlations of the electronic structure and structural chemistry of these intriguing nanomaterials are presented, ranging from the nano to the bulk scale. In this work, variations in the shape, position, and intensity of the O K-edge and Fe L-edge NEXAFS spectra have been analyzed in terms of electronic structure and surface chemistry of the FeMONS materials as compared with that of the bulk. We hypothesize that surface imperfection and surface strain anisotropies in nanoparticles induce distortion and site inequivalency of the oxygen Oh sites around the Fe ion located close to the surface, resulting in an increase in the degree of multiplicity as well as in nonstoichiometric effects in FeMONS materials.

Park,T.; Sambasivan, S.; Fischer, D.; Yoon, W.; Misewich, J.; Wong, S.

2008-01-01

324

Connecting [NiFe]- and [FeFe]-Hydrogenases: Mixed-Valence Nickel-Iron Dithiolates With Rotated Structures  

PubMed Central

A series of mixed-valence iron-nickel dithiolates is described that exhibits structures similar to those of mixed-valence diiron dithiolates. Interaction of tricarbonyl salt [(dppe)Ni(pdt)Fe(CO)3]BF4 ([1]BF4, dppe = Ph2PCH2CH2PPh2, pdtH2 = HSCH2CH2CH2SH) with P-donor ligands (L) afforded the substituted derivatives [(dppe)Ni(pdt)Fe(CO)2L]BF4 incorporating L = PHCy2 ([1a]BF4), PPh(NEt2)2 ([1b]BF4), P(NMe2)3 ([1c]BF4), P(i-Pr)3 ([1d]BF4) and PCy3 ([1e]BF4). The related precursor [(dcpe)Ni(pdt)Fe(CO)3]BF4 ([2]BF4, dcpe = Cy2PCH2CH2PCy2) gave the more electron-rich family of compounds [(dcpe)Ni(pdt)Fe(CO)2L]BF4 for L = PPh2(2-pyridyl) ([2a]BF4), PPh3 ([2b]BF4) and PCy3 ([2c]BF4). For bulky and strongly basic monophosphorus ligands, the salts feature distorted Fe coordination geometries: crystallographic analyses of [1e]BF4 and [2c]BF4 showed they adopt ‘rotated’ Fe(I) centers, in which PCy3 occupies a basal site and one CO ligand partially bridges the Ni and Fe centers. Like the undistorted mixed-valence derivatives, the new class of complexes are described as Ni(II)Fe(I) (S = ½) systems according to EPR spectroscopy, although with attenuated 31P hyperfine interactions. DFT calculations using the BP86, B3LYP, and PBE0 exchange-correlation functionals agree with the structural and spectroscopic data, suggesting that the spin for [1e]+ is localized in a Fe(I)-centered d(z2) orbital, orthogonal to the Fe-P bond. The PCy3 complexes, rare examples of species featuring ‘rotated’ Fe centers, both structurally and spectroscopically resemble mixed-valence diiron dithiolates. Also reproducing the NiS2Fe core of the [NiFe]-H2ase active site, the hybrid models incorporate key features of the two major classes of H2ase. Furthermore, cyclic voltammetry experiments suggest that the highly basic phosphine ligands enable a second oxidation corresponding to the couple [(dxpe)Ni(pdt)Fe(CO)2L]+/2+. The resulting unsaturated 32e? dications represent the closest approach to modeling the highly electrophilic Ni-SIa state. In the case of L = PPh2(2-pyridyl) chelation of this ligand accompanies the second oxidation.

Schilter, David; Rauchfuss, Thomas B.; Stein, Matthias

2012-01-01

325

A computational library for multiscale modeling of material failure  

NASA Astrophysics Data System (ADS)

We present an open-source software framework called PERMIX for multiscale modeling and simulation of fracture in solids. The framework is an object oriented open-source effort written primarily in Fortran 2003 standard with Fortran/C++ interfaces to a number of other libraries such as LAMMPS, ABAQUS, LS-DYNA and GMSH. Fracture on the continuum level is modeled by the extended finite element method (XFEM). Using several novel or state of the art methods, the piece software handles semi-concurrent multiscale methods as well as concurrent multiscale methods for fracture, coupling two continuum domains or atomistic domains to continuum domains, respectively. The efficiency of our open-source software is shown through several simulations including a 3D crack modeling in clay nanocomposites, a semi-concurrent FE-FE coupling, a 3D Arlequin multiscale example and an MD-XFEM coupling for dynamic crack propagation.

Talebi, Hossein; Silani, Mohammad; Bordas, Stéphane P. A.; Kerfriden, Pierre; Rabczuk, Timon

2014-05-01

326

Coordination Chemistry of [HFe(CN)2(CO)3? and Its Derivatives: Toward a Model for the Iron Subsite of the [NiFe]-Hydrogenases  

PubMed Central

The photoreaction of Fe(CO)5 and cyanide salts in MeCN solution affords the dianion [Fe(CN)2(CO)3]2?, conveniently isolated as [K(18-crown-6)]2[Fe(CN)2(CO)3]. Solutions of [Fe(CN)2(CO)3]2? oxidize irreversibly at ?600 mV (vs. Ag/AgCl) to give primarily [Fe(CN)3(CO)3]?. Protonation of the dianion affords the hydride [K(18-crown-6)][HFe(CN)2(CO)3] with a pKa ? 17 (MeCN). The ferrous hydride exhibits enhanced electrophilicity vs. its dianionic precursor, which resists substitution. Treatment of [K(18-crown-6)][Fe(CN)2(CO)3] with tertiary phosphines and phosphites gives isomeric mixtures of [HFe(CN)2(CO)2L]? (L = P(OPh)3 and PPh3). Carbonyl substitution on [1H(CO)2]? by P(OPh)3 is first-order in both the phosphite and iron (k = 0.18 M?1 s?1 at 22 °C) with ?H‡ = 51.6 kJ mol?1 and ?S‡ = ?83.0 J K?1 mol?1. These ligands are displaced under an atmosphere of CO. With cis-Ph2PCH=CHPPh2 (dppv), we obtained the monocarbonyl, [HFe(CN)2(CO)(dppv)]?, a highly basic hydride (pKa > 23.3) that rearranges in solution to a single isomer. Treatment of [K(18-crown-6)][HFe(CN)2(CO)3] with Et4NCN resulted in rapid proton transfer to give [Fe(CN)2(CO)3]2? and HCN. The tricyano hydride [HFe(CN)3(CO)2]2? is prepared by the reaction of [HFe(CN)2(CO)2(PPh3)]? and [K(18-crown-6)]CN. Similar to the phosphine and phosphite derivatives, [HFe(CN)3(CO)2]2? exists as a mixture of all three possible isomers. Protonation of the hydrides [HFe(CN)2(CO)(dppv)]? and [HFe(CN)3(CO)2]? in acetonitrile solutions releases H2 and gives the corresponding acetonitrile complexes [K(18-crown-6)][Fe(CN)3(NCMe)(CO)2] and Fe(CN)2(NCMe)(CO)(dppv). Alkylation of [K(18-crown-6)]2[Fe(CN)2(CO)3] with MeOTf gives the thermally-unstable [MeFe(CN)2(CO)3]?, which was characterized spectroscopically at ?40 °C. Reaction of dppv with [MeFe(CN)2(CO)3]? gives the acetyl complex, [Fe(CN)2(COMe)(CO)(dppv)]?. Whereas [Fe(CN)2(CO)3]2? undergoes protonation and methylation at Fe, acid chlorides give the iron(0) N-acylisocyanides [Fe(CN)(CO)3(CNCOR)]? (R = Ph, CH3). The solid state structures of [K(18-crown-6)][HFe(CN)2(CO)(dppv)], Fe(CN)2(NCMe)(CO)(dppv), and [K(18-crown-6)]2[HFe(CN)3(CO)2] were confirmed crystallographically. In all three cases, the cyanide ligands are cis to the hydride or acetonitrile ligands.

Whaley, C. Matthew; Wilson, Scott R.

2009-01-01

327

EPR spectroscopic studies of the Fe-S clusters in the O2-tolerant [NiFe]-hydrogenase Hyd-1 from Escherichia coli and characterization of the unique [4Fe-3S] cluster by HYSCORE.  

PubMed

The unusual [4Fe-3S] cluster proximal to the active site plays a crucial role in allowing a class of [NiFe]-hydrogenases to function in the presence of O(2) through its unique ability to undergo two rapid, consecutive one-electron transfers. This property helps to neutralize reactive oxygen species. Mechanistic details and the role of the medial and distal clusters remain unresolved. To probe the Fe-S relay, continuous wave and pulse electron paramagnetic resonance (EPR) studies were conducted on the O(2)-tolerant hydrogenase from Escherichia coli (Hyd-1) and three variants with point mutations at the proximal and/or medial clusters. Reduction potentials of the proximal ([4Fe-3S](5+/4+/3+)) and medial ([3Fe-4S](+/0)) clusters were determined by potentiometry. The medial [3Fe-4S](+/0) reduction potential is exceptionally high, implicating a mechanistic role in O(2)-tolerance. Numerous experiments establish that the distal cluster has a ground state S > 1/2 in all three variants and indicate that this is also the case for native Hyd-1. Concurrent with the Hyd-1 crystal structure, EPR data for the 'superoxidized' P242C variant, in which the medial cluster is 'magnetically silenced', reveal two conformations of the proximal [4Fe-3S](5+) cluster, and X-band HYSCORE spectroscopy shows two (14)N hyperfine couplings attributed to one conformer. The largest, A((14)N) = [11.5,11.5,16.0] ± 1.5 MHz, characterizes the unusual bond between one Fe (Fe(4)) and the backbone amide-N of cysteine-20. The second, A((14)N) = [2.8,4.6,3.5] ± 0.3 MHz, is assigned to N(C19). The (14)N hyperfine couplings are conclusive evidence that Fe(4) is a valence-localized Fe(3+) in the superoxidized state, whose formation permits an additional electron to be transferred rapidly back to the active site during O(2) attack. PMID:22900997

Roessler, Maxie M; Evans, Rhiannon M; Davies, Rosalind A; Harmer, Jeffrey; Armstrong, Fraser A

2012-09-19

328

Fe-Mn alloys: A mixed-bond spin-1/2 Ising model version  

NASA Astrophysics Data System (ADS)

In this work, we apply the mixed-bond spin-1/2 Ising model to study the magnetic properties of Fe-Mn alloys in the ? phase by employing the effective field theory (EFT). Here, we suggest a new approach to the ferromagnetic coupling between nearest neighbours Fe-Fe that depends on the ratio between the Mn-Mn coupling and the Fe-Mn coupling and of second power of the Mn concentration q in contrast to linear dependence considered in the other articles. Also, we propose a new probability distribution for binary alloys with mixed-bonds based on the distribution for ternary alloys and we obtain a very good agreement for all considered values of q in T-q plane, in particular for q>0.11.

