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1

Organometallic Complexes that Model the Active Sites of the [FeFe]- and [Fe]-Hydrogenases  

E-print Network

in the FeIFeI diiron models ((mu- pdt)[Fe(CO)2L][Fe(CO)2L'] ( L, L' = CO, PPh3, or PMe3) is thermodynamically favored to produce the mu-oxo or oxidative addition product, FeII-O-FeII, nevertheless the sulfurbased HOMO-1 accounts for the experimentally...

Liu, Tianbiao

2011-02-22

2

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. PMID:23049878

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

2012-01-01

3

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

4

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. PMID:20479937

Stapleton, James A.; Swartz, James R.

2010-01-01

5

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

6

Functional Studies of [FeFe] Hydrogenase Maturation in an Escherichia coli Biosynthetic System  

Microsoft Academic Search

Maturation of (FeFe) hydrogenases requires the biosynthesis and insertion of the catalytic iron-sulfur cluster, the H cluster. Two radical S-adenosylmethionine (SAM) proteins proposed to function in H cluster biosynthesis, HydEF and HydG, were recently identified in the hydEF-1 mutant of the green alga Chlamydo- monas reinhardtii (M. C. Posewitz, P. W. King, S. L. Smolinski, L. Zhang, M. Seibert, and

Paul W. King; Matthew C. Posewitz; Maria L. Ghirardi; Michael Seibert

2006-01-01

7

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

8

Activation Barriers of Oxygen Transformation at the Active Site of [FeFe] Hydrogenases.  

PubMed

Oxygen activation at the active sites of [FeFe] hydrogenases has been proposed to be the initial step of irreversible oxygen-induced inhibition of these enzymes. On the basis of a first theoretical study into the thermodynamics of O2 activation [Inorg. Chem. 2009, 48, 7127] we here investigate the kinetics of possible reaction paths at the distal iron atom of the active site by means of density functional theory. A sequence of steps is proposed to either form a reactive oxygen species (ROS) or fully reduce O2 to water. In this reaction cascade, two branching points are identified where water formation directly competes with harmful oxygen activation reactions. The latter are water formation by O-O bond cleavage of a hydrogen peroxide-bound intermediate competing with H2O2 dissociation and CO2 formation by a putative iron-oxo species competing with protonation of the iron-oxo species to form a hydroxyo ligand. Furthermore, we show that proton transfer to activated oxygen is fast and that proton supply to the active site is vital to prevent ROS dissociation. If sufficiently many reduction equivalents are available, oxygen activation reactions are accelerated, and oxygen reduction to water becomes possible. PMID:25345467

Finkelmann, Arndt R; Stiebritz, Martin T; Reiher, Markus

2014-11-17

9

Advanced electron paramagnetic resonance and density functional theory study of a {2Fe3S} cluster mimicking the active site of [FeFe] hydrogenase.  

PubMed

Despite extensive investigations of the active site of the [FeFe] hydrogenases, many details concerning the properties of the "hydrogen converting cluster" are not yet fully understood. The complexity of the so-called H-cluster is one of the main difficulties in studying the properties of its components. The present study is aimed at the mixed-valence EPR active [Fe2(?-CO)(CO)3(CN)2{MeSCH2C(Me)(CH2S)2}](1-) that is structurally closely related to the redox active binuclear part of the H-cluster in its CO-inhibited oxidized state. In this work, we present a characterization of this compound by advanced pulse EPR methods. The accurate determination of the (57)Fe, (1)H, (2)H, (14)N, and (15)N electron nuclear hyperfine interactions provided a very detailed picture of the electronic structure of this complex. A theoretical study using density functional theory (DFT) calculations identified possible isomers of the compound and further refined the knowledge about its properties. It was found that upon one electron oxidation of the parent Fe(I)-Fe(I) complex, the dominant mixed-valence Fe(I)-Fe(II) species is the one in which the CN ligand of the iron center that is distal to the thioether moves from the basal to the apical position. The unpaired spin distribution of the model complex is found to be clearly different from that of the native H-cluster. These differences are discussed and provide new insight into the functional features of the [FeFe] hydrogenase active site. PMID:21082840

Silakov, Alexey; Shaw, Jennifer L; Reijerse, Eduard J; Lubitz, Wolfgang

2010-12-15

10

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

11

Hydrogen-producing microflora and Fe-Fe hydrogenase diversities in seaweed bed associated with marine hot springs of Kalianda, Indonesia.  

PubMed

Microbial fermentation is a promising technology for hydrogen (H(2)) production. H(2) producers in marine geothermal environments are thermophilic and halotolerant. However, no one has surveyed an environment specifically for thermophilic bacteria that produce H(2) through Fe-Fe hydrogenases (H(2)ase). Using heterotrophic medium, several microflora from a seaweed bed associated with marine hot springs were enriched and analyzed for H(2) production. A H(2)-producing microflora was obtained from Sargassum sp., 16S rRNA genes and Fe-Fe H(2)ase diversities of this enrichment were also analyzed. Based on 16S rRNA genes analysis, 10 phylotypes were found in the H(2)-producing microflora showing 90.0-99.5 % identities to known species, and belonged to Clostridia, Gammaproteobacteria, and Bacillales. Clostridia were the most abundant group, and three Clostridia phylotypes were most related to known H(2) producers such as Anaerovorax odorimutans (94.0 % identity), Clostridium papyrosolvens (98.4 % identity), and Clostridium tepidiprofundi (93.1 % identity). For Fe-Fe H(2)ases, seven phylotypes were obtained, showing 63-97 % identities to known Fe-Fe H(2)ases, and fell into four distinct clusters. Phylotypes HW55-3 and HM55-1 belonged to thermophilic and salt-tolerant H(2)-producing Clostridia, Halothermothrix orenii-like Fe-Fe H(2)ases (80 % identity), and cellulolytic H(2)-producing Clostridia, C. papyrosolvens-like Fe-Fe H(2)ases (97 % identity), respectively. The results of both 16S rRNA genes and Fe-Fe H(2)ases surveys suggested that the thermophilic and halotolerant H(2)-producing microflora in seaweed bed of hot spring area represented previously unknown H(2) producers, and have potential application for H(2) production. PMID:23325032

Xu, Shou-Ying; He, Pei-Qing; Dewi, Seswita-Zilda; Zhang, Xue-Lei; Ekowati, Chasanah; Liu, Tong-Jun; Huang, Xiao-Hang

2013-05-01

12

(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

13

Non-innocent bma ligand in a dissymetrically disubstituted diiron dithiolate related to the active site of the [FeFe] hydrogenases.  

PubMed

The purpose of the present study was to evaluate the use of a non-innocent ligand as a surrogate of the anchored [4Fe4S] cubane in a synthetic mimic of the [FeFe] hydrogenase active site. Reaction of 2,3-bis(diphenylphosphino) maleic anhydride (bma) with [Fe(2)(CO)(6)(mu-pdt)] (propanedithiolate, pdt=S(CH(2))(3)S) in the presence of Me(3)NO-2H(2)O afforded the monosubstituted derivative [Fe(2)(CO)(5)(Me(2)NCH(2)PPh(2))(mu-pdt)] (1). This results from the decomposition of the bma ligand and the apparent C-H bond cleavage in the released trimethylamine. Reaction under photolytic conditions afforded [Fe(2)(CO)(4)(bma)(mu-pdt)] (2). Compounds 1 and 2 were characterized by IR, NMR and X-ray diffraction. Voltammetric study indicated that the primary reduction of 2 is centered on the bma ligand. PMID:20547420

Si, Youtao; Charreteur, Kévin; Capon, Jean-François; Gloaguen, Frederic; Pétillon, François Y; Schollhammer, Philippe; Talarmin, Jean

2010-10-01

14

Facilitated hydride binding in an Fe-Fe hydrogenase active-site biomimic revealed by X-ray absorption spectroscopy and DFT calculations.  

PubMed

Iron-only hydrogenases are high-efficiency biocatalysts for the synthesis and cleavage of molecular hydrogen. Their active site is a diiron center, which carries CO and CN ligands. Remarkably, the two iron atoms likely are connected by a non-protein azadithiolate (adt = S-CH2-NH-CH2-S). To dwell on the role of the adt in H2 catalysis, a specific biomimetic diiron compound, 1 = [Fe2(mu-adt-CH2-Ph)(CO)4(PMe3)2], with unprecedented positive reduction potential, has been synthesized and crystallized previously. It comprises two protonation sites, the N-benzyl-adt nitrogen that can hold a proton (H) and the Fe-Fe bond that will formally carry a hydride (Hy). We investigated changes in the solution structure of 1 in its four different protonation states (1', [1H]+, [1HHy]2+, and [1Hy]+) by X-ray absorption spectroscopy at the iron K-edge. EXAFS reveals that already protonation at the adt nitrogen atom causes a change of the ligand geometry involving a significant lengthening of the Fe-Fe distance and CO and PMe3 repositioning, respectively, thereby facilitating the subsequent binding of a bridging hydride. Hydride binding clearly is discernible in the XANES spectra of [1HHy]2+ and [1Hy]+. DFT calculations are in excellent agreement with the experimentally derived structural parameters and provide complementary insights into the electronic structure of the four protonation states. In the iron-only hydrogenases, protonation of the putative adt ligand may cause the bridging CO to move to a terminal position, thereby preparing the active site for hydride binding en route to H2 formation. PMID:18041829

Löscher, Simone; Schwartz, Lennart; Stein, Matthias; Ott, Sascha; Haumann, Michael

2007-12-24

15

The HydG enzyme generates an Fe(CO)2(CN) synthon in assembly of the FeFe hydrogenase H-cluster.  

PubMed

Three iron-sulfur proteins--HydE, HydF, and HydG--play a key role in the synthesis of the [2Fe](H) component of the catalytic H-cluster of FeFe hydrogenase. The radical S-adenosyl-L-methionine enzyme HydG lyses free tyrosine to produce p-cresol and the CO and CN(-) ligands of the [2Fe](H) cluster. Here, we applied stopped-flow Fourier transform infrared and electron-nuclear double resonance spectroscopies to probe the formation of HydG-bound Fe-containing species bearing CO and CN(-) ligands with spectroscopic signatures that evolve on the 1- to 1000-second time scale. Through study of the (13)C, (15)N, and (57)Fe isotopologs of these intermediates and products, we identify the final HydG-bound species as an organometallic Fe(CO)2(CN) synthon that is ultimately transferred to apohydrogenase to form the [2Fe](H) component of the H-cluster. PMID:24458644

Kuchenreuther, Jon M; Myers, William K; Suess, Daniel L M; Stich, Troy A; Pelmenschikov, Vladimir; Shiigi, Stacey A; Cramer, Stephen P; Swartz, James R; Britt, R David; George, Simon J

2014-01-24

16

Solution-phase photochemistry of a [FeFe]hydrogenase model compound: Evidence of photoinduced isomerisation  

SciTech Connect

The solution-phase photochemistry of the [FeFe] hydrogenase subsite model ({mu}-S(CH{sub 2}){sub 3}S)Fe{sub 2}(CO){sub 4}(PMe{sub 3}){sub 2} has been studied using ultrafast time-resolved infrared spectroscopy supported by density functional theory calculations. In three different solvents, n-heptane, methanol, and acetonitrile, relaxation of the tricarbonyl intermediate formed by UV photolysis of a carbonyl ligand leads to geminate recombination with a bias towards a thermodynamically less stable isomeric form, suggesting that facile interconversion of the ligand groups at the Fe center is possible in the unsaturated species. In a polar or hydrogen bonding solvent, this process competes with solvent substitution leading to the formation of stable solvent adduct species. The data provide further insight into the effect of incorporating non-carbonyl ligands on the dynamics and photochemistry of hydrogenase-derived biomimetic compounds.

Kania, Rafal; Hunt, Neil T. [Department of Physics, University of Strathclyde, SUPA, Glasgow G4 0NG (United Kingdom); Frederix, Pim W. J. M. [Department of Physics, University of Strathclyde, SUPA, Glasgow G4 0NG (United Kingdom); WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1XL (United Kingdom); Wright, Joseph A.; Pickett, Christopher J. [Energy Materials Laboratory, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ (United Kingdom); Ulijn, Rein V. [WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1XL (United Kingdom)

2012-01-28

17

Solution-phase photochemistry of a [FeFe]hydrogenase model compound: evidence of photoinduced isomerisation.  

PubMed

The solution-phase photochemistry of the [FeFe] hydrogenase subsite model (?-S(CH(2))(3)S)Fe(2)(CO)(4)(PMe(3))(2) has been studied using ultrafast time-resolved infrared spectroscopy supported by density functional theory calculations. In three different solvents, n-heptane, methanol, and acetonitrile, relaxation of the tricarbonyl intermediate formed by UV photolysis of a carbonyl ligand leads to geminate recombination with a bias towards a thermodynamically less stable isomeric form, suggesting that facile interconversion of the ligand groups at the Fe center is possible in the unsaturated species. In a polar or hydrogen bonding solvent, this process competes with solvent substitution leading to the formation of stable solvent adduct species. The data provide further insight into the effect of incorporating non-carbonyl ligands on the dynamics and photochemistry of hydrogenase-derived biomimetic compounds. PMID:22299905

Kania, Rafal; Frederix, Pim W J M; Wright, Joseph A; Ulijn, Rein V; Pickett, Christopher J; Hunt, Neil T

2012-01-28

18

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. PMID:17660315

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

2007-01-01

19

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

20

Immobilized metallodithiolate ligand supports for construction of bioinorganic model complexes  

E-print Network

to the analogous NiN2S2 2- systems. As the active site of [FeFe] Hydrogenase utilizes a unique peptide-bound propane dithiolate bridge to support the FeFe organometallic unit, [FeFe]Hydrogenase models have been covalently anchored to the resin-beads via similar...

Green, Kayla Nalynn

2009-05-15

21

Vibrational analysis of the model complex (mu-edt)[Fe(CO)(3)](2) and comparison to iron-only hydrogenase: the activation scale of hydrogenase model systems.  

PubMed

Research on simple [FeFe] hydrogenase model systems of type (mu-S(2)R)[Fe(CO)(3)](2) (R = C(2)H(4) (edt), C(3)H(6) (pdt)) 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 state Raman spectra of (mu-edt)[Fe(CO)(3)](2) and of the corresponding (13)CO-labeled complex are presented and analyzed in detail, with focus on the nu(C=O) and nu(Fe-CO)/delta(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 nu(C=O), nu(Fe-CO), and delta(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, fifteen mixed nu(Fe-CO)/delta(Fe-C=O) modes have been identified. The most prominent Raman peaks at 454, 456, and 483 cm(-1) correspond to a combination of nu(Fe-CO) stretching and delta(Fe-C=O) linear bending modes. The less intense peaks at 416 cm(-1) and 419 cm(-1) correspond to pure delta(Fe-C=O) linear bends. In the nu(C=O) region, the nu(C=O) normal modes at lower energy (1968 and 1964 cm(-1)) are almost pure equatorial (eq) nu(C=O)(eq) stretching vibrations, whereas the remaining four nu(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 pi-backdonation. Compared to the reduced form of [FeFe] hydrogenase (H(red)), the nu(C=O) vibrational frequencies of (mu-edt)[Fe(CO)(3)](2) are higher in energy, indicating that the dinuclear iron core in (mu-edt)[Fe(CO)(3)](2) is less electron rich compared to H(red) in the actual enzyme. Finally, quantum yields for the photodecomposition of (mu-edt)[Fe(CO)(3)](2) have been determined. PMID:20225804

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

2010-04-01

22

EPR/ENDOR, M?ssbauer, and Quantum Chemical Investigation of Di-iron Complexes Mimicking the Active Oxidized State of [FeFe] Hydrogenase  

PubMed Central

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 [Fe2(S2C2H4NH)(CN)2(CO)2(µ-CO)] active center uniquely found in the [FeFe]-hydrogenases, we present a detailed spectroscopic and theoretical analysis of its inorganic model [Fe2(S2X)(CO)3(dppv)(PMe3)]+ in two forms with S2X = ethanedithiolate (1edt) and azadithiolate (1adt) (dppv =cis-1,2-bis(diphenylphosphino)ethylene). These complexes represent models for the oxidized mixed-valent Fe(I)Fe(II) state analogous to the active oxidized "Hox" state of the native H-cluster. For both complexes, the 31P hyperfine (HF) interactions were determined by pulse EPR and ENDOR methods. For 1edt, the 57Fe parameters were measured by ESEEM and Mössbauer spectroscopy, while for 1adt 14N and selected 1H couplings could be obtained by ENDOR and HYSCORE. The spin density was found to be predominantly localized on the Fe(dppv) site. This spin distribution is different from the H-cluster where both the spin and charge density are delocalized over the two Fe centers. This difference is attributed to the influence of “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 14N 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

Olsen, Matthew T.; Sproules, Stephen; Reijerse, Eduard J.; Rauchfuss, Thomas B.

2012-01-01

23

Electron transfer and hydrogen generation from a molecular dyad: platinum(II) alkynyl complex anchored to [FeFe] hydrogenase subsite mimic.  

PubMed

A PS-Fe(2)S(2) molecular dyad 1a directly anchoring a platinum(II) alkynyl complex to a Fe(2)S(2) active site of a [FeFe] H(2)ase mimic, and an intermolecular system of its reference complexes 1b and 2, have been successfully constructed. Time-dependence of H(2) evolution shows that PS-Fe(2)S(2)1a as well as complex 2 with 1b can produce H(2) in the presence of a proton source and sacrificial donor under visible light irradiation. Spectroscopic and electrochemical studies on the electron transfer event reveal that the reduced Fe(I)Fe(0) species generated by the first electron transfer from the excited platinum(II) complex to the Fe(2)S(2) active site in PS-Fe(2)S(2)1a and complex 2 with 1b is essential for photochemical H(2) evolution, while the second electron transfer from the excited platinum(II) complex to the protonated Fe(I)Fe(0) species is thermodynamically unfeasible, which might be an obstacle for the relatively small amount of H(2) obtained by PS-Fe(2)S(2) molecular dyads reported so far. PMID:22218815

Wang, Wen-Guang; Wang, Feng; Wang, Hong-Yan; Tung, Chen-Ho; Wu, Li-Zhu

2012-02-28

24

A [NiFe]hydrogenase model that catalyses the release of hydrogen from formic acid.  

PubMed

We report the decomposition of formic acid to hydrogen and carbon dioxide, catalysed by a NiRu complex originally developed as a [NiFe]hydrogenase model. This is the first example of H2 evolution, catalysed by a [NiFe]hydrogenase model, which does not require additional energy. PMID:25234420

Nguyen, Nga T; Mori, Yuki; Matsumoto, Takahiro; Yatabe, Takeshi; Kabe, Ryota; Nakai, Hidetaka; Yoon, Ki-Seok; Ogo, Seiji

2014-11-11

25

Selenium is involved in regulation of periplasmic hydrogenase gene expression in Desulfovibrio vulgaris Hildenborough.  

PubMed

Desulfovibrio vulgaris Hildenborough is a good model organism to study hydrogen metabolism in sulfate-reducing bacteria. Hydrogen is a key compound for these organisms, since it is one of their major energy sources in natural habitats and also an intermediate in the energy metabolism. The D. vulgaris Hildenborough genome codes for six different hydrogenases, but only three of them, the periplasmic-facing [FeFe], [FeNi]1, and [FeNiSe] hydrogenases, are usually detected. In this work, we studied the synthesis of each of these enzymes in response to different electron donors and acceptors for growth as well as in response to the availability of Ni and Se. The formation of the three hydrogenases was not very strongly affected by the electron donors or acceptors used, but the highest levels were observed after growth with hydrogen as electron donor and lowest with thiosulfate as electron acceptor. The major effect observed was with inclusion of Se in the growth medium, which led to a strong repression of the [FeFe] and [NiFe]1 hydrogenases and a strong increase in the [NiFeSe] hydrogenase that is not detected in the absence of Se. Ni also led to increased formation of the [NiFe]1 hydrogenase, except for growth with H2, where its synthesis is very high even without Ni added to the medium. Growth with H2 results in a strong increase in the soluble forms of the [NiFe]1 and [NiFeSe] hydrogenases. This study is an important contribution to understanding why D. vulgaris Hildenborough has three periplasmic hydrogenases. It supports their similar physiological role in H2 oxidation and reveals that element availability has a strong influence in their relative expression. PMID:16621815

Valente, Filipa M A; Almeida, Cláudia C; Pacheco, Isabel; Carita, João; Saraiva, Lígia M; Pereira, Inês A C

2006-05-01

26

Roles of HynAB and Ech, the Only Two Hydrogenases Found in the Model Sulfate Reducer Desulfovibrio gigas  

PubMed Central

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

2013-01-01

27

Flexibility in Anaerobic Metabolism as Revealed in a Mutant of Chlamydomonas reinhardtii Lacking Hydrogenase Activity  

SciTech Connect

The green alga Chlamydomonas reinhardtii has a network of fermentation pathways that become active when cells acclimate to anoxia. Hydrogenase activity is an important component of this metabolism, and we have compared metabolic and regulatory responses that accompany anaerobiosis in wild-type C. reinhardtii cells and a null mutant strain for the HYDEF gene (hydEF-1 mutant), which encodes an [FeFe] hydrogenase maturation protein. This mutant has no hydrogenase activity and exhibits elevated accumulation of succinate and diminished production of CO2 relative to the parental strain during dark, anaerobic metabolism. In the absence of hydrogenase activity, increased succinate accumulation suggests that the cells activate alternative pathways for pyruvate metabolism, which contribute to NAD(P)H reoxidation, and continued glycolysis and fermentation in the absence of O2. Fermentative succinate production potentially proceeds via the formation of malate, and increases in the abundance of mRNAs encoding two malateforming enzymes, pyruvate carboxylase and malic enzyme, are observed in the mutant relative to the parental strain following transfer of cells from oxic to anoxic conditions. Although C. reinhardtii has a single gene encoding pyruvate carboxylase, it has six genes encoding putative malic enzymes. Only one of the malic enzyme genes, MME4, shows a dramatic increase in expression (mRNA abundance) in the hydEF-1 mutant during anaerobiosis. Furthermore, there are marked increases in transcripts encoding fumarase and fumarate reductase, enzymes putatively required to convert malate to succinate. These results illustrate the marked metabolic flexibility of C. reinhardtii and contribute to the development of an informed model of anaerobic metabolism in this and potentially other algae.

Dubini, A.; Mus, F.; Seibert, M.; Grossman, A. R.; Posewitz, M. C.

2009-03-13

28

Brownian Dynamics and Molecular Dynamics Study of the Association between Hydrogenase and Ferredoxin from Chlamydomonas reinhardtii  

PubMed Central

The [FeFe] hydrogenase from the green alga Chlamydomonas reinhardtii can catalyze the reduction of protons to hydrogen gas using electrons supplied from photosystem I and transferred via ferredoxin. To better understand the association of the hydrogenase and the ferredoxin, we have simulated the process over multiple timescales. A Brownian dynamics simulation method gave an initial thorough sampling of the rigid-body translational and rotational phase spaces, and the resulting trajectories were used to compute the occupancy and free-energy landscapes. Several important hydrogenase-ferredoxin encounter complexes were identified from this analysis, which were then individually simulated using atomistic molecular dynamics to provide more details of the hydrogenase and ferredoxin interaction. The ferredoxin appeared to form reasonable complexes with the hydrogenase in multiple orientations, some of which were good candidates for inclusion in a transition state ensemble of configurations for electron transfer. PMID:18621810

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

2008-01-01

29

Hydrogen-Activation Mechanism of [Fe] Hydrogenase Revealed by Multi-Scale Modeling  

E-print Network

When investigating the mode of hydrogen activation by [Fe] hydrogenases, not only the chemical reactivity at the active site is of importance but also the large-scale conformational change between the so-called open and closed conformations, which leads to a special spatial arrangement of substrate and iron cofactor. To study H2 activation, a complete model of the solvated and cofactor-bound enzyme in complex with the substrate methenyl-H4MPT+ was constructed. Both the closed and open conformations were simulated with classical molecular dynamics on the 100 ns time scale. Quantum-mechanics/molecular-mechanics calculations on snapshots then revealed the features of the active site that enable the facile H2 cleavage. The hydroxyl group of the pyridinol ligand can easily be deprotonated. With the deprotonated hydroxyl group and the structural arrangement in the closed conformation, H2 coordinated to the Fe center is subject to an ionic and orbital push-pull effect and can be rapidly cleaved with a concerted hydr...

Finkelmann, Arndt Robert; Reiher, Markus

2014-01-01

30

Flexibility in Anaerobic Metabolism as Revealed in a Mutant of Chlamydomonas reinhardtii Lacking Hydrogenase Activity*S?  

PubMed Central

The green alga Chlamydomonas reinhardtii has a network of fermentation pathways that become active when cells acclimate to anoxia. Hydrogenase activity is an important component of this metabolism, and we have compared metabolic and regulatory responses that accompany anaerobiosis in wild-type C. reinhardtii cells and a null mutant strain for the HYDEF gene (hydEF-1 mutant), which encodes an [FeFe] hydrogenase maturation protein. This mutant has no hydrogenase activity and exhibits elevated accumulation of succinate and diminished production of CO2 relative to the parental strain during dark, anaerobic metabolism. In the absence of hydrogenase activity, increased succinate accumulation suggests that the cells activate alternative pathways for pyruvate metabolism, which contribute to NAD(P)H reoxidation, and continued glycolysis and fermentation in the absence of O2. Fermentative succinate production potentially proceeds via the formation of malate, and increases in the abundance of mRNAs encoding two malateforming enzymes, pyruvate carboxylase and malic enzyme, are observed in the mutant relative to the parental strain following transfer of cells from oxic to anoxic conditions. Although C. reinhardtii has a single gene encoding pyruvate carboxylase, it has six genes encoding putative malic enzymes. Only one of the malic enzyme genes, MME4, shows a dramatic increase in expression (mRNA abundance) in the hydEF-1 mutant during anaerobiosis. Furthermore, there are marked increases in transcripts encoding fumarase and fumarate reductase, enzymes putatively required to convert malate to succinate. These results illustrate the marked metabolic flexibility of C. reinhardtii and contribute to the development of an informed model of anaerobic metabolism in this and potentially other algae. PMID:19117946

Dubini, Alexandra; Mus, Florence; Seibert, Michael; Grossman, Arthur R.; Posewitz, Matthew C.

2009-01-01

31

Brownian Dynamics and Molecular Dynamics Study of the Association Between Hydrogenase and Ferredoxin from the Chlamydomonas reinhardtii  

SciTech Connect

The [FeFe] hydrogenase from the green alga Chlamydomonas reinhardtii can catalyze the reduction of protons to hydrogen gas using electrons supplied from photosystem I and transferred via ferredoxin. To better understand the association of the hydrogenase and the ferredoxin, we have simulated the process over multiple timescales. A Brownian dynamics simulation method gave an initial thorough sampling of the rigid-body translational and rotational phase spaces, and the resulting trajectories were used to compute the occupancy and free-energy landscapes. Several important hydrogenase-ferredoxin encounter complexes were identified from this analysis, which were then individually simulated using atomistic molecular dynamics to provide more details of the hydrogenase and ferredoxin interaction. The ferredoxin appeared to form reasonable complexes with the hydrogenase in multiple orientations, some of which were good candidates for inclusion in a transition state ensemble of configurations for electron transfer.

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

2008-10-01

32

Interaction of [FeFe]-hydrogenases with single-walled carbon nanotubes  

NASA Astrophysics Data System (ADS)

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 II. 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.

Svedruzic Chang, Drazenka; McDonald, Timothy J.; Kim, Yong-Hyun; Blackburn, Jeffrey L.; Heben, Michael J.; King, Paul W.

2007-09-01

33

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

34

Hydrogen Activation by Biomimetic [NiFe]-Hydrogenase Model Containing Protected Cyanide Cofactors  

PubMed Central

Described are experiments that allow incorporation of cyanide cofactors and hydride substrate into active site models [NiFe]-hydrogenases (H2ases). Complexes of the type (CO)2(CN)2Fe(pdt)Ni(dxpe), (dxpe = dppe, 1; dxpe = dcpe, 2) bind the Lewis acid B(C6F5)3 (BArF3) to give the adducts (CO)2(CNBArF3)2Fe(pdt)Ni(dxpe), (1(BArF3)2, 2(BArF3)2). Upon decarbonylation using amine oxides, these adducts react with H2 to give hydrido derivatives Et4N[(CO)(CNBArF3)2Fe(H)(pdt)Ni(dxpe)], (dxpe = dppe, Et4N[H3(BArF3)2]; dxpe = dcpe, Et4N[H4(BArF3)2]). Crystallographic analysis shows that Et4N[H3(BArF3)2] generally resembles the active site of the enzyme in the reduced, hydride-containing states (Ni-C/R). The Fe-H…Ni center is unsymmetrical with rFe-H = 1.51(3) and rNi-H = 1.71(3) Å. Both crystallographic and 19F NMR analysis show that the CNBArF3? ligands occupy basal and apical sites. Unlike cationic Ni-Fe hydrides, [H3(BArF3)2]? and [H4(BArF3)2]? oxidize at mild potentials, near the Fc+/0 couple. Electrochemical measurements indicate that in the presence of base, [H3(BArF3)2]? catalyzes the oxidation of H2. NMR evidence indicates dihydrogen bonding between these anionic hydrides and ammonium salts, which is relevant to the mechanism of hydrogenogenesis. In the case of Et4N[H3(BArF3)2], strong acids such as HCl induce H2 release to give the chloride Et4N[(CO)(CNBArF3)2Fe(pdt)(Cl)Ni(dppe)]. PMID:23899049

Manor, Brian C.; Rauchfuss, Thomas B.

2013-01-01

35

Accurate calculations of geometries and singlet-triplet energy differences for active-site models of [NiFe] hydrogenase.  

PubMed

We have studied the geometry and singlet-triplet energy difference of two mono-nuclear Ni(2+) models related to the active site in [NiFe] hydrogenase. Multiconfigurational second-order perturbation theory based on a complete active-space wavefunction with an active space of 12 electrons in 12 orbitals, CASPT2(12,12), reproduces experimental bond lengths to within 1 pm. Calculated singlet-triplet energy differences agree with those obtained from coupled-cluster calculations with single, double and (perturbatively treated) triple excitations (CCSD(T)) to within 12 kJ mol(-1). For a bimetallic model of the active site of [NiFe] hydrogenase, the CASPT2(12,12) results were compared with the results obtained with an extended active space of 22 electrons in 22 orbitals. This is so large that we need to use restricted active-space theory (RASPT2). The calculations predict that the singlet state is 48-57 kJ mol(-1) more stable than the triplet state for this model of the Ni-SIa state. However, in the [NiFe] hydrogenase protein, the structure around the Ni ion is far from the square-planar structure preferred by the singlet state. This destabilises the singlet state so that it is only ?24 kJ mol(-1) more stable than the triplet state. Finally, we have studied how various density functional theory methods compare to the experimental, CCSD(T), CASPT2, and RASPT2 results. Semi-local functionals predict the best singlet-triplet energy differences, with BP86, TPSS, and PBE giving mean unsigned errors of 12-13 kJ mol(-1) (maximum errors of 25-31 kJ mol(-1)) compared to CCSD(T). For bond lengths, several methods give good results, e.g. TPSS, BP86, and M06, with mean unsigned errors of 2 pm for the bond lengths if relativistic effects are considered. PMID:24647807

Delcey, Mickaël G; Pierloot, Kristine; Phung, Quan M; Vancoillie, Steven; Lindh, Roland; Ryde, Ulf

2014-05-01

36

Determination of the photolysis products of [FeFe]hydrogenase enzyme model systems using ultrafast multidimensional infrared spectroscopy.  

PubMed

Ultrafast transient 2D-IR (T-2D-IR) spectroscopy has been used to study the photolysis products of the [FeFe]hydrogenase enzyme model compound (?-propanedithiolate)Fe(2)(CO)(6) in heptane solution following irradiation at ultraviolet wavelengths. Observation of coupling patterns between the vibrational modes of the photoproduct species formed alongside examination of the appearance time scales of these signals has uniquely enabled assignment of the photoproduct spectrum to a single pentacarbonyl species. Comparison of the vibrational relaxation rate of the photoproduct with that of the parent is consistent with the formation of a solvent adduct at the vacant coordination site, while anisotropy data in conjunction with density functional theory simulations indicates substitution in an axial rather than equatorial position. No firm evidence of additional short-lived intermediates is seen, indicating that the subsequent chemistry of these species is likely to be strongly defined by the nature of the first solvation shell. PMID:20845922

Stewart, Andrew I; Wright, Joseph A; Greetham, Gregory M; Kaziannis, Spiridon; Santabarbara, Stefano; Towrie, Michael; Parker, Anthony W; Pickett, Christopher J; Hunt, Neil T

2010-10-18

37

The iron-site structure of [Fe]-hydrogenase and model systems: an X-ray absorption near edge spectroscopy study†‡  

PubMed Central

The [Fe]-hydrogenase is an ideal system for studying the electronic properties of the low spin iron site that is common to the catalytic centres of all hydrogenases. Because they have no auxiliary iron-sulfur clusters and possess a cofactor containing a single iron centre, the [Fe]-hydrogenases are well suited for spectroscopic analysis of those factors required for the activation of molecular hydrogen. Specifically, in this study we shed light on the electronic and molecular structure of the iron centre by XAS analysis of [Fe]-hydrogenase from Methanocaldococcus jannashii and five model complexes (Fe(ethanedithiolate)-(CO)2(PMe3)2, [K(18-crown-6)]2[Fe(CN)2(CO)3], K[Fe(CN)(CO)4], K3[Fe(iii)(CN)6], K4[Fe(ii)(CN)6]). The different electron donors have a strong influence on the iron absorption K-edge energy position, which is frequently used to determine the metal oxidation state. Our results demonstrate that the K-edges of Fe(ii) complexes, achieved with low-spin ferrous thiolates, are consistent with a ferrous centre in the [Fe]-hydrogenase from Methanocaldococcus jannashii. The metal geometry also strongly influences the XANES and thus the electronic structure. Using in silico simulation, we were able to reproduce the main features of the XANES spectra and describe the effects of individual donor contributions on the spectra. Thereby, we reveal the essential role of an unusual carbon donor coming from an acyl group of the cofactor in the determination of the electronic structure required for the activity of the enzyme. PMID:20221540

Salomone-Stagni, Marco; Stellato, Francesco; Whaley, C. Matthew; Vogt, Sonja; Morante, Silvia; Shima, Seigo; Rauchfuss, Thomas B.; Meyer-Klaucke, Wolfram

2012-01-01

38

Studies of Hybrid Nano-Bio-System: Single-Walled Carbon Nanotubes and Hydrogenase  

SciTech Connect

We have examined changes in single-walled carbon nanotubes (SWNT) optical signals upon addition of recombinant [FeFe] hydrogenases from Clostridium acetobutylicum or Chlamydomonas reinhardtii. We found evidence that novel and stable charge-transfer complexes are formed only under conditions of hydrogenase catalytic turnover. Formation of the complex sensitizes the nanotubes to the proton-to-hydrogen redox half-reaction. Thus, the experimental potential can be altered by changing the pH or molecular hydrogen concentration. In the presence of molecular hydrogen, hydrogenase mediates electron injection into the conduction band of semiconducting SWNT, which was observed as a quenching of the photoluminescence signals. Here, we will present recent Raman studies, which revealed that SWNTs in a complex with hydrogenase may undergo either oxidation or reduction, depending on the electronic structure of the SWNT and the oxidation state of the enzyme. In addition, we will describe our efforts to prepare stable, solubilized SWNT/hydrogenase complexes in the absence of detergent. This work shows that SWNT/hydrogenase complexes have potential applications as a component of an energy conversion device.

Svedruzic-Chang, D.; Blackburn, J. L.; McDonald, T. J.; Heben, M. J.; King, P. W.

2008-01-01

39

Diiron Dithiolato Carbonyls Related to the HoxCO State of [FeFe]-Hydrogenase  

PubMed Central

Oxidation of the electron-rich (E1/2 = ?175 vs Ag/AgCl) ethanedithiolato complex Fe2(S2C2H4)-(CO)2(dppv)2 (1) under a CO atmosphere yielded [Fe2(S2C2H4)(?-CO)(CO)2(dppv)2]+ ([1(CO)]+), a model for the HoxCO state of the [FeFe]-hydrogenases. This complex exists as two isomers: a kinetically favored unsymmetrical derivative, unsym-[1(CO)]+, and a thermodynamically favored isomer, sym-[1(CO)]+, wherein both diphosphines span apical and basal sites. Crystallographic characterization of sym-[1(CO)]+ confirmed a C2-symmetric structure with a bridging CO ligand and an elongated Fe–Fe bond of 2.7012(14) Å, as predicted previously. Oxidation of sym-[1(CO)]+ and unsym-[1(CO)]+ again by 1e? oxidation afforded the respective diamagnetic diferrous derivatives where the relative stabilities of the sym and unsym isomers are reversed. DFT calculations indicate that the stabilities of sym and unsym isomers are affected differently by the oxidation state of the diiron unit: the mutually trans CO ligands in the sym isomer are more destabilizing in the mixed-valence state than in the diferrous state. EPR analysis of mixed-valence complexes revealed that, for [1]+, the unpaired spin is localized on a single iron center, whereas for unsym/sym-[1(CO)]+, the unpaired spin was delocalized over both iron centers, as indicated by the magnitude of the hyperfine coupling to the phosphine ligands trans to the Fe–Fe vector. Oxidation of 1 by 2 equiv of acetylferrocenium afforded the dication [1]2+, which, on the basis of low-temperature IR spectrum, is structurally similar to [1]+. Treatment of [1]2+ with CO gives unsym-[1(CO)]2+. PMID:18341276

Justice, Aaron K.; Nilges, Mark J.; Rauchfuss, Thomas B.; Wilson, Scott R.; De Gioia, Luca; Zampella, Giuseppe

2008-01-01

40

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. PMID:23318679

YAGI, Tatsuhiko; HIGUCHI, Yoshiki

2013-01-01

41

Hydride Binding to the Active Site of [FeFe]-Hydrogenase.  

PubMed

[FeFe]-hydrogenase from green algae (HydA1) is the most efficient hydrogen (H2) producing enzyme in nature and of prime interest for (bio)technology. Its active site is a unique six-iron center (H-cluster) composed of a cubane cluster, [4Fe4S]H, cysteine-linked to a diiron unit, [2Fe]H, which carries unusual carbon monoxide (CO) and cyanide ligands and a bridging azadithiolate group. We have probed the molecular and electronic configurations of the H-cluster in functional oxidized, reduced, and super-reduced or CO-inhibited HydA1 protein, in particular searching for intermediates with iron-hydride bonds. Site-selective X-ray absorption and emission spectroscopy were used to distinguish between low- and high-spin iron sites in the two subcomplexes of the H-cluster. The experimental methods and spectral simulations were calibrated using synthetic model complexes with ligand variations and bound hydride species. Distinct X-ray spectroscopic signatures of electronic excitation or decay transitions in [4Fe4S]H and [2Fe]H were obtained, which were quantitatively reproduced by density functional theory calculations, thereby leading to specific H-cluster model structures. We show that iron-hydride bonds are absent in the reduced state, whereas only in the super-reduced state, ligand rotation facilitates hydride binding presumably to the Fe-Fe bridging position at [2Fe]H. These results are in agreement with a catalytic cycle involving three main intermediates and at least two protonation and electron transfer steps prior to the H2 formation chemistry in [FeFe]-hydrogenases. PMID:25369169

Chernev, Petko; Lambertz, Camilla; Brünje, Annika; Leidel, Nils; Sigfridsson, Kajsa G V; Kositzki, Ramona; Hsieh, Chung-Hung; Yao, Shenglai; Schiwon, Rafael; Driess, Matthias; Limberg, Christian; Happe, Thomas; Haumann, Michael

2014-11-17

42

Sulfonated diiron complexes as water-soluble models of the [Fe-Fe]-hydrogenase enzyme active site.  

PubMed

A series of diiron complexes developed as fundamental models of the two-iron subsite in the [FeFe]-hydrogenase enzyme active site show water-solubility by virtue of a sulfonate group incorporated into the -SCH(2)NRCH(2)S- dithiolate unit that bridges two Fe(I)(CO)(2)L moieties. The sulfanilic acid group imparts even greater water solubility in the presence of ?-cyclodextrin, ?-CyD, for which NMR studies suggest aryl-sulfonate inclusion into the cyclodextrin cavity as earlier demonstrated in the X-ray crystal structure of 1Na·2 ?-CyD clathrate, where 1Na = Na(+)(?-SCH(2)N(C(6)H(4)SO(3)(-))CH(2)S-)[Fe(CO)(3)](2), (Singleton et al., J. Am. Chem. Soc.2010, 132, 8870). Electrochemical analysis of the complexes for potential as electrocatalysts for proton reduction to H(2) finds the presence of ?-CyD to diminish response, possibly reflecting inhibition of structural rearrangements required of the diiron unit for a facile catalytic cycle. Advantages of the aryl sulfonate approach include entry into a variety of water-soluble derivatives from the well-known (?-SRS)[Fe(CO)(3)](2) parent biomimetic, that are stable in O(2)-free aqueous solutions. PMID:21524099

Singleton, Michael L; Crouthers, Danielle J; Duttweiler, Robert P; Reibenspies, Joseph H; Darensbourg, Marcetta Y

2011-06-01

43

Photocatalytic hydrogen production using models of the iron-iron hydrogenase active site dispersed in micellar solution.  

PubMed

Iron-thiolate complexes of the type [Fe2 (?-bdt)(CO)6-x P(OMe3 )x ] (bdt=S2 C6 H4 =benzenedithiolate, x?2) are simplified models of iron-iron hydrogenase enzymes. Recently, we have shown that these water-insoluble organometallic complexes, when included into micelles formed by sodium dodecyl sulfate (SDS), are good catalysts for the electrochemical production of hydrogen in aqueous solutions at pH<6. We herein report that the all-CO derivative [Fe2 (?-bdt)(CO)6 ] (1), owing to its comparatively low reduction potential, is also a robust molecular catalyst for visible-light-driven production of H2 in aqueous SDS solutions at pH 10.5. Irradiation at ?=455 nm of a system consisting of complex 1, Eosin Y as a sensitizer, and triethylamine as an electron donor produced up to 0.86 mL of H2 in 4.5 h, corresponding to a turnover number of 117 mol of H2 per mol of catalyst. In the presence of a large excess of sensitizer, the production of H2 lasted for more than 30 h, stressing the relative stability of complex 1 under the photocatalytic conditions used herein. Thermodynamic considerations and UV/Vis spectroscopy experiments suggest that the catalytic cycle begins with the photo-driven reduction of complex 1. The reduced intermediate reacts with a proton source to yield iron hydride. Subsequent reduction and protonation steps produce H2 , regenerating the starting complex. As a result, the iron-thiolate complex 1 is a versatile proton reduction catalyst that can utilize either solar or electrical energy inputs, providing a starting point for the construction of noble metal-free molecular systems for renewable H2 production. PMID:24127363

Orain, Christophe; Quentel, François; Gloaguen, Frederic

2014-02-01

44

Computational Investigation of [FeFe]-Hydrogenase Models: Characterization of Singly and Doubly Protonated Intermediates and Mechanistic Insights.  

PubMed

The [FeFe]-hydrogenase enzymes catalyze hydrogen oxidation and production efficiently with binuclear Fe metal centers. Recently the bioinspired H2-producing model system Fe2(adt)(CO)2(dppv)2 (adt=azadithiolate and dppv=diphosphine) was synthesized and studied experimentally. In this system, the azadithiolate bridge facilitates the formation of a doubly protonated ammonium-hydride species through a proton relay. Herein computational methods are utilized to examine this system in the various oxidation states and protonation states along proposed mechanistic pathways for H2 production. The calculated results agree well with the experimental data for the geometries, CO vibrational stretching frequencies, and reduction potentials. The calculations illustrate that the NH···HFe dihydrogen bonding distance in the doubly protonated species is highly sensitive to the effects of ion-pairing between the ammonium and BF4(-) counterions, which are present in the crystal structure, in that the inclusion of BF4(-) counterions leads to a significantly longer dihydrogen bond. The non-hydride Fe center was found to be the site of reduction for terminal hydride species and unsymmetric bridging hydride species, whereas the reduced symmetric bridging hydride species exhibited spin delocalization between the Fe centers. According to both experimental measurements and theoretical calculations of the relative pKa values, the Fed center of the neutral species is more basic than the amine, and the bridging hydride species is more thermodynamically stable than the terminal hydride species. The calculations implicate a possible pathway for H2 evolution that involves an intermediate with H2 weakly bonded to one Fe, a short H2 distance similar to the molecular bond length, the spin density delocalized over the two Fe centers, and a nearly symmetrically bridged CO ligand. Overall, this study illustrates the mechanistic roles of the ammonium-hydride interaction, flexibility of the bridging CO ligand, and intramolecular electron transfer between the Fe centers in the catalytic cycle. Such insights will assist in the design of more effective bioinspired catalysts for H2 production. PMID:25207842

Huynh, Mioy T; Wang, Wenguang; Rauchfuss, Thomas B; Hammes-Schiffer, Sharon

2014-10-01

45

Absolute potential of the Fermi level of single-walled carbon nanotubes via hydrogenase complex formation.  

NASA Astrophysics Data System (ADS)

The absolute potential of the Fermi level of nanotubes as a function of nanotube type is not presently understood, and is important for many nanotube applications and sorting strategies. Here, we study complexes of recombinant [FeFe] hydrogenases and single-walled carbon nanotubes. We find evidence that novel charge-transfer complexes are formed and are stable, which enables further study and application of this system. The hydrogenase functions as a hydrogen electrode sensitizing the nanotubes to the redox half-reaction for hydrogen. Thus the potential can be altered by changing the molecular hydrogen concentration, and this tunability is utilized to bleach various semiconducting nanotube transitions. By observing which are bleached and which remain emissive, we determine the alignment of the potential of the Fermi level of semiconducting single-walled carbon nanotubes. The experimentally determined Fermi level alignment is confirmed theoretically by the first-principles DFT-PBE method.

McDonald, Timothy; Svedruzic, Drazenka; Kim, Yong-Hyun; Blackburn, Jeffrey; Zhang, Shengbai; King, Paul; Heben, Michael

2007-03-01

46

Protein induced singlet-triplet quasidegeneracy in the active site of [NiFe]-hydrogenase  

NASA Astrophysics Data System (ADS)

Molecular hydrogen oxidation and reduction on [NiFe]-hydrogenase is an inspiring example of using abundant first row transition metals to catalyze biologically and industrially important chemical reactions. We demonstrate that by rotating terminal thiolate ligands in the active site of [NiFe]-hydrogenase, either the singlet or triplet electronic state can be made a ground state. The two states become degenerate when the ligand orientations are similar to those observed in [NiFe]-hydrogenase, where this orientation is enforced by the protein backbone. The unusual distorted coordination geometry of Ni can explain the inability of the structural models of [NiFe]-hydrogenase to bind molecular hydrogen.

Yson, Renante L.; Gilgor, Jessica L.; Guberman, Benjamin A.; Varganov, Sergey A.

2013-07-01

47

Favorable Protonation of the (?-edt)[Fe2(PMe3)4(CO)2(H-terminal)]+ Hydrogenase Model Complex Over Its Bridging ?-H Counterpart: A Spectroscopic and DFT Study  

PubMed Central

The mechanism of hydrogen production in [FeFe] hydrogenase remains elusive. However, a species featuring a terminal hydride bound to the distal Fe is thought to be the key intermediate leading to hydrogen production. In this study, density functional theory (DFT) calculations on the terminal (H-term) and bridging (?-H) hydride isomers of (?-edt)-[Fe2(PMe3)4(CO)2H]+ are presented in order to understand the factors affecting their propensity for protonation. Relative to H-term, ?-H is 12.7 kcal/mol more stable, which contributes to its decreased reactivity towards an acid. Potential energy surface (PES) calculations for the reaction of the H-term isomer with 4-nitropyridinium, a proton source, further reveal a lower activation energy barrier (14.5 kcal/mol) for H-term than for ?-H (29 kcal/mol). Besides these energetic considerations, the H-term isomer displays a key molecular orbital (MO <139>) that has a relatively strong hydride (1s) contribution (23%), which is not present in the ?-H isomer. This indicates a potential orbital control of the reaction of the hydride complexes with acid. The lower activation energy barrier and this key MO together control the overall catalytic activity of (?-edt)[Fe2(PMe3)4(CO)2(H-term)]+. Lastly, Raman and IR spectroscopy were performed in order to probe the ?(Fe-H) stretching mode of the two isomers and their deuterated counterparts. A ?(Fe-H) stretching mode was observed for the ?-H complex at 1220 cm?1. However, the corresponding mode is not observed for the less stable H-term isomer. PMID:23162378

Galinato, Mary Grace I.; Whaley, C. Matthew; Roberts, Dean; Wang, Peng; Lehnert, Nicolai

2012-01-01

48

Fe?FeS eutectic temperatures to 620 kbar  

Microsoft Academic Search

Eutectic melting temperatures for the system Fe?FeS have been measured for the first time in the diamond anvil cell, using improved techniques to identify the solidus temperatures. Results at low pressure are in excellent agreement with previous measurements. The eutectic temperature increases linearly with pressure and remains lower than the melting temperatures of either Fe or FeS throughout the pressure

R. Boehler

1996-01-01

49

Characterization of the Fe Site in Iron-Sulfur-Cluster-Free Hydrogenase (Hmd) and of a Model Compound via Nuclear Resonance Vibrational Spectroscopy (NRVS)  

PubMed Central

We have used 57Fe nuclear resonance vibrational spectroscopy (NRVS) to study the iron site in the iron-sulfur-cluster-free hydrogenase Hmd from the methanogenic archaeon Methanothermobacter marburgensis. The spectra have been interpreted by comparison with a cis-(CO)2-ligated Fe model compound, Fe(S2C2H4)(CO)2(PMe3)2, as well as by normal mode simulations of plausible active site structures. For this model complex, normal mode analyses both from an optimized Urey-Bradley force field and from complementary density functional theory (DFT) calculations produced consistent results. Previous IR spectroscopic studies found strong CO stretching modes at 1944 and 2011 cm?1, interpreted as evidence for cis-Fe(CO)2 ligation. The NRVS data provide further insight into the dynamics of the Fe site, revealing Fe-CO stretch and Fe-CO bend modes at 494, 562, 590, and 648 cm?1, consistent with the proposed cis-Fe(CO)2 ligation. The NRVS also reveals a band assigned to Fe-S stretching motion at ~311 cm?1, and another reproducible feature at ~380 cm?1. The 57Fe partial vibrational densities of states (PVDOS) for Hmd can be reasonably well simulated by a normal mode analysis based on a Urey-Bradley force field for a 5-coordinate cis-(CO)2-ligated Fe site with additional cysteine, water, and pyridone cofactor ligands. A final interpretation of the Hmd NRVS data, including DFT analysis, awaits a 3-dimensional structure for the active site. PMID:18407624

Guo, Yisong; Wang, Hongxin; Xiao, Yuming; vogt, Sonja; Shima, Seigo; Volkers, Phillip I.; Pelmentschikov, Vladimir; Alp, Ercan E.; Sturhahn, Wolfgang; Yada, Yoshitaka

2009-01-01

50

H 2 consumption by Escherichia coli coupled via hydrogenase 1 or hydrogenase 2 to different terminal electron acceptors  

Microsoft Academic Search

Hydrogen uptake in the presence of various terminal electron acceptors was examined in Escherichia coli mutants synthesizing either hydrogenase 1 or hydrogenase 2. Both hydrogenases mediated nitrate-dependent H2 consumption but neither of them was coupled with nitrite. Unlike hydrogenase 2, hydrogenase 1 demonstrated poor activity with electron acceptors of low midpoint redox potential. Oxygen-linked H2 uptake via hydrogenase 1 was

Tatyana V Laurinavichene; Anatoly A Tsygankov

2001-01-01

51

Cyanide inactivation of hydrogenase from Azotobacter vinelandii  

SciTech Connect

The effects of cyanide on membrane-associated and purified hydrogenase from Azotobacter vinelandii were characterized. Inactivation of hydrogenase by cyanide was dependent on the activity (oxidation) state of the enzyme. Active (reduced) hydrogenase showed no inactivation when treated with cyanide over several hours. Treatment of reversibly inactive (oxidized) states of both membrane-associated and purified hydrogenase, however, resulted in a time-dependent, irreversible loss of hydrogenase activity. The rate of cyanide inactivation was dependent on the cyanide concentration and was an apparent first-order process for purified enzyme (bimolecular rate constant, 23.1 M{sup {minus}1} min{sup {minus}1} for CN{sup {minus}}). The rate of inactivation decreased with decreasing pH. ({sup 14}C)cyanide remained associated with cyanide-inactivated hydrogenase after gel filtration chromatography, with a stoichiometry of 1.7 mol of cyanide bound per mol of inactive enzyme. The presence of saturating concentrations of CO had no effect on the rate or extent of cyanide inactivation of hydrogenases. The results indicate that cyanide can cause a time-dependent, irreversible inactivation of hydrogenase in the oxidized, activatable state but has no effect when hydrogenase is in the reduced, active state.

