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1

Process and genes for expression and overexpression of active [FeFe] hydrogenases  

DOEpatents

A process for expression of active [FeFe]-hydrogenase in a host organism that does not contain either the structural gene(s) for [FeFe]-hydrogenases and/or homologues for the maturation genes HydE, HydF and HyG, comprising: cloning the structural hydrogenase gene(s) and/or the maturation genes HydE, HydF and HydG from an organisms that contains these genes into expression plasmids; transferring the plasmids into an organism that lacks a native [FeFe]-hydrogenase or that has a disrupted [FeFe]-hydrogenase and culturing it aerobically; and inducing anaerobiosis to provide [FeFe] hydrogenase biosynthesis and H?2#191 production.

Seibert, Michael; King, Paul W; Ghirardi, Maria Lucia; Posewitz, Matthew C; Smolinski, Sharon L

2014-09-16

2

Nuclear resonance vibrational spectroscopy and electron paramagnetic resonance spectroscopy of 57Fe-enriched [FeFe] hydrogenase indicate stepwise assembly of the H-cluster.  

PubMed

The [FeFe] hydrogenase from Clostridium pasteurianum (CpI) harbors four Fe-S clusters that facilitate the transfer of an electron to the H-cluster, a ligand-coordinated six-iron prosthetic group that catalyzes the redox interconversion of protons and H(2). Here, we have used (57)Fe nuclear resonance vibrational spectroscopy (NRVS) to study the iron centers in CpI, and we compare our data to that for a [4Fe-4S] ferredoxin as well as a model complex resembling the [2Fe](H) catalytic domain of the H-cluster. To enrich the hydrogenase with (57)Fe nuclei, we used cell-free methods to post-translationally mature the enzyme. Specifically, inactive CpI apoprotein with (56)Fe-labeled Fe-S clusters was activated in vitro using (57)Fe-enriched maturation proteins. This approach enabled us to selectively label the [2Fe](H) subcluster with (57)Fe, which NRVS confirms by detecting (57)Fe-CO and (57)Fe-CN normal modes from the H-cluster nonprotein ligands. The NRVS and iron quantification results also suggest that the hydrogenase contains a second (57)Fe-S cluster. Electron paramagnetic resonance (EPR) spectroscopy indicates that this (57)Fe-enriched metal center is not the [4Fe-4S](H) subcluster of the H-cluster. This finding demonstrates that the CpI hydrogenase retained an (56)Fe-enriched [4Fe-4S](H) cluster during in vitro maturation, providing unambiguous evidence of stepwise assembly of the H-cluster. In addition, this work represents the first NRVS characterization of [FeFe] hydrogenases. PMID:23249091

Kuchenreuther, Jon M; Guo, Yisong; Wang, Hongxin; Myers, William K; George, Simon J; Boyke, Christine A; Yoda, Yoshitaka; Alp, E Ercan; Zhao, Jiyong; Britt, R David; Swartz, James R; Cramer, Stephen P

2013-02-01

3

Hydrogenases of the model hyperthermophiles.  

PubMed

Hydrogenases are enzymes found in all domains of life that catalyze a remarkably simple chemistry, the reversible oxidation of molecular hydrogen to protons and electrons. In order to perform this chemistry, cells have evolved, several different times, intricate organometal complexes built around a binuclear Ni-Fe or Fe-Fe center, with bound CO and CN(-) groups, as well as multiple FeS centers. These complicated enzymes have been an area of intense study for many decades, with interest peaking on the occasions of major increases in national energy costs. Interest in biologically generated hydrogen as a potential substitute for fossil fuels is again at the forefront, and the new tools of the postgenomic world available for manipulating these enzymes make it a truly viable possibility. Hydrogenases from hyperthermophilic microorganisms such as Pyrococcus furiosus and Thermotoga maritima, with optimal growth temperatures near 100 degrees C, are of particular interest and promise for elucidating and manipulating these enzymatic mechanisms. PMID:18378597

Jenney, Francis E; Adams, Michael W W

2008-03-01

4

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

5

Artificially maturated [FeFe] hydrogenase from Chlamydomonas reinhardtii: a HYSCORE and ENDOR study of a non-natural H-cluster.  

PubMed

Hydrogenases are enzymes that catalyze the oxidation of H2 as well as the reduction of protons to form H2. The active site of [FeFe] hydrogenase is referred to as the "H-cluster" and consists of a "classical" [4Fe-4S] cluster connected via a bridging cysteine thiol group to a unique [2Fe]H sub-cluster, containing CN(-) and CO ligands as well as a bidentate azadithiolate ligand. It has been recently shown that the biomimetic [Fe2(adt)(CO)4(CN)2](2-) (adt(2-) = azadithiolate) complex resembling the diiron sub-cluster can be inserted in vitro into the apo-protein of [FeFe] hydrogenase, which contains only the [4Fe-4S] part of the H-cluster, resulting in a fully active enzyme. This synthetic tool allows convenient incorporation of a variety of diiron mimics, thus generating hydrogenases with artificial active sites. [FeFe] hydrogenase from Chlamydomonas reinhardtii maturated with the biomimetic complex [Fe2(pdt)(CO)4(CN)2](2-) (pdt(2-) = propanedithiolate), in which the bridging adt(2-) ligand is replaced by pdt(2-), can be stabilized in a state strongly resembling the active oxidized (Hox) state of the native protein. This state is EPR active and the signal originates from the mixed valence Fe(I)Fe(II) state of the diiron sub-cluster. Taking advantage of the variant with (15)N and (13)C isotope labeled CN(-) ligands we performed HYSCORE and ENDOR studies on this hybrid protein. The (13)C hyperfine couplings originating from both CN(-) ligands were determined and assigned. Only the (15)N coupling from the CN(-) ligand bound to the terminal iron was observed. Detailed orientation selective ENDOR and HYSCORE experiments at multiple field positions enabled the extraction of accurate data for the relative orientations of the nitrogen and carbon hyperfine tensors. These data are consistent with the crystal structure assuming a g-tensor orientation following the local symmetry of the binuclear sub-cluster. PMID:25613229

Adamska-Venkatesh, Agnieszka; Simmons, Trevor R; Siebel, Judith F; Artero, Vincent; Fontecave, Marc; Reijerse, Edward; Lubitz, Wolfgang

2015-02-01

6

Synthetic hydrogenases: incorporation of an iron carbonyl thiolate into a designed peptide.  

PubMed

[FeFe] hydrogenases catalyze reversible hydrogen oxidation at an unusual organometallic active site. Neither enzymatic studies nor synthesis of small molecule models has managed to elucidate the mechanisms of these enzymes. In this paper, we demonstrate the incorporation of an iron carbonyl thiolate mimic of the hydrogenase active site into a de novo artificial peptide, creating the first peptide-based model system for hydrogenases. PMID:17997557

Jones, Anne K; Lichtenstein, Bruce R; Dutta, Arnab; Gordon, Gwyneth; Dutton, P Leslie

2007-12-01

7

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

PubMed Central

Research on simple [FeFe] hydrogenase model systems of type (?-S2R)[Fe(CO)3]2 (R = ethane, propane) which have been shown to function as robust electrocatalysts for proton reduction, provides a reference to understand the electronic and vibrational properties of the active site of [FeFe] hydrogenases and of more sophisticated model systems. In this study, the solution and solid Raman spectra of (?-S2R)[Fe(CO)3]2 (R = ethane) and of the corresponding 13CO-labeled complex are presented and analyzed in detail, with focus on the ?(C=O) and ?(Fe-CO)/?(Fe-C=O) vibrational regions. These regions are specifically important as vibrations involving CO ligands serve as probes for the ‘electron richness’ of low-valent transition metal centers and the geometric structures of the complexes. The obtained vibrational spectra have been completely assigned in terms of the ?(C=O), ?(Fe-CO) and ?(Fe-C=O) modes, and the force constants of the important C=O and Fe-CO bonds have been determined using our Quantum Chemistry Centered Normal Coordinate Analysis (QCC-NCA). In the 400–650 cm?1 region, 15 mixed ?(Fe-CO)/?(Fe-C=O) modes have been identified. The most prominent Raman peaks at 454, 456 and 483 cm?1 correspond to a combination of ?(Fe-CO) stretching and ?(Fe-C=O) linear bending modes. The less intense peaks at 416 cm?1 and 419 cm?1 correspond to pure ?(Fe-C=O) linear bends. In the ?(C=O) region, the ?(C=O) normal modes at lower energy (1968 and 1964 cm?1) are almost pure equatorial (eq) ?(C=O)eq stretching vibrations, whereas the remaining four ?(C=O) normal modes show dominant (C=O)eq (2070 and 1961 cm?1) and (C=O)ax (2005 and 1979 cm?1; ax = axial) contributions. Importantly, an inverse correlation between the f(C=O)ax/eq and f(Fe-CO)ax/eq force constants is obtained, in agreement with the idea that the Fe(I)-CO bond in these types of complexes is dominated by ? backdonation. Compared to the reduced form of [FeFe] hydrogenase (Hred), the ?(C=O) vibrational frequencies of (?-edt)[Fe(CO)3]2 are higher in energy, indicating that the dinuclear iron core in (?-edt)[Fe(CO)3]2 is less electron rich compared to Hred in the actual enzyme. Finally, quantum yields for the photodecomposition of (?-edt)[Fe(CO)3]2 have been determined. PMID:20225804

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

2010-01-01

8

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

PubMed

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

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

2012-07-12

9

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

10

Extended X-ray absorption fine structure of the [Fe]-hydrogenase Hmd active site  

NASA Astrophysics Data System (ADS)

Hydrogenases are enzymes that catalyze the reversible oxidation of molecular hydrogen. Although their structure and catalytic mechanism are of considerable applied interest as models for the development of efficient catalysts for hydrogen fueled processes, the understanding of how hydrogenases react with H2 is only in its infancy. Two of the three known types of hydrogenases are iron-sulfur proteins that contain a dinuclear metal center, either [NiFe] or [FeFe]. In contrast, [Fe]-hydrogenase is the only mononuclear hydrogenase and thus a perfect system for studying the structural and electronic determinants of these enzymes. Here we summarize recent improvements in modeling based on the EXAFS signal and the geometric structure of this metalloenzyme in its as isolated or reconstituted form. The individual contributions to the EXAFS resulting in two different structural models are presented and discussed. Inspired by the new crystal structure, we show an advanced EXAFS model for the enzyme from Methanothermobacter marburgensis.

Salomone-Stagni, Marco; Vogt, Sonja; Shima, Seigo; Meyer-Klaucke, Wolfram

2009-11-01

11

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

E-print Network

).. .................................................................... 64 Figure III. 2 Solution IR spectra (CH 2 Cl 2 ) showing the reversibility of the one- electron oxidation of III-1 (A), III-2 (B), and III-3 (C)............................67 Figure III. 3 Experimental (black) and simulated (red) EPR.... ....................................................................................79 Figure III. 10 IR spectra monitoring the reaction of III-2 ox with 13 CO at -78 ?C in CH 2 Cl 2 over a 1 hour time period in the absence of light. .......................83 Figure III. 11 IR spectra of the mixture of isotopically...

Liu, Tianbiao

2011-02-22

12

[FeFe]-hydrogenase models assembled into vesicular structures.  

PubMed

Compartmentalization is a major prerequisite for the origin of life on earth according to Wächtershäuser "Iron-Sulfur-World". The hypothesis is mainly based on an autocatalytic inorganic energy reproducing redox system consisting of iron and sulfur as requirement for the subsequent synthesis of complex organic structures. Here, we modified [FeFe]-hydrogenase models by means of covalent coupling to either oleic acid or the amphiphilic block copolymer polybutadiene-polyethyleneoxide (PB-PEO) and incorporated those into the membranes of vesicles composed of phospholipids (liposomes) or the unmodified amphiphilic polymer (polymersomes). We employed a [2Fe-2S] cluster as a hydrogenase model, since these structures are known to be suitable catalysts for the generation of H2 in the presence of weak acids. Successful incorporation was confirmed by spectrophotometric iron quantification and the vesicles formed were characterized by size determination (photon correlation spectroscopy (PCS)), and zeta potential as well as by cryo-transmission electron microscopy (Cryo-TEM). The modified models could be incorporated into liposomes or polymersomes up to molar proportions of 3.15% and 28%, respectively. Due to the immobilization in vesicular bilayers the [FeFe]-hydrogenase models can even exhibit catalytic action under the particular conditions of the intravesicular microenvironment. Our results suggest that the vesicular systems described may be applied as a nanoreactor for the reduction of encapsulated substances by generating hydrogen and thus as a minimal cell model. PMID:24006843

Menzel, Kristin; Apfel, Ulf-Peter; Wolter, Nonio; Rüger, Ronny; Alpermann, Theodor; Steiniger, Frank; Gabel, Detlef; Förster, Stephan; Weigand, Wolfgang; Fahr, Alfred

2014-03-01

13

Artificial Hydrogenases  

PubMed Central

Decades of biophysical study on the hydrogenase (H2ase) enzymes have yielded sufficient information to guide the synthesis of analogues of their active sites. Three families of enzymes serve as inspiration for this work: the [FeFe]-, [NiFe]-, and [Fe]-H2ases, all of which feature iron centers bound to both CO and thiolate. Artificial H2ases effect the oxidation of H2 of H2 and the reverse reaction, the reduction of protons. These reactions occur via the intermediacy of metal hydrides. The inclusion of amine bases within the catalysts is an important design feature that is emulated in related bioinspired catalysts. Continuing challenges are the low reactivity of H2 towards biomimetic H2ases. PMID:20356731

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

2010-01-01

14

Mössbauer and computational investigation of a functional [NiFe] hydrogenase model complex.  

PubMed

Developing biomimetic complexes that model the active site of [NiFe] hydrogenase enzymes in order to catalyze the activation of H2 is a topic of major interest. A functional [NiFe] hydrogenase model complex has recently been described by Ogo et al. (Science, 2013, 339, 682-683). Here, we report a Mössbauer and computational investigation of this model complex. This study affords deeper understanding of the electronic structure, the reactivity and the mechanism of H2 activation by this complex. PMID:25535725

Kochem, A; Bill, E; Neese, F; van Gastel, M

2015-01-22

15

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

16

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

17

Functional model for the [Fe] hydrogenase inspired by the frustrated Lewis pair concept.  

PubMed

[Fe] hydrogenase (Hmd) catalyzes the heterolytic splitting of H2 by using, in its active site, a unique organometallic iron-guanylylpyridinol (FeGP) cofactor and, as a hydride acceptor, the substrate methenyltetrahydromethanopterin (methenyl-H4MPT(+)). The combination FeGP/methenyl-H4MPT(+) and its reactivity bear resemblance to the concept of frustrated Lewis pairs (FLPs), some of which have been shown to heterolytically activate H2. The present work exploits this interpretation of Hmd reactivity by using the combination of Lewis basic ruthenium metalates, namely K[CpRu(CO)2] (KRp) and a related polymeric Cp/Ru/CO compound (Rs), with the new imidazolinium salt 1,3-bis(2,6-difluorophenyl)-2-(4-tolyl)imidazolinium bromide ([(Tol)Im(F4)](+)Br(-)) that was designed to emulate the hydride acceptor properties of methenyl-H4MPT(+). Solid-state structures of [(Tol)Im(F4)](+)Br(-) and the corresponding imidazolidine H(Tol)Im(F4) reveal that the heterocycle undergoes similar structural changes as in the biological substrate. DFT calculations indicate that heterolytic splitting of dihydrogen by the FLP Rp(-)/[(Tol)Im(F4)](+) is exothermic, but the formation of the initial Lewis pair should be unfavorable in polar solvents. Consequently the combination Rp(-)/[(Tol)Im(F4)](+) does not react with H2 but leads instead to side products from nucleophilic substitution (k = 4 × 10(-2) L mol (-1) s(-1) at room temperature). In contrast, the heterogeneous combination Rs/[(Tol)Im(F4)](+) does split H2 heterolytically to give H(Tol)Im(F4) and HRuCp(CO)2 (HRp) or D(Tol)Im(F4) and DRp when using D2. The reaction has been followed by (1)H/(2)H and (19)F NMR spectroscopy as well as by IR spectroscopy and reaches 96% conversion after 1 d. Formation of H(Tol)Im(F4) under these conditions demonstrates that superelectrophilic activation by protonation, which has been proposed for methenyl-H4MPT(+) to increase its carbocationic character, is not necessarily required for an imidazolinium ion to serve as a hydride acceptor. This unprecedented functional model for the [Fe] hydrogenase, using a Lewis acidic imidazolinium salt as a biomimetic hydride acceptor in combination with an organometallic Lewis base, may provide new inspiration for biomimetic H2 activation. PMID:25353322

Kalz, Kai F; Brinkmeier, Alexander; Dechert, Sebastian; Mata, Ricardo A; Meyer, Franc

2014-11-26

18

Fundamental Studies of Recombinant Hydrogenases  

SciTech Connect

This research addressed the long term goals of understanding the assembly and organization of hydrogenase enzymes, of reducing them in size and complexity, of determining structure/function relationships, including energy conservation via charge separation across membranes, and in screening for novel H2 catalysts. A key overall goal of the proposed research was to define and characterize minimal hydrogenases that are produced in high yields and are oxygen-resistant. Remarkably, in spite of decades of research carried out on hydrogenases, it is not possible to readily manipulate or design the enzyme using molecular biology approaches since a recombinant form produced in a suitable host is not available. Such resources are essential if we are to understand what constitutes a “minimal” hydrogenase and design such catalysts with certain properties, such as resistance to oxygen, extreme stability and specificity for a given electron donor. The model system for our studies is Pyrococcus furiosus, a hyperthermophile that grows optimally at 100°C, which contains three different nickel-iron [NiFe-] containing hydrogenases. Hydrogenases I and II are cytoplasmic while the other, MBH, is an integral membrane protein that functions to both evolve H2 and pump protons. Three important breakthroughs were made during the funding period with P. furiosus soluble hydrogenase I (SHI). First, we produced an active recombinant form of SHI in E. coli by the co-expression of sixteen genes using anaerobically-induced promoters. Second, we genetically-engineered P. furiosus to overexpress SHI by an order of magnitude compared to the wild type strain. Third, we generated the first ‘minimal’ form of SHI, one that contained two rather than four subunits. This dimeric form was stable and active, and directly interacted with a pyruvate-oxidizing enzyme with any intermediate electron carrier. The research resulted in five peer-reviewed publications.