Freitas, A. S.; de Albuquerque, Douglas F.; Moreno, N. O.

2014-06-01

329

Reaction of Fe3(CO)12 with octreotide--chemical, electrochemical and biological investigations.  

PubMed

In search for peptidic [FeFe] hydrogenase mimics, the cyclic disulfide Sandostatin (octreotide) was allowed to react with Fe(3)(CO)(12). An octreotide-Fe(2)(CO)(6) complex was isolated and characterized spectroscopically as well as by elemental and thermochemical analysis. The complex catalyzes the electrochemical reduction of H(+) to H(2). It is suggested by radioligand binding assays that the complex retains much of the binding affinity for the somatostatin hsst(1-5) receptors of octreotide. PMID:20221541

Apfel, Ulf-Peter; Rudolph, Manfred; Apfel, Christina; Robl, Christian; Langenegger, Daniel; Hoyer, Daniel; Jaun, Bernhard; Ebert, Marc-Olivier; Alpermann, Theodor; Seebach, Dieter; Weigand, Wolfgang

2010-03-28

330

Principles of sustained enzymatic hydrogen oxidation in the presence of oxygen--the crucial influence of high potential Fe-S clusters in the electron relay of [NiFe]-hydrogenases.  

PubMed

"Hyd-1", produced by Escherichia coli , exemplifies a special class of [NiFe]-hydrogenase that can sustain high catalytic H(2) oxidation activity in the presence of O(2)-an intruder that normally incapacitates the sulfur- and electron-rich active site. The mechanism of "O(2) tolerance" involves a critical role for the Fe-S clusters of the electron relay, which is to ensure the availability-for immediate transfer back to the active site-of all of the electrons required to reduce an attacking O(2) molecule completely to harmless H(2)O. The unique [4Fe-3S] cluster proximal to the active site is crucial because it can rapidly transfer two of the electrons needed. Here we investigate and establish the equally crucial role of the high potential medial [3Fe-4S] cluster, located >20 Å from the active site. A variant, P242C, in which the medial [3Fe-4S] cluster is replaced by a [4Fe-4S] cluster, is unable to sustain steady-state H(2) oxidation activity in 1% O(2). The [3Fe-4S] cluster is essential only for the first stage of complete O(2) reduction, ensuring the supply of all three electrons needed to form the oxidized inactive state "Ni-B" or "Ready" (Ni(III)-OH). Potentiometric titrations show that Ni-B is easily reduced (E(m) ? +0.1 V at pH 6.0); this final stage of the O(2)-tolerance mechanism regenerates active enzyme, effectively completing a competitive four-electron oxidase cycle and is fast regardless of alterations at the proximal or medial clusters. As a consequence of all these factors, the enzyme's response to O(2), viewed by its electrocatalytic activity in protein film electrochemistry (PFE) experiments, is merely to exhibit attenuated steady-state H(2) oxidation activity; thus, O(2) behaves like a reversible inhibitor rather than an agent that effectively causes irreversible inactivation. The data consolidate a rich picture of the versatile role of Fe-S clusters in electron relays and suggest that Hyd-1 can function as a proficient hydrogen oxidase. PMID:23398301

Evans, Rhiannon M; Parkin, Alison; Roessler, Maxie M; Murphy, Bonnie J; Adamson, Hope; Lukey, Michael J; Sargent, Frank; Volbeda, Anne; Fontecilla-Camps, Juan C; Armstrong, Fraser A

2013-02-20

331

Nitrosyl Derivatives of Diiron(I) Dithiolates Mimic the Structure and Lewis Acidity of the FeFe-Hydrogenase Active Site  

PubMed Central

This study probes the impact of electronic asymmetry of diiron(I) dithiolato carbonyls. Treatment of Fe2(S2CnH2n)(CO)6-x(PMe3)x compounds (n = 2, 3) with NOBF4 gave the derivatives [Fe2(S2CnH2n)(CO)5-x(PMe3)x(NO)]BF4 (x = 1, 2, 3) which are electronically unsymmetrical due to the presence of a single NO+ ligand. Whereas the mono phosphine derivative is largely undistorted, the bis PMe3 derivatives are distorted such that the CO ligand on the Fe(CO)(PMe3)(NO)+ subunit is semibridging. Two isomers of [Fe2(S2C3H6)(CO)3(PMe3)2(NO)]BF4 were characterized spectroscopically and crystallographically. Each isomer features electron-rich [Fe(CO)2PMe3] and electrophilic [Fe(CO)(PMe3)(NO)]+ subunits. These species are in equilibrium with an unobserved isomer that reversibly binds CO (?H = ?35 kJ/mol, ?S = ?139 J/mol•K) to give the symmetrical adduct [Fe2(S2C3H6)(?-NO)(CO)4(PMe3)2]BF4. In contrast to Fe2(S2C3H6)(CO)4(PMe3)2, the bis(PMe3) nitrosyls readily undergo CO-substitution to give the (PMe3)3 derivatives. The nitrosyl complexes reduce at potentials that are ~1 V milder than their carbonyl counterparts. DFT calculations, specifically NBO values, reinforce the electronic resemblance of the nitrosyl complexes with the corresponding mixed-valence diiron complexes. Unlike other diiron dithiolato carbonyls, these species undergo reversible reductions at mild conditions. The results show that the novel structural and chemical features associated with mixed valence diiron dithiolates – the so-called Hox models - can be replicated in the absence of mixed-valency by introducing electronic asymmetry.

Olsen, Matthew T.; Bruschi, Maurizio; Wilson, Scott R.

2008-01-01

332

Modelling the Thermal History of Asteroid 4 Vesta  

NASA Technical Reports Server (NTRS)

The asteroid 4 Vesta is widely thought to be the source of the HED (Howardite, Eucrite and Diogenite) meteorites, with this link supported by spectroscopic and dynamical studies. The availability of the HED meteorites for study and the new data being gained from the Dawn mission provides an excellent opportunity to investigate Vesta s history. In this study, modelling of Vesta has been undertaken to investigate its evolution from an unconsolidated chondritic body to a differentiated body with an iron core. In contrast to previous modelling, both heat and mass transfer are considered as coupled processes. This work draws on models of melt segregation in terrestrial environments to inform the evolution of Vesta into the differentiated body observed today. In order for a core to form in this body, a separation of the metallic iron from the silicates must take place. Temperatures in excess of the solidus temperatures for the Fe-FeS system and the silicates are therefore required. Thermal modelling has shown accretion before 2Myr leads to temperatures in excess of the silicate solidus.

Solano, James M.; Kiefer, W. S.; Mittlefehldt, D. W.

2012-01-01

333

First-principles thermodynamic modeling of lanthanum chromate perovskites  

NASA Astrophysics Data System (ADS)

Tendencies toward local atomic ordering in (A,A')(B,B')O3-? mixed composition perovskites are modeled to explore their influence on thermodynamic, transport, and electronic properties. In particular, dopants and defects within lanthanum chromate perovskites are studied under various simulated redox environments. (La1-x,Srx)(Cr1-y,Fey)O3-? (LSCF) and (La1-x,Srx)(Cr1-y,Ruy)O3-? (LSCR) are modeled using a cluster expansion statistical thermodynamics method built upon a density functional theory database of structural energies. The cluster expansions are utilized in lattice Monte Carlo simulations to compute the ordering of Sr and Fe(Ru) dopant and oxygen vacancies (Vac). Reduction processes are modeled via the introduction of oxygen vacancies, effectively forcing excess electronic charge onto remaining atoms. LSCR shows increasingly extended Ru-Vac associates and short-range Ru-Ru and Ru-Vac interactions upon reduction; LSCF shows long-range Fe-Fe and Fe-Vac interaction ordering, inhibiting mobility. First principles density functional calculations suggest that Ru-Vac associates significantly decrease the activation energy of Ru-Cr swaps in reduced LSCR. These results are discussed in view of experimentally observed extrusion of metallic Ru from LSCR nanoparticles under reducing conditions at elevated temperature.

Dalach, P.; Ellis, D. E.; van de Walle, A.

2012-01-01

334

Iron-sulfur clusters—new features in enzymes and synthetic models  

NASA Astrophysics Data System (ADS)

Mössbauer spectroscopy is very important for the characterization of iron sulfur clusters in biological and synthetic molecules. The electric and magnetic hyperfine parameters obtained for 57Fe provide valuable information about the electronic structure of the different iron sites occurring in Fe:S clusters. Although known since more than four decades, research in this field is very active, revealing unexpected functions, structures and redox states. In this overview, new aspects of double exchange and vibronic coupling in a structurally well-characterized two-iron model compound are discussed, the electronic structure of extremely reduced clusters with all iron in ferrous or even in iron(I) state is elucidated, and an exciting new type of cubane cluster occurring in oxygen-insensitive hydrogenases is presented. The latter cluster involves structural changes during function and it supports more than one redox transition, which may be essential for oxygen protection of the enzymes.