Seefeldt, L.C.; Arp, D.J. (Univ. of California, Riverside (USA))

1989-06-01

52

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. PMID:19284580

2009-01-01

53

Combined spectroscopic/computational study of binuclear Fe(I)-Fe(I) complexes: implications for the fully-reduced active-site cluster of Fe-only hydrogenases.  

PubMed

The Fe(I)-Fe(I) dimer complex [Fe2(pdt)(CO)4(CN)2][Et4N]2 (2), where pdt = 1,3-propane dithiolate, serves as a model of the fully reduced [2Fe]H component of the H cluster, which is the active site for catalysis in Fe-only hydrogenases (FeHases). Electronic absorption, magnetic circular dichroism (MCD), and resonance Raman (rR) spectroscopies have been employed to characterize both the ground and excited states of 2 as well as those of the related complex Fe2(pdt)(CO)6 (1). These results have been combined with density functional theory (DFT) computations to produce experimentally validated bonding descriptions of 1 and 2. It is shown that Fe(I)-S covalency is significantly reduced upon dicyano substitution (i.e., conversion of 1 --> 2), while the corresponding Fe(I)-CO/CN pi-backbonding interactions are strengthened, results that are corroborated by normal-coordinate analyses of the vibrational data. Detailed assignments of the features observed in the electronic absorption spectra of 1 and 2 have been developed on the basis of time-dependent DFT (TD-DFT) calculations, which provide remarkably accurate simulations of the experimental data. For both complexes, all bands below 32,000 cm(-1) arise from transitions involving electronic excitation within the binuclear Fe-Fe core, with the most intense feature assigned to the Fe(sigma(b)) --> Fe(sigma*) transition. Analysis of the corresponding rR excitation profiles within the framework of time-dependent Heller theory reveals that in each case the Fe-Fe bond is elongated by approximately 0.3 A in the Fe(sigma(b)) --> Fe(sigma*) excited state. Finally, building upon the insights gained from the spectroscopic/computational studies of 1 and 2, our computational methodology has been extended to the reduced enzyme active site, providing insights into the electronic structure of the [2Fe]H subcluster in the H(red) state and its relationship to catalysis. PMID:15762706

Fiedler, Adam T; Brunold, Thomas C

2005-03-21

54

Redox interaction of cytochrome c3 with [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F.  

PubMed

Cytochrome c3 isolated from a sulfate-reducing bacterium, Desulfovibrio vulgaris Miyazaki F, is a tetraheme protein. Its physiological partner, [NiFe] hydrogenase, catalyzes the reversible oxidoreduction of molecular hydrogen. To elucidate the mechanism of electron transfer between cytochrome c3 and [NiFe] hydrogenase, the transient complex formation by these proteins was investigated by means of NMR. All NH signals of uniformly 15N-labeled ferric cytochrome c3 except N-terminus, Pro, and Gly73 were assigned. 1H-15N HSQC spectra were recorded for 15N-labeled ferric and ferrous cytochrome c3, in the absence and presence of hydrogenase. Chemical shift perturbations were observed in the region around heme 4 in both oxidation states. Additionally, the region between hemes 1 and 3 in ferrous cytochrome c3 was affected in the presence of hydrogenase, suggesting that the mode of interaction is different in each redox state. Heme 3 is probably the electron gate for ferrous cytochrome c3. To investigate the transient complex of cytochrome c3 and hydrogenase in detail, modeling of the complex was performed for the oxidized proteins using a docking program, ZDOCK 2.3, and NMR data. Furthermore, the roles of lysine residues of cytochrome c3 in the interaction with hydrogenase were investigated by site-directed mutagenesis. When the lysine residues around heme 4 were replaced by an uncharged residue, methionine, one by one, the Km of the electron-transfer kinetics increased. The results showed that the positive charges of Lys60, Lys72, Lys95, and Lys101 around heme 4 are important for formation of the transient complex with [NiFe] hydrogenase in the initial stage of the cytochrome c3 reduction. This finding is consistent with the most possible structure of the transient complex obtained by modeling. PMID:16460012

Yahata, Naoki; Saitoh, Takashi; Takayama, Yuki; Ozawa, Kiyoshi; Ogata, Hideaki; Higuchi, Yoshiki; Akutsu, Hideo

2006-02-14

55

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

56

Site saturation mutagenesis demonstrates a central role for cysteine 298 as proton donor to the catalytic site in CaHydA [FeFe]-hydrogenase.  

PubMed

[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 k(cat) 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 O(2) 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. PMID:23133586

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

2012-01-01

57

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

58

Influence of Escherichia coli hydrogenases on hydrogen fermentation from glycerol  

E-print Network

production, organic acids production, and ethanol production. Inacti- vation of hydrogenase 2 and hydrogenase 3 reduced cell growth, hydrogen and succinate production as well as glycerol utilization while synthesis activity through the formate hydrogen lyase complex. Hydrogenase 2 seems mainly required

Wood, Thomas K.

59

Purification of hydrogenase from Chlamydomonas reinhardtii  

SciTech Connect

A method is described which results in a 2750-fold purification of hydrogenase from Chlamydomonas reinhardtii, yielding a preparation which is approximately 40% pure. With a saturating amount of ferredoxin as the electron mediator, the specific activity of pure enzyme was calculated to be 1800 micromoles H/sub 2/ produced per milligram protein per minute. The molecular weight was determined to be 4.5 x 10/sup 4/ by gel filtration and 4.75 x 10/sub 4/ by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The enzyme has an abundance of acidic side groups, contains iron, and has an activation energy of 55.1 kilojoules per mole for H/sub 2/ production; these properties are similar to those of bacterial hydrogenases. The enzyme is less thermally stable than those of bacterial hydrogenases, however, losing 50% of its activity in 1 hour at 55/sup 0/C. The K/sub m/ of purified hydrogenase for ferredoxin is 10 micromolar, and the binding of these proteins to each other is enhanced under slightly acidic conditions. Purified hydrogenase also accepts electrons from a variety of artificial electron mediators, including sodium metatungstate, sodium silicotungstate, and several viologen dyes. A lag period is frequently observed before maximal activity is expressed with these artificial electron mediators, although the addition of sodium thiosulfate at least partially overcomes this lag. 22 references, 5 figures, 2 tables.

Roessler, P.G.; Lien, S.

1984-07-01

60

De novo modeling of the F420-reducing [NiFe]-hydrogenase from a methanogenic archaeon by cryo-electron microscopy  

PubMed Central

Methanogenic archaea use a [NiFe]-hydrogenase, Frh, for oxidation/reduction of F420, an important hydride carrier in the methanogenesis pathway from H2 and CO2. Frh accounts for about 1% of the cytoplasmic protein and forms a huge complex consisting of FrhABG heterotrimers with each a [NiFe] center, four Fe-S clusters and an FAD. Here, we report the structure determined by near-atomic resolution cryo-EM of Frh with and without bound substrate F420. The polypeptide chains of FrhB, for which there was no homolog, was traced de novo from the EM map. The 1.2-MDa complex contains 12 copies of the heterotrimer, which unexpectedly form a spherical protein shell with a hollow core. The cryo-EM map reveals strong electron density of the chains of metal clusters running parallel to the protein shell, and the F420-binding site is located at the end of the chain near the outside of the spherical structure. DOI: http://dx.doi.org/10.7554/eLife.00218.001 PMID:23483797

Mills, Deryck J; Vitt, Stella; Strauss, Mike; Shima, Seigo; Vonck, Janet

2013-01-01

61

Atomic model of the F420-reducing [NiFe] hydrogenase by electron cryo-microscopy using a direct electron detector.  

PubMed

The introduction of direct electron detectors with higher detective quantum efficiency and fast read-out marks the beginning of a new era in electron cryo-microscopy. Using the FEI Falcon II direct electron detector in video mode, we have reconstructed a map at 3.36 Å resolution of the 1.2 MDa F420-reducing hydrogenase (Frh) from methanogenic archaea from only 320,000 asymmetric units. Videos frames were aligned by a combination of image and particle alignment procedures to overcome the effects of beam-induced motion. The reconstructed density map shows all secondary structure as well as clear side chain densities for most residues. The full coordination of all cofactors in the electron transfer chain (a [NiFe] center, four [4Fe4S] clusters and an FAD) is clearly visible along with a well-defined substrate access channel. From the rigidity of the complex we conclude that catalysis is diffusion-limited and does not depend on protein flexibility or conformational changes. DOI: http://dx.doi.org/10.7554/eLife.01963.001. PMID:24569482

Allegretti, Matteo; Mills, Deryck J; McMullan, Greg; Kühlbrandt, Werner; Vonck, Janet

2014-01-01

62

Evolutionary Significance of an Algal Gene Encoding an [FeFe]-Hydrogenase with F-Domain Homology and Hydrogenase Activity in Chlorella Variabilis NC64A  

SciTech Connect

[FeFe]-hydrogenases (HYDA) link the production of molecular H{sub 2} to anaerobic metabolism in many green algae. Similar to Chlamydomonas reinhardtii, Chlorella variabilis NC64A (Trebouxiophyceae, Chlorophyta) exhibits [FeFe]-hydrogenase (HYDA) activity during anoxia. In contrast to C. reinhardtii and other chlorophycean algae, which contain hydrogenases with only the HYDA active site (H-cluster), C. variabilis NC64A is the only known green alga containing HYDA genes encoding accessory FeS cluster-binding domains (F-cluster). cDNA sequencing confirmed the presence of F-cluster HYDA1 mRNA transcripts, and identified deviations from the in silico splicing models. We show that HYDA activity in C. variabilis NC64A is coupled to anoxic photosynthetic electron transport (PSII linked, as well as PSII-independent) and dark fermentation. We also show that the in vivo H{sub 2}-photoproduction activity observed is as O2 sensitive as in C. reinhardtii. The two C. variabilis NC64A HYDA sequences are similar to homologs found in more deeply branching bacteria (Thermotogales), diatoms, and heterotrophic flagellates, suggesting that an F-cluster HYDA is the ancestral enzyme in algae. Phylogenetic analysis indicates that the algal HYDA H-cluster domains are monophyletic, suggesting that they share a common origin, and evolved from a single ancestral F-cluster HYDA. Furthermore, phylogenetic reconstruction indicates that the multiple algal HYDA paralogs are the result of gene duplication events that occurred independently within each algal lineage. Collectively, comparative genomic, physiological, and phylogenetic analyses of the C. variabilis NC64A hydrogenase has provided new insights into the molecular evolution and diversity of algal [FeFe]-hydrogenases.

Meuser, J. E.; Boyd, E. S.; Ananyev, G.; Karns, D.; Radakovits, R.; Murthy, U. M. N.; Ghirardi, M. L.; Dismukes, G. C.; Peters, J. W.; Posewitz, M. C.

2011-10-01

63

The regeneration of coenzymes using immobilized hydrogenase  

Microsoft Academic Search

A new enzymatic approach to the regeneration of coenzymes has been developed. It uses the reduction of natural or artificial cofactors with H2, catalyzed by hydrogenase activity in immobilized whole cells ofA. eutrophus. The method has been employed for regeneration of such coenzymes as NAD+, FMN, phenazine methosulfate, Janus green, methylene blue, and 2,6-dichlorophenol-indophenol.

Alexander M. Klibanov; Austin V. Puglisi

1980-01-01

64

Action of inhibitors on hydrogenase in Azotobacter  

Microsoft Academic Search

The inhibitors usually associated with the activity of the cytochrome oxidase system - cyanide and carbon monoxide - are also effective in reducing the oxidation of Hâ by intact cells of Azotobacter vinclandii. The hydrogenase system is more sensitive to CO than is the respiratory system. Oxidation of a carbon source and of hydrogen by Azotobacter cells is inhibited in

J. B. Wilson; P. W. Wilson

1943-01-01

65

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. PMID:22511957

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

2012-01-01

66

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. PMID:24934472

2014-01-01

67

Regulation of hydrogenase activity in vegetative cells of Anabaena variabilis.  

PubMed Central

Heterocyst-free (NH4+-grown) cultures of the cyanobacterium Anabaena variabilis produce a hydrogenase which is reversibly inhibited by light and O2. White or red light at an intensity of 5,000 lx inhibited greater than 95% of the activity. Oxygen at concentrations as low as 0.5% inhibited more than 85% of the hydrogenase in the vegetative cells of CO2-NH4+-grown cultures. The vegatative cell hydrogenase is also sensitive to strong oxidants like ferricyanide. In the presence of strong reductants like S2O4(2-), hydrogenase activity was not inhibited by light. However, hydrogenase activity in the heterocysts was insensitive to both light (greater than 5,000 lx) and O2 (10%). Heterocysts and light-insensitive hydrogenase activity appear simultaneously during differentiation of the vegetative cells into heterocysts (an NH4+-grown culture transferred to NH4+-free, N2-containing medium). This light-insensitive hydrogenase activity was detected several hours before the induction of nitrogenase activity. These results suggest a mode of regulation of hydrogenase in the vegetative cells of A. variabilis that is similar to "redox control" of hydrogenase and other "anaerobic" proteins in enteric bacteria like Escherichia coli. PMID:6408057

Spiller, H; Bookjans, G; Shanmugam, K T

1983-01-01

68

Hydrogenases and Hydrogen Metabolism of Cyanobacteria  

PubMed Central

Cyanobacteria may possess several enzymes that are directly involved in dihydrogen metabolism: nitrogenase(s) catalyzing the production of hydrogen concomitantly with the reduction of dinitrogen to ammonia, an uptake hydrogenase (encoded by hupSL) catalyzing the consumption of hydrogen produced by the nitrogenase, and a bidirectional hydrogenase (encoded by hoxFUYH) which has the capacity to both take up and produce hydrogen. This review summarizes our knowledge about cyanobacterial hydrogenases, focusing on recent progress since the first molecular information was published in 1995. It presents the molecular knowledge about cyanobacterial hupSL and hoxFUYH, their corresponding gene products, and their accessory genes before finishing with an applied aspect—the use of cyanobacteria in a biological, renewable production of the future energy carrier molecular hydrogen. In addition to scientific publications, information from three cyanobacterial genomes, the unicellular Synechocystis strain PCC 6803 and the filamentous heterocystous Anabaena strain PCC 7120 and Nostoc punctiforme (PCC 73102/ATCC 29133) is included. PMID:11875125

Tamagnini, Paula; Axelsson, Rikard; Lindberg, Pia; Oxelfelt, Fredrik; Wunschiers, Robbe; Lindblad, Peter

2002-01-01

69

Relation between anaerobic inactivation and oxygen tolerance in a large series of NiFe hydrogenase mutants.  

PubMed

Nickel-containing hydrogenases, the biological catalysts of oxidation and production, reversibly inactivate under anaerobic, oxidizing conditions. We aim at understanding the mechanism of (in)activation and what determines its kinetics, because there is a correlation between fast reductive reactivation and oxygen tolerance, a property of some hydrogenases that is very desirable from the point of view of biotechnology. Direct electrochemistry is potentially very useful for learning about the redox-dependent conversions between active and inactive forms of hydrogenase, but the voltammetric signals are complex and often misread. Here we describe simple analytical models that we used to characterize and compare 16 mutants, obtained by substituting the position-74 valine of the -sensitive NiFe hydrogenase from Desulfovibrio fructosovorans. We observed that this substitution can accelerate reactivation up to 1,000-fold, depending on the polarity of the position 74 amino acid side chain. In terms of kinetics of anaerobic (in)activation and oxygen tolerance, the valine-to-histidine mutation has the most spectacular effect: The V74H mutant compares favorably with the -tolerant hydrogenase from Aquifex aeolicus, which we use here as a benchmark. PMID:23169623

Abou Hamdan, Abbas; Liebgott, Pierre-Pol; Fourmond, Vincent; Gutiérrez-Sanz, Oscar; De Lacey, Antonio L; Infossi, Pascale; Rousset, Marc; Dementin, Sébastien; Léger, Christophe

2012-12-01

70

Connection between the membrane electron transport system and Hyn hydrogenase in the purple sulfur bacterium, Thiocapsa roseopersicina BBS.  

PubMed

Thiocapsa. roseopersicina BBS has four active [NiFe] hydrogenases, providing an excellent opportunity to examine their metabolic linkages to the cellular redox processes. Hyn is a periplasmic membrane-associated hydrogenase harboring two additional electron transfer subunits: Isp1 is a transmembrane protein, while Isp2 is located on the cytoplasmic side of the membrane. In this work, the connection of HynSL to various electron transport pathways is studied. During photoautotrophic growth, electrons, generated from the oxidation of thiosulfate and sulfur, are donated to the photosynthetic electron transport chain via cytochromes. Electrons formed from thiosulfate and sulfur oxidation might also be also used for Hyn-dependent hydrogen evolution which was shown to be light and proton motive force driven. Hyn-linked hydrogen uptake can be promoted by both sulfur and nitrate. The electron flow from/to HynSL requires the presence of Isp2 in both directions. Hydrogenase-linked sulfur reduction could be inhibited by a QB site competitive inhibitor, terbutryne, suggesting a redox coupling between the Hyn hydrogenase and the photosynthetic electron transport chain. Based on these findings, redox linkages of Hyn hydrogenase are modeled. PMID:25111750

Tengölics, Roland; Mészáros, Lívia; Gy?ri, E; Doffkay, Zsolt; Kovács, Kornél L; Rákhely, Gábor

2014-10-01

71

Structure and mechanism of iron-only hydrogenases.  

PubMed

The recent elucidation of the structures of iron-only hydrogenases from the microorganisms Clostridium pasteurianum and Desulfovibrio desulfuricans has revealed that the presumed site of reversible hydrogen oxidation exists as a unique, protein-associated organometallic prosthetic group. Details of the hydrogenase structures provide insight into the chemical mechanism of this highly evolved catalyst. PMID:10607666

Peters, J W

1999-12-01

72

Cell-free synthesis of the H-cluster: a model for the in vitro assembly of metalloprotein metal centers.  

PubMed

Many organometallic cofactors are highly complex and require multiple accessory proteins for both their assembly and transfer to a target protein. A cell-free system in which the biosynthetic pathway for a prosthetic group has been fully or even partially reconstructed enables investigations of the reaction sequence as well as the cofactor itself. As a model for the in vitro assembly of protein-bound metal centers, we describe a procedure for the cell-free synthesis of the H-cluster in the context of producing purified and active [FeFe] hydrogenase samples for spectroscopic studies. In general terms, this in vitro system is a combination of non-purified accessory proteins, exogenous substrates, and purified hydrogenase apoprotein. We also describe methods for making the required components used in the cell-free system. Specifically, these procedures include anaerobic expression of heterologous metalloproteins in Escherichia coli, anaerobic cell lysate production, and anaerobic metalloprotein purification using Strep-Tactin(®) chromatography. PMID:24639253

Kuchenreuther, Jon M; Shiigi, Stacey A; Swartz, James R

2014-01-01

73

Enhanced decomposition of dimethyl phthalate via molecular oxygen activated by Fe@Fe2O3/AC under microwave irradiation.  

PubMed

In this study, we demonstrate that the decomposition of dimethyl phthalate under microwave irradiation could be greatly enhanced over Fe@Fe(2)O(3) nanowires supported on activated carbon (Fe@Fe(2)O(3)/AC). The great enhanced decomposition of dimethyl phthalate could be attributed to a unique microwave induced molecular oxygen activation process. Upon microwave irradiation, electrons could be transferred from activated carbon to zero-valent iron, and then react with molecular oxygen to form O(2)(-) and OH radicals for the decomposition of dimethyl phthalate. The deactivation and the regeneration of Fe@Fe(2)O(3)/AC catalyst were systematically studied. We also found that microwave heating could accelerate the electron transferring from AC to Fe@Fe(2)O(3) to generate more reactive oxygen species for the decomposition of DMP than conventional oil bath heating. This novel molecular oxygen activation approach may find applications for wastewater treatment and drinking water purification. PMID:22883705

Chen, Yiling; Ai, Zhihui; Zhang, Lizhi

2012-10-15

74

Activation and de novo synthesis of hydrogenase in Chlamydomonas  

SciTech Connect

Two distinct processes are involved in the formation of active hydrogenase during anaerobic adaptation of Chlamydomonas reinhardtii cells. In the first 30 minutes of anaerobiosis, nearly all of the hydrogenase activity can be attributed to activation of constituitive polypeptide precursor, based on the insensitivity of the process to treatment with cycloheximide (15 micrograms per milliliter). This concentration of cycloheximide inhibits protein synthesis by greater than 98%. After the initial activation period, de novo protein synthesis plays a critical role in the adaptation process since cycloheximide inhibits the expression of hydrogenase in maximally adapted cells by 70%. Chloramphenicol (500 micrograms per milliliter) has a much lesser effect on the adaptation process. Incubation of cell-free extracts under anaerobic conditions in the presence of dithionite, dithiothreitol, NADH, NADP, ferredoxin, ATP, Mg/sup 2 +/, Ca/sup 2 +/, and iron does not lead to active hydrogenase formation. Furthermore, in vivo reactivation of oxygen-inactivated hydrogenase does not appear to take place. The adaptation process is very sensitive to the availability of iron. Iron-deficient cultures lose the ability to form active hydrogenase before growth, photosynthesis, and respiration are significantly affected. Preincubation of iron-deficient cells with iron 2 hours prior to the adaptation period fully restores the capacity of the cells to synthesize functional hydrogenase.

Roessler, P.G.; Lien, S.

1984-12-01

75

Melting relationships in the Fe-Fe3S system up to the outer core conditions  

NASA Astrophysics Data System (ADS)

In situ X-ray diffraction experiments in the Fe-Fe3S system were performed up to 175 GPa and 3500 K using a laser-heated diamond anvil cell to investigate melting relationships in the system. Partial melting in the Fe-Fe3S system was observed based on the disappearance of X-ray diffraction peaks of solid Fe3S and texture observation of the recovered samples. The melting relationship of the Fe-Fe3S system as a function of pressure is evaluated based on Kraut-Kennedy law. Our results of melting relationships suggest that the temperature at the inner core boundary is between 4700(160) and 4930(330) K if sulfur is the only light element in the Earth's core. Assuming the adiabatic temperature gradient in the outer core, the temperature at the core-mantle boundary is estimated to be in the range of 3600-3770 K. The present temperature profile of the core is consistent with the core-mantle boundary temperature that can explain the core heat flux to maintain the core dynamo and the seismic structure at the base of the lower mantle.

Kamada, Seiji; Ohtani, Eiji; Terasaki, Hidenori; Sakai, Takeshi; Miyahara, Masaaki; Ohishi, Yasuo; Hirao, Naohisa

2012-12-01

76

Hydrogenase in actinorhizal root nodules and root nodule homogenates.  

PubMed

Hydrogenases were measured in intact actinorhizal root nodules and from disrupted nodules of Alnus glutinosa, Alnus rhombifolia, Alnus rubra, and Myrica pensylvanica. Whole nodules took up H2 in an O2-dependent reaction. Endophyte preparations oxidized H2 through the oxyhydrogen reaction, but rates were enhanced when hydrogen uptake was coupled to artificial electron acceptors. Oxygen inhibited artifical acceptor-dependent H2 uptake. The hydrogenase system from M. pensylvanica had a different pattern of coupling to various electron acceptors than the hydrogenase systems from the alders; only the bayberry system evolved H2 from reduced viologen dyes. PMID:6989799

Benson, D R; Arp, D J; Burris, R H

1980-04-01

77

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

78

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

79

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. PMID:23803769

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

2013-01-01

80

Synthesis of the H-Cluster Framework of Iron-Only Hydrogenase  

SciTech Connect

The reversible reduction of protons to dihydrogen is deceptively the simplest of reactions but one which requires multi-step catalysis to proceed at practical rates. How the metal-sulfur of the hydrogenases catalyse this interconversion has been the subject has been the subject of intensive structural, spectroscopic and mechanistic studies of the enzymes, of synthetic assemblies and of in silico models. Beyond the intrinsic desire to understand how metallo-sulfur clusters in biology catalyses a range of difficult chemistry, including nitrogen fixation, research on hydrogenase chemistry is particularly driven by the view that understanding active-site structure and function will inform the design of new materials for hydrogen production or uptake, pertinent to energy transduction technology and a hydrogen economy. Herein we report the assembly of the first materials with di-iron sub-sites linked by a thiolate bridge to a (4Fe4S) ? cluster, as found at the active site of the iron-only hydrogenase, the H-cluster.

Tard, Cedric; Liu, Xiaohong; Ibrahim, S K.; Mauizio, Bruschi; De Gioia, Luca; Davies, Sian; Yang, Xin; Wang, Lai S.; Sawers, G; Pickett, Chris J.

2005-02-10

81

Synthesis, structural characterization, and electrochemical properties of dinuclear Ni/Mn model complexes for the active site of [NiFe]-hydrogenases.  

PubMed

Four new dinuclear Ni/Mn model complexes RN(PPh2)2Ni(?-SEt)2(?-Cl)Mn(CO)3 (7, R = p-MeC6H4CH2; 8, R = EtO2CCH2) and RN(PPh2)2Ni(?-SEt)2(?-Br)Mn(CO)3 (9, R = p-MeC6H4CH2; 10, R = EtO2CCH2) have been prepared via the four separated step-reactions involving six new precursors RN(PPh2)2 (1, R = p-MeC6H4CH2; 2, R = EtO2CCH2), RN(PPh2)2NiCl2 (3, R = p-MeC6H4CH2; 4, R = EtO2CCH2), and RN(PPh2)2Ni(SEt)2 (5, R = p-MeC6H4CH2; 6, R = EtO2CCH2). The Et3N-assisted aminolysis of Ph2PCl with p-MeC6H4CH2NH2 or EtO2CCH2NH2·HCl in CH2Cl2 gave the azadiphosphine ligands 1 and 2 in 38% and 53% yields, whereas the coordination reaction of 1 or 2 with NiCl2·6H2O in CH2Cl2/MeOH afforded the mononuclear Ni dichloride complexes 3 and 4 in 59% and 78% yields, respectively. While thiolysis of 3 or 4 with EtSH under the assistance of Et3N in CH2Cl2 produced the mononuclear Ni dithiolate complexes 5 and 6 in 64% and 68% yields, further treatment of 5 and 6 with Mn(CO)5Cl or Mn(CO)5Br resulted in formation of the dinuclear Ni/Mn model complexes 7-10 in 31-73% yields. All the new compounds 1-10 have been structurally characterized, while model complexes 7 and 9 have been found to be catalysts for HOAc proton reduction to hydrogen under CV conditions. PMID:24063734

Song, Li-Cheng; Li, Jia-Peng; Xie, Zhao-Jun; Song, Hai-Bin

2013-10-01

82

Structural and gene expression analyses of uptake hydrogenases and other proteins involved in nitrogenase protection in Frankia.  

PubMed

The actinorhizal bacterium Frankia expresses nitrogenase and can therefore convert molecular nitrogen into ammonia and the by-product hydrogen. However, nitrogenase is inhibited by oxygen. Consequently, Frankia and its actinorhizal hosts have developed various mechanisms for excluding oxygen from their nitrogen-containing compartments. These include the expression of oxygen-scavenging uptake hydrogenases, the formation of hopanoid-rich vesicles, enclosed by multi-layered hopanoid structures, the lignification of hyphal cell walls, and the production of haemoglobins in the symbiotic nodule. In this work, we analysed the expression and structure of the so-called uptake hydrogenase (Hup), which catalyses the in vivo dissociation of hydrogen to recycle the energy locked up in this 'waste' product. Two uptake hydrogenase syntons have been identified in Frankia: synton 1 is expressed under freeliving conditions while synton 2 is expressed during symbiosis. We used qPCR to determine synton 1 hup gene expression in two Frankia strains under aerobic and anaerobic conditions. We also predicted the 3D structures of the Hup protein subunits based on multiple sequence alignments and remote homology modelling. Finally, we performed BLAST searches of genome and protein databases to identify genes that may contribute to the protection of nitrogenase against oxygen in the two Frankia strains. Our results show that in Frankia strain ACN14a, the expression patterns of the large (HupL1) and small (HupS1) uptake hydrogenase subunits depend on the abundance of oxygen in the external environment. Structural models of the membrane-bound hydrogenase subunits of ACN14a showed that both subunits resemble the structures of known [NiFe] hydrogenases (Volbeda et al. 1995), but contain fewer cysteine residues than the uptake hydrogenase of the Frankia DC12 and Eu1c strains. Moreover, we show that all of the investigated Frankia strains have two squalene hopane cyclase genes (shc1 and shc2). The only exceptions were CcI3 and the symbiont of Datisca glomerata, which possess shc1 but not shc2. Four truncated haemoglobin genes were identified in Frankia ACN14a and Eu1f, three in CcI3, two in EANpec1 and one in the Datisca glomerata symbiont (Dg). PMID:24287649

Richau, K H; Kudahettige, R L; Pujic, P; Kudahettige, N P; Sellstedt, A

2013-11-01

83

Magnetic properties of fluffy Fe@?-Fe2O3 core-shell nanowires  

PubMed Central

Novel fluffy Fe@?-Fe2O3 core-shell nanowires have been synthesized using the chemical reaction of ferrous sulfate and sodium borohydride, as well as the post-annealing process in air. The coercivity of the as-synthesized nanowires is above 684 Oe in the temperature range of 5 to 300 K, which is significantly higher than that of the bulk Fe (approximately 0.9 Oe). Through the annealing process in air, the coercivity and the exchange field are evidently improved. Both the coercivity and the exchange field increase with increasing annealing time (TA) and reach their maximum values of 1,042 and 78 Oe, respectively, at TA?=?4 h. The magnetic measurements show that the effective anisotropy is increased with increasing the thickness of the?-Fe2O3 by annealing. The large values of coercivity and exchange field, as well as the high surface area to volume ratio, may make the fluffy Fe@?-Fe2O3 core-shell nanowire a promising candidate for the applications of the magnetic drug delivery, electrochemical energy storage, gas sensors, photocatalysis, and so forth. PMID:24134440

2013-01-01

84

High-valent [MnFe] and [FeFe] cofactors in ribonucleotide reductases.  

PubMed

Ribonucleotide reductases (RNRs) are essential for DNA synthesis in most organisms. In class-Ic RNR from Chlamydia trachomatis (Ct), a MnFe cofactor in subunit R2 forms the site required for enzyme activity, instead of an FeFe cofactor plus a redox-active tyrosine in class-Ia RNRs, for example in mouse (Mus musculus, Mm). For R2 proteins from Ct and Mm, either grown in the presence of, or reconstituted with Mn and Fe ions, structural and electronic properties of higher valence MnFe and FeFe sites were determined by X-ray absorption spectroscopy and complementary techniques, in combination with bond-valence-sum and density functional theory calculations. At least ten different cofactor species could be tentatively distinguished. In Ct R2, two different Mn(IV)Fe(III) site configurations were assigned either L(4)Mn(IV)(?O)(2)Fe(III)L(4) (metal-metal distance of ~2.75Å, L = ligand) prevailing in metal-grown R2, or L(4)Mn(IV)(?O)(?OH)Fe(III)L(4) (~2.90Å) dominating in metal-reconstituted R2. Specific spectroscopic features were attributed to an Fe(IV)Fe(III) site (~2.55Å) with a L(4)Fe(IV)(?O)(2)Fe(III)L(3) core structure. Several Mn,Fe(III)Fe(III) (~2.9-3.1Å) and Mn,Fe(III)Fe(II) species (~3.3-3.4Å) likely showed 5-coordinated Mn(III) or Fe(III). Rapid X-ray photoreduction of iron and shorter metal-metal distances in the high-valent states suggested radiation-induced modifications in most crystal structures of R2. The actual configuration of the MnFe and FeFe cofactors seems to depend on assembly sequences, bound metal type, valence state, and previous catalytic activity involving subunit R1. In Ct R2, the protonation of a bridging oxide in the Mn(IV)(?O)(?OH)Fe(III) core may be important for preventing premature site reduction and initiation of the radical chemistry in R1. PMID:22222354

Leidel, Nils; Popovi?-Bijeli?, Ana; Havelius, Kajsa G V; Chernev, Petko; Voevodskaya, Nina; Gräslund, Astrid; Haumann, Michael

2012-03-01

85

Hydrogen evolution from dithionite and H2 photoproduction by hydrogenase incorporated into various hydrophobic matrices.  

PubMed

The effects of surfactants, lipids and amphiphilic viologen mediators on H2 production from dithionite as well as on Ru(bpy) sensitized H2 photoproduction by hydrogenase from Thiocapsa roseopersicina was studied. Three systems which differed as to the nature of the hydrophobic matrix around the hydrogenase were tested. An enhanced hydrogenase activity was observed in the presence of surfactants, in the 1-6 mM concentration range. Hydrogenase showed a selectivity for the amphiphilic viologens, 2C7-diCl was the most efficient electron mediator in both reactions. H2 photoproduction seemed not to be feasible in the detergent-hydrogenase system because of intensive foaming. Hydrogenase incorporated into liposomes catalyzed H2 photoevolution efficiently but the rate was decreasing in time, though reversibly. Using intact bacterial cells instead of purified hydrogenase yielded stable H2 photoevolution for at least 12 hours. This system offers several advantages for potential practical applications. PMID:3089309

Kovács, K L; Dér, A

1986-01-01

86

Application of Gene-Shuffling for the Rapid Generation of Novel [FeFe]-Hydrogenase Libraries  

SciTech Connect

A gene-shuffling technique was identified, optimized and used to generate diverse libraries of recombinant [FeFe]-hydrogenases. Six native [FeFe]-hydrogenase genes from species of Clostridia were first cloned and separately expressed in Escherichia coli concomitantly with the assembly proteins required for [FeFe]-hydrogenase maturation. All enzymes, with the exception of C. thermocellum HydA, exhibited significant activity when expressed. Single-stranded DNA fragments from genes encoding the two most active [FeFe]-hydrogenases were used to optimize a gene-shuffling protocol and generate recombinant enzyme libraries. Random sampling demonstrates that several shuffled products are active. This represents the first successful application of gene-shuffling using hydrogenases. Moreover, we demonstrate that a single set of [FeFe]-hydrogenase maturation proteins is sufficient for the heterologous assembly of the bioinorganic active site of several native and shuffled [FeFe]-hydrogenases.

Nagy, L. E.; Meuser, J. E.; Plummer, S.; Seibert, M.; Ghirardi, M. L.; King, P. W.; Ahmann, D.; Posewitz, M. C.

2007-01-01

87

Distribution and activity of hydrogenase enzymes in subsurface sediments  

NASA Astrophysics Data System (ADS)

Metabolically active microbial communities are present in a wide range of subsurface environments. Techniques like enumeration of microbial cells, activity measurements with radiotracer assays and the analysis of porewater constituents are currently being used to explore the subsurface biosphere, alongside with molecular biological analyses. However, many of these techniques reach their detection limits due to low microbial activity and abundance. Direct measurements of microbial turnover not just face issues of insufficient sensitivity, they only provide information about a single specific process rather than an overall microbial activity. Since hydrogenase enzymes are intracellular and ubiquitous in subsurface microbial communities, the enzyme activity represents a measure of total activity of the entire microbial community. A hydrogenase activity assay could quantify total metabolic activity without having to identify specific processes. This would be a major advantage in subsurface biosphere studies, where several metabolic processes can occur simultaneously. We quantified hydrogenase enzyme activity and distribution in sediment samples from different aquatic subsurface environments (Lake Van, Barents Sea, Equatorial Pacific and Gulf of Mexico) using a tritium-based assay. We found enzyme activity at all sites and depths. Volumetric hydrogenase activity did not show much variability between sites and sampling depths, whereas cell-specific activity ranged from 10-5 to 1 nmol H2 cell-1 d-1. Activity was lowest in sediment layers where nitrate was detected. Higher activity was associated with samples in which sulfate was the predominant electron acceptor. We found highest activity in samples from environments with >10 ppm methane in the pore water. The results show that cell-specific hydrogenase enzyme activity increases with decreasing energy yield of the electron acceptor used. It is not possible to convert volumetric or cell-specific hydrogenase activity into a turnover rate of a specific process like sulfate reduction. However, we can use the cell-specific hydrogenase activity to estimate the size of the metabolically active microbial population. The conversion factors vary according to the predominant electron-accepting process. In subsurface sediment standard methods for quantification of the metabolically active microbial population (e.g. CARD-FISH) are at their lower detection limit. The hydrogenase enzyme activity measurement provides an alternative and sensitive way of quantification.

Adhikari, R.; Nickel, J.; Glombitza, C.; Spivack, A. J.; D'Hondt, S. L.; Kallmeyer, J.

2013-12-01

88

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

89

Immobilisation of Hydrogenase Systems for the Photochemical Production of Hydrogen.  

National Technical Information Service (NTIS)

Desulfovibrio vulgaris has been grown under a variety of conditions to maximise the yield of oxygen-stable 12Fe-12S hydrogenase. The enzyme forms up to 1% of the total cellular protein in cells grown in the presence of EDTA. Techniques have also been deve...

C. Veeger, A. Harder, H. M. Van Der Westen

1982-01-01

90

Hydrogen fuel electrode based on bioelectrocatalysis by the enzyme hydrogenase  

Microsoft Academic Search

Our aim is to show, that the enzymes as electrocatalysts are able to improve the performance characteristics of the fuel cells. The hydrogen fuel electrode based on hydrogenase from Thiocapsa roseopersicina immobilized directly on carbon filament material has been made. The enzyme electrode has operated according to electron tunneling between the enzyme active site and the electrode support; this mechanism

A. A. Karyakin; S. V. Morozov; E. E. Karyakina; S. D. Varfolomeyev; N. A. Zorin; S. Cosnier

2002-01-01

91

Hydrogenases in Desulfovibrio vulgaris Hildenborough: structural and physiologic characterisation of the membrane-bound [NiFeSe] hydrogenase.  

PubMed

The genome of Desulfovibrio vulgaris Hildenborough (DvH) encodes for six hydrogenases (Hases), making it an interesting organism to study the role of these proteins in sulphate respiration. In this work we address the role of the [NiFeSe] Hase, found to be the major Hase associated with the cytoplasmic membrane. The purified enzyme displays interesting catalytic properties, such as a very high H(2) production activity, which is dependent on the presence of phospholipids or detergent, and resistance to oxygen inactivation since it is isolated aerobically in a Ni(II) oxidation state. Evidence was obtained that the [NiFeSe] Hase is post-translationally modified to include a hydrophobic group bound to the N-terminal, which is responsible for its membrane association. Cleavage of this group originates a soluble, less active form of the enzyme. Sequence analysis shows that [NiFeSe] Hases from Desulfovibrionacae form a separate family from the [NiFe] enzymes of these organisms, and are more closely related to [NiFe] Hases from more distant bacterial species that have a medial [4Fe4S](2+/1+) cluster, but not a selenocysteine. The interaction of the [NiFeSe] Hase with periplasmic cytochromes was investigated and is similar to the [NiFe](1) Hase, with the Type I cytochrome c (3) as the preferred electron acceptor. A model of the DvH [NiFeSe] Hase was generated based on the structure of the Desulfomicrobium baculatum enzyme. The structures of the two [NiFeSe] Hases are compared with the structures of [NiFe] Hases, to evaluate the consensual structural differences between the two families. Several conserved residues close to the redox centres were identified, which may be relevant to the higher activity displayed by [NiFeSe] Hases. PMID:16187073

Valente, Filipa M A; Oliveira, A Sofia F; Gnadt, Nicole; Pacheco, Isabel; Coelho, Ana V; Xavier, António V; Teixeira, Miguel; Soares, Cláudio M; Pereira, Inês A C

2005-10-01

92

Crystallographic and FTIR spectroscopic evidence of changes in Fe coordination upon reduction of the active site of the Fe-only hydrogenase from Desulfovibrio desulfuricans.  

PubMed

Fe-only hydrogenases, as well as their NiFe counterparts, display unusual intrinsic high-frequency IR bands that have been assigned to CO and CN(-) ligation to iron in their active sites. FTIR experiments performed on the Fe-only hydrogenase from Desulfovibrio desulfuricans indicate that upon reduction of the active oxidized form, there is a major shift of one of these bands that is provoked, most likely, by the change of a CO ligand from a bridging position to a terminal one. Indeed, the crystal structure of the reduced active site of this enzyme shows that the previously bridging CO is now terminally bound to the iron ion that most likely corresponds to the primary hydrogen binding site (Fe2). The CO binding change may result from changes in the coordination sphere of Fe2 or its reduction. Superposition of this reduced active site with the equivalent region of a NiFe hydrogenase shows a remarkable coincidence between the coordination of Fe2 and that of the Fe ion in the NiFe cluster. Both stereochemical and mechanistic considerations suggest that the small organic molecule found at the Fe-only hydrogenase active site and previously modeled as 1,3-propanedithiolate may, in fact, be di-(thiomethyl)-amine. PMID:11456758

Nicolet, Y; de Lacey, A L; Vernède, X; Fernandez, V M; Hatchikian, E C; Fontecilla-Camps, J C

2001-02-28

93

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. PMID:23934246

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

2013-01-01

94

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

95

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

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. PMID:1711025

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

1991-06-01

96

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. PMID:21079771

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

97

Interaction between Hydrogenase Maturation Factors HypA and HypB Is Required for [NiFe]-Hydrogenase Maturation  

PubMed Central

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

98

Enhancement of photoheterotrophic biohydrogen production at elevated temperatures by the expression of a thermophilic clostridial hydrogenase.  

PubMed

The working temperature of a photobioreactor under sunlight can be elevated above the optimal growth temperature of a microorganism. To improve the biohydrogen productivity of photosynthetic bacteria at higher temperatures, a [FeFe]-hydrogenase gene from the thermophile Clostridium thermocellum was expressed in the mesophile Rhodopseudomonas palustris CGA009 (strain CGA-CThydA) using a log-phase expression promoter P( pckA ) to drive the expression of heterogeneous hydrogenase gene. In contrast, a mesophilic Clostridium acetobutylicum [FeFe]-hydrogenase gene was also constructed and expressed in R. palustris (strain CGA-CAhydA). Both transgenic strains were tested for cell growth, in vivo hydrogen production rate, and in vitro hydrogenase activity at elevated temperatures. Although both CGA-CThydA and CGA-CAhydA strains demonstrated enhanced growth over the vector control at temperatures above 38 °C, CGA-CThydA produced more hydrogen than the other strains. The in vitro hydrogenase activity assay, measured at 40 °C, confirmed that the activity of the CGA-CThydA hydrogenase was higher than the CGA-CAhydA hydrogenase. These results showed that the expression of a thermophilic [FeFe]-hydrogenase in R. palustris increased the growth rate and biohydrogen production at elevated temperatures. This transgenic strategy can be applied to a broad range of purple photosynthetic bacteria used to produce biohydrogen under sunlight. PMID:22460592

Lo, Shou-Chen; Shih, Shau-Hua; Chang, Jui-Jen; Wang, Chun-Ying; Huang, Chieh-Chen

2012-08-01

99

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. PMID:21637846

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

2011-01-01

100

The bidirectional hydrogenase of Synechocystis sp. PCC 6803 works as an electron valve during photosynthesis  

Microsoft Academic Search

The activity of the bidirectional hydrogenase of the cyanobacterium Synechocystis sp. PCC 6803 was found not to be regulated in parallel to respiration but to photosynthesis. A mutant with a deletion in the large hydrogenase subunit gene (hoxH), which contains the active site, was impaired in the oxidation of photosystem I (PSI) when illuminated with light, which excites either PSI

Jens Appel; Saranya Phunpruch; Klaus Steinmüller; Rüdiger Schulz

2000-01-01

101

THE [Fe-Fe]-HYDROGENASE MATURATION PROTEIN HydF FROM Thermotoga maritima IS A GTPase WITH AN IRON-SULFUR CLUSTER  

E-print Network

1 THE [Fe-Fe]-HYDROGENASE MATURATION PROTEIN HydF FROM Thermotoga maritima IS A GTPase WITH AN IRON-SULFUR-Fe]-hydrogenases (1), [Fe-Fe]-hydrogenases (2,3) and "Iron-Sulfur cluster- free" hydrogenase (4,5,6), which do for activity (10). Infrared spectroscopy studies have also demonstrated the presence of CO ligands in the "Iron-Sulfur

Paris-Sud XI, Université de

102

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

103

Hydrogenase-based nanomaterials as anode electrode catalyst in polymer electrolyte fuel cells  

NASA Astrophysics Data System (ADS)

We consider hydrogenase-based nanomaterials for possible use as anode electrode catalysts in polymer electrolyte fuel cells (PEFCs). We choose Fe-only hydrogenase component of Desulfovibrio desulfuricans (DdHase) as a hydrogenase complex, and investigate its catalytic activity for H 2 dissociation using ab initio calculations based on density functional theory (DFT). We found two possible H-H bond cleavage pathways, which are heterolytic and possess low activation barriers. Moreover, the H 2 dissociation can be promoted by inducing spin polarization of the H 2 adduct. We report that hydrogenase or hydrogenase-based nanomaterials can manipulate to exhibit the catalytic activity equivalent to the well-known platinum catalyst.

Tsuda, Muneyuki; Diño, Wilson Agerico; Kasai, Hideaki

2005-03-01

104

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

105

Structure-Function Relationships in [FeFe]-Hydrogenase Active Site Maturation*  

PubMed Central

Since the discovery that, despite the active site complexity, only three gene products suffice to obtain active recombinant [FeFe]-hydrogenase, significant light has been shed on this process. Both the source of the CO and CN? ligands to iron and the assembly site of the catalytic subcluster are known, and an apo structure of HydF has been published recently. However, the nature of the substrate(s) for the synthesis of the bridging dithiolate ligand to the subcluster remains to be established. From both spectroscopy and model chemistry, it is predicted that an amine function in this ligand plays a central role in catalysis, acting as a base in the heterolytic cleavage of hydrogen. PMID:22389497

Nicolet, Yvain; Fontecilla-Camps, Juan C.

2012-01-01

106

Structure prediction and molecular simulation of gases diffusion pathways in hydrogenase.  

PubMed

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 H(2) catalysts found in ecologically and phylogenetically diverse microorganisms, including the photosynthetic green alga, Chlamydomonas reinhardtii. While 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. 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 H(2) molecules were randomly inserted in the solvated box and two simulations of 50 and 100 ps were performed. Similarly 100 O(2) 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. PMID:21364783

Sundaram, Shanthy; Tripathi, Ashutosh; Gupta, Vipul

2010-01-01

107

Structural and functional investigations of biological catalysts for optimization of solar-driven H II production systems  

NASA Astrophysics Data System (ADS)

Research efforts to develop efficient systems for H II production encompass a variety of biological and chemical approaches. For solar-driven H II production we are investigating an approach that integrates biological catalysts, the [FeFe] hydrogenases, with a photoelectrochemical cell as a novel bio-hybrid system. Structurally the [FeFe] hydrogenases consist of an iron-sulfur catalytic site that in some instances is electronically wired to accessory iron-sulfur clusters proposed to function in electron transfer. The inherent structural complexity of most examples of these enzymes is compensated by characteristics desired for bio-hybrid systems (i.e., low activation energy, high catalytic activity and solubility) with the benefit of utilizing abundant, less costly non-precious metals. Redesign and modification of [FeFe] hydrogenases is being undertaken to reduce complexity and to optimize structural properties for various integration strategies. The least complex examples of [FeFe] hydrogenase are found in the species of photosynthetic green algae and are being studied as design models for investigating the effects of structural minimization on substrate transfer, catalytic activity and oxygen sensitivity. Redesigning hydrogenases for effective use in bio-hybrid systems requires a detailed understanding of the relationship between structure and catalysis. To achieve better mechanistic understanding of [FeFe] hydrogenases both structural and dynamic models are being used to identify potential substrate transfer mechanisms which are tested in an experimental system. Here we report on recent progress of our investigations in the areas of [FeFe] hydrogenase overexpression, minimization and biochemical characterization.

King, Paul W.; Svedruzic, Drazenka; Cohen, Jordi; Schulten, Klaus; Seibert, Michael; Ghirardi, Maria L.

2006-08-01

108

The role of Hox hydrogenase in the H2 metabolism of Thiocapsa roseopersicina.  