Adams, Michael W

2014-01-25

19

Hydride-Containing Models for the Active Site of the Nickel-Iron Hydrogenases  

PubMed Central

The [NiFe]-hydrogenase model complex NiFe(pdt)(dppe)(CO)3 (1) (pdt = 1,3-propanedithiolate) has been efficiently synthesized and found to be robust. This neutral complex sustains protonation to give the first nickel-iron hydride [1H]BF4. One CO ligand in [1H]BF4 is readily substituted by organophosphorus ligand to afford the substituted derivatives [HNiFe(pdt)(dppe)(CO)2(PR3)]BF4, where PR3 = P(OPh)3 ([2H]BF4); PPh3 ([3H]BF4); PPh2Py ([4H]BF4, where Py = 2-pyridyl). Variable temperature NMR measurements show that the neutral and protonated derivatives are dynamic on the NMR timescale, which partially symmetrizes the phosphine complex. The proposed stereodynamics involve twisting of the Ni(dppe) center, not rotation at the Fe(CO)2(PR3) center. In MeCN solution, 3, which can be prepared by deprotonation of [3H]BF4 with NaOMe, is about 104 stronger base than is 1. X-ray crystallographic analysis of [3H]BF4 revealed a highly unsymmetrical bridging hydride, the Fe-H bond being 0.40 Å shorter than the Ni-H distance. Complexes [2H]BF4, [3H]BF4, [4H]BF4 undergo reductions near ?1.46 V vs Fc0/+. For [2H]BF4, this reduction process is reversible, and we assign it as a one-electron process. In the presence of trifluoroacetic acid, proton reduction catalysis coincides with this reductive event. The dependence of ic/ip on the concentration of the acid indicates that H2 evolution entails protonation of a reduced hydride. For [2H]+, [3H]+, and [4H]+, the acid-independent rate constants are 50-75 s?1. For [2H]+ and [3H]+, the overpotentials for H2 evolution are ~430 mV, whereas the overpotential for the N-protonated pyridinium complex [4H2]2+ is estimated to be 260 mV. The mechanism of H2 evolution is proposed to follow an ECEC sequence, where E and C correspond to one-electron reductions and protonations, respectively. On the basis of their values for its pKa and redox potentials, ?GH• and ?GH? are 57 and 79 kcal/mol for [1H]+ and [1]2+, respectively. PMID:20925337

Barton, Bryan E.; Rauchfuss, Thomas B.

2010-01-01

20

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

21

Role of the Azadithiolate Cofactor in Models for the [FeFe]-Hydrogenase: Novel Structures and Catalytic Implications  

PubMed Central

The report summarizes studies on the redox behavior of synthetic models for the [FeFe]-hydrogenases, consisting of diiron dithiolato carbonyl complexes bearing the amine cofactor and its N-benzyl derivative. Of specific interest are the causes of the low reactivity of oxidized models toward H2, which contrasts with the high activity of these enzymes for H2 oxidation. The redox and acid-base properties of the model complexes [Fe2[(SCH2)2NR](CO)3(dppv)(PMe3)]+ ([2]+ for R = H and [2?]+ for R = CH2C6H5, dppv = cis-1,2-bis(diphenylphosphino)ethylene)) indicate that addition of H2 and followed by deprotonation are (i) endothermic for the mixed valence (FeIIFeI) state and (ii) exothermic for the diferrous (FeIIFeII) state. The diferrous state is shown to be unstable with respect to coordination of the amine to Fe, a derivative of which was characterized crystallographically. The redox and acid-base properties for the mixed valence models differ strongly for those containing the amine cofactor versus those derived from propanedithiolate. Protonation of [2?]+ induces disproportionation to a 1:1 mixture of the ammonium-FeIFeI and the dication [2?]2+ (FeIIFeII). This effect is consistent with substantial enhancement of the basicity of the amine in the FeIFeI state vs the FeIIFeI state. The FeIFeI ammonium compounds are rapid and efficient H-atom donors toward the nitroxyl compound TEMPO. The atom transfer is proposed to proceed via the hydride, as indicated by the reaction of [HFe2[(SCH2)2NH](CO)2(dppv)2]+ with TEMPO. Collectively, the results suggest that proton-coupled electron-transfer pathways should be considered for H2 activation by the [FeFe]-hydrogenases. PMID:21114298

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

2010-01-01

22

Hydrogenases and Hydrogen Photoproduction in Oxygenic Photosynthetic Organisms  

SciTech Connect

The photobiological production of H{sub 2} gas, using water as the only electron donor, is a property of two types of photosynthetic microorganisms: green algae and cyanobacteria. In these organisms, photosynthetic water splitting is functionally linked to H{sub 2} production by the activity of hydrogenase enzymes. Interestingly, each of these organisms contains only one of two major types of hydrogenases, [FeFe] or [NiFe] enzymes, which are phylogenetically distinct but perform the same catalytic reaction, suggesting convergent evolution. This idea is supported by the observation that each of the two classes of hydrogenases has a different metallo-cluster, is encoded by entirely different sets of genes (apparently under the control of different promoter elements), and exhibits different maturation pathways. The genetics, biosynthesis, structure, function, and O{sub 2} sensitivity of these enzymes have been the focus of extensive research in recent years. Some of this effort is clearly driven by the potential for using these enzymes in future biological or biohybrid systems to produce renewable fuel or in fuel cell applications.

Ghirardi, M. L.; Posewitz, M. C.; Maness, P. C.; Dubini, A.; Yu, J.; Seibert, M.

2007-01-01

23

Hydrogenases and hydrogen photoproduction in oxygenic photosynthetic organisms.  

PubMed

The photobiological production of H2 gas, using water as the only electron donor, is a property of two types of photosynthetic microorganisms: green algae and cyanobacteria. In these organisms, photosynthetic water splitting is functionally linked to H(2) production by the activity of hydrogenase enzymes. Interestingly, each of these organisms contains only one of two major types of hydrogenases, [FeFe] or [NiFe] enzymes, which are phylogenetically distinct but perform the same catalytic reaction, suggesting convergent evolution. This idea is supported by the observation that each of the two classes of hydrogenases has a different metallo-cluster, is encoded by entirely different sets of genes (apparently under the control of different promoter elements), and exhibits different maturation pathways. The genetics, biosynthesis, structure, function, and O2 sensitivity of these enzymes have been the focus of extensive research in recent years. Some of this effort is clearly driven by the potential for using these enzymes in future biological or biohybrid systems to produce renewable fuel or in fuel cell applications. PMID:17150028

Ghirardi, Maria L; Posewitz, Matthew C; Maness, Pin-Ching; Dubini, Alexandra; Yu, Jianping; Seibert, Michael

2007-01-01

24

Heterolytic Cleavage of Hydrogen by an Iron Hydrogenase Model: An Fe-H - - - H-N Dihydorgen Bond Characterized by Neutron Diffraction  

SciTech Connect

Use of hydrogen as a fuel by [FeFe]-hydrogenase enzymes in nature requires heterolytic cleavage of the H-H bond into a proton (H+) and hydride (H-), a reaction that is also a critical step in homogeneous catalysts for hydrogenation of C=O and C=N bonds. An understanding of the catalytic oxidation of H2 by hydrogenases provides insights into the design of synthetic catalysts that are sought as cost-effective alternatives to the use of the precious metal platinum in fuel cells. Crystallographic studies on the [FeFe]-hydrogenase enzyme were critical to understanding of its reactivity, but the key H-H cleavage step is not readily observed experimentally in natural hydrogenases. Synthetic biomimics have provided evidence for H2 cleavage leading to hydride transfer to the metal and proton transfer to an amine. Limitations on the precise location of hydrogen atoms by x-ray diffraction can be overcome by use of neutron diffraction, though its use is severely limited by the difficulty of obtaining suitable crystals and by the scarcity of neutron sources. Here we show that an iron complex with a pendant amine in the diphosphine ligand cleaves hydrogen heterolytically under mild conditions, leading to [CpC5F4NFeH(PtBu2NtBu2H)]+BArF4-, [PtBu2NtBu2 = 1,5-di(tert-butyl)-3,7-di(tert-butyl)-1,5-diaza-3,7-diphosphacyclooctane; ArF = 3,5-bis(trifluoromethyl)phenyl]. The Fe-H- - - H-N moiety has a strong dihydrogen bond, with a remarkably short H • • • H distance of 1.489(10) Å between the protic N-H?+ and hydridic Fe-H?-. The structural data for [CpC5F4NFeH(PtBu2NtBu2H)]+ provide a glimpse of how the H-H bond is oxidized or generated in hydrogenase enzymes, with the pendant amine playing a key role as a proton relay. The iron complex [CpC5F4NFeH(PtBu2NtBu2H)]+BArF4- is an electrocatalyst for oxidation of H2 (1 atm) at 22 °C, so the structural data are obtained on a complex that is a functional model for catalysis by [FeFe]-hydrogenase enzymes. This research was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences. Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy.

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

2014-05-19

25

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

26

Mild Redox Complementation Enables H2 Activation by [FeFe]-Hydrogenase Models  

PubMed Central

Mild oxidants such as [Fe(C5Me5)2]+ accelerate the activation of H2 by [Fe2[(SCH2)2NBn](CO)3(dppv)(PMe3)]+ ([1]+). The reaction is first order in [1]+ and [H2] but is independent of the E1/2 and concentration of the oxidant. The analogous reaction occurs with D2 and proceeds with an inverse isotope effect of 0.75(8). The activation of H2 is further enhanced with the tetracarbonyl [Fe2[(SCH2)2NBn](CO)4(dppn)]+ ([2]+), the first crystallographically characterized Hox model containing an amine cofactor. These studies point to rate-determining binding of H2 followed by proton-coupled electron-transfer (PCET). In comparison with [1]+, the rate of H2 activation by [2]+/Fc+ is enhanced by 104 (25 °C). PMID:21548619

Camara, James M.; Rauchfuss, Thomas B.

2011-01-01

27

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

28

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

PubMed

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

Shi, Jingu; Ai, Zhihui; Zhang, Lizhi

2014-08-01

29

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

E-print Network

of the model. The X-ray crystal structure of the inclusion complex, Na (?-SCH2N(C6H4SO3-)CH2S-)[Fe(CO)3]2?2 ?-cyclodextrin shows complete enclosure of the diiron model within two cyclodextrin units. Solution studies support the formation of an inclusion complex...

Singleton, Michael Lee

2012-02-14

30

Purification of Hydrogenase from Chlamydomonas reinhardtii1  

PubMed Central

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 H2 produced per milligram protein per minute. The molecular weight was determined to be 4.5 × 104 by gel filtration and 4.75 × 104 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 H2 production; these properties are similar to those of bacterial hydrogenases. The enzyme is less thermally stable than most bacterial hydrogenases, however, losing 50% of its activity in 1 hour at 55°C. The Km 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. Images Fig. 2 PMID:16663691

Roessler, Paul G.; Lien, Stephen

1984-01-01

31

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

PubMed

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

Kaur-Ghumaan, Sandeep; Stein, Matthias

2014-07-01

32

Cobaloxime-based artificial hydrogenases.  

PubMed

Cobaloximes are popular H2 evolution molecular catalysts but have so far mainly been studied in nonaqueous conditions. We show here that they are also valuable for the design of artificial hydrogenases for application in neutral aqueous solutions and report on the preparation of two well-defined biohybrid species via the binding of two cobaloxime moieties, {Co(dmgH)2} and {Co(dmgBF2)2} (dmgH2 = dimethylglyoxime), to apo Sperm-whale myoglobin (SwMb). All spectroscopic data confirm that the cobaloxime moieties are inserted within the binding pocket of the SwMb protein and are coordinated to a histidine residue in the axial position of the cobalt complex, resulting in thermodynamically stable complexes. Quantum chemical/molecular mechanical docking calculations indicated a coordination preference for His93 over the other histidine residue (His64) present in the vicinity. Interestingly, the redox activity of the cobalt centers is retained in both biohybrids, which provides them with the catalytic activity for H2 evolution in near-neutral aqueous conditions. PMID:25029381

Bacchi, Marine; Berggren, Gustav; Niklas, Jens; Veinberg, Elias; Mara, Michael W; Shelby, Megan L; Poluektov, Oleg G; Chen, Lin X; Tiede, David M; Cavazza, Christine; Field, Martin J; Fontecave, Marc; Artero, Vincent

2014-08-01

33

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

PubMed Central

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

34

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

35

Multi-edge X-ray absorption spectroscopy. 1. X-ray absorption near-edge structure analysis of a biomimetic model of FeFe-hydrogenase.  

PubMed

In this work, we demonstrate the potential of multi-edge X-ray absorption near-edge structure (XANES) analysis in completely defining the ground state electronic structure of a prototypical biomimetic complex of the [2Fe]-subcluster of the catalytic H-cluster of FeFe-hydrogenase. The spectral features at the ionization thresholds for Fe, S, C, and O 1s (K-edge) and Fe 2p (L-edge) core electrons were considered simultaneously to obtain the atomic compositions of the unoccupied frontier molecular orbitals. A systematic error analysis was carried out at the most informative S K-edge for spectra collected by multiple detection methods, at various data collection temperatures, and different sample preparation protocols. As expected for the difference in bonding between bridging and terminal Fe-S(thiolate) coordination, the Fe-S bond is more covalent in the [2Fe]-biomimetic complex with formally iron(I) centers (36 ± 2% S character per Fe-S bond) than in the previously described [2Fe-2S] clusters (25 ± 3% S character per Fe-S bond) with formally iron(III) centers. An electron hole-based analysis of the pre-edge features at Fe K-, Fe L-, and S K-edges experimentally defines the composition of the first three frontier unoccupied molecular orbitals to contain 4% Fe 4p, 44% Fe 3d, and 24% S 3p contributions per electron hole, respectively. The complementary CO ligand contribution thus can be defined as 28% per electron hole. These experimental orbital covalency values are important in rationalizing redox properties, electrophilicity of the metals, or nucleophilicity of the ligands, and critically evaluating the absolute accuracy of electronic structure calculations. PMID:23145835

Giles, Logan J; Grigoropoulos, Alexios; Szilagyi, Robert K

2012-12-20

36

Biodiversity of uptake hydrogenase systems from legume endosymbiotic bacteria.  

PubMed

Uptake hydrogenases in legume endosymbiotic bacteria recycle hydrogen produced during the nitrogen fixation process in legume nodules. Despite the described beneficial effect on plant productivity, the hydrogen oxidation capability is not widespread in the Rhizobiaceae family. Characterization of hydrogenase gene clusters in strains belonging to Rhizobium, Bradyrhizobium and Azorhizobium reveals a similar overall genetic organization along with important differences in gene regulation. In addition, phylogenetic analysis of hup genes indicates distinct evolutionary origins for hydrogenase genes in Rhizobia. PMID:15667257

Brito, B; Baginsky, C; Palacios, J M; Cabrera, E; Ruiz-Argüeso, T; Imperial, J

2005-02-01

37

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

38

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; Wünschiers, Röbbe; Lindblad, Peter

2002-01-01

39

A Bacterial Electron-bifurcating Hydrogenase*  

PubMed Central

The Wood-Ljungdahl pathway of anaerobic CO2 fixation with hydrogen as reductant is considered a candidate for the first life-sustaining pathway on earth because it combines carbon dioxide fixation with the synthesis of ATP via a chemiosmotic mechanism. The acetogenic bacterium Acetobacterium woodii uses an ancient version of the pathway that has only one site to generate the electrochemical ion potential used to drive ATP synthesis, the ferredoxin-fueled, sodium-motive Rnf complex. However, hydrogen-based ferredoxin reduction is endergonic, and how the steep energy barrier is overcome has been an enigma for a long time. We have purified a multimeric [FeFe]-hydrogenase from A. woodii containing four subunits (HydABCD) which is predicted to have one [H]-cluster, three [2Fe2S]-, and six [4Fe4S]-clusters consistent with the experimental determination of 32 mol of Fe and 30 mol of acid-labile sulfur. The enzyme indeed catalyzed hydrogen-based ferredoxin reduction, but required NAD+ for this reaction. NAD+ was also reduced but only in the presence of ferredoxin. NAD+ and ferredoxin reduction both required flavin. Spectroscopic analyses revealed that NAD+ and ferredoxin reduction are strictly coupled and that they are reduced in a 1:1 stoichiometry. Apparently, the multimeric hydrogenase of A. woodii is a soluble energy-converting hydrogenase that uses electron bifurcation to drive the endergonic ferredoxin reduction by coupling it to the exergonic NAD+ reduction. PMID:22810230

Schuchmann, Kai; Müller, Volker

2012-01-01

40

A bacterial electron-bifurcating hydrogenase.  

PubMed

The Wood-Ljungdahl pathway of anaerobic CO(2) fixation with hydrogen as reductant is considered a candidate for the first life-sustaining pathway on earth because it combines carbon dioxide fixation with the synthesis of ATP via a chemiosmotic mechanism. The acetogenic bacterium Acetobacterium woodii uses an ancient version of the pathway that has only one site to generate the electrochemical ion potential used to drive ATP synthesis, the ferredoxin-fueled, sodium-motive Rnf complex. However, hydrogen-based ferredoxin reduction is endergonic, and how the steep energy barrier is overcome has been an enigma for a long time. We have purified a multimeric [FeFe]-hydrogenase from A. woodii containing four subunits (HydABCD) which is predicted to have one [H]-cluster, three [2Fe2S]-, and six [4Fe4S]-clusters consistent with the experimental determination of 32 mol of Fe and 30 mol of acid-labile sulfur. The enzyme indeed catalyzed hydrogen-based ferredoxin reduction, but required NAD(+) for this reaction. NAD(+) was also reduced but only in the presence of ferredoxin. NAD(+) and ferredoxin reduction both required flavin. Spectroscopic analyses revealed that NAD(+) and ferredoxin reduction are strictly coupled and that they are reduced in a 1:1 stoichiometry. Apparently, the multimeric hydrogenase of A. woodii is a soluble energy-converting hydrogenase that uses electron bifurcation to drive the endergonic ferredoxin reduction by coupling it to the exergonic NAD(+) reduction. PMID:22810230

Schuchmann, Kai; Müller, Volker

2012-09-01

41

ASSESSING SHOOT-ROOT COMMUNICATION IN THE REGULATION OF IRON HOMEOSTASIS IN THE FEFE MELON MUTANT  

Technology Transfer Automated Retrieval System (TEKTRAN)

The fefe mutant of musk melon exhibits characteristics of iron deficiency such as interveinal chlorosis of leaves, retarded growth, and finally death unless supplemental Fe is provided. The seedlings have normal green cotyledons but the first true leaves are yellow with green veins. To determine the...

42

The hydrogenases and formate dehydrogenases of Escherichia coli  

Microsoft Academic Search

Escherichia coli has the capacity to synthesise three distinct formate dehydrogenase isoenzymes and three hydrogenase isoenzymes. All six are multisubunit, membrane-associated proteins that are functional in the anaerobic metabolism of the organism. One of the formate dehydrogenase isoenzymes is also synthesised in aerobic cells. Two of the formate dehydrogenase enzymes and two hydrogenases have a respiratory function while the formate

Gary Sawers

1994-01-01

43

Immobilization of selenite on Fe3O4 and Fe/Fe3C ultrasmall particles.  