Bill, Eckhard

2012-03-01

335

Integrated analysis of transcriptomic and proteomic data of Desulfovibrio vulgaris: Zero-Inflated Poisson regression models to predict abundance of undetected proteins  

SciTech Connect

Abstract Advances in DNA microarray and proteomics technologies have enabled high-throughput measurement of mRNA expression and protein abundance. Parallel profiling of mRNA and protein on a global scale and integrative analysis of these two data types could provide additional insight into the metabolic mechanisms underlying complex biological systems. However, because protein abundance and mRNA expression are affected by many cellular and physical processes, there have been conflicting results on the correlation of these two measurements. In addition, as current proteomic methods can detect only a small fraction of proteins present in cells, no correlation study of these two data types has been done thus far at the whole-genome level. In this study, we describe a novel data-driven statistical model to integrate whole-genome microarray and proteomic data collected from Desulfovibrio vulgaris grown under three different conditions. Based on the Poisson distribution pattern of proteomic data and the fact that a large number of proteins were undetected (excess zeros), Zero-inflated Poisson models were used to define the correlation pattern of mRNA and protein abundance. The models assumed that there is a probability mass at zero representing some of the undetected proteins because of technical limitations. The models thus use abundance measurements of transcripts and proteins experimentally detected as input to generate predictions of protein abundances as output for all genes in the genome. We demonstrated the statistical models by comparatively analyzing D. vulgaris grown on lactate-based versus formate-based media. The increased expressions of Ech hydrogenase and alcohol dehydrogenase (Adh)-periplasmic Fe-only hydrogenase (Hyd) pathway for ATP synthesis were predicted for D. vulgaris grown on formate.

Nie, Lei; Wu, Gang; Brockman, Fred J.; Zhang, Weiwen

2006-05-04

336

Numerical models of the thermomechanical evolution of planetesimals: Application to the acapulcoite-lodranite parent body  

NASA Astrophysics Data System (ADS)

The acapulcoite-lodranite meteorites are members of the primitive achondrite class. The observation of partial melting and resulting partial removal of Fe-FeS indicates that this meteorite group could be an important link between achondrite and iron meteorites, on the one hand, and chondrite meteorites, on the other. Thus, a better understanding of the thermomechanical evolution of the parent body of this meteorite group can help improve our understanding of the evolution of early planetesimals. Here, we use 2-D and 3-D finite-difference numerical models to determine the formation time, initial radius of the parent body of the acapulcoite-lodranite meteorites, and their formation depth inside the body by applying available geochronological, thermal, and textural constraints to our numerical data. Our results indicate that the best fit to the data can be obtained for a parent body with 25-65 km radius, which formed around 1.3 Ma after calcium-aluminum-rich inclusions. The 2-D and 3-D results considering various initial temperatures and the effect of porosity indicate possible formation depths of the acapulcoite-lodranite meteorites of 9-19 and 14-25 km, respectively. Our data also suggest that other meteorite classes could form at different depths inside the same parent body, supporting recently proposed models (Elkins-Tanton et al.

Golabek, Gregor J.; Bourdon, Bernard; Gerya, Taras V.

2014-06-01

337

Growth of thin Fe/Fe2O3 films on the Cu(110) surface  

NASA Astrophysics Data System (ADS)

The growth of Fe/Fe-oxide double-layers on Cu(110) was studied with thermal energy atom scattering (TEAS), Auger electron spectroscopy, and low-energy electron diffraction (LEED). An iron film with a thickness of about 0.6 nm was evaporated at low temperature (130 K) on a smooth, well-ordered thin film of Fe2O3 prepared on Cu(110). This Fe film is disordered. Ordering of the film was observed at temperatures between 400 and 600 K. At 530 K, a structure corresponding to that of a well-ordered ?-Fe(001) surface was observed with TEAS and LEED. Clear evidence was found for a mixing of the Fe and Fe2O3 layers at the interface, already beginning at the deposition temperature of 130 K. With increasing temperature, the mixing of the Fe and Fe2O3 layers became gradually more effective until, at around 600 K, it was essentially completed. Upon annealing the sample to 1000 K the structure of the film changes and a very thin (less than 2 ML) FeO film on top of the Cu(110) surface is obtained.

Pflitsch, Christian; David, Rudolf; Verheij, Laurens K.; Franchy, René

2001-08-01

338

Structure and magnetic properties of irradiated Fe-Fe oxide core-shell nanoclusters  

SciTech Connect

A cluster deposition method was used to produce a film of loosely aggregated particles of Fe-Fe{sub 3}O{sub 4} coreshell nanoclusters with an 8 nm iron core size and 2 nm oxide shell thickness. The film of particles on a silicon substrate was irradiated with 5.5 MeV Si{sup 2+} ions to a fluence of 10{sup 16} cm{sup -2} near room temperature, and computer simulations based on the SRIM (Stopping and Range of Ions in Matter) code show that the implanted Si species stops near the filmsubstrate interface. The ion irradiation creates a structural change in the film with corresponding chemical and magnetic changes. X-ray diffraction shows that the core size and chemistry stay the same but the shell becomes FeO that grows to a thickness of 17 nm. Helium ion microscopy shows that the previously separate particles have densified into a nearly continuous film. Major loop magnetic hysteresis measurements show a decrease in saturation magnetization that we attribute to the presence of the antiferromagnetic (AFM) FeO shell. First-order reversal curve measurements on the irradiated film performed with a vibrating sample magnetometer show that the AFM shell prevents the particles from interacting magnetically, leading to low coercivity from the iron core and little bias field from the core interactions. These results, and others reported previously on different compositions (Fe{sub 3}O{sub 4} or FeO+Fe{sub 3}N nanoclusters), show that the ion irradiation behavior of nanocluster films such as these depends strongly on the initial nanostructure and chemistry.

McCloy, John S.; Jiang Weilin [Pacific Northwest National Laboratory, 902 Battelle Blvd., PO Box 999, Richland, WA 99352 (United States); Sundararajan, Jennifer A.; Qiang, You [Department of Physics, University of Idaho, Moscow, ID 83844 (United States); Burks, Edward; Liu Kai [Department of Physics, University of California, Davis, CA 95616 (United States)

2013-04-19

339

Construction of Martian Interior Model  

NASA Astrophysics Data System (ADS)

We present the results of extensive numerical modeling of the Martian interior. Yoder et al. in 2003 reported a mean moment of inertia of Mars that was somewhat smaller than the previously used value and the Love number k 2 obtained from observations of solar tides on Mars. These values of k 2 and the mean moment of inertia impose a strong new constraint on the model of the planet. The models of the Martian interior are elastic, while k 2 contains both elastic and inelastic components. We thoroughly examined the problem of partitioning the Love number k 2 into elastic and inelastic components. The information necessary to construct models of the planet (observation data, choice of a chemical model, and the cosmogonic aspect of the problem) are discussed in the introduction. The model of the planet comprises four submodels—a model of the outer porous layer, a model of the consolidated crust, a model of the silicate mantle, and a core model. We estimated the possible content of hydrogen in the core of Mars. The following parameters were varied while constructing the models: the ferric number of the mantle (Fe#) and the sulfur and hydrogen content in the core. We used experimental data concerning the pressure and temperature dependence of elastic properties of minerals and the information about the behavior of Fe(?-Fe ), FeS, FeH, and their mixtures at high P and T. The model density, pressure, temperature, and compressional and shear velocities are given as functions of the planetary radius. The trial model M13 has the following parameters: Fe#=0.20; 14 wt % of sulfur in the core; 50 mol % of hydrogen in the core; the core mass is 20.9 wt %; the core radius is 1699 km; the pressure at the mantle-core boundary is 20.4 GPa; the crust thickness is 50 km; Fe is 25.6 wt %; the Fe/Si weight ratio is 1.58, and there is no perovskite layer. The model gives a radius of the Martian core within 1600 1820 km while ?30 mol % of hydrogen is incorporated into the core. When the inelasticity of the Martian interior is taken into account, the Love number k 2 increases by several thousandths; therefore, the model radius of the planetary core increases as well. The prognostic value of the Chandler period of Mars is 199.5 days, including one day due to inelasticity. Finally, we calculated parameters of the equilibrium figure of Mars for the M13 model: J 2 0 = 1.82 × 10-3, J 4 0 = -7.79 × 10-6, e c-m D = 1/242.3 (the dynamical flattening of the core-mantle boundary).

Zharkov, V. N.; Gudkova, T. V.

2005-09-01

340

Modelling \\  

Microsoft Academic Search

We determine criteria for modelling plan-based “but” in task-oriented dialogue (TOD), following work by Lagerwerf [5] and focusing on cases in which it signals denial of expectation (DofE) and concession, to which end we propose a novel treatment of concession in TOD. We present initial considerations for an algorithm to address\\u000a plan-based “but” in an Information State (IS) model of

Kavita E. Thomas

2003-01-01

341

Modeling  

NASA Technical Reports Server (NTRS)

A prediction of the future population of satellites, satellite fragments, and assorted spacecraft debris in Earth orbit can be reliably made only after three conditions are satisfied: (1) the size and spatial distributions of these Earth-orbiting objects are established at some present-day time; (2) the processes of orbital evolution, explosions, hypervelocity impact fragmentation, and atmospheric drag are understood; and (3) a reasonable traffic model for the future launch rate of Earth-orbiting objects is assumed. The theoretician will then take these three quantities as input data and will carry through the necessary mathematica and numerical analyses to project the present-day orbital population into the future.

Zook, H. A.

1985-01-01

342

Modeling  

SciTech Connect

Slurry flows occur in many circumstances, including chemical manufacturing processes, pipeline transfer of coal, sand, and minerals; mud flows; and disposal of dredged materials. In this section we discuss slurry flow applications related to radioactive waste management. The Hanford tank waste solids and interstitial liquids will be mixed to form a slurry so it can be pumped out for retrieval and treatment. The waste is very complex chemically and physically. The ARIEL code is used to model the chemical interactions and fluid dynamics of the waste.