PubMed

The purple sulfur phototrophic bacterium Thiocapsa roseopersicina BBS synthesizes at least three NiFe hydrogenases (Hox, Hup, Hyn). We characterized the physiological H(2) 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 and Hyn hydrogenases) catalyzed the dark fermentative H(2) evolution and the light-dependent H(2) production in the presence of thiosulfate. Both Hox(+) and Hup(+) mutants demonstrated light-dependent H(2) uptake stimulated by CO(2) but only the Hup(+) mutant was able to mediate O(2)-dependent H(2) consumption in the dark. The ability of the Hox(+) mutant to evolve or consume hydrogen was found to depend on a number of interplaying factors including both growth and reaction conditions (availability of glucose, sulfur compounds, CO(2), H(2), light). The study of the redox properties of Hox hydrogenase supported the reversibility of its action. Based on the results a scheme is suggested to describe the role of Hox hydrogenase in light-dependent and dark hydrogen metabolism in T. roseopersicina BBS. PMID:17376400

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

2007-06-01

109

The Role of Frozen Spins in the Exchange Anisotropy of Core-Shell Fe@Fe3O4 Nanoparticles  

PubMed Central

Core–shell Fe@Fe3O4 nanoparticles exhibit substantial exchange bias at low temperatures, mediated by unidirectionally aligned moments at the core–shell interface. These spins are frozen into magnetic alignment with field cooling, and are depinned in a temperature-dependent manner. The population of such frozen spins has a direct impact on both coercivity (HC) and the exchange-bias field (HE), which are modulated by external physical parameters such as the strength of the applied cooling field and the cycling history of magnetic field sweeps (training effect). Aging of the core–shell nanoparticles under ambient conditions results in a gradual decrease in magnetization but overall retention of HC and HE, as well as a large increase in the population of frozen spins. These changes are accompanied by a structural evolution from well-defined core–shell structures to particles containing multiple voids, attributable to the Kirkendall effect. Energy-filtered and high-resolution transmission electron microscopy both indicate further oxidation of the shell layer, but the Fe core is remarkably well preserved. The increase in frozen spin population with age is responsible for the overall retention of exchange bias, despite void formation and other oxidation-dependent changes. The exchange-bias field becomes negligible upon deliberate oxidation of Fe@Fe3O4 nanoparticles into yolk–shell particles, with a nearly complete physical separation of core and shell. PMID:21321674

Ong, Quy Khac; Lin, Xiao-Min; Wei, Alexander

2011-01-01

110

Activities, occurrence, and localization of hydrogenase in free-living and symbiotic frankia.  

PubMed

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. PMID:16667353

Sellstedt, A; Lindblad, P

1990-03-01

111

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 PMID:16667353

Sellstedt, Anita; Lindblad, Peter

1990-01-01

112

FTIR spectroelectrochemical characterization of the Ni-Fe-Se hydrogenase from Desulfovibrio vulgaris Hildenborough.  

PubMed

For the first time a complete characterization by infrared spectroscopy of a Ni-Fe-Se hydrogenase in its different redox states is reported. The Ni-Fe-Se hydrogenase was isolated from Desulfovibrio vulgaris Hildenborough. Two different electron paramagnetic resonance silent and air-stable redox states that are not in equilibrium were detected. Upon reduction of these states the catalytically active states Ni-R and Ni-C appear immediately. These states are in redox equilibrium and their formal redox potential has been measured. Putative structural differences between the redox states of the active site of the Ni-Fe-Se hydrogenase are discussed. PMID:18704522

De Lacey, Antonio L; Gutiérrez-Sánchez, Cristina; Fernández, Víctor M; Pacheco, Isabel; Pereira, Inês A C

2008-11-01

113

Turning Cellulose Waste Into Electricity: Hydrogen Conversion by a Hydrogenase Electrode  

PubMed Central

Hydrogen-producing thermophilic cellulolytic microorganisms were isolated from cow faeces. Rates of cellulose hydrolysis and hydrogen formation were 0.2 mM L-1 h-1 and 1 mM L-1 h-1, respectively. An enzymatic fuel cell (EFC) with a hydrogenase anode was used to oxidise hydrogen produced in a microbial bioreactor. The hydrogenase electrode was exposed for 38 days (912 h) to a thermophilic fermentation medium. The hydrogenase activity remaining after continuous operation under load was 73% of the initial value. PMID:24312437

Abramov, Sergey M.; Sadraddinova, Elmira R.; Shestakov, Andrey I.; Voronin, Oleg G.; Karyakin, Arkadiy A.; Zorin, Nikolay A.; Netrusov, Alexander I.

2013-01-01

114

Interaction between hydrogenase, nitrogenase, and respiratory activities in a Frankia isolate from Alnus rubra.  

PubMed

H2 uptake and H2-supported O2 uptake were measured in N2-fixing cultures of Frankia strain ArI3 isolated from root nodules of Alnus rubra. H2 uptake by intact cells was O2 dependent and maximum rates were observed at ambient O2 concentrations. No hydrogenase activity could be detected in NH4+-grown, undifferentiated filaments cultured aerobically indicating that uptake hydrogenase activity was associated with the vesicles, the cellular site of nitrogen fixation in Frankia. Hydrogenase activity was inhibited by acetylene but inhibition could be alleviated by pretreatment with H2. H2 stimulated acetylene reduction at supraoptimal but not suboptimal O2 concentrations. These results suggest that uptake hydrogenase activity in ArI3 may play a role in O2 protection of nitrogenase, especially under conditions of carbon limitation. PMID:2766117

Murry, M A; Lopez, M F

1989-06-01

115

BIOTECHNOLOGICALLY RELEVANT ENZYMES AND PROTEINS Protein engineering of hydrogenase 3 to enhance  

E-print Network

production by an error-prone polymerase chain reaction (epPCR) using a host that lacked hydrogenase activity and CO ligands may be synthesized from carbamoylphosphate via the postulated reaction: 2LnFe þ 2H2NCOOPO�

Wood, Thomas K.

116

HypD is the scaffold protein for Fe-(CN)2CO cofactor assembly in [NiFe]-hydrogenase maturation.  

PubMed

[NiFe]-hydrogenases bind a NiFe-(CN)2CO cofactor in their catalytic large subunit. The iron-sulfur protein HypD and the small accessory protein HypC play a central role in the generation of the CO and CN(-) ligands. Infrared spectroscopy identified signatures on an anaerobically isolated HypCD complex that are reminiscent of those in the hydrogenase active site, suggesting that this complex is the assembly site of the Fe-(CN)2CO moiety of the cofactor prior to its transfer to the hydrogenase large subunit. Here, we report that HypD isolated in the absence of HypC shows infrared bands at 1956 cm(-1), 2072 cm(-1), and 2092 cm(-1) that can be assigned to CO, CN(1), and CN(2), respectively, and which are indistinguishable from those observed for the HypCD complex. HypC could not be isolated with CO or CN(-) ligand contribution. Treatment of HypD with EDTA led to the concomitant loss of Fe and the CO and CN(-) signatures, while oxidation by H2O2 resulted in a positive shift of the CO and CN(-) bands by 35 cm(-1) and 20 cm(-1), respectively, indicative of the ferrous iron as an immediate ligation site for the diatomic ligands. Analysis of HypD amino acid variants identified cysteines 41, 69, and 72 to be essential for maturation of the cofactor. We propose a refined model for the ligation of Fe-(CN)2CO to HypD and the role of HypC in [NiFe]-hydrogenase maturation. PMID:23597401

Stripp, Sven T; Soboh, Basem; Lindenstrauss, Ute; Braussemann, Mario; Herzberg, Martin; Nies, Dietrich H; Sawers, R Gary; Heberle, Joachim

2013-05-14

117

Function of periplasmic hydrogenases in the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough.  

PubMed

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. PMID:17601789

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

2007-09-01

118

Involvement of a single periplasmic hydrogenase for both hydrogen uptake and production in some Desulfovibrio species.  

PubMed

Various sulphate-reducing bacteria differing in the number of genes encoding hydrogenase were shown to ferment lactate in coculture with Methanospirillum hungatei, in the absence of sulphate. The efficiency of interspecies H2 transfer carried out by these species of sulphate-reducing bacteria does not appear to correlate with the distribution of genes coding for hydrogenase. Desulfovibrio vulgaris Groningen, which possesses only the gene for [NiFe] hydrogenase, oxidizes hydrogen in the presence of sulphate and produces some hydrogen during fermentation of pyruvate without electron acceptor. The hydrogenase of D. vulgaris was purified and characterized. It exhibits a molecular mass of 87 kDa and is composed of two different subunits (60 and 28 kDa). D. vulgaris hydrogenase contains 10.6 iron atoms, 0.9 nickel atom and 12 acid-labile sulphur atoms/molecule, and the absorption spectrum of the enzyme is characteristic of an iron-sulphur protein. Maximal H2 uptake and H2 evolution activities were 332 and 230 units/mg protein, respectively. D. vulgaris cells contain exclusively the [NiFe] hydrogenase, whatever the growth conditions, as shown by biochemical and immunological studies. Immunocytolocalization in ultrathin frozen sections of cells grown on lactate and sulphate, on H2 and sulphate and on pyruvate showed that the [NiFe] hydrogenase was located in the periplasmic space. Labelling was enhanced in cells grown on H2 and sulphate and on pyruvate. The results enable us to conclude that D. vulgaris Groningen contains a single hydrogenase of the [NiFe] type, located in the periplasmic space like that described for D. gigas. This enzyme appears to be involved in both H2 uptake and H2 production, depending on the growth conditions. PMID:7652207

Hatchikian, E C; Forget, N; Bernadac, A; Alazard, D; Ollivier, B

1995-02-01

119

Hydrogen evolution and consumption in AOT–isooctane reverse micelles by Desulfovibrio gigas hydrogenase  

Microsoft Academic Search

The enzyme hydrogenase isolated from the sulphate reducing anaerobic bacterium Desulfovibrio gigas was encapsulated in reverse micelles of AOT–water–isooctane. The enzyme ability to consume molecular hydrogen was studied as a function of the micelle size (given by Wo=[H2O]\\/[organic solvent]). A peak of catalytic activity was obtained for Wo=18, a micelle size theoretically fitting the heterodimeric hydrogenase molecule. At this Wo

Susana L. A. Andrade; José J. G. Moura

2002-01-01

120

Energy-Converting [NiFe] Hydrogenases from Archaea and Extremophiles: Ancestors of Complex I  

Microsoft Academic Search

[NiFe] hydrogenases are well-characterized enzymes that have a key function in the H2 metabolism of various microorganisms. In the recent years a subfamily of [NiFe] hydrogenases with unique properties has been identified. The members of this family form multisubunit membrane-bound enzyme complexes composed of at least four hydrophilic and two integral membrane proteins. These six conserved subunits, which built the

Reiner Hedderich

2004-01-01

121

Function of Periplasmic Hydrogenases in the Sulfate-ReducingBacterium Desulfovibrio vulgaris Hildenborough  

SciTech Connect

The sulfate-reducing bacterium Desulfovibrio vulgarisHildenborough possesses four periplasmic hydrogenases to facilitate theoxidation 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 theircellular functions, we have compared the growth rates of existing (hydand hyn1) and newly constructed (hys and hyn-1 hyd) mutants to those ofthe wild type in defined media in which lactate or hydrogen at either 5or 50 percent (vol/vol) was used as the sole electron donor for sulfatereduction. Only strains missing the [Fe]hydrogenase were significantlyaffected during growth with lactate or with 50 percent (vol/vol) hydrogenas the sole electron donor. When the cells were grown at low (5 percent[vol/vol]) hydrogen concentrations, those missing the [NiFeSe]hydrogenase suffered the greatest impairment. The growth rate datacorrelated strongly with gene expression results obtained from microarrayhybridizations and real-time PCR using mRNA extracted from cells grownunder the three conditions. Expression of the hys genes followed theorder 5 percent hydrogen>50 percent hydrogen>lactate, whereasexpression of the hyd genes followed the reverse order. These resultssuggest that growth with lactate and 50 percent hydrogen is associatedwith high intracellular hydrogen concentrations, which are best capturedby the higher activity, lower affinity [Fe]hydrogenase. In contrast,growth with 5 percent hydrogen is associated with a low intracellularhydrogen concentration, requiring the lower activity, higher affinity[NiFeSe]hydrogenase.

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

2007-09-24

122

[Fe]-hydrogenases in green algae: photo-fermentation and hydrogen evolution under sulfur deprivation  

Microsoft Academic Search

Recent studies indicate that [Fe]-hydrogenases and H2 metabolism are widely distributed among green algae. The enzymes are simple structured and catalyze H2 evolution with similar rates than the more complex [Fe]-hydrogenases from bacteria. Different green algal species developed diverse strategies to survive under sulfur deprivation. Chlamydomonas reinhardtii evolves large quantities of hydrogen gas in the absence of sulfur. In a

Martin Winkler; Anja Hemschemeier; Cecilia Gotor; Anastasios Melis; Thomas Happe

2002-01-01

123

Structural Basis for GTP-Dependent Dimerization of Hydrogenase Maturation Factor HypB  

PubMed Central

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

Wong, Ching-On; Wong, Kam-Bo

2012-01-01

124

Acetylene, Not Ethylene, Inactivates the Uptake Hydrogenase of Actinorhizal Nodules during Acetylene Reduction Assays.  

PubMed

Acetylene reduction assays were shown to inactivate uptake hydrogenase activity to different extents in one Casuarina and two Alnus symbioses. Inactivation was found to be caused by C(2)H(2) and not by C(2)H(4). Acetylene completely inactivated the hydrogenase activity of intact root systems of Alnus incana inoculated with Frankia strain Avcl1 in 90 minutes, as shown by a drop in the relative efficiency of nitrogenase from 1.0 to 0.73. The hydrogenase of Frankia preparations (containing vesicles) and of cell-free extracts (not containing vesicles) from the same symbiosis was much more susceptible to acetylene inactivation. Cell-free extracts lost all hydrogenase activity after 5 minutes of exposure to acetylene. The hydrogenase activity of intact root systems of Casuarina obesa was less sensitive to acetylene than that of root systems of A. incana, since the relative efficiency of nitrogenase changed only from 1.0 to 0.95 over 90 minutes. Frankia preparations and cell-free extracts of C. obesa still retained hydrogenase activity after a 10 minute-exposure to acetylene. PMID:16667724

Sellstedt, A; Winship, L J

1990-09-01

125

Theoretical Studies of Structures and Mechanisms in Organometallic and Bioinorganic Chemistry: Heck Reaction with Palladium Phosphines, Active Sites of Superoxide Reductase and Cytochrome P450 Monooxygenase, and Tetrairon Hexathiolate Hydrogenase Model  

E-print Network

The electronic structures and reaction mechanisms of transition-metal complexes can be calculated accurately by density functional theory (DFT) in cooperation with the continuum solvation model. The palladium catalyzed Heck reaction, iron...

Surawatanawong, Panida

2010-07-14

126

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

PubMed Central

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 gene cluster coding for a cytoplasmic, NAD+-reducing NiFe hydrogenase was identified and sequenced. The deduced gene products exhibited the highest similarity to the corresponding subunits of the cyanobacterial bidirectional soluble hydrogenases (HoxEFUYH). The five genes were localized on a single transcript according to reverse transcription-PCR experiments. A ?54-type promoter preceded the gene cluster, suggesting that there was inducible expression of the operon. The Hox hydrogenase was proven to function as a truly bidirectional hydrogenase; it produced H2 under nitrogenase-repressed conditions, and it recycled the hydrogen produced by the nitrogenase in cells fixing N2. In-frame deletion of the hoxE gene eliminated hydrogen evolution derived from the Hox enzyme in vivo, although it had no effect on the hydrogenase activity in vitro. This suggests that HoxE has a hydrogenase-related role; it likely participates in the electron transfer processes. This is the first example of the presence of a cyanobacterial-type, NAD+-reducing hydrogenase in a phototrophic bacterium that is not a cyanobacterium. The potential physiological implications are discussed. PMID:14766547

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

2004-01-01

127

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

128

Spectroscopic and electrochemical characterization of the [NiFeSe] hydrogenase from Desulfovibrio vulgaris Miyazaki F: reversible redox behavior and interactions between electron transfer centers.  

PubMed

Characterizing a new hydrogenase: The newly isolated [NiFeSe] hydrogenase from Desulfovibrio vulgaris Miyazaki F displays catalytic properties distinct from other hydrogenase proteins. Here we apply site-specific spectroscopic and electrochemical techniques to characterize these unique features at the molecular level. PMID:24038675

Riethausen, Jana; Rüdiger, Olaf; Gärtner, Wolfgang; Lubitz, Wolfgang; Shafaat, Hannah S

2013-09-23

129

Nickel-Iron Dithiolates Related to the Deactivated [NiFe]-Hydrogenases  

PubMed Central

Described herein are preparations of synthetic models for the deactivated Ni(II)Fe(II) states of the [NiFe]-hydrogenases. Iodination of the S = ½ species [(dppe)Ni(pdt)Fe(CO)3]+ afforded the diamagnetic iodo complex [(dppe)Ni(pdt)IFe(CO)3]+. Crystallographic analysis of this species confirmed the presence of square-pyramidal Ni linked to an octahedral Fe centre. The Ni···Fe separation of 3.018 Å indicated the absence of metal-metal bonding. This complex could be reduced to give (dppe)Ni(pdt)Fe(CO)3 and, in the presence of iodide, decarbonylated to afford (dppe)Ni(pdt)FeI2. Derivatives of the type [(diphosphine)Ni(dithiolate)XFe(CO)2L]+ (X = Cl, Br, I) were prepared by halogenation of mixed-valence precursors [(diphosphine)Ni(dithiolate)Fe(CO)2L]+ (diphosphine = dppe, dcpe; L = tertiary phosphine or CO). The Fe(CO)2(PR3)-containing derivatives are more robust than the related tricarbonyl derivatives. Exploiting this greater stability, we characterised examples of chloride and bromide derivatives. Related fluorides could be prepared by F? abstraction from BF4?. Spectroscopic evidence is presented for the hydroperoxide [(diphosphine)Ni(dithiolate)(OOH)Fe(CO)2L]+, which was prepared by oxidation of a model for Ni-SU and Ni-SIr states. PMID:22992700

Schilter, David

2012-01-01

130

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 PMID:3056905

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

1988-01-01

131

Hybrid molecular assemblies composed of hydrogenase enzymes and quantum dots helps to pave the way for the  

E-print Network

, Smita; Ai, Xin; Rumbles, Garry; and King, Paul W."Controlled Assembly of Hydrogenase-CdTe Nanocrystal measurements showed that the photocatalytic efficiency varied with the quantum dot/hydrogenase ratio, which was maximal at low enzyme coverages favoring one-to-one ratios. The efficiency of photocatalytic H2 production

132

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

133

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

134

Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803  

PubMed Central

Background Molecular hydrogen is an environmentally-clean fuel and the reversible (bi-directional) hydrogenase of the cyanobacterium Synechocystis sp. PCC 6803 as well as the native Escherichia coli hydrogenase 3 hold great promise for hydrogen generation. These enzymes perform the simple reaction 2H+ + 2e- ? H2 (g). Results Hydrogen yields were enhanced up to 41-fold by cloning the bidirectional hydrogenase (encoded by hoxEFUYH) from the cyanobacterium into E. coli. Using an optimized medium, E. coli cells expressing hoxEFUYH also produced twice as much hydrogen as the well-studied Enterobacter aerogenes HU-101, and hydrogen gas bubbles are clearly visible from the cultures. Overexpression of HoxU alone (small diaphorase subunit) accounts for 43% of the additional hydrogen produced by HoxEFUYH. In addition, hydrogen production in E. coli mutants with defects in the native formate hydrogenlyase system show that the cyanobacterial hydrogenase depends on both the native E. coli hydrogenase 3 as well as on its maturation proteins. Hydrogen absorption by cells expressing hoxEFUYH was up to 10 times lower than cells which lack the cloned cyanobacterial hydrogenase; hence, the enhanced hydrogen production in the presence of hoxEFUYH is due to inhibition of hydrogen uptake activity in E. coli. Hydrogen uptake by cells expressing hoxEFUYH was suppressed in three wild-type strains and in two hycE mutants but not in a double mutant defective in hydrogenase 1 and hydrogenase 2; hence, the active cyanobacterial locus suppresses hydrogen uptake by hydrogenase 1 and hydrogenase 2 but not by hydrogenase 3. Differential gene expression indicated that overexpression of HoxEFUYH does not alter expression of the native E. coli hydrogenase system; instead, biofilm-related genes are differentially regulated by expression of the cyanobacterial enzymes which resulted in 2-fold elevated biofilm formation. This appears to be the first enhanced hydrogen production by cloning a cyanobacterial enzyme into a heterologous host. Conclusion Enhanced hydrogen production in E. coli cells expressing the cyanobacterial HoxEFUYH is by inhibiting hydrogen uptake of both hydrogenase 1 and hydrogenase 2. PMID:17521447

Maeda, Toshinari; Vardar, Gonul; Self, William T; Wood, Thomas K

2007-01-01

135

A 2.8 Å Fe-Fe Separation in the Fe2III/IV Intermediate (X) from Escherichia coli Ribonucleotide Reductase  

PubMed Central

A class Ia ribonucleotide reductase (RNR) employs a µ-oxo-Fe2III/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 Fe2II/II complex with O2 results in accumulation of an Fe2III/IV cluster, termed X, which oxidizes the adjacent tyrosine (Y) 122 to the radical (Y122•) as the cluster is converted to the µ-oxo-Fe2III/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 2.5 Å Fe-Fe separation (dFe-Fe), which was interpreted to imply the presence of three single-atom bridges (O2?, HO?, and/or µ-1,1-carboxylates). This short dFe-Fe has been irreconcilable with computational and synthetic models, which all have dFe-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, > 2.5 times the concentration realized in the previous EXAFS study. The measured dFe-Fe of 2.78 Å is fully consistent with computational models containing a (µ-oxo)2-Fe2III/IV core. The correction of dFe–Fe brings the experimental data and computational models into full conformity and thus 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.

2014-01-01

136

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. 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

137

Engineering Hyperthermophilic Archaeon Pyrococcus furiosus to Overproduce Its Cytoplasmic [NiFe]-Hydrogenase*  

PubMed Central

The cytoplasmic hydrogenase (SHI) of the hyperthermophilic archaeon Pyrococcus furiosus is an NADP(H)-dependent heterotetrameric enzyme that contains a nickel-iron catalytic site, flavin, and six iron-sulfur clusters. It has potential utility in a range of bioenergy systems in vitro, but a major obstacle in its use is generating sufficient amounts. We have engineered P. furiosus to overproduce SHI utilizing a recently developed genetic system. In the overexpression (OE-SHI) strain, transcription of the four-gene SHI operon was under the control of a strong constitutive promoter, and a Strep-tag II was added to the N terminus of one subunit. OE-SHI and wild-type P. furiosus strains had similar rates of growth and H2 production on maltose. Strain OE-SHI had a 20-fold higher transcription of the polycistronic hydrogenase mRNA encoding SHI, and the specific activity of the cytoplasmic hydrogenase was ?10-fold higher when compared with the wild-type strain, although the expression levels of genes encoding processing and maturation of SHI were the same in both strains. Overexpressed SHI was purified by a single affinity chromatography step using the Strep-tag II, and it and the native form had comparable activities and physical properties. Based on protein yield per gram of cells (wet weight), the OE-SHI strain yields a 100-fold higher amount of hydrogenase when compared with the highest homologous [NiFe]-hydrogenase system previously reported (from Synechocystis). This new P. furiosus system will allow further engineering of SHI and provide hydrogenase for efficient in vitro biohydrogen production. PMID:22157005

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

2012-01-01

138

Hydrogen Formation and Its Regulation in Ruminococcus albus: Involvement of an Electron-Bifurcating [FeFe]-Hydrogenase, of a Non-Electron-Bifurcating [FeFe]-Hydrogenase, and of a Putative Hydrogen-Sensing [FeFe]-Hydrogenase.  

PubMed

Ruminococcus albus 7 has played a key role in the development of the concept of interspecies hydrogen transfer. The rumen bacterium ferments glucose to 1.3 acetate, 0.7 ethanol, 2 CO2, and 2.6 H2 when growing in batch culture and to 2 acetate, 2 CO2, and 4 H2 when growing in continuous culture in syntrophic association with H2-consuming microorganisms that keep the H2 partial pressure low. The organism uses NAD(+) and ferredoxin for glucose oxidation to acetyl coenzyme A (acetyl-CoA) and CO2, NADH for the reduction of acetyl-CoA to ethanol, and NADH and reduced ferredoxin for the reduction of protons to H2. Of all the enzymes involved, only the enzyme catalyzing the formation of H2 from NADH remained unknown. Here, we report that R. albus 7 grown in batch culture on glucose contained, besides a ferredoxin-dependent [FeFe]-hydrogenase (HydA2), a ferredoxin- and NAD-dependent electron-bifurcating [FeFe]-hydrogenase (HydABC) that couples the endergonic formation of H2 from NADH to the exergonic formation of H2 from reduced ferredoxin. Interestingly, hydA2 is adjacent to the hydS gene, which is predicted to encode an [FeFe]-hydrogenase with a C-terminal PAS domain. We showed that hydS and hydA2 are part of a larger transcriptional unit also harboring putative genes for a bifunctional acetaldehyde/ethanol dehydrogenase (Aad), serine/threonine protein kinase, serine/threonine protein phosphatase, and a redox-sensing transcriptional repressor. Since HydA2 and Aad are required only when R. albus grows at high H2 partial pressures, HydS could be a H2-sensing [FeFe]-hydrogenase involved in the regulation of their biosynthesis. PMID:25157086

Zheng, Yanning; Kahnt, Jörg; Kwon, In Hyuk; Mackie, Roderick I; Thauer, Rudolf K

2014-11-15

139

Regulation of the Periplasmic [Fe] Hydrogenase by Ferrous Iron in Desulfovibrio vulgaris (Hildenborough)  

PubMed Central

The periplasmic [Fe] hydrogenase from the sulfate-reducing bacterium Desulfovibrio vulgaris (Hildenborough) DSM 8303 was found to be regulated by ferrous iron availability. During growth with 5 ppm of iron, the enzyme derepressed and the specific activity increased approximately fourfold, whereas the presence of 100 ppm of ferrous iron repressed the enzyme. The repression-derepression phenomenon with ferrous iron was found to be operative when the cells were cultured under either hydrogen or nitrogen gas. This is the first reported case showing that the hydrogenase enzyme is regulated by iron, and the implications of this finding relative to the corrosion industry are discussed. PMID:16348873

Bryant, Richard D.; Van Ommen Kloeke, Fintan; Laishley, Edward J.

1993-01-01

140

Effects of deletion of genes encoding Fe-only hydrogenase of Desulfovibrio vulgaris Hildenborough on hydrogen and lactate metabolism.  

PubMed

The physiological properties of a hyd mutant of Desulfovibrio vulgaris Hildenborough, lacking periplasmic Fe-only hydrogenase, have been compared with those of the wild-type strain. Fe-only hydrogenase is the main hydrogenase of D. vulgaris Hildenborough, which also has periplasmic NiFe- and NiFeSe-hydrogenases. The hyd mutant grew less well than the wild-type strain in media with sulfate as the electron acceptor and H(2) as the sole electron donor, especially at a high sulfate concentration. Although the hyd mutation had little effect on growth with lactate as the electron donor for sulfate reduction when H(2) was also present, growth in lactate- and sulfate-containing media lacking H(2) was less efficient. The hyd mutant produced, transiently, significant amounts of H(2) under these conditions, which were eventually all used for sulfate reduction. The results do not confirm the essential role proposed elsewhere for Fe-only hydrogenase as a hydrogen-producing enzyme in lactate metabolism (W. A. M. van den Berg, W. M. A. M. van Dongen, and C. Veeger, J. Bacteriol. 173:3688-3694, 1991). This role is more likely played by a membrane-bound, cytoplasmic Ech-hydrogenase homolog, which is indicated by the D. vulgaris genome sequence. The physiological role of periplasmic Fe-only hydrogenase is hydrogen uptake, both when hydrogen is and when lactate is the electron donor for sulfate reduction. PMID:11790737

Pohorelic, Brant K J; Voordouw, Johanna K; Lojou, Elisabeth; Dolla, Alain; Harder, Jens; Voordouw, Gerrit

2002-02-01

141

Immunolocalization of the uptake hydrogenase in the marine cyanobacterium Lyngbya majuscula CCAP 1446/4 and two Nostoc strains.  

PubMed

In N(2)-fixing cyanobacteria, the reduction of N(2) to NH(3) is coupled with the production of molecular hydrogen, which is rapidly consumed by an uptake hydrogenase, an enzyme that is present in almost all diazotrophic cyanobacteria. The cellular and subcellular localization of the cyanobacterial uptake hydrogenase remains uncertain, and it is definitely strain dependent. Previous studies focused mainly on heterocystous cyanobacteria and used heterologous antisera. The present work represents the first effort to establish the subcellular localization of the uptake hydrogenase in a N(2)-fixing filamentous nonheterocystous cyanobacterium, Lyngbya majuscula CCAP 1446/4, using the first antiserum produced against a cyanobacterial uptake hydrogenase. The data obtained revealed higher specific labelling associated with the thylakoid membranes of L. majuscula, reinforcing the idea that the cyanobacterial uptake hydrogenase is indeed a membrane-bound protein. For comparative purposes, the localization of the uptake hydrogenase was also investigated in two distinct heterocystous cyanobacterial strains, and while in Nostoc sp. PCC 7120 the labelling was only observed in the heterocysts, in Nostoc punctiforme, the presence of uptake hydrogenase antigens was detected in both the vegetative cells and heterocysts, corresponding most probably to an inactive and an active form of the enzyme. PMID:19222582

Seabra, Rui; Santos, Arlete; Pereira, Sara; Moradas-Ferreira, Pedro; Tamagnini, Paula

2009-03-01

142

Function of the chloroplast hydrogenase in the microalga Chlamydomonas: the role of hydrogenase and state transitions during photosynthetic activation in anaerobiosis.  

PubMed

Like a majority of photosynthetic microorganisms, the green unicellular alga Chlamydomonas reinhardtii may encounter O2 deprived conditions on a regular basis. In response to anaerobiosis or in a respiration defective context, the photosynthetic electron transport chain of Chlamydomonas is remodeled by a state transition process to a conformation that favours the photoproduction of ATP at the expense of reductant synthesis. In some unicellular green algae including Chlamydomonas, anoxia also triggers the induction of a chloroplast-located, oxygen sensitive hydrogenase, which accepts electrons from reduced ferredoxin to convert protons into molecular hydrogen. Although microalgal hydrogen evolution has received much interest for its biotechnological potential, its physiological role remains unclear. By using specific Chlamydomonas mutants, we demonstrate that the state transition ability and the hydrogenase function are both critical for induction of photosynthesis in anoxia. These two processes are thus important for survival of the cells when they are transiently placed in an anaerobic environment. PMID:23717558

Ghysels, Bart; Godaux, Damien; Matagne, René F; Cardol, Pierre; Franck, Fabrice

2013-01-01

143

Function of the Chloroplast Hydrogenase in the Microalga Chlamydomonas: The Role of Hydrogenase and State Transitions during Photosynthetic Activation in Anaerobiosis  

PubMed Central

Like a majority of photosynthetic microorganisms, the green unicellular alga Chlamydomonas reinhardtii may encounter O2 deprived conditions on a regular basis. In response to anaerobiosis or in a respiration defective context, the photosynthetic electron transport chain of Chlamydomonas is remodeled by a state transition process to a conformation that favours the photoproduction of ATP at the expense of reductant synthesis. In some unicellular green algae including Chlamydomonas, anoxia also triggers the induction of a chloroplast-located, oxygen sensitive hydrogenase, which accepts electrons from reduced ferredoxin to convert protons into molecular hydrogen. Although microalgal hydrogen evolution has received much interest for its biotechnological potential, its physiological role remains unclear. By using specific Chlamydomonas mutants, we demonstrate that the state transition ability and the hydrogenase function are both critical for induction of photosynthesis in anoxia. These two processes are thus important for survival of the cells when they are transiently placed in an anaerobic environment. PMID:23717558

Ghysels, Bart; Godaux, Damien; Matagne, Rene F.; Cardol, Pierre; Franck, Fabrice

2013-01-01

144

Mechanistic Modeling of Sulfur-Deprived Photosynthesis and Hydrogen Production in  

E-print Network

Mechanistic Modeling of Sulfur-Deprived Photosynthesis and Hydrogen Production in Suspensions of Chlamydomonas Reinhardtii C. R. Williams,1 M.A. Bees2 1 British Antarctic Survey, Natural Environment Research hydrogen gas via iron- hydrogenase is well known. However, the oxygen-sensitive hydrogenase is closely

Bees, Martin

145

A Reversible Electron-Bifurcating Ferredoxin- and NAD-Dependent [FeFe]-Hydrogenase (HydABC) in Moorella thermoacetica  

PubMed Central

Moorella thermoacetica was long the only model organism used to study the biochemistry of acetogenesis from CO2. Depending on the growth substrate, this Gram-positive bacterium can either form H2 or consume it. Despite the importance of H2 in its metabolism, a hydrogenase from the organism has not yet been characterized. We report here the purification and properties of an electron-bifurcating [FeFe]-hydrogenase from M. thermoacetica and show that the cytoplasmic enzyme efficiently catalyzes both H2 formation and H2 uptake. The purified heterotrimeric iron-sulfur flavoprotein (HydABC) catalyzed the coupled reduction of ferredoxin (Fd) and NAD+ with H2 at 55°C at pH 7.5 at a specific rate of about 100 ?mol min?1 mg protein?1 and the reverse reaction, the coupled reduction of protons to H2 with reduced ferredoxin and NADH, at a specific rate of about 10 ?mol min?1 mg protein?1 in the stoichiometry Fdox + NAD+ + 2H2 ? Fdred2? + NADH + 3H+. When ferredoxin from Clostridium pasteurianum, NAD+, and the enzyme were incubated at pH 7.0 under 100% H2 in the gas phase (E0? = ?414 mV), more than 95% of the ferredoxin (E0? = ?400 mV) was reduced, which indicated that ferredoxin reduction with H2 is driven by the exergonic reduction of NAD+ (E0? = ?320 mV) with H2. In the absence of NAD+, ferredoxin was not reduced. We identified the genes encoding HydABC within the transcriptional unit hydCBAX and mapped the transcription start site. PMID:23316038

Wang, Shuning; Huang, Haiyan; Kahnt, Jorg

2013-01-01

146

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

147

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

2014-06-01

148

Regulation and genetic organization of hydrogenase: Final progress report for the period June 1, 1985--July 31, 1988  

SciTech Connect

Hydrogenase is an enzyme which plays an important role in the anaerobic metabolism of many bacteria. The objectives of the research were to elucidate the regulation and genetic organization of hydrogenase in microorganisms. A mutation in the E. coli hydE gene leads to loss of all hydrogenase activities and isoenzymes as well as all formate-related activities. A 0.9 kb DNA fragment has been cloned from an E. coli genomic DNA library which restored all hydrogenase and formate activities to a hydE mutant strain. This gene coded for a polypeptide of subunit mw 36 kDa which is required for hydrogenase synthesis. It is involved in incorporation of nickel into hydrogenase. A mutation in the E coli hupB gene leads to the loss of the uptake of H/sub 2/ by dyes and the ability to grow on fumarate plus H/sub 2/, but expresses normal levels of hydrogenase when assayed by deuterium exchange. This mutation also leads to loss of all formate-related activities. The mutation mapped near minute 17 and a single mutation was responsible for loss of both activities. A 1.4 kb DNA fragment was isolated which restored the hydrogen uptake activities and coded for a polypeptide of subunit mw 30 kDa. Dna fragments have been isolated from Chromatium vinosum and Proteus vulgaris which restored hydrogenase activities to E. coli strains with mutations in the hydA or hydB regulatory genes and which lack all hydrogenase activities. 6 refs., 12 figs.

Krasna, A.I.

1988-10-01

149

Disclosure of key stereoelectronic factors for efficient H2 binding and cleavage in the active site of [NiFe]-hydrogenases.  

PubMed

A comparative analysis of a series of DFT models of [NiFe]-hydrogenases, ranging from minimal NiFe clusters to very large systems including both the first and second coordination sphere of the bimetallic cofactor, was carried out with the aim of unraveling which stereoelectronic properties of the active site of [NiFe]-hydrogenases are crucial for efficient H2 binding and cleavage. H2 binding to the Ni-SIa redox state is energetically favored (by 4.0 kcal mol(-1)) only when H2 binds to Ni, the NiFe metal cluster is in a low spin state, and the Ni cysteine ligands have a peculiar seesaw coordination geometry, which in the enzyme is stabilized by the protein environment. The influence of the Ni coordination geometry on the H2 binding affinity was then quantitatively evaluated and rationalized analyzing frontier molecular orbitals and populations. Several plausible reaction pathways leading to H2 cleavage were also studied. It turned out that a two-step pathway, where H2 cleavage takes place on the Ni-SIa redox state of the enzyme, is characterized by very low reaction barriers and favorable reaction energies. More importantly, the seesaw coordination geometry of Ni was found to be a key feature for facile H2 cleavage. The discovery of the crucial influence of the Ni coordination geometry on H2 binding and activation in the active site of [NiFe]-hydrogenases could be exploited in the design of novel biomimetic synthetic catalysts. PMID:24392667

Bruschi, Maurizio; Tiberti, Matteo; Guerra, Alessandro; De Gioia, Luca

2014-02-01

150

Oriented immobilization of a membrane-bound hydrogenase onto an electrode for direct electron transfer.  

PubMed

The interaction of redox enzymes with electrodes is of great interest for studying the catalytic mechanisms of redox enzymes and for bioelectronic applications. Efficient electron transport between the biocatalysts and the electrodes has achieved more success with soluble enzymes than with membrane enzymes because of the higher structural complexity and instability of the latter proteins. In this work, we report a strategy for immobilizing a membrane-bound enzyme onto gold electrodes with a controlled orientation in its fully active conformation. The immobilized redox enzyme is the Ni-Fe-Se hydrogenase from Desulfovibrio vulgaris Hildenborough, which catalyzes H(2)-oxidation reversibly and is associated with the cytoplasmic membrane by a lipidic tail. Gold surfaces modified with this enzyme and phospholipids have been studied by atomic force microscopy (AFM) and electrochemical methods. The combined study indicates that by a two-step immobilization procedure the hydrogenase can be inserted via its lipidic tail onto a phospholipidic bilayer formed over the gold surface, allowing only mediated electron transfer between the enzyme and electrode. However, a one-step immobilization procedure favors the formation of a hydrogenase monolayer over the gold surface with its lipidic tail inserted into a phospholipid bilayer formed on top of the hydrogenase molecules. This latter method has allowed for the first time efficient electron transfer between a membrane-bound enzyme in its native conformation and an electrode. PMID:21491850

Gutiérrez-Sánchez, Cristina; Olea, David; Marques, Marta; Fernández, Victor M; Pereira, Inês A C; Vélez, Marisela; De Lacey, Antonio L

2011-05-17

151

A redox hydrogel protects hydrogenase from high-potential deactivation and oxygen damage  

NASA Astrophysics Data System (ADS)

Hydrogenases are nature's efficient catalysts for both the generation of energy via oxidation of molecular hydrogen and the production of hydrogen via the reduction of protons. However, their O2 sensitivity and deactivation at high potential limit their applications in practical devices, such as fuel cells. Here, we show that the integration of an O2-sensitive hydrogenase into a specifically designed viologen-based redox polymer protects the enzyme from O2 damage and high-potential deactivation. Electron transfer between the polymer-bound viologen moieties controls the potential applied to the active site of the hydrogenase and thus insulates the enzyme from excessive oxidative stress. Under catalytic turnover, electrons provided from the hydrogen oxidation reaction induce viologen-catalysed O2 reduction at the polymer surface, thus providing self-activated protection from O2. The advantages of this tandem protection are demonstrated using a single-compartment biofuel cell based on an O2-sensitive hydrogenase and H2/O2 mixed feed under anode-limiting conditions.

Plumeré, Nicolas; Rüdiger, Olaf; Oughli, Alaa Alsheikh; Williams, Rhodri; Vivekananthan, Jeevanthi; Pöller, Sascha; Schuhmann, Wolfgang; Lubitz, Wolfgang

2014-09-01

152

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

153

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

E-print Network

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, ...

Yacoby, Iftach

154

[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

155

Two different hydrogenase enzymes from sulphate-reducing bacteria are responsible for the bioreductive mechanism of platinum into nanoparticles  

Microsoft Academic Search

A mixed consortium of sulphate-reducing bacteria was used to investigate the enzymatic mechanism for the total bioreduction of platinum (IV) into platinum (0) nanoparticles. It was established that two different hydrogenase enzymes were involved. First the platinum (IV) was reduced to platinum (II) by a two-electron bioreduction using an oxygen-sensitive novel cytoplasmic hydrogenase. Second the platinum (II) ion was reduced

T. L. Riddin; Y. Govender; M. Gericke; C. G. Whiteley

2009-01-01

156

Hydrogen yield from a hydrogenase in Frankia R43 at different levels of the carbon source propionate.  

PubMed

Fermentative hydrogen yield was investigated in the Frankia strain R43, which was grown in different amounts of the carbon source propionate. In relation to hydrogen yield, the hydrogenase enzyme was characterized by use of Western blot. A bioreactor study revealed a 10-fold increase in growth within 50 h. The study showed that there is an active anaerobic hydrogen production in Frankia R43 and that this hydrogenase is immunologically related to the subunit HoxU of Ralstonia eutropha. PMID:21276650

Chatchai, Kosawang; Lasanthi, Kudahettige Rasika; Lars, Resman; Anita, Sellstedt

2012-03-01

157

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

158

Flow-FISH analysis and isolation of clostridial strains in an anaerobic semi-solid bio-hydrogen producing system by hydrogenase gene target  

Microsoft Academic Search

By using hydrogenase gene-targeted polymerase chain reaction (PCR) and reverse transcriptase PCR (RT-PCR), the predominant\\u000a clostridial hydrogenase that may have contributed to biohydrogen production in an anaerobic semi-solid fermentation system\\u000a has been monitored. The results revealed that a Clostridium pasteurianum-like hydrogenase gene sequence can be detected by both PCR and RT-PCR and suggested that the bacterial strain possessing\\u000a this specific

Chang Jui Jen; Chia-Hung Chou; Ping-Chi Hsu; Sian-Jhong Yu; Wei-En Chen; Jiunn-Jyi Lay; Chieh-Chen Huang; Fu-Shyan Wen

2007-01-01

159

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

160

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

161

Survey of the Distribution of Different Types of Nitrogenases and Hydrogenases in Heterocyst-Forming Cyanobactera  

Microsoft Academic Search

As a first step toward developing the methodology for screening large numbers of heterocyst-forming freshwater cyanobacteria\\u000a strains for the presence of various types of nitrogenases and hydrogenases, we surveyed the distribution of these genes and\\u000a their activities in 14 strains from culture collections. The nitrogenase genes include nif1 encoding a Mo-type nitrogenase expressed in heterocysts, nif2 expressed in vegetative cells

Hajime Masukawa; Xiaohui Zhang; Emi Yamazaki; Syunsuke Iwata; Kensuke Nakamura; Mari Mochimaru; Kazuhito Inoue; Hidehiro Sakurai

2009-01-01

162

RESEARCH ARTICLE The Hyb Hydrogenase Permits Hydrogen-Dependent Respiratory Growth of Salmonella enterica Serovar Typhimurium  

E-print Network

ABSTRACT Salmonella enterica serovar Typhimurium contains three distinct respiratory hydrogenases, all of which contribute to virulence. Addition of H2 significantly enhanced the growth rate and yield of S. Typhimurium in an amino acid-containing medium; this occurred with three different terminal respiratory electron acceptors. Based on studies with site-specific doublehydrogenase mutant strains, most of this H2-dependent growth increase was attributed to the Hyb hydrogenase, rather than to the Hya or Hyd respiratory H2-oxidizing enzymes. The wild type strain with H2 had 4.0-fold greater uptake of 14C-labeled amino acids over a period of minutes than did cells incubated without H2. The double-uptake hydrogenase mutant containing only the Hyb hydrogenase transported amino acids H2 dependently like the wild type. The Hyb-only-containing strain produced a membrane potential comparable to that of the wild type. The H2-stimulated amino acid uptake of the wild type and the Hyb-only strain was inhibited by the protonophore carbonyl cyanide m-chlorophenylhydrazone but was less affected by the ATP synthase inhibitor sodium orthovanadate. In the wild type, proteins TonB and ExbD, which are known to couple proton motive force (PMF) to transport processes, were induced by H2 exposure, as were the genes corresponding to these periplasmic PMF-coupling factors. However, studies on tonB and exbD single mutant strains could not confirm a major role for these proteins in amino acid transport. The results link H2 oxidation via the Hyb enzyme to growth, amino acid transport, and expression of periplasmic proteins that facilitate PMF-mediated transport across the outer membrane. IMPORTANCE Complex carbohydrates consumed by animals are fermented by intestinal microflora, and this leads to molecular

Reena Lamichhane-khadka; Andrea Kwiatkowski; Robert J. Maier

163

Anionic modulation of the catalytic activity of hydrogenase from Chlamydomonas reinhardtii  

SciTech Connect

Hydrogen production by cell-free extracts of Chlamydomonas reinhardtii is stimulated by anions when methyl viologen, reduced by dithionite, is used as the electron donor to hydrogenase. The increasing effectiveness of various anions closely follows their position in the Hofmeister chaotropic sequence. The most stimulatory anion tested, I/sup -/, gives a six-fold increase in activity at a concentration of 0.5 N. The K/sub m/ of the enzyme for methyl viologen is not affected by anions, while the V is greatly increased. H/sub 2/ oxidation coupled to methyl viologen reduction is also greatly stimulated by anions. However, when reduced ferredoxin is used as the electron donor to hydrogenase, there is a very strong inhibition of H/sub 2/ production by salts. In this case, the V of the enzyme is unaffected, but there is a large increase in the K/sub m/ of the enzyme for ferredoxin. The most inhibitory salt tested, KI, decreases hydrogenase activity by 93% at a concentration of 0.2 N.

Roessler, P.; Lien, S.

1982-01-01

164

Hydrogen evolution and hydrogenase activity in synchronous culture of Chlamydomonas reinhardii in connection with anaerobic digradation of starch  

SciTech Connect

The course of anaerobic activation of hydrogenase, H/sub 2/ evolution and anaerobic degradation of starch were compared in cells at the start, middle, and end of the light period (designated 0-, 6-, and 14-h cells, respectively) in synchronous culture of Chlamydomonas reinhardii (14 h of light followed by 10 h of darkness). In 0- and 14-h cells, activation of hydrogenase began after 10-12 min of anaerobiosis both in the dark and under light. In 6-h cells, hydrogenase was activated only under light after 30 min of anaerobiosis. In the event that these cells were preliminarily put in the dark with preservation of aerobic conditions, then activation of hydrogenase began after 10-12 min of anaerobiosis both under light and in the dark. In all cases, anaerobic degradation of starch in the dark coincided with such degradation under light. Its nature in 6-h cells did not change after dark aerobic incubation. In 0- and 6-h cells with low content of starch, its degradation was curtailed after 3 and 1 h, respectively. Curtailment of H/sub 2/ evolution and decrease of hydrogenase activity set in parallel with this in the dark, but not under light. The data do not enable us to establish whether activation of hydrogenase depends upon degradation of starch. However, H/sub 2/ evolution and maintenance of hydrogenase activity (at least in the dark) are determined by such degradation. Characteristics of H/sub 2/ metabolism in cells taken at the stage of 6 h are not associated with metabolism of starch. (Refs. 10).

Yanyushin, M.F.

1982-02-01

165

Spectroscopic Insights into the Oxygen-tolerant Membrane-associated [NiFe] Hydrogenase of Ralstonia eutropha H16*  

PubMed Central

This study provides the first spectroscopic characterization of the membrane-bound oxygen-tolerant [NiFe] hydrogenase (MBH) from Ralstonia eutropha H16 in its natural environment, the cytoplasmic membrane. The H2-converting MBH is composed of a large subunit, harboring the [NiFe] active site, and a small subunit, capable in coordinating one [3Fe4S] and two [4Fe4S] clusters. The hydrogenase dimer is electronically connected to a membrane-integral cytochrome b. EPR and Fourier transform infrared spectroscopy revealed a strong similarity of the MBH active site with known [NiFe] centers from strictly anaerobic hydrogenases. Most redox states characteristic for anaerobic [NiFe] hydrogenases were identified except for one remarkable difference. The formation of the oxygen-inhibited Niu-A state was never observed. Furthermore, EPR data showed the presence of an additional paramagnetic center at high redox potential (+290 mV), which couples magnetically to the [3Fe4S] center and indicates a structural and/or redox modification at or near the proximal [4Fe4S] cluster. Additionally, significant differences regarding the magnetic coupling between the Nia-C state and [4Fe4S] clusters were observed in the reduced form of the MBH. The spectroscopic properties are discussed with regard to the unusual oxygen tolerance of this hydrogenase and in comparison with those of the solubilized, dimeric form of the MBH. PMID:19304663

Saggu, Miguel; Zebger, Ingo; Ludwig, Marcus; Lenz, Oliver; Friedrich, Barbel; Hildebrandt, Peter; Lendzian, Friedhelm

2009-01-01

166

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. PMID:9361423

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

1997-01-01

167

Naphthalene adsorptions on graphene using Cr/Cr2/Fe/Fe2 linkages: Stability and spin perspectives from first-principles calculations  

NASA Astrophysics Data System (ADS)

We present a first-principles study of naphthalene adsorption on graphene via coordination bonds with Cr/Cr2/Fe/Fe2. The obtained structures possess great binding stability, and the geometry alignment of C10H8 is distorted. Especially, the use of Cr/Fe dimer further enhances the binding stability of C10H8 on graphene. From binding energy analysis, the adsorption of C10H8 on metal-graphene is observed to be more favorable than the adsorption of metal-C10H8 on graphene. When empirical dispersion corrections are introduced, the binding energy is improved by 0.78-1.40 eV. Interestingly, various degrees of magnetism are observed with respect to the metal identity, atom/dimer utilization, and bonding interactions.

Bui, Viet Q.; Le, Hung M.

2014-10-01

168

Determination of Hydrogenase in Free-living Cultures of Rhizobium japonicum and Energy Efficiency of Soybean Nodules 1  

PubMed Central

A sensitive tritium exchange assay was applied to the Rhizobium system for measuring the expression of uptake hydrogenase in free-living cultures of Rhizobium japonicum. Hydrogenase was detected about 45 hours after inoculation of cultures maintained under microaerophilic conditions (about 0.1% O2). The tritium exchange assay was used to screen a variety of different strains of R. japonicum (including major production strains) with the findings that about 30% of the strains expressed hydrogenase activity with identical results being observed using an alternative assay based on uptake of H2. The relative efficiency of intact soybean nodules inoculated with 10 different rhizobial strains gave results identical to those obtained using free-living cultures. The tritium exchange assay provides an easy, quick, and accurate assessment of H2 uptake efficiency of intact nodules. PMID:16660568

Lim, Soo T.