PubMed

The sorption of selenite ions onto Fe3O4 and Fe/Fe3C nanoparticles (NPs) was studied in aqueous solutions under anoxic conditions using gamma spectrometry and X-ray absorption spectrometry (XAS) techniques. This is the first study related to the remedial applications of Fe/Fe3C NPs. FesO4 NPs have been prepared by conventional coprecipitation of Fe(II) and Fe(III) in basic solutions. Stable Fe/Fe3C NPs have been prepared by Fe(CO)5 sonicating in diphenylmethane solutions and subsequently annealing the as-prepared product. Kinetic study demonstrated that Se(IV) sorption is extremely rapid: the equilibrium is reached in approximately 10 and 30 min for Fe3O4 and Fe/Fe3C NPs, respectively, at pH = 4.9-5.1 in solutions of 0.1 M NaCl. The distribution coefficients are also very high for both kinds of NPs (Kd > 3000). Increasing the pH to 10.3 or adsorption of organic ligands, like L-lysine or dodecanoate, at the surface of NPs causes the decrease in Kd values. However, even in these cases Kd values exceed 150. Magnetic NPs loaded with selenium can be easily and completely removed from solution with a 0.4 T permanent magnet. XAS study revealed the absence of Se(IV) reduction during the sorption onto Fe3O4 NPs in the pH range of 4.8-8.0. By contrast, the removal of Se(IV) with Fe/Fe3C NPs in anaerobic conditions occurs via Se(IV) reduction to Se(-II) and subsequent formation of iron selenide at the particle surface. Thus, the Fe/Fe3C NPs are superior to Fe3O4 NPs due to their ability to immobilize rapidly and irreversibly Se(IV) via reductive mechanism. Presumably these particles could be also effective for the removal of other contaminants such as hexavalent chromium, actinides, technetium, and toxic organic compounds. PMID:18504980

Loyo, Raquel López de Arroyabe; Nikitenko, Sergei I; Scheinost, Andreas C; Simonoff, Monique

2008-04-01

44

Biomimetic assembly and activation of [FeFe]-hydrogenases.  

PubMed

Hydrogenases are the most active molecular catalysts for hydrogen production and uptake, and could therefore facilitate the development of new types of fuel cell. In [FeFe]-hydrogenases, catalysis takes place at a unique di-iron centre (the [2Fe] subsite), which contains a bridging dithiolate ligand, three CO ligands and two CN(-) ligands. Through a complex multienzymatic biosynthetic process, this [2Fe] subsite is first assembled on a maturation enzyme, HydF, and then delivered to the apo-hydrogenase for activation. Synthetic chemistry has been used to prepare remarkably similar mimics of that subsite, but it has failed to reproduce the natural enzymatic activities thus far. Here we show that three synthetic mimics (containing different bridging dithiolate ligands) can be loaded onto bacterial Thermotoga maritima HydF and then transferred to apo-HydA1, one of the hydrogenases of Chlamydomonas reinhardtii algae. Full activation of HydA1 was achieved only when using the HydF hybrid protein containing the mimic with an azadithiolate bridge, confirming the presence of this ligand in the active site of native [FeFe]-hydrogenases. This is an 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. PMID:23803769

Berggren, G; Adamska, A; Lambertz, C; Simmons, T R; Esselborn, J; Atta, M; Gambarelli, S; Mouesca, J-M; Reijerse, E; Lubitz, W; Happe, T; Artero, V; Fontecave, M

2013-07-01

45

Salmonella enterica serovar Typhimurium NiFe uptake-type hydrogenases are differentially expressed in vivo.  

PubMed

Salmonella enterica serovar Typhimurium, a common enteric pathogen, possesses three NiFe uptake-type hydrogenases. The results from mouse infection studies suggest that the H(2) oxidation capacity provided by these hydrogenases is important for virulence. Since the three enzymes are similar in structure and function, it may be expected that they are utilized under different locations and times during an infection. A recombination-based method to examine promoter activity in vivo (RIVET) was used to determine hydrogenase gene expression in macrophages, polymorphonuclear leukocyte (PMN)-like cells, and a mouse model of salmonellosis. The hyd and hya promoters showed increased expression in both murine macrophages and human PMN-like cells compared to that in the medium-only controls. Quantitative reverse transcription-PCR results suggested that hyb is also expressed in phagocytes. A nonpolar hya mutant was compromised for survival in macrophages compared to the wild type. This may be due to lower tolerance to acid stress, since the hya mutant was much more acid sensitive than the wild type. In addition, hya mutant cells were internalized by macrophages the same as wild-type cells. Mouse studies (RIVET) indicate that hyd is highly expressed in the liver and spleen early during infection but is expressed poorly in the ileum in infected animals. Late in the infection, the hyd genes were expressed at high levels in the ileum as well as in the liver and spleen. The hya genes were expressed at low levels in all locations tested. These results suggest that the hydrogenases are used to oxidize hydrogen in different stages of an infection. PMID:18625729

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

2008-10-01

46

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

47

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

PubMed Central

Hydrogen gas is an attractive alternative fuel as it is carbon neutral and has higher energy content per unit mass than fossil fuels. The biological enzyme responsible for utilizing molecular hydrogen is hydrogenase, a heteromeric metalloenzyme requiring a complex maturation process to assemble its O2-sensitive dinuclear-catalytic site containing nickel and iron atoms. To facilitate their utility in applied processes, it is essential that tools are available to engineer hydrogenases to tailor catalytic activity and electron carrier specificity, and decrease oxygen sensitivity using standard molecular biology techniques. As a model system we are using hydrogen-producing Pyrococcus furiosus, which grows optimally at 100°C. We have taken advantage of a recently developed genetic system that allows markerless chromosomal integrations via homologous recombination. We have combined a new gene marker system with a highly-expressed constitutive promoter to enable high-level homologous expression of an engineered form of the cytoplasmic NADP-dependent hydrogenase (SHI) of P. furiosus. In a step towards obtaining ‘minimal’ hydrogenases, we have successfully produced the heterodimeric form of SHI that contains only two of the four subunits found in the native heterotetrameric enzyme. The heterodimeric form is highly active (150 units mg?1 in H2 production using the artificial electron donor methyl viologen) and thermostable (t1/2 ?0.5 hour at 90°C). Moreover, the heterodimer does not use NADPH and instead can directly utilize reductant supplied by pyruvate ferredoxin oxidoreductase from P. furiosus. The SHI heterodimer and POR therefore represent a two-enzyme system that oxidizes pyruvate and produces H2 in vitro without the need for an intermediate electron carrier. PMID:22039508

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

2011-01-01

48

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

49

Resonant inelastic X-ray scattering on synthetic nickel compounds and Ni-Fe hydrogenase protein  

NASA Astrophysics Data System (ADS)

Ni-Fe hydrogenases are proteins catalyzing the oxidative cleavage of dihydrogen (H2) and proton reduction to H2 at high turnover rates. Their active site is a heterobimetallic center comprising one Ni and one Fe atom. To understand the function of the site, well resolved structural and electronic information is required. Such information is expected to become accessible by high resolution X-ray absorption and emission techniques, which are rapidly developing at third generation synchrotron radiation sources. We studied a number of synthetic Ni compounds, which mimic relevant features of the Ni site in hydrogenases, and the Ni site in the soluble, NAD-reducing hydrogenase (SH) from the bacterium Ralstonia eutropha by resonant inelastic X-ray scattering (RIXS) using a Rowland-type spectrometer at the ESRF. The SH is particularly interesting because its H2-cleavage reaction is highly resistant against inhibition by O2. K?-fluorescence detected RIXS planes in the 1s?3d region of the X-ray absorption spectrum were recorded on the protein which allow to extract L3-edge type spectra Spectral features of the protein are compared to those of the model compounds.

Sanganas, Oliver; Löscher, Simone; Pfirrmann, Stefan; Marinos, Nicolas; Glatzel, Pieter; Weng, Tsu-Chien; Limberg, Christian; Driess, Matthias; Dau, Holger; Haumann, Michael

2009-11-01

50

Transcriptomic and physiological characterization of the fefe mutant of melon (Cucumis melo) reveals new aspects of iron-copper crosstalk.  

PubMed

Iron (Fe) and copper (Cu) homeostasis are tightly linked across biology. In previous work, Fe deficiency interacted with Cu-regulated genes and stimulated Cu accumulation. The C940-fe (fefe) Fe-uptake mutant of melon (Cucumis melo) was characterized, and the fefe mutant was used to test whether Cu deficiency could stimulate Fe uptake. Wild-type and fefe mutant transcriptomes were determined by RNA-seq under Fe and Cu deficiency. FeFe-regulated genes included core Fe uptake, metal homeostasis, and transcription factor genes. Numerous genes were regulated by both Fe and Cu. The fefe mutant was rescued by high Fe or by Cu deficiency, which stimulated ferric-chelate reductase activity, FRO2 expression, and Fe accumulation. Accumulation of Fe in Cu-deficient plants was independent of the normal Fe-uptake system. One of the four FRO genes in the melon and cucumber (Cucumis sativus) genomes was Fe-regulated, and one was Cu-regulated. Simultaneous Fe and Cu deficiency synergistically up-regulated Fe-uptake gene expression. Overlap in Fe and Cu deficiency transcriptomes highlights the importance of Fe-Cu crosstalk in metal homeostasis. The fefe gene is not orthologous to FIT, and thus identification of this gene will provide clues to help understand regulation of Fe uptake in plants. PMID:24975482

Waters, Brian M; McInturf, Samuel A; Amundsen, Keenan

2014-09-01

51

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

NASA Astrophysics Data System (ADS)

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

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

2014-02-01

52

Oxygen-tolerant hydrogenases in hydrogen-based technologies.  

PubMed

To develop a viable H2 technology, production of H2 has to be significantly enlarged by using renewable resources. One option of generating H2 is the photosynthetic conversion of sunlight and water directly to H2 and O2. Photosystems and hydrogenases are currently being exploited for the design of efficient H2-producing systems that require highly active and O2-tolerant biocatalysts. This communication focuses on two challenging features: hydrogenases that produce H2 in the presence of O2, and direct electron transfer between photosystem I (PS I) and hydrogenase. The latter is accomplished by connecting both modules through a protein fusion or a synthetic molecular wire. These are first steps toward a photosynthetic microbial cell or a semi-synthetic system that may be employed in future H2-based technologies. PMID:21334190

Friedrich, Bärbel; Fritsch, Johannes; Lenz, Oliver

2011-06-01

53

Purification of the membrane-bound hydrogenase of Escherichia coli.  

PubMed Central

The membrane-bound hydrogenase (EC class 1.12) of aerobically grown Escherichia coli cells was solubilized by treatment with deoxycholate and pancreatin. The enzyme was further purified to electrophoretic homogeneity by chromoatographic methods, including hydrophobic-interaction chromatography, with a yield of 10% as judged by activity and an overall purification of 2140-fold. The hydrogenase was a dimer of identical subunits with a mol.wt. of 113,000 and contained 12 iron and 12 acid-labile sulphur atoms per molecule. The epsilon 400 was 49,000M-1 . cm-1. The hydrogenase catalysed both H2 evolution and H2 uptake with a variety of artificial electron carriers, but would not interact with flavodoxin, ferredoxin or nicotinamide and flavin nucleotides. We were unable to identify any physiological electron carrier for the hydrogenase. With Methyl Viologen as the electron carrier, the pH optimum for H2 evolution and H2 uptake was 6.5 and 8.5 respectively. The enzyme was stable for long periods at neutral pH, low temperatures and under anaerobic conditions. The half-life of the hydrogenase under air at room temperature was about 12 h, but it could be stabilized by Methyl Viologen and Benzyl Viologen, both of which are electron carriers for the enzyme, and by bovine serum albumin. The hydrogenase was strongly inhibited by carbon monoxide (Ki = 1870Pa), heavy-metal salts and high concentrations of buffers, but was resistant to inhibition by thiol-blocking and metal-complexing reagents. These aerobically grown E. coli cells lacked formate hydrogenlyase activity and cytochrome c552. PMID:393247

Adams, M W; Hall, D O

1979-01-01

54

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

55

Desulfovibrio desulfuricans iron hydrogenase: the structure shows unusual coordination to an active site Fe binuclear center  

Microsoft Academic Search

Background: Many microorganisms have the ability to either oxidize molecular hydrogen to generate reducing power or to produce hydrogen in order to remove low-potential electrons. These reactions are catalyzed by two unrelated enzymes: the Ni–Fe hydrogenases and the Fe-only hydrogenases.Results: We report here the structure of the heterodimeric Fe-only hydrogenase from Desulfovibrio desulfuricans – the first for this class of

Yvain Nicolet; Claudine Piras; Pierre Legrand; Claude E Hatchikian; Juan C Fontecilla-Camps

1999-01-01

56

Oxygen-resistant hydrogenases and methods for designing and making same  

DOEpatents

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

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

2009-03-10

57

Oxygen-resistant hydrogenases and methods for designing and making same  

DOEpatents

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

King, Paul; Ghirardi, Maria Lucia; Seibert, Michael

2014-03-04

58

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

NASA Astrophysics Data System (ADS)

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

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

2011-12-01

59

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

Microsoft Academic Search

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

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

2004-01-01

60

Hydrogenase does not confer significant benefits to Azotobacter vinelandii growing diazotrophically under conditions of glucose limitation.  

PubMed Central

The presumed beneficial effect of hydrogenase on growth of diazotrophic bacteria was reinvestigated with carbon-limited chemostat cultures of the hydrogenase-deficient mutant hoxKG of Azotobacter vinelandii and its parent. The results revealed that hydrogen recycling was too low to benefit the cellular energy metabolism or activities of nitrogenase and respiration. PMID:7592361

Linkerhägner, K; Oelze, J

1995-01-01

61

Competition between electron transfer, trapping, and recombination in CdS nanorod-hydrogenase complexes.  

PubMed

Electron transfer from photoexcited CdS nanorods to [FeFe]-hydrogenase is a critical step in photochemical H2 production by CdS-hydrogenase complexes. By accounting for the distributions in the numbers of electron traps and enzymes adsorbed, we determine rate constants and quantum efficiencies for electron transfer from transient absorption measurements. PMID:25623885

Utterback, James K; Wilker, Molly B; Brown, Katherine A; King, Paul W; Eaves, Joel D; Dukovic, Gordana

2015-02-10

62

[FeFe]-hydrogenase-catalyzed H2 production in a photoelectrochemical biofuel cell.  

PubMed

The Clostridium acetobutylicum [FeFe]-hydrogenase HydA has been investigated as a hydrogen production catalyst in a photoelectrochemical biofuel cell. Hydrogenase was adsorbed to pyrolytic graphite edge and carbon felt electrodes. Cyclic voltammograms of the immobilized hydrogenase films reveal cathodic proton reduction and anodic hydrogen oxidation, with a catalytic bias toward hydrogen evolution. When corrected for the electrochemically active surface area, the cathodic current densities are similar for both carbon electrodes, and approximately 40% of those obtained with a platinum electrode. The high surface area carbon felt/hydrogenase electrode was subsequently used as the cathode in a photoelectrochemical biofuel cell. Under illumination, this device is able to oxidize a biofuel substrate and reduce protons to hydrogen. Similar photocurrents and hydrogen production rates were observed in the photoelectrochemical biofuel cell using either hydrogenase or platinum cathodes. PMID:18205358

Hambourger, Michael; Gervaldo, Miguel; Svedruzic, Drazenka; King, Paul W; Gust, Devens; Ghirardi, Maria; Moore, Ana L; Moore, Thomas A

2008-02-13

63

[FeFe]-Hydrogenase-Catalyzed H2 Production in a Photoelectrochemical Biofuel Cell  

SciTech Connect

The Clostridium acetobutylicum [FeFe]-hydrogenase HydA has been investigated as a hydrogen production catalyst in a photoelectrochemical biofuel cell. Hydrogenase was adsorbed to pyrolytic graphite edge and carbon felt electrodes. Cyclic voltammograms of the immobilized hydrogenase films reveal cathodic proton reduction and anodic hydrogen oxidation, with a catalytic bias toward hydrogen evolution. When corrected for the electrochemically active surface area, the cathodic current densities are similar for both carbon electrodes, and 40% of those obtained with a platinum electrode. The high surface area carbon felt/hydrogenase electrode was subsequently used as the cathode in a photoelectrochemical biofuel cell. Under illumination, this device is able to oxidize a biofuel substrate and reduce protons to hydrogen. Similar photocurrents and hydrogen production rates were observed in the photoelectrochemical biofuel cell using either hydrogenase or platinum cathodes.

Hambourger, M.; Gervaldo, M.; Svedruzic, D.; King, P. W.; Gust, D.; Ghirardi, M.; Moore, A. L.; Moore, T. A.

2008-01-01

64

H, not O or pressure, causes eutectic T depression in the Fe-FeS System to 8 GPa  

NASA Astrophysics Data System (ADS)

The Fe-FeS system maintains a eutectic temperature of 990 ± 10 °C to at least 8 GPa if starting materials and pressure media are rigorously dehydrated. Literature reports of pressure-induced freezing point depression of the eutectic for the Fe-FeS system are not confirmed. Modest addition of oxygen alone is confirmed to cause negligible freezing point depression at 6 GPa. Addition of H alone causes a progressive decrease in the eutectic temperature with P in the Fe-FeS-H system to below 965 °C at 6 GPa to below 950 °C at 8 GPa. It is our hypothesis that moisture contamination in unrigorously dried experiments may be an H source for freezing point depression. O released from H2O disproportionation reacts with Fe and is sequestered as ferropericlase along the sample capsules walls, leaving the H to escape the system and/or enter the Fe-FeS mixture. The observed occurrence of ferropericlase on undried MgO capsule margins is otherwise difficult to explain, because an alternate source for the oxygen in the ferropericlase layer is difficult to identify. This study questions the use of pressure-depressed Fe-S eutectic temperatures and suggests that the lower eutectic temperatures sometimes reported are achieved by moving into the ternary Fe-S-H system. These results adjust slightly the constraints on eutectic temperatures allowed for partly solidified cores on small planets. H substantially diminishes the temperature extent of the melting interval in Fe-S by reducing the melting points of the crystalline phases more than it depresses the eutectic.