Loth, E.; Tryggvason, G.; Tsuji, Y.; Elghobashi, S. E.; Crowe, Clayton T.; Berlemont, A.; Reeks, M.; Simonin, O.; Frank, Th; Onishi, Yasuo; Van Wachem, B.

2005-09-01

343

Modeling and computations of the intramolecular electron transfer process in the two-heme protein cytochrome c(4).  

PubMed

The di-heme protein Pseudomonas stutzeri cytochrome c(4) (cyt c(4)) has emerged as a useful model for studying long-range protein electron transfer (ET). Recent experimental observations have shown a dramatically different pattern of intramolecular ET between the two heme groups in different local environments. Intramolecular ET in homogeneous solution is too slow (>10 s) to be detected but fast (ms-?s) intramolecular ET in an electrochemical environment has recently been achieved by controlling the molecular orientation of the protein assembled on a gold electrode surface. In this work we have performed computational modeling of the intramolecular ET process by a combination of density functional theory (DFT) and quantum mechanical charge transfer theory to disclose reasons for this difference. We first address the electronic structures of the model heme core with histidine and methionine axial ligands in both low- and high-spin states by structure-optimized DFT. The computations enable estimating the intramolecular reorganization energy of the ET process for different combinations of low- and high-spin heme couples. Environmental reorganization free energies, work terms ("gating") and driving force were determined using dielectric continuum models. We then calculated the electronic transmission coefficient of the intramolecular ET rate using perturbation theory combined with the electronic wave functions determined by the DFT calculations for different heme group orientations and Fe-Fe separations. The reactivity of low- and high-spin heme groups was notably different. The ET rate is exceedingly low for the crystallographic equilibrium orientation but increases by several orders of magnitude for thermally accessible non-equilibrium configurations. Deprotonation of the propionate carboxyl group was also found to enhance the ET rate significantly. The results are discussed in relation to the observed surface immobilization effect and support the notion of conformationally gated ET. PMID:22430606

Nazmutdinov, Renat R; Bronshtein, Michael D; Zinkicheva, Tamara T; Chi, Qijin; Zhang, Jingdong; Ulstrup, Jens

2012-05-01

344

Hydrogenases in sulfate-reducing bacteria function as chromium reductase  

Microsoft Academic Search

The ability of sulfate-reducing bacteria (SRB) to reduce chromate VI has been studied for possible application to the decontamination of polluted environments. Metal reduction can be achieved both chemically, by H 2S produced by the bacteria, and enzymatically, by polyhemic cytochromes c 3. We demonstrate that, in addition to low potential polyheme c-type cytochromes, the ability to reduce chromate is

B. Chardin; M.-T. Giudici-Orticoni; G. De Luca; B. Guigliarelli; M. Bruschi

2003-01-01

345

Survey of Hydrogenase Activity in Algae: Final Report  

SciTech Connect

The capacity for hydrogen gas production was examined in nearly 100 strains of Eukaryotic algae. Each strain was assessed for rate of H2 production in darkness, at compensating light intensity and at saturating Tight intensity. Maximum H2 yield on illumination and sensitivity to molecular oxygen were also measured.

Brand, J. J.

1982-04-01

346

Hydrogen Production Using Hydrogenase-Containing Oxygenic Photosynthetic Organisms  

DOEpatents

A reversible physiological process provides for the temporal separation of oxygen evolution and hydrogen production in a microorganism, which includes the steps of growing a culture of the microorganism in medium under illuminated conditions to accumulate an endogenous substrate, depleting from the medium a nutrient selected from the group consisting of sulfur, iron, and/or manganese, sealing the culture from atmospheric oxygen, incubating the culture in light whereby a rate of light-induced oxygen production is equal to or less than a rate of respiration, and collecting an evolved gas. The process is particularly useful to accomplish a sustained photobiological hydrogen gas production in cultures of microorganisms, such as Chlamydomonas reinhardtii.

Melis, A.; Zhang, L.; Benemann, J. R.; Forestier, M.; Ghirardi, M.; Seibert, M.

2006-01-24

347

A model study on the possible effects of an external electrical field on enzymes having dinuclear iron cluster [2Fe-2S].  

PubMed

Hydrogenases which catalyze the H(2)? 2H(+) + 2e(-) reaction are metalloenzymes that can be divided into two classes, the NiFe and Fe enzymes, on the basis of their metal content. Iron-sulfur clusters [2Fe-2S] and [4Fe-4S] are common in ironhydrogenases. In the present model study, [2Fe-2S] cluster has been considered to visualize the effect of external electric field on various quantum chemical properties of it. In the model, all the cysteinyl residues are in the amide form. The PM3 type semiempirical calculations have been performed for the geometry optimization of the model structure in the absence and presence of the external field. Then, single point DFT calculations (B3LYP/6-31+G(d)) have been carried out. Depending on the direction of the field, the chemical reactivity of the model enzyme varies which suggests that an external electric field could, under proper conditions, improve the enzymatic hydrogen production. PMID:22629229

Türker, Lemi

2012-01-01

348

An atomistic model for the graphite-alumina/liquid iron system: Monte-Carlo simulations on carbon dissolution  

SciTech Connect

A Monte-Carlo (MC) simulation study has been carried out at 1600 deg C on graphite-alumina/liquid iron system with an aim to develop an atomistic model with optimum interaction parameters. The atomistic model of the graphite/liquid iron system was extended to include alumina molecules in the solid graphitic lattice. A molecule of alumina was represented as a rigid unified group of five atoms and occupied five neighbouring lattice sites. Using a canonical ensemble, simulations were carried out for a range of compositions and alumina interaction parameters. As non-wetting of alumina by liquid iron was expected to significantly affect carbon dissolution from graphite-alumina mixtures, interaction between alumina and iron was assumed to be strongly repulsive. Dissolution of carbon from alumina-graphite into liquid iron was monitored and compared with the experimental results. Even for a wide choice of alumina interaction parameters, it was not possible to get a good fit between simulation and experimental results. Another attempt was made to incorporate non-wetting at an atomic level by modifying the nature of interactions on the solid/liquid interface. While these simulations produced a much better agreement with experiment, some gaps still persisted at high alumina concentrations. A third attempt was then made to simulate non-wetting behaviour in terms of mutual exclusion of alumina and iron from their immediate neighbourhood. An excellent fit was obtained with experimental results in the entire composition range. In addition, alumina interaction parameters were found to have no effect on carbon dissolution and were therefore redundant. The optimum interaction parameters for the graphite-alumina/liquid iron system are: J{sub 1}(C-C) = -J,J{sub 1}(C-Fe) = 0.6J,J{sub 1}(Fe-Fe) = J and no interaction parameters for alumina.

Khanna, R. [School of Materials Science and Engineering, University of New South Wales, UNSW, Sydney NSW 2052 (Australia)]. E-mail: ritakhanna@unsw.edu.au; Sahajwalla, V. [School of Materials Science and Engineering, University of New South Wales, UNSW, Sydney NSW 2052 (Australia)

2005-02-01

349

Geochemical modeling of low melt-fraction anatexis in a peraluminous system: The Pena Negra complex (central Spain)  

SciTech Connect

A study was made of the chemical fractionation associated with four cases of anatectic segregation of low melt-fraction cordieritic granites from migmatized meta-greywackes. The aims of the study were to (1) reveal the fractionation patterns of major and trace elements, (2) compare the major element chemistry of leucogranites and the quantitative behavior of source minerals during anatexis - inferred by mass-balance adjustment - with available experimental data for peraluminous systems, and (3) discuss the behavior of trace elements in crustal melting by comparing the chemically determined composition of leucogranites with the results of three fractionation models. Two of these assume a perfect diffusive behavior of trace elements within residual solids, but they use a different set of distribution coefficients. The third assumes a perfect nondiffusive behavior. In relation to their source rocks, the leucogranites are strongly depleted in Li, Transition Elements, and Light Rare Earth Elements, but enriched in K{sub 2}O, SiO{sub 2}, and Ba. Mass balance analysis using the Anatexis Mixing Model shows that the chemistry of cordierite leucogranites is compatible with its having originated by closed-system, water-undersaturated anatexis on previously migmatized meta-greywackes, leaving a residue enriched in cordierite plus biotite and exhausted in K-feldspar. Biotite melts congruently unless important amounts of sillimanite were also present in the source. Compared with experimental metals obtained from sources with the same chemical composition but with a different femic mineralogy (biotite + sillimanite, instead of cordierite + biotite), the Pena Negra leucogranites are richer in K{sub 2}O and MgO with a lower Fe/(Fe + Mg) ratio. The differences in magnesium are believed to result from the changes in the mineral assemblage of the source rocks.

Bea, F. (Univ. of Salamanca (Spain))

1991-07-01

350

First-principles study of point defects in an fcc Fe-10Ni-20Cr model alloy  

NASA Astrophysics Data System (ADS)

The influence of the local environment on vacancy and self-interstitial formation energies has been investigated in a face-centered-cubic (fcc) Fe-10Ni-20Cr model alloy by analyzing an extensive set of first-principle calculations based on density functional theory. Chemical disorder has been considered by designing special quasirandom structures and four different collinear magnetic structures have been investigated in order to determine a relevant reference state to perform point defect calculations at 0 K. Two different convergence methods have also been used to characterize the importance of the method on the results. Although our fcc Fe-10Ni-20Cr would be better represented in terms of applications by the paramagnetic state, we found that the antiferromagnetic single-layer magnetic structure was the most stable at 0 K and we chose it as a reference state to determine the point defect properties. Point defects have been introduced in this reference state, i.e., vacancies and Fe-Fe, Fe-Ni, Fe-Cr, Cr-Cr, Ni-Ni, and Ni-Cr dumbbell interstitials oriented either parallel or perpendicular to the single layer antiferromagnetic planes. Each point defect studied was introduced at different lattice sites to consider a sufficient variety of local environments and analyze its influence on the formation energy values. We have estimated the point defect formation energies with linear regressions using variables which describe the local environment surrounding the point defects. The number and the position of Ni and Cr first nearest neighbors to the point defects were found to drive the evolution of the formation energies. In particular, Ni is found to decrease and Cr to increase the vacancy formation energy of the model alloy, while the opposite trends are found for the dumbbell interstitials. This study suggested that, to a first approximation, the first nearest atoms to point defects can provide reliable estimates of point defect formation energies.