1978-01-01

169

Penta-carbonyl-1?2 C,2?3 C-(ferrocenyl-diphenyl-phosphine-1?P)[?-2-(4-methyl-phen-yl)-2-aza-propane-1,3-dithiol-ato-1:2?4 S,S?:S,S?]diiron(I)(Fe--Fe)  

PubMed Central

The title compound, [Fe2(C9H11NS2){Fe(C5H5)(C17H14P)}(CO)5], was prepared as an aza­dithiol­ato–iron model for the iron-only hydrogenase active site. The Fe2S2 unit exhibits a butterfly conformation and the ferrocenyldiphenyl­phosphine ligand is trans to the Fe—Fe bond. The Fe—Fe distance of 2.5160?(8)?Å is longer than found in related model structures. Intra­molecular C—H?S and inter­molecular C—H?O hydrogen bonds are observed. PMID:21580868

Tang, Yan-Feng; Zhu, Jin-Li

2008-01-01

170

Photocatalytic Hydrogen Production using Polymeric Carbon Nitride with a Hydrogenase and a Bioinspired Synthetic Ni Catalyst  

E-print Network

1 Photocatalysis DOI: 10.1002/anie.201 Photocatalytic Hydrogen Production using Polymeric Carbon Nitride with a Hydrogenase and a Bio-inspired Synthetic Ni Catalyst** Christine A. Caputo,a Manuela A. Gross,a Vincent W. Lau,b,c Christine Cavazza... -inspired synthetic catalysts containing non-noble metal centers have been developed by DuBois and co-workers.[7] These nickel complexes are considered among the best synthetic H2 evolution catalysts. They possess a bis(diphosphine) ligand core bearing pendant amino...

Caputo, Christine A.; Gross, Manuela A.; Lau, Vincent W.; Cavazza, Christine; Lotsch, Bettina V.; Reisner, Erwin

2014-09-09

171

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

172

Photoinduced hydrogen production by direct electron transfer from photosystem I cross-linked with cytochrome c3 to [NiFe]-hydrogenase.  

PubMed

The photosynthetic reaction center is an efficient molecular device for the conversion of light energy to chemical energy. In a previous study, we synthesized the hydrogenase/photosystem I (PSI) complex, in which Ralstonia hydrogenase was linked to the cytoplasmic side of Synechocystis PSI, to modify PSI so that it photoproduced molecular hydrogen (H2). In that study, hydrogenase was fused with a PSI subunit, PsaE, and the resulting hydrogenase-PsaE fusion protein was self-assembled with PsaE-free PSI to give the hydrogenase/PSI complex. Although the hydrogenase/PSI complex served as a direct light-to-H2 conversion system in vitro, the activity was totally suppressed by adding physiological PSI partners, ferredoxin (Fd) and ferredoxin-NADP+-reductase (FNR). In the present study, to establish an H2 photoproduction system in which the activity is not interrupted by Fd and FNR, position 40 of PsaE from Synechocystis sp. PCC6803, corresponding to the Fd-binding site on PSI, was selected and targeted for the cross-linking with cytochrome c3 (cytc3) from Desulfovibrio vulgaris. The covalent adduct of cytc3 and PsaE was stoichiometrically assembled with PsaE-free PSI to form the cytc3/PSI complex. The NADPH production by the cytc3/PSI complex coupled with Fd and FNR decreased to approximately 20% of the original activity, whereas the H2 production by the cytc3/PSI complex coupled with hydrogenase from Desulfovibrio vulgaris was enhanced 7-fold. Consequently, in the simultaneous presence of hydrogenase, Fd, and FNR, the light-driven H2 production by the hydrogenase/cytc3/PSI complex was observed (0.30 pmol Hz/mg chlorophyll/h). These results suggest that the cytc3/PSI complex may produce H2 in vivo. PMID:16836469

Ihara, Masaki; Nakamoto, Hitoshi; Kamachi, Toshiaki; Okura, Ichiro; Maeda, Mizuo

2006-01-01

173

Rates of intra- and intermolecular electron transfers in hydrogenase deduced from steady-state activity measurements.  

PubMed

Electrons are transferred over long distances along chains of FeS clusters in hydrogenases, mitochondrial complexes, and many other respiratory enzymes. It is usually presumed that electron transfer is fast in these systems, despite the fact that there has been no direct measurement of rates of FeS-to-FeS electron transfer in any respiratory enzyme. In this context, we propose and apply to NiFe hydrogenase an original strategy that consists of quantitatively interpreting the variations of steady-state activity that result from changing the nature of the FeS clusters which connect the active site to the redox partner, and/or the nature of the redox partner. Rates of intra- and intermolecular electron transfer are deduced from such large data sets. The mutation-induced variations of electron transfer rates cannot be explained by changes in intercenter distances and reduction potentials. This establishes that FeS-to-FeS rate constants are extremely sensitive to the nature and coordination of the centers. PMID:21615141

Dementin, Sébastien; Burlat, Bénédicte; Fourmond, Vincent; Leroux, Fanny; Liebgott, Pierre-Pol; Abou Hamdan, Abbas; Léger, Christophe; Rousset, Marc; Guigliarelli, Bruno; Bertrand, Patrick

2011-07-01

174

Spectroelectrochemical characterization of the [NiFe] hydrogenase of Desulfovibrio vulgaris Miyazaki F.  

PubMed

The active site in the [NiFe] hydrogenase of Desulfovibrio vulgaris Miyazaki F has been investigated by Fourier transform infrared (FTIR) spectroscopy. Analysis of the spectra allowed the three diatomic inorganic ligands to Fe in this enzyme to be identified as one CO molecule and two CN(-) molecules. Furthermore, pH-dependent redox titrations were performed to determine the midpoint potentials as well as the pK value of the respective reactions and revealed that each single-electron redox transition is accompanied by a single-proton transfer step. The comparison of these spectra with those published for other [NiFe] hydrogenases shows that the electronic structure of the active sites of these enzymes and their redox processes are essentially the same. Nevertheless, differences with respect to the frequency of the CO band and the pH dependence of the Ni-R states have been observed. Finally, the frequency shifts of the bands in the IR spectra were interpreted with respect to the electronic configuration of the redox intermediates in the catalytic cycle. PMID:16893172

Fichtner, Caroline; Laurich, Christoph; Bothe, Eberhard; Lubitz, Wolfgang

2006-08-15

175

Interaction of cellular hydrogenase, cytochrome c3, and desulfoviridin in Desulfovibrio vulgaris Miyazaki with their antibodies.  

PubMed

Anti-sera for hydrogenase, cytochrome c3, and desulfoviridin (abbreviated as anti-hyd, anti-c3, and anti-dvn, respectively) were raised in mice, and used to locate these antigens in cells of Desulfovibrio vulgaris Miyazaki. The activity of the intact cells to absorb H2 with methyl viologen or sulfite as an electron acceptor was cumulatively inhibited by treating the cells with anti-hyd and anti-c3 but unaffected by anti-dvn treatment. The activity of the intact cells to produce H2 from formate was also inhibited by anti-c3 treatment, but the inhibition by anti-hyd treatment was not significant. The fluorescent antibody technique applied to intact cells of D. vulgaris Miyazaki indicated that both hydrogenase and cytochrome c3 are localized on the surface of the cell. These results are not exactly in conformity with the hydrogen-cycling hypothesis for proton gradient formation in the energy metabolism in Desulfovibrio. The procedure described in the present paper provides a new technique to elucidate the roles of proteins by applying anti-sera to intact cells without destroying the cellular structure. PMID:2853157

Tamura, A; Kawate, T; Ogata, M; Yagi, T

1988-11-01

176

Fast and efficient molecular electrocatalysts for H2 production: Using hydrogenase enzymes as guides  

SciTech Connect

Hydrogen generation using solar energy will require the development of efficient electrocatalysts for proton reduction. This article discusses the important role that proton movement plays in hydrogenase enzymes and potentials devices for solar generation. Studies of hydrogenase enzymes provide many import design principles for the development of simpler molecular catalysts. These principles are illustrated with examples from the literature and from the authors’ laboratories. In particular, pendant bases incorporated in the second coordination sphere of catalytic molecules play a number of important roles that are crucial to efficient catalysis. These include acting as relays to move protons between the metal center and solution, promoting intra- and inter-molecular proton transfer reactions, coupling proton and electron transfer reactions, assisting heterolytic cleavage of hydrogen, and stabilizing critical reaction intermediates. The importance of controlling proton movement on the molecular scale underscores the importance of a similar degree of control in devices designed for the solar production of hydrogen or any fuel generation process involving multiple electrons and protons. 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.

Yang, Jenny Y.; Bullock, R. Morris; Rakowski DuBois, Mary; DuBois, Daniel L.

2011-01-15

177

Strategies for reliable and improved large-scale production of Pyrococcus furiosus with integrated purification of hydrogenase I.  

PubMed

The hyperthermophilic archaeon Pyrococcus furiosus is an interesting organism for research and application, especially owing to its unique NADPH-dependent hydrogenase I. However, mass production of P. furiosus through fermentation is susceptible to fault because of its sensitivity to oxygen, a short exponential and stationary phase and a rapid cell lysis in typical cultivation process. In this study, significant improvement for pilot plant scale production processes for P. furiosus biomass was made by investigations of the fermentation process with subsequent hydrogenase I enzyme purification. Scale-up in a 300-L stirred tank bioreactor was successfully achieved. A repeated-batch cultivation process with high reproducibility and productivity was realized. Furthermore, the enzyme hydrogenase I was purified, and its activity tested and verified. The improvements in this production process for the production of large amount of P. furiosus biomass and hydrogenase I have been achieved, especially by successfully implementing the following key measures and steps: unsterile cultivation setup, skipping typical intermediate preculture and inoculation steps, accelerating the cultivation process by defining an optimal state of the inoculation, optimal time point of biomass harvesting and finally by choosing a one-step purification procedure for enzyme recovery. PMID:24894374

Rieckenberg, Fabian; Götz, Katharina; Hilterhaus, Lutz; Liese, Andreas; Zeng, An-Ping

2014-12-01

178

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

179

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. PMID:23023750

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

2012-01-01

180

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. PMID:19801638

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

2009-01-01

181

Comparison of N(2) Fixation and Yields in Cajanus cajan between Hydrogenase-Positive and Hydrogenase-Negative Rhizobia by In Situ Acetylene Reduction Assays and Direct N Partitioning.  

PubMed

Pigeon peas [Cajanus cajan (L.) Millsp.] were grown in soil columns containing (15)N-enriched organic matter. Seasonal N(2) fixation activity was determined by periodically assaying plants for reduction of C(2)H(2). N(2) fixation rose sharply from the first assay period at 51 days after planting to a peak of activity between floral initiation and fruit set. N(2) fixation (acetylene reduction) activity dropped concomitantly with pod maturation but recovered after pod harvests. Analysis of (15)N content of plant shoots revealed that approximately 91 to 94% of plant N was derived from N(2) 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. H(2) was never detected, even in columns containing pigeon peas inoculated with hydrogenase-negative rhizobia. This was attributed to H(2) consumption by soil bacteria. Estimation of N(2) fixation by acetylene reduction activity was closest to the direct (15)N 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 (15)N 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. PMID:16663148

La Favre, J S; Focht, D D

1983-08-01

182

Photo-induced H2 production by [NiFe]-hydrogenase from T. roseopersicina covalently linked to a Ru(II) photosensitizer.  

PubMed

The potential of hydrogen as a clean renewable fuel source and the finite reserves of platinum metal to be utilized in hydrogen production catalysts have provided the motivation for the development of non-noble metal-based solutions for catalytic hydrogen production. There are a number of microorganisms that possess highly efficient hydrogen production catalysts termed hydrogenases that generate hydrogen under certain metabolic conditions. Although hydrogenases occur in photosynthetic microorganisms, the oxygen sensitivity of these enzymes represents a significant barrier in directly coupling hydrogen production to oxygenic photosynthesis. To overcome this barrier, there has been considerable interest in identifying or engineering oxygen tolerant hydrogenases or generating mimetic systems that do not rely on oxygen producing photocatalysts. In this work, we demonstrate photo-induced hydrogen production from a stable [NiFe]-hydrogenase coupled to a [Ru(2,2'-bipyridine)(2)(5-amino-1,10-phenanthroline)](2+) photocatalyst. When the Ru(II) complex is covalently attached to the hydrogenase, photocatalytic hydrogen production occurs more efficiently in the presence of a redox mediator than if the Ru(II) complex is simply present in solution. Furthermore, sustained hydrogen production occurs even in the presence of oxygen by presumably creating a local anoxic environment through the reduction of oxygen similar to what is proposed for oxygen tolerant hydrogenases. These results provide a strong proof of concept for engineering photocatalytic hydrogen production in the presence of oxygen using biohybrid mimetic systems. PMID:22119807

Zadvornyy, Oleg A; Lucon, Janice E; Gerlach, Robin; Zorin, Nikolay A; Douglas, Trevor; Elgren, Timothy E; Peters, John W

2012-01-01

183

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. PMID:24240187

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

2013-01-01

184

Photocatalytic Hydrogen Production using Polymeric Carbon Nitride with a Hydrogenase and a Bioinspired Synthetic Ni Catalyst.  

PubMed

Solar-light-driven H2 production in water with a [NiFeSe]-hydrogenase (H2 ase) and a bioinspired synthetic nickel catalyst (NiP) in combination with a heptazine carbon nitride polymer, melon (CNx ), is reported. The semibiological and purely synthetic systems show catalytic activity during solar light irradiation with turnover numbers (TONs) of more than 50?000?mol?H2 ?(mol?H2 ase)(-1) and approximately 155?mol?H2 ?(mol?NiP)(-1) in redox-mediator-free aqueous solution at pH?6 and 4.5, respectively. Both systems maintained a reduced photoactivity under UV-free solar light irradiation (?>420?nm). PMID:25205168

Caputo, Christine A; Gross, Manuela A; Lau, Vincent W; Cavazza, Christine; Lotsch, Bettina V; Reisner, Erwin

2014-10-20

185

Enhanced photocatalytic hydrogen production from an MCM-41-immobilized photosensitizer-[Fe-Fe] hydrogenase mimic dyad.  

PubMed

A covalently linked photosensitizer-catalytic center dyad Ps-Hy, consisting of two bis(2-phenylpyridine)(2,2'-bipyridine)iridium(iii) chromophores (Ps) and a diiron hydrogenase mimic (Hy) was constructed by using click reaction. Ps-Hy was incorporated into K(+)-exchanged molecular sieve MCM-41 to form a composite (Ps-Hy@MCM-41), which has been successfully applied to the photochemical production of hydrogen. The catalytic activity of Ps-Hy@MCM-41 is ?3-fold higher as compared with that of Ps-Hy in the absence of MCM-41. The incorporation of Ps-Hy into MCM-41 stabilizes the catalyst, and consequently, advances the photocatalysis. The present study provides a potential strategy for improving catalytic efficiency of artificial photosynthesis systems using mesoporous molecular sieves. PMID:25238441

Wang, Wen; Yu, Tianjun; Zeng, Yi; Chen, Jinping; Yang, Guoqiang; Li, Yi

2014-10-15

186

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. PMID:23649626

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

2013-01-01

187

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. PMID:24866391

2014-01-01

188

Mechanistic insight into the blocking of CO diffusion in [NiFe]-hydrogenase mutants through multiscale simulation  

PubMed Central

[NiFe]-hydrogenases are fascinating biological catalysts with potential application in biofuel cells. However, a severe problem in practical application is the strong sensitivity of hydrogenase to gaseous inhibitor molecules such as CO and O2. Recently, a number of successful protein engineering studies have been reported that aimed at lowering the access of diatomic inhibitors to the active site pocket, but the molecular mechanism conferring increased resistance remained unclear. Here we use a multiscale simulation approach combining molecular dynamics with a master equation formalism to explain the steady drop in CO diffusion rate observed for the mutants V74M L122A, V74M L122M, and V74M of Desulfovibrio fructosovorans [NiFe]-hydrogenase. We find that diffusion in these variants is controlled by two gates, one between residues 74 and 476 and the other between residues 74 and 122. The existence of two control points in different locations explains why the reduction in the experimental diffusion rate does not simply correlate with the width of the main gas channel. We also find that in the more effective mutation (V74M) CO molecules are still able to reach the active site through transitions that are gated by the microsecond dihedral motions of the side chain of R476 and the thermal fluctuations of the width of the gas channel defined by M74 and L122. Reflecting on the molecular information gained from simulation, we discuss future mutation experiments that could further lower the diffusion rates of small ligands inhibiting [NiFe]-hydrogenase. PMID:22493222

Wang, Po-hung; Blumberger, Jochen

2012-01-01

189

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

2014-05-21

190

A Binuclear Isocyanide Azadithiolatoiron Complex Relevant to the Active Site of Fe-Only Hydrogenases: Synthesis, Structure and Electrochemical Properties  

Microsoft Academic Search

An aromatic isocyanide-substituted diiron complex 5 has been synthesized as a mimic for the active site of Fe-only hydrogenases. Its structure has been fully characterized by X-ray crystallography. The 4-iodophenylisocyanide ligands in 5 are in the basal positions and are nearly parallel to each other, with ?-? stacking interactions. Four isomeric geome- tries of complex 5 have been optimized by

Jun Hou; Xiaojun Peng; Jifeng Liu; Yunling Gao; Xing Zhao; Shang Gao; Keli Han

2006-01-01

191

Salmonella Typhimurium Strain ATCC14028 Requires H2-Hydrogenases for Growth in the Gut, but Not at Systemic Sites  

PubMed Central

Salmonella enterica is a common cause of diarrhea. For eliciting disease, the pathogen has to colonize the gut lumen, a site colonized by the microbiota. This process/initial stage is incompletely understood. Recent work established that one particular strain, Salmonella enterica subspecies 1 serovar Typhimurium strain SL1344, employs the hyb H2-hydrogenase for consuming microbiota-derived H2 to support gut luminal pathogen growth: Protons from the H2-splitting reaction contribute to the proton gradient across the outer bacterial membrane which can be harvested for ATP production or for import of carbon sources. However, it remained unclear, if other Salmonella strains would use the same strategy. In particular, earlier work had left unanswered if strain ATCC14028 might use H2 for growth at systemic sites. To clarify the role of the hydrogenases, it seems important to establish if H2 is used at systemic sites or in the gut and if Salmonella strains may differ with respect to the host sites where they require H2 in vivo. In order to resolve this, we constructed a strain lacking all three H2-hydrogenases of ATCC14028 (14028hyd3) and performed competitive infection experiments. Upon intragastric inoculation, 14028hyd3 was present at 100-fold lower numbers than 14028WT in the stool and at systemic sites. In contrast, i.v. inoculation led to equivalent systemic loads of 14028hyd3 and the wild type strain. However, the pathogen population spreading to the gut lumen featured again up to 100-fold attenuation of 14028hyd3. Therefore, ATCC14028 requires H2-hydrogenases for growth in the gut lumen and not at systemic sites. This extends previous work on ATCC14028 and supports the notion that H2-utilization might be a general feature of S. Typhimurium gut colonization. PMID:25303479

Maier, Lisa; Barthel, Manja; Stecher, Barbel; Maier, Robert J.; Gunn, John S.; Hardt, Wolf-Dietrich

2014-01-01

192

Mechanistic insight into the blocking of CO diffusion in [NiFe]-hydrogenase mutants through multiscale simulation.  

PubMed

[NiFe]-hydrogenases are fascinating biological catalysts with potential application in biofuel cells. However, a severe problem in practical application is the strong sensitivity of hydrogenase to gaseous inhibitor molecules such as CO and O(2). Recently, a number of successful protein engineering studies have been reported that aimed at lowering the access of diatomic inhibitors to the active site pocket, but the molecular mechanism conferring increased resistance remained unclear. Here we use a multiscale simulation approach combining molecular dynamics with a master equation formalism to explain the steady drop in CO diffusion rate observed for the mutants V74M L122A, V74M L122M, and V74M of Desulfovibrio fructosovorans [NiFe]-hydrogenase. We find that diffusion in these variants is controlled by two gates, one between residues 74 and 476 and the other between residues 74 and 122. The existence of two control points in different locations explains why the reduction in the experimental diffusion rate does not simply correlate with the width of the main gas channel. We also find that in the more effective mutation (V74M) CO molecules are still able to reach the active site through transitions that are gated by the microsecond dihedral motions of the side chain of R476 and the thermal fluctuations of the width of the gas channel defined by M74 and L122. Reflecting on the molecular information gained from simulation, we discuss future mutation experiments that could further lower the diffusion rates of small ligands inhibiting [NiFe]-hydrogenase. PMID:22493222

Wang, Po-hung; Blumberger, Jochen

2012-04-24

193

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

194

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

195

Genetic Analysis of the Hox Hydrogenase in the Cyanobacterium Synechocystis sp. PCC 6803 Reveals Subunit Roles in Association, Assembly, Maturation, and Function*  

PubMed Central

Hydrogenases are metalloenzymes that catalyze 2H+ + 2e? ? H2. A multisubunit, bidirectional [NiFe]-hydrogenase has been identified and characterized in a number of bacteria, including cyanobacteria, where it is hypothesized to function as an electron valve, balancing reductant in the cell. In cyanobacteria, this Hox hydrogenase consists of five proteins in two functional moieties: a hydrogenase moiety (HoxYH) with homology to heterodimeric [NiFe]-hydrogenases and a diaphorase moiety (HoxEFU) with homology to NuoEFG of respiratory Complex I, linking NAD(P)H ? NAD(P)+ as a source/sink for electrons. Here, we present an extensive study of Hox hydrogenase in the cyanobacterium Synechocystis sp. PCC 6803. We identify the presence of HoxEFUYH, HoxFUYH, HoxEFU, HoxFU, and HoxYH subcomplexes as well as association of the immature, unprocessed large subunit (HoxH) with other Hox subunits and unidentified factors, providing a basis for understanding Hox maturation and assembly. The analysis of mutants containing individual and combined hox gene deletions in a common parental strain reveals apparent alterations in subunit abundance and highlights an essential role for HoxF and HoxU in complex/subcomplex association. In addition, analysis of individual and combined hox mutant phenotypes in a single strain background provides a clear view of the function of each subunit in hydrogenase activity and presents evidence that its physiological function is more complicated than previously reported, with no outward defects apparent in growth or photosynthesis under various growth conditions. PMID:23139416

Eckert, Carrie; Boehm, Marko; Carrieri, Damian; Yu, Jianping; Dubini, Alexandra; Nixon, Peter J.; Maness, Pin-Ching

2012-01-01

196

Initial cloning and sequencing of hydHG, an operon homologous to ntrBC and regulating the labile hydrogenase activity in Escherichia coli K-12.  

PubMed Central

To isolate genes from Escherichia coli which regulate the labile hydrogenase activity, a plasmid library was used to transform hydL mutants lacking the labile hydrogenase. A single type of gene, designated hydG, was isolated. This gene also partially restored the hydrogenase activity in hydF mutants (which are defective in all hydrogenase isoenzymes), although the low hydrogenase 1 and 2 levels were not induced. Therefore, hydG apparently regulates, specifically, the labile hydrogenase activity. Restoration of this latter activity in hydF mutants was accompanied by a proportional increase of the H2 uptake activity, suggesting a functional relationship. H2:fumarate oxidoreductase activity was not restored in complemented hydL mutants. These latter strains may therefore lack, in addition to the labile hydrogenase, a second component (provisionally designated component R), possibly an electron carrier coupling H2 oxidation to the anerobic respiratory chain. Sequence analysis showed an open reading frame of 1,314 base pairs for hydG. It was preceded by a ribosome-binding site but apparently lacked a promoter. Minicell experiments revealed a single polypeptide of approximately 50 kilodaltons. Comparison of the predicted amino acid sequence with a protein sequence data base revealed strong homology to NtrC from Klebsiella pneumoniae, a DNA-binding transcriptional activator. The 411 base pairs upstream from pHG40 contained a second open reading frame overlapping hydG by four bases. The deduced amino acid sequence showed considerable homology with the C-terminal part of NtrB. This sequence was therefore assumed to be part of a second gene, encoding the NtrB-like component, and was designated hydH. The labile hydrogenase activity in E. coli is apparently regulated by a multicomponent system analogous to the NtrB-NtrC system. This conclusion is in agreement with the results of Birkmann et al. (A. Birkmann, R. G. Sawers, and A. Böck, Mol. Gen. Genet. 210:535-542, 1987), who demonstrated ntrA dependence for the labile hydrogenase activity. Images PMID:2666400

Stoker, K; Reijnders, W N; Oltmann, L F; Stouthamer, A H

1989-01-01

197

HybF, a zinc-containing protein involved in NiFe hydrogenase maturation.  

PubMed

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 K(D) of 1.87 microM 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. PMID:15090500

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

2004-05-01

198

Comparison of the membrane-bound [NiFe] hydrogenases from R. eutropha H16 and D. vulgaris Miyazaki F in the oxidized ready state by pulsed EPR.  

PubMed

The geometric and electronic structures of the active sites in the oxidized Ni(r)-B state of the [NiFe] hydrogenases from Ralstonia eutropha H16 and Desulfovibrio vulgaris Miyazaki F were investigated in pulsed EPR and ENDOR experiments at two different microwave frequencies (X- and Q-band). Two hyperfine-couplings were clearly resolved in the frozen solution spectra arising from the beta-protons of the nickel-coordinating cysteine residues Cys549 and Cys586 from the Desulfovibrio vulgaris and Ralstonia eutropha hydrogenase, respectively. ESEEM spectroscopic experiments reveal the presence of a histidine in the second coordination sphere of the Ni. The spectroscopic data indicate that the electronic structures of the [NiFe] centers in both hydrogenases are identical in the Ni(r)-B state. However, additional spin couplings of the active site to further paramagnetic centers were identified for the Ralstonia eutropha hydrogenase. The respective couplings could be clearly resolved and simulated. The results from this study are discussed in view of the exceptional O(2)-tolerance of the Ralstonia hydrogenase. PMID:20165762

Saggu, Miguel; Teutloff, Christian; Ludwig, Marcus; Brecht, Marc; Pandelia, Maria-Eirini; Lenz, Oliver; Friedrich, Bärbel; Lubitz, Wolfgang; Hildebrandt, Peter; Lendzian, Friedhelm; Bittl, Robert

2010-03-01

199

Direct evidence of active-site reduction and photodriven catalysis in sensitized hydrogenase assemblies.  

PubMed

We report photocatalytic H(2) production by hydrogenase (H(2)ase)-quantum dot (QD) hybrid assemblies. Quenching of the CdTe exciton emission was observed, consistent with electron transfer from the quantum dot to H(2)ase. GC analysis showed light-driven H(2) production in the presence of a sacrificial electron donor with an efficiency of 4%, which is likely a lower limit for these hybrid systems. FTIR spectroscopy was employed for direct observation of active-site reduction in unprecedented detail for photodriven H(2)ase catalysis with sensitivity toward both H(2)ase and the sacrificial electron donor. Photosensitization with Ru(bpy)(3)(2+) showed distinct FTIR photoreduction properties, generating all of the states along the steady-state catalytic cycle with minimal H(2) production, indicating slow, sequential one-electron reduction steps. Comparing the H(2)ase activity and FTIR results for the two systems showed that QDs bind more efficiently for electron transfer and that 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. PMID:22716776

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

2012-07-11

200

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. PMID:23805134

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

2013-01-01

201

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

202

Molecular basis of [FeFe]-hydrogenase function: an insight into the complex interplay between protein and catalytic cofactor.  

PubMed

The precise electrochemical features of metal cofactors that convey the functions of redox enzymes are essentially determined by the specific interaction pattern between cofactor and enclosing protein environment. However, while biophysical techniques allow a detailed understanding of the features characterizing the cofactor itself, knowledge about the contribution of the protein part is much harder to obtain. [FeFe]-hydrogenases are an interesting class of enzymes that catalyze both, H2 oxidation and the reduction of protons to molecular hydrogen with significant efficiency. The active site of these proteins consists of an unusual prosthetic group (H-cluster) with six iron and six sulfur atoms. While H-cluster architecture and catalytic states during the different steps of H2 turnover have been thoroughly investigated during the last 20 years, possible functional contributions from the polypeptide framework were only assumed according to the level of conservancy and X-ray structure analyses. Due to the recent development of simpler and more efficient expression systems the role of single amino acids can now be experimentally investigated. This article summarizes, compares and categorizes the results of recent investigations based on site directed and random mutagenesis according to their informative value about structure function relationships in [FeFe]-hydrogenases. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems. PMID:23507618

Winkler, Martin; Esselborn, Julian; Happe, Thomas

2013-01-01

203

Disruption of the Operon Encoding Ehb Hydrogenase Limits AnabolicCO2 Assimilation in the Archaeon Methanococcus maripaludis  

SciTech Connect

Methanococcus maripaludis is a mesophilic archaeon thatreduces CO2 to methane with H2 or formate as an energy source. Itcontains two membrane-bound energy-conserving hydrogenases, Eha and Ehb.To determine therole of Ehb, a deletion in the ehb operon wasconstructed to yield the mutant, strain S40. Growth of S40 was severelyimpaired in minimal medium. Both acetate and yeast extract were necessaryto restore growth to nearly wild-type levels, suggesting that Ehb wasinvolved in multiple steps in carbon assimilation. However, nodifferences in the total hydrogenase specific activities were foundbetween the wild type and mutant in either cell extracts ormembrane-purified fractions. Methanogenesis by resting cells withpyruvate as the electron donor was also reduced by 30 percent in S40,suggesting a defect in pyruvate oxidation. CO dehydrogenase/acetylcoenzyme A (CoA) synthase and pyruvate oxidoreductase had higher specificactivities in the mutant, and genes encoding these enzymes, as well asAMP-forming acetyl-CoA synthetase, were expressed at increased levels.These observations support a role for Ehb in anabolic CO2 assimilation inmethanococci.

Porat, Iris; Kim, Wonduck; Hendrickson, Erik L.; Xia, Qiangwei; Zhang, Yi; Wang, Tiansong; Taub, Fred; Moore, Brian C.; Anderson, IainJ.; Hackett, Murray; Leigh, John A.; Whitman, William B.

2006-02-01

204

Effect of the protonation degree of a self-assembled monolayer on the immobilization dynamics of a [NiFe] hydrogenase.  

PubMed

Understanding the interaction and immobilization of [NiFe] hydrogenases on functionalized surfaces is important in the field of biotechnology and, in particular, for the development of biofuel cells. In this study, we investigated the adsorption behavior of the standard [NiFe] hydrogenase of Desulfovibrio gigas on amino-terminated alkanethiol self-assembled monolayers (SAMs) with different levels of protonation. Classical all-atom molecular dynamics (MD) simulations revealed a strong correlation between the adsorption behavior and the level of ionization of the chemically modified electrode surface. While the hydrogenase undergoes a weak but stable initial adsorption process on SAMs with a low degree of protonation, a stronger immobilization is observable on highly ionized SAMs, affecting protein reorientation and conformation. These results were validated by complementary surface-enhanced infrared absorption (SEIRA) measurements on the comparable [NiFe] standard hydrogenases from Desulfovibrio vulgaris Miyazaki F and allowed in this way for a detailed insight into the adsorption mechanism at the atomic level. PMID:23215250

Utesch, Tillmann; Millo, Diego; Castro, Maria Ana; Hildebrandt, Peter; Zebger, Ingo; Mroginski, Maria Andrea

2013-01-15

205

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. PMID:23136119

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

206

DFT investigation of structural, electronic, and catalytic properties of diiron complexes related to the [2Fe](H) subcluster of Fe-only hydrogenases.  

PubMed

Hydrogenases catalyze the reversible oxidation of dihydrogen to protons and electrons. The structures of two Fe-only hydrogenases have been recently reported [Peters, J. W.; Lanzilotta, W. N.; Lemon, B. J.; Seefeldt, L. C. Science 1998, 282, 1853-1858. Nicolet, Y.; Piras, C.; Legrand, P.; Hatchikian, E. C.; Fontecilla-Camps, J. C. Structure 1999, 7, 13-23], showing that the likely site of dihydrogen activation is the so-called [2Fe](H) cluster, where each Fe ion is coordinated by CO and CN(-) ligands and the two metals are bridged by a chelating S-X(3)-S ligand. Moreover, the presence of a water molecule coordinated to the distal Fe2 center suggested that the Fe2 atom could be a suitable site for binding and activation of H(2). In this contribution, we report a density functional theory investigation of the structural and electronic properties of complexes derived from the [(CO)(CH(3)S)(CN)Fe(II)(mu-PDT)Fe(II)(CO)(2)(CN)](-1) species, which is related to the [2Fe](H) cluster observed in Fe-only hydrogenases. Our results show that the structure of the [2Fe](H) cluster observed in the enzyme does not correspond to a stable form of the isolated cluster, in the absence of the protein. As a consequence, the reactivity of [(CO)(CH(3)S)(CN)Fe(II)(mu-PDT)Fe(II)(CO)(2)(CN)](-1) derivatives in solution may be expected to be quite different from that of the active site of Fe-only hydrogenases. In fact, the most favorable path for H(2) activation involves the two metal atoms and one of the bridging S atoms and is associated with a very low activation energy (5.3 kcal mol(-1)). The relevance of these observations for the catalytic properties of Fe-only hydrogenases is discussed in light of available experimental and theoretical data. PMID:11896710

Bruschi, Maurizio; Fantucci, Piercarlo; De Gioia, Luca

2002-03-25

207

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. PMID:23233392

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

2012-01-01

208

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. PMID:21724888

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

209

Explorations of iron-iron hydrogenase active site models by experiment and theory  

E-print Network

to form a 3c-2eâ Fe-H-Fe bond, while Et+ reacts to form a new C-S bond. The instability of a bridging ethyl complex is attributed to the inability of the ethyl group, in contrast to a hydride, to form a stable 3c-2eâ bond with the two iron centers. Gas...

Tye, Jesse Wayne

2009-05-15

210

Mixed-Valence Nickel-Iron Dithiolate Models of the [NiFe]-Hydrogenase Active Site  

PubMed Central

A series of mixed-valence iron-nickel dithiolates is described. Oxidation of (diphosphine)Ni(dithiolate)Fe(CO)3 complexes 1, 2, and 3 with ferrocenium salts affords the corresponding tricarbonyl cations [(dppe)Ni(pdt)Fe(CO)3]+ ([1]+), [(dppe)Ni(edt)Fe(CO)3]+ ([2]+) and [(dcpe)Ni(pdt)Fe(CO)3]+ ([3]+), respectively, where dppe = Ph2PCH2CH2PPh2, dcpe = Cy2PCH2CH2PCy2, pdtH2 = HSCH2CH2CH2SH and edtH2 = HSCH2CH2SH. The cation [2]+ proved unstable, but the propanedithiolates are robust. IR and EPR spectroscopic measurements indicate that these species exist as Cs-symmetric species. Crystallographic characterization of [3]BF4 shows that Ni is square planar. Interaction of [1]BF4 with P-donor ligands (L) afforded a series of substituted derivatives of type [(dppe)Ni(pdt)Fe(CO)2L]BF4 for L = P(OPh)3 ([4a]BF4), P(p-C6H4Cl)3 ([4b]BF4), PPh2(2-py) ([4c]BF4), PPh2(OEt) ([4d]BF4), PPh3 ([4e]BF4), PPh2(o-C6H4OMe) ([4f]BF4), PPh2(o-C6H4OCH2OMe) ([4g]BF4), P(p-tol)3 ([4h]BF4), P(p-C6H4OMe)3 ([4i]BF4), PMePh2 ([4j]BF4). EPR analysis indicates that ethanedithiolate [2]+ exists as a single species at 110 K, whereas the propanedithiolate cations exist as a mixture of two conformers, which are proposed to be related through a flip of the chelate ring. Mössbauer spectra of 1 and oxidized S = ½ [4e]BF4 are both consistent with a low-spin Fe(i) state. The hyperfine coupling tensor of [4e]BF4 has a small isotropic component and significant anisotropy. DFT calculations using the BP86, B3LYP, and PBE0 exchange-correlation functionals agree with the structural and spectroscopic data, suggesting that the SOMOs in complexes of the present type are localized in a Fe(i)-centered d(z2) orbital. The DFT calculations allow an assignment of oxidation states of the metals and rationalization of the conformers detected by EPR spectroscopy. Treatment of [1]+ with CN- and compact basic phosphines results in complex reactions. With dppe, [1]+ undergoes quasi-disproportionation to give 1 and the diamagnetic complex [(dppe)Ni(pdt)Fe(CO)2(dppe)]2+ ([5]2+), which features square-planar Ni linked to an octahedral Fe center. PMID:22304696

Schilter, David; Nilges, Mark J.; Chakrabarti, Mrinmoy; Lindahl, Paul A.; Rauchfuss, Thomas B.; Stein, Matthias

2012-01-01

211

Research on Soluble Metal Sulfides: From Polysulfido Complexes to Functional Models for the Hydrogenases  

E-print Network

-S bonds to generate H2S and more readily processed and more cleanly combusted hydrocarbon product. A range theme uncovered the useful role of donor solvents on the reaction of metals with sulfur. It was found

Rauchfuss, Thomas B.

212

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. PMID:21441514

Fritsch, Johannes; Lenz, Oliver; Friedrich, Barbel

2011-01-01

213

[NiFe]Hydrogenase from Citrobacter sp. S-77 surpasses platinum as an electrode for H2 oxidation reaction.  

PubMed

Reported herein is an electrode for dihydrogen (H2) oxidation, and it is based on [NiFe]Hydrogenase from Citrobacter sp. S-77 ([NiFe]S77). It has a 637 times higher mass activity than Pt (calculated based on 1?mg of [NiFe]S77 or Pt) at 50?mV in a hydrogen half-cell. The [NiFe]S77 electrode is also stable in air and, unlike Pt, can be recovered 100?% after poisoning by carbon monoxide. Following characterization of the [NiFe]S77 electrode, a fuel cell comprising a [NiFe]S77 anode and Pt cathode was constructed and shown to have a a higher power density than that achievable by Pt. PMID:24895095

Matsumoto, Takahiro; Eguchi, Shigenobu; Nakai, Hidetaka; Hibino, Takashi; Yoon, Ki-Seok; Ogo, Seiji

2014-08-18

214

Crystals of the hydrogenase maturation factor HypF N-terminal domain grown in microgravity, display improved internal order  

NASA Astrophysics Data System (ADS)

Synthesis of the active [Ni-Fe]-hydrogenase in prokaryotes requires a series of ancillary maturation factors. Among them, the HypF maturation factor is a multidomain 82 kDa protein, whose N-terminal domain displays sequence and structural similarities to acylphosphatases. Acylphosphatases are small enzymes that are able to catalyze carboxyl-phosphate bond hydrolysis in acylphosphates, as well as in nucleoside di- and tri-phosphates and in arylphosphates. Here, we present a crystallographic comparison between microgravity and earth-grown crystals of the HypF N-terminal domain. Both crystals were of excellent quality, thereby allowing us to collect very high resolution datasets. A detailed analysis of data collection and refinement statistics, together with an analysis of the diffraction pattern showed that microgravity would appear to further improve the internal order of crystals.

Ponassi, Marco; Felli, Lamberto; Parodi, Stefania; Valbusa, Ugo; Rosano, Camillo

2011-01-01

215

Investigations on the Role of Proton-Coupled Electron Transfer in Hydrogen Activation by [FeFe]-Hydrogenase.  

PubMed

Proton-coupled electron transfer (PCET) is a fundamental process at the core of oxidation-reduction reactions for energy conversion. The [FeFe]-hydrogenases catalyze the reversible activation of molecular H2 through a unique metallocofactor, the H-cluster, which is finely tuned by the surrounding protein environment to undergo fast PCET transitions. The correlation of electronic and structural transitions at the H-cluster with proton-transfer (PT) steps has not been well-resolved experimentally. Here, we explore how modification of the conserved PT network via a Cys ? Ser substitution at position 169 proximal to the H-cluster of Chlamydomonas reinhardtii [FeFe]-hydrogenase (CrHydA1) affects the H-cluster using electron paramagnetic resonance (EPR) and Fourier transform infrared (FTIR) spectroscopy. Despite a substantial decrease in catalytic activity, the EPR and FTIR spectra reveal different H-cluster catalytic states under reducing and oxidizing conditions. Under H2 or sodium dithionite reductive treatments, the EPR spectra show signals that are consistent with a reduced [4Fe-4S]H(+) subcluster. The FTIR spectra showed upshifts of ?CO modes to energies that are consistent with an increase in oxidation state of the [2Fe]H subcluster, which was corroborated by DFT analysis. In contrast to the case for wild-type CrHydA1, spectra associated with Hred and Hsred states are less populated in the Cys ? Ser variant, demonstrating that the exchange of -SH with -OH alters how the H-cluster equilibrates among different reduced states of the catalytic cycle under steady-state conditions. PMID:25286239

Mulder, David W; Ratzloff, Michael W; Bruschi, Maurizio; Greco, Claudio; Koonce, Evangeline; Peters, John W; King, Paul W

2014-10-29

216

Intact functional fourteen-subunit respiratory membrane-bound [NiFe]-hydrogenase complex of the hyperthermophilic archaeon Pyrococcus furiosus.  

PubMed

The archaeon Pyrococcus furiosus grows optimally at 100 °C by converting carbohydrates to acetate, CO2, and H2, obtaining energy from a respiratory membrane-bound hydrogenase (MBH). This conserves energy by coupling H2 production to oxidation of reduced ferredoxin with generation of a sodium ion gradient. MBH is encoded by a 14-gene operon with both hydrogenase and Na(+)/H(+) antiporter modules. Herein a His-tagged MBH was expressed in P. furiosus and the detergent-solubilized complex purified under anaerobic conditions by affinity chromatography. Purified MBH contains all 14 subunits by electrophoretic analysis (13 subunits were also identified by mass spectrometry) and had a measured iron:nickel ratio of 15:1, resembling the predicted value of 13:1. The as-purified enzyme exhibited a rhombic EPR signal characteristic of the ready nickel-boron state. The purified and membrane-bound forms of MBH both preferentially evolved H2 with the physiological donor (reduced ferredoxin) as well as with standard dyes. The O2 sensitivities of the two forms were similar (half-lives of ? 15 h in air), but the purified enzyme was more thermolabile (half-lives at 90 °C of 1 and 25 h, respectively). Structural analysis of purified MBH by small angle x-ray scattering indicated a Z-shaped structure with a mass of 310 kDa, resembling the predicted value (298 kDa). The angle x-ray scattering analyses reinforce and extend the conserved sequence relationships of group 4 enzymes and complex I (NADH quinone oxidoreductase). This is the first report on the properties of a solubilized form of an intact respiratory MBH complex that is proposed to evolve H2 and pump Na(+) ions. PMID:24860091

McTernan, Patrick M; Chandrayan, Sanjeev K; Wu, Chang-Hao; Vaccaro, Brian J; Lancaster, W Andrew; Yang, Qingyuan; Fu, Dax; Hura, Greg L; Tainer, John A; Adams, Michael W W

2014-07-11

217

X-ray crystallographic and computational studies of the O2-tolerant [NiFe]-hydrogenase 1 from Escherichia coli  

PubMed Central

The crystal structure of the membrane-bound O2-tolerant [NiFe]-hydrogenase 1 from Escherichia coli (EcHyd-1) has been solved in three different states: as-isolated, H2-reduced, and chemically oxidized. As very recently reported for similar enzymes from Ralstonia eutropha and Hydrogenovibrio marinus, two supernumerary Cys residues coordinate the proximal [FeS] cluster in EcHyd-1, which lacks one of the inorganic sulfide ligands. We find that the as-isolated, aerobically purified species contains a mixture of at least two conformations for one of the cluster iron ions and Glu76. In one of them, Glu76 and the iron occupy positions that are similar to those found in O2-sensitive [NiFe]-hydrogenases. In the other conformation, this iron binds, besides three sulfur ligands, the amide N from Cys20 and one O? of Glu76. Our calculations show that oxidation of this unique iron generates the high-potential form of the proximal cluster. The structural rearrangement caused by oxidation is confirmed by our H2-reduced and oxidized EcHyd-1 structures. Thus, thanks to the peculiar coordination of the unique iron, the proximal cluster can contribute two successive electrons to secure complete reduction of O2 to H2O at the active site. The two observed conformations of Glu76 are consistent with this residue playing the role of a base to deprotonate the amide moiety of Cys20 upon iron binding and transfer the resulting proton away, thus allowing the second oxidation to be electroneutral. The comparison of our structures also shows the existence of a dynamic chain of water molecules, resulting from O2 reduction, located near the active site. PMID:22431599

Volbeda, Anne; Amara, Patricia; Darnault, Claudine; Mouesca, Jean-Marie; Parkin, Alison; Roessler, Maxie M.; Armstrong, Fraser A.; Fontecilla-Camps, Juan C.

2012-01-01

218

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. PMID:24297906

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

2013-01-01

219

Quantification of microbial activity in subsurface environments using a hydrogenase enzyme assay  

NASA Astrophysics Data System (ADS)

The subsurface biosphere is the largest microbial ecosystem on Earth. Despite its large size and extensive industrial exploitation, very little is known about the role of microbial activity in the subsurface. Subsurface microbial activity plays a fundamental role in geochemical cycles of carbon and other biologically important elements. How the indigenous microbial communities are supplied with energy is one of the most fundamental questions in subsurface research. It is still an enigma how these communities can survive with such recalcitrant carbon over geological time scales. Despite its usually very low concentration, hydrogen is an important element in subsurface environments. Heterotrophic and chemoautotrophic microorganisms use hydrogen in their metabolic pathways; they either obtain protons from the radiolysis of water and/or cleavage of hydrogen generated by the alteration of basaltic crust, or they dispose of protons by formation of water. Hydrogenase (H2ase) is a ubiquitous intracellular enzyme that catalyzes the interconversion of molecular hydrogen and/or water into protons and electrons. The protons are used for the synthesis of ATP, thereby coupling energy-generating metabolic processes to electron acceptors such as carbon dioxide or sulfate. H2ase activity can therefore be used as a measure for total microbial activity as it targets a key metabolic compound rather than a specific turnover process. Using a highly sensitive tritium assay we measured H2ase enzyme activity in the organic-rich sediments of Lake Van, a saline, alkaline lake in eastern Turkey and in marine subsurface sediments of the Barents Sea. Additionally, sulfate reduction rates (SRRs) were measured to compare the results of the H2ase enzyme assay with the quantitatively most important electron acceptor process. H2ase activity was found at all sites, measured values and distribution of activity varied widely with depth and between sites. At the Lake Van sites H2ase activity ranged from ca. 20 mmol H2 cm-3 d-1 close to the sediment-water interface to 0.5 mmol H2 cm-3 d-1 at a depth of 0.8 m. In samples from the Barents Sea H2ase activity ranged between 0.1 to 2.5 mmol H2 cm-3 d-1 down to a depth of 1.60 m. At all sites the SRR profile followed the H2ase activity profile until SRR declined to values close to the minimum detection limit (~10 pmol cm-3 d-1). H2ase activity increased again after SRR declined, indicating that other microbial processes are becoming quantitatively more important. The H2ase and SRR data show that our assay has a potential to become a valuable tool to measure total subsurface microbial activity.

Adhikari, R. R.; Nickel, J.; Kallmeyer, J.

2012-04-01

220

Stereochemical studies of a selenium-containing hydrogenase from Methanococcus vannielii: determination of the absolute configuration of C-5 chirally labeled dihydro-8-hydroxy-5-deazaflavin cofactor.  

PubMed

Reduction of 7,8-didemethyl-8-hydroxy-[5-2H]-5-deazariboflavin by the selenium-containing hydrogenase from Methanococcus vannielii gave a C-5 chirally labeled 1,5-dihydro derivative. The absolute configuration of the chiral label was shown to be (R) by comparison of the chemically degraded product with authentic samples of known absolute configurations. Therefore, the steric course of the enzymic reactions involving the 8-hydroxy-5-deazaflavin cofactor can be defined as follows: (a) reduction occurs on the si face of the 5-deazaflavin molecule; (b) oxidation proceeds by the abstraction of the pro-S hydrogen at C-5 of the 1,5-dihydro-5-deazaflavin. Thus, the selenium-containing hydrogenase and 8-hydroxy-5-deazaflavin-dependent NADP+ reductase from M. vannielii are si face specific. PMID:3883357

Yamazaki, S; Tsai, L; Stadtman, T C; Teshima, T; Nakaji, A; Shiba, T

1985-03-01

221

Stereochemical Studies of a Selenium-Containing Hydrogenase from Methanococcus vannielii: Determination of the Absolute Configuration of C-5 Chirally Labeled Dihydro8-hydroxy-5-deazaflavin Cofactor  

Microsoft Academic Search

Reduction of 7,8-didemethyl-8-hydroxy-[5-2H]-5-deazariboflavin by the selenium-containing hydrogenase from Methanococcus vannielii gave a C-5 chirally labeled 1,5-dihydro derivative. The absolute configuration of the chiral label was shown to be (R) by comparison of the chemically degraded product with authentic samples of known absolute configurations. Therefore, the steric course of the enzymic reactions involving the 8-hydroxy-5-deazaflavin cofactor can be defined as follows:

Shigeko Yamazaki; Lin Tsai; Thressa C. Stadtman; Tadashi Teshima; Akira Nakaji; Tetsuo Shiba

1985-01-01

222

Electronic structure of the unique [4Fe-3S] cluster in O2-tolerant hydrogenases characterized by 57Fe M?ssbauer and EPR spectroscopy  

PubMed Central

Iron–sulfur clusters are ubiquitous electron transfer cofactors in hydrogenases. Their types and redox properties are important for H2 catalysis, but, recently, their role in a protection mechanism against oxidative inactivation has also been recognized for a [4Fe-3S] cluster in O2-tolerant group 1 [NiFe] hydrogenases. This cluster, which is uniquely coordinated by six cysteines, is situated in the proximity of the catalytic [NiFe] site and exhibits unusual redox versatility. The [4Fe-3S] cluster in hydrogenase (Hase) I from Aquifex aeolicus performs two redox transitions within a very small potential range, forming a superoxidized state above +200 mV vs. standard hydrogen electrode (SHE). Crystallographic data has revealed that this state is stabilized by the coordination of one of the iron atoms to a backbone nitrogen. Thus, the proximal [4Fe-3S] cluster undergoes redox-dependent changes to serve multiple purposes beyond classical electron transfer. In this paper, we present field-dependent 57Fe-Mössbauer and EPR data for Hase I, which, in conjunction with spectroscopically calibrated density functional theory (DFT) calculations, reveal the distribution of Fe valences and spin-coupling schemes for the iron–sulfur clusters. The data demonstrate that the electronic structure of the [4Fe-3S] core in its three oxidation states closely resembles that of corresponding conventional [4Fe-4S] cubanes, albeit with distinct differences for some individual iron sites. The medial and distal iron–sulfur clusters have similar electronic properties as the corresponding cofactors in standard hydrogenases, although their redox potentials are higher. PMID:23267108

Pandelia, Maria-Eirini; Bykov, Dmytro; Izsak, Robert; Infossi, Pascale; Giudici-Orticoni, Marie-Therese; Bill, Eckhard; Neese, Frank; Lubitz, Wolfgang

2013-01-01

223

Significance of hydrogen burst from growing cultures of Desulfovibrio vulgaris , Miyazaki, and the role of hydrogenase and cytochrome c 3 in energy production system  

Microsoft Academic Search

In an early stage of the growth of Desulfovibrio vulgaris, Miyazaki, a burst of H2 occurred, and lasted for a few hours. The H2S production which paralleled the cell proliferation was very low in the H2 burst period, and began to increase thereafter. Hydrogenase (hydrogen: ferricytochrome c3 oxidoreductase, EC1. 12.2.1), cytochrome c3 and desulfoviridin also increased after the H2 burst.