Buono, Antonio S.; Walker, David

2014-12-01

65

A synthetic system links FeFe-hydrogenases to essential E. coli sulfur metabolism  

PubMed Central

Background FeFe-hydrogenases are the most active class of H2-producing enzymes known in nature and may have important applications in clean H2 energy production. Many potential uses are currently complicated by a crucial weakness: the active sites of all known FeFe-hydrogenases are irreversibly inactivated by O2. Results We have developed a synthetic metabolic pathway in E. coli that links FeFe-hydrogenase activity to the production of the essential amino acid cysteine. Our design includes a complementary host strain whose endogenous redox pool is insulated from the synthetic metabolic pathway. Host viability on a selective medium requires hydrogenase expression, and moderate O2 levels eliminate growth. This pathway forms the basis for a genetic selection for O2 tolerance. Genetically selected hydrogenases did not show improved stability in O2 and in many cases had lost H2 production activity. The isolated mutations cluster significantly on charged surface residues, suggesting the evolution of binding surfaces that may accelerate hydrogenase electron transfer. Conclusions Rational design can optimize a fully heterologous three-component pathway to provide an essential metabolic flux while remaining insulated from the endogenous redox pool. We have developed a number of convenient in vivo assays to aid in the engineering of synthetic H2 metabolism. Our results also indicate a H2-independent redox activity in three different FeFe-hydrogenases, with implications for the future directed evolution of H2-activating catalysts. PMID:21615937

2011-01-01

66

Intracellular Location and O2 Sensitivity of Uptake Hydrogenase in Azospirillum spp  

PubMed Central

Uptake hydrogenase activity of Azospirillum brasilense in vitro (cell-free extract) was very much more sensitive to O2 than was that of A. amazonense, and the O2 pressure optima for uptake hydrogenase activities were 0.01 and 0.4 to 3 kPa for A. brasilense and A. amazonense, respectively. The addition of superoxide dismutase did not increase uptake hydrogenase activity of A. brasilense either in vivo or in vitro. The O2 uptake rates of A. brasilense and A. amazonense were nearly the same. Inhibition of A. brasilense O2-dependent uptake hydrogenase activity by O2 was highly reversible under the conditions tested. O2 also markedly inhibited in vitro methylene blue-dependent uptake hydrogenase activity of A. brasilense, and this inhibition was highly reversible. It is concluded that the difference in O2 tolerance of the uptake hydrogenases is not due to a difference in respiratory protection in the two species and may be due to inherent differences in the two enzymes. For the three species, A. brasilense, A. amazonense, and A. lipoferum, almost all the recovered methylene blue-dependent uptake hydrogenase activity was associated with the membrane fraction. PMID:16348011

Fu, Changlin; Knowles, Roger

1989-01-01

67

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

68

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

69

Insight into Core-Shell Dependent Anoxic Cr(VI) Removal with Fe@Fe2O3 Nanowires: Indispensable Role of Surface Bound Fe(II).  

PubMed

In this study, we investigated the anoxic Cr(VI) removal with core-shell Fe@Fe2O3 nanowires. It was found the surface area normalized Cr(VI) removal rate constants of Fe@Fe2O3 nanowires first increased with increasing the iron oxide shell thickness and then decreased, suggesting that Fe@Fe2O3 nanowires possessed an interesting core-shell structure dependent Cr(VI) removal property. Meanwhile, the Cr(VI) removal efficiency was positively correlated to the amount of surface bound Fe(II). This result revealed that the core-shell structure dependent Cr(VI) removal property of Fe@Fe2O3 nanowires was mainly attributed to the reduction of Cr(VI) by the surface bound Fe(II) besides the reduction of Cr(VI) adsorbed on the iron oxide shell via the electrons transferred from the iron core. The indispensable role of surface bound Fe(II) was confirmed by Tafel polarization and high-resolution X-ray photoelectron spectroscopic depth profiles analyses. X-ray diffraction patterns and scanning electron microscope images of the fresh and used Fe@Fe2O3 nanowires revealed the formation of Fe(III)/Cr(III)/Cr(VI) composite oxides during the anoxic Cr(VI) removal process. This study sheds a deep insight into the anoxic Cr(VI) removal mechanism of core-shell Fe@Fe2O3 nanowires and also provides an efficient Cr(VI) removal method. PMID:25543716

Mu, Yi; Ai, Zhihui; Zhang, Lizhi; Song, Fahui

2015-01-28

70

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

71

Structural differences of oxidized iron-sulfur and nickel-iron cofactors in O2-tolerant and O2-sensitive hydrogenases studied by X-ray absorption spectroscopy.  

PubMed

The class of [NiFe]-hydrogenases comprises oxygen-sensitive periplasmic (PH) and oxygen-tolerant membrane-bound (MBH) enzymes. For three PHs and four MBHs from six bacterial species, structural features of the nickel-iron active site of hydrogen turnover and of the iron-sulfur clusters functioning in electron transfer were determined using X-ray absorption spectroscopy (XAS). Fe-XAS indicated surplus oxidized iron and a lower number of ~2.7Å Fe-Fe distances plus additional shorter and longer distances in the oxidized MBHs compared to the oxidized PHs. This supported a double-oxidized and modified proximal FeS cluster in all MBHs with an apparent trimer-plus-monomer arrangement of its four iron atoms, in agreement with crystal data showing a [4Fe3S] cluster instead of a [4Fe4S] cubane as in the PHs. Ni-XAS indicated coordination of the nickel by the thiol group sulfurs of four conserved cysteines and at least one iron-oxygen bond in both MBH and PH proteins. Structural differences of the oxidized inactive [NiFe] cofactor of MBHs in the Ni-B state compared to PHs in the Ni-A state included a ~0.05Å longer Ni-O bond, a two times larger spread of the Ni-S bond lengths, and a ~0.1Å shorter Ni-Fe distance. The modified proximal [4Fe3S] cluster, weaker binding of the Ni-Fe bridging oxygen species, and an altered localization of reduced oxygen species at the active site may each contribute to O2 tolerance. PMID:25316302

Sigfridsson, Kajsa G V; Leidel, Nils; Sanganas, Oliver; Chernev, Petko; Lenz, Oliver; Yoon, Ki-Seok; Nishihara, Hirofumi; Parkin, Alison; Armstrong, Fraser A; Dementin, Sébastien; Rousset, Marc; De Lacey, Antonio L; Haumann, Michael

2015-02-01

72

Gd[subscript 13]Fe[subscript 10]C[subscript 13]: Indications of Fe?Fe Multiple Bonding Emerging from Chemical Frustration  

SciTech Connect

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

Hadler, Amelia B.; Fredrickson, Daniel C. (UW)

2012-10-25

73

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

PubMed Central

The importance of hydrogenase activity to corrosion of steel was assessed by using mixed populations of sulfate-reducing bacteria isolated from corroded and noncorroded oil pipelines. Biofilms which developed on the steel studs contained detectable numbers of sulfate-reducing bacteria (104 increasing to 107/0.5 cm2). However, the biofilm with active hydrogenase activity (i.e., corrosion pipeline organisms), as measured by a semiquantitative commercial kit, was associated with a significantly higher corrosion rate (7.79 mm/year) relative to noncorrosive biofilm (0.48 mm/year) with 105 sulfate-reducing bacteria per 0.5 cm2 but no measurable hydrogenase activity. The importance of hydrogenase and the microbial sulfate-reducing bacterial population making up the biofilm are discussed relative to biocorrosion. Images PMID:16348560

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

1991-01-01

74

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

Microsoft Academic Search

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

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

1987-01-01

75

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

SciTech Connect

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

Arp, D.J.

1991-01-01

76

Catalytic mechanism of hydrogenase from Azotobacter vinelandii. Final technical report, August 1, 1994--July 31, 1997  

SciTech Connect

This project is focused on investigations of the catalytic mechanism of the hydrogenase found in the aerobic, N{sub 2}-fixing microorganism Azotobacter vinelandii. This report summarizes the progress during the first two years of the current project and include the anticipated course of the research for the remaining year of the current project. Because the current proposal represents a change in direction, the authors also include a brief progress report of prior DOE-sponsored research dealing with hydrogenases.

Arp, D.J.

1997-10-01

77

Hydrogenase Genes from Rhizobium leguminosarum bv. viciae are Controlled by the Nitrogen Fixation Regulatory Protein NifA  

Microsoft Academic Search

Rhizobium leguminosarum bv. viciae expresses an uptake hydrogenase in symbiosis with peas (Pisum sativum) but, unlike all other characterized hydrogen-oxidizing bacteria, cannot express it in free-living conditions. The hydrogenase-specific transcriptional activator gene hoxA described in other species was shown to have been inactivated in R. leguminosarum by accumulation of frameshift and deletion mutations. Symbiotic transcription of hydrogenase structural genes hupSL

Belen Brito; Marta Martinez; Domingo Fernandez; Luis Rey; Ezequiel Cabrera; Jose Manuel Palacios; Juan Imperial; Tomas Ruiz-Argueso

1997-01-01

78

Acetylene, Not Ethylene, Inactivates the Uptake Hydrogenase of Actinorhizal Nodules during Acetylene Reduction Assays 1  

PubMed Central

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 C2H2 and not by C2H4. 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, Anita; Winship, Lawrence J.

1990-01-01

79

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

80

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

PubMed Central

Two distinct types of hydrogenase occur in Anabaena 7120 and are distinguishable in whole filaments by the application of selective assay methods. A reversible hydrogenase occurs both in heterocysts and vegetative cells and can be selectively assayed by measuring H2 evolution from reduced methyl viologen. Activities in aerobically grown filaments were low but could be increased by 2 to 3 orders of magnitude by growing cells microaerobically. The presence of the reversible hydrogenase was independent of the N2-fixing properties of the organism, and activity did not respond to added H2 in the culture. Illumination was necessary during derepression of the reversible hydrogenase, and addition of 3-(3',4'-dichlorophenyl)-1,1-dimethylurea increased the amount of enzyme that was synthesized. An uptake hydrogenase occurred only in heterocysts of aerobically grown filaments, but a small amount of activity also was present in the vegetative cells of filaments grown microaerobically with 20% H2. It was assayed selectively by measuring an oxyhydrogen reaction at atmospheric levels of O2. Additional uptake hydrogenase could be elicited by including H2 or by removing O2 from the sparging gas of a culture. PMID:6783614

Houchins, J P; Burris, R H

1981-01-01

81

Hydrogenase Activity of Mineral-Associated and Suspended Populations of Desulfovibrio desulfuricans Essex 6  

SciTech Connect

The interactions between sulfate-reducing microorganisms and iron oxides influence a number of important redox-sensitive biogeochemical processes including the formation of iron sulfides. Enzymes, such as hydrogenase which catalyze the reversible oxidation of molecular hydrogen, are known to mediate electron transfer to metals and may contribute to the formation and speciation of ferrous sulfides formed at the cell–mineral interface. In the present study, we compared the whole cell hydrogenase activity of Desulfovibrio desulfuricans strain Essex 6 growing as biofilms on hematite (hematite-associated) or as suspended populations using different metabolic pathways. Hematite-associated cells exhibited significantly greater hydrogenase activity than suspended populations during sulfate respiration but not during pyruvate fermentation. The enhanced activity of the hematite-associated, sulfate-grown cells appears to be dependent on iron availability rather than a general response to surface attachment since the activity of glass-associated cells did not differ from that of suspended populations. Hydrogenase activity of pyruvate-fermenting cells was stimulated by addition of iron as soluble Fe(II)Cl2 and, in the absence of added iron, both sulfate-reducing and pyruvate-fermenting cells displayed similar rates of hydrogenase activity. These data suggest that iron exerts a stronger influence on whole cell hydrogenase activity than either metabolic pathway or mode of growth. The location of hydrogenase to the cell envelope and the enhanced activity at the hematite surface in sulfate-reducing cells may influence the redox conditions that control the species of iron sulfides on the mineral surface.

C.L. Reardon; T.S. Magnuson; E.S. Boyd; W.D. Leavitt; D.W. Reed; G.G. Geesey

2014-02-01

82

Hydrogenase activity of mineral-associated and suspended populations of Desulfovibrio desulfuricans Essex 6.  

PubMed

The interactions between sulfate-reducing microorganisms and iron oxides influence a number of important redox-sensitive biogeochemical processes including the formation of iron sulfides. Enzymes, such as hydrogenase which catalyze the reversible oxidation of molecular hydrogen, are known to mediate electron transfer to metals and may contribute to the formation and speciation of ferrous sulfides formed at the cell-mineral interface. In the present study, we compared the whole cell hydrogenase activity of Desulfovibrio desulfuricans strain Essex 6 growing as biofilms on hematite (hematite-associated) or as suspended populations using different metabolic pathways. Hematite-associated cells exhibited significantly greater hydrogenase activity than suspended populations during sulfate respiration but not during pyruvate fermentation. The enhanced activity of the hematite-associated, sulfate-grown cells appears to be dependent on iron availability rather than a general response to surface attachment since the activity of glass-associated cells did not differ from that of suspended populations. Hydrogenase activity of pyruvate-fermenting cells was stimulated by addition of iron as soluble Fe(II)Cl2 and, in the absence of added iron, both sulfate-reducing and pyruvate-fermenting cells displayed similar rates of hydrogenase activity. These data suggest that iron exerts a stronger influence on whole cell hydrogenase activity than either metabolic pathway or mode of growth. The location of hydrogenase to the cell envelope and the enhanced activity at the hematite surface in sulfate-reducing cells may influence the redox conditions that control the species of iron sulfides on the mineral surface. PMID:24194097

Reardon, C L; Magnuson, T S; Boyd, E S; Leavitt, W D; Reed, D W; Geesey, G G

2014-02-01

83

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

E-print Network

Hybrid molecular assemblies composed of hydrogenase enzymes and quantum dots helps to pave the way selectivity and fast turnover of hydrogenase enzymes to achieve light-driven hydrogen (H2) production was maximal at low enzyme coverages favoring one-to-one ratios. The efficiency of photocatalytic H2 production

84

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

SciTech Connect

Hydrogenases are enzymes which catalyze reactions involving dihydrogen. They serve integral roles in a number of microbial metabolic pathways. Our research is focussed on investigations of the catalytic mechanism of the hydrogenases found in aerobic, N{sub 2}-fixing microorganisms such as Azotobacter vinelandii and the agronomically important Bradyrhizobium japonicum as well as microorganisms with similar hydrogenases. The hydrogenases isolated from these microorganisms are Ni- and Fe-containing heterodimers. Our work has focussed on three areas during the last grant period. In all cases, a central theme has been the role of inhibitors in the characteristics under investigation. In addition, a number of collaborative efforts have yielded interesting results. In metalloenzymes such as hydrogenase, inhibitors often influence the activity of the enzyme through ligand interactions with redox centers, often metals, within the enzyme. Therefore, investigations of the ability of various compounds to inhibit an enzyme's activity, as well as the mechanism of inhibition, can provide insight into the catalytic mechanism of the enzyme as well as the role of various redox centers in catalysis. We have investigated in detail four inhibitors of A. vinelandii and the results are summarized here. The influence of these inhibitors on the spectral properties of the enzyme are summarized. Electron paramagnetic resonance and ultraviolet spectra investigations are discussed. 9 figs.

Arp, D.J.

1990-01-01

85

A gene complex coding for the membrane-bound hydrogenase of Alcaligenes eutrophus H16.  

PubMed Central

One of the key enzymes in the chemolithoautotrophic metabolism of Alcaligenes eutrophus H16 is a dimeric, membrane-associated hydrogenase. The genetic determinants of this enzyme are located on the endogenous megaplasmid pHG1 (G. Eberz, C. Hogrefe, C. Kortlüke, A. Kamienski, and B. Friedrich, J. Bacteriol. 168:636-641, 1986). Complementation studies showed that the information required for the formation of active membrane-bound hydrogenase occupies more than 7.5 kb of megaplasmid DNA. We cloned and sequenced this region and identified the genes encoding the two hydrogenase subunits (hoxK and hoxG). The nucleotide sequence contains nine additional closely spaced open reading frames. Immunoelectron microscopy showed that the gene product of one of these open reading frames (hoxM) is involved in the process leading to the attachment of hydrogenase to the membrane. Other open reading frames may encode additional processing functions and components of a hydrogenase-linked electron transport chain. Analysis of Tn5-B21-mediated transcriptional fusions provided evidence that the structural genes and accessory functions belong to at least three coordinately regulated transcriptional units. Images PMID:1383192

Kortlüke, C; Horstmann, K; Schwartz, E; Rohde, M; Binsack, R; Friedrich, B

1992-01-01

86

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

87

Approaches to efficient molecular catalyst systems for photochemical H2 production using [FeFe]-hydrogenase active site mimics.  

PubMed

The research on structural and functional biomimics of the active site of [FeFe]-hydrogenases is in an attempt to elucidate the mechanisms of H(2)-evolution and uptake at the [FeFe]-hydrogenase active site, and to learn from Nature how to create highly efficient H(2)-production catalyst systems. Undoubtedly, it is a challenging, arduous, and long-term work. In this perspective, the progresses in approaches to photochemical H(2) production using mimics of the [FeFe]-hydrogenase active site as catalysts in the last three years are reviewed, with emphasis on adjustment of the redox potentials and hydrophilicity of the [FeFe]-hydrogenase active site mimics to make them efficient catalysts for H(2) production. With gradually increasing understanding of the chemistry of the [FeFe]-hydrogenases and their mimics, more bio-inspired proton reduction catalysts with significantly improved efficiency of H(2) production will be realized in the future. PMID:21983599

Wang, Mei; Chen, Lin; Li, Xueqiang; Sun, Licheng

2011-12-28

88

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

Microsoft Academic Search

Sensitive electrochemical sensing for the DNA damage in situ based on a cathodic process of Fe@Fe2O3 core–shell nanonecklace and Au nanoparticles was performed by a novel biosensor, which was constructed via a glassy carbon electrode (GCE) modified with a multilayer film comprising of separate layers of poly(dimethyldiallylammonium chloride) (PDDA), the mixture of Fe@Fe2O3 core–shell nanonecklace and Au nanoparticles, PDDA and

Xueliang Wang; Tao Yang; Kui Jiao

2009-01-01

89

Advances in the Function and Regulation of Hydrogenase in the Cyanobacterium Synechocystis PCC6803  

PubMed Central

In order to use cyanobacteria for the biological production of hydrogen, it is important to thoroughly study the function and the regulation of the hydrogen-production machine in order to better understand its role in the global cell metabolism and identify bottlenecks limiting H2 production. Most of the recent advances in our understanding of the bidirectional [Ni-Fe] hydrogenase (Hox) came from investigations performed in the widely-used model cyanobacterium Synechocystis PCC6803 where Hox is the sole enzyme capable of combining electrons with protons to produce H2 under specific conditions. Recent findings suggested that the Hox enzyme can receive electrons from not only NAD(P)H as usually shown, but also, or even preferentially, from ferredoxin. Furthermore, plasmid-encoded functions and glutathionylation (the formation of a mixed-disulfide between the cysteines residues of a protein and the cysteine residue of glutathione) are proposed as possible new players in the function and regulation of hydrogen production. PMID:25365180

Cassier-Chauvat, Corinne; Veaudor, Théo; Chauvat, Franck

2014-01-01

90

Advances in the function and regulation of hydrogenase in the cyanobacterium Synechocystis PCC6803.  