Piochaud, J. B.; Klaver, T. P. C.; Adjanor, G.; Olsson, P.; Domain, C.; Becquart, C. S.

2014-01-01

351

Modeling modeling.  

PubMed Central

Models are tools; they need to fit both the hand and the task. Presence or absence of a feature such as a pacemaker or a cascade is not in itself good. Or bad. Criteria for model evaluation involve benefit-cost ratios, with the numerator a function of the range of phenomena explained, goodness of fit, consistency with other nearby models, and intangibles such as beauty. The denominator is a function of complexity, the number of phenomena that must be ignored, and the effort necessary to incorporate the model into one's parlance. Neither part of the ratio can yet be evaluated for MTS, whose authors provide some cogent challenges to SET.

Killeen, P R

1999-01-01

352

Toward a rigorous network of protein-protein interactions of the model sulfate reducer Desulfovibrio vulgaris Hildenborough  

SciTech Connect

Protein–protein interactions offer an insight into cellular processes beyond what may be obtained by the quantitative functional genomics tools of proteomics and transcriptomics. The aforementioned tools have been extensively applied to study E. coli and other aerobes and more recently to study the stress response behavior of Desulfovibrio 5 vulgaris Hildenborough, a model anaerobe and sulfate reducer. In this paper we present the first attempt to identify protein-protein interactions in an obligate anaerobic bacterium. We used suicide vector-assisted chromosomal modification of 12 open reading frames encoded by this sulfate reducer to append an eight amino acid affinity tag to the carboxy-terminus of the chosen proteins. Three biological replicates of the 10 ‘pulled-down’ proteins were separated and analyzed using liquid chromatography-mass spectrometry. Replicate agreement ranged between 35% and 69%. An interaction network among 12 bait and 90 prey proteins was reconstructed based on 134 bait-prey interactions computationally identified to be of high confidence. We discuss the biological significance of several unique metabolic features of D. vulgaris revealed by this protein-protein interaction data 15 and protein modifications that were observed. These include the distinct role of the putative carbon monoxide-induced hydrogenase, unique electron transfer routes associated with different oxidoreductases, and the possible role of methylation in regulating sulfate reduction.

Chhabra, S.R.; Joachimiak, M.P.; Petzold, C.J.; Zane, G.M.; Price, M.N.; Gaucher, S.; Reveco, S.A.; Fok, V.; Johanson, A.R.; Batth, T.S.; Singer, M.; Chandonia, J.M.; Joyner, D.; Hazen, T.C.; Arkin, A.P.; Wall, J.D.; Singh, A.K.; Keasling, J.D.

2011-05-01

353

Towards a Rigorous Network of Protein-Protein Interactions of the Model Sulfate Reducer Desulfovibrio vulgaris Hildenborough  

PubMed Central

Protein–protein interactions offer an insight into cellular processes beyond what may be obtained by the quantitative functional genomics tools of proteomics and transcriptomics. The aforementioned tools have been extensively applied to study Escherichia coli and other aerobes and more recently to study the stress response behavior of Desulfovibrio vulgaris Hildenborough, a model obligate anaerobe and sulfate reducer and the subject of this study. Here we carried out affinity purification followed by mass spectrometry to reconstruct an interaction network among 12 chromosomally encoded bait and 90 prey proteins based on 134 bait-prey interactions identified to be of high confidence. Protein-protein interaction data are often plagued by the lack of adequate controls and replication analyses necessary to assess confidence in the results, including identification of potential false positives. We addressed these issues through the use of biological replication, exponentially modified protein abundance indices, results from an experimental negative control, and a statistical test to assign confidence to each putative interacting pair applicable to small interaction data studies. We discuss the biological significance of metabolic features of D. vulgaris revealed by these protein-protein interaction data and the observed protein modifications. These include the distinct role of the putative carbon monoxide-induced hydrogenase, unique electron transfer routes associated with different oxidoreductases, and the possible role of methylation in regulating sulfate reduction.

Petzold, Christopher J.; Zane, Grant M.; Price, Morgan N.; Reveco, Sonia A.; Fok, Veronica; Johanson, Alyssa R.; Batth, Tanveer S.; Singer, Mary; Chandonia, John-Marc; Joyner, Dominique; Hazen, Terry C.; Arkin, Adam P.; Wall, Judy D.; Singh, Anup K.; Keasling, Jay D.

2011-01-01

354

Kinetics and mechanism of a catalytic chloride ion effect on the dissociation of model siderophore hydroxamate-iron(III) complexes.  

PubMed

Proton-driven ligand dissociation kinetics in the presence of chloride, bromide, and nitrate ions have been investigated for model siderophore complexes of Fe(III) with the mono- and dihydroxamic acid ligands R(1)C(=O)N(OH)R(2) (R(1) = CH(3), R(2) = H; R(1) = CH(3), R(2) = CH(3); R(1) = C(6)H(5), R(2) = H; R(1) = C(6)H(5), R(2) = C(6)H(5)) and CH(3)N(OH)C(=O)[CH(2)](n)C(=O)N(OH)CH(3) (H(2)L(n); n = 2, 4, 6). Significant rate acceleration in the presence of chloride ion is observed for ligand dissociation from the bis(hydroxamate)- and mono(hydroxamate)-bound complexes. Rate acceleration was also observed in the presence of bromide and nitrate ions but to a lesser extent. A mechanism for chloride ion catalysis of ligand dissociation is proposed which involves chloride ion dependent parallel paths with transient Cl(-) coordination to Fe(III). The labilizing effect of Cl(-) results in an increase in microscopic rate constants on the order of 10(2)-10(3). Second-order rate constants for the proton driven dissociation of dinuclear Fe(III) complexes formed with H(2)L(n)() were found to vary with Fe-Fe distance. An analysis of these data permits us to propose a reactive intermediate of the structure (H(2)O)(4)Fe(L(n)())Fe(HL(n))(Cl)(OH(2))(2+) for the chloride ion dependent ligand dissociation path. Environmental and biological implications of chloride ion enhancement of Fe(III)-ligand dissociation reactions are presented. PMID:11487321

Boukhalfa, H; Crumbliss, A L

2001-08-13

355

Ion irradiation of Fe-Fe oxide core-shell nanocluster films: Effect of interface on stability of magnetic properties  

SciTech Connect

A cluster deposition method was used to produce films of loosely aggregated nanoclusters (NC) of Fe core-Fe3O4 shell or fully oxidized Fe3O4. Films of these NC on Si(100) or MgO(100)/Fe3O4(100) were irradiated to 1016 Si2+/cm2 near room temperature using an ion accelerator. Ion irradiation creates structural change in the NC film with corresponding chemical and magnetic changes which depend on the initial oxidation state of the cluster. Films were characterized using magnetometry (hysteresis, first order reversal curves), microscopy (transmission electron, helium ion), and x-ray diffraction. In all cases, the particle sizes increased due to ion irradiation, and when a core of Fe is present, irradiation reduces the oxide shells to lower valent Fe species. These results show that ion irradiated behavior of the nanocluster films depends strongly on the initial nanostructure and chemistry, but in general saturation magnetization decreases slightly.

McCloy, John S.; Jiang, Weilin; Droubay, Timothy C.; Varga, Tamas; Kovarik, Libor; Sundararajan, Jennifer A.; Kaur, Maninder; Qiang, You; Burks, Edward; Liu, Kai

2013-08-23

356

Thermal Equations of State in the Fe-FeS, Fe-FeO, and Ammonia-Water Systems  

Microsoft Academic Search

With the maturing of laser heating systems for the diamond anvil coupled to 3rd generation synchrotron radiation sources, studies at high pressures are moving from end member to binary and even more complex systems. Interesting discoveries are being made, for instance the addition of Si to pure Fe stabilizes the bcc phase to exceptionally high pressures [Lin, et al., 2002,

D. L. Heinz; C. T. Seagle; A. J. Campbell; N. Miller; V. B. Prakapenka; G. Shen

2007-01-01

357

Hepta-carbonyl-bis-(?-propane-1,3-di-thiol-ato)triiron(I,II)(2 Fe--Fe)  

PubMed Central

The trinuclear title compound, [Fe3(C3H6S2)2(CO)7], is a mixed-valent FeI/FeII complex and crystallizes with two mol­ecules of similar configuration in the asymmetric unit. The three Fe atoms in each mol­ecule display a bent arrangement [Fe—Fe—Fe = 156.22?(4) and 157.06?(3)°]. Both outer FeI atoms are six-coordinated in a distorted ocahedral coordination geometry defined by the bridging FeII atom, three carbonyl C atoms and two bridging S atoms. The coordination number of the central FeII atom is seven and includes bonding to the two outer FeI atoms, four bridging S atoms and one carbonyl C atom. The resulting coordination polyhedron might be described as a highly distorted monocapped trigonal prism. In the crystal packing, the mol­ecules exhibit a chain-like arrangement parallel to [100] and [001], and the resulting layers are stacked along [010]. The cohesion of the structure is dominated by van der Waals inter­actions.