Keiko Tsuji; Tatsuhiko Yagi

1980-01-01

224

Identification of an Uptake Hydrogenase Required for Hydrogen-Dependent Reduction of Fe(III) and Other Electron Acceptors by Geobacter sulfurreducens  

Microsoft Academic Search

Geobacter sulfurreducens, a representative of the family Geobacteraceae that predominates in Fe(III)-reducing subsurface environments, can grow by coupling the oxidation of hydrogen to the reduction of a variety of electron acceptors, including Fe(III), fumarate, and quinones. An examination of the G. sulfurreducens genome revealed two operons, hya and hyb, which appeared to encode periplasmically oriented respiratory uptake hydrogenases. In order

Maddalena V. Coppi; Regina A. O'Neil; Derek R. Lovley

2004-01-01

225

[NiFe]-hydrogenase maturation in vitro: analysis of the roles of the HybG and HypD accessory proteins1.  

PubMed

[NiFe]-hydrogenases (Hyd) bind a nickel-iron-based cofactor. The Fe ion of the cofactor is bound by two cyanide ligands and a single carbon monoxide ligand. Minimally six accessory proteins (HypA-HypF) are necessary for NiFe(CN)2CO cofactor biosynthesis in Escherichia coli. It has been shown that the anaerobically purified HypC-HypD-HypE scaffold complex carries the Fe(CN)2CO moiety of this cofactor. In the present study, we have purified the HybG-HypDE complex and used it to successfully reconstitute in vitro active Hyd from E. coli. HybG is a homologue of HypC that is specifically required for the maturation of Hyd-2 and also functions in the maturation of Hyd-1 of E. coli. Maturation of active Hyd-1 and Hyd-2 could be demonstrated in extracts derived from HybG- and HypD-deficient E. coli strains by adding anaerobically purified HybG-HypDE complex. In vitro maturation was dependent on ATP, carbamoylphosphate, nickel and reducing conditions. Hydrogenase maturation was prevented when the purified HybG-HypDE complex used in the maturation assay lacked a bound Fe(CN)2CO moiety. These findings demonstrate that it is possible to isolate incompletely processed intermediates on the maturation pathway and to use these to activate apo-forms of [NiFe]-hydrogenase large subunits. PMID:25184670

Soboh, Basem; Lindenstrauss, Ute; Granich, Claudia; Javed, Mahwish; Herzberg, Martin; Thomas, Claudia; Stripp, Sven T

2014-12-01

226

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. PMID:21444783

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

2011-01-01

227

Fractionation of Sulfur Isotopes by Desulfovibrio vulgaris Mutants Lacking Periplasmic Hydrogenases or the Type I Tetraheme Cytochrome c3  

NASA Astrophysics Data System (ADS)

A large fraction of anaerobic mineralization of organic compounds relies on microbial sulfate reduction. Sulfur isotope fractionation by these microbes has been widely used to trace the biogeochemical cycling of sulfur and carbon, but intracellular mechanisms behind the wide range of fractionations observed in nature and cultures are not fully understood. In this study, we investigated the influence of electron transport chain components on the fractionation of sulfur isotopes by culturing Desulfovibrio vulgaris Hildenborough mutants lacking hydrogenases or type I tetraheme cytochrome c3 (Tp1-c3). The mutants were grown both in batch and continuous cultures. All tested mutants grew on lactate or pyruvate as the sole carbon and energy sources, generating sulfide. Mutants lacking cytoplasmic and periplasmic hydrogenases exhibited similar growth physiologies and sulfur isotope fractionations to their parent strains. On the other hand, a mutant lacking Tp1-c3 (?cycA) fractionated the 34S/32S ratio more than the wild type, evolving H2 in the headspace and exhibiting a lower specific respiration rate. In the presence of high concentrations of pyruvate, the growth of ?cycA relied largely on fermentation rather than sulfate reduction, even when sulfate was abundant, producing the largest sulfur isotope effect observed in this study. Differences between sulfur isotope fractionation by ?cycA and the wild type highlight the effect of electron transfer chains on the magnitude of sulfur isotope fractionation. Because Tp1-c3 is known to exclusively shuttle electrons from periplasmic hydrogenases to transmembrane complexes, electron transfers in the absence of Tp1-c3 should bypass the periplasmic hydrogen cycling, and the loss of reducing equivalents in the form of H2 can impair the flow of electrons from organic acids to sulfur, increasing isotope fractionation. Larger fractionation by ?cycA can inform interpretations of sulfur isotope data at an environmental scale as well, because intracellular concentrations of electron transport components can be altered by environmental factors such as iron availability. Simultaneous sulfate reduction and fermentation, and their corresponding sulfur isotope effects, also generate a hypothesis that links sulfur isotope fractionation to the cellular energy budget. Theoretically, the largest fractionation during microbial sulfate reduction occurs when the backward fluxes equal the forward fluxes in sulfate reduction pathway. However, when the generation of ATP depends exclusively on sulfate respiration, a minimum respiration rate is required to fulfill the maintenance energy requirement. In contrast, when sulfate reduction occurs simultaneously with fermentation, the latter process may contribute toward maintenance energy, enabling slower and more reversible sulfate reduction, and leading to larger fractionation. Given that many sulfate-reducing microbes are also facultative fermenters, fermentation by sulfate reducing microbes in natural habitats and sulfur isotope signatures produced by such communities deserve further exploration.

Sim, M.; Ono, S.; Bosak, T.

2012-12-01

228

Crystal structure and anion binding in the prokaryotic hydrogenase maturation factor HypF acylphosphatase-like domain.  

PubMed

[NiFe]-hydrogenases require a set of complementary and regulatory proteins for correct folding and maturation processes. One of the essential regulatory proteins, HypF (82kDa) contains a N-terminal acylphosphatase (ACT)-like domain, a sequence motif shared with enzymes catalyzing O-carbamoylation, and two zinc finger motifs similar to those found in the DnaJ chaperone. The HypF acylphosphatase domain is thought to support the conversion of carbamoylphosphate into CO and CN(-), promoting coordination of these ligands to the hydrogenase metal cluster. It has been shown recently that the HypF N-terminal domain can aggregate in vitro to yield fibrils matching those formed by proteins linked to amyloid diseases. The 1.27A resolution HypF acylphosphatase domain crystal structure (residues 1-91; R-factor 13.1%) shows a domain fold of betaalphabetabetaalphabeta topology, as observed in mammalian acylphosphatases specifically catalyzing the hydrolysis of the carboxyl-phosphate bonds in acylphosphates. The HypF N-terminal domain can be assigned to the ferredoxin structural superfamily, to which RNA-binding domains of small nuclear ribonucleoproteins and some metallochaperone proteins belong. Additionally, the HypF N-terminal domain displays an intriguing structural relationship to the recently discovered ACT domains. The structures of different HypF acylphosphatase domain complexes show a phosphate binding cradle comparable to the P-loop observed in unrelated phosphatase families. On the basis of the catalytic mechanism proposed for acylphosphatases, whereby residues Arg23 and Asn41 would support substrate orientation and the nucleophilic attack of a water molecule on the phosphate group, fine structural features of the HypF N-terminal domain putative active site region may account for the lack of acylphosphatase activity observed for the expressed domain. The crystallographic analyses here reported were undertaken to shed light on the molecular bases of inactivity, folding, misfolding and aggregation of the HypF N-terminal acylphosphatase domain. PMID:12206761

Rosano, Camillo; Zuccotti, Simone; Bucciantini, Monica; Stefani, Massimo; Ramponi, Giampietro; Bolognesi, Martino

2002-08-30

229

How Escherichia coli Is Equipped to Oxidize Hydrogen under Different Redox Conditions*S  

E-print Network

accommodating one to three electron-transfer- ring iron-sulfur clusters. The active sites of [Ni: di-iron [FeFe]-, nickel-iron [NiFe]-, and mono-iron [Fe]-hydrogenases (1). Nickel-iron hydrogenasesFe]-hydroge- nases contain a nickel atom coordinated by four cysteine-S ligands, two of which bridge to an iron atom

Palmer, Tracy

230

Modulation of active site electronic structure by the protein matrix to control [NiFe] hydrogenase reactivity.  

PubMed

Control of the reactivity of the nickel center of the [NiFe] hydrogenase and other metalloproteins commonly involves outer coordination sphere ligands that act to modify the geometry and physical properties of the active site metal centers. We carried out a combined set of classical molecular dynamics and quantum/classical mechanics calculations to provide quantitative estimates of how dynamic fluctuations of the active site within the protein matrix modulate the electronic structure at the catalytic center. Specifically we focused on the dynamics of the inner and outer coordination spheres of the cysteinate-bound Ni-Fe cluster in the catalytically active Ni-C state. There are correlated movements of the cysteinate ligands and the surrounding hydrogen-bonding network, which modulate the electron affinity at the active site and the proton affinity of a terminal cysteinate. On the basis of these findings, we hypothesize a coupling between protein dynamics and electron and proton transfer reactions critical to dihydrogen production. PMID:25285653

Smith, Dayle M A; Raugei, Simone; Squier, Thomas C

2014-11-21

231

Original design of an oxygen-tolerant [NiFe] hydrogenase: major effect of a valine-to-cysteine mutation near the active site.  

PubMed

Hydrogenases are efficient biological catalysts of H(2) oxidation and production. Most of them are inhibited by O(2), and a prerequisite for their use in biotechnological applications under air is to improve their oxygen tolerance. We have previously shown that exchanging the residue at position 74 in the large subunit of the oxygen-sensitive [NiFe] hydrogenase from Desulfovibrio fructosovorans could impact the reaction of the enzyme with O(2) (Dementin, S.; J. Am. Chem. Soc. 2009, 131, 10156-10164; Liebgott, P. P.; Nat. Chem. Biol. 2010, 6, 63-70). This residue, a valine in the wild-type enzyme, located at the bottleneck of the gas channel near the active site, has here been exchanged with a cysteine. A thorough characterization using a combination of kinetic, spectroscopic (EPR, FTIR), and electrochemical studies demonstrates that the V74C mutant has features of the naturally occurring oxygen-tolerant membrane-bound hydrogenases (MBH). The mutant is functional during several minutes under O(2), has impaired H(2)-production activity, and has a weaker affinity for CO than the WT. Upon exposure to O(2), it is converted into the more easily reactivatable inactive form, Ni-B, and this inactive state reactivates about 20 times faster than in the WT enzyme. Control experiments carried out with the V74S and V74N mutants indicate that protonation of the position 74 residue is not the reason the mutants reactivate faster than the WT enzyme. The electrochemical behavior of the V74C mutant toward O(2) is intermediate between that of the WT enzyme from D. fructosovorans and the oxygen-tolerant MBH from Aquifex aeolicus. PMID:21175174

Liebgott, Pierre-Pol; de Lacey, Antonio L; Burlat, Bénédicte; Cournac, Laurent; Richaud, Pierre; Brugna, Myriam; Fernandez, Victor M; Guigliarelli, Bruno; Rousset, Marc; Léger, Christophe; Dementin, Sébastien

2011-02-01

232

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

233

Replication of Bacteriophage SH-133 in the Facultative Autotroph Hydrogenomonas facilis II. Bacteriophage Synthesis and Hydrogenase Induction Under Step-Up and Step-Down Growth Conditions  

PubMed Central

Autotrophically grown infected cells are able to replicate phage SH-133 after being switched to a heterotrophic environment (step-up growth). The effect of step-down growth on phage replication varies with the choice of organic substrate. Phage replication and the induction of cellular hydrogenase occur under step-down growth from acetate but not peptone broth. The requirement of a continued source of energy for phage replication in either heterotrophically or autotrophically grown cells could be uniquely demonstrated in this phage-host system by the deletion of hydrogen from the growth medium. PMID:4203084

Aron, Gary M.; Pootjes, Christine F.

1973-01-01

234

The active site of the [FeFe]-hydrogenase from Desulfovibrio desulfuricans . I. Light sensitivity and magnetic hyperfine interactions as observed by electron paramagnetic resonance  

Microsoft Academic Search

The hydrogen-activating cluster (H cluster) in [FeFe]-hydrogenases consists of two moieties. The [2Fe]H subcluster is a (L)(CO)(CN)Fe(?-RS2)(?-CO)Fe(CysS)(CO)(CN) centre. The Cys-bound Fe is called Fe1, the other iron Fe2. The Cys-thiol forms a bridge to a [4Fe–4S]\\u000a cluster, the [4Fe–4S]H subcluster. We report that electron paramagnetic resonance (EPR) spectra of the 57Fe-enriched enzyme from Desulfovibrio desulfuricans in the Hox–CO state are

Simon P. J. Albracht; Winfried Roseboom; E. Claude Hatchikian

2006-01-01

235

The active site of the [FeFe]-hydrogenase from Desulfovibrio desulfuricans . II. Redox properties, light sensitivity and CO-ligand exchange as observed by infrared spectroscopy  

Microsoft Academic Search

In [FeFe]-hydrogenases, the H cluster (hydrogen-activating cluster) contains a di-iron centre ([2Fe]H subcluster, a (L)(CO)(CN)Fe(?-RS2)(?-CO)Fe(CysS)(CO)(CN) group) covalently attached to a cubane iron-sulphur cluster ([4Fe-4S]H subcluster). The Cys-thiol functions as the link between one iron (called Fe1) of the [2Fe]H subcluster and one iron of the cubane subcluster. The other iron in the [2Fe]H subcluster is called Fe2. The light sensitivity

Winfried Roseboom; Antonio L. De Lacey; Victor M. Fernandez; E. Claude Hatchikian; Simon P. J. Albracht

2006-01-01

236

Hydrogen-oxidizing hydrogenases 1 and 2 of Escherichia coli regulate the onset of hydrogen evolution and ATPase activity, respectively, during glucose fermentation at alkaline pH.  

PubMed

Simultaneous measurement of redox potential (Eh ) and determination of H2 evolution kinetics using a pair of titanium silicate and platinum redox electrodes in fermenting cultures of Escherichia coli wild type and different mutants lacking hydrogenases 1 (Hyd-1) or 2 (Hyd-2) revealed that Hyd-1 controls the onset of H2 evolution at slightly alkaline pH (pH 7.5) and under oxidizing Eh . In addition, Hyd-2 influences the N,N'-dicyclohexylcarbodiimide-inhibited ATPase activity in fermenting cells and thus regulates the proton F0 F1 -ATPase at the alkaline pH but under reducing Eh . PMID:24111652

Poladyan, Anna; Trchounian, Karen; Sawers, R Gary; Trchounian, Armen

2013-11-01

237

Characterization of Photochemical Processes for H2 Production by CdS Nanorod-[FeFe] Hydrogenase Complexes  

SciTech Connect

We have developed complexes of CdS nanorods capped with 3-mercaptopropionic acid (MPA) and Clostridium acetobutylicum [FeFe]-hydrogenase I (CaI) that photocatalyze reduction of H{sup +} to H{sub 2} at a CaI turnover frequency of 380-900 s{sup -1} and photon conversion efficiencies of up to 20% under illumination at 405 nm. In this paper, we focus on the compositional and mechanistic aspects of CdS:CaI complexes that control the photochemical conversion of solar energy into H{sub 2}. Self-assembly of CdS with CaI was driven by electrostatics, demonstrated as the inhibition of ferredoxin-mediated H{sub 2} evolution by CaI. Production of H{sub 2} by CdS:CaI was observed only under illumination and only in the presence of a sacrificial donor. We explored the effects of the CdS:CaI molar ratio, sacrificial donor concentration, and light intensity on photocatalytic H{sub 2} production, which were interpreted on the basis of contributions to electron transfer, hole transfer, or rate of photon absorption, respectively. Each parameter was found to have pronounced effects on the CdS:CaI photocatalytic activity. Specifically, we found that under 405 nm light at an intensity equivalent to total AM 1.5 solar flux, H{sub 2} production was limited by the rate of photon absorption ({approx}1 ms{sup -1}) and not by the turnover of CaI. Complexes were capable of H{sub 2} production for up to 4 h with a total turnover number of 106 before photocatalytic activity was lost. This loss correlated with inactivation of CaI, resulting from the photo-oxidation of the CdS capping ligand MPA.

Brown, K. A.; Wilker, M. B.; Boehm, M.; Dukovic, G.; King, P. W.

2012-03-28

238

Synthetic analogues of [Fe4S4(Cys)3(His)] in hydrogenases and [Fe4S4(Cys)4] in HiPIP derived from all-ferric [Fe4S4{N(SiMe3)2}4  

PubMed Central

The all-ferric [Fe4S4]4+ cluster [Fe4S4{N(SiMe3)2}4] 1 and its one-electron reduced form [1]- serve as convenient precursors for the synthesis of 3?1-site differentiated [Fe4S4] clusters and high-potential iron-sulfur protein (HiPIP) model clusters. The reaction of 1 with four equivalents (equiv) of the bulky thiol HSDmp (Dmp = 2,6-(mesityl)2C6H3, mesityl = 2,4,6-Me3C6H2) followed by treatment with tetrahydrofuran (THF) resulted in the isolation of [Fe4S4(SDmp)3(THF)3] 2. Cluster 2 contains an octahedral iron atom with three THF ligands, and its Fe(S)3(O)3 coordination environment is relevant to that in the active site of substrate-bound aconitase. An analogous reaction of [1]- with four equiv of HSDmp gave [Fe4S4(SDmp)4]- 3, which models the oxidized form of HiPIP. The THF ligands in 2 can be replaced by tetramethyl-imidazole (Me4Im) to give [Fe4S4(SDmp)3(Me4Im)] 4 modeling the [Fe4S4(Cys)3(His)] cluster in hydrogenases, and its one-electron reduced form [4]- was synthesized from the reaction of 3 with Me4Im. The reversible redox couple between 3 and [3]- was observed at E1/2 = -820 mV vs. Ag/Ag+, and the corresponding reversible couple for 4 and [4]- is positively shifted by +440 mV. The cyclic voltammogram of 3 also exhibited a reversible oxidation couple, which indicates generation of the all-ferric [Fe4S4]4+ cluster, [Fe4S4(SDmp)4]. PMID:21768339

Ohki, Yasuhiro; Tanifuji, Kazuki; Yamada, Norihiro; Imada, Motosuke; Tajima, Tomoyuki; Tatsumi, Kazuyuki

2011-01-01

239

Hydrogen bonding affects the [NiFe] active site of Desulfovibrio vulgaris Miyazaki F hydrogenase: a hyperfine sublevel correlation spectroscopy and density functional theory study.  

PubMed

Pulse electron paramagnetic resonance and hyperfine sublevel correlation spectroscopy have been used to investigate nitrogen coordination of the active site of [NiFe] hydrogenase of Desulfovibrio vulgaris Miyazaki F in its oxidized "ready" state. The obtained (14)N hyperfine (A = [+1.32, +1.32, +2.07] MHz) and nuclear quadrupole (e(2)qQ/h = -1.9 MHz, eta = 0.37) coupling constants were assigned to the N(epsilon) of a highly conserved histidine (His88) by studying a hydrogenase preparation in which the histidines were (15)N labeled. The histidine is hydrogen-bonded via its N(epsilon)-H to the nickel-coordinating sulfur of a cysteine (Cys549) that carries an appreciable amount of spin density. Through the hydrogen bond a small fraction of the spin density ( approximately 1%) is delocalized onto the histidine ring giving rise to an isotropic (14)N hyperfine coupling constant of about 1.6 MHz. These conclusions are supported by density functional calculations. The measured (14)N quadrupole coupling constants are related to the polarization of the N(epsilon)-H bond, and the respective hydrogen bond can be classified as being weak. PMID:16610917

Agrawal, Aruna Goenka; van Gastel, Maurice; Gärtner, Wolfgang; Lubitz, Wolfgang

2006-04-20

240

Novel arrangement of enhancer sequences for NifA-dependent activation of the hydrogenase gene promoter in Rhizobium leguminosarum bv. viciae.  

PubMed

The transcriptional activation of the NifA-dependent sigma(54) promoter of the Rhizobium leguminosarum hydrogenase structural genes hupSL (P(1)) has been studied through gel retardation analysis and detailed mutagenesis. Gel retardation analysis indicated the existence of a physical interaction between NifA and the promoter. Extensive mutagenesis followed by in vivo expression analysis showed that three sequences of 4 bases each (-170 ACAA -167, -161 ACAA -158, and -145 TTGT -142) are required for maximal stimulation of in vivo transcription of the P(1) promoter. The arrangement of these upstream activating sequences (ACAA N(5) ACAA N(12) TTGT) differs from the canonical 5'ACA N(10) TGT 3' UAS structure involved in NifA-dependent activation of nif/fix genes. Mutant promoter analysis indicated that the relative contribution of each of these sequences to P(1) promoter activity increases with its proximity to the transcription start site. Analysis of double mutants altered in two out of the three enhancer sequences suggests that each of these sequences functions in NifA-dependent activation of the P(1) promoter in an independent but cooperative mode. The similarities and differences between cis elements of hup and nif/fix promoters suggest that the structure of the P(1) promoter has adapted to activation by NifA in order to coexpress hydrogenase and nitrogenase activities in legume nodules. PMID:18310336

Martínez, Marta; Colombo, Maria-Victoria; Palacios, Jose-Manuel; Imperial, Juan; Ruiz-Argüeso, Tomás

2008-05-01

241

Contributions of the [NiFe]- and [FeFe]-hydrogenase to H2 production in Shewanella oneidensis MR-1 as revealed by isotope ratio analysis of evolved H(2).  

PubMed

Shewanella oneidensis MR-1 encodes both a [NiFe]- and an [FeFe]-hydrogenase. While the output of these proteins has been characterized in mutant strains expressing only one of the enzymes, the contribution of each to H2 synthesis in the wild-type organism is not clear. Here, we use stable isotope analysis of H2 in the culture headspace, along with transcription data and measurements of the concentrations of gases in the headspace, to characterize H2 production in the wild-type strain. After most of the O2 in the headspace had been consumed, H2 was produced and then consumed by the bidirectional [NiFe]-hydrogenase. Once the cultures were completely anaerobic, a new burst of H2 synthesis catalyzed by both enzymes took place. Our data are consistent with the hypothesis that at this point in the culture cycle, a pool of electrons is shunted toward both hydrogenases in the wild-type organisms, but that in the absence of one of the hydrogenases, the flux is redirected to the available enzyme. To our knowledge, this is the first use of natural-abundance stable isotope analysis of a metabolic product to elucidate substrate flux through two alternative enzymes in the same cellular system. PMID:24372594

Kreuzer, Helen W; Hill, Eric A; Moran, James J; Bartholomew, Rachel A; Yang, Hui; Hegg, Eric L

2014-03-01

242

Designing interfaces of hydrogenase-nanomaterial hybrids for efficient solar conversion.  

PubMed

The direct conversion of sunlight into biofuels is an intriguing alternative to a continued reliance on fossil fuels. Natural photosynthesis has long been investigated both as a potential solution, and as a model for utilizing solar energy to drive a water-to-fuel cycle. The molecules and organizational structure provide a template to inspire the design of efficient molecular systems for photocatalysis. A clear design strategy is the coordination of molecular interactions that match kinetic rates and energetic levels to control the direction and flow of energy from light harvesting to catalysis. Energy transduction and electron-transfer reactions occur through interfaces formed between complexes of donor-acceptor molecules. Although the structures of several of the key biological complexes have been solved, detailed descriptions of many electron-transfer complexes are lacking, which presents a challenge to designing and engineering biomolecular systems for solar conversion. Alternatively, it is possible to couple the catalytic power of biological enzymes to light harvesting by semiconductor nanomaterials. In these molecules, surface chemistry and structure can be designed using ligands. The passivation effect of the ligand can also dramatically affect the photophysical properties of the semiconductor, and energetics of external charge-transfer. The length, degree of bond saturation (aromaticity), and solvent exposed functional groups of ligands can be manipulated to further tune the interface to control molecular assembly, and complex stability in photocatalytic hybrids. The results of this research show how ligand selection is critical to designing molecular interfaces that promote efficient self-assembly, charge-transfer and photocatalysis. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems. PMID:23541891

King, Paul W

2013-01-01

243

The [NiFe]-hydrogenase accessory chaperones HypC and HybG of Escherichia coli are iron- and carbon dioxide-binding proteins.  

PubMed

[NiFe]-hydrogenase accessory proteins HypC and HypD form a complex that binds a Fe-(CN)?CO moiety and CO?. In this study two HypC homologues from Escherichia coli were purified under strictly anaerobic conditions and both contained sub-stoichiometric amounts of iron (approx. 0.3 molFe/mol HypC). Infrared spectroscopic analysis identified a signature at 2337 cm?¹ indicating bound CO?. Aerobically isolated HypC lacked both Fe and CO?. Exchange of either of the highly conserved amino acid residues Cys2 or His51 abolished both Fe- and CO?-binding. Our results suggest that HypC delivers CO? bound directly to Fe for reduction to CO by HypD. PMID:23851071

Soboh, Basem; Stripp, Sven T; Bielak, Claudia; Lindenstrauß, Ute; Braussemann, Mario; Javaid, Mahwish; Hallensleben, Magnus; Granich, Claudia; Herzberg, Martin; Heberle, Joachim; Sawers, R Gary

2013-08-19

244

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. PMID:17026754

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

245

Nonaheme cytochrome c, a new physiological electron acceptor for [Ni,Fe] hydrogenase in the sulfate-reducing bacterium Desulfovibrio desulfuricans Essex: primary sequence, molecular parameters, and redox properties.  

PubMed

A nonaheme cytochrome c was purified to homogeneity from the soluble and the membrane fractions of the sulfate-reducing bacterium Desulfovibrio desulfuricans Essex. The gene encoding for the protein was cloned and sequenced. The primary structure of the multiheme protein was highly homologous to that of the nonaheme cytochrome c from D. desulfuricans ATCC 27774 and to that of the 16-heme HmcA protein from Desulfovibrio vulgaris Hildenborough. The analysis of the sequence downstream of the gene encoding for the nonaheme cytochrome c from D. desulfuricans Essex revealed an open reading frame encoding for an HmcB homologue. This operon structure indicated the presence of an Hmc complex in D. desulfuricans Essex, with the nonaheme cytochrome c replacing the 16-heme HmcA protein found in D. vulgaris. The molecular and spectroscopic parameters of nonaheme cytochrome c from D. desulfuricans Essex in the oxidized and reduced states were analyzed. Upon reduction, the pI of the protein changed significantly from 8.25 to 5.0 when going from the Fe(III) to the Fe(II) state. Such redox-induced changes in pI have not been reported for cytochromes thus far; most likely they are the result of a conformational rearrangement of the protein structure, which was confirmed by CD spectroscopy. The reactivity of the nonaheme cytochrome c toward [Ni,Fe] hydrogenase was compared with that of the tetraheme cytochrome c(3); both the cytochrome c(3) and the periplasmic [Ni,Fe] hydrogenase originated from D. desulfuricans Essex. The nonaheme protein displayed an affinity and reactivity toward [Ni,Fe] hydrogenase [K(M) = 20.5 +/- 0.9 microM; v(max) = 660 +/- 20 nmol of reduced cytochrome min(-1) (nmol of hydrogenase)(-1)] similar to that of cytochrome c(3) [K(M) = 12.6 +/- 0.7 microM; v(max) = 790 +/- 30 nmol of reduced cytochrome min(-1) (nmol of hydrogenase)(-1)]. This shows that nonaheme cytochrome c is a competent physiological electron acceptor for [Ni,Fe] hydrogenase. PMID:11170458

Fritz, G; Griesshaber, D; Seth, O; Kroneck, P M

2001-02-01

246

Effect of Secondary Interactions on the Fundamental Properties of Small Molecule Models of the Diiron Hydrogenase Active Site  

E-print Network

mixed-valent FeIFeII complexes. An X-ray crystal structure of one of these complexes, (?-SCH2C(CH3)2CH2S-)[Fe(CO)2PMe3]2PF6 shows both a semi-bridging carbonyl and an open site similar to the 2-Fe subsite in the Hox state of the enzyme active site...

Singleton, Michael Lee

2012-02-14

247

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. PMID:22698670

Benoit, Stéphane L.; McMurry, Jonathan L.; Hill, Stephanie A.; Maier, Robert J.

2014-01-01

248

Biosynthesis of the iron-guanylylpyridinol cofactor of [Fe]-hydrogenase in methanogenic archaea as elucidated by stable-isotope labeling.  

PubMed

[Fe]-hydrogenase catalyzes the reversible hydride transfer from H(2) to methenyltetrahydromethanoptherin, which is an intermediate in methane formation from H(2) and CO(2) in methanogenic archaea. The enzyme harbors a unique active site iron-guanylylpyridinol (FeGP) cofactor, in which a low-spin Fe(II) is coordinated by a pyridinol-N, an acyl group, two carbon monoxide, and the sulfur of the enzyme's cysteine. Here, we studied the biosynthesis of the FeGP cofactor by following the incorporation of (13)C and (2)H from labeled precursors into the cofactor in growing methanogenic archaea and by subsequent NMR, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS), electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FT-ICR-MS) and IR analysis of the isolated cofactor and reference compounds. The pyridinol moiety of the cofactor was found to be synthesized from three C-1 of acetate, two C-2 of acetate, two C-1 of pyruvate, one carbon from the methyl group of l-methionine, and one carbon directly from CO(2). The metabolic origin of the two CO-ligands was CO(2) rather than C-1 or C-2 of acetate or pyruvate excluding that the two CO are derived from dehydroglycine as has previously been shown for the CO-ligands in [FeFe]-hydrogenases. A formation of CO from CO(2) via direct reduction catalyzed by a nickel-dependent CO dehydrogenase or from formate could also be excluded. When the cells were grown in the presence of (13)CO, the two CO-ligands and the acyl group became (13)C-labeled, indicating either that free CO is an intermediate in their synthesis or that free CO can exchange with these iron-bound ligands. Based on these findings, we propose pathways for how the FeGP cofactor might be synthesized. PMID:22260087

Schick, Michael; Xie, Xiulan; Ataka, Kenichi; Kahnt, Jörg; Linne, Uwe; Shima, Seigo

2012-02-15

249

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. PMID:22669892

Pape, Miriam; Lambertz, Camilla; Happe, Thomas; Hemschemeier, Anja

2012-01-01

250

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

251

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

252

Molecular recognition and self-assembly special feature: Self-assembled biomimetic [2Fe2S]-hydrogenase-based photocatalyst for molecular hydrogen evolution.  

PubMed

The large-scale production of clean energy is one of the major challenges society is currently facing. Molecular hydrogen is envisaged as a key green fuel for the future, but it becomes a sustainable alternative for classical fuels only if it is also produced in a clean fashion. Here, we report a supramolecular biomimetic approach to form a catalyst that produces molecular hydrogen using light as the energy source. It is composed of an assembly of chromophores to a bis(thiolate)-bridged diiron ([2Fe2S]) based hydrogenase catalyst. The supramolecular building block approach introduced in this article enabled the easy formation of a series of complexes, which are all thoroughly characterized, revealing that the photoactivity of the catalyst assembly strongly depends on its nature. The active species, formed from different complexes, appears to be the [Fe(2)(micro-pdt)(CO)(4){PPh(2)(4-py)}(2)] (3) with 2 different types of porphyrins (5a and 5b) coordinated to it. The modular supramolecular approach was important in this study as with a limited number of building blocks several different complexes were generated. PMID:19164541

Kluwer, A M; Kapre, R; Hartl, F; Lutz, M; Spek, A L; Brouwer, A M; van Leeuwen, P W N M; Reek, J N H

2009-06-30

253

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

254

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. PMID:16349280

Boogerd, Fred C.; Ferdinandy-van Vlerken, Marijke M. A.; Mawadza, Crispen; Pronk, Annemieke F.; Stouthamer, Adriaan H.; van Verseveld, Henk W.

1994-01-01

255

Relationship of proton motive force and the F(0)F (1)-ATPase with bio-hydrogen production activity of Rhodobacter sphaeroides: effects of diphenylene iodonium, hydrogenase inhibitor, and its solvent dimethylsulphoxide.  

PubMed

Rhodobacter sphaeroides MDC 6521 was able to produce bio-hydrogen (H(2)) in anaerobic conditions under illumination. In this study the effects of the hydrogenase inhibitor-diphenylene iodonium (Ph(2)I) and its solvent dimethylsulphoxide (DMSO) on growth characteristics and H(2) production by R. sphaeroides were investigated. The results point out the concentration dependent DMSO effect: in the presence of 10 mM DMSO H(2) yield was ~6 fold lower than that of the control. The bacterium was unable to produce H(2) in the presence of Ph(2)I. In order to examine the mediatory role of proton motive force (?p) or the F(0)F(1)-ATPase in H(2) production by R. sphaeroides, the effects of Ph(2)I and DMSO on ?p and its components (membrane potential (??) and transmembrane pH gradient), and ATPase activity were determined. In these conditions ?? was of -98 mV and the reversed ?pH was +30 mV, resulting in ?p of -68 mV. Ph(2)I decreased ?? in concentrations of 20 ?M and higher; lower concentrations of Ph(2)I as DMSO had no valuable effect on ??. The R. sphaeroides membrane vesicles demonstrated significant ATPase activity sensitive to N,N'-dicyclohexylcarbodiimide. The 10-20 ?M Ph(2)I did not affect the ATPase activity, whereas 40 ?M Ph(2)I caused a marked inhibition (~2 fold) in ATPase activity. The obtained results provide novel evidence on the involvement of hydrogenase and the F(0)F(1)-ATPase in H(2) production by R. sphaeroides. Moreover, these data indicate the role of hydrogenase and the F(0)F(1)-ATPase in ?p generation. In addition, DMSO might increase an interaction of nitrogenase with CO(2), decreasing nitrogenase activity and affecting H(2) production. PMID:22689145

Hakobyan, Lilit; Gabrielyan, Lilit; Trchounian, Armen

2012-08-01

256

Inhibition of the [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F by carbon monoxide: an FTIR and EPR spectroscopic study.  

PubMed

X-ray crystallographic studies [Ogata et al., J. Am. Chem. Soc. 124 (2002) 11628-11635] have shown that carbon monoxide binds to the nickel ion at the active site of the [NiFe] hydrogenase from Desulfovibriovulgaris Miyazaki F and inhibits its catalytic function. In the present work spectroscopic aspects of the CO inhibition for this bacterial organism are reported for the first time and enable a direct comparison with the existing crystallographic data. The binding affinity of each specific redox state for CO is probed by FTIR spectro-electrochemistry. It is shown that only the physiological state Ni-SI(a) reacts with CO. The CO-inhibited product state is EPR-silent (Ni2+) and exists in two forms, Ni-SCO and Ni-SCO(red). At very negative potentials, the exogenous CO is electrochemically detached from the active site and the active Ni-R states are obtained. At temperatures below 100 K, photodissociation of the extrinsic CO from the Ni-SCO state results in Ni-SI(a) that is identified to be the only light-induced state. In the dark, rebinding of CO takes place; the recombination rate constants are of biexponential character and the activation barrier is determined to be approximately 9 kJ mol(-1). In addition, formation of a paramagnetic CO-inhibited state (Ni-CO) was observed that results from the interaction of carbon monoxide with the Ni-L state. It is proposed that the nickel in Ni-CO is in a formal monovalent state (Ni1+). PMID:19925776

Pandelia, Maria-Eirini; Ogata, Hideaki; Currell, Leslie J; Flores, Marco; Lubitz, Wolfgang

2010-02-01

257

Hydrogen photoproduction by immobilized n2-fixing cyanobacteria: understanding the role of the uptake hydrogenase in the long-term process.  

PubMed

We have investigated two approaches to enhance and extend H2 photoproduction yields in heterocystous, N2-fixing cyanobacteria entrapped in thin alginate films. In the first approach, periodic CO2 supplementation was provided to alginate-entrapped, N-deprived cells. N deprivation led to the inhibition of photosynthetic activity in vegetative cells and the attenuation of H2 production over time. Our results demonstrated that alginate-entrapped ?hupL cells were considerably more sensitive to high light intensity, N deficiency, and imbalances in C/N ratios than wild-type cells. In the second approach, Anabaena strain PCC 7120, its ?hupL mutant, and Calothrix strain 336/3 films were supplemented with N2 by periodic treatments of air, or air plus CO2. These treatments restored the photosynthetic activity of the cells and led to a high level of H2 production in Calothrix 336/3 and ?hupL cells (except for the treatment air plus CO2) but not in the Anabaena PCC 7120 strain (for which H2 yields did not change after air treatments). The highest H2 yield was obtained by the air treatment of ?hupL cells. Notably, the supplementation of CO2 under an air atmosphere led to prominent symptoms of N deficiency in the ?hupL strain but not in the wild-type strain. We propose that uptake hydrogenase activity in heterocystous cyanobacteria not only supports nitrogenase activity by removing excess O2 from heterocysts but also indirectly protects the photosynthetic apparatus of vegetative cells from photoinhibition, especially under stressful conditions that cause an imbalance in the C/N ratio in cells. PMID:25015894

Kosourov, Sergey; Leino, Hannu; Murukesan, Gayathri; Lynch, Fiona; Sivonen, Kaarina; Tsygankov, Anatoly A; Aro, Eva-Mari; Allahverdiyeva, Yagut

2014-09-01

258

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. PMID:16664984

Mahon, John D.; Nelson, Louise M.

1986-01-01

259

Biochemical studies on sulfate-reducing bacteria. XIV. Enzyme levels of adenylylsulfate reductase, inorganic pyrophosphatase, sulfite reductase, hydrogenase, and adenosine triphosphatase in cells grown on sulfate, sulfite, and thiosulfate.  

PubMed

Sulfate-reducing bacteria, Desulfovibrio vulgaris, strain Miyazaki, were grown on either sulfate, sulfite, or thiosulfate as the terminal electron acceptor. Better growth was observed on sulfite and less growth on thiosulfate than on sulfate. Enzyme levels of adenylylsulfate (APS) reductase [EC 1.8.99.2], reductant-activated inorganic pyrophosphatase [EC 3.6.1.1], sulfite reductase [EC 1.8.99.1] (desulfoviridin), hydrogenase [EC 1.12.2.1], and Mg2+-activated ATPase [EC 3.6.1.3] were compared in crude extracts of these cells at various stages of growth. 1) The specific activity of APS reductase in sulfite-grown cells was only one-fourth that in sulfate-grown cells throughout growth. Thiosulfate-grown cells had an activity intermediate between those of sulfate- and sulfite-grown cells. 2) Cells grown on sulfite had lower specific activity of reductant-activated inorganic pyrophosphatase than cells grown on sulfate or thiosulfate. 3) The specific activity of sulfite reductase (desulfoviridin) was highest in sulfite-grown cells. The sulfite medium gave the enzyme in high yield as well as with high specific activity. 4) The specific activities of hydrogenase and Mg2+-ATPase were not significantly altered by electron acceptors in the growth medium. PMID:175050

Kobayashi, K; Morisawa, Y; Ishituka, T; Ishimoto, M

1975-11-01

260

Role of different Escherichia coli hydrogenases in H+ efflux and F?F(o)-ATPase activity during glycerol fermentation at different pH values.  

PubMed

Escherichia coli is able to ferment glycerol and produce H2 by different Hyds (hydrogenases). Wild-type whole cells were shown to extrude H+ through the F1Fo-ATPase and by other means with a lower rate compared with that under glucose fermentation. At pH 7.5, H+ efflux was stimulated in fhlA mutant (with defective transcriptional activator of Hyd-3 or Hyd-4) and was lowered in hyaB or hybC mutants (with defective Hyd-1 or Hyd-2) and hyaB hybC double mutant; DCCD (dicyclohexylcarbodi-imide)-sensitive H+ efflux was observed. At pH 5.5, H+ efflux in wild-type was lower compared with that at pH 7.5; it was increased in fhlA mutant and absent in hyaB hybC mutant. Membrane vesicle ATPase activity was lower in wild-type glycerol-fermented cells at pH 7.5 compared with that in glucose-fermented cells; 100 mM K+ did not stimulate ATPase activity. The latter at pH 7.5, compared with that in wild-type, was lower in hyaB and less in hybC mutants, stimulated in the hyaB hybC mutant and suppressed in the fhlA mutant; DCCD inhibited ATPase activity. At pH 5.5, the ATPase activities of hyaB and hybC mutants had similar values and were higher compared with that in wild-type; ATPase activity was suppressed in hyaB hybC and fhlA mutants. The results indicate that during glycerol fermentation, H+ was expelled also via F1Fo. At pH 7.5 Hyd-1 and Hyd-2 but not FhlA or Hyd-4 might be related to F1Fo or have their own H+-translocating ability. At pH 5.5, both Hyd-1 and Hyd-2 more than F1Fo might be involved in H+ efflux. PMID:20662772

Blbulyan, Syuzanna; Avagyan, Arev; Poladyan, Anna; Trchounian, Armen

2011-06-01

261

The active site of the [FeFe]-hydrogenase from Desulfovibrio desulfuricans. I. Light sensitivity and magnetic hyperfine interactions as observed by electron paramagnetic resonance.  

PubMed

The hydrogen-activating cluster (H cluster) in [FeFe]-hydrogenases consists of two moieties. The [2Fe]H subcluster is a (L)(CO)(CN)Fe(mu-RS2)(mu-CO)Fe(CysS)(CO)(CN) centre. The Cys-bound Fe is called Fe1, the other iron Fe2. The Cys-thiol forms a bridge to a [4Fe-4S] cluster, the [4Fe-4S]H subcluster. We report that electron paramagnetic resonance (EPR) spectra of the 57Fe-enriched enzyme from Desulfovibrio desulfuricans in the H(ox)-CO state are consistent with a magnetic hyperfine interaction of the unpaired spin with all six Fe atoms of the H cluster. In contrast to the inactive aerobic enzyme, the active enzyme is easily destroyed by light. The [2Fe]H subcluster in some enzyme molecules loses CO by photolysis, whereupon other molecules firmly bind the released CO to form the H(ox)-CO state giving rise to the so-called axial 2.06 EPR signal. Though not destroyed by light, the H(ox)-CO state is affected by it. As demonstrated in the accompanying paper [49] two of the intrinsic COs, both bound to Fe2, can be exchanged by extrinsic 13CO during illumination at 2 degrees C. We found that only one of the three 13COs, the one at the extrinsic position, gives an EPR-detectable isotropic superhyperfine interaction of 0.6 mT. At 30 K both the inhibiting extrinsic CO bound to Fe2 and one more CO can be photolysed. EPR spectra of the photolysed products are consistent with a 3d7 system of Fe with the formal oxidation state +1. The damaged enzyme shows a light-sensitive g = 5 signal which is ascribed to an S = 3/2 form of the [2Fe](H) subcluster. The light sensitivity of the enzyme explains the occurrence of the g = 5 signal and the axial 2.06 signal in published EPR spectra of nearly all preparations studied thus far. PMID:16323020

Albracht, Simon P J; Roseboom, Winfried; Hatchikian, E Claude

2006-01-01

262

The active site of the [FeFe]-hydrogenase from Desulfovibrio desulfuricans. II. Redox properties, light sensitivity and CO-ligand exchange as observed by infrared spectroscopy.  

PubMed

In [FeFe]-hydrogenases, the H cluster (hydrogen-activating cluster) contains a di-iron centre ([2Fe]H subcluster, a (L)(CO)(CN)Fe(mu-RS2)(mu-CO)Fe(CysS)(CO)(CN) group) covalently attached to a cubane iron-sulphur cluster ([4Fe-4S]H subcluster). The Cys-thiol functions as the link between one iron (called Fe1) of the [2Fe]H subcluster and one iron of the cubane subcluster. The other iron in the [2Fe]H subcluster is called Fe2. The light sensitivity of the Desulfovibrio desulfuricans enzyme in a variety of states has been studied with infrared (IR) spectroscopy. The aerobic inactive enzyme (H(inact) state) and the CO-inhibited active form (H(ox)-CO state) were stable in light. Illumination of the H(ox) state led to a kind of cannibalization; in some enzyme molecules the H cluster was destroyed and the released CO was captured by the H clusters in other molecules to form the light-stable H(ox)-CO state. Illumination of active enzyme under 13CO resulted in the complete exchange of the two intrinsic COs bound to Fe2. At cryogenic temperatures, light induced the photodissociation of the extrinsic CO and the bridging CO of the enzyme in the H(ox)-CO state. Electrochemical redox titrations showed that the enzyme in the H(inact) state converts to the transition state (H(trans)) in a reversible one-electron redox step (E (m, pH 7) = -75 mV). IR spectra demonstrate that the added redox equivalent not only affects the [4Fe-4S]H subcluster, but also the di-iron centre. Enzyme in the H(trans) state reacts with extrinsic CO, which binds to Fe2. The H(trans) state converts irreversibly into the H(ox) state in a redox-dependent reaction most likely involving two electrons (E (m, pH 7) = -261 mV). These electrons do not end up on any of the six Fe atoms of the H cluster; the possible destiny of the two redox equivalents is discussed. An additional reversible one-electron redox reaction leads to the H(red) state (E (m, pH 7) = -354 mV), where both Fe atoms of the [2Fe]H subcluster have the same formal oxidation state. The possible oxidation states of Fe1 and Fe2 in the various enzyme states are discussed. Low redox potentials (below -500 mV) lead to destruction of the [2Fe]H subcluster. PMID:16323019

Roseboom, Winfried; De Lacey, Antonio L; Fernandez, Victor M; Hatchikian, E Claude; Albracht, Simon P J

2006-01-01

263

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

264

Mechanistic modeling of sulfur-deprived photosynthesis and hydrogen production in suspensions of Chlamydomonas reinhardtii.  

PubMed

The ability of unicellular green algal species such as Chlamydomonas reinhardtii to produce hydrogen gas via iron-hydrogenase is well known. However, the oxygen-sensitive hydrogenase is closely linked to the photosynthetic chain in such a way that hydrogen and oxygen production need to be separated temporally for sustained photo-production. Under illumination, sulfur-deprivation has been shown to accommodate the production of hydrogen gas by partially-deactivating O2 evolution activity, leading to anaerobiosis in a sealed culture. As these facets are coupled, and the system complex, mathematical approaches potentially are of significant value since they may reveal improved or even optimal schemes for maximizing hydrogen production. Here, a mechanistic model of the system is constructed from consideration of the essential pathways and processes. The role of sulfur in photosynthesis (via PSII) and the storage and catabolism of endogenous substrate, and thus growth and decay of culture density, are explicitly modeled in order to describe and explore the complex interactions that lead to H2 production during sulfur-deprivation. As far as possible, functional forms and parameter values are determined or estimated from experimental data. The model is compared with published experimental studies and, encouragingly, qualitative agreement for trends in hydrogen yield and initiation time are found. It is then employed to probe optimal external sulfur and illumination conditions for hydrogen production, which are found to differ depending on whether a maximum yield of gas or initial production rate is required. The model constitutes a powerful theoretical tool for investigating novel sulfur cycling regimes that may ultimately be used to improve the commercial viability of hydrogen gas production from microorganisms. PMID:24026984

Williams, C R; Bees, M A

2014-02-01

265

Using Stable Isotopes to Trace Microbial Hydrogen Production Pathways  

NASA Astrophysics Data System (ADS)

Biological H2 production by hydrogenase enzymes (H2ases) plays an important role in anaerobic microbial metabolism and community structure. Despite considerable progress in elucidating H2 metabolism, the regulation of and flux through key H2 production pathways remain largely undefined. Our goal is to improve understanding of biological H2 production by using H isotope ratios to dissect proton fluxes through different H2ase enzymes and from different substrates. We hypothesized that the isotope ratio of H2 produced by various hydrogenases (H2ase) would differ, and that the H isotope ratios would allow us to define the contribution of different enzymes when more than one is present in vivo. We chose Shewanella oneidensis (S.o.) MR-1, a facultative anaerobe capable of transferring electrons to a variety of terminal acceptors, including protons, as a model system for in vivo studies. S. o. encodes one [FeFe]- and one [NiFe]-H2ase. We purified three [FeFe]-H2ases (S.o., Clostridium pasteurianum, and Chlamydomonas reinhardtii) and two [NiFe]-H2ases (S. o. and Desulfovibrio fructosovorans) to test the isotope fractionation associated with activity by each enzyme in vitro. For in vivo analysis we used wild-type S.o. as well as electron transfer-deficient and H2ase-deficient strains. We employed batch cultures using lactate as an electron donor and O2 as an initial electron acceptor (with H2 production after O2 consumption). The five H2ases we tested all had a unique isotope fractionation. Measurements of H2 produced in vivo showed distinct periods of H2 production having isotope signatures consistent with in vitro results. Isotope data as well as studies of H2 production by mutants in the genes encoding either the [NiFe]-H2ase or the [FeFe]-H2ase, respectively, show that the [NiFe]- and [FeFe]- H2ases became active at different times. The [NiFe]-H2ase both produces and consumes H2 before the [FeFe]-H2ase becomes active. RNA analysis is consistent with up regulation of different hydrogenases at different points in the culture’s growth, but presents a mystery. Transcription of the [NiFe]-H2ase is more coincident with detection of H2 production and uptake by the protein. The [FeFe]-H2ase gene, however, undergoes a burst of transcription long before H2 production by the protein is detected. A second burst of transcription of the gene coincides with H2 production. We are working towards identifying key conditions that direct hydrogenase activity (including redox conditions and availability of auxiliary electron acceptors). Taken together we show that different H2ases express different fractionation factors in vitro, and H isotope ratios can be exploited to dissect pathways of H2 production in vivo.

Moran, J.; Hill, E.; Bartholomew, R.; Yang, H.; Shi, L.; Ostrom, N. E.; Gandhi, H.; Hegg, E.; Kreuzer, H.

2010-12-01

266

Ferric iron reduction by Desulfovibrio vulgaris Hildenborough wild type and energy metabolism mutants.  