PubMed

In order to use cyanobacteria for the biological production of hydrogen, it is important to thoroughly study the function and the regulation of the hydrogen-production machine in order to better understand its role in the global cell metabolism and identify bottlenecks limiting H2 production. Most of the recent advances in our understanding of the bidirectional [Ni-Fe] hydrogenase (Hox) came from investigations performed in the widely-used model cyanobacterium Synechocystis PCC6803 where Hox is the sole enzyme capable of combining electrons with protons to produce H2 under specific conditions. Recent findings suggested that the Hox enzyme can receive electrons from not only NAD(P)H as usually shown, but also, or even preferentially, from ferredoxin. Furthermore, plasmid-encoded functions and glutathionylation (the formation of a mixed-disulfide between the cysteines residues of a protein and the cysteine residue of glutathione) are proposed as possible new players in the function and regulation of hydrogen production. PMID:25365180

Cassier-Chauvat, Corinne; Veaudor, Théo; Chauvat, Franck

2014-01-01

91

[Studies on transference of hydrogenase genes of Rhizobium arachis].  

PubMed

The hydrogen-uptake genes were transferred into wild Rhizobium arachis Ra strains (Hup-, Nif+, Apr) by triparental mating using pRK2013 as help plasmid. A transconjugant R. arachis Rz34-2(Hup+, Nif+, Apr, Tcr) which expressed high activities of hydrogenase and nitrogenase under free-living and symbiotic state was screened. Peanut inoculation test with recipient R. arachis Ra34, transcojugant Rz34-2 and control strain R. arachis L8-3 (Hup+, Nif+) was carried out respectively. The results showed that, compare to treatment without inoculation, inoculation with R. arachis Ra34 and R. arachis L8-3, the dry weight of leaf inoculated with transconjuant Rz34-2 increased 6.2%, 7.6% and 6.3% respectively; the N-content of seed increased 8.8%, 10.0% and 6.0%; the output increased 18.8%, 10.5% and 10.7%. This suggested that legume plants inoculated with Rhizobium strains (Hup+) were more efficient to accumulate N and to increase its output. PMID:12552906

Wang, Z; Long, M; Liu, Y; Zhang, F; Xu, L; Zhu, T; Jiang, S

2001-08-01

92

Understanding and tuning the catalytic bias of hydrogenase.  

PubMed

When enzymes are optimized for biotechnological purposes, the goal often is to increase stability or catalytic efficiency. However, many enzymes reversibly convert their substrate and product, and if one is interested in catalysis in only one direction, it may be necessary to prevent the reverse reaction. In other cases, reversibility may be advantageous because only an enzyme that can operate in both directions can turnover at a high rate even under conditions of low thermodynamic driving force. Therefore, understanding the basic mechanisms of reversibility in complex enzymes should help the rational engineering of these proteins. Here, we focus on NiFe hydrogenase, an enzyme that catalyzes H(2) oxidation and production, and we elucidate the mechanism that governs the catalytic bias (the ratio of maximal rates in the two directions). Unexpectedly, we found that this bias is not mainly determined by redox properties of the active site, but rather by steps which occur on sites of the proteins that are remote from the active site. We evidence a novel strategy for tuning the catalytic bias of an oxidoreductase, which consists in modulating the rate of a step that is limiting only in one direction of the reaction, without modifying the properties of the active site. PMID:22540997

Abou Hamdan, Abbas; Dementin, Sébastien; Liebgott, Pierre-Pol; Gutierrez-Sanz, Oscar; Richaud, Pierre; De Lacey, Antonio L; Rousset, Marc; Bertrand, Patrick; Cournac, Laurent; Léger, Christophe

2012-05-23

93

Cloning and sequence of the structural (hupSLC) and accessory (hupDHI) genes for hydrogenase biosynthesis in Thiocapsa roseopersicina.  

PubMed

The first molecular biology study on the purple sulfur photosynthetic bacterium Thiocapsa roseopersicina is reported, namely, the construction of cosmid libraries and isolation of a hydrogenase gene cluster by hybridization with hydrogenase structural genes from the purple non-sulfur bacterium, Rhodobacter capsulatus. The sequenced gene cluster contains six open reading frames, the products of which show significant degrees of identity (from 40 to 78%) with hydrogenase gene products necessary for biosynthesis of the group-I of [NiFe]hydrogenases. The structural hupSLC genes encode the small and large hydrogenase subunits and a hydrophobic protein shown to accept electrons from hydrogenase in R. capsulatus. They are followed downstream by three genes, hupDHI, which are similar to hydrogenase accessory genes found in other bacteria. PMID:8125335

Colbeau, A; Kovacs, K L; Chabert, J; Vignais, P M

1994-03-11

94

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

PubMed

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

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

2014-01-01

95

Novel, Oxygen-Insensitive Group 5 [NiFe]-Hydrogenase in Ralstonia eutropha  

PubMed Central

Recently, a novel group of [NiFe]-hydrogenases has been defined that appear to have a great impact in the global hydrogen cycle. This so-called group 5 [NiFe]-hydrogenase is widespread in soil-living actinobacteria and can oxidize molecular hydrogen at atmospheric levels, which suggests a high affinity of the enzyme toward H2. Here, we provide a biochemical characterization of a group 5 hydrogenase from the betaproteobacterium Ralstonia eutropha H16. The hydrogenase was designated an actinobacterial hydrogenase (AH) and is catalytically active, as shown by the in vivo H2 uptake and by activity staining in native gels. However, the enzyme does not sustain autotrophic growth on H2. The AH was purified to homogeneity by affinity chromatography and consists of two subunits with molecular masses of 65 and 37 kDa. Among the electron acceptors tested, nitroblue tetrazolium chloride was reduced by the AH at highest rates. At 30°C and pH 8, the specific activity of the enzyme was 0.3 ?mol of H2 per min and mg of protein. However, an unexpectedly high Michaelis constant (Km) for H2 of 3.6 ± 0.5 ?M was determined, which is in contrast to the previously proposed low Km of group 5 hydrogenases and makes atmospheric H2 uptake by R. eutropha most unlikely. Amperometric activity measurements revealed that the AH maintains full H2 oxidation activity even at atmospheric oxygen concentrations, showing that the enzyme is insensitive toward O2. PMID:23793632

Schäfer, Caspar; Friedrich, Bärbel

2013-01-01

96

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

97

Positive Transcriptional Feedback Controls Hydrogenase Expression in Alcaligenes eutrophus H16  

PubMed Central

The protein HoxA is the central regulator of the Alcaligenes eutrophus H16 hox regulon, which encodes two hydrogenases, a nickel permease and several accessory proteins required for hydrogenase biosynthesis. Expression of the regulatory gene hoxA was analyzed. Screening of an 8-kb region upstream of hoxA with a promoter probe vector localized four promoter activities. One of these was found in the region immediately 5? of hoxA; the others were correlated with the nickel metabolism genes hypA1, hypB1, and hypX. All four activities were independent of HoxA and of the minor transcription factor ?54. Translational fusions revealed that hoxA is expressed constitutively at low levels. In contrast to these findings, immunoblotting studies revealed a clear fluctuation in the HoxA pool in response to conditions which induce the hox regulon. Quantitative transcript assays indicated elevated levels of hyp mRNA under hydrogenase-derepressing conditions. Using interposon mutagenesis, we showed that the activity of a remote promoter is required for hydrogenase expression and autotrophic growth. Site-directed mutagenesis revealed that PMBH, which directs transcription of the structural genes of the membrane-bound hydrogenase, contributes to the expression of hoxA under hydrogenase-derepressing conditions. Thus, expression of the hox regulon is governed by a positive feedback loop mediating amplification of the regulator HoxA. These results imply the existence of an unusually large (ca. 17,000-nucleotide) transcript. PMID:10482509

Schwartz, Edward; Buhrke, Thorsten; Gerischer, Ulrike; Friedrich, Bärbel

1999-01-01

98

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

SciTech Connect

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

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

2008-10-22

99

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

PubMed

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

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

2013-11-13

100

Powerful fermentative hydrogen evolution of photosynthate in the cyanobacterium Lyngbya aestuarii BL J mediated by a bidirectional hydrogenase  

PubMed Central

Cyanobacteria are considered good models for biohydrogen production because they are relatively simple organisms with a demonstrable ability to generate H2 under certain physiological conditions. However, most produce only little H2, revert readily to H2 consumption, and suffer from hydrogenase sensitivity to O2. Strains of the cyanobacteria Lyngbya aestuarii and Microcoleus chthonoplastes obtained from marine intertidal cyanobacterial mats were recently found to display much better H2 production potential. Because of their ecological origin in environments that become quickly anoxic in the dark, we hypothesized that this differential ability may have evolved to serve a role in the fermentation of the photosynthate. Here we show that, when forced to ferment internal substrate, these cyanobacteria display desirable characteristics of physiological H2 production. Among them, the strain L. aestuarii BL J had the fastest specific rates and attained the highest H2 concentrations during fermentation of photosynthate, which proceeded via a mixed acid fermentation pathway to yield acetate, ethanol, lactate, H2, CO2, and pyruvate. Contrary to expectations, the H2 yield per mole of glucose was only average compared to that of other cyanobacteria. Thermodynamic analyses point to the use of electron donors more electronegative than NAD(P)H in Lyngbya hydrogenases as the basis for its strong H2 production ability. In any event, the high specific rates and H2 concentrations coupled with the lack of reversibility of the enzyme, at the expense of internal, photosynthetically generated reductants, makes L. aestuarii BL J and/or its enzymes, a potentially feasible platform for large-scale H2 production.

Kothari, Ankita; Parameswaran, Prathap; Garcia-Pichel, Ferran

2014-01-01

101

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

102

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

103

Hydrogenase activity of mineral-associated and suspended populations of Desulfovibrio Desulfuricans Essex 6  

Technology Transfer Automated Retrieval System (TEKTRAN)

The interactions between sulfate-reducing microorganisms and iron oxides influence a number of important redox-sensitive biogeochemical processes including the formation of iron sulfides. Enzymes, such as hydrogenase which catalyze the reversible oxidation of molecular hydrogen, are known to mediate...

104

Purification and characterization of Desulfovibrio vulgaris (Hildenborough) hydrogenase expressed in Escherichia coli.  

PubMed

Hydrogenase from Desulfovibrio vulgaris (Hildenborough) is a heterologous dimer of molecular mass 46 + 13.5 kDa. Its two structural genes have been cloned on a 4664-base-pair fragment of known sequence in the vector pUC9. Expression of hydrogenase polypeptides in Escherichia coli transformed with this plasmid is poor (approximately 0.1% w/w of total protein). Deletion of up to 1.9 kb of insert DNA brings the gene encoding for the large subunit in close proximity to the lac promotor of pUC9 and results in a 50-fold increased expression of hydrogenase polypeptides in E. coli. The protein formed is inactive and was purified in order to delineate its defect. Complete purification was achieved with a procedure similar to that used for the isolation of active hydrogenase from D. vulgaris H. The derived protein is also an alpha beta dimer and electron-paramagnetic resonance studies indicate the presence of the electron-transferring ferredoxin-type iron-sulfur clusters. In contrast to the native protein from D. vulgaris H, these can only be reduced with dithionite, not with hydrogen, indicating that the hydrogen-binding active centre which also contains an iron-sulfur cluster is missing. PMID:3028789

Voordouw, G; Hagen, W R; Krüse-Wolters, K M; van Berkel-Arts, A; Veeger, C

1987-01-01

105

Designed Surface Residue Substitutions in [NiFe] Hydrogenase that Improve Electron Transfer Characteristics  

PubMed Central

Photobiological hydrogen production is an attractive, carbon-neutral means to convert solar energy to hydrogen. We build on previous research improving the Alteromonas macleodii “Deep Ecotype” [NiFe] hydrogenase, and report progress towards creating an artificial electron transfer pathway to supply the hydrogenase with electrons necessary for hydrogen production. Ferredoxin is the first soluble electron transfer mediator to receive high-energy electrons from photosystem I, and bears an electron with sufficient potential to efficiently reduce protons. Thus, we engineered a hydrogenase-ferredoxin fusion that also contained several other modifications. In addition to the C-terminal ferredoxin fusion, we truncated the C-terminus of the hydrogenase small subunit, identified as the available terminus closer to the electron transfer region. We also neutralized an anionic patch surrounding the interface Fe-S cluster to improve transfer kinetics with the negatively charged ferredoxin. Initial screening showed the enzyme tolerated both truncation and charge neutralization on the small subunit ferredoxin-binding face. While the enzyme activity was relatively unchanged using the substrate methyl viologen, we observed a marked improvement from both the ferredoxin fusion and surface modification using only dithionite as an electron donor. Combining ferredoxin fusion and surface charge modification showed progressively improved activity in an in vitro assay with purified enzyme. PMID:25603181

Yonemoto, Isaac T.; Smith, Hamilton O.; Weyman, Philip D.

2015-01-01

106

Role of the NiFe Hydrogenase Hya in Oxidative Stress Defense in Geobacter sulfurreducens  

PubMed Central

Geobacter sulfurreducens, an Fe(III)-reducing deltaproteobacterium found in anoxic subsurface environments, contains 4 NiFe hydrogenases. Hyb, a periplasmically oriented membrane-bound NiFe hydrogenase, is essential for hydrogen-dependent growth. The functions of the three other hydrogenases are unknown. We show here that the other periplasmically oriented membrane-bound NiFe hydrogenase, Hya, is necessary for growth after exposure to oxidative stress when hydrogen or a highly limiting concentration of acetate is the electron source. The beneficial impact of Hya on growth was dependent on the presence of H2 in the atmosphere. Moreover, the Hya-deficient strain was more sensitive to the presence of superoxide or hydrogen peroxide. Hya was also required to safeguard Hyb hydrogen oxidation activity after exposure to O2. Overexpression studies demonstrated that Hya was more resistant to oxidative stress than Hyb. Overexpression of Hya also resulted in the creation of a recombinant strain better fitted for exposure to oxidative stress than wild-type G. sulfurreducens. These results demonstrate that one of the physiological roles of the O2-resistant Hya is to participate in the oxidative stress defense of G. sulfurreducens. PMID:22366414

Lovley, Derek R.

2012-01-01

107

Antigenic determinants of the membrane-bound hydrogenase in Alcaligenes eutrophus are exposed toward the periplasm.  

PubMed Central

Electron microscopic immunogold labeling experiments were performed with ultrathin sections of plasmolyzed cells of Alcaligenes eutrophus and "whole-mount" samples of spheroplasts and protoplasts. They demonstrated that antigenic determinants of the membrane-bound hydrogenase are exposed, at the outside of the cytoplasmic membrane, to the periplasm. PMID:7592402

Eismann, K; Mlejnek, K; Zipprich, D; Hoppert, M; Gerberding, H; Mayer, F

1995-01-01

108

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

109

Designed Surface Residue Substitutions in [NiFe] Hydrogenase that Improve Electron Transfer Characteristics.  

PubMed

Photobiological hydrogen production is an attractive, carbon-neutral means to convert solar energy to hydrogen. We build on previous research improving the Alteromonas macleodii "Deep Ecotype" [NiFe] hydrogenase, and report progress towards creating an artificial electron transfer pathway to supply the hydrogenase with electrons necessary for hydrogen production. Ferredoxin is the first soluble electron transfer mediator to receive high-energy electrons from photosystem I, and bears an electron with sufficient potential to efficiently reduce protons. Thus, we engineered a hydrogenase-ferredoxin fusion that also contained several other modifications. In addition to the C-terminal ferredoxin fusion, we truncated the C-terminus of the hydrogenase small subunit, identified as the available terminus closer to the electron transfer region. We also neutralized an anionic patch surrounding the interface Fe-S cluster to improve transfer kinetics with the negatively charged ferredoxin. Initial screening showed the enzyme tolerated both truncation and charge neutralization on the small subunit ferredoxin-binding face. While the enzyme activity was relatively unchanged using the substrate methyl viologen, we observed a marked improvement from both the ferredoxin fusion and surface modification using only dithionite as an electron donor. Combining ferredoxin fusion and surface charge modification showed progressively improved activity in an in vitro assay with purified enzyme. PMID:25603181

Yonemoto, Isaac T; Smith, Hamilton O; Weyman, Philip D

2015-01-01

110

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

111

The Crystal Structure of the [NiFe] Hydrogenase from the Photosynthetic Bacterium Allochromatium vinosum: Characterization of the Oxidized Enzyme (Ni-A State)  

Microsoft Academic Search

The crystal structure of the membrane-associated [NiFe] hydrogenase from Allochromatium vinosum has been determined to 2.1 Å resolution. Electron paramagnetic resonance (EPR) and Fourier transform infrared spectroscopy on dissolved crystals showed that it is present in the Ni-A state (>90%). The structure of the A. vinosum [NiFe] hydrogenase shows significant similarities with [NiFe] hydrogenase structures derived from Desulfovibrio species. The amino

Hideaki Ogata; Petra Kellers; Wolfgang Lubitz

2010-01-01

112

New FeFe-hydrogenase genes identified in a metagenomic fosmid library from a municipal wastewater treatment plant as revealed by high-throughput sequencing.  