Hu, Mingqiang; Ma, Chengbing; Wen, Huimin; Cui, Honghua; Chen, Changneng

2014-01-01

358

Ion irradiation of Fe-Fe oxide core-shell nanocluster films: Effect of interface on stability of magnetic properties  

SciTech Connect

A cluster deposition method was used to produce films of loosely aggregated nanoclusters (NCs) of Fe core-Fe{sub 3}O{sub 4} shell or fully oxidized Fe{sub 3}O{sub 4}. Films of these NC on Si(100) or MgO(100)/Fe{sub 3}O{sub 4}(100) were irradiated to 10{sup 16} Si{sup 2+}/cm{sup 2} near room temperature using an ion accelerator. Ion irradiation creates structural change in the NC film with corresponding chemical and magnetic changes which depend on the initial oxidation state of the cluster. Films were characterized using magnetometry (hysteresis, first order reversal curves), microscopy (transmission electron, helium ion), and x-ray diffraction. In all cases, the particle sizes increased due to ion irradiation, and when a core of Fe is present, irradiation reduces the oxide shells to lower valent Fe species. These results show that ion irradiated behavior of the NC films depends strongly on the initial nanostructure and chemistry, but in general saturation magnetization decreases slightly.

McCloy, John S.; Jiang, Weilin; Droubay, Timothy C.; Varga, Tamas; Kovarik, Libor [Pacific Northwest National Laboratory, 902 Battelle Blvd., PO Box 999, Richland, Washington 99352 (United States)] [Pacific Northwest National Laboratory, 902 Battelle Blvd., PO Box 999, Richland, Washington 99352 (United States); Sundararajan, Jennifer A.; Kaur, Maninder; Qiang, You [Department of Physics, University of Idaho, Moscow, Idaho 83844 (United States)] [Department of Physics, University of Idaho, Moscow, Idaho 83844 (United States); Burks, Edward C.; Liu, Kai [Department of Physics, University of California, Davis, California 95616 (United States)] [Department of Physics, University of California, Davis, California 95616 (United States)

2013-08-28

359

Bioinspired Hydrogenase Models: The Mixed-Valence Triiron Complex [Fe3(CO)7(?-edt)2] and Phosphine Derivatives [Fe3(CO)7–x(PPh3)x(?-edt)2] (x = 1, 2) and [Fe3(CO)5(?2-diphosphine)(?-edt)2] as Proton Reduction Catalysts  

PubMed Central

The mixed-valence triiron complexes [Fe3(CO)7–x(PPh3)x(?-edt)2] (x = 0–2; edt = SCH2CH2S) and [Fe3(CO)5(?2-diphosphine)(?-edt)2] (diphosphine = dppv, dppe, dppb, dppn) have been prepared and structurally characterized. All adopt an anti arrangement of the dithiolate bridges, and PPh3 substitution occurs at the apical positions of the outer iron atoms, while the diphosphine complexes exist only in the dibasal form in both the solid state and solution. The carbonyl on the central iron atom is semibridging, and this leads to a rotated structure between the bridged diiron center. IR studies reveal that all complexes are inert to protonation by HBF4·Et2O, but addition of acid to the pentacarbonyl complexes results in one-electron oxidation to yield the moderately stable cations [Fe3(CO)5(PPh3)2(?-edt)2]+ and [Fe3(CO)5(?2-diphosphine)(?-edt)2]+, species which also result upon oxidation by [Cp2Fe][PF6]. The electrochemistry of the formally Fe(I)–Fe(II)–Fe(I) complexes has been investigated. Each undergoes a quasi-reversible oxidation, the potential of which is sensitive to phosphine substitution, generally occurring between 0.15 and 0.50 V, although [Fe3(CO)5(PPh3)2(?-edt)2] is oxidized at ?0.05 V. Reduction of all complexes is irreversible and is again sensitive to phosphine substitution, varying between ?1.47 V for [Fe3(CO)7(?-edt)2] and around ?1.7 V for phosphine-substituted complexes. In their one-electron-reduced states, all complexes are catalysts for the reduction of protons to hydrogen, the catalytic overpotential being increased upon successive phosphine substitution. In comparison to the diiron complex [Fe2(CO)6(?-edt)], [Fe3(CO)7(?-edt)2] catalyzes proton reduction at 0.36 V less negative potentials. Electronic structure calculations have been carried out in order to fully elucidate the nature of the oxidation and reduction processes. In all complexes, the HOMO comprises an iron–iron bonding orbital localized between the two iron atoms not ligated by the semibridging carbonyl, while the LUMO is highly delocalized in nature and is antibonding between both pairs of iron atoms but also contains an antibonding dithiolate interaction.

2014-01-01

360

Formation and properties of high Fe-content Fe-(B-Si)-Zr bulk amorphous alloys  

NASA Astrophysics Data System (ADS)

The present work is devoted to the development of Fe-(B-Si)-Zr amorphous alloys with high glass-forming ability and good magnetic properties. Using the cluster-plus-glue-atom model proposed for ideal amorphous structures, [FeFe11B3Si](Fe1- x Zr x ) was determined as the cluster formula of Fe-(B-Si)-Zr alloys. The glass formation and thermal stability of the serial alloys, namely, [FeFe11B3Si](Fe1- x Zr x ) ( x = 0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.75, and 1.0), were studied by the combination of copper mold casting, X-ray diffraction, and differential thermal analysis techniques. The maxima of glass-forming ability and thermal stability were found to occur at the compositions of [FeFe11B3Si](Fe0.6Zr0.4) and [FeFe11B3Si](Fe0.5Zr0.5). The alloys can be cast into amorphous rods with 1.5 mm diameter, and upon reheating, the amorphous alloys exhibit a large undercooled liquid span of 37 K. The saturation magnetization of the [FeFe11B3Si](Fe0.5Zr0.5) amorphous alloy was measured to be 1.4 T.

Geng, Yao-xiang; Wang, Ying-min; Qiang, Jian-bing; Wang, Qing; Kong, Fan-yang; Zhang, Gui-feng; Dong, Chuang

2013-04-01

361

A Synthetic Nickel Electrocatalyst With a Turnover Frequency Above 100,000 s-1 for H2 Production  

SciTech Connect

Increased worldwide energy demand will require greater use of carbon-neutral sustainable energy sources. The intermittent nature of solar and wind power requires storage of energy, so electrocatalysts that convert electrical energy to chemical bonds in fuels are needed. Platinum is an excellent catalyst, but it is of low abundance and high cost. Hydrogenase enzymes in Nature catalyze the evolution of H2 and use earth-abundant metals such as nickel and iron. We report that a synthetic nickel catalyst, [Ni(7PPh2NPh)2](BF4)2, (7PPh2NPh = 1,3,6-triphenyl-1-aza-3,6-diphosphacycloheptane) catalyzes the production of H2 using [(DMF)H]+OTf as the proton source, with turnover frequencies of 31,000 s-1 in dry acetonitrile and 108,000 s-1 in the presence of H2O (1.2 M), at a potential of -1.13 V (vs. the ferrocenium/ferrocene couple). These turnover frequencies exceed those reported for the [FeFe] hydrogenase enzyme by more than an order of magnitude, and are the fastest reported for any molecular catalyst for H2 production. This material is based upon work supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the US Department of Energy, Office of Science, Office of Basic Energy Sciences.

Helm, Monte L.; Stewart, Michael P.; Bullock, R. Morris; Rakowski DuBois, Mary; DuBois, Daniel L.

2011-08-12

362

Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052  

PubMed Central

Background Solventogenic clostridia offer a sustainable alternative to petroleum-based production of butanol--an important chemical feedstock and potential fuel additive or replacement. C. beijerinckii is an attractive microorganism for strain design to improve butanol production because it (i) naturally produces the highest recorded butanol concentrations as a byproduct of fermentation; and (ii) can co-ferment pentose and hexose sugars (the primary products from lignocellulosic hydrolysis). Interrogating C. beijerinckii metabolism from a systems viewpoint using constraint-based modeling allows for simulation of the global effect of genetic modifications. Results We present the first genome-scale metabolic model (iCM925) for C. beijerinckii, containing 925 genes, 938 reactions, and 881 metabolites. To build the model we employed a semi-automated procedure that integrated genome annotation information from KEGG, BioCyc, and The SEED, and utilized computational algorithms with manual curation to improve model completeness. Interestingly, we found only a 34% overlap in reactions collected from the three databases--highlighting the importance of evaluating the predictive accuracy of the resulting genome-scale model. To validate iCM925, we conducted fermentation experiments using the NCIMB 8052 strain, and evaluated the ability of the model to simulate measured substrate uptake and product production rates. Experimentally observed fermentation profiles were found to lie within the solution space of the model; however, under an optimal growth objective, additional constraints were needed to reproduce the observed profiles--suggesting the existence of selective pressures other than optimal growth. Notably, a significantly enriched fraction of actively utilized reactions in simulations--constrained to reflect experimental rates--originated from the set of reactions that overlapped between all three databases (P = 3.52 × 10-9, Fisher's exact test). Inhibition of the hydrogenase reaction was found to have a strong effect on butanol formation--as experimentally observed. Conclusions Microbial production of butanol by C. beijerinckii offers a promising, sustainable, method for generation of this important chemical and potential biofuel. iCM925 is a predictive model that can accurately reproduce physiological behavior and provide insight into the underlying mechanisms of microbial butanol production. As such, the model will be instrumental in efforts to better understand, and metabolically engineer, this microorganism for improved butanol production.