PubMed

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 weight cytochrome (Hmc) complex, respectively, were able to reduce Fe(III) chelated with nitrilotriacetic acid (NTA), but not insoluble ferric oxide, with lactate as the electron donor. The rate and extent of Fe(III)-NTA reduction followed the order hyn = WT > hmc > hyd, suggesting that reduction of soluble Fe(III) is a periplasmic process that requires the presence of periplasmic [FeFe] hydrogenase. Reduction of Fe(III)-NTA was not coupled to cell growth. In fact cell concentrations declined when D. vulgaris was incubated with Fe(III)-NTA as the only electron acceptor. Wild type and mutant cells reducing a limiting concentration of sulfate (2 mM), reduced Fe(III)-NTA with similar rates. However, these were similarly incapable of catalyzing subsequent lactate-dependent reduction of Fe(III)-NTA to completion. Periplasmic reduction of Fe(III)-NTA appeared to inhibit the productive, sulfate-reducing metabolism of D. vulgaris, possibly because it prevents the cycling of reducing equivalents needed to achieve a net bioenergetic benefit. PMID:17588123

Park, Hyung Soo; Lin, Shiping; Voordouw, Gerrit

2008-01-01

267

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

268

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

269

Microstructure, mechanical property, biodegradation behavior, and biocompatibility of biodegradable FeFe2O3 composites  

E-print Network

applications. On the other hand, from the mechanical point of view, the properties of 316L stainless steelMicrostructure, mechanical property, biodegradation behavior, and biocompatibility of biodegradable behaviors, and in vitro biocompatibility of Fe� Fe2O3 composites fabricated by spark plasma sintering were

Zheng, Yufeng

270

Shock compression of Fe-FeS mixture up to 204 GPa  

NASA Astrophysics Data System (ADS)