PubMed

A fosmid metagenomic library was constructed with total community DNA obtained from a municipal wastewater treatment plant (MWWTP), with the aim of identifying new FeFe-hydrogenase genes encoding the enzymes most important for hydrogen metabolism. The dataset generated by pyrosequencing of a fosmid library was mined to identify environmental gene tags (EGTs) assigned to FeFe-hydrogenase. The majority of EGTs representing FeFe-hydrogenase genes were affiliated with the class Clostridia, suggesting that this group is the main hydrogen producer in the MWWTP analyzed. Based on assembled sequences, three FeFe-hydrogenase genes were predicted based on detection of the L2 motif (MPCxxKxxE) in the encoded gene product, confirming true FeFe-hydrogenase sequences. These sequences were used to design specific primers to detect fosmids encoding FeFe-hydrogenase genes predicted from the dataset. Three identified fosmids were completely sequenced. The cloned genomic fragments within these fosmids are closely related to members of the Spirochaetaceae, Bacteroidales and Firmicutes, and their FeFe-hydrogenase sequences are characterized by the structure type M3, which is common to clostridial enzymes. FeFe-hydrogenase sequences found in this study represent hitherto undetected sequences, indicating the high genetic diversity regarding these enzymes in MWWTP. Results suggest that MWWTP have to be considered as reservoirs for new FeFe-hydrogenase genes. PMID:25446611

Tomazetto, Geizecler; Wibberg, Daniel; Schlüter, Andreas; Oliveira, Valéria M

2015-01-01

113

Hydrogenase of the hyperthermophile Pyrococcus furiosus is an elemental sulfur reductase or sulfhydrogenase: Evidence for a sulfur-reducing hydrogenase ancestor  

SciTech Connect

Microorganisms growing near and above 100[degrees]C have recently been discovered near shallow and deep sea hydrothermal vents. Most are obligately dependent upon the reduction of elemental sulfur (S[sup 0]) to hydrogen sulfide (H[sub 2]S) for optimal growth, even though S[sup 0] reduction readily occurs abiotically at their growth temperatures. The sulfur reductase activity of the anaerobic archaeon Pyrococcus furiosus, which grows optimally at 100[degrees]C by a metabolism that produces H[sub 2]S if S[sup 0] is present, was found in the cytoplasm. It was purified anaerobically and was shown to be identical to the hydrogenase that had been previously purified from this organism. Both S[sup 0] and polysulfide served as substrates for H[sub 2]S production, and the S[sub 0] reduction activity but not the H[sub 2]-oxidation activity was enhanced by the redox protein rubredoxin. The H[sub 2]-oxidizing and S[sup 0]-reduction activities of the enzyme also showed different responses to pH, temperature, and inhibitors. This bifunctional [open quotes]sulfhydrogenase[close quotes] enzyme can, therefore, dispose of the excess reductant generated during fermentation using either protons or polysulfides as the electron acceptor. In addition, purified hydrogenases from both hyperthermophilic and mesophilic representatives of the archaeal and bacterial domains were shown to reduce S[sup 0] to H[sub 2]S. It is suggested that the function of some form of ancestral hydrogenase was S[sup 0] reduction rather than, or in addition, to the reduction of protons. 33 refs., 4 figs., 2 tabs.

Ma, K.; Adams, M.W.W. (Univ. of Georgia, Athens (United States)); Schicho, R.N. (Johns Hopkins Univ., Baltimore, MD (United States)); Kelly, R.M. (North Carolina State Univ., Raleigh (United States))

1993-06-01

114

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

115

Crystal structure of the nickel-iron hydrogenase from Desulfovibrio gigas  

Microsoft Academic Search

The X-ray structure of the heterodimeric Ni-Fe hydrogenase from Desulfovibrio gigas, the enzyme responsible for the metabolism of molecular hydrogen, has been solved at 2.85 Å resolution. The active site, which appears to contain, besides nickel, a second metal ion, is buried in the 60K subunit. The 28K subunit, which coordinates one [3Fe-4S] and two [4Fe-4S] clusters, contains an amino-terminal

Anne Volbeda; Marie-Hélène Charon; Claudine Piras; E. Claude Hatchikian; Michel Frey; Juan C. Fontecilla-Camps

1995-01-01

116

Rhizobium leguminosarum hupE Encodes a Nickel Transporter Required for Hydrogenase Activity?  

PubMed Central

Synthesis of the hydrogen uptake (Hup) system in Rhizobium leguminosarum bv. viciae requires the function of an 18-gene cluster (hupSLCDEFGHIJK-hypABFCDEX). Among them, the hupE gene encodes a protein showing six transmembrane domains for which a potential role as a nickel permease has been proposed. In this paper, we further characterize the nickel transport capacity of HupE and that of the translated product of hupE2, a hydrogenase-unlinked gene identified in the R. leguminosarum genome. HupE2 is a potential membrane protein that shows 48% amino acid sequence identity with HupE. Expression of both genes in the Escherichia coli nikABCDE mutant strain HYD723 restored hydrogenase activity and nickel transport. However, nickel transport assays revealed that HupE and HupE2 displayed different levels of nickel uptake. Site-directed mutagenesis of histidine residues in HupE revealed two motifs (HX5DH and FHGX[AV]HGXE) that are required for HupE functionality. An R. leguminosarum double mutant, SPF22A (hupE hupE2), exhibited reduced levels of hydrogenase activity in free-living cells, and this phenotype was complemented by nickel supplementation. Low levels of symbiotic hydrogenase activity were also observed in SPF22A bacteroid cells from lentil (Lens culinaris L.) root nodules but not in pea (Pisum sativum L.) bacteroids. Moreover, heterologous expression of the R. leguminosarum hup system in bacteroid cells of Rhizobium tropici and Mesorhizobium loti displayed reduced levels of hydrogen uptake in the absence of hupE. These data support the role of R. leguminosarum HupE as a nickel permease required for hydrogen uptake under both free-living and symbiotic conditions. PMID:20023036

Brito, Belén; Prieto, Rosa-Isabel; Cabrera, Ezequiel; Mandrand-Berthelot, Marie-Andrée; Imperial, Juan; Ruiz-Argüeso, Tomás; Palacios, José-Manuel

2010-01-01

117

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

118

Photosynthetic hydrogen production by a hybrid complex of photosystem I and [NiFe]-hydrogenase.  

PubMed

Nature provides key components for generating fuels from renewable resources in the form of enzymatic nanomachines which catalyze crucial steps in biological energy conversion, for example, the photosynthetic apparatus, which transforms solar power into chemical energy, and hydrogenases, capable of generating molecular hydrogen. As sunlight is usually used to synthesize carbohydrates, direct generation of hydrogen from light represents an exception in nature. On the molecular level, the crucial step for conversion of solar energy into H(2) lies in the efficient electronic coupling of photosystem I and hydrogenase. Here we show the stepwise assembly of a hybrid complex consisting of photosystem I and hydrogenase on a solid gold surface. This device gave rise to light-induced H(2) evolution. Hydrogen production is possible at far higher potential and thus lower energy compared to those of previously described (bio)nanoelectronic devices that did not employ the photosynthesis apparatus. The successful demonstration of efficient solar-to-hydrogen conversion may serve as a blueprint for the establishment of this system in a living organism with the paramount advantage of self-replication. PMID:19947646

Krassen, Henning; Schwarze, Alexander; Friedrich, Bärbel; Ataka, Kenichi; Lenz, Oliver; Heberle, Joachim

2009-12-22

119

[FeFe]-Hydrogenase Oxygen Inactivation Is Initiated at the H Cluster 2Fe Subcluster.  

PubMed

The [FeFe]-hydrogenase catalytic site H cluster is a complex iron sulfur cofactor that is sensitive to oxygen (O2). The O2 sensitivity is a significant barrier for production of hydrogen as an energy source in water-splitting, oxygenic systems. Oxygen reacts directly with the H cluster, which results in rapid enzyme inactivation and eventual degradation. To investigate the progression of O2-dependent [FeFe]-hydrogenase inactivation and the process of H cluster degradation, the highly O2-sensitive [FeFe]-hydrogenase HydA1 from the green algae Chlamydomonas reinhardtii was exposed to defined concentrations of O2 while monitoring the loss of activity and accompanying changes in H cluster spectroscopic properties. The results indicate that H cluster degradation proceeds through a series of reactions, the extent of which depend on the initial enzyme reduction/oxidation state. The degradation process begins with O2 interacting and reacting with the 2Fe subcluster, leading to degradation of the 2Fe subcluster and leaving an inactive [4Fe-4S] subcluster state. This final inactive degradation product could be reactivated in vitro by incubation with 2Fe subcluster maturation machinery, specifically HydF(EG), which was observed by recovery of enzyme activity. PMID:25579778

Swanson, Kevin D; Ratzloff, Michael W; Mulder, David W; Artz, Jacob H; Ghose, Shourjo; Hoffman, Andrew; White, Spencer; Zadvornyy, Oleg A; Broderick, Joan B; Bothner, Brian; King, Paul W; Peters, John W

2015-02-11

120

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

NASA Technical Reports Server (NTRS)

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

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

2004-01-01

121

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

122

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

PubMed Central

We developed a broad-ranging method for identifying key hydrogen-producing and consuming microorganisms through analysis of hydrogenase gene content and expression in complex anaerobic microbial communities. The method is based on a tiling hydrogenase gene oligonucleotide DNA microarray (Hydrogenase Chip), which implements a high number of probes per gene by tiling probe sequences across genes of interest at 1.67 × –2 × coverage. This design favors the avoidance of false positive gene identification in samples of DNA or RNA extracted from complex microbial communities. We applied this technique to interrogate interspecies hydrogen transfer in complex communities in (i) lab-scale reductive dehalogenating microcosms enabling us to delineate key H2-consuming microorganisms, and (ii) hydrogen-generating microbial mats where we found evidence for significant H2 production by cyanobacteria. Independent quantitative PCR analysis on selected hydrogenase genes showed that this Hydrogenase Chip technique is semiquantitative. We also determined that as microbial community complexity increases, specificity must be traded for sensitivity in analyzing data from tiling DNA microarrays. PMID:21993396

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

2012-01-01

123

FnrN Controls Symbiotic Nitrogen Fixation and Hydrogenase Activities in Rhizobium leguminosarum Biovar viciae UPM791  

Microsoft Academic Search

sarum fnrN1 and fnrN2 mutants exhibited a Fix 1 phenotype and near wild-type levels of nitrogenase and hydrogenase activities in pea (Pisum sativum L.) nodules. In contrast, an fnrN1 fnrN2 double mutant formed ineffective nodules lacking both nitrogenase and hydrogenase activities. Unlike the wild-type strain and single fnrN1 or fnrN2 mutants, the fnrN1 fnrN2 double mutant was unable to induce

DELIA GUTIERREZ; YOLANDA HERNANDO; JOSE ´-MANUEL PALACIOS; JUAN IMPERIAL; TOMAS RUIZ-ARGUESO; Consejo Superior de Investigaciones

1997-01-01

124

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

125

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

PubMed Central

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

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

2014-01-01

126

Expression of Shewanella oneidensis MR-1 [FeFe]-hydrogenase genes in Anabaena sp. strain PCC 7120.  

PubMed

H(2) 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 H(2) 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 O(2) sensitive. Certain filamentous cyanobacteria protect nitrogenase from O(2) 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 P(hetN). 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 O(2). PMID:23023750

Gärtner, Katrin; Lechno-Yossef, Sigal; Cornish, Adam J; Wolk, C Peter; Hegg, Eric L

2012-12-01

127

Electron transfer activation of a second water channel for proton transport in [FeFe]-hydrogenase  

NASA Astrophysics Data System (ADS)

Hydrogenase enzymes are important because they can reversibly catalyze the production of molecular hydrogen. Proton transport mechanisms have been previously studied in residue pathways that lead to the active site of the enzyme via residues Cys299 and Ser319. The importance of this pathway and these residues has been previously exhibited through site-specific mutations, which were shown to interrupt the enzyme activity. It has been shown recently that a separate water channel (WC2) is coupled with electron transport to the active site of the [FeFe]-hydrogenase. The water-mediated proton transport mechanisms of the enzyme in different electronic states have been studied using the multistate empirical valence bond reactive molecular dynamics method, in order to understand any role WC2 may have in facilitating the residue pathway in bringing an additional proton to the enzyme active site. In a single electronic state A2-, a water wire was formed through which protons can be transported with a low free energy barrier. The remaining electronic states were shown, however, to be highly unfavorable to proton transport in WC2. A double amino acid substitution is predicted to obstruct proton transport in electronic state A2- by closing a cavity that could otherwise fill with water near the proximal Fe of the active site.

Sode, Olaseni; Voth, Gregory A.

2014-12-01

128

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

PubMed Central

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

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

2014-01-01

129

Transcriptional and Mutational Analysis of the Uptake Hydrogenase of the Filamentous Cyanobacterium Anabaena variabilis ATCC 29413  

PubMed Central

A 10-kb DNA region of the cyanobacterium Anabaena variabilis ATCC 29413 containing the structural genes of the uptake hydrogenase (hupSL) was cloned and sequenced. In contrast to the hupL gene of Anabaena sp. strain PCC 7120, which is interrupted by a 10.5-kb DNA fragment in vegetative cells, there is no programmed rearrangement within the hupL gene during the heterocyst differentiation of A. variabilis. The hupSL genes were transcribed as a 2.7-kb operon and were induced only under nitrogen-fixing conditions, as shown by Northern blot experiments and reverse transcriptase PCR. Primer extension experiments with a fluorescence-labeled oligonucleotide primer confirmed these results and identified the 5? start of the mRNA transcript 103 bp upstream of the ATG initiation codon. A consensus sequence in the promoter that is recognized by the fumarate nitrate reductase regulator (Fnr) could be detected. The hupSL operon in A. variabilis was interrupted by an interposon deletion (mutant strain AVM13). Under N2-fixing conditions, the mutant strain exhibited significantly increased rates in H2 accumulation and produced three times more hydrogen than the wild type. These results indicate that the uptake hydrogenase is catalytically active in the wild type and that the enzyme reoxidizes the H2 developed by the nitrogenase. The Nif phenotype of the mutant strain showed a slight decrease of acetylene reduction compared to that of the wild type. PMID:10692368

Happe, Thomas; Schütz, Kathrin; Böhme, Herbert

2000-01-01

130

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

Microsoft Academic Search

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

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

1998-01-01

131

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

PubMed

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

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

2005-02-01

132

The Bidirectional NiFe-hydrogenase in Synechocystis sp. PCC 6803 Is Reduced by Flavodoxin and Ferredoxin and Is Essential under Mixotrophic, Nitrate-limiting Conditions*  

PubMed Central

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

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

2014-01-01

133

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

NASA Astrophysics Data System (ADS)

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

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

2012-07-01

134

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

PubMed Central

Pigeon peas [Cajanus cajan (L.) Millsp.] were grown in soil columns containing 15N-enriched organic matter. Seasonal N2 fixation activity was determined by periodically assaying plants for reduction of C2H2. N2 fixation rose sharply from the first assay period at 51 days after planting to a peak of activity between floral initiation and fruit set. N2 fixation (acetylene reduction) activity dropped concomitantly with pod maturation but recovered after pod harvests. Analysis of 15N content of plant shoots revealed that approximately 91 to 94% of plant N was derived from N2 fixation. The effect of inoculation with hydrogenase-positive and hydrogenase-negative rhizobia was examined. Pigeon peas inoculated with strain P132 (hydrogenase-positive) yielded significantly more total shoot N than other inoculated or uninoculated treatments. However, two other hydrogenase-positive strains did not yield significantly more total shoot N than a hydrogenase-negative strain. The extent of nodulation by inoculum strains compared to indigenous rhizobia was determined by typing nodules according to intrinsic antibiotic resistance of the inoculum strains. The inoculum strains were detected in almost all typed nodules of inoculated plants. Gas samples were taken from soil columns several times during the growth cycle of the plants. H2 was never detected, even in columns containing pigeon peas inoculated with hydrogenase-negative rhizobia. This was attributed to H2 consumption by soil bacteria. Estimation of N2 fixation by acetylene reduction activity was closest to the direct 15N method when ethylene concentrations in the gas headspace (between the column lid and soil surface) were extrapolated to include the soil pore space as opposed solely to measurement in the headspace. There was an 8-fold difference between the two acetylene reduction assay methods of estimation. Based on a planting density of 15,000 plants per hectare, the direct 15N fixation rates ranged from 67 (noninoculated) to 134 kilograms per hectare, while grain yields ranged from 540 to 825 kilograms per hectare. Grain yields were not increased with N fertilizer. PMID:16663148

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

1983-01-01

135

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

PubMed Central

Background Solar energy is the ultimate energy source on the Earth. The conversion of solar energy into fuels and energy sources can be an ideal solution to address energy problems. The recent discovery of proteorhodopsin in uncultured marine ?-proteobacteria has made it possible to construct recombinant Escherichia coli with the function of light-driven proton pumps. Protons that translocate across membranes by proteorhodopsin generate a proton motive force for ATP synthesis by ATPase. Excess protons can also be substrates for hydrogen (H2) production by hydrogenase in the periplasmic space. In the present work, we investigated the effect of the co-expression of proteorhodopsin and hydrogenase on H2 production yield under light conditions. Results Recombinant E. coli BL21(DE3) co-expressing proteorhodopsin and [NiFe]-hydrogenase from Hydrogenovibrio marinus produced ~1.3-fold more H2 in the presence of exogenous retinal than in the absence of retinal under light conditions (70 ?mole photon/(m2·s)). We also observed the synergistic effect of proteorhodopsin with endogenous retinal on H2 production (~1.3-fold more) with a dual plasmid system compared to the strain with a single plasmid for the sole expression of hydrogenase. The increase of light intensity from 70 to 130 ?mole photon/(m2·s) led to an increase (~1.8-fold) in H2 production from 287.3 to 525.7 mL H2/L-culture in the culture of recombinant E. coli co-expressing hydrogenase and proteorhodopsin in conjunction with endogenous retinal. The conversion efficiency of light energy to H2 achieved in this study was ~3.4%. Conclusion Here, we report for the first time the potential application of proteorhodopsin for the production of biohydrogen, a promising alternative fuel. We showed that H2 production was enhanced by the co-expression of proteorhodopsin and [NiFe]-hydrogenase in recombinant E. coli BL21(DE3) in a light intensity-dependent manner. These results demonstrate that E. coli can be applied as light-powered cell factories for biohydrogen production by introducing proteorhodopsin. PMID:22217184

2012-01-01

136

Single crystal EPR study of the Ni center of NiFe hydrogenase  

NASA Astrophysics Data System (ADS)

EPR spectra of single crystals of NiFe hydrogenase from Desulfovibrio vulgaris Miyazaki F were evaluated and yielded the g-tensors of the Ni center for two different states of enzyme. The g-values associated with these states are identical to those measured in frozen solutions for the ready (Ni?B) and the unready (Ni?A) form of the Ni center. Directions of the g-tensor axes were determined relative to the crystal symmetry axes. The obtained changes of g-values and tensor axes orientations between Ni?A and Ni?B can be explained by a structural difference involving modification of a cysteine sulfur ligand.

Geßner, Ch.; Trofanchuk, O.; Kawagoe, K.; Higuchi, Y.; Yasuoka, N.; Lubitz, W.

1996-07-01

137

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

2014-11-01

138

Comprehensive phylogenetic diversity of [FeFe]-hydrogenase genes in termite gut microbiota.  

PubMed

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

139

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, Patrícia; Kellers, Petra; Lindblad, Peter; Styring, Stenbjörn; Magnuson, Ann

2013-01-01

140

Enhanced oxygen-tolerance of the full heterotrimeric membrane-bound [NiFe]-hydrogenase of Ralstonia eutropha.  

PubMed

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

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

2014-06-18

141

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, Bärbel; Maier, Robert J.; Gunn, John S.; Hardt, Wolf-Dietrich

2014-01-01

142

Characterization of a [2Fe-2S] protein encoded in the iron-hydrogenase operon of Thermotoga maritima.  