2011-01-01

363

Involvement of NADH:Acceptor Oxidoreductase and Butyryl Coenzyme A Dehydrogenase in Reversed Electron Transport during Syntrophic Butyrate Oxidation by Syntrophomonas wolfei? †  

PubMed Central

Methanogenic oxidation of butyrate to acetate requires a tight cooperation between the syntrophically fermenting Syntrophomonas wolfei and the methanogen Methanospirillum hungatei, and a reversed electron transport system in S. wolfei was postulated to shift electrons from butyryl coenzyme A (butyryl-CoA) oxidation to the redox potential of NADH for H2 generation. The metabolic activity of butyrate-oxidizing S. wolfei cells was measured via production of formazan and acetate from butyrate, with 2,3,5-triphenyltetrazolium chloride as electron acceptor. This activity was inhibited by trifluoperazine (TPZ), an antitubercular agent known to inhibit NADH:menaquinone oxidoreductase. In cell extracts of S. wolfei, the oxidation of NADH could be measured with quinones, viologens, and tetrazolium dyes as electron acceptors, and also this activity was inhibited by TPZ. The TPZ-sensitive NADH:acceptor oxidoreductase activity appeared to be membrane associated but could be dissociated from the membrane as a soluble protein and was semipurified by anion-exchange chromatography. Recovered proteins were identified by peptide mass fingerprinting, which indicated the presence of an NADH:acceptor oxidoreductase as part of a three-component [FeFe] hydrogenase complex and a selenocysteine-containing formate dehydrogenase. Furthermore, purification of butyryl-CoA dehydrogenase (Bcd) activity and peptide mass fingerprinting revealed two Bcd proteins different from the Bcd subunit of the Bcd/electron-transfer flavoprotein complex (Bcd/EtfAB) predicted from the genome sequence of S. wolfei. The results suggest that syntrophic oxidation of butyrate in S. wolfei involves a membrane-associated TPZ-sensitive NADH:acceptor oxidoreductase as part of a hydrogenase complex similar to the recently discovered “bifurcating” hydrogenase in Thermotoga maritima and butyryl-CoA dehydrogenases that are different from Bcd of the Bcd/EtfAB complex.

Muller, Nicolai; Schleheck, David; Schink, Bernhard

2009-01-01

364

Insights Into the P-To-Q Conversion in the Catalytic Cycle of Methane Monooxygenase From a Synthetic Model System  

SciTech Connect

For the catalytic cycle of soluble methane monooxygenase (sMMO), it has been proposed that cleavage of the O-O bond in the ({mu}-peroxo)diiron(III) intermediate P gives rise to the diiron(IV) intermediate Q with an Fe{sub 2}({mu}-O){sub 2} diamond core, which oxidizes methane to methanol. As a model for this conversion, ({mu}-oxo) diiron(III) complex 1 ([Fe{sup III}{sub 2}({mu}-O)({mu}-O{sub 2}H{sub 3})(L){sub 2}]{sup 3+}, L = tris(3,5-dimethyl-4-methoxypyridyl-2-methyl)amine) has been treated consecutively with one eq of H{sub 2}O{sub 2} and one eq of HClO{sub 4} to form 3 ([Fe{sup IV}{sub 2}({mu}-O){sub 2}(L){sub 2}]{sup 4+}). In the course of this reaction a new species, 2, can be observed before the protonation step; 2 gives rise to a cationic peak cluster by ESI-MS at m/z 1,399, corresponding to the [Fe{sub 2}O{sub 3}L{sub 2}H](OTf){sub 2}{sup +} ion in which 1 oxygen atom derives from 1 and the other two originate from H{sub 2}O{sub 2}. Moessbauer studies of 2 reveal the presence of two distinct, exchange coupled iron(IV) centers, and EXAFS fits indicate a short Fe-O bond at 1.66 {angstrom} and an Fe-Fe distance of 3.32 {angstrom}. Taken together, the spectroscopic data point to an HO-Fe{sup IV}-O-Fe{sup IV} = O core for 2. Protonation of 2 results in the loss of H{sub 2}O and the formation of 3. Isotope labeling experiments show that the [Fe{sup IV}{sub 2}({mu}-O){sub 2}] core of 3 can incorporate both oxygen atoms from H{sub 2}O{sub 2}. The reactions described here serve as the only biomimetic precedent for the conversion of intermediates P to Q in the sMMO reaction cycle and shed light on how a peroxodiiron(III) unit can transform into an [Fe{sup IV}{sub 2}({mu}-O){sub 2}] core.

Xue, G.; Fiedler, A.T.; Martinho, M.; Munck, E.; Que, L.; Jr.

2009-05-28

365

Fermentation of biomass-generated synthesis gas: effects of nitric oxide.  

PubMed

The production of renewable fuels, such as ethanol, has been steadily increasing owing to the need for a reduced dependency on fossil fuels. It was demonstrated previously that biomass-generated synthesis gas (biomass-syngas) can be converted to ethanol and acetic acid using a microbial catalyst. The biomass-syngas (primarily CO, CO(2), H(2), and N(2)) was generated in a fluidized-bed gasifier and used as a substrate for Clostridium carboxidivorans P7(T). Results showed that the cells stopped consuming H(2) when exposed to biomass-syngas, thus indicating that there was an inhibition of the hydrogenase enzyme due to some biomass-syngas contaminant. It was hypothesized that nitric oxide (NO) detected in the biomass-syngas could be the possible cause of this inhibition. The specific activity of hydrogenase was monitored with time under varying concentrations of H(2) and NO. Results indicated that NO (at gas concentrations above 40 ppm) was a non-competitive inhibitor of hydrogenase activity, although the loss of hydrogenase activity was reversible. In addition, NO also affected the cell growth and increased the amount of ethanol produced. A kinetic model of hydrogenase activity with inhibition by NO was demonstrated with results suggesting there are multiple binding sites of NO on the hydrogenase enzyme. Since other syngas-fermenting organisms utilize the same metabolic pathways, this study estimates that NO < 40 ppm can be tolerated by cells in a syngas-fermentation system without compromising the hydrogenase activity, cell growth, and product distribution. PMID:17171719

Ahmed, Asma; Lewis, Randy S

2007-08-01

366

Experimental partitioning studies near the Fe-FeS eutectic, with an emphasis on elements important to iron meteorite chronologies (Pb, Ag, Pd, and Tl)  

NASA Technical Reports Server (NTRS)

Partitioning coefficients for metal/sulfide liquid, troilite/sulfide liquid, and schreibersite/sulfide liquid were determined for Ag, Au, Mo, Ni, Pd, and Tl (using EMPA and proton-induced X-ray microprobe and ion microprobe analyses) in order to understand the chronometer systems of iron meteorites. In general, the obtained schreibersite/metal and troilite/metal partition coefficients for 'compatible' elements were quite similar to those inferred from natural assemblages, reinforcing an earlier made conclusion that there is a class of elements for which experimental troilite/metal and schreibersite/metal partition coefficients approximate those inferred from natural samples. The consistency between experimental and natural assemblages, however, was not observed for Ag, Pb, and Tl, indicating that the abundances of these elements determined in 'metal' and 'troilite' separates from iron meteorites are influenced by trace minerals that concentrate incompatible elements.

Jones, J. H.; Hart, S. R.; Benjamin, T. M.

1993-01-01

367

Hydrogenases, Their Cloning, Preparation, Characterization and Modification for Use in Photobioreactors. Final Report.  

National Technical Information Service (NTIS)

The screen for hydrogen evolving activity involved some 40 organisms and strains including photosynthetic bacteria, sulfate reducers, several thermophilic blue green algae, as well as soil bacteria such as Alcaligenes eutrophus and various clostridia. Des...

1984-01-01

368

Distribution Analysis of Hydrogenases in Surface Waters of Marine and Freshwater Environments  

Microsoft Academic Search

BackgroundSurface waters of aquatic environments have been shown to both evolve and consume hydrogen and the ocean is estimated to be the principal natural source. In some marine habitats, H2 evolution and uptake are clearly due to biological activity, while contributions of abiotic sources must be considered in others. Until now the only known biological process involved in H2 metabolism

Martin Barz; Christian Beimgraben; Torsten Staller; Frauke Germer; Friederike Opitz; Claudia Marquardt; Christoph Schwarz; Kirstin Gutekunst; Klaus Heinrich Vanselow; Ruth Schmitz; Julie LaRoche; Rüdiger Schulz; Jens Appel

2010-01-01

369

Models, Fiction, and Fictional Models  

NASA Astrophysics Data System (ADS)

The following sections are included: * Introduction * Why Most Models in Science Are Not Fictional * Typically Fictional Models in Science * Modeling the Unobservable * Fictional Models for the Unobservable? * References

Liu, Chuang

2014-03-01

370

The importance of hydrogen and formate transfer for syntrophic fatty, aromatic and alicyclic metabolism.  

PubMed

We used a combination of genomic, transcriptional and enzymatic analyses to determine the mechanism of interspecies electron transfer by two model syntrophic microorganisms, Syntrophomonas wolfei and Syntrophus aciditrophicus. Both organisms contain multiple hydrogenase and formate dehydrogenase genes, but lack genes for outer membrane cytochromes and nanowire formation. Syntrophically grown cells and cell-free extracts of S. aciditrophicus and S. wolfei had both hydrogenase and formate dehydrogenase activities. Butyrate metabolism and CH4 production by washed cell suspensions of S.?wolfei and Methanospirillum hungatei were inhibited by hydrogenase inhibitors (cyanide and carbon monoxide), but not by a formate dehydrogenase inhibitor (hypophosphite). Syntrophic benzoate oxidation and CH4 production by washed cell suspensions of S. aciditrophicus and M. hungatei were inhibited by hypophosphite, but not cyanide and carbon monoxide. All three inhibitors halted syntrophic cyclohexane-1-carboxylate metabolism. Two hydrogenase genes, hydA1 and hydA2, were more highly expressed when S. wolfei was grown syntrophically. S. aciditrophicus expressed multiple hydrogenase and formate dehydrogenase genes during syntrophic benzoate and cyclohexane-1-carboxylate growth, one of which (fdhA2) was highly differentially expressed during syntrophic benzoate growth. Thus, these syntrophic microorganisms have flexible metabolisms that allow them to use either H2 or formate transfer depending on the substrate involved. PMID:24387041