AbstractUsing a two-stage light gas gun, we obtained new shock wave Hugoniot data for an iron-sulfur alloy (Fe-11.8wt%S) over the pressure range of 94-204 GPa. A least-squares fit to the Hugoniot data yields a linear relationship between shock velocity DS and particle velocity u, DS (km/s) =3.60(0.14) +1.57(0.05) u. The measured Hugoniot data for Fe-11.8wt%S agree well with the calculated results based on the thermodynamic parameters of Fe and FeS using the additive law. By comparing the calculated densities along the adiabatic core temperature with the PREM density profile, an iron core with 10 wt.% sulfur (S) provides the best solution for the composition of the Earth's outer core.</p> <div class="credits"> <p class="dwt_author">Huang, Haijun; Wu, Shijie; Hu, Xiaojun; Wang, Qingsong; Wang, Xiang; Fei, Yingwei</p> <p class="dwt_publisher"></p> <p class="publishDate">2013-02-01</p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">271</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://cdsweb.cern.ch/record/1702520"> <span id="translatedtitle">A hidden reservoir of <span class="hlt">Fe/FeS</span> in interstellar silicates?</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.osti.gov/epsearch/">E-print Network</a></p> <p class="result-summary">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. We study the incorporation of iron and sulphur into amorphous silicates of olivine- and pyroxene-type and their effects on the dust spectroscopy and thermal emission. 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. Iron sulphide inclusions within amorphous silicates that contain iron metal inclusions shows 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 $\\mu$m silicate band. The assumption of amorphous olivine-type and pyroxene-typ...</p> <div class="credits"> <p class="dwt_author">Köhler, M; Ysard, N</p> <p class="dwt_publisher"></p> <p class="publishDate">2014-01-01</p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">272</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://ntrs.nasa.gov/search.jsp?R=19850012911&hterms=Mathematica&qs=Ntx%3Dmode%2Bmatchall%26Ntk%3DAll%26N%3D0%26No%3D30%26Ntt%3DMathematica"> <span id="translatedtitle"><span class="hlt">Modeling</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p class="result-summary">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 <span class="hlt">model</span> 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.</p> <div class="credits"> <p class="dwt_author">Zook, H. A.</p> <p class="dwt_publisher"></p> <p class="publishDate">1985-01-01</p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">273</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1056147"> <span id="translatedtitle">Sodium Stimulation of Uptake <span class="hlt">Hydrogenase</span> Activity In Symbiotic Rhizobium1</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p class="result-summary">Initial observations showed a 100% increase in H2-uptake (Hup) activity of Rhizobium leguminosarum strain 3855 in pea root nodules (Pisum sativum L. cv Alaska) on plants growing in a baked clay substrate relative to those growing in vermiculite, and an investigation of nutrient factors responsible for the phenomenon was initiated. Significantly greater Hup activity was first measured in the clay-grown plants 24 days after germination, and higher activity was maintained relative to the vermiculite treatment until experiments were terminated at day 32. The increase in Hup activity was associated with a decrease in H2 evolution for plants with comparable rates of acetylene reduction. Analyses of the clay showed that it contained more Na+ (29 versus 9 milligrams per kilogram) and less K+ (6 versus 74 milligrams per kilogram) than the vermiculite. Analyses of plants, however, showed a large increase in Na+ concentration of clay-grown plants with a much smaller reduction in K+ concentration. In tests with the same organisms in a hydroponic system with controlled pH, 40 millimolar NaCl increased Hup activity more than 100% over plants grown in solutions lacking NaCl. Plants with increased Hup activity, however, did not have greater net carbon or total nitrogen assimilation. KCl treatments from 5 to 80 millimolar produced slight increased in Hup activity at 10 millimolar KCl, and tests with other salts in the hydroponic system indicated that only Na+ strongly promoted Hup activity. Treating vermiculite with 50 millimolar NaCl increased Na+ concentration in pea plant tissue and greatly promoted Hup activity of root nodules in a manner analogous to the original observation with the clay rooting medium. A wider generality of the phenomenon was suggested by demonstrating that exogenous Na+ increased Hup activity of other R. leguminosarum strains and promoted Hup activity of R. meliloti strain B300 in alfalfa (Medicago sativa L.). PMID:16665057</p> <div class="credits"> <p class="dwt_author">Kapulnik, Yoram; Phillips, Donald A.</p> <p class="dwt_publisher"></p> <p class="publishDate">1986-01-01</p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">274</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://inside.mines.edu/~jspear/pdf/publications/Boyd%20et%20al_2010_hydA%20in%20YNP.pdf"> <span id="translatedtitle">ORIGINAL ARTICLE [FeFe]-<span class="hlt">hydrogenase</span> in Yellowstone National Park</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.osti.gov/epsearch/">E-print Network</a></p> <p class="result-summary">), hydrothermal vents (Jannasch and Mottl, 1985), salt-evaporation ponds (Hoehler et al., 2001) and a range of terrestrial geothermal features (Conrad et al., 1985; Inskeep and McDermott, 2005; Spear et al., 2005). H2</p> <div class="credits"> <p class="dwt_author"></p> <p class="dwt_publisher"></p> <p class="publishDate"></p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">275</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.lifesci.dundee.ac.uk/groups/tracy_palmer/pdfs/2005/Jack2005.pdf"> <span id="translatedtitle">International <span class="hlt">Hydrogenases</span> Conference 2004 105 Common principles in the biosynthesis</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.osti.gov/epsearch/">E-print Network</a></p> <p class="result-summary">nitrate, nitrite, fumarate, trimethylamine N-oxide and DMSO as terminal electron acceptors as alter electron acceptors. In addition, NADH, formate, glycerol 3-phos- phate, succinate, lactate, pyruvate from the cytoplasm by the twin-arginine transport apparatus. Such proteins contain distinctive N-terminal</p> <div class="credits"> <p class="dwt_author">Palmer, Tracy</p> <p class="dwt_publisher"></p> <p class="publishDate"></p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">276</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.osti.gov/doepatents/biblio/894277"> <span id="translatedtitle">Hydrogen Production Using <span class="hlt">Hydrogenase</span>-Containing Oxygenic Photosynthetic Organisms</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.osti.gov/doepatents">DOEpatents</a></p> <p class="result-summary">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.</p> <div class="credits"> <p class="dwt_author">Melis, A.; Zhang, L.; Benemann, J. R.; Forestier, M.; Ghirardi, M.; Seibert, M.</p> <p class="dwt_publisher"></p> <p class="publishDate">2006-01-24</p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">277</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.osti.gov/scitech/biblio/1091462"> <span id="translatedtitle">Ion irradiation of <span class="hlt">Fe-Fe</span> oxide core-shell nanocluster films: Effect of interface on stability of magnetic properties</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p class="result-summary">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.</p> <div class="credits"> <p class="dwt_author">McCloy, John S.; Jiang, Weilin; Droubay, Timothy C.; Varga, Tamas; Kovarik, Libor; Sundararajan, Jennifer A.; Kaur, Maninder; Qiang, You; Burks, Edward; Liu, Kai</p> <p class="dwt_publisher"></p> <p class="publishDate">2013-08-23</p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">278</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.osti.gov/scitech/biblio/22218100"> <span id="translatedtitle">Ion irradiation of <span class="hlt">Fe-Fe</span> oxide core-shell nanocluster films: Effect of interface on stability of magnetic properties</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p class="result-summary">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.</p> <div class="credits"> <p class="dwt_author">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)</p> <p class="dwt_publisher"></p> <p class="publishDate">2013-08-28</p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">279</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.osti.gov/scitech/servlets/purl/1051787"> <span id="translatedtitle">Toward a rigorous network of protein-protein interactions of the <span class="hlt">model</span> sulfate reducer Desulfovibrio vulgaris Hildenborough</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p class="result-summary">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 <span class="hlt">model</span> 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 <span class="hlt">hydrogenase</span>, unique electron transfer routes associated with different oxidoreductases, and the possible role of methylation in regulating sulfate reduction.</p> <div class="credits"> <p class="dwt_author">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.</p> <p class="dwt_publisher"></p> <p class="publishDate">2011-05-01</p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">280</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.ncbi.nlm.nih.gov/pubmed/21738675"> <span id="translatedtitle">Towards a rigorous network of protein-protein interactions of the <span class="hlt">model</span> sulfate reducer Desulfovibrio vulgaris Hildenborough.</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p class="result-summary">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 <span class="hlt">model</span> 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 <span class="hlt">hydrogenase</span>, unique electron transfer routes associated with different oxidoreductases, and the possible role of methylation in regulating sulfate reduction. PMID:21738675</p> <div class="credits"> <p class="dwt_author">Chhabra, Swapnil R; Joachimiak, Marcin P; 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</p> <p class="dwt_publisher"></p> <p class="publishDate">2011-01-01</p> </div> </div> </div> </div> <div id="filter_results_form" class="filter_results_form floatContainer" style="visibility: visible;"> <div style="width:100%" id="PaginatedNavigation" class="paginatedNavigationElement"> <a id="FirstPageLink" onclick='return showDiv("page_1");' href="#" title="First Page"> <img id="FirstPageLinkImage" class="Icon" src="http://www.science.gov/scigov/images/icon.first.18x20.png" alt="First Page" /></a> <a id="PreviousPageLink" onclick='return showDiv("page_13");' href="#" title="Previous Page"> <img id="PreviousPageLinkImage" 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showDiv("page_24");' href="#">24</a> <a onClick='return showDiv("page_25");' href="#">25</a> </span> </span> <a id="NextPageLink" onclick='return showDiv("page_16");' href="#" title="Next Page"> <img id="NextPageLinkImage" class="Icon" src="http://www.science.gov/scigov/images/icon.next.18x20.png" alt="Next Page" /></a> <a id="LastPageLink" onclick='return showDiv("page_25.0");' href="#" title="Last Page"> <img id="LastPageLinkImage" class="Icon" src="http://www.science.gov/scigov/images/icon.last.18x20.png" alt="Last Page" /></a> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">281</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3985925"> <span id="translatedtitle">Bioinspired <span class="hlt">Hydrogenase</span> <span class="hlt">Models</span>: 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</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p class="result-summary">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. PMID:24748710</p> <div class="credits"> <p class="dwt_author"></p> <p class="dwt_publisher"></p> <p class="publishDate">2014-01-01</p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">282</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.ncbi.nlm.nih.gov/pubmed/25055974"> <span id="translatedtitle">Genome sequence of the <span class="hlt">model</span> sulfate reducer Desulfovibrio gigas: a comparative analysis within the Desulfovibrio genus.</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p class="result-summary">Desulfovibrio gigas is a <span class="hlt">model</span> organism of sulfate-reducing bacteria of which energy metabolism and stress response have been extensively studied. The complete genomic context of this organism was however, not yet available. The sequencing of the D. gigas genome provides insights into the integrated network of energy conserving complexes and structures present in this bacterium. Comparison with genomes of other Desulfovibrio spp. reveals the presence of two different CRISPR/Cas systems in D. gigas. Phylogenetic analysis using conserved protein sequences (encoded by rpoB and gyrB) indicates two main groups of Desulfovibrio spp, being D. gigas more closely related to D. vulgaris and D. desulfuricans strains. Gene duplications were found such as those encoding fumarate reductase, formate dehydrogenase, and superoxide dismutase. Complexes not yet described within Desulfovibrio genus were identified: Mnh complex, a v-type ATP-synthase as well as genes encoding the MinCDE system that could be responsible for the larger size of D. gigas when compared to other members of the genus. A low number of <span class="hlt">hydrogenases</span> and the absence of the codh/acs and pfl genes, both present in D. vulgaris strains, indicate that intermediate cycling mechanisms may contribute substantially less to the energy gain in D. gigas compared to other Desulfovibrio spp. This might be compensated by the presence of other unique genomic arrangements of complexes such as the Rnf and the Hdr/Flox, or by the presence of NAD(P)H related complexes, like the Nuo, NfnAB or Mnh. PMID:25055974</p> <div class="credits"> <p class="dwt_author">Morais-Silva, Fabio O; Rezende, Antonio Mauro; Pimentel, Catarina; Santos, Catia I; Clemente, Carla; Varela-Raposo, Ana; Resende, Daniela M; da Silva, Sofia M; de Oliveira, Luciana Márcia; Matos, Marcia; Costa, Daniela A; Flores, Orfeu; Ruiz, Jerónimo C; Rodrigues-Pousada, Claudina</p> <p class="dwt_publisher"></p> <p class="publishDate">2014-08-01</p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">283</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://academic.research.microsoft.com/Publication/59790863"> <span id="translatedtitle">Self-assembled biomimetic [2Fe2S]-<span class="hlt">hydrogenase</span>-based photocatalyst for molecular hydrogen evolution</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://academic.research.microsoft.com/">Microsoft Academic Search </a></p> <p class="result-summary">The large-scale production of clean energy is one of the major challenges society is currently facing. Molecular hydrogen is envisaged as a key green fuel for the future, but it becomes a sustainable alternative for classical fuels only if it is also produced in a clean fashion. Here, we report a supramolecular biomimetic approach to form a catalyst that produces</p> <div class="credits"> <p class="dwt_author">A. M. Kluwer; R. Kapre; F. Hartl; M. Lutz; A. L. Spek; A. M. Brouwer; Leeuwen van P. W. N. M; J. N. H. Reek</p> <p class="dwt_publisher"></p> <p class="publishDate">2009-01-01</p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">284</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://academic.research.microsoft.com/Publication/59694119"> <span id="translatedtitle">Self-assembled biomimetic [2Fe2S]-<span class="hlt">hydrogenase</span>-based photocatalyst for molecular hydrogen evolution</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://academic.research.microsoft.com/">Microsoft Academic Search </a></p> <p class="result-summary">The large-scale production of clean energy is one of the major\\u000achallenges society is currently facing. Molecular hydrogen is envisaged\\u000aas a key green fuel for the future, but it becomes a\\u000asustainable alternative for classical fuels only if it is also produced\\u000ain a clean fashion. Here, we report a supramolecular biomimetic\\u000aapproach to form a catalyst that produces</p> <div class="credits"> <p class="dwt_author">A. M. Kluwer; R. Kapre; F. Hartl; M. Lutz; A. L. Spek; A. M. Brouwer; P. W. N. M. van Leeuwen; J. N. H. Reek</p> <p class="dwt_publisher"></p> <p class="publishDate">2009-01-01</p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">285</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://carnegiedpb.stanford.edu/sites/dpb.carnegiescience.edu/files/DubiniJBC2009.pdf"> <span id="translatedtitle">Flexibility in Anaerobic Metabolism as Revealed in a Mutant of Chlamydomonas reinhardtii Lacking <span class="hlt">Hydrogenase</span> Activity</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.osti.gov/epsearch/">E-print Network</a></p> <p class="result-summary">contribute to NAD(P)H reoxidation, and continued glycolysis and fermentation in the absence of O2 in the abundance of mRNAs encoding two malate forming enzymes, pyruvate carboxylase and malic enzyme, are observed Chlamydomonas has a single gene encoding pyruvate carboxylase, it has six genes encoding putative malic enzymes</p> <div class="credits"> <p class="dwt_author"></p> <p class="dwt_publisher"></p> <p class="publishDate"></p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">286</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://jb.asm.org/cgi/reprint/188/17/6143.pdf"> <span id="translatedtitle">Regulation of Uptake <span class="hlt">Hydrogenase</span> and Effects of Hydrogen Utilization on Gene Expression in Rhodopseudomonas palustris</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://academic.research.microsoft.com/">Microsoft Academic Search </a></p> <p class="result-summary">Rhodopseudomonas palustris is a purple, facultatively phototrophic bacterium that uses hydrogen gas as an electron donor for carbon dioxide fixation during photoautotrophic growth or for ammonia synthesis during nitrogen fixation. It also uses hydrogen as an electron supplement to enable the complete assim- ilation of oxidized carbon compounds, such as malate, into cell material during photoheterotrophic growth. The R. palustris</p> <div class="credits"> <p class="dwt_author">Federico E. Rey; Yasuhiro Oda; Caroline S. Harwood</p> <p class="dwt_publisher"></p> <p class="publishDate">2006-01-01</p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">287</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://academic.research.microsoft.com/Publication/34388591"> <span id="translatedtitle">Autotrophic growth of nitrogen-fixing Azospirillum species and partial characterization of <span class="hlt">hydrogenase</span> from strain CC</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://academic.research.microsoft.com/">Microsoft Academic Search </a></p> <p class="result-summary">Out of 15 strains ofAzospirillum spp. isolated from the roots of different plants, only 4 (CY, M, CC, and AM) were able to grow autotrophically with H2 and CO2. All of them showed H2 uptake in the presence of oxygen or methylene blue and ribulose-1,5-bisphosphate carboxylase activity. Among the four strains, strain CC isolated from the roots ofCenchrus cilliaris showed</p> <div class="credits"> <p class="dwt_author">Kolluru V. B. R. Tilak; Klaus Schneider; Hans G. Schlegel</p> <p class="dwt_publisher"></p> <p class="publishDate">1986-01-01</p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">288</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://kuscholarworks.ku.edu/handle/1808/10059"> <span id="translatedtitle">Niche <span class="hlt">Modeling</span>: <span class="hlt">Model</span> Evaluation</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.osti.gov/epsearch/">E-print Network</a></p> <p class="result-summary">Ecological niche <span class="hlt">modeling</span> has become a very popular tool in ecological and biogeographic studies across broad extents. The tool is used in hundreds of publications each year now, but some fundamental aspects of the approach have seen a fair amount...</p> <div class="credits"> <p class="dwt_author">Peterson, A. Townsend</p> <p class="dwt_publisher"></p> <p class="publishDate">2012-08-29</p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">289</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.math.tamu.edu/~rowell/RowellQCSem.pdf"> <span id="translatedtitle">Quantum Circuit <span class="hlt">Model</span> Topological <span class="hlt">Model</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.osti.gov/epsearch/">E-print Network</a></p> <p class="result-summary">Quantum Circuit <span class="hlt">Model</span> Topological <span class="hlt">Model</span> Comparison of <span class="hlt">Models</span> Topological Quantum Computation Eric Rowell Texas A&M University October 2010 Eric Rowell Topological Quantum Computation #12;Quantum Circuit <span class="hlt">Model</span> Topological <span class="hlt">Model</span> Comparison of <span class="hlt">Models</span> Outline 1 Quantum Circuit <span class="hlt">Model</span> Gates, Circuits</p> <div class="credits"> <p class="dwt_author">Rowell, Eric C.</p> <p class="dwt_publisher"></p> <p class="publishDate"></p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">290</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.im.ufrj.br/~coloquiomea/apresentacoes/lopes.pdf"> <span id="translatedtitle">Basic <span class="hlt">model</span> Basic <span class="hlt">model</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.osti.gov/epsearch/">E-print Network</a></p> <p class="result-summary">Spearman's (1904) seminal paper on the American Journal of Psychology entitled "General Inteligente, British Journal of Mathematical and Statistical Psychology, 48, 211-220. 3 / 66 #12;Early days Basic <span class="hlt">model</span> that Spearman invented factor analysis but his almost exclusive concern with the notion of a general factor</p> <div class="credits"> <p class="dwt_author">Liu, I-Shih</p> <p class="dwt_publisher"></p> <p class="publishDate"></p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">291</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://oaspub.epa.gov/eims/eimsapi.dispdetail?deid=137225"> <span id="translatedtitle"><span class="hlt">MODEL</span> DEVELOPMENT - DOSE <span class="hlt">MODELS</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://oaspub.epa.gov/eims/query.page">EPA Science Inventory</a></p> <p class="result-summary"><span class="hlt">Model</span> Development Humans are exposed to mixtures of chemicals from multiple pathways and routes. These exposures may result from a single event or may accumulate over time if multiple exposure events occur. The traditional approach of assessing risk from a single chemica...</p> <div class="credits"> <p class="dwt_author"></p> <p class="dwt_publisher"></p> <p class="publishDate"></p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">292</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3807489"> <span id="translatedtitle">Flexibility of Syntrophic Enzyme Systems in Desulfovibrio Species Ensures Their Adaptation Capability to Environmental Changes</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p class="result-summary">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 <span class="hlt">hydrogenases</span>) and the ratio shift in electron carriers used for interspecies metabolite exchange (hydrogen/formate). A putative monomeric [<span class="hlt">Fe-Fe</span>] <span class="hlt">hydrogenase</span> 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. PMID:23974031</p> <div class="credits"> <p class="dwt_author">Meyer, Birte; Kuehl, Jennifer V.; Deutschbauer, Adam M.; Arkin, Adam P.</p> <p class="dwt_publisher"></p> <p class="publishDate">2013-01-01</p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">293</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://ntrs.nasa.gov/search.jsp?R=19860023426&hterms=louis+owen&qs=Ntx%3Dmode%2Bmatchall%26Ntk%3DAll%26N%3D0%26No%3D30%26Ntt%3D%2528louis%2Bowen%2529"> <span id="translatedtitle">Assessment <span class="hlt">models</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p class="result-summary">The types of <span class="hlt">models</span> used in assessment of possible chemical perturbations to the stratosphere are reviewed. The statue of one and two dimensional <span class="hlt">models</span> are discussed. The problem of <span class="hlt">model</span> validation is covered before the status of photochemical <span class="hlt">modeling</span> efforts is discussed. A hierarchy of tests for photochemical <span class="hlt">models</span> is presented.</p> <div class="credits"> <p class="dwt_author">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.</p> <p class="dwt_publisher"></p> <p class="publishDate">1985-01-01</p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">294</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.exo.net/~donr/activities/Toilet_Model.pdf"> <span id="translatedtitle">Toilet <span class="hlt">Model</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://nsdl.org/nsdl_dds/services/ddsws1-1/service_explorer.jsp">NSDL National Science Digital Library</a></p> <p class="result-summary">In this activity, PVC pipe, plastic water bottles and vinyl tubing are used to make a simple working toilet <span class="hlt">model</span>. The <span class="hlt">model</span> shows the role of a siphon in the flushing of a toilet. Educators can pre-assemble this <span class="hlt">model</span> and use it for demonstration purposes or engage learners in the <span class="hlt">model</span> building process.</p> <div class="credits"> <p class="dwt_author">Rathjen, Don</p> <p class="dwt_publisher"></p> <p class="publishDate">2005-01-01</p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">295</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://learningcenter.nsta.org/product_detail.aspx?id=10.2505/9780873552264.1"> <span id="translatedtitle">Understanding <span class="hlt">Models</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://nsdl.org/nsdl_dds/services/ddsws1-1/service_explorer.jsp">NSDL National Science Digital Library</a></p> <p class="result-summary">Chapter 1 defines and discusses <span class="hlt">models</span> in a broad, and perhaps unusual, way. In particular, the chapter stresses the framework of personal <span class="hlt">models</span> that underlie science and learning across fields. Subsequent chapters will deal more with particular kinds of expressed <span class="hlt">models</span> that are important in science and science teaching: physical <span class="hlt">models</span>, analog <span class="hlt">models</span> and plans, mathematical <span class="hlt">models</span>, and computer simulations. Throughout, the book examines how all <span class="hlt">models</span> are important to science, how they are used, and how to use them effectively. They can and should be used not only to teach science, but also to teach students something about the process of learning and about the nature of knowledge itself.</p> <div class="credits"> <p class="dwt_author">Ireton, Shirley W.; Gilbert, Steven W.</p> <p class="dwt_publisher"></p> <p class="publishDate">2003-01-01</p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">296</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3238660"> <span id="translatedtitle">Penta-carbonyl-1?2 C,2?3 C-(4-iodo-phenyl isocyanide-1?C)(?-propane-1,3-dithiol-ato-1:2?4 S,S?:S,S?)iron(I)(Fe--Fe)</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p class="result-summary">In the title compound, [Fe2(C7H4IN)(C3H6S2)(CO)5], the <span class="hlt">Fe—Fe</span> distance of 2.5156?(11)?Å compares well with that in related <span class="hlt">model</span> structures. The phenyl isocyanide ligand is in the basal position and trans to the S atoms of the propane­dithiol­ate ligand due to steric hindrance. The crystal structure features C—H?O inter­actions. PMID:22199551</p> <div class="credits"> <p class="dwt_author">Zhu, Jinli; Tang, Yanfeng; Jiang, Guo -Min; Wang, Miao; Hua, Ping</p> <p class="dwt_publisher"></p> <p class="publishDate">2011-01-01</p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">297</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.math.uic.edu/~jbaldwin/pub/ist09a.pdf"> <span id="translatedtitle"><span class="hlt">Model</span> Theory: Infinitary <span class="hlt">Model</span> Theory</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.osti.gov/epsearch/">E-print Network</a></p> <p class="result-summary">'. #12;Infinitary <span class="hlt">Model</span> Theory: Covers of Abelian Varieties John T. Baldwin Hierarchy for L1, 1 completeInfinitary <span class="hlt">Model</span> Theory: Covers of Abelian Varieties John T. Baldwin Infinitary <span class="hlt">Model</span> Theory: Covers of Abelian Varieties John T. Baldwin August 16, 2009 #12;Infinitary <span class="hlt">Model</span> Theory: Covers</p> <div class="credits"> <p class="dwt_author">Baldwin, John T.</p> <p class="dwt_publisher"></p> <p class="publishDate"></p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">298</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.osti.gov/scitech/servlets/purl/5813096"> <span id="translatedtitle">Supermatrix <span class="hlt">models</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p class="result-summary">Radom matrix <span class="hlt">models</span> based on an integral over supermatrices are proposed as a natural extension of bosonic matrix <span class="hlt">models</span>. The subtle nature of superspace integration allows these <span class="hlt">models</span> to have very different properties from the analogous bosonic <span class="hlt">models</span>. Two choices of integration slice are investigated. One leads to a perturbative structure which is reminiscent of, and perhaps identical to, the usual Hermitian matrix <span class="hlt">models</span>. Another leads to an eigenvalue reduction which can be described by a two component plasma in one dimension. A stationary point of the <span class="hlt">model</span> is described.</p> <div class="credits"> <p class="dwt_author">Yost, S.A.</p> <p class="dwt_publisher"></p> <p class="publishDate">1991-05-01</p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">299</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://eric.ed.gov/?q=3%2c1&pg=2&id=EJ770219"> <span id="translatedtitle">Synthesis, Purification, and Characterization of a [mu]-(1,3-Propanedithiolato)-Hexacarbonyldiiron</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.eric.ed.gov/ERICWebPortal/search/extended.jsp?_pageLabel=advanced">ERIC Educational Resources Information Center</a></p> <p class="result-summary">A project which exposes students to biologically important transition-metal chemistry is illustrated by taking an example of the iron-carbonyl compound, [mu]-(1,3-Propanedithiolaro)-hexa-carbonyldiiron as a structural <span class="hlt">model</span> for an iron-only <span class="hlt">hydro-genase</span>. The project provides the students with experience of Schlenk line techniques, purification,…</p> <div class="credits"> <p class="dwt_author">Works, Carmen F.</p> <p class="dwt_publisher"></p> <p class="publishDate">2007-01-01</p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">300</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3647810"> <span id="translatedtitle">[?-3-(Methyl-sulfan-yl)benzene-1,2-di-thiol-ato-1:2?4 S,S?:S,S?]bis-[tri-carbonyl-iron(I)</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p class="result-summary">The title compound, [Fe2(C7H6S3)(CO)6], was prepared as a biomimic for the active site of [FeFe]-<span class="hlt">hydrogenases</span>. The central Fe2S2 core is in a butterfly conformation and each FeI atom has a pseudo-square-pyramidal coordination by three O atoms and two S atoms. The <span class="hlt">Fe—Fe</span> distance is 2.471?(2)?Å and the dihedral angle between the two Fe—S—Fe planes is 78.96?(7)°. The least-squares plane through the –S(C7H6S)S– bridge nearly bis­ects the mol­ecular structure: except for the two Fe(CO)3 units, all atoms are in this plane with an average deviation from the plane of 0.028?(3)?Å. In the crystal, the mol­ecules are linked into chains along [001] by C—H??(arene) inter­actions. PMID:23723776</p> <div class="credits"> <p class="dwt_author">Yang, Yong; Wang, Ning; Chen, Lin</p> <p class="dwt_publisher"></p> <p class="publishDate">2013-01-01</p> </div> </div> </div> </div> <div id="filter_results_form" class="filter_results_form floatContainer" style="visibility: visible;"> <div style="width:100%" id="PaginatedNavigation" class="paginatedNavigationElement"> <a id="FirstPageLink" onclick='return showDiv("page_1");' href="#" title="First Page"> <img id="FirstPageLinkImage" class="Icon" src="http://www.science.gov/scigov/images/icon.first.18x20.png" alt="First Page" /></a> <a id="PreviousPageLink" onclick='return showDiv("page_14");' href="#" title="Previous Page"> <img id="PreviousPageLinkImage" class="Icon" src="http://www.science.gov/scigov/images/icon.previous.18x20.png" alt="Previous Page" /></a> <span id="PageLinks" class="pageLinks"> <span> <a onClick='return showDiv("page_1");' href="#">1</a> <a onClick='return showDiv("page_2");' href="#">2</a> <a 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href="#">10</a> <a onClick='return showDiv("page_11");' href="#">11</a> <a onClick='return showDiv("page_12");' href="#">12</a> <a onClick='return showDiv("page_13");' href="#">13</a> <a onClick='return showDiv("page_14");' href="#">14</a> <a onClick='return showDiv("page_15");' href="#">15</a> <a style="font-weight: bold;">16</a> <a onClick='return showDiv("page_17");' href="#">17</a> <a onClick='return showDiv("page_18");' href="#">18</a> <a onClick='return showDiv("page_19");' href="#">19</a> <a onClick='return showDiv("page_20");' href="#">20</a> <a onClick='return showDiv("page_21");' href="#">21</a> <a onClick='return showDiv("page_22");' href="#">22</a> <a onClick='return showDiv("page_23");' href="#">23</a> <a onClick='return showDiv("page_24");' href="#">24</a> <a onClick='return showDiv("page_25");' href="#">25</a> </span> </span> <a id="NextPageLink" onclick='return showDiv("page_17");' href="#" title="Next Page"> <img id="NextPageLinkImage" class="Icon" src="http://www.science.gov/scigov/images/icon.next.18x20.png" alt="Next Page" /></a> <a id="LastPageLink" onclick='return showDiv("page_25.0");' href="#" title="Last Page"> <img id="LastPageLinkImage" class="Icon" src="http://www.science.gov/scigov/images/icon.last.18x20.png" alt="Last Page" /></a> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">301</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://oaspub.epa.gov/eims/eimsapi.dispdetail?deid=2808"> <span id="translatedtitle"><span class="hlt">MODELS</span> - 3</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://oaspub.epa.gov/eims/query.page">EPA Science Inventory</a></p> <p class="result-summary"><span class="hlt">Models</span>-3 is a third generation air quality <span class="hlt">modeling</span> system that contains a variety of tools to perform research and analysis of critical environmental questions and problems. These tools provide regulatory analysts and scientists with quicker results, greater scientific accuracy ...</p> <div class="credits"> <p class="dwt_author"></p> <p class="dwt_publisher"></p> <p class="publishDate"></p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">302</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://oaspub.epa.gov/eims/eimsapi.dispdetail?deid=151530"> <span id="translatedtitle">ENTRAINMENT <span class="hlt">MODELS</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://oaspub.epa.gov/eims/query.page">EPA Science Inventory</a></p> <p class="result-summary">This presentation presented information on entrainment <span class="hlt">models</span>. Entrainment <span class="hlt">models</span> use entrainment hypotheses to express the continuity equation. The advantage is that plume boundaries are known. A major disadvantage is that the problems that can be solved are rather simple. The ...</p> <div class="credits"> <p class="dwt_author"></p> <p class="dwt_publisher"></p> <p class="publishDate"></p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">303</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://grad.bio.uci.edu/ecoevo/ahebling/Research/GK-12_files/Modeling_Presentation.pdf"> <span id="translatedtitle"><span class="hlt">Modeling</span> Transformation</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.osti.gov/epsearch/">E-print Network</a></p> <p class="result-summary"><span class="hlt">Modeling</span> Transformation What does each step do? #12;Transformation Procedure #12;Transformation Procedure #12;Building Your <span class="hlt">Model</span> Yarn = chromosomal DNA Beads = ribosomes Black velcro = plasmid DNA Green velcro = GFP gene Pink velcro</p> <div class="credits"> <p class="dwt_author">Rose, Michael R.</p> <p class="dwt_publisher"></p> <p class="publishDate"></p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">304</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://learningcenter.nsta.org/product_detail.aspx?id=10.2505/4/tst04_071_07_48"> <span id="translatedtitle"><span class="hlt">Modeling</span> Convection</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://nsdl.org/nsdl_dds/services/ddsws1-1/service_explorer.jsp">NSDL National Science Digital Library</a></p> <p class="result-summary">Typically, teachers use simple <span class="hlt">models</span> that employ differences in temperature and density to help students visualize convection. However, most of these <span class="hlt">models</span> are incomplete or merely hint at (instead of <span class="hlt">model</span>) convective circulation. In order to make the use of <span class="hlt">models</span> more effective, the authors developed an alternative system that uses a simple, low-cost apparatus that not only maintains dynamic convective circulation, but also illustrates two adjacent cells that teaches students about Earth's processes.</p> <div class="credits"> <p class="dwt_author">Schulz, Amanda; Ebert, James R.; Elliott, Nancy A.</p> <p class="dwt_publisher"></p> <p class="publishDate">2004-09-01</p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">305</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.dnalc.org/resources/animations/model_organisms.html"> <span id="translatedtitle"><span class="hlt">Model</span> Organisms</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://nsdl.org/nsdl_dds/services/ddsws1-1/service_explorer.jsp">NSDL National Science Digital Library</a></p> <p class="result-summary">Each <span class="hlt">model</span> organism has its own advantages and disadvantages. Choosing an appropriate <span class="hlt">model</span> depends on the question being asked. Many laboratories find it useful to perform parallel experiments in two or more <span class="hlt">model</span> systems to understand different aspects of a biochemical process. This animation from Cold Spring Harbor Laboratory's Dolan DNA Learning Center presents <span class="hlt">Model</span> Organisms through a series of illustrations of the processes involved.</p> <div class="credits"> <p class="dwt_author"></p> <p class="dwt_publisher"></p> <p class="publishDate">2012-11-19</p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">306</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://oaspub.epa.gov/eims/eimsapi.dispdetail?deid=240424"> <span id="translatedtitle">Phoenix <span class="hlt">model</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://oaspub.epa.gov/eims/query.page">EPA Science Inventory</a></p> <p class="result-summary">Phoenix (formerly referred to as the Second Generation <span class="hlt">Model</span> or SGM) is a global general equilibrium <span class="hlt">model</span> designed to analyze energy-economy-climate related questions and policy implications in the medium- to long-term. This <span class="hlt">model</span> disaggregates the global economy into 26 industr...</p> <div class="credits"> <p class="dwt_author"></p> <p class="dwt_publisher"></p> <p class="publishDate"></p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">307</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://folk.uio.no/rnymoen/imfpcg.pdf"> <span id="translatedtitle">Econometric <span class="hlt">Modelling</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://academic.research.microsoft.com/">Microsoft Academic Search </a></p> <p class="result-summary">The theory of reduction explains the origins of empirical <span class="hlt">models</span>, by delineating all the steps involved in mapping from the actual data generation process (DGP) in the economy - far too com- plicated and high dimensional ever to be completely <span class="hlt">modeled</span> - to an empirical <span class="hlt">model</span> thereof. Each reduction step involves a potential loss of information from: aggregating, marginalizing, condition-</p> <div class="credits"> <p class="dwt_author">David F. Hendry</p> <p class="dwt_publisher"></p> <p class="publishDate"></p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">308</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://academic.research.microsoft.com/Publication/13006453"> <span id="translatedtitle">Graphical <span class="hlt">Models</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://academic.research.microsoft.com/">Microsoft Academic Search </a></p> <p class="result-summary">Statistical applications in fields such as bioinformatics, information retrieval, speech processing, image processing and communications often involve large-scale <span class="hlt">models</span> in which thousands or millions of random variables are linked in complex ways. Graphical <span class="hlt">models</span> provide a general methodology for approaching these problems, and indeed many of the <span class="hlt">models</span> developed by researchers in these applied fields are instances of the general</p> <div class="credits"> <p class="dwt_author">Michael I. Jordan</p> <p class="dwt_publisher"></p> <p class="publishDate">2004-01-01</p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">309</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.ncbi.nlm.nih.gov/pubmed/22938964"> <span id="translatedtitle">Animal <span class="hlt">models</span>.</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p class="result-summary">Epilepsy accounts for a significant portion of the dis-ease burden worldwide. Research in this field is fundamental and mandatory. Animal <span class="hlt">models</span> have played, and still play, a substantial role in understanding the patho-physiology and treatment of human epilepsies. A large number and variety of approaches are available, and they have been applied to many animals. In this chapter the in vitro and in vivo animal <span class="hlt">models</span> are discussed,with major emphasis on the in vivo studies. <span class="hlt">Models</span> have used phylogenetically different animals - from worms to monkeys. Our attention has been dedicated mainly to rodents.In clinical practice, developmental aspects of epilepsy often differ from those in adults. Animal <span class="hlt">models</span> have often helped to clarify these differences. In this chapter, developmental aspects have been emphasized.Electrical stimulation and chemical-induced <span class="hlt">models</span> of seizures have been described first, as they represent the oldest and most common <span class="hlt">models</span>. Among these <span class="hlt">models</span>, kindling raised great interest, especially for the study of the epileptogenesis. Acquired focal <span class="hlt">models</span> mimic seizures and occasionally epilepsies secondary to abnormal cortical development, hypoxia, trauma, and hemorrhage.Better knowledge of epileptic syndromes will help to create new animal <span class="hlt">models</span>. To date, absence epilepsy is one of the most common and (often) benign forms of epilepsy. There are several <span class="hlt">models</span>, including acute pharmacological <span class="hlt">models</span> (PTZ, penicillin, THIP, GBL) and chronic <span class="hlt">models</span> (GAERS, WAG/Rij). Although atypical absence seizures are less benign, thus needing more investigation, only two <span class="hlt">models</span> are so far available (AY-9944,MAM-AY). Infantile spasms are an early childhood encephalopathy that is usually associated with a poor out-come. The investigation of this syndrome in animal <span class="hlt">models</span> is recent and fascinating. Different approaches have been used including genetic (Down syndrome,ARX mutation) and acquired (multiple hit, TTX, CRH,betamethasone-NMDA) <span class="hlt">models</span>.An entire section has been dedicated to genetic <span class="hlt">models</span>, from the older <span class="hlt">models</span> obtained with spontaneous mutations (GEPRs) to the new engineered knockout, knocking, and transgenic <span class="hlt">models</span>. Some of these <span class="hlt">models</span> have been created based on recently recognized patho-genesis such as benign familial neonatal epilepsy, early infantile encephalopathy with suppression bursts, severe myoclonic epilepsy of infancy, the tuberous sclerosis <span class="hlt">model</span>, and the progressive myoclonic epilepsy. The contribution of animal <span class="hlt">models</span> to epilepsy re-search is unquestionable. The development of further strategies is necessary to find novel strategies to cure epileptic patients, and optimistically to allow scientists first and clinicians subsequently to prevent epilepsy and its consequences. PMID:22938964</p> <div class="credits"> <p class="dwt_author">Coppola, Antonietta; Moshé, Solomon L</p> <p class="dwt_publisher"></p> <p class="publishDate">2012-01-01</p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">310</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://ntrs.nasa.gov/search.jsp?R=20000024740&hterms=why+people+lie&qs=Ntx%3Dmode%2Bmatchall%26Ntk%3DAll%26N%3D0%26No%3D10%26Ntt%3D%2528%2528why%2Bpeople%2529%2Blie%2529"> <span id="translatedtitle"><span class="hlt">Model</span> Experiments and <span class="hlt">Model</span> Descriptions</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p class="result-summary">The Second Workshop on Stratospheric <span class="hlt">Models</span> and Measurements Workshop (M&M II) is the continuation of the effort previously started in the first Workshop (M&M I, Prather and Remsberg [1993]) held in 1992. As originally stated, the aim of M&M is to provide a foundation for establishing the credibility of stratospheric <span class="hlt">models</span> used in environmental assessments of the ozone response to chlorofluorocarbons, aircraft emissions, and other climate-chemistry interactions. To accomplish this, a set of measurements of the present day atmosphere was selected. The intent was that successful simulations of the set of measurements should become the prerequisite for the acceptance of these <span class="hlt">models</span> as having a reliable prediction for future ozone behavior. This section is divided into two: <span class="hlt">model</span> experiment and <span class="hlt">model</span> descriptions. In the <span class="hlt">model</span> experiment, participant were given the charge to design a number of experiments that would use observations to test whether <span class="hlt">models</span> are using the correct mechanisms to simulate the distributions of ozone and other trace gases in the atmosphere. The purpose is closely tied to the needs to reduce the uncertainties in the <span class="hlt">model</span> predicted responses of stratospheric ozone to perturbations. The specifications for the experiments were sent out to the <span class="hlt">modeling</span> community in June 1997. Twenty eight <span class="hlt">modeling</span> groups responded to the requests for input. The first part of this section discusses the different <span class="hlt">modeling</span> group, along with the experiments performed. Part two of this section, gives brief descriptions of each <span class="hlt">model</span> as provided by the individual <span class="hlt">modeling</span> groups.</p> <div class="credits"> <p class="dwt_author">Jackman, Charles H.; Ko, Malcolm K. W.; Weisenstein, Debra; Scott, Courtney J.; Shia, Run-Lie; Rodriguez, Jose; Sze, N. D.; Vohralik, Peter; Randeniya, Lakshman; Plumb, Ian</p> <p class="dwt_publisher"></p> <p class="publishDate">1999-01-01</p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">311</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.modelingandsimulation.org"> <span id="translatedtitle"><span class="hlt">Modeling</span> & Simulation</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://nsdl.org/nsdl_dds/services/ddsws1-1/service_explorer.jsp">NSDL National Science Digital Library</a></p> <p class="result-summary"><span class="hlt">Modeling</span> & Simulation is a journal published by The Society for <span class="hlt">Modeling</span> and Simulation International. The Society has made its 2004 <span class="hlt">Modeling</span> and Simulation Resource Guide available free to download. The directory provides descriptions and contact information for the many <span class="hlt">modeling</span> and simulation software packages currently available, as well as listings for various <span class="hlt">modeling</span> and simulation organizations worldwide. Two guest articles describe techniques for the application of real-time simulation in simulations that are complex. Previously published articles are also posted in the online archive.</p> <div class="credits"> <p class="dwt_author"></p> <p class="dwt_publisher"></p> <p class="publishDate"></p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">312</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://learningcenter.nsta.org/product_detail.aspx?id=10.2505/4/sc03_040_04_29"> <span id="translatedtitle">Rethinking <span class="hlt">Models</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://nsdl.org/nsdl_dds/services/ddsws1-1/service_explorer.jsp">NSDL National Science Digital Library</a></p> <p class="result-summary">While <span class="hlt">models</span> and analogies are integral to both the learning and practice of science, their use is complex and potentially troublesome. Misconceptions can arise when parts of a <span class="hlt">model</span> are misleading, missing, or misapplied. Students begin to look critically at <span class="hlt">models</span> as they investigate a question of personal interest and develop related lessons for use in a local elementary school. This article suggests techniques you can use to analyze <span class="hlt">models</span> and describes preservice teachers' experiences as they critically examined popular <span class="hlt">models</span> used in many elementary classrooms.</p> <div class="credits"> <p class="dwt_author">Frazier, Richard</p> <p class="dwt_publisher"></p> <p class="publishDate">2003-01-01</p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">313</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.met.tamu.edu/class/atmo151/tut/models/modelmain.html"> <span id="translatedtitle">Computer <span class="hlt">Models</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://nsdl.org/nsdl_dds/services/ddsws1-1/service_explorer.jsp">NSDL National Science Digital Library</a></p> <p class="result-summary">This undergraduate meteorology tutorial from Texas A&M University focuses on computer <span class="hlt">models</span> that are run by the National Weather Service (NWS) National Centers for Environmental Prediction (NCEP) and are used for forecasting day-to-day weather in the United States. NCEP has four basic <span class="hlt">models</span>: the Eta <span class="hlt">Model</span>, the Nested Grid <span class="hlt">model</span> (NGM), the Rapid Update Cycle (RUC), and the Global Forecast System (GFS). Each <span class="hlt">model</span> is a self-contained set of computer programs, which include means of analyzing data and computing the evolution of the atmosphere's winds, temperature, pressure, and moisture based on the analyses. Students are given some basic terminology and learn to identify the <span class="hlt">models</span> and to read <span class="hlt">model</span> output.</p> <div class="credits"> <p class="dwt_author">Nielsen-Gammon, John</p> <p class="dwt_publisher"></p> <p class="publishDate">1996-01-01</p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">314</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.osti.gov/scitech/servlets/purl/6245971"> <span id="translatedtitle">ICRF <span class="hlt">modelling</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p class="result-summary">This lecture provides a survey of the methods used to <span class="hlt">model</span> fast magnetosonic wave coupling, propagation, and absorption in tokamaks. The validity and limitations of three distinct types of <span class="hlt">modelling</span> codes, which will be contrasted, include discrete <span class="hlt">models</span> which utilize ray tracing techniques, approximate continuous field <span class="hlt">models</span> based on a parabolic approximation of the wave equation, and full field <span class="hlt">models</span> derived using finite difference techniques. Inclusion of mode conversion effects in these <span class="hlt">models</span> and modification of the minority distribution function will also be discussed. The lecture will conclude with a presentation of time-dependent global transport simulations of ICRF-heated tokamak discharges obtained in conjunction with the ICRF <span class="hlt">modelling</span> codes. 52 refs., 15 figs.</p> <div class="credits"> <p class="dwt_author">Phillips, C.K.</p> <p class="dwt_publisher"></p> <p class="publishDate">1985-12-01</p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">315</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://ntrs.nasa.gov/search.jsp?R=20120013440&hterms=internet+finance&qs=Ntx%3Dmode%2Bmatchall%26Ntk%3DAll%26N%3D0%26No%3D20%26Ntt%3Dinternet%2Bfinance"> <span id="translatedtitle">Climate <span class="hlt">Models</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p class="result-summary">Climate <span class="hlt">models</span> is a very broad topic, so a single volume can only offer a small sampling of relevant research activities. This volume of 14 chapters includes descriptions of a variety of <span class="hlt">modeling</span> studies for a variety of geographic regions by an international roster of authors. The climate research community generally uses the rubric climate <span class="hlt">models</span> to refer to organized sets of computer instructions that produce simulations of climate evolution. The code is based on physical relationships that describe the shared variability of meteorological parameters such as temperature, humidity, precipitation rate, circulation, radiation fluxes, etc. Three-dimensional climate <span class="hlt">models</span> are integrated over time in order to compute the temporal and spatial variations of these parameters. <span class="hlt">Model</span> domains can be global or regional and the horizontal and vertical resolutions of the computational grid vary from <span class="hlt">model</span> to <span class="hlt">model</span>. Considering the entire climate system requires accounting for interactions between solar insolation, atmospheric, oceanic and continental processes, the latter including land hydrology and vegetation. <span class="hlt">Model</span> simulations may concentrate on one or more of these components, but the most sophisticated <span class="hlt">models</span> will estimate the mutual interactions of all of these environments. Advances in computer technology have prompted investments in more complex <span class="hlt">model</span> configurations that consider more phenomena interactions than were possible with yesterday s computers. However, not every attempt to add to the computational layers is rewarded by better <span class="hlt">model</span> performance. Extensive research is required to test and document any advantages gained by greater sophistication in <span class="hlt">model</span> formulation. One purpose for publishing climate <span class="hlt">model</span> research results is to present purported advances for evaluation by the scientific community.</p> <div class="credits"> <p class="dwt_author">Druyan, Leonard M.</p> <p class="dwt_publisher"></p> <p class="publishDate">2012-01-01</p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">316</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.compadre.org/Repository/document/ServeFile.cfm?ID=8632&DocID=1003"> <span id="translatedtitle">Kac <span class="hlt">Model</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://nsdl.org/nsdl_dds/services/ddsws1-1/service_explorer.jsp">NSDL National Science Digital Library</a></p> <p class="result-summary">The EJS Kac <span class="hlt">Model</span> simulates the relaxation of a gas to equilibrium by randomly selecting and then colliding gas molecules but without keeping track of the molecules' positions. As long as the collisions are consistent with spatial isotropy, the Boltzmann speed distribution will emerge. You can modify this simulation if you have Ejs installed by right-clicking within the plot and selecting âOpen Ejs Modelâ from the pop-up menu item. The Kac <span class="hlt">model</span> was created using the Easy Java Simulations (Ejs) <span class="hlt">modeling</span> tool. It is distributed as a ready-to-run (compiled) Java archive. Double clicking the ejs_stp_Kac<span class="hlt">Model</span>.jar file will run the program if Java is installed. Ejs is a part of the Open Source Physics Project and is designed to make it easier to access, modify, and generate computer <span class="hlt">models</span>. Additional Ejs <span class="hlt">models</span> are available. They can be found by searching ComPADRE for Open Source Physics, OSP, or Ejs.</p> <div class="credits"> <p class="dwt_author">Christian, Wolfgang</p> <p class="dwt_publisher"></p> <p class="publishDate">2009-03-05</p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">317</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.osti.gov/scitech/servlets/purl/6365078"> <span id="translatedtitle">Phenomenological <span class="hlt">models</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p class="result-summary">The biological effects of ionizing radiation exposure are the result of a complex sequence of physical, chemical, biochemical, and physiological interactions. One way to begin a search for an understanding of health effects of radiation is through the development of phenomenological <span class="hlt">models</span> of the response. Many <span class="hlt">models</span> have been presented and tested in the slowly evolving process of characterizing cellular response. A range of <span class="hlt">models</span> covering different endpoints and phenomena has developed in parallel. Many of these <span class="hlt">models</span> employ similar assumptions about some underlying processes while differing about the nature of others. An attempt is made to organize many of the <span class="hlt">models</span> into groups with similar features and to compare the consequences of those features with the actual experimental observations. It is assumed that by showing that some assumptions are inconsistent with experimental observations, the job of devising and testing mechanistic <span class="hlt">models</span> can be simplified. 43 refs., 13 figs.</p> <div class="credits"> <p class="dwt_author">Braby, L.A.</p> <p class="dwt_publisher"></p> <p class="publishDate">1990-09-01</p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">318</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.compadre.org/Repository/document/ServeFile.cfm?ID=11530&DocID=2485"> <span id="translatedtitle">Gimbal <span class="hlt">Model</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://nsdl.org/nsdl_dds/services/ddsws1-1/service_explorer.jsp">NSDL National Science Digital Library</a></p> <p class="result-summary">The Gimbal <span class="hlt">Model</span> illustrates the pitch, roll and yaw of a 3D object. Independent axis mode allows each axes to be rotated without affecting the others axes. If this mode is not selected, the <span class="hlt">model</span> can be used to explore the phenomena of gimbal lock. This <span class="hlt">model</span> tests the Java 3D implementation of the EJS 3D library. If the Java 3D option is selected, a airplane VMRL file (wrl) is rendered inside the gimbals. A warning message will appear if the Java 3D library is not available. The Gimbal <span class="hlt">Model</span> was developed using the Easy Java Simulations (EJS) <span class="hlt">modeling</span> tool. It is distributed as a ready-to-run (compiled) Java archive. Double clicking the ejs_ntnu_Gimbal.jar file will run the program if Java is installed. You can modify this simulation if you have EJS installed by right-clicking within the map and selecting "Open Ejs <span class="hlt">Model</span>" from the pop-up menu item.</p> <div class="credits"> <p class="dwt_author">Hwang, Fu-Kwun; Wee, Loo K.</p> <p class="dwt_publisher"></p> <p class="publishDate">2011-12-30</p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">319</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://serc.carleton.edu/quantskills/activities/locke_scarp.html"> <span id="translatedtitle">SCARP <span class="hlt">Model</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://nsdl.org/nsdl_dds/services/ddsws1-1/service_explorer.jsp">NSDL National Science Digital Library</a></p> <p class="result-summary">SCARP is the first in a sequence of spreadsheet <span class="hlt">modeling</span> exercises (SCARP2, LONGPRO, and GLACPRO). In this exercise, students use a simple arithmetic <span class="hlt">model</span> (a running mean) to simulate the evolution of a scarp (escarpment) across time. Although the output closely resembles an evolving scarp, no real variables are included in the <span class="hlt">model</span>. The purpose of the exercise, in addition to the simulation, is to develop basic skills in spreadsheeting and especially in graphical display.</p> <div class="credits"> <p class="dwt_author">Locke, Bill</p> <p class="dwt_publisher"></p> <p class="publishDate"></p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">320</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://academic.research.microsoft.com/Publication/655249"> <span id="translatedtitle"><span class="hlt">Model</span> Cheking</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://academic.research.microsoft.com/">Microsoft Academic Search </a></p> <p class="result-summary"><span class="hlt">Model</span> checking is an automatic technique for verifying finite-state reactive systems, such as sequential circuit designs and\\u000a communication protocols. Specifications are expressed in temporal logic, and the reactive system is <span class="hlt">modeled</span> as a statetransition\\u000a graph. An efficient search procedure is used to determine whether or not the state-transition graph satisfies the specifications.\\u000a \\u000a We describe the basic <span class="hlt">model</span> checking algorithm and</p> <div class="credits"> <p class="dwt_author">Edmund M. Clarke</p> <p class="dwt_publisher"></p> <p class="publishDate">1997-01-01</p> </div> </div> </div> </div> <div id="filter_results_form" class="filter_results_form floatContainer" style="visibility: visible;"> <div style="width:100%" id="PaginatedNavigation" class="paginatedNavigationElement"> <a id="FirstPageLink" onclick='return showDiv("page_1");' href="#" title="First Page"> <img id="FirstPageLinkImage" class="Icon" src="http://www.science.gov/scigov/images/icon.first.18x20.png" alt="First Page" /></a> <a id="PreviousPageLink" onclick='return showDiv("page_15");' href="#" title="Previous Page"> <img id="PreviousPageLinkImage" class="Icon" src="http://www.science.gov/scigov/images/icon.previous.18x20.png" alt="Previous Page" /></a> <span id="PageLinks" class="pageLinks"> <span> <a onClick='return showDiv("page_1");' href="#">1</a> <a onClick='return showDiv("page_2");' href="#">2</a> <a onClick='return showDiv("page_3");' href="#">3</a> <a onClick='return showDiv("page_4");' 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onclick='return showDiv("page_25.0");' href="#" title="Last Page"> <img id="LastPageLinkImage" class="Icon" src="http://www.science.gov/scigov/images/icon.last.18x20.png" alt="Last Page" /></a> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">321</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.osti.gov/scitech/biblio/5587042"> <span id="translatedtitle">PREDICTIVE <span class="hlt">MODELS</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p class="result-summary">PREDICTIVE <span class="hlt">MODELS</span> is a collection of five <span class="hlt">models</span> - CFPM, CO2PM, ICPM, PFPM, and SFPM - used in the 1982-1984 National Petroleum Council study of enhanced oil recovery (EOR) potential. Each pertains to a specific EOR process designed to squeeze additional oil from aging or spent oil fields. The processes are: 1) chemical flooding; 2) carbon dioxide miscible flooding; 3) in-situ combustion; 4) polymer flooding; and 5) steamflood. CFPM, the Chemical Flood Predictive <span class="hlt">Model</span>, <span class="hlt">models</span> micellar (surfactant)-polymer floods in reservoirs, which have been previously waterflooded to residual oil saturation. Thus, only true tertiary floods are considered. An option allows a rough estimate of oil recovery by caustic or caustic-polymer processes. CO2PM, the Carbon Dioxide miscible flooding Predictive <span class="hlt">Model</span>, is applicable to both secondary (mobile oil) and tertiary (residual oil) floods, and to either continuous CO2 injection or water-alternating gas processes. ICPM, the In-situ Combustion Predictive <span class="hlt">Model</span>, computes the recovery and profitability of an in-situ combustion project from generalized performance predictive algorithms. PFPM, the Polymer Flood Predictive <span class="hlt">Model</span>, is switch-selectable for either polymer or waterflooding, and an option allows the calculation of the incremental oil recovery and economics of polymer relative to waterflooding. SFPM, the Steamflood Predictive <span class="hlt">Model</span>, is applicable to the steam drive process, but not to cyclic steam injection (steam soak) processes. The IBM PC/AT version includes a plotting capability to produces a graphic picture of the predictive <span class="hlt">model</span> results.</p> <div class="credits"> <p class="dwt_author">Ray, R.M. (DOE Bartlesville Energy Technology Center, Bartlesville, OK (United States))</p> <p class="dwt_publisher"></p> <p class="publishDate">1988-10-01</p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">322</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://ntrs.nasa.gov/search.jsp?R=19950020245&hterms=cscm&qs=Ntx%3Dmode%2Bmatchall%26Ntk%3DAll%26N%3D0%26No%3D10%26Ntt%3Dcscm"> <span id="translatedtitle">Turbulence <span class="hlt">modeling</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p class="result-summary">The objective of this work is to develop, verify, and incorporate the baseline two-equation turbulence <span class="hlt">models</span> which account for the effects of compressibility into the three-dimensional Reynolds averaged Navier-Stokes (RANS) code and to provide documented descriptions of the <span class="hlt">models</span> and their numerical procedures so that they can be implemented into 3-D CFD codes for engineering applications.</p> <div class="credits"> <p class="dwt_author">Bardina, Jorge E.</p> <p class="dwt_publisher"></p> <p class="publishDate">1995-01-01</p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">323</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://serc.carleton.edu/quantskills/activities/locke_glacpro.html"> <span id="translatedtitle">GLACPRO <span class="hlt">Model</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://nsdl.org/nsdl_dds/services/ddsws1-1/service_explorer.jsp">NSDL National Science Digital Library</a></p> <p class="result-summary">In the GLACPRO exercise student teams (1-3 members) use a numerical <span class="hlt">model</span> to reconstruct a former glacial flowline from moraines to source. They must interact with teams studying adjacent flowlines to accurately place ice divides. They can calculate average thicknesses, volumes, ice loading, and sea level equivalent from the class <span class="hlt">model</span>.</p> <div class="credits"> <p class="dwt_author">Locke, Bill</p> <p class="dwt_publisher"></p> <p class="publishDate"></p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">324</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www3.geosc.psu.edu/~dmb53/DaveSTELLA/Daisyworld/daisyworld_model.htm"> <span id="translatedtitle">Daisyworld <span class="hlt">Model</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://nsdl.org/nsdl_dds/services/ddsws1-1/service_explorer.jsp">NSDL National Science Digital Library</a></p> <p class="result-summary">The simulation exercise uses a STELLA-based <span class="hlt">model</span> called Daisyworld to explore concepts associated with Earth's energy balance and climate change. Students examine the evolution of a simplified <span class="hlt">model</span> of an imaginary planet with only two species of life on its surface -- white and black daisies -- with different albedos. The daisies can alter the temperature of the surface where they are growing.</p> <div class="credits"> <p class="dwt_author">Lovelock, James; Watson, Andrew; Bice, Dave; Dept. Of Geosciences, Penn S.</p> <p class="dwt_publisher"></p> <p class="publishDate"></p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">325</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.econ.surrey.ac.uk/people/rpierse/files/arima.pdf"> <span id="translatedtitle">Animal <span class="hlt">models</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://academic.research.microsoft.com/">Microsoft Academic Search </a></p> <p class="result-summary">Time Series Analysis looks at the properties of time series from a purely statistical point of view. No attempt is made to relate variables using a priori economic theory (c.f. econometrics). Why use time series methods? 1) Short term forecasting. Time series <span class="hlt">models</span> may well forecast better than econometric <span class="hlt">models</span> over the short term. One would expect that they would</p> <div class="credits"> <p class="dwt_author">Hartmut Wekerle; Kimikazu Kojima; Joseli Lannes-Vieira; Hans Lassmann; Christopher Linington</p> <p class="dwt_publisher"></p> <p class="publishDate">1983-01-01</p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">326</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.cancer.gov/aboutnci/budget_planning_leg/plan-2012/cancerbiology/computational-models"> <span id="translatedtitle">Computational <span class="hlt">Models</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.cancer.gov">Cancer.gov</a></p> <p class="result-summary">The <span class="hlt">models</span> work by investigating relationships between the pathways that control a cell's response to inflammation, growth factors, DNA damage, and other events. The goal is to create a dynamic <span class="hlt">model</span> of the biological processes related to cancer initiation, progression, and metastasis.</p> <div class="credits"> <p class="dwt_author"></p> <p class="dwt_publisher"></p> <p class="publishDate"></p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">327</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.osti.gov/scitech/servlets/purl/1062195"> <span id="translatedtitle">OSPREY <span class="hlt">Model</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p class="result-summary">The absence of industrial scale nuclear fuel reprocessing in the U.S. has precluded the necessary driver for developing the advanced simulation capability now prevalent in so many other countries. Thus, it is essential to <span class="hlt">model</span> complex series of unit operations to simulate, understand, and predict inherent transient behavior and feedback loops. A capability of accurately simulating the dynamic behavior of advanced fuel cycle separation processes will provide substantial cost savings and many technical benefits. The specific fuel cycle separation process discussed in this report is the off-gas treatment system. The off-gas separation consists of a series of scrubbers and adsorption beds to capture constituents of interest. Dynamic <span class="hlt">models</span> are being developed to simulate each unit operation involved so each unit operation can be used as a stand-alone <span class="hlt">model</span> and in series with multiple others. Currently, an adsorption <span class="hlt">model</span> has been developed within Multi-physics Object Oriented Simulation Environment (MOOSE) developed at the Idaho National Laboratory (INL). Off-gas Separation and REcoverY (OSPREY) <span class="hlt">models</span> the adsorption of off-gas constituents for dispersed plug flow in a packed bed under non-isothermal and non-isobaric conditions. Inputs to the <span class="hlt">model</span> include gas, sorbent, and column properties, equilibrium and kinetic data, and inlet conditions. The simulation outputs component concentrations along the column length as a function of time from which breakthrough data is obtained. The breakthrough data can be used to determine bed capacity, which in turn can be used to size columns. It also outputs temperature along the column length as a function of time and pressure drop along the column length. Experimental data and parameters were input into the adsorption <span class="hlt">model</span> to develop <span class="hlt">models</span> specific for krypton adsorption. The same can be done for iodine, xenon, and tritium. The <span class="hlt">model</span> will be validated with experimental breakthrough curves. Customers will be given access to OSPREY to used and evaluate the <span class="hlt">model</span>.</p> <div class="credits"> <p class="dwt_author">Veronica J. Rutledge</p> <p class="dwt_publisher"></p> <p class="publishDate">2013-01-01</p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">328</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://adsabs.harvard.edu/abs/2012ISPAr39B5...99G"> <span id="translatedtitle">Stereometric <span class="hlt">Modelling</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p class="result-summary">These mandatory guidelines are provided for preparation of papers accepted for publication in the series of Volumes of The The stereometric <span class="hlt">modelling</span> means <span class="hlt">modelling</span> achieved with : - the use of a pair of virtual cameras, with parallel axes and positioned at a mutual distance average of 1/10 of the distance camera-object (in practice the realization and use of a stereometric camera in the <span class="hlt">modeling</span> program); - the shot visualization in two distinct windows - the stereoscopic viewing of the shot while <span class="hlt">modelling</span>. Since the definition of "3D vision" is inaccurately referred to as the simple perspective of an object, it is required to add the word stereo so that "3D stereo vision " shall stand for "three-dimensional view" and ,therefore, measure the width, height and depth of the surveyed image. Thanks to the development of a stereo metric <span class="hlt">model</span> , either real or virtual, through the "materialization", either real or virtual, of the optical-stereo metric <span class="hlt">model</span> made visible with a stereoscope. It is feasible a continuous on line updating of the cultural heritage with the help of photogrammetry and stereometric <span class="hlt">modelling</span>. The catalogue of the Architectonic Photogrammetry Laboratory of Politecnico di Bari is available on line at: <a href = "http://rappresentazione.stereofot.it:591/StereoFot/FMPro?-db=StereoFot.fp5&-lay=Scheda&-format=cerca.htm&-view" target="_blank">http://rappresentazione.stereofot.it:591/StereoFot/FMPro?-db=StereoFot.fp5&-lay=Scheda&-format=cerca.htm&-view</a></p> <div class="credits"> <p class="dwt_author">Grimaldi, P.</p> <p class="dwt_publisher"></p> <p class="publishDate">2012-07-01</p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">329</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://adsabs.harvard.edu/abs/2011AIPC.1406..523I"> <span id="translatedtitle"><span class="hlt">Modeling</span> Arcs</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p class="result-summary">Although vacuum arcs were first identified over 110 years ago, they are not yet well understood. We have since developed a <span class="hlt">model</span> of breakdown and gradient limits that tries to explain, in a self-consistent way: arc triggering, plasma initiation, plasma evolution, surface damage and gradient limits. We use simple PIC codes for <span class="hlt">modeling</span> plasmas, molecular dynamics for <span class="hlt">modeling</span> surface breakdown, and surface damage, and mesoscale surface thermodynamics and finite element electrostatic codes for to evaluate surface properties. Since any given experiment seems to have more variables than data points, we have tried to consider a wide variety of arcing (rf structures, e beam welding, laser ablation, etc.) to help constrain the problem, and concentrate on common mechanisms. While the mechanisms can be comparatively simple, <span class="hlt">modeling</span> can be challenging.</p> <div class="credits"> <p class="dwt_author">Insepov, Z.; Norem, J.; Vetizer, S.; Mahalingam, S.</p> <p class="dwt_publisher"></p> <p class="publishDate">2011-12-01</p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">330</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://cdsweb.cern.ch/record/1373092"> <span id="translatedtitle"><span class="hlt">Modeling</span> Arcs</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.osti.gov/epsearch/">E-print Network</a></p> <p class="result-summary">Although vacuum arcs were first identified over 110 years ago, they are not yet well understood. We have since developed a <span class="hlt">model</span> of breakdown and gradient limits that tries to explain, in a self-consistent way: arc triggering, plasma initiation, plasma evolution, surface damage and gra- dient limits. We use simple PIC codes for <span class="hlt">modeling</span> plasmas, molecular dynamics for <span class="hlt">modeling</span> surface breakdown, and surface damage, and mesoscale surface thermodynamics and finite element electrostatic codes for to evaluate surface properties. Since any given experiment seems to have more variables than data points, we have tried to consider a wide variety of arcing (rf structures, e beam welding, laser ablation, etc.) to help constrain the problem, and concentrate on common mechanisms. While the mechanisms can be comparatively simple, <span class="hlt">modeling</span> can be challenging.</p> <div class="credits"> <p class="dwt_author">Insepov, Zeke; Veitzer, Seth; Mahalingam, Sudhakar</p> <p class="dwt_publisher"></p> <p class="publishDate">2011-01-01</p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">331</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.osti.gov/scitech/biblio/21612529"> <span id="translatedtitle"><span class="hlt">Modeling</span> Arcs</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p class="result-summary">Although vacuum arcs were first identified over 110 years ago, they are not yet well understood. We have since developed a <span class="hlt">model</span> of breakdown and gradient limits that tries to explain, in a self-consistent way: arc triggering, plasma initiation, plasma evolution, surface damage and gradient limits. We use simple PIC codes for <span class="hlt">modeling</span> plasmas, molecular dynamics for <span class="hlt">modeling</span> surface breakdown, and surface damage, and mesoscale surface thermodynamics and finite element electrostatic codes for to evaluate surface properties. Since any given experiment seems to have more variables than data points, we have tried to consider a wide variety of arcing (rf structures, e beam welding, laser ablation, etc.) to help constrain the problem, and concentrate on common mechanisms. While the mechanisms can be comparatively simple, <span class="hlt">modeling</span> can be challenging.</p> <div class="credits"> <p class="dwt_author">Insepov, Z.; Norem, J. [Argonne National Lab, Argonne, IL 60439 (United States); Vetizer, S.; Mahalingam, S. [Tech-X Corp., Boulder, CO (United States)</p> <p class="dwt_publisher"></p> <p class="publishDate">2011-12-23</p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">332</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.ntis.gov/search/product.aspx?ABBR=AD860650"> <span id="translatedtitle">Theaterspiel <span class="hlt">Model</span>.</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.ntis.gov/search/index.aspx">National Technical Information Service (NTIS)</a></p> <p class="result-summary">THEATERSPIEL is a two-sided, closed, computer-assisted, theater-level war game with resolution at division level. The THEATERSPIEL game <span class="hlt">model</span> consists of the cyclical application of flexible sets of rules, procedures, mathematical expressions, empirical f...</p> <div class="credits"> <p class="dwt_author"></p> <p class="dwt_publisher"></p> <p class="publishDate">1969-01-01</p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">333</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.g2conline.org/548"> <span id="translatedtitle"><span class="hlt">Model</span> Center</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://nsdl.org/nsdl_dds/services/ddsws1-1/service_explorer.jsp">NSDL National Science Digital Library</a></p> <p class="result-summary">A human is a complicated organism, and it is considered unethical to do many kinds of experiments on human subjects. For these reasons, biologists often use simpler '<span class="hlt">model</span>' organisms that are easy to keep and manipulate in the laboratory. Despite obvious differences, <span class="hlt">model</span> organisms share with humans many key biochemical and physiological functions that have been conserved (maintained) by evolution. Each of the following <span class="hlt">model</span> organisms has its advantages and disadvantages in different research applications. This tool allows you to examine the similarities between different systems by comparing the proteins they share and the proportion of DNA they have in common. Choose a gene from the drop-down menu and select the species you want to compare. Rolling over the images will give you a more detailed description of each <span class="hlt">model</span>. Clicking on a geneâÃÂÃÂs name will take you to the National Center for Biological Information, where you can explore the latest relevant scientific literature.</p> <div class="credits"> <p class="dwt_author"></p> <p class="dwt_publisher"></p> <p class="publishDate">2009-04-14</p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">334</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://oaspub.epa.gov/eims/eimsapi.dispdetail?deid=199951"> <span id="translatedtitle">Energy <span class="hlt">Models</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://oaspub.epa.gov/eims/query.page">EPA Science Inventory</a></p> <p class="result-summary">Energy <span class="hlt">models</span> characterize the energy system, its evolution, and its interactions with the broader economy. The energy system consists of primary resources, including both fossil fuels and renewables; power plants, refineries, and other technologies to process and convert these r...</p> <div class="credits"> <p class="dwt_author"></p> <p class="dwt_publisher"></p> <p class="publishDate"></p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">335</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.osti.gov/scitech/biblio/5392640"> <span id="translatedtitle">PREDICTIVE <span class="hlt">MODELS</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p class="result-summary">PREDICTIVE <span class="hlt">MODELS</span> is a collection of five <span class="hlt">models</span> - CFPM, CO2PM, ICPM, PFPM, and SFPM - used in the 1982-1984 National Petroleum Council study of enhanced oil recovery (EOR) potential. Each pertains to a specific EOR process designed to squeeze additional oil from aging or spent oil fields. The processes are: 1) chemical flooding, where soap-like surfactants are injected into the reservoir to wash out the oil; 2) carbon dioxide miscible flooding, where carbon dioxide mixes with the lighter hydrocarbons making the oil easier to displace; 3) in-situ combustion, which uses the heat from burning some of the underground oil to thin the product; 4) polymer flooding, where thick, cohesive material is pumped into a reservoir to push the oil through the underground rock; and 5) steamflood, where pressurized steam is injected underground to thin the oil. CFPM, the Chemical Flood Predictive <span class="hlt">Model</span>, <span class="hlt">models</span> micellar (surfactant)-polymer floods in reservoirs, which have been previously waterflooded to residual oil saturation. Thus, only true tertiary floods are considered. An option allows a rough estimate of oil recovery by caustic or caustic-polymer processes. CO2PM, the Carbon Dioxide miscible flooding Predictive <span class="hlt">Model</span>, is applicable to both secondary (mobile oil) and tertiary (residual oil) floods, and to either continuous CO2 injection or water-alternating gas processes. ICPM, the In-situ Combustion Predictive <span class="hlt">Model</span>, computes the recovery and profitability of an in-situ combustion project from generalized performance predictive algorithms. PFPM, the Polymer Flood Predictive <span class="hlt">Model</span>, is switch-selectable for either polymer or waterflooding, and an option allows the calculation of the incremental oil recovery and economics of polymer relative to waterflooding. SFPM, the Steamflood Predictive <span class="hlt">Model</span>, is applicable to the steam drive process, but not to cyclic steam injection (steam soak) processes.</p> <div class="credits"> <p class="dwt_author">Ray, R.M. (DOE Bartlesville Energy Technology Technology Center, Bartlesville, OK (United States))</p> <p class="dwt_publisher"></p> <p class="publishDate">1986-12-01</p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">336</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://adsabs.harvard.edu/abs/2003AGUFMNG31A0602S"> <span id="translatedtitle">Everglades <span class="hlt">Modeling</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p class="result-summary">The Florida Everglades is a vast, low-relief, nearly horizontal, densely vegetated subtropical wetland with slow-moving water and only trace inputs of sediment and nutrients. The natural system is a classic example of a self-organizing system, with feedbacks between hydrology, vegetation, and soil evolution, but not all controls on landscape patterns are well understood. Engineered features (roads, canals, levees, etc.) have since the 1920s greatly modified the hydrologic regime, resulting in significant loss of peat and degraded patterning. We are developing a nested flow and transport <span class="hlt">model</span> to try to understand dominant processes in landscape formation. Flow is described in 2D, vertically integrated over the surficial aquifer and surface water (using vegetative-drag <span class="hlt">models</span> rather than Manning's equation). Transport is described in 3D, with sediment and (in the future) nutrient transport considered. High correlation between vegetative resistance and microtopography allows a parsimonious large-scale [O(1~km)] flow <span class="hlt">model</span> based on a truncated normal distribution for microtopography that is partitioned by vegetation class. A more complex landscape-unit <span class="hlt">model</span> describes both flow and transport at the large scale, with the potential of considering landscape evolution. The landscape-unit <span class="hlt">model</span> considers typical landscape units as additional embedded continua within a slough continuum. The large-scale <span class="hlt">models</span> can be used on their own, and also to provide boundary conditions for fine-scale [O(10~m)] simulations considering individual landscape features and the local effect of engineered systems.</p> <div class="credits"> <p class="dwt_author">Stothoff, S. A.; Mitchell-Bruker, S.</p> <p class="dwt_publisher"></p> <p class="publishDate">2003-12-01</p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">337</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://warnercnr.colostate.edu/docs/hdnr/mor2/Fassnacht_Modelling.pdf"> <span id="translatedtitle"><span class="hlt">Modelling</span> Tools<span class="hlt">Modelling</span> Tools Steven Fassnacht</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.osti.gov/epsearch/">E-print Network</a></p> <p class="result-summary"><span class="hlt">Modelling</span> Tools · Data Analysis ­ Trend identification ­ Projections · Computer <span class="hlt">Models</span> ­ Process ­ Ensemble Analysis Transpiration Evaporation Precipitation surface runoff groundwater flow Infiltration <span class="hlt">Model</span> Schematic computer <span class="hlt">model</span> streamflow precipitation landcover data temperature #12;3 <span class="hlt">Modelling</span></p> <div class="credits"> <p class="dwt_author"></p> <p class="dwt_publisher"></p> <p class="publishDate"></p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">338</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://dspace.mit.edu/handle/1721.1/80786"> <span id="translatedtitle">Fractionation of sulfur isotopes by Desulfovibrio vulgaris mutants lacking <span class="hlt">hydrogenases</span> or type I tetraheme cytochrome c[subscript 3</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.osti.gov/epsearch/">E-print Network</a></p> <p class="result-summary">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 ...</p> <div class="credits"> <p class="dwt_author">Sim, Min Sub</p> <p class="dwt_publisher"></p> <p class="publishDate"></p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">339</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://academic.research.microsoft.com/Publication/26487295"> <span id="translatedtitle">Improved hydrogen production by coupled systems of <span class="hlt">hydrogenase</span> negative photosynthetic bacteria and fermentative bacteria in reverse micelles</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://academic.research.microsoft.com/">Microsoft Academic Search </a></p> <p class="result-summary">Significant improvement in biological hydrogen production is achieved by the use of coupled bacterial cells in reverse micellar systems. Two coupled systems (a) Rhodopseudomonas palustris CGA009\\/Citrobacter Y19, and (b) Rhodobacter sphaeroides 2.4.1\\/Citrobacter Y19 bacteria have been immobilized separately in aqueous pool of the reverse micelles fabricated by various surfactants (AOT, CBAC and SDS) and apolar organic solvents (benzene and isooctane).