PubMed

Thermotoga maritima grows optimally at 80 degrees C by fermenting carbohydrates to organic acids, CO(2), and H(2). The production of H(2) is catalyzed by a cytoplasmic, heterotrimeric (alphabetagamma) Fe-hydrogenase. This is encoded by three genes, hydC (gamma), hydB (beta) and hydA (alpha), organized within a single operon that contains five additional open reading frames (ORFs). The recombinant form of the first ORF of the operon, TM1420, was produced in Escherichia coli. It has a molecular mass of 8537+/-3 Da as determined by mass spectrometry, in agreement with the predicted amino acid sequence. Purified TM1420 is red in color, has a basic p I (8.8), and contains 1.9 Fe atoms/mol that are present as a single [2Fe-2S] cluster, as determined by UV-visible absorption and EPR spectroscopy. The protein contains five cysteine residues, but their arrangement is characteristic of a subunit or domain rather than of a ferredoxin-type protein. The reduction potential of the [2Fe-2S] cluster (-233 mV at pH 6.5 and 25 degrees C) is pH independent but decreases linearly with temperature to -296 mV (-1.15 mV/ degrees C) at 80 degrees C. TM1420 is not reduced, in vitro, by the Fe-hydrogenase nor by a pyruvate ferredoxin oxidoreductase. The protein was unstable at 70 degrees C under anaerobic conditions with a half-life of approximately 30 min. The basic nature of TM1420, its instability at the growth temperature of T. maritima, and the unusual spacing of its cysteine residues suggest that this protein does not function as a ferredoxin-type electron carrier for the Fe-hydrogenase. Instead, TM1420 is more likely part of a thermostable multi-protein complex that is involved in metal cluster assembly of the hydrogenase holoenzyme. PMID:12605255

Pan, Guangliang; Menon, Angeli Lal; Adams, Michael W W

2003-04-01

143

Participation of hyf-encoded hydrogenase 4 in molecular hydrogen release coupled with proton-potassium exchange in Escherichia coli.  

PubMed

In a previous work (Trchounian et al., Biol. Membrany 16:416-428 (1999) (in Russian)) we reported the interrelations between production of H2 and H+-K+ exchange in fermenting Escherichia coli grown under anaerobic conditions at pH 7.5. The ion fluxes had stable stoichiometry 2H+/K+ and were N,N'-dicyclohexylcarbodiimide (DCC)-inhibitable at different external pH and K+ activity. In the present study, the H2 production was further studied in fermenting bacteria grown at pH 7.5 or 6.5. The H2 production was inhibited by DCC and did not occur if bacteria were grown at pH 7.5 in a medium containing formate or upon hypoosmotic stress. The H2 production was not sensitive to osmotic stress when bacteria were grown at pH 6.5. Formation of H2 and 2H+/K+ exchange were not observed in mutants with deletions of the hyfoperon genes, encoding membrane-associated hydrogenase 4. K+ influx in these mutants was not sensitive to valinomycin, in contrast to the K+ influx in the parental strain. If grown at pH 6.5, the mutants produced H2 and carried out 2H+/K+ exchange, when subjected to the hyperosmotic stress. The results suggest a participation of hydrogenase 4 in the production of H2 and proton-potassium exchange in fermenting E. coli grown at pH 7.5. In bacteria grown at pH 6.5 or in a medium containing formate, another membrane-bound hydrogenase, namely hydrogenase 3, may be responsible for the H2 production. PMID:11817571

Bagramyan, K; Vassilian, A; Mnatsakanyan, N; Trchounian, A

2001-01-01

144

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

145

Hydrogenase genes from Rhizobium leguminosarum bv. viciae are controlled by the nitrogen fixation regulatory protein nifA.  

PubMed

Rhizobium leguminosarum bv. viciae expresses an uptake hydrogenase in symbiosis with peas (Pisum sativum) but, unlike all other characterized hydrogen-oxidizing bacteria, cannot express it in free-living conditions. The hydrogenase-specific transcriptional activator gene hoxA described in other species was shown to have been inactivated in R. leguminosarum by accumulation of frameshift and deletion mutations. Symbiotic transcription of hydrogenase structural genes hupSL originates from a -24/-12 type promoter (hupSp). A regulatory region located in the -173 to -88 region was essential for promoter activity in R. leguminosarum. Activation of hupSp was observed in Klebsiella pneumoniae and Escherichia coli cells expressing the K. pneumoniae nitrogen fixation regulator NifA, and in E. coli cells expressing R. meliloti NifA. This activation required direct interaction of NifA with the essential -173 to -88 regulatory region. However, no sequences resembling known NifA-binding sites were found in or around this region. NifA-dependent activation was also observed in R. etli bean bacteroids. NifA-dependent hupSp activity in heterologous hosts was also absolutely dependent on the RpoN sigma-factor and on integration host factor. Proteins immunologically related to integration host factor were identified in R. leguminosarum. The data suggest that hupSp is structurally and functionally similar to nitrogen fixation promoters. The requirement to coordinate nitrogenase-dependent H2 production and H2 oxidation in nodules might be the reason for the loss of HoxA in R. leguminosarum and the concomitant NifA control of hup gene expression. This evolutionary acquired control would ensure regulated synthesis of uptake hydrogenase in the most common H2-rich environment for rhizobia, the legume nodule. PMID:9177161

Brito, B; Martínez, M; Fernández, D; Rey, L; Cabrera, E; Palacios, J M; Imperial, J; Ruiz-Argüeso, T

1997-06-10

146

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

147

Molecular Dynamics Study of the Proposed Proton Transport Pathways in [FeFe]-Hydrogenase  

SciTech Connect

Possible proton channels in Clostridium pasteurianum [FeFe]-hydrogenase were investigated with molecular dynamics simulations. This study was undertaken to discern proposed channels, compare their properties, evaluate the functional channel, and to provide insight into the features of an active proton channel. Our simulations suggest that protons are not transported through water wires. Instead, a five-residue motif (E282, S319, E279, HOH, C299) was found to be the likely channel, consistent with experimental observations. This channel connects the surface of the enzyme and the di-thiomethylamine bridge of the catalytic H-cluster, permitting the transport of protons. The channel was found to have a persistent hydrogen bonded core (residues E279 to S319), with less persistent hydrogen bonds at the ends of the channel. The hydrogen bond occupancy in this network was found to be sensitive to the protonation state of the residues in the channel, with different protonation states enhancing or stabilizing hydrogen bonding in different regions of the network. Single site mutations to non-hydrogen bonding residues break the hydrogen bonding network at that residue, consistent with experimental observations showing catalyst inactivation. In many cases, these mutations alter the hydrogen bonding in other regions of the channel which may be equally important in catalytic failure. A correlation between the protein dynamics near the proton channel and the redox partner binding regions was also found as a function of protonation state. The likely mechanism of proton movement in [FeFe]-hydrogenases is discussed based on the structural analysis presented here. This work was funded by the DOE Office of Science Early Career Research Program through the Office of Basic Energy Sciences. Computational resources were provided at W. R. Wiley Environmental Molecular Science Laboratory (EMSL), a national scientific user facility sponsored by the Department of Energy’s Office of Biological and Environmental Research located at Pacific Northwest National Laboratory, and a portion of the research was performed using PNNL Institutional Computing at Pacific Northwest National Laboratory. Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy.

Ginovska-Pangovska, Bojana; Ho, Ming-Hsun; Linehan, John C.; Cheng, Yuhui; Dupuis, Michel; Raugei, Simone; Shaw, Wendy J.

2014-01-15

148

Protonation, electrochemical properties and molecular structures of halogen-functionalized diiron azadithiolate complexes related to the active site of iron-only hydrogenases.  

PubMed

Diiron complexes [{(micro-SCH2)2NCH2C6H4X}{Fe(CO)2L}2] (L = CO, X = 2-Br, 1; 2-F, 2; 3-Br, 3; L = PMe(3), X = 2-Br, 4) were prepared as biomimetic models of the iron-only hydrogenase active site. The N-protonated species [(NH)]+ClO(4)(-), [(NH)](+)ClO(4)(-) and the micro-hydride diiron complex [4(FeHFe)]+PF(6)(-) were obtained in the presence of proton acids and well characterized. The protonation process of 4 was studied by in-situ IR and NMR spectroscopy, which suggests the formation of the diprotonated species [4(NH)(FeHFe)](2+) in the presence of an excess of proton acid. The molecular structures of 1, [(NH)]+ClO(4)(-), 4 and [4(FeHFe)]+PF(6)(-) were determined by X-ray crystallography. The single-crystal X-ray analysis reveals that an intramolecular H...Br contact (2.82 A) in the crystalline state of [1(NH)]+ClO(4)(-). In the presence of 1-6 equiv of the stronger acid HOTf, complex 1 is readily protonated on the bridged-N atom and can electrochemically catalyze the proton reduction at a relatively mild potential (ca.-1.0 V). Complex 4 is also electrocatalytic active at -1.4 V in the presence of HOTf with formation of the micro-hydride diiron species. PMID:17712448

Wang, Fujun; Wang, Mei; Liu, Xiaoyang; Jin, Kun; Dong, Weibing; Sun, Licheng

2007-09-14

149

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

PubMed Central

The genes encoding the periplasmic [Fe] hydrogenase from Desulfovibrio vulgaris subsp. oxamicus Monticello were cloned by exploiting their homology with the hydAB genes from D. vulgaris subsp. vulgaris Hildenborough, in which this enzyme is present as a heterologous dimer of alpha and beta subunits. Nucleotide sequencing showed that the enzyme is encoded by an operon in which the gene for the 46-kilodalton (kDa) alpha subunit precedes that of the 13.5-kDa beta subunit, exactly as in the Hildenborough strain. The pairs of hydA and hydB genes are highly homologous; both alpha subunits (420 amino acid residues) share 79% sequence identity, while the unprocessed beta subunits (124 and 123 amino acid residues, respectively) share 71% sequence identity. In contrast, there appears to be no sequence homology outside these coding regions, with the exception of a possible promoter element, which was found approximately 90 base pairs upstream from the translational start of the hydA gene. The recently discovered hydC gene, which may code for a 65.8-kDa fusion protein (gamma) of the alpha and beta subunits and is present immediately downstream from the hydAB genes in the Hildenborough strain, was found to be absent from the Monticello strain. The implication of this result for the possible function of the hydC gene product in Desulfovibrio species is discussed. Images PMID:2661538

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

1989-01-01

150

Characterization of the frhAGB-encoding hydrogenase from a non-methanogenic hyperthermophilic archaeon.  

PubMed

The F420-reducing hydrogenase has been known as a key enzyme in methanogenesis. Its homologs have been identified in non-methanogenic hyperthermophilic archaea, including Thermococcus onnurineus NA1, but neither physiological function nor biochemical properties have been reported to date. The enzyme of T. onnurineus NA1 was distinguished from those of other methanogens and the members of the family Desulfurobacteriaceae with respect to the phylogenetic distribution of the ? and ? subunits, organization of frhAGB genes and conservation of F420-coordinating residues. RT-qPCR and Western blot analyses revealed frhA gene is not silent but is expressed in T. onnurineus NA1 grown in the presence of sulfur, carbon monoxide, or formate. The trimeric enzyme complex was purified to homogeneity via affinity chromatography from T. onnurineus NA1 and exhibited catalytic activity toward the electron acceptors such as viologens and flavins but not the deazaflavin coenzyme F420. This is the first biochemical study on the function of the frhAGB-encoding enzyme from a non-methanogenic archaea. PMID:25142159

Jeon, Jeong Ho; Lim, Jae Kyu; Kim, Min-Sik; Yang, Tae-Jun; Lee, Seong-Hyuk; Bae, Seung Seob; Kim, Yun Jae; Lee, Sang Hee; Lee, Jung-Hyun; Kang, Sung Gyun; Lee, Hyun Sook

2015-01-01

151

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

152

Crystal Structure of HydG from Carboxydothermus hydrogenoformans: A Trifunctional [FeFe]-Hydrogenase Maturase.  

PubMed

The structure of the radical S-adenosyl-L-methionine (SAM) [FeFe]-hydrogenase maturase HydG involved in CN(-) /CO synthesis is characterized by two internal tunnels connecting its tyrosine-binding pocket with the external medium and the C-terminal Fe4 S4 cluster-containing region. A comparison with a tryptophan-bound NosL structure suggests that substrate binding causes the closing of the first tunnel and, along with mutagenesis studies, that tyrosine binds to HydG with its amino group well positioned for H-abstraction by SAM. In this orientation the dehydroglycine (DHG) fragment caused by tyrosine C??C? bond scission can readily migrate through the second tunnel towards the C-terminal domain where both CN(-) and CO are synthesized. Our HydG structure appears to be in a relaxed state with its C-terminal cluster CysX2 CysX22 Cys motif exposed to solvent. A rotation of this domain coupled to Fe4 S4 cluster assembly would bury its putatively reactive unique Fe ion thereby allowing it to interact with DHG. PMID:25504963

Nicolet, Yvain; Pagnier, Adrien; Zeppieri, Laura; Martin, Lydie; Amara, Patricia; Fontecilla-Camps, Juan C

2015-02-01

153

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

PubMed

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

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

2007-02-01

154

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

PubMed

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

Ogata, Hideaki; Kellers, Petra; Lubitz, Wolfgang

2010-09-17

155

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

PubMed

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

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

2014-03-14

156

FnrN controls symbiotic nitrogen fixation and hydrogenase activities in Rhizobium leguminosarum biovar viciae UPM791.  

PubMed

Rhizobium leguminosarum bv. viciae UPM791 contains a second copy of the fnrN gene, which encodes a redox-sensitive transcriptional activator functionally homologous to Escherichia coli Fnr. This second copy (fnrN2) is located in the symbiotic plasmid, while fnrN1 is in the chromosome. Isolation and sequencing of the fnrN2 gene revealed that the deduced amino acid sequence of FnrN2 is 87.5% identical to the sequence of FnrN1, including a conserved cysteine-rich motif characteristic of Fnr-like proteins. Individual R. leguminosarum fnrN1 and fnrN2 mutants exhibited a Fix+ phenotype and near wild-type levels of nitrogenase and hydrogenase activities in pea (Pisum sativum L.) nodules. In contrast, an fnrN1 fnrN2 double mutant formed ineffective nodules lacking both nitrogenase and hydrogenase activities. Unlike the wild-type strain and single fnrN1 or fnrN2 mutants, the fnrN1 fnrN2 double mutant was unable to induce micro-oxic or bacteroid activation of the hypBFCDEX operon, which encodes proteins essential for hydrogenase synthesis. In the search for symbiotic genes that could be controlled by FnrN, a fixNOQP operon, putatively encoding a micro-oxically induced, bacteroid-specific cbb3-type terminal cytochrome oxidase, was isolated from strain UPM791 and partially sequenced. The fixNOQP operon was present in a single copy located in the symbiotic plasmid, and an anaerobox was identified in the fixN promoter region. Consistent with this, a fixNOQP'-lacZ fusion was shown to be highly induced in micro-oxic cells of the wild-type strain. A high level of micro-oxic induction was also observed in single fnrN1 and fnrN2 mutants, but no detectable induction was observed in the fnrN1 fnrN2 double mutant. The lack of expression of fixNOQP in the fnrN1 fnrN2 double mutant is likely to cause the observed Fix- phenotype. These data demonstrate that, contrary to the situation in other rhizobia, FnrN controls both hydrogenase and nitrogenase activities of R. leguminosarum bv. viciae UPM791 in the nodule and suggest that this strain lacks a functional fixK gene. PMID:9286975

Gutiérrez, D; Hernando, Y; Palacios, J M; Imperial, J; Ruiz-Argüeso, T

1997-09-01

157

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

PubMed Central

The hupT gene, which represses hydrogenase gene expression in the purple photosynthetic bacterium Rhodobacter capsulatus, has been identified and sequenced. The nucleotide sequence of hupT and of the contiguous downstream open reading frame, hupU, is reported. The HupT protein of 456 amino acids (48,414 Da) has sequence similarity with the FixL, DctB, NtrB, and ArcB proteins and is predicted to be a soluble sensor kinase. Insertional inactivation of the hupT gene led to deregulation of transcriptional control, so that the hydrogenase structural operon hupSLC became overexpressed in cells grown anaerobically or aerobically. The HupT- mutants were complemented in trans by a plasmid containing an intact copy of the hupT gene. The hupU open reading frame, capable of encoding a protein of 84,879 Da, shared identity with [NiFe]hydrogenase subunits; the strongest similarity was observed with the periplasmic hydrogenase of Desulfovibrio baculatus. Images PMID:8226687

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

1993-01-01

158

The hydrogenase-like Nar1p is essential for maturation of cytosolic and nuclear iron–sulphur proteins  

PubMed Central

The genome of the yeast Saccharomyces cerevisiae encodes the essential protein Nar1p that is conserved in virtually all eukaryotes and exhibits striking sequence similarity to bacterial iron-only hydrogenases. A human homologue of Nar1p was shown previously to bind prenylated prelamin A in the nucleus. However, yeast neither exhibits hydrogenase activity nor contains nuclear lamins. Here, we demonstrate that Nar1p is predominantly located in the cytosol and contains two adjacent iron–sulphur (Fe/S) clusters. Assembly of its Fe/S clusters crucially depends on components of the mitochondrial Fe/S cluster biosynthesis apparatus such as the cysteine desulphurase Nfs1p, the ferredoxin Yah1p and the ABC transporter Atm1p. Using functional studies in vivo, we show that Nar1p is required for maturation of cytosolic and nuclear, but not of mitochondrial, Fe/S proteins. Nar1p-depleted cells do not accumulate iron in mitochondria, distinguishing these cells from mutants in components of the mitochondrial Fe/S cluster biosynthesis apparatus. In conclusion, Nar1p represents a crucial, novel component of the emerging cytosolic Fe/S protein assembly machinery that catalyses an essential and ancient process in eukaryotes. PMID:15103330

Balk, Janneke; Pierik, Antonio J; Netz, Daili J Aguilar; Mühlenhoff, Ulrich; Lill, Roland

2004-01-01

159

Cloning and sequencing of a putative Escherichia coli [NiFe] hydrogenase-1 operon containing six open reading frames.  

PubMed Central

DNA encompassing the structural genes of an Escherichia coli [NiFe] hydrogenase has been cloned and sequenced. The genes were identified as those encoding the large and small subunits of hydrogenase isozyme 1 based on NH2-terminal sequences of purified subunits (kindly provided by K. Francis and K. T. Shanmugam). The structural genes formed part of a putative operon that contained four additional open reading frames. We have designated the operon hya and the six open reading frames hyaA through F. hyaA and hyaB encode the small and large structural subunits, respectively. The nucleotide-derived amino acid sequence of hyaC has a calculated molecular mass of 27.6 kilodaltons, contains 20% aromatic residues, and has four potential membrane-spanning regions. Open reading frames hyaD through F could encode polypeptides of 21.5, 14.9, and 31.5 kilodaltons, respectively. These putative peptides have no homology to other reported protein sequences, and their functions are unknown. Images FIG. 2 FIG. 3 PMID:2180913

Menon, N K; Robbins, J; Peck, H D; Chatelus, C Y; Choi, E S; Przybyla, A E

1990-01-01

160

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

161

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, Hervé; Squier, Thomas C.; Zachara, John M.; Fredrickson, James K.