Sieber, Jessica R; Le, Huynh M; McInerney, Michael J

2014-01-01

371

Modeling the Syn-Disposition of Nitrogen Donors in Non-Heme Diiron Enzymes. Synthesis, Characterization, and Hydrogen Peroxide Reactivity of Diiron(III) Complexes with the Syn N-Donor Ligand H2BPG2DEV  

PubMed Central

In order to model the syn disposition of histidine residues in carboxylate-bridged non-heme diiron enzymes, we prepared a new dinucleating ligand, H2BPG2DEV, that provides this geometric feature. The ligand incorporates biologically relevant carboxylate functionalities, which have not been explored as extensively as nitrogen-only analogs. Three novel oxo-bridged diiron(III) complexes [Fe2(?-O)(H2O)2-(BPG2DEV)](ClO4)2 (6), [Fe2(?-O)(?-O CAriPrO)(BPG2DEV)](ClO4) (7), and [Fe2(?-O)(?-CO3)(BPG2DEV)] (8) were prepared. Single crystal X-ray structural characterization confirms that two pyridines are bound syn with respect to the Fe–Fe vector in these compounds. The carbonato-bridged complex 8 forms quantitatively from 6 in a rapid reaction with gaseous CO2 in organic solvents. A common maroon-colored intermediate (?max = 490 nm; ? = 1500 M?1 cm?1) forms in reactions of 6, 7, or 8 with H2O2 and NEt3 in CH3CN/H2O solutions. Mass spectrometric analyses of this species, formed using 18O-labeled H2O2, indicate the presence of a peroxide ligand bound to the oxo-bridged diiron(III) center. The Mössbauer spectrum at 90 K of the EPR-silent intermediate exhibits a quadrupole doublet with ?. = 0.58 mm/s and ?EQ = 0.58 mm/s. The isomer shift is typical for a peroxodiiron(III) species, but the quadrupole splitting parameter is unusually small compared to related complexes. These Mössbauer parameters are comparable to those observed for a peroxo intermediate formed in the reaction of reduced toluene/o-xylene monooxygenase hydroxylase (ToMOH) with dioxygen. Resonance Raman studies reveal an unusually low-energy O–O stretching mode in the peroxo intermediate that is consistent with a short diiron distance. Although peroxodiiron(III) intermediates generated from 6, 7, and 8 are poor O-atom transfer catalysts, they display highly efficient catalase activity, with turnover numbers up to 10,000. In contrast to hydrogen peroxide reactions of diiron(III) complexes that lack a dinucleating ligand, the intermediates generated here could be reformed in significant quantities after a second addition of H2O2, as observed spectroscopically and by mass spectrometry.

Friedle, Simone; Kodanko, Jeremy J.; Morys, Anna J.; Hayashi, Takahiro; Moenne-Loccoz, Pierre; Lippard, Stephen J.

2009-01-01

372

Flexibility of Syntrophic Enzyme Systems in Desulfovibrio Species Ensures Their Adaptation Capability to Environmental Changes  

PubMed Central

The mineralization of organic matter in anoxic environments relies on the cooperative activities of hydrogen producers and consumers obligately linked by interspecies metabolite exchange in syntrophic consortia that may include sulfate reducing species such as Desulfovibrio. To evaluate the metabolic flexibility of syntrophic Desulfovibrio to adapt to naturally fluctuating methanogenic environments, we studied Desulfovibrio alaskensis strain G20 grown in chemostats under respiratory and syntrophic conditions with alternative methanogenic partners, Methanococcus maripaludis and Methanospirillum hungatei, at different growth rates. Comparative whole-genome transcriptional analyses, complemented by G20 mutant strain growth experiments and physiological data, revealed a significant influence of both energy source availability (as controlled by dilution rate) and methanogen on the electron transfer systems, ratios of interspecies electron carriers, energy generating systems, and interspecies physical associations. A total of 68 genes were commonly differentially expressed under syntrophic versus respiratory lifestyle. Under low-energy (low-growth-rate) conditions, strain G20 further had the capacity to adapt to the metabolism of its methanogenic partners, as shown by its differing gene expression of enzymes involved in the direct metabolic interactions (e.g., periplasmic hydrogenases) and the ratio shift in electron carriers used for interspecies metabolite exchange (hydrogen/formate). A putative monomeric [Fe-Fe] hydrogenase and Hmc (high-molecular-weight-cytochrome c3) complex-linked reverse menaquinone (MQ) redox loop become increasingly important for the reoxidation of the lactate-/pyruvate oxidation-derived redox pair, DsrCred and Fdred, relative to the Qmo-MQ-Qrc (quinone-interacting membrane-bound oxidoreductase; quinone-reducing complex) loop. Together, these data underscore the high enzymatic and metabolic adaptive flexibility that likely sustains Desulfovibrio in naturally fluctuating methanogenic environments.

Meyer, Birte; Kuehl, Jennifer V.; Deutschbauer, Adam M.; Arkin, Adam P.

2013-01-01

373

Correcting for electrocatalyst desorption and inactivation in chronoamperometry experiments.  

PubMed

Chronoamperometric experiments with adsorbed electrocatalysts are commonly performed either for analytical purposes or for studying the catalytic mechanism of a redox enzyme. In the context of amperometric sensors, the current may be recorded as a function of time while the analyte concentration is being increased to determine a linearity range. In mechanistic studies of redox enzymes, chronoamperometry proved powerful for untangling the effects of electrode potential and time, which are convoluted in cyclic voltammetric measurements, and for studying the energetics and kinetics of inhibition. In all such experiments, the fact that the catalyst's coverage and/or activity decreases over time distorts the data. This may hide meaningful features, introduce systematic errors, and limit the accuracy of the measurements. We propose a general and surprisingly simple method for correcting for electrocatalyst desorption and inactivation, which greatly increases the precision of chronoamperometric experiments. Rather than subtracting a baseline, this consists in dividing the current, either by a synthetic signal that is proportional to the instant electroactive coverage or by the signal recorded in a control experiment. In the latter, the change in current may result from film loss only or from film loss plus catalyst inactivation. We describe the different strategies for obtaining the control signal by analyzing various data recorded with adsorbed redox enzymes: nitrate reductase, NiFe hydrogenase, and FeFe hydrogenase. In each case we discuss the trustfulness and the benefit of the correction. This method also applies to experiments where electron transfer is mediated, rather than direct, providing the current is proportional to the time-dependent concentration of catalyst. PMID:19298055

Fourmond, Vincent; Lautier, Thomas; Baffert, Carole; Leroux, Fanny; Liebgott, Pierre-Pol; Dementin, Sébastien; Rousset, Marc; Arnoux, Pascal; Pignol, David; Meynial-Salles, Isabelle; Soucaille, Phillippe; Bertrand, Patrick; Léger, Christophe

2009-04-15

374

Local structures of Sr2FeMnO5+y (y=0, 0.5) and Sr2Fe1.5Cr0.5O5 from reverse Monte Carlo modeling of pair distribution function data and implications for magnetic order  

NASA Astrophysics Data System (ADS)

The local structures of the oxygen deficient perovskites Sr2FeMnO5, Sr2FeMnO5.5, and Sr2Fe1.5Cr0.5O5 have been analyzed using neutron pair distribution function data. The results show that locally all three structures are more complex than implied by their average cubic structures and that the distributions of oxygen vacancies are not completely random on a local level. For both Sr2FeMnO5+y compounds it is found that there is no short range ordering of the Fe and Mn cations. For Sr2Fe1.5Cr0.5O5 there is evidence to suggest that the Fe/Cr distribution is not completely random and is locally ordered such that there are fewer Fe?Fe nearest neighbor pairs than in a random distribution. Reverse Monte Carlo modeling of the pair distribution function data has provided the Fe?O, Mn?O, and Cr?O bond length distributions and information on the coordination numbers of the Fe, Mn, and Cr cations. In Sr2FeMnO5 it is found that the Fe3+ cations are most often in 4-fold coordination but there is also a large amount of Fe3+ in 5-fold coordination and a small amount in 6-fold coordination. The Mn3+ is split between 5-fold and 6-fold coordination. The Mn?O bond length distributions indicate that the Mn3+O6 octahedra and Mn3+O5 square pyramids are locally Jahn-Teller distorted. In Sr2FeMnO5.5 the Fe3+ is almost entirely 5 coordinate while the Mn4+ is almost entirely 6 coordinate. The Cr3+ in Sr2Fe1.5Cr0.5O5 is almost entirely 6-fold coordinated, giving the Fe3+ an average coordination number of 4.67. In Sr2FeMnO5 and Sr2Fe1.5Cr0.5O5 the Fe3+ and Sr2+ cations undergo local displacements which are driven by the oxygen vacancies, while the Mn3+ and Cr3+ cations remain near their positions in the average structures. In Sr2FeMnO5.5 these cations are not significantly displaced. The local coordination geometries are used to explain previously observed but yet poorly understood magnetic properties of these materials.

King, Graham; Ramezanipour, Farshid; Llobet, Anna; Greedan, John E.

2013-02-01

375

Assessment models  

NASA Technical Reports Server (NTRS)

The types of models used in assessment of possible chemical perturbations to the stratosphere are reviewed. The statue of one and two dimensional models are discussed. The problem of model validation is covered before the status of photochemical modeling efforts is discussed. A hierarchy of tests for photochemical models is presented.

Pyle, J. A.; Butler, D. M.; Cariolle, D.; Garcia, R. R.; Grose, W. L.; Guthrie, P. D.; Ko, M.; Owens, A. J.; Plumb, R. A.; Prather, M. J.

1985-01-01

376

Fair Model  

NSDL National Science Digital Library

The Fair model web site includes a freely available United States macroeconomic econometric model and a multicounty econometric model. The models run on the Windows OS. Instructors can use the models to teach forecasting, run policy experiments, and evaluate historical episodes of macroeconomic behavior. The web site includes extensive documentation for both models. The simulation is for upper-division economics courses in macroeconomics or econometrics. The principle developer is Ray Fair at Yale University.

Blecha, Betty