</p> <div class="credits"> <p class="dwt_author">Anita Singh; Krishna Misra</p> <p class="dwt_publisher"></p> <p class="publishDate">2008-01-01</p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">340</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.springerlink.com/index/9q8q73757jw89065.pdf"> <span id="translatedtitle"><span class="hlt">Modelling</span> Experiments as Mediating <span class="hlt">Models</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://academic.research.microsoft.com/">Microsoft Academic Search </a></p> <p class="result-summary">Syntactic and structural <span class="hlt">models</span> specify relationships between their constituents but cannot show what outcomes their interaction\\u000a would produce over time in the world. Simulation consists in iterating the states of a <span class="hlt">model</span>, so as to produce behaviour over\\u000a a period of simulated time. Iteration enables us to trace the implications and outcomes of inference rules and other assumptions\\u000a implemented in</p> <div class="credits"> <p class="dwt_author">D. C. Gooding; T. R. Addis</p> <p class="dwt_publisher"></p> <p class="publishDate">2008-01-01</p> </div> </div> </div> </div> <div id="filter_results_form" class="filter_results_form floatContainer" style="visibility: visible;"> <div style="width:100%" id="PaginatedNavigation" class="paginatedNavigationElement"> <a id="FirstPageLink" onclick='return showDiv("page_1");' href="#" title="First Page"> <img id="FirstPageLinkImage" class="Icon" src="http://www.science.gov/scigov/images/icon.first.18x20.png" alt="First Page" /></a> <a id="PreviousPageLink" onclick='return showDiv("page_16");' href="#" title="Previous Page"> <img id="PreviousPageLinkImage" class="Icon" src="http://www.science.gov/scigov/images/icon.previous.18x20.png" alt="Previous Page" /></a> <span id="PageLinks" class="pageLinks"> <span> <a onClick='return showDiv("page_1");' href="#">1</a> <a onClick='return showDiv("page_2");' href="#">2</a> <a onClick='return showDiv("page_3");' href="#">3</a> <a onClick='return showDiv("page_4");' 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onclick='return showDiv("page_25.0");' href="#" title="Last Page"> <img id="LastPageLinkImage" class="Icon" src="http://www.science.gov/scigov/images/icon.last.18x20.png" alt="Last Page" /></a> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">341</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.compadre.org/Repository/document/ServeFile.cfm?ID=9378&DocID=1276"> <span id="translatedtitle">Gnomon <span class="hlt">Model</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://nsdl.org/nsdl_dds/services/ddsws1-1/service_explorer.jsp">NSDL National Science Digital Library</a></p> <p class="result-summary">The EJS Gnomon <span class="hlt">model</span> simulates the shadow cast by a gnomon (the part of a sundial that casts the shadow) over the course of a day for any day of the year and any latitude on Earth. The program gives you the option to use mean Sun (which moves relative to the stars at a constant rate throughout the year) or true Sun (which varies its apparent speed relative to the background stars). The default is to use true Sun. The program also shows the observer's horizon plane on the spherical Earth, as well as the ecliptic and the apparent path of Sun. The Earth View can be set to let Earth rotate or remain fixed EJS Gnomon <span class="hlt">model</span> was created using the Easy Java Simulations (Ejs) <span class="hlt">modeling</span> tool. It is distributed as a ready-to-run (compiled) Java archive. Double clicking the ejs_astronomy_Gnomon.jar file will run the program if Java is installed. Ejs is a part of the Open Source Physics Project and is designed to make it easier to access, modify, and generate computer <span class="hlt">models</span>. Additional Ejs <span class="hlt">models</span> for astronomy are available. They can be found by searching ComPADRE for Open Source Physics, OSP, or Ejs.</p> <div class="credits"> <p class="dwt_author">Timberlake, Todd</p> <p class="dwt_publisher"></p> <p class="publishDate">2009-08-19</p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">342</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://ntrs.nasa.gov/search.jsp?R=19920001089&hterms=peter+the+great+economics&qs=Ntx%3Dmode%2Bmatchall%26Ntk%3DAll%26N%3D0%26No%3D60%26Ntt%3D%2528%2528%2528peter%2Bthe%2529%2Bgreat%2529%2Beconomics%2529"> <span id="translatedtitle"><span class="hlt">Modeling</span> reality</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p class="result-summary">Although powerful computers have allowed complex physical and manmade hardware systems to be <span class="hlt">modeled</span> successfully, we have encountered persistent problems with the reliability of computer <span class="hlt">models</span> for systems involving human learning, human action, and human organizations. This is not a misfortune; unlike physical and manmade systems, human systems do not operate under a fixed set of laws. The rules governing the actions allowable in the system can be changed without warning at any moment, and can evolve over time. That the governing laws are inherently unpredictable raises serious questions about the reliability of <span class="hlt">models</span> when applied to human situations. In these domains, computers are better used, not for prediction and planning, but for aiding humans. Examples are systems that help humans speculate about possible futures, offer advice about possible actions in a domain, systems that gather information from the networks, and systems that track and support work flows in organizations.</p> <div class="credits"> <p class="dwt_author">Denning, Peter J.</p> <p class="dwt_publisher"></p> <p class="publishDate">1990-01-01</p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">343</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3439679"> <span id="translatedtitle"><span class="hlt">Modelling</span> osteomyelitis</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p class="result-summary">Background This work focuses on the computational <span class="hlt">modelling</span> of osteomyelitis, a bone pathology caused by bacteria infection (mostly Staphylococcus aureus). The infection alters the RANK/RANKL/OPG signalling dynamics that regulates osteoblasts and osteoclasts behaviour in bone remodelling, i.e. the resorption and mineralization activity. The infection rapidly leads to severe bone loss, necrosis of the affected portion, and it may even spread to other parts of the body. On the other hand, osteoporosis is not a bacterial infection but similarly is a defective bone pathology arising due to imbalances in the RANK/RANKL/OPG molecular pathway, and due to the progressive weakening of bone structure. Results Since both osteoporosis and osteomyelitis cause loss of bone mass, we focused on comparing the dynamics of these diseases by means of computational <span class="hlt">models</span>. Firstly, we performed meta-analysis on a gene expression data of normal, osteoporotic and osteomyelitis bone conditions. We mainly focused on RANKL/OPG signalling, the TNF and TNF receptor superfamilies and the NF-kB pathway. Using information from the gene expression data we estimated parameters for a novel <span class="hlt">model</span> of osteoporosis and of osteomyelitis. Our <span class="hlt">models</span> could be seen as a hybrid ODE and probabilistic verification <span class="hlt">modelling</span> framework which aims at investigating the dynamics of the effects of the infection in bone remodelling. Finally we discuss different diagnostic estimators defined by formal verification techniques, in order to assess different bone pathologies (osteopenia, osteoporosis and osteomyelitis) in an effective way. Conclusions We present a <span class="hlt">modeling</span> framework able to reproduce aspects of the different bone remodeling defective dynamics of osteomyelitis and osteoporosis. We report that the verification-based estimators are meaningful in the light of a feed forward between computational medicine and clinical bioinformatics. PMID:23095605</p> <div class="credits"> <p class="dwt_author"></p> <p class="dwt_publisher"></p> <p class="publishDate">2012-01-01</p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">344</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://citeseerx.ist.psu.edu/viewdoc/summary;jsessionid=2E64C7AF55BC711C5498C3051B076811?doi=10.1.1.334.5330&rank=1"> <span id="translatedtitle">The hydrogen-sensing apparatus in Ralstonia eutropha</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.osti.gov/epsearch/">E-print Network</a></p> <p class="result-summary">Molecular hydrogen is widely used by microorganisms as a source of energy. One of the best studied aerobic hydrogen oxidizers, the b-proteobacterium Ralstonia eutropha (formerly Alcaligenes eutrophus), harbors two distinct [NiFe]-<span class="hlt">hydrogenases</span> which catalyze the heterolytic cleavage of H2 into 2H + and 2e. The genes encoding the <span class="hlt">hydrogenase</span> subunits are arranged in two large operons together with accessory and regulatory genes involved in <span class="hlt">hydrogenase</span> biosynthesis. Both operons are transcribed from strong s 54-dependent promoters. Transcription requires the activation by the HoxA protein, a member of the NtrC family of response regulators. HoxA is only active when H2 is present in the environment. H2 recognition is mediated by a signal transduction complex consisting of the soluble histidine protein kinase HoxJ and a regulatory [NiFe]-<span class="hlt">hydrogenase</span> which acts as an H2 receptor. Biochemical and genetic data suggest that signal transduction between the RH and HoxJ involves an electron transport process. According to our current <span class="hlt">model</span> the histidine protein kinase HoxJ inactivates HoxA by phosphorylation in the absence H2. This property of the HoxJ-HoxA regulator pair is quite different from the behaviour of common two-component regulatory systems. Phosphorylation of HoxA is blocked in the presence of H2 provided the RH can contact HoxJ and transmit the signal to the kinase. Furthermore, <span class="hlt">hydrogenase</span> gene expression is subject to a global regulatory network in response to the carbon and energy source. HoxA is a major component of this epistatic control the molecular mechanism of which is not yet understood.</p> <div class="credits"> <p class="dwt_author">Oliver Lenz; Michael Bernhard; Thorsten Buhrke; Edward Schwartz; Bärbel Friedrich</p> <p class="dwt_publisher"></p> <p class="publishDate">2002-01-01</p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">345</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://lawrencehallofscience.org/kidsite/activities/files/ee_pdf_activities/recipes/marshmallow_models.pdf"> <span id="translatedtitle">Marshmallow <span class="hlt">Models</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://nsdl.org/nsdl_dds/services/ddsws1-1/service_explorer.jsp">NSDL National Science Digital Library</a></p> <p class="result-summary">No glue is needed for learners of any age to become marshmallow architects or engineers. Using marshmallows and water (and maybe edible decorations like peanut butter, pretzels, gumdrops, etc.), learners wet a few marshamallows at a time and stick them together bit by bit to construct whatever <span class="hlt">models</span> they want.</p> <div class="credits"> <p class="dwt_author">Science, Lawrence H.</p> <p class="dwt_publisher"></p> <p class="publishDate">2010-01-01</p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">346</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.epa.gov/region07/education_resources/teachers/activities/wateractivity1.htm"> <span id="translatedtitle">Groundwater <span class="hlt">Model</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://nsdl.org/nsdl_dds/services/ddsws1-1/service_explorer.jsp">NSDL National Science Digital Library</a></p> <p class="result-summary">In this activity, students build a <span class="hlt">model</span> to demonstrate how aquifers are formed and ground water becomes polluted. For younger students, the teacher can perform this activity as a demonstration, or older students can perform it themselves. A materials list, instructions, and extension activities are provided.</p> <div class="credits"> <p class="dwt_author"></p> <p class="dwt_publisher"></p> <p class="publishDate"></p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">347</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://eric.ed.gov/?q=holloway&id=EJ767023"> <span id="translatedtitle"><span class="hlt">Model</span> Behavior</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.eric.ed.gov/ERICWebPortal/search/extended.jsp?_pageLabel=advanced">ERIC Educational Resources Information Center</a></p> <p class="result-summary">There are dozens of books and hundreds of resources that address the issue of character development in students: how to raise them to be good people, how to teach them to be good citizens, how to help them to make good decisions. Little is written, however, about the character development of principals and school leaders, whose behavior is a <span class="hlt">model</span>…</p> <div class="credits"> <p class="dwt_author">Holloway, John</p> <p class="dwt_publisher"></p> <p class="publishDate">2006-01-01</p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">348</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://eric.ed.gov/?q=Wide+AND+%22The+Water%22&id=EJ758568"> <span id="translatedtitle"><span class="hlt">Modeling</span> Convection</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.eric.ed.gov/ERICWebPortal/search/extended.jsp?_pageLabel=advanced">ERIC Educational Resources Information Center</a></p> <p class="result-summary">Students must understand the fundamental process of convection before they can grasp a wide variety of Earth processes, many of which may seem abstract because of the scales on which they operate. Presentation of a very visual, concrete <span class="hlt">model</span> prior to instruction on these topics may facilitate students' understanding of processes that are largely…</p> <div class="credits"> <p class="dwt_author">Ebert, James R.; Elliott, Nancy A.; Hurteau, Laura; Schulz, Amanda</p> <p class="dwt_publisher"></p> <p class="publishDate">2004-01-01</p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">349</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://eric.ed.gov/?q=Wylie&pg=7&id=EJ584115"> <span id="translatedtitle"><span class="hlt">Model</span> Behavior.</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.eric.ed.gov/ERICWebPortal/search/extended.jsp?_pageLabel=advanced">ERIC Educational Resources Information Center</a></p> <p class="result-summary">Statistical <span class="hlt">modeling</span> provides a method for colleges to use alumni-development information to create an equation predicting who is likely to respond positively to fund-raising appeals. This can make fund raising more cost-effective, provide higher returns on minimal investment, provide results quickly, and improve competitiveness. Resources…</p> <div class="credits"> <p class="dwt_author">Wylie, Peter B.</p> <p class="dwt_publisher"></p> <p class="publishDate">1999-01-01</p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">350</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://home.comcast.net/~sharov/PopEcol/lec12/diffus.html"> <span id="translatedtitle">Diffusion <span class="hlt">Models</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://nsdl.org/nsdl_dds/services/ddsws1-1/service_explorer.jsp">NSDL National Science Digital Library</a></p> <p class="result-summary">Web-based intructional material describing the use of diffusion <span class="hlt">models</span> in population ecology. This page is part of a set of on-line lectures on Quantitative Population Ecology produced by Alexei Sharov in the Department of Entomology at Virginia Tech.</p> <div class="credits"> <p class="dwt_author">Sharov, Alexei</p> <p class="dwt_publisher"></p> <p class="publishDate"></p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">351</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://oaspub.epa.gov/eims/eimsapi.dispdetail?deid=47008"> <span id="translatedtitle">ATMOSPHERIC <span class="hlt">MODELING</span>: <span class="hlt">MODEL</span> AND ACCURACY</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://oaspub.epa.gov/eims/query.page">EPA Science Inventory</a></p> <p class="result-summary">The development of <span class="hlt">models</span> to assess the emission control requirements of primary precursor pollutants in the production of photochemical oxidants has been underway for approximately 20 years. Over the period there has been a considerable increase in our understanding of the basic...</p> <div class="credits"> <p class="dwt_author"></p> <p class="dwt_publisher"></p> <p class="publishDate"></p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">352</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.compadre.org/Repository/document/ServeFile.cfm?ID=9422&DocID=1315"> <span id="translatedtitle">Micrometer <span class="hlt">Model</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://nsdl.org/nsdl_dds/services/ddsws1-1/service_explorer.jsp">NSDL National Science Digital Library</a></p> <p class="result-summary">This interactive simulation gives students practice in the operation and the physical parts of a real micrometer, a measuring device that employs a screw to amplify distances that are too small to measure easily. The accuracy of a micrometer derives from the accuracy of the thread that is at its heart. The basic operating principle of a micrometer is that the rotation of an accurately made screw can be directly and precisely correlated to a certain amount of axial movement (and vice-versa), through the constant known as the screw's lead. The Micrometer <span class="hlt">model</span> was created using the Easy Java Simulations (EJS) <span class="hlt">modeling</span> tool. It is distributed as a ready-to-run (compiled) Java archive. Double click the ejs_ntnu_Micrometer.jar file to run the program (Java must be installed).</p> <div class="credits"> <p class="dwt_author">Hwang, Fu-Kwun</p> <p class="dwt_publisher"></p> <p class="publishDate">2014-06-10</p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">353</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://ntrs.nasa.gov/search.jsp?R=20020066502&hterms=small+molecules&qs=Ntx%3Dmode%2Bmatchall%26Ntk%3DAll%26N%3D0%26No%3D90%26Ntt%3Dsmall%2Bmolecules"> <span id="translatedtitle"><span class="hlt">Modeling</span> Molecules</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p class="result-summary">The molecule <span class="hlt">modeling</span> method known as Multibody Order (N) Dynamics, or MBO(N)D, was developed by Moldyn, Inc. at Goddard Space Flight Center through funding provided by the SBIR program. The software can <span class="hlt">model</span> the dynamics of molecules through technology which stimulates low-frequency molecular motions and properties, such as movements among a molecule's constituent parts. With MBO(N)D, a molecule is substructured into a set of interconnected rigid and flexible bodies. These bodies replace the computation burden of mapping individual atoms. Moldyn's technology cuts computation time while increasing accuracy. The MBO(N)D technology is available as Insight II 97.0 from Molecular Simulations, Inc. Currently the technology is used to account for forces on spacecraft parts and to perform molecular analyses for pharmaceutical purposes. It permits the solution of molecular dynamics problems on a moderate workstation, as opposed to on a supercomputer.</p> <div class="credits"> <p class="dwt_author"></p> <p class="dwt_publisher"></p> <p class="publishDate">2000-01-01</p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">354</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://learningcenter.nsta.org/product_detail.aspx?id=10.2505/9780873552394.1"> <span id="translatedtitle">Simple <span class="hlt">Models</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://nsdl.org/nsdl_dds/services/ddsws1-1/service_explorer.jsp">NSDL National Science Digital Library</a></p> <p class="result-summary">As stated in "About This Book," the author isn't going to take the usual approach to the subject of chemistry. Because virtually all explanations of chemical reactions are based on our current <span class="hlt">model</span> of atoms and molecules, the first thing to do here is to help you understand why we believe that atoms and molecules look and act the way they do. That's not a trivial issue, because despite the impression you might have gotten from textbooks, no one has ever seen an atom in the sense that you can see this page in front of you. What we have are observations and experiments that lead us to formulate <span class="hlt">models</span> of atoms. This free selection includes the Table of Contents, Preface, About This Book section, a Safety Note, and the Glossary.</p> <div class="credits"> <p class="dwt_author">Robertson, William C.</p> <p class="dwt_publisher"></p> <p class="publishDate">2007-01-01</p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">355</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.math.montana.edu/frankw/ccp/modeling/discrete/linear/learn.htm"> <span id="translatedtitle">Linear <span class="hlt">Models</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://nsdl.org/nsdl_dds/services/ddsws1-1/service_explorer.jsp">NSDL National Science Digital Library</a></p> <p class="result-summary">This site uses linear <span class="hlt">models</span> to demonstrate the change in bird populations on a barren island over time, supply and demand, and the natural cleaning of a polluted lake by fresh water over time. The problems are laid out and turned into both graphic and equation form in order to understand the rate of change happening in each scenario. There are also links to previously covered materials that can help student review material from past math lessons.</p> <div class="credits"> <p class="dwt_author">Wattenberg, Frank</p> <p class="dwt_publisher"></p> <p class="publishDate">1997-01-01</p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">356</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.math.uah.edu/stat/buffon/index.html"> <span id="translatedtitle">Geometric <span class="hlt">Models</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://nsdl.org/nsdl_dds/services/ddsws1-1/service_explorer.jsp">NSDL National Science Digital Library</a></p> <p class="result-summary">Created by Kyle Siegrist of the University of Alabama-Huntsville, this is an online, interactive lesson on geometric <span class="hlt">models</span>. The author provides examples, exercises, and applets which include Buffon's problems, Bertrand's paradox, and random triangles. Additionally, the author provides links to external resources for students wanting to engage further in this topic. This is simply one lesson in a series of seventeen. They are all easily accessible as the author has formated his site much like an online textbook.</p> <div class="credits"> <p class="dwt_author">Siegrist, Kyle</p> <p class="dwt_publisher"></p> <p class="publishDate">2009-02-23</p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">357</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://pbskids.org/dragonflytv/web_assets/pdf/dftv_nanoedguide_watercleanup.pdf#page=2"> <span id="translatedtitle"><span class="hlt">Model</span> Well</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://nsdl.org/nsdl_dds/services/ddsws1-1/service_explorer.jsp">NSDL National Science Digital Library</a></p> <p class="result-summary">In this quick activity about pollutants and groundwater (page 2 of PDF), learners build a <span class="hlt">model</span> well with a toilet paper tube. Learners use food coloring to simulate pollutants and observe how they can be carried by groundwater and eventually enter water sources such as wells, rivers, and streams. This activity is associated with nanotechnology and relates to linked video, DragonflyTV Nano: Water Clean-up.</p> <div class="credits"> <p class="dwt_author">Twin Cities Public Television, Inc.</p> <p class="dwt_publisher"></p> <p class="publishDate">2008-01-01</p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">358</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.osti.gov/scitech/servlets/purl/875627"> <span id="translatedtitle"><span class="hlt">Modeling</span> biomembranes.</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p class="result-summary">Understanding the properties and behavior of biomembranes is fundamental to many biological processes and technologies. Microdomains in biomembranes or ''lipid rafts'' are now known to be an integral part of cell signaling, vesicle formation, fusion processes, protein trafficking, and viral and toxin infection processes. Understanding how microdomains form, how they depend on membrane constituents, and how they act not only has biological implications, but also will impact Sandia's effort in development of membranes that structurally adapt to their environment in a controlled manner. To provide such understanding, we created physically-based <span class="hlt">models</span> of biomembranes. Molecular dynamics (MD) simulations and classical density functional theory (DFT) calculations using these <span class="hlt">models</span> were applied to phenomena such as microdomain formation, membrane fusion, pattern formation, and protein insertion. Because lipid dynamics and self-organization in membranes occur on length and time scales beyond atomistic MD, we used coarse-grained <span class="hlt">models</span> of double tail lipid molecules that spontaneously self-assemble into bilayers. DFT provided equilibrium information on membrane structure. Experimental work was performed to further help elucidate the fundamental membrane organization principles.</p> <div class="credits"> <p class="dwt_author">Plimpton, Steven James; Heffernan, Julieanne; Sasaki, Darryl Yoshio; Frischknecht, Amalie Lucile; Stevens, Mark Jackson; Frink, Laura J. Douglas</p> <p class="dwt_publisher"></p> <p class="publishDate">2005-11-01</p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">359</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://adsabs.harvard.edu/abs/1999JChEd..76..871H"> <span id="translatedtitle">Molecular <span class="hlt">Modeling</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p class="result-summary">Molecular <span class="hlt">modeling</span> has trickled down from the realm of pharmaceutical and research laboratories into the realm of undergraduate chemistry instruction. It has opened avenues for the visualization of chemical concepts that previously were difficult or impossible to convey. I am sure that many of you have developed exercises using the various molecular <span class="hlt">modeling</span> tools. It is the desire of this Journal to become an avenue for you to share these exercises among your colleagues. It is to this end that Ron Starkey has agreed to edit such a column and to publish not only the description of such exercises, but also the software documents they use. The WWW is the obvious medium to distribute this combination and so accepted submissions will appear online as a feature of JCE Internet. <img src="Images/jun99p871_1.gif" width=211 heighth=164 align=right> Typical molecular <span class="hlt">modeling</span> exercise: finding conformation energies. Molecular <span class="hlt">Modeling</span> Exercises and Experiments is the latest feature column of JCE Internet, joining Conceptual Questions and Challenge Problems, Hal's Picks, and Mathcad in the Chemistry Curriculum. JCE Internet continues to seek submissions in these areas of interest and submissions of general interest. If you have developed materials and would like to submit them, please see our Guide to Submissions for more information. The Chemical Education Resource Shelf, Equipment Buyers Guide, and WWW Site Review would also like to hear about chemistry textbooks and software, equipment, and WWW sites, respectively. Please consult JCE Internet Features to learn more about these resources at JCE Online. Email Announcements Would you like to be informed by email when the latest issue of the Journal is available online? when a new JCE Software title is shipping? when a new JCE Internet article has been published or is available for Open Review? when your subscription is about to expire? A new feature of JCE Online makes this possible. Visit our Guestbook to learn how. When you submit the form on this page, which includes your email address, you may choose to receive an email notice about a Journal event that interests you. Currently such events include availability of the latest issue of the Journal at JCE Online, expiration of your Journal subscription, shipment of a new JCE Software issue, publication of a new JCE Internet article or its availability for Open Review, and other announcements from the Journal. You may choose any number of these options independently. <img src="Images/jun99p871_2.gif" width=213 heighth=226 align=right> JCE Online Guestbook. Your Privacy JCE Online promises to you that we will not use the information that you provide in our Guestbook for anything other than our own internal information. We will not provide this information to third parties. We will use the information you provide only in our effort to help make the JCE serve you better. You only need to provide your email address to take advantage of this service; the other information you provide is optional. Molecular <span class="hlt">Modeling</span> Exercises and Experiments: Mission Statement We are seeking in this JCE Internet feature column to publish molecular <span class="hlt">modeling</span> exercises and experiments that have been used successfully in undergraduate instruction. The exercises will be published here on JCE Internet. An abstract of published submissions will appear in print in the Journal of Chemical Education. Acceptable exercises could be used in either a chemistry laboratory or a chemistry computer laboratory. The exercise could cover any area of chemistry, but should be limited to undergraduate instructional applications. We envision that most of the exercises/experiments will utilize one of the popular instructional molecular <span class="hlt">modeling</span> software programs (e.g. HyperChem, Spartan, CAChe, PC <span class="hlt">Model</span>). Exercises that are specific to a particular <span class="hlt">modeling</span> program are acceptable, but those usable with any <span class="hlt">modeling</span> program are preferred. Ideally the exercises/experiments will be of the type where the "correct"answer is not obvious so </p> <div class="credits"> <p class="dwt_author">Holmes, Jon L.</p> <p class="dwt_publisher"></p> <p class="publishDate">1999-06-01</p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">360</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://academic.research.microsoft.com/Publication/47814340"> <span id="translatedtitle">Atomic <span class="hlt">Models</span>, Nagaoka's Saturnian <span class="hlt">Model</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://academic.research.microsoft.com/">Microsoft Academic Search </a></p> <p class="result-summary">In late 1903, Hantaro Nagaoka (1865–1950) developed the earliest published quasi-planetary <span class="hlt">model</span> of the atom. This graduate\\u000a of the University of Tokyo from 1887 spent his postdoctoral period in Vienna, Berlin and Munich before obtaining a professorship\\u000a in Tokyo to become Japan's foremost modern physicist. Nagaoka assumed that the atom is a large, massive, positively charged\\u000a sphere, encircled by very</p> <div class="credits"> <p class="dwt_author">Klaus Hentschel</p> <p class="dwt_publisher"></p> <p class="publishDate"></p> </div> </div> </div> </div> <div id="filter_results_form" class="filter_results_form floatContainer" style="visibility: visible;"> <div style="width:100%" id="PaginatedNavigation" class="paginatedNavigationElement"> <a id="FirstPageLink" onclick='return showDiv("page_1");' href="#" title="First Page"> <img id="FirstPageLinkImage" class="Icon" src="http://www.science.gov/scigov/images/icon.first.18x20.png" alt="First Page" /></a> <a id="PreviousPageLink" onclick='return showDiv("page_17");' href="#" title="Previous Page"> <img id="PreviousPageLinkImage" class="Icon" src="http://www.science.gov/scigov/images/icon.previous.18x20.png" alt="Previous Page" /></a> <span id="PageLinks" class="pageLinks"> <span> <a onClick='return showDiv("page_1");' href="#">1</a> <a 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title="Next Page"> <img id="NextPageLinkImage" class="Icon" src="http://www.science.gov/scigov/images/icon.next.18x20.png" alt="Next Page" /></a> <a id="LastPageLink" onclick='return showDiv("page_25.0");' href="#" title="Last Page"> <img id="LastPageLinkImage" class="Icon" src="http://www.science.gov/scigov/images/icon.last.18x20.png" alt="Last Page" /></a> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">361</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.osti.gov/scitech/biblio/22150046"> <span id="translatedtitle">Local structures of Sr{sub 2}FeMnO{sub 5+y} (y=0, 0.5) and Sr{sub 2}Fe{sub 1.5}Cr{sub 0.5}O{sub 5} from reverse Monte Carlo <span class="hlt">modeling</span> of pair distribution function data and implications for magnetic order</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p class="result-summary">The local structures of the oxygen deficient perovskites Sr{sub 2}FeMnO{sub 5}, Sr{sub 2}FeMnO{sub 5.5}, and Sr{sub 2}Fe{sub 1.5}Cr{sub 0.5}O{sub 5} 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 Sr{sub 2}FeMnO{sub 5+y} compounds it is found that there is no short range ordering of the Fe and Mn cations. For Sr{sub 2}Fe{sub 1.5}Cr{sub 0.5}O{sub 5} there is evidence to suggest that the Fe/Cr distribution is not completely random and is locally ordered such that there are fewer <span class="hlt">Fe--Fe</span> nearest neighbor pairs than in a random distribution. Reverse Monte Carlo <span class="hlt">modeling</span> 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 Sr{sub 2}FeMnO{sub 5} it is found that the Fe{sup 3+} cations are most often in 4-fold coordination but there is also a large amount of Fe{sup 3+} in 5-fold coordination and a small amount in 6-fold coordination. The Mn{sup 3+} is split between 5-fold and 6-fold coordination. The Mn--O bond length distributions indicate that the Mn{sup 3+}O{sub 6} octahedra and Mn{sup 3+}O{sub 5} square pyramids are locally Jahn-Teller distorted. In Sr{sub 2}FeMnO{sub 5.5} the Fe{sup 3+} is almost entirely 5 coordinate while the Mn{sup 4+} is almost entirely 6 coordinate. The Cr{sup 3+} in Sr{sub 2}Fe{sub 1.5}Cr{sub 0.5}O{sub 5} is almost entirely 6-fold coordinated, giving the Fe{sup 3+} an average coordination number of 4.67. In Sr{sub 2}FeMnO{sub 5} and Sr{sub 2}Fe{sub 1.5}Cr{sub 0.5}O{sub 5} the Fe{sup 3+} and Sr{sup 2+} cations undergo local displacements which are driven by the oxygen vacancies, while the Mn{sup 3+} and Cr{sup 3+} cations remain near their positions in the average structures. In Sr{sub 2}FeMnO{sub 5.5} 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. - Graphical abstract: The actual bond angle distributions in the cubic perovskite Sr{sub 2}FeMnO{sub 5} obtained from reverse Monte Carlo <span class="hlt">modeling</span> of the local structure using neutron pair distribution function data. Highlights: Black-Right-Pointing-Pointer No long range ordering of oxygen vacancies, but short range order is present. Black-Right-Pointing-Pointer No short range Fe/Mn order but short range Fe/Cr order is present. Black-Right-Pointing-Pointer Fe tends to have lower coordination numbers while Mn and Cr have higher ones. Black-Right-Pointing-Pointer Local bond distances and bond angles have been determined. Black-Right-Pointing-Pointer Local structures can help explain long range magnetic ordering behavior.</p> <div class="credits"> <p class="dwt_author">King, Graham, E-mail: gking@lanl.gov [Lujan Neutron Scattering Center, Los Alamos National Laboratory, MS H805, Los Alamos, NM 87545 (United States)] [Lujan Neutron Scattering Center, Los Alamos National Laboratory, MS H805, Los Alamos, NM 87545 (United States); Ramezanipour, Farshid [Department of Chemistry and Brockhouse Institute for Materials Research, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4M1 (Canada)] [Department of Chemistry and Brockhouse Institute for Materials Research, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4M1 (Canada); Llobet, Anna [Lujan Neutron Scattering Center, Los Alamos National Laboratory, MS H805, Los Alamos, NM 87545 (United States)] [Lujan Neutron Scattering Center, Los Alamos National Laboratory, MS H805, Los Alamos, NM 87545 (United States); Greedan, John E. [Department of Chemistry and Brockhouse Institute for Materials Research, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4M1 (Canada)] [Department of Chemistry and Brockhouse Institute for Materials Research, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4M1 (Canada)</p> <p class="dwt_publisher"></p> <p class="publishDate">2013-02-15</p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">362</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://svr-www.eng.cam.ac.uk/~wjb31/ppubs/jjjbNAACL2009yPres.pdf"> <span id="translatedtitle">Introduction <span class="hlt">Model</span> training</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.osti.gov/epsearch/">E-print Network</a></p> <p class="result-summary">Introduction <span class="hlt">Model</span> training Experimental results Conclusion Context-Dependent Alignment <span class="hlt">Models</span> and William Byrne Context-Dependent Alignment <span class="hlt">Models</span> for SMT #12;Introduction <span class="hlt">Model</span> training Experimental trees <span class="hlt">Model</span> training Experimental results Evaluation of alignment quality Translation results Jamie</p> <div class="credits"> <p class="dwt_author">Byrne, William</p> <p class="dwt_publisher"></p> <p class="publishDate"></p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">363</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://pubs.er.usgs.gov/publication/70006394"> <span id="translatedtitle"><span class="hlt">Modeling</span> uncertainty: quicksand for water temperature <span class="hlt">modeling</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://pubs.er.usgs.gov/pubs/index.jsp?view=adv">USGS Publications Warehouse</a></p> <p class="result-summary">Uncertainty has been a hot topic relative to science generally, and <span class="hlt">modeling</span> specifically. <span class="hlt">Modeling</span> uncertainty comes in various forms: measured data, limited <span class="hlt">model</span> domain, <span class="hlt">model</span> parameter estimation, <span class="hlt">model</span> structure, sensitivity to inputs, <span class="hlt">modelers</span> themselves, and users of the results. This paper will address important components of uncertainty in <span class="hlt">modeling</span> water temperatures, and discuss several areas that need attention as the <span class="hlt">modeling</span> community grapples with how to incorporate uncertainty into <span class="hlt">modeling</span> without getting stuck in the quicksand that prevents constructive contributions to policy making. The material, and in particular the reference, are meant to supplement the presentation given at this conference.</p> <div class="credits"> <p class="dwt_author">Bartholow, John M.</p> <p class="dwt_publisher"></p> <p class="publishDate">2003-01-01</p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">364</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://eric.ed.gov/?q=cad&pg=4&id=EJ916642"> <span id="translatedtitle">Pre-<span class="hlt">Modeling</span> Ensures Accurate Solid <span class="hlt">Models</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.eric.ed.gov/ERICWebPortal/search/extended.jsp?_pageLabel=advanced">ERIC Educational Resources Information Center</a></p> <p class="result-summary">Successful solid <span class="hlt">modeling</span> requires a well-organized design tree. The design tree is a list of all the object's features and the sequential order in which they are <span class="hlt">modeled</span>. The solid-<span class="hlt">modeling</span> process is faster and less prone to <span class="hlt">modeling</span> errors when the design tree is a simple and geometrically logical definition of the <span class="hlt">modeled</span> object. Few high…</p> <div class="credits"> <p class="dwt_author">Gow, George</p> <p class="dwt_publisher"></p> <p class="publishDate">2010-01-01</p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">365</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.hss.cmu.edu/philosophy/spirtes/jem05.pdf"> <span id="translatedtitle">Graphical <span class="hlt">models</span>, causal inference, and econometric <span class="hlt">models</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.osti.gov/epsearch/">E-print Network</a></p> <p class="result-summary">Graphical <span class="hlt">models</span>, causal inference, and econometric <span class="hlt">models</span> Peter Spirtes Abstract A graphical <span class="hlt">model</span> <span class="hlt">modeling</span> has historical ties to causal <span class="hlt">modeling</span> in econometrics and other social sciences, there have been isolated from the econometric tradition. In this paper I will describe a number of recent developments</p> <div class="credits"> <p class="dwt_author">Spirtes, Peter</p> <p class="dwt_publisher"></p> <p class="publishDate"></p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">366</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://academic.research.microsoft.com/Publication/38748075"> <span id="translatedtitle">Technological Forecasting---<span class="hlt">Model</span> Selection, <span class="hlt">Model</span> Stability, and Combining <span class="hlt">Models</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://academic.research.microsoft.com/">Microsoft Academic Search </a></p> <p class="result-summary">The paper identifies 29 <span class="hlt">models</span> that the literature suggests are appropriate for technological forecasting. These <span class="hlt">models</span> are divided into three classes according to the timing of the point of inflexion in the innovation or substitution process. Faced with a given data set and such a choice, the issue of <span class="hlt">model</span> selection needs to be addressed. Evidence used to aid <span class="hlt">model</span></p> <div class="credits"> <p class="dwt_author">Nigel Meade; Towhidul Islam</p> <p class="dwt_publisher"></p> <p class="publishDate">1998-01-01</p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">367</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://academic.research.microsoft.com/Publication/375035"> <span id="translatedtitle">Software interconnection <span class="hlt">models</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://academic.research.microsoft.com/">Microsoft Academic Search </a></p> <p class="result-summary">We present a formulation of interconnection <span class="hlt">models</span> and present the unit and syntactic <span class="hlt">models</span> — the primary <span class="hlt">models</span> used for managing the evolution of large software systems. We discuss various tools that use these <span class="hlt">models</span> and evaluate how well these <span class="hlt">models</span> support the management of system evolution. We then introduce the semantic interconnection <span class="hlt">model</span>. The semantic interconnection <span class="hlt">model</span> incorporates the</p> <div class="credits"> <p class="dwt_author">Dewayne E. Perry</p> <p class="dwt_publisher"></p> <p class="publishDate">1987-01-01</p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">368</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.stat.columbia.edu/~regina/research/dimacs.pdf"> <span id="translatedtitle">Epidemic <span class="hlt">Modeling</span>: SIRS <span class="hlt">Models</span> Regina Dolgoarshinnykh</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.osti.gov/epsearch/">E-print Network</a></p> <p class="result-summary">Epidemic <span class="hlt">Modeling</span>: SIRS <span class="hlt">Models</span> Regina Dolgoarshinnykh Columbia University joint with Steven P. Lalley University of Chicago #12;Threshold Phenomena in Epidemic <span class="hlt">Models</span> · Epidemic <span class="hlt">models</span> often exhibit the reproductive number is above one, a major epidemic is possible. · The final outcome of the infection spread</p> <div class="credits"> <p class="dwt_author">Dolgoarshinnykh, Regina</p> <p class="dwt_publisher"></p> <p class="publishDate"></p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">369</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://academic.research.microsoft.com/Publication/50687214"> <span id="translatedtitle">Parametric uncertainty <span class="hlt">modeling</span> for LFT <span class="hlt">model</span> realization</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://academic.research.microsoft.com/">Microsoft Academic Search </a></p> <p class="result-summary">This paper presents a procedure for parametric uncertainty <span class="hlt">modeling</span> of a small unmanned aerial vehicle flight dynamics for the purpose of LFT <span class="hlt">model</span> realization. Experimental data measurements were taken to construct the parametric uncertainties in the 6-DOF nonlinear simulation <span class="hlt">model</span> for the vehicle . A new approach is used to linearize the uncertain nonlinear simulation <span class="hlt">model</span> developed and a physically</p> <div class="credits"> <p class="dwt_author">Yew Chai Paw; Gary J. Balas</p> <p class="dwt_publisher"></p> <p class="publishDate">2008-01-01</p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">370</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.fil.ion.ucl.ac.uk/~wpenny/bdb/hdm.pdf"> <span id="translatedtitle">Hierarchical Dynamic <span class="hlt">Models</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.osti.gov/epsearch/">E-print Network</a></p> <p class="result-summary">Hierarchical Dynamic <span class="hlt">Models</span> Will Penny OU Processes Embedding OU(2) process Dynamic <span class="hlt">Models</span> Generalised coordinates Joint Likelihood Filtering Mode Following Dynamic Expectation Maximisation Generative Generative <span class="hlt">Model</span> Generated Data Filtering Triple Estimation Hierarchical Dynamic <span class="hlt">Models</span> References</p> <div class="credits"> <p class="dwt_author">Penny, Will</p> <p class="dwt_publisher"></p> <p class="publishDate"></p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">371</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.osti.gov/scitech/servlets/purl/1046069"> <span id="translatedtitle">I&C <span class="hlt">Modeling</span> in SPAR <span class="hlt">Models</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p class="result-summary">The Standardized Plant Analysis Risk (SPAR) <span class="hlt">models</span> for the U.S. commercial nuclear power plants currently have very limited instrumentation and control (I&C) <span class="hlt">modeling</span> [1]. Most of the I&C components in the operating plant SPAR <span class="hlt">models</span> are related to the reactor protection system. This was identified as a finding during the industry peer review of SPAR <span class="hlt">models</span>. While the Emergency Safeguard Features (ESF) actuation and control system was incorporated into the Peach Bottom Unit 2 SPAR <span class="hlt">model</span> in a recent effort [2], various approaches to expend resources for detailed I&C <span class="hlt">modeling</span> in other SPAR <span class="hlt">models</span> are investigated.</p> <div class="credits"> <p class="dwt_author">John A. Schroeder</p> <p class="dwt_publisher"></p> <p class="publishDate">2012-06-01</p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">372</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4186674"> <span id="translatedtitle">Comparative Protein Structure <span class="hlt">Modeling</span> Using <span class="hlt">Modeller</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p class="result-summary">Functional characterization of a protein sequence is one of the most frequent problems in biology. This task is usually facilitated by accurate three-dimensional (3-D) structure of the studied protein. In the absence of an experimentally determined structure, comparative or homology <span class="hlt">modeling</span> can sometimes provide a useful 3-D <span class="hlt">model</span> for a protein that is related to at least one known protein structure. Comparative <span class="hlt">modeling</span> predicts the 3-D structure of a given protein sequence (target) based primarily on its alignment to one or more proteins of known structure (templates). The prediction process consists of fold assignment, target-template alignment, <span class="hlt">model</span> building, and <span class="hlt">model</span> evaluation. This unit describes how to calculate comparative <span class="hlt">models</span> using the program <span class="hlt">MODELLER</span> and discusses all four steps of comparative <span class="hlt">modeling</span>, frequently observed errors, and some applications. <span class="hlt">Modeling</span> lactate dehydrogenase from Trichomonas vaginalis (TvLDH) is described as an example. The download and installation of the <span class="hlt">MODELLER</span> software is also described. PMID:18428767</p> <div class="credits"> <p class="dwt_author">Eswar, Narayanan; Marti-Renom, Marc A.; Madhusudhan, M.S.; Eramian, David; Shen, Min-yi; Pieper, Ursula</p> <p class="dwt_publisher"></p> <p class="publishDate">2014-01-01</p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">373</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://academic.research.microsoft.com/Publication/60574079"> <span id="translatedtitle">Composite Load <span class="hlt">Model</span> Evaluation</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://academic.research.microsoft.com/">Microsoft Academic Search </a></p> <p class="result-summary">The WECC load <span class="hlt">modeling</span> task force has dedicated its effort in the past few years to develop a composite load <span class="hlt">model</span> that can represent behaviors of different end-user components. The <span class="hlt">modeling</span> structure of the composite load <span class="hlt">model</span> is recommended by the WECC load <span class="hlt">modeling</span> task force. GE Energy has implemented this composite load <span class="hlt">model</span> with a new function CMPLDW in</p> <div class="credits"> <p class="dwt_author">Ning Lu; Hong Qiao</p> <p class="dwt_publisher"></p> <p class="publishDate">2007-01-01</p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">374</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.osti.gov/scitech/biblio/21153921"> <span id="translatedtitle">Standard Solar <span class="hlt">Model</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p class="result-summary">Solar <span class="hlt">models</span> are important in our understanding of stars and stellar evolution. Solar <span class="hlt">models</span> have been constructed using different methods. In this work, a solar <span class="hlt">model</span> will be built using the fitting method. The <span class="hlt">model</span> will incorporate the most recent input data. The <span class="hlt">model</span> will be evolved to the current epoch starting from the zero-age main sequence <span class="hlt">model</span>.</p> <div class="credits"> <p class="dwt_author">Loong, Lim Yaw; Yusof, Norhasliza; Kassim, Hasan Abu [Physics Department, Faculty of Science, University of Malaya, 50603 Kuala Lumpur (Malaysia)</p> <p class="dwt_publisher"></p> <p class="publishDate">2008-05-20</p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">375</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://endo.endojournals.org/cgi/reprint/146/2/913.pdf"> <span id="translatedtitle">Reduced Adipose Glucocorticoid Reactivation and Increased Hepatic Glucocorticoid Clearance as an Early Adaptation to High-Fat Feeding in Wistar Rats</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://academic.research.microsoft.com/">Microsoft Academic Search </a></p> <p class="result-summary">Altered peripheral glucocorticoid metabolism may be impor- tant in the pathogenesis of obesity in humans and animal <span class="hlt">models</span>. Genetically obese Zucker rats, Lep\\/ob mice, and obese humans exhibit increased regeneration of active glucocorti- coids selectively in adipose tissue by 11-hydroxysteroid de- <span class="hlt">hydrogenase</span> type 1 (11-HSD-1) and increased glucocorticoid clearance by hepatic A-ring reductases. We have examined whether dietary obesity in</p> <div class="credits"> <p class="dwt_author">Amanda J. Drake; Dawn E. W. Livingstone; Ruth Andrew; Jonathan R. Seckl; Nicholas M. Morton; Brian R. Walker</p> <p class="dwt_publisher"></p> <p class="publishDate">2004-01-01</p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">376</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://academic.research.microsoft.com/Publication/13024064"> <span id="translatedtitle">The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://academic.research.microsoft.com/">Microsoft Academic Search </a></p> <p class="result-summary">Desulfovibrio vulgaris Hildenborough is a <span class="hlt">model</span> organism for studying the energy metabolism of sulfate-reducing bacteria (SRB) and for understanding the economic impacts of SRB, including biocorrosion of metal infrastructure and bioremediation of toxic metal ions. The 3,570,858 base pair (bp) genome sequence reveals a network of novel c-type cytochromes, connecting multiple periplasmic <span class="hlt">hydrogenases</span> and formate dehydrogenases, as a key feature</p> <div class="credits"> <p class="dwt_author">Rekha Seshadri; Shelley A Haveman; Christopher L Hemme; Ian T Paulsen; James F Kolonay; Jonathan A Eisen; Barbara Methe; Lauren M Brinkac; Sean C Daugherty; Robert T Deboy; Robert J Dodson; A Scott Durkin; Ramana Madupu; William C Nelson; Steven A Sullivan; Derrick Fouts; Daniel H Haft; Jeremy Selengut; Jeremy D Peterson; Tanja M Davidsen; Nikhat Zafar; Liwei Zhou; Diana Radune; George Dimitrov; Mark Hance; Kevin Tran; Hoda Khouri; John Gill; Terry R Utterback; Tamara V Feldblyum; Judy D Wall; Gerrit Voordouw; Claire M Fraser; John F Heidelberg</p> <p class="dwt_publisher"></p> <p class="publishDate">2004-01-01</p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">377</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4238032"> <span id="translatedtitle"><span class="hlt">Modeling</span> cholera outbreaks</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p class="result-summary">Mathematical <span class="hlt">modeling</span> can be a valuable tool for studying infectious disease outbreak dynamics and simulating the effects of possible interventions. Here, we describe approaches to <span class="hlt">modeling</span> cholera outbreaks and how <span class="hlt">models</span> have been applied to explore intervention strategies, particularly in Haiti. Mathematical <span class="hlt">models</span> can play an important role in formulating and evaluating complex cholera outbreak response options. Major challenges to cholera <span class="hlt">modeling</span> are insufficient data for calibrating <span class="hlt">models</span> and the need to tailor <span class="hlt">models</span> for different outbreak scenarios. PMID:23412687</p> <div class="credits"> <p class="dwt_author">Longini, Ira M.; Morris, J. Glenn</p> <p class="dwt_publisher"></p> <p class="publishDate">2014-01-01</p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">378</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://ntrs.nasa.gov/search.jsp?R=19890016849&hterms=iodine+laser&qs=Ntx%3Dmode%2Bmatchall%26Ntk%3DAll%26N%3D0%26No%3D60%26Ntt%3Diodine%2Blaser"> <span id="translatedtitle">Comparison of laser <span class="hlt">models</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p class="result-summary">Progress on the comparison of laser <span class="hlt">models</span> is reported. Equations for an oscillatory <span class="hlt">model</span> and a nonoscillatory <span class="hlt">model</span> for the simulation of iodine laser operation are solved. Reaction rate coefficients used in both <span class="hlt">models</span> are listed. Currently there are four <span class="hlt">models</span> for the simulation of iodine laser operation are solved. Reaction rate coefficients used in both <span class="hlt">models</span> are listed. Currently there are four <span class="hlt">models</span> for the simulation of an iodine laser. They are: (1) a time dependent <span class="hlt">model</span>; (2) a quasi-steady state <span class="hlt">model</span>; (3) a noncompressible <span class="hlt">model</span>; and (4) a compressible flow laser <span class="hlt">model</span>. Current research is being directed toward: (1) parameter studies using the compressible flow laser <span class="hlt">model</span>; (2) development of a two-pass amplifier <span class="hlt">model</span>; and (3) solving a system of equations describing operation of the high powered iodine MOPA (master oscillator power amplifier).</p> <div class="credits"> <p class="dwt_author">Heinbockel, John H.</p> <p class="dwt_publisher"></p> <p class="publishDate">1989-01-01</p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">379</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://people.irisa.fr/Jean-Marc.Jezequel/enseignement/M2RI/MDE/ModelTyping.pdf"> <span id="translatedtitle"><span class="hlt">Model</span> Transformation Reuse with <span class="hlt">Model</span> Typing</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.osti.gov/epsearch/">E-print Network</a></p> <p class="result-summary">machines More and more <span class="hlt">model</span> manipulation operators · Need for a systematic engineering Software Language manipulation 7 8 · Motivating example: <span class="hlt">model</span> transformation [SoSyM'07] takes as input a state machine Rennes Triskell Research Team http://www.irisa.fr/triskell · A <span class="hlt">model</span> · Its metamodel · Adding Operational</p> <div class="credits"> <p class="dwt_author"></p> <p class="dwt_publisher"></p> <p class="publishDate"></p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">380</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.cscamm.umd.edu/programs/cxf07/presentations/Wang.pdf"> <span id="translatedtitle"><span class="hlt">Modeling</span> Biofilms Using Complex Fluid <span class="hlt">Models</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.osti.gov/epsearch/">E-print Network</a></p> <p class="result-summary"><span class="hlt">Modeling</span> Biofilms Using Complex Fluid <span class="hlt">Models</span> Qi Wang Department of Mathematics Florida State · Phase field <span class="hlt">models</span> for biofilms · Linear stability analysis of constant steady states · Numerical (optional). · Conclusion #12;Introduction to Biofilms · Biofilms are ubiquitous in nature and manmade</p> <div class="credits"> <p class="dwt_author">Maryland at College Park, University of</p> <p class="dwt_publisher"></p> <p class="publishDate"></p> </div> </div> </div> </div> <div id="filter_results_form" class="filter_results_form floatContainer" style="visibility: visible;"> <div style="width:100%" id="PaginatedNavigation" 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class="floatContainer result odd" lang="en"> <div class="resultNumber element">381</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.math.uni-leipzig.de/~frey/frey-mcneil-02a.pdf"> <span id="translatedtitle">Dependence <span class="hlt">Modelling</span>, <span class="hlt">Model</span> Risk and <span class="hlt">Model</span> Calibration in <span class="hlt">Models</span> of Portfolio Credit Risk</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.osti.gov/epsearch/">E-print Network</a></p> <p class="result-summary">Dependence <span class="hlt">Modelling</span>, <span class="hlt">Model</span> Risk and <span class="hlt">Model</span> Calibration in <span class="hlt">Models</span> of Portfolio Credit Risk R@mathematik.uni-leipzig.de Alexander J. McNeil Department of Mathematics Federal Institute of Technology ETH Zentrum CH-8092 Zurich the mathe- matical structure and in particular the <span class="hlt">modelling</span> of dependence between default events</p> <div class="credits"> <p class="dwt_author">Frey, Rüdiger</p> <p class="dwt_publisher"></p> <p class="publishDate"></p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">382</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://academic.research.microsoft.com/Publication/70894"> <span id="translatedtitle">The Mobius <span class="hlt">modeling</span> tool</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://academic.research.microsoft.com/">Microsoft Academic Search </a></p> <p class="result-summary">Despite the development of many <span class="hlt">modeling</span> formalisms and <span class="hlt">model</span> solution methods, most tool implementations support only a single formalism. Furthermore, <span class="hlt">models</span> expressed in the chosen formalism cannot be combined with <span class="hlt">models</span> expressed in other formalisms. This monolithic approach both limits the usefulness of such tools to practitioners, and hampers <span class="hlt">modeling</span> research, since it is difficult to compare new and existing</p> <div class="credits"> <p class="dwt_author">Graham Clark; Tod Courtney; David Daly; Dan Deavours; Salem Derisavi; Jay M. Doyle; William H. Sanders; Patrick Webster</p> <p class="dwt_publisher"></p> <p class="publishDate">2001-01-01</p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">383</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://eric.ed.gov/?q=unified+AND+equation&pg=2&id=EJ922103"> <span id="translatedtitle">Multilevel <span class="hlt">Model</span> Prediction</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.eric.ed.gov/ERICWebPortal/search/extended.jsp?_pageLabel=advanced">ERIC Educational Resources Information Center</a></p> <p class="result-summary">Multilevel <span class="hlt">models</span> are proven tools in social research for <span class="hlt">modeling</span> complex, hierarchical systems. In multilevel <span class="hlt">modeling</span>, statistical inference is based largely on quantification of random variables. This paper distinguishes among three types of random variables in multilevel <span class="hlt">modeling--model</span> disturbances, random coefficients, and future response…</p> <div class="credits"> <p class="dwt_author">Frees, Edward W.; Kim, Jee-Seon</p> <p class="dwt_publisher"></p> <p class="publishDate">2006-01-01</p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">384</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.apsarchive.org/resource.cfm?submissionID=1174&BEN=1"> <span id="translatedtitle"><span class="hlt">Modeling</span> the Heart</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://nsdl.org/nsdl_dds/services/ddsws1-1/service_explorer.jsp">NSDL National Science Digital Library</a></p> <p class="result-summary"><span class="hlt">Models</span> of the heart have been developed since 1960, starting with the discovery and <span class="hlt">modeling</span> of potassium channels. The first <span class="hlt">models</span> of calcium balance were made in the 1980s and have now reached a high degree of physiological detail. During the 1990s, these cell <span class="hlt">models</span> were incorporated into anatomically detailed tissue and organ <span class="hlt">models</span>.</p> <div class="credits"> <p class="dwt_author">Denis Noble (Oxford University Department of Physiology)</p> <p class="dwt_publisher"></p> <p class="publishDate">2004-08-01</p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">385</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.siggraph.org/education/materials/HyperGraph/modeling/cgmodel.htm"> <span id="translatedtitle"><span class="hlt">Modeling</span> in Computer Graphics</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://nsdl.org/nsdl_dds/services/ddsws1-1/service_explorer.jsp">NSDL National Science Digital Library</a></p> <p class="result-summary">A discussion of different <span class="hlt">modeling</span> techniques in computer graphics including t polygon mesh, parametric cubic curves and patches, implicit functions such as metaballs, procedural <span class="hlt">modeling</span> (plants and flowers) and <span class="hlt">modeling</span> transformations.</p> <div class="credits"> <p class="dwt_author"></p> <p class="dwt_publisher"></p> <p class="publishDate">2003-02-15</p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">386</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.ntis.gov/search/product.aspx?ABBR=N20030093737"> <span id="translatedtitle">Earth System <span class="hlt">Model</span>.</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.ntis.gov/search/index.aspx">National Technical Information Service (NTIS)</a></p> <p class="result-summary">The Earth System <span class="hlt">Model</span> is the natural evolution of current climate <span class="hlt">models</span> and will be the ultimate embodiment of our geophysical understanding of the planet. These <span class="hlt">models</span> are constructed from components - atmosphere, ocean, ice, land, chemistry, solid ear...</p> <div class="credits"> <p class="dwt_author">M. Schoeberl, R. B. Rood, P. Hildebrand, C. Raymond</p> <p class="dwt_publisher"></p> <p class="publishDate">2003-01-01</p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">387</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://dx.doi.org/10.1080/0950069980200308"> <span id="translatedtitle"><span class="hlt">Models</span> of magnetism</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://nsdl.org/nsdl_dds/services/ddsws1-1/service_explorer.jsp">NSDL National Science Digital Library</a></p> <p class="result-summary">This study investigates the mental <span class="hlt">models</span> that people construct about magnetic phenomena. The project involved students, physics teachers, engineers, and practitioners. The researchers propose five <span class="hlt">models</span> following a progression from simple description to a field <span class="hlt">model</span>. Contains 28 references.</p> <div class="credits"> <p class="dwt_author">Borges, A. T.; Gilbert, John; Tecnico, Colegio</p> <p class="dwt_publisher"></p> <p class="publishDate">2006-05-23</p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">388</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://learningcenter.nsta.org/product_detail.aspx?id=10.2505/4/tst11_078_02_34"> <span id="translatedtitle"><span class="hlt">Modeling</span> Natural Selection</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://nsdl.org/nsdl_dds/services/ddsws1-1/service_explorer.jsp">NSDL National Science Digital Library</a></p> <p class="result-summary">In their research, scientists generate, test, and modify scientific <span class="hlt">models</span>. These <span class="hlt">models</span> can be shared with others and demonstrate a scientist's understanding of how the natural world works. Similarly, students can generate and modify <span class="hlt">models</span> to gain a bet</p> <div class="credits"> <p class="dwt_author">Lotter, Christine; Bogiages, Christopher A.</p> <p class="dwt_publisher"></p> <p class="publishDate">2011-02-01</p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">389</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://serc.carleton.edu/introgeo/mathstatmodels/index.html"> <span id="translatedtitle">Mathematics and Statistics <span class="hlt">Models</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://nsdl.org/nsdl_dds/services/ddsws1-1/service_explorer.jsp">NSDL National Science Digital Library</a></p> <p class="result-summary">Developed by Bob MacKay, Clark College. What are Mathematical and Statistical <span class="hlt">Models</span> These types of <span class="hlt">models</span> are obviously related, but there are also real differences between them. Mathematical <span class="hlt">Models</span>: grow out of ...</p> <div class="credits"> <p class="dwt_author"></p> <p class="dwt_publisher"></p> <p class="publishDate"></p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">390</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://eric.ed.gov/?q=physics+AND+engineers&id=EJ574269"> <span id="translatedtitle"><span class="hlt">Models</span> of Magnetism.</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.eric.ed.gov/ERICWebPortal/search/extended.jsp?_pageLabel=advanced">ERIC Educational Resources Information Center</a></p> <p class="result-summary">Investigates the mental <span class="hlt">models</span> that people construct about magnetic phenomena. Involves students, physics teachers, engineers, and practitioners. Proposes five <span class="hlt">models</span> following a progression from simple description to a field <span class="hlt">model</span>. Contains 28 references. (DDR)</p> <div class="credits"> <p class="dwt_author">Borges, A. Tarciso; Gilbert, John K.</p> <p class="dwt_publisher"></p> <p class="publishDate">1998-01-01</p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">391</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://adsabs.harvard.edu/abs/2014NJPh...16i3035F"> <span id="translatedtitle">Quantum <span class="hlt">model</span> averaging</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p class="result-summary">Standard tomographic analyses ignore <span class="hlt">model</span> uncertainty. It is assumed that a given <span class="hlt">model</span> generated the data and the task is to estimate the quantum state, or a subset of parameters within that <span class="hlt">model</span>. Here we apply a <span class="hlt">model</span> averaging technique to mitigate the risk of overconfident estimates of <span class="hlt">model</span> parameters in two examples: (1) selecting the rank of the state in tomography and (2) selecting the <span class="hlt">model</span> for the fidelity decay curve in randomized benchmarking.</p> <div class="credits"> <p class="dwt_author">Ferrie, Christopher</p> <p class="dwt_publisher"></p> <p class="publishDate">2014-09-01</p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">392</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.osti.gov/scitech/servlets/purl/5801890"> <span id="translatedtitle"><span class="hlt">Modeling</span> of geothermal systems</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p class="result-summary">During the last decade the use of numerical <span class="hlt">modeling</span> for geothermal resource evaluation has grown significantly, and new <span class="hlt">modeling</span> approaches have been developed. In this paper we present a summary of the present status in numerical <span class="hlt">modeling</span> of geothermal systems, emphasizing recent developments. Different <span class="hlt">modeling</span> approaches are described and their applicability discussed. The various <span class="hlt">modeling</span> tasks, including natural-state, exploitation, injection, multi-component and subsidence <span class="hlt">modeling</span>, are illustrated with geothermal field examples. 99 refs., 14 figs.</p> <div class="credits"> <p class="dwt_author">Bodvarsson, G.S.; Pruess, K.; Lippmann, M.J.</p> <p class="dwt_publisher"></p> <p class="publishDate">1985-03-01</p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">393</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://academic.research.microsoft.com/Publication/923146"> <span id="translatedtitle">Validating simulation <span class="hlt">models</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://academic.research.microsoft.com/">Microsoft Academic Search </a></p> <p class="result-summary">In this paper we give a general introduction to <span class="hlt">model</span> validation, define the various validation techniques, discuss conceptual and operational validity, and present a recommended <span class="hlt">model</span> validation procedure.</p> <div class="credits"> <p class="dwt_author">Robert G. Sargent</p> <p class="dwt_publisher"></p> <p class="publishDate">1983-01-01</p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">394</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.ebi.ac.uk/biomodels-main/"> <span id="translatedtitle">Bio<span class="hlt">Models</span> Database</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://nsdl.org/nsdl_dds/services/ddsws1-1/service_explorer.jsp">NSDL National Science Digital Library</a></p> <p class="result-summary">Hosted by the European Bioinformatics Institute, the Bio<span class="hlt">Models</span> Database is a collaborative, "new effort to develop a data resource that will allow biologist to store, search and retrieve published mathematical <span class="hlt">models</span> of biological interests. The <span class="hlt">models</span> in the Bio<span class="hlt">Models</span> Database are annotated and linked to relevant data resources, such as publications, databases of compounds and pathways, controlled vocabularies, etc." The website allows visitors to browse and search the Database for <span class="hlt">models</span>. The site also provides information about submitting <span class="hlt">models</span> for the Database. It should be noted that submitted <span class="hlt">models</span> must undergo tests conducted by Bio<span class="hlt">Models</span> Database curators before they are incorporated. [NL</p> <div class="credits"> <p class="dwt_author"></p> <p class="dwt_publisher"></p> <p class="publishDate"></p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">395</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://ntrs.nasa.gov/search.jsp?R=19920057858&hterms=circuit+modeling&qs=Ntx%3Dmode%2Bmatchall%26Ntk%3DAll%26N%3D0%26No%3D10%26Ntt%3Dcircuit%2Bmodeling"> <span id="translatedtitle">Continuous system <span class="hlt">modeling</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p class="result-summary">A comprehensive and systematic introduction is presented for the concepts associated with '<span class="hlt">modeling</span>', involving the transition from a physical system down to an abstract description of that system in the form of a set of differential and/or difference equations, and basing its treatment of <span class="hlt">modeling</span> on the mathematics of dynamical systems. Attention is given to the principles of passive electrical circuit <span class="hlt">modeling</span>, planar mechanical systems <span class="hlt">modeling</span>, hierarchical modular <span class="hlt">modeling</span> of continuous systems, and bond-graph <span class="hlt">modeling</span>. Also discussed are <span class="hlt">modeling</span> in equilibrium thermodynamics, population dynamics, and system dynamics, inductive reasoning, artificial neural networks, and automated <span class="hlt">model</span> synthesis.</p> <div class="credits"> <p class="dwt_author">Cellier, Francois E.</p> <p class="dwt_publisher"></p> <p class="publishDate">1991-01-01</p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">396</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.osti.gov/scitech/biblio/10192285"> <span id="translatedtitle">PREDICTIVE <span class="hlt">MODELS</span>. Enhanced Oil Recovery <span class="hlt">Model</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p class="result-summary">PREDICTIVE <span class="hlt">MODELS</span> is a collection of five <span class="hlt">models</span> - CFPM, CO2PM, ICPM, PFPM, and SFPM - used in the 1982-1984 National Petroleum Council study of enhanced oil recovery (EOR) potential. Each pertains to a specific EOR process designed to squeeze additional oil from aging or spent oil fields. The processes are: 1 chemical flooding; 2 carbon dioxide miscible flooding; 3 in-situ combustion; 4 polymer flooding; and 5 steamflood. CFPM, the Chemical Flood Predictive <span class="hlt">Model</span>, <span class="hlt">models</span> micellar (surfactant)-polymer floods in reservoirs, which have been previously waterflooded to residual oil saturation. Thus, only true tertiary floods are considered. An option allows a rough estimate of oil recovery by caustic or caustic-polymer processes. CO2PM, the Carbon Dioxide miscible flooding Predictive <span class="hlt">Model</span>, is applicable to both secondary (mobile oil) and tertiary (residual oil) floods, and to either continuous CO2 injection or water-alternating gas processes. ICPM, the In-situ Combustion Predictive <span class="hlt">Model</span>, computes the recovery and profitability of an in-situ combustion project from generalized performance predictive algorithms. PFPM, the Polymer Flood Predictive <span class="hlt">Model</span>, is switch-selectable for either polymer or waterflooding, and an option allows the calculation of the incremental oil recovery and economics of polymer relative to waterflooding. SFPM, the Steamflood Predictive <span class="hlt">Model</span>, is applicable to the steam drive process, but not to cyclic steam injection (steam soak) processes. The IBM PC/AT version includes a plotting capability to produces a graphic picture of the predictive <span class="hlt">model</span> results.</p> <div class="credits"> <p class="dwt_author">Ray, R.M. [DOE Bartlesville Energy Technology Center, Bartlesville, OK (United States)</p> <p class="dwt_publisher"></p> <p class="publishDate">1992-02-26</p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">397</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://adsabs.harvard.edu/abs/2010AIPC.1309..769R"> <span id="translatedtitle">AIDS Epidemiological <span class="hlt">models</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p class="result-summary">The aim of this paper is to present mathematical <span class="hlt">modelling</span> of the spread of infection in the context of the transmission of the human immunodeficiency virus (HIV) and the acquired immune deficiency syndrome (AIDS). These <span class="hlt">models</span> are based in part on the <span class="hlt">models</span> suggested in the field of th AIDS mathematical <span class="hlt">modelling</span> as reported by ISHAM [6].</p> <div class="credits"> <p class="dwt_author">Rahmani, Fouad Lazhar</p> <p class="dwt_publisher"></p> <p class="publishDate">2010-11-01</p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">398</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://academic.research.microsoft.com/Publication/122300"> <span id="translatedtitle">Relevance based language <span class="hlt">models</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://academic.research.microsoft.com/">Microsoft Academic Search </a></p> <p class="result-summary">We explore the relation between classical probabilistic <span class="hlt">models</span> of information retrieval and the emerging language <span class="hlt">modeling</span> approaches. It has long been recognized that the primary obstacle to effective performance of classical <span class="hlt">models</span> is the need to estimate arelevance <span class="hlt">model</span>: probabilities of words in the relevant class. We propose a novel technique for estimating these probabilities using the query alone. We</p> <div class="credits"> <p class="dwt_author">Victor Lavrenko; W. Bruce Croft</p> <p class="dwt_publisher"></p> <p class="publishDate">2001-01-01</p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">399</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://eric.ed.gov/?q=Trees&pg=7&id=ED519318"> <span id="translatedtitle">Generative <span class="hlt">Models</span> of Disfluency</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.eric.ed.gov/ERICWebPortal/search/extended.jsp?_pageLabel=advanced">ERIC Educational Resources Information Center</a></p> <p class="result-summary">This thesis describes a generative <span class="hlt">model</span> for representing disfluent phenomena in human speech. This <span class="hlt">model</span> makes use of observed syntactic structure present in disfluent speech, and uses a right-corner transform on syntax trees to <span class="hlt">model</span> this structure in a very natural way. Specifically, the phenomenon of speech repair is <span class="hlt">modeled</span> by explicitly…</p> <div class="credits"> <p class="dwt_author">Miller, Timothy A.</p> <p class="dwt_publisher"></p> <p class="publishDate">2010-01-01</p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">400</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://eric.ed.gov/?q=artificial+AND+intelligence+AND+computer+AND+simulation&pg=7&id=ED301147"> <span id="translatedtitle">Qualitative Student <span class="hlt">Models</span>.</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.eric.ed.gov/ERICWebPortal/search/extended.jsp?_pageLabel=advanced">ERIC Educational Resources Information Center</a></p> <p class="result-summary">The concept of a qualitative <span class="hlt">model</span> is used as the focus of this review of qualitative student <span class="hlt">models</span> in order to compare alternative computational <span class="hlt">models</span> and to contrast domain requirements. The report is divided into eight sections: (1) Origins and Goals (adaptive instruction, qualitative <span class="hlt">models</span> of processes, components of an artificial…</p> <div class="credits"> <p class="dwt_author">Clancey, William J.</p> <p class="dwt_publisher"></p> <p class="publishDate"></p> </div> </div> </div> </div> <div id="filter_results_form" class="filter_results_form floatContainer" style="visibility: visible;"> <div style="width:100%" id="PaginatedNavigation" class="paginatedNavigationElement"> <a id="FirstPageLink" onclick='return showDiv("page_1");' href="#" title="First Page"> <img id="FirstPageLinkImage" class="Icon" src="http://www.science.gov/scigov/images/icon.first.18x20.png" alt="First Page" /></a> <a id="PreviousPageLink" onclick='return showDiv("page_19");' href="#" title="Previous Page"> <img id="PreviousPageLinkImage" class="Icon" src="http://www.science.gov/scigov/images/icon.previous.18x20.png" alt="Previous Page" /></a> <span id="PageLinks" 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id="NextPageLink" onclick='return showDiv("page_22");' href="#" title="Next Page"> <img id="NextPageLinkImage" class="Icon" src="http://www.science.gov/scigov/images/icon.next.18x20.png" alt="Next Page" /></a> <a id="LastPageLink" onclick='return showDiv("page_25.0");' href="#" title="Last Page"> <img id="LastPageLinkImage" class="Icon" src="http://www.science.gov/scigov/images/icon.last.18x20.png" alt="Last Page" /></a> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">401</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://math.umons.ac.be/logic/sources/sonia_3.pdf"> <span id="translatedtitle"><span class="hlt">Model</span> Theory and Quantum</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.osti.gov/epsearch/">E-print Network</a></p> <p class="result-summary"><span class="hlt">Model</span> Theory and Quantum Groups Sonia L'Innocente <span class="hlt">Model</span> Theory and Quantum Groups Sonia L'Innocente (University of Mons) <span class="hlt">Model</span> Theory and Quantum Groups 1 / 40 #12;<span class="hlt">Model</span> Theory and Quantum Groups Sonia L quantum plane, submitted. This work is inspired by Ivo Herzog's paper: The pseudo-finite dimensional</p> <div class="credits"> <p class="dwt_author">Mons-Hainaut, Université de</p> <p class="dwt_publisher"></p> <p class="publishDate"></p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">402</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.sci.utah.edu/~chengu/street_sig08/street_talk_S2008.pdf"> <span id="translatedtitle">Interactive Street <span class="hlt">Modeling</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://www.osti.gov/epsearch/">E-print Network</a></p> <p class="result-summary">field T street graph G 9 #12;Tensor Field DesignTensor Field Design - = ab ba yx1 #12;Interactive Procedural Street <span class="hlt">Modeling</span> Interactive Procedural Street <span class="hlt">Modeling</span> Guoning Chen1 University 3 Procedural Inc. / ETH Zürich #12;Street <span class="hlt">Modeling</span>Street <span class="hlt">Modeling</span> Images by Eric Hanson and Ben</p> <div class="credits"> <p class="dwt_author">Chen, Guoning</p> <p class="dwt_publisher"></p> <p class="publishDate"></p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">403</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://academic.research.microsoft.com/Publication/56483154"> <span id="translatedtitle">Heat pump <span class="hlt">modeling</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://academic.research.microsoft.com/">Microsoft Academic Search </a></p> <p class="result-summary">Computer <span class="hlt">models</span> of the performance of heat pumps and of individual components are described; preliminary results from system improvement studies using these <span class="hlt">models</span> are presented. Heat exchanger <span class="hlt">models</span>, based on a tube-by-tube computational approach, may be used by the system <span class="hlt">model</span> when appropriate. Comparisons of calculated and observed performance parameters for heat exchangers in the laboratory are shown.</p> <div class="credits"> <p class="dwt_author">R. D. Ellison; F. A. Creswick; C. K. Rice; W. L. Jackson; S. K. Fischer</p> <p class="dwt_publisher"></p> <p class="publishDate">1979-01-01</p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">404</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=https://www.meted.ucar.edu/training_module.php?id=524"> <span id="translatedtitle">Mesoscale Ocean Circulation <span class="hlt">Models</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://nsdl.org/nsdl_dds/services/ddsws1-1/service_explorer.jsp">NSDL National Science Digital Library</a></p> <p class="result-summary">This module examines mesoscale ocean circulation <span class="hlt">models</span> and features and processes that they predict. These <span class="hlt">models</span> simulate temperature, salinity, currents, and elevation in 3 dimensions through a period of time. They have sufficient resolution to simulate features like fronts, eddies, upwelling, and internal tides. In this module, we examine current operational <span class="hlt">models</span>, limitations to <span class="hlt">model</span> forecasts, examples of predicted ocean features, and potential applications.</p> <div class="credits"> <p class="dwt_author">Comet</p> <p class="dwt_publisher"></p> <p class="publishDate">2009-05-21</p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">405</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://www.cs.cmu.edu/~emc/papers/Papers%20In%20Refereed%20Journals/Model%20Checking%20and%20Abstraction94.pdf"> <span id="translatedtitle"><span class="hlt">Model</span> checking and abstraction</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://academic.research.microsoft.com/">Microsoft Academic Search </a></p> <p class="result-summary">We describe a method for using abstraction to reduce the complexity of temporal logic <span class="hlt">model</span> checking. The basis of this method is a way of constructing an abstract <span class="hlt">model</span> of a program without ever examining the corresponding unabstracted <span class="hlt">model</span>. We show how this abstract <span class="hlt">model</span> can be used to verify properties of the original program. We have implemented a system</p> <div class="credits"> <p class="dwt_author">Edmund M. Clarke; Orna Grumberg; David E. Long</p> <p class="dwt_publisher"></p> <p class="publishDate">1992-01-01</p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">406</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://academic.research.microsoft.com/Publication/857254"> <span id="translatedtitle"><span class="hlt">Model</span> checking and abstraction</span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://academic.research.microsoft.com/">Microsoft Academic Search </a></p> <p class="result-summary">We describe a method for using abstraction to reduce the complexity of temporal-logic <span class="hlt">model</span> checking. Using techniques similar to those involved in abstract interpretation, we construct an abstract <span class="hlt">model</span> of a program without ever examining the corresponding unabstracted <span class="hlt">model</span>. We show how this abstract <span class="hlt">model</span> can be used to verify properties of the original program. We have implemented a system</p> <div class="credits"> <p class="dwt_author">Edmund M. Clarke; Orna Grumberg; David E. Long</p> <p class="dwt_publisher"></p> <p class="publishDate">1994-01-01</p> </div> </div> </div> </div> <div class="floatContainer result odd" lang="en"> <div class="resultNumber element">407</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://classweb.gmu.edu/kersch/infs770/Topics/ADBPapers/PostgresDM.pdf"> <span id="translatedtitle">The POSTGRES Data <span class="hlt">Model</span></span></a>  </p> <div class="result-meta"> <p class="source"><a target="_blank" id="logoLink" href="http://academic.research.microsoft.com/">Microsoft Academic Search </a></p> <p class="result-summary">The design of the POSTGRES data <span class="hlt">model</span> is described. The data <span class="hlt">model</span> is a relational <span class="hlt">model</span> that has been extended with abstract data types including user-defined operators and procedures, relation attributes of type pro- cedure, and attribute and procedure inheri- tance. These mechanism can be used to simu- late a wide variety of semantic and object- oriented data <span class="hlt">modeling</span> constructs</p> <div class="credits"> <p class="dwt_author">Lawrence A. Rowe; Michael Stonebraker</p> <p class="dwt_publisher"></p> <p class="publishDate">1987-01-01</p> </div> </div> </div> </div> <div class="floatContainer result " lang="en"> <div class="resultNumber element">408</div> <div class="resultBody element"> <p class="result-title"><a target="resultTitleLink" href="http://science.gov/scigov/link.html?type=RESULT&redirectUrl=http://academic.research.microsoft.com/Publication/387368">