2011-01-01

162

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, Bärbel

2011-01-01

163

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

E-print Network

-phase density functional theory calculations are used to predict the solutionphase infrared spectra for a series of CO and CN-containing dinuclear iron complexes dithiolate. It is shown that simple linear scaling of the computed C-O and C-N stretching...

Tye, Jesse Wayne

2009-05-15

164

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

E-print Network

.; Andrade, S. L. A.; Schmid, B.; Yoshida, M.; Howard, J. B.; Rees, D. C. Science 2002, 297, 1696-1700. (4 of feedstock and environmental considerations continue to * E-mail: rauchfuz@uiuc.edu. (1) Rees, D. C. Annu. ReV. Biochem. 2002, 71, 221-246. (2) Thauer, R. K. Science 2001, 293, 1264-1265. (3) Einsle, O.; Tezcan, A

Rauchfuss, Thomas B.

165

A possible iron delivery function of the dinuclear iron center of HcgD in [Fe]-hydrogenase cofactor biosynthesis.  

PubMed

HcgD, a homolog of the ubiquitous Nif3-like protein family, is found in a gene cluster involved in the biosynthesis of the iron-guanylylpyridinol (FeGP) cofactor of [Fe]-hydrogenase. The presented crystal structure and biochemical analyses indicated that HcgD has a dinuclear iron-center, which provides a pronounced binding site for anionic ligands. HcgD contains a stronger and a weaker bound iron; the latter being removable by chelating reagents preferentially in the oxidized state. Therefore, we propose HcgD as an iron chaperone in FeGP cofactor biosynthesis, which might also stimulate investigations on the functionally unknown but physiologically important eukaryotic Nif3-like protein family members. PMID:24931373

Fujishiro, Takashi; Ermler, Ulrich; Shima, Seigo

2014-08-25

166

Modulation of Active Site Electronic Structure by the Protein Matrix to Control [NiFe] Hydrogenase Reactivity  

SciTech Connect

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.

Smith, Dayle MA; Raugei, Simone; Squier, Thomas C.

2014-09-30

167

[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

168

[FeFe]-Hydrogenase Abundance and Diversity along a Vertical Redox Gradient in Great Salt Lake, USA  

PubMed Central

The use of [FeFe]-hydrogenase enzymes for the biotechnological production of H2 or other reduced products has been limited by their sensitivity to oxygen (O2). Here, we apply a PCR-directed approach to determine the distribution, abundance, and diversity of hydA gene fragments along co-varying salinity and O2 gradients in a vertical water column of Great Salt Lake (GSL), UT. The distribution of hydA was constrained to water column transects that had high salt and relatively low O2 concentrations. Recovered HydA deduced amino acid sequences were enriched in hydrophilic amino acids relative to HydA from less saline environments. In addition, they harbored interesting variations in the amino acid environment of the complex H-cluster metalloenzyme active site and putative gas transfer channels that may be important for both H2 transfer and O2 susceptibility. A phylogenetic framework was created to infer the accessory cluster composition and quaternary structure of recovered HydA protein sequences based on phylogenetic relationships and the gene contexts of known complete HydA sequences. Numerous recovered HydA are predicted to harbor multiple N- and C-terminal accessory iron-sulfur cluster binding domains and are likely to exist as multisubunit complexes. This study indicates an important role for [FeFe]-hydrogenases in the functioning of the GSL ecosystem and provides new target genes and variants for use in identifying O2 tolerant enzymes for biotechnological applications. PMID:25464382

Boyd, Eric S.; Hamilton, Trinity L.; Swanson, Kevin D.; Howells, Alta E.; Baxter, Bonnie K.; Meuser, Jonathan E.; Posewitz, Matthew C.; Peters, John W.

2014-01-01

169

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

170

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

171

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 Central

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

1985-01-01

172

Analysis and comparison of nucleotide sequences encoding the genes for (NiFe) and (NiFeSe) hydrogenases from Desulfovibrio gigas and Desulfovibrio baculatus  

SciTech Connect

The nucleotide sequences encoding the (NiFe) hydrogenase from Desulfovibrio gigas and the (NiFeSe) hydrogenase from Desulfovibrio baculatus were analyzed by the codon usage method of Staden and McLachlan. The reported reading frames were found to contain regions of low codon probability which are matched by more probable sequences in other frames. Renewed nucleotide sequencing showed the probable frames to be correct. The corrected sequences of the two small and large subunits share a significant degree of sequence homology. The small subunit, which contains 10 conserved cysteine residues, is likely to coordinate at least 2 iron-sulfur clusters, while the finding of a selenocystein codon (TGA) near the 3{prime} end of the (NiFeSe) large-subunit gene matched by a regular cysteine codon (TGC) in the (NiFe) large subunit gene indicates the presence of some of the ligands to the active-site nickel in the large subunit.

Voordouw, G. (Univ. of Calgary, Alberta (Canada)); Menon, N.K.; LeGall, J.; Euisung Choi; Peck, H.D. Jr.; Przybyla, A.E. (Univ. of Georgia, Athens (United States))

1989-05-01

173

Impact of the Iron-Sulfur Cluster Proximal to the Active Site on the Catalytic Function of an O2-Tolerant NAD(+)-Reducing [NiFe]-Hydrogenase.  

PubMed

The soluble NAD(+)-reducing hydrogenase (SH) from Ralstonia eutropha H16 belongs to the O2-tolerant subtype of pyridine nucleotide-dependent [NiFe]-hydrogenases. To identify molecular determinants for the O2 tolerance of this enzyme, we introduced single amino acids exchanges in the SH small hydrogenase subunit. The resulting mutant strains and proteins were investigated with respect to their physiological, biochemical, and spectroscopic properties. Replacement of the four invariant conserved cysteine residues, Cys41, Cys44, Cys113, and Cys179, led to unstable protein, strongly supporting their involvement in the coordination of the iron-sulfur cluster proximal to the catalytic [NiFe] center. The Cys41Ser exchange, however, resulted in an SH variant that displayed up to 10% of wild-type activity, suggesting that the coordinating role of Cys41 might be partly substituted by the nearby Cys39 residue, which is present only in O2-tolerant pyridine nucleotide-dependent [NiFe]-hydrogenases. Indeed, SH variants carrying glycine, alanine, or serine in place of Cys39 showed increased O2 sensitity compared to that of the wild-type enzyme. Substitution of further amino acids typical for O2-tolerant SH representatives did not greatly affect the H2-oxidizing activity in the presence of O2. Remarkably, all mutant enzymes investigated by electron paramagnetic resonance spectroscopy did not reveal significant spectral changes in relation to wild-type SH, showing that the proximal iron-sulfur cluster does not contribute to the wild-type spectrum. Interestingly, exchange of Trp42 by serine resulted in a completely redox-inactive [NiFe] site, as revealed by infrared spectroscopy and H2/D(+) exchange experiments. The possible role of this residue in electron and/or proton transfer is discussed. PMID:25517969

Karstens, Katja; Wahlefeld, Stefan; Horch, Marius; Grunzel, Miriam; Lauterbach, Lars; Lendzian, Friedhelm; Zebger, Ingo; Lenz, Oliver

2015-01-20

174

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

175

Exposure studies of core-shell Fe/Fe(3)O(4) and Cu/CuO NPs to lettuce (Lactuca sativa) plants: Are they a potential physiological and nutritional hazard?  

PubMed

Iron and copper nanomaterials are widely used in environmental remediation and agriculture. However, their effects on physiological parameters and nutritional quality of terrestrial plants such as lettuce (Lactuca sativa) are still unknown. In this research, 18-day-old hydroponically grown lettuce seedlings were treated for 15 days with core-shell nanoscale materials (Fe/Fe(3)O(4), Cu/CuO) at 10 and 20mg/L, and FeSO(4)·7H(2)O and CuSO(4)·5H(2)O at 10mg/L. At harvest, Fe, Cu, micro and macronutrients were determined by ICP-OES. Also, we evaluated chlorophyll content, plant growth, and catalase (CAT) and ascorbate peroxidase (APX) activities. Our results showed that iron ions/NPs did not affect the physiological parameters with respect to water control. Conversely, Cu ions/NPs reduced water content, root length, and dry biomass of the lettuce plants. ICP-OES results showed that nano-Cu/CuO treatments produced significant accumulation of Cu in roots compared to the CuSO(4)·5H(2)O treatment. In roots, all Cu treatments increased CAT activity but decreased APX activity. In addition, relative to the control, nano-Cu/CuO altered the nutritional quality of lettuce, since the treated plants had significantly more Cu, Al and S but less Mn, P, Ca, and Mg. PMID:24462971

Trujillo-Reyes, J; Majumdar, S; Botez, C E; Peralta-Videa, J R; Gardea-Torresdey, J L

2014-02-28

176

Control of the Transition between Ni-C and Ni-SIa States by the Redox State of the Proximal Fe?S Cluster in the Catalytic Cycle of [NiFe] Hydrogenase.  

PubMed

[NiFe] hydrogenase catalyzes the reversible cleavage of H2 . The electrons produced by the H2 cleavage pass through three Fe-S clusters in [NiFe] hydrogenase to its redox partner. It has been reported that the Ni-SIa , Ni-C, and Ni-R states of [NiFe] hydrogenase are involved in the catalytic cycle, although the mechanism and regulation of the transition between the Ni-C and Ni-SIa states remain unrevealed. In this study, the FT-IR spectra under light irradiation at 138-198?K show that the Ni-L state of [NiFe] hydrogenase is an intermediate between the transition of the Ni-C and Ni-SIa states. The transition of the Ni-C state to the Ni-SIa state occurred when the proximal [Fe4 S4 ]p (2+/+) cluster was oxidized, but not when it was reduced. These results show that the catalytic cycle of [NiFe] hydrogenase is controlled by the redox state of its [Fe4 S4 ]p (2+/+) cluster, which may function as a gate for the electron flow from the NiFe active site to the redox partner. PMID:25297065

Tai, Hulin; Nishikawa, Koji; Suzuki, Masayuki; Higuchi, Yoshiki; Hirota, Shun

2014-12-01

177

The hydrogenase gene cluster of Rhizobium leguminosarum bv. viciae contains an additional gene (hypX), which encodes a protein with sequence similarity to the N10-formyltetrahydrofolate-dependent enzyme family and is required for nickel-dependent hydrogenase processing and activity.  

PubMed

Plasmid pAL618 contains the genetic determinants for H2 uptake (hup) from Rhizobium leguminosarum bv. viciae, including a cluster of 17 genes named hupSLCDEFGHIJK-hypABFCDE. A 1.7-kb segment of insert DNA located downstream of hypE has now been sequenced, thus completing the sequence of the 20441-bp insert DNA in plasmid pAL618. An open reading frame (designated hypX) encoding a protein with a calculated M(r) of 62300 that exhibits extensive sequence similarity with HoxX from Alcaligenes eutrophus (52% identity) and Bradyrhizobium japonicum (57% identity) was identified 10 bp downstream of hypE. Nodule bacteroids produced by hypX mutants in pea (Pisum sativum L.) plants grown at optimal nickel concentrations (100 microM) for hydrogenase expression, exhibited less than 5% of the wild-type levels of hydrogenase activity. These bacteroids contained wild-type levels of mRNA from hydrogenase structural genes (hupSL) but accumulated large amounts of the immature form of HupL protein. The Hup-deficient mutants were complemented for normal hydrogenase activity and nickel-dependent maturation of HupL by a hypX gene provided in trans. From expression analysis of hypX-lacZ fusion genes, it appears that hypX gene is transcribed from the FnrN-dependent hyp promoter, thus placing hypX in the hyp operon (hypBFCDEX). Comparisons of the HypX/HoxX sequences with those in databases provided unexpected insights into their function in hydrogenase synthesis. Similarities were restricted to two distinct regions in the HypX/HoxX sequences. Region I, corresponding to a sequence conserved in N10-formyltetrahydrofolate-dependent enzymes involved in transferring one-carbon units (C1), was located in the N-terminal half of the protein, whereas region II, corresponding to a sequence conserved in enzymes of the enoyl-CoA hydratase/isomerase family, was located in the C-terminal half. These similarities strongly suggest that HypX/HoxX have dual functions: binding of the C1 donor N10-formyltetrahydrofolate and transfer of the C1 to an unknown substrate, and catalysis of a reaction involving polarization of the C = O bond of an X-CO-SCoA substrate. These results also suggest the involvement of a small organic molecule, possibly synthesized with the participation of an X-CO-SCoA precursor and of formyl groups, in the synthesis of the metal-containing active centre of hydrogenase. PMID:8842143

Rey, L; Fernández, D; Brito, B; Hernando, Y; Palacios, J M; Imperial, J; Ruiz-Argüeso, T

1996-09-13

178

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

179

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

180

Enhanced nematic and antiferromagnetic phases in the spin-fermion model for strained iron pnictides  

NASA Astrophysics Data System (ADS)

The effects of anisotropic superexchange and Fe-Fe hoppings on phase transitions in the undoped three-orbital spin-fermion model are investigated to understand the experimentally reported strain effect in BaFe2As2. Monte Carlo simulated phase diagrams show that both the collinear antiferromagnetic and nematic transitions shift toward high temperature with the increasing magnitude of anisotropies, qualitatively consistent with experimental observation. Thus, both the anisotropic superexchange and Fe-Fe hoppings are suggested to be responsible for the variation of the transition temperatures of BaFe2As2 with uniaxial stress. In addition, we observed a 90 degree rotation of the collinear antiferromagnetic order, accompanied with a reversal of the orbital occupancy at the Fermi surface when the sign of the superexchange anisotropy changes, further supporting previous predictions by first principles calculation.

Qin, Minghui; Dong, Shuai; Liu, Junming; Ren, Zhifeng

2015-01-01

181

Branched Polyethylenimine Improves Hydrogen Photoproduction from a CdSe Quantum Dot/[FeFe]-Hydrogenase Mimic System in Neutral Aqueous Solutions.  

PubMed

Nature uses hydrogenase enzyme to catalyze proton reduction at pH?7 with overpotentials and catalytic efficiencies that rival platinum electrodes. Over the past several years, [FeFe]-hydrogenase ([FeFe]-H2 ase) mimics have been demonstrated to be effective catalysts for light-driven H2 evolution. However, it remains a significant challenge to realize H2 production by such an artificial photosynthetic system in neutral aqueous solution. Herein, we report a new system for photocatalytic H2 evolution working in a broad pH range, especially under neutral conditions. This unique system is consisted of branched polyethylenimine (PEI)-grafted [FeFe]-H2 ase mimic (PEI-g-Fe2 S2 ), MPA-CdSe quantum dots (MPA=mercaptopropionic acid), and ascorbic acid (H2 A) in water. Due to the secondary coordination sphere of PEI, which has high buffering capacity and stabilizing ability, the system is able to produce H2 under visible-light irradiation with turnover number of 10?600 based on the Fe2 S2 active site in PEI-g-Fe2 S2 . The stability and activity are much better than that of the same system under acidic or basic conditions and they are, to the best of our knowledge, the highest known to date for photocatalytic H2 evolution from a [FeFe]-H2 ase mimic in neutral aqueous solution. PMID:25572459

Liang, Wen-Jing; Wang, Feng; Wen, Min; Jian, Jing-Xin; Wang, Xu-Zhe; Chen, Bin; Tung, Chen-Ho; Wu, Li-Zhu

2015-02-16

182

NADP-Specific Electron-Bifurcating [FeFe]-Hydrogenase in a Functional Complex with Formate Dehydrogenase in Clostridium autoethanogenum Grown on CO  

PubMed Central

Flavin-based electron bifurcation is a recently discovered mechanism of coupling endergonic to exergonic redox reactions in the cytoplasm of anaerobic bacteria and archaea. Among the five electron-bifurcating enzyme complexes characterized to date, one is a heteromeric ferredoxin- and NAD-dependent [FeFe]-hydrogenase. We report here a novel electron-bifurcating [FeFe]-hydrogenase that is NADP rather than NAD specific and forms a complex with a formate dehydrogenase. The complex was found in high concentrations (6% of the cytoplasmic proteins) in the acetogenic Clostridium autoethanogenum autotrophically grown on CO, which was fermented to acetate, ethanol, and 2,3-butanediol. The purified complex was composed of seven different subunits. As predicted from the sequence of the encoding clustered genes (fdhA/hytA-E) and from chemical analyses, the 78.8-kDa subunit (FdhA) is a selenocysteine- and tungsten-containing formate dehydrogenase, the 65.5-kDa subunit (HytB) is an iron-sulfur flavin mononucleotide protein harboring the NADP binding site, the 51.4-kDa subunit (HytA) is the [FeFe]-hydrogenase proper, and the 18.1-kDa (HytC), 28.6-kDa (HytD), 19.9-kDa (HytE1), and 20.1-kDa (HytE2) subunits are iron-sulfur proteins. The complex catalyzed both the reversible coupled reduction of ferredoxin and NADP+ with H2 or formate and the reversible formation of H2 and CO2 from formate. We propose the complex to have two functions in vivo, namely, to normally catalyze CO2 reduction to formate with NADPH and reduced ferredoxin in the Wood-Ljungdahl pathway and to catalyze H2 formation from NADPH and reduced ferredoxin when these redox mediators get too reduced during unbalanced growth of C. autoethanogenum on CO (E0? = ?520 mV). PMID:23893107

Wang, Shuning; Huang, Haiyan; Kahnt, Jörg; Mueller, Alexander P.; Köpke, Michael

2013-01-01

183

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

184

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

185

Physiology and Bioenergetics of [NiFe]-Hydrogenase 2-Catalyzed H2-Consuming and H2-Producing Reactions in Escherichia coli.  

PubMed

Escherichia coli uptake hydrogenase 2 (Hyd-2) catalyzes the reversible oxidation of H2 to protons and electrons. Hyd-2 synthesis is strongly upregulated during growth on glycerol or on glycerol-fumarate. Membrane-associated Hyd-2 is an unusual heterotetrameric [NiFe]-hydrogenase that lacks a typical cytochrome b membrane anchor subunit, which transfers electrons to the quinone pool. Instead, Hyd-2 has an additional electron transfer subunit, termed HybA, with four predicted iron-sulfur clusters. Here, we examined the physiological role of the HybA subunit. During respiratory growth with glycerol and fumarate, Hyd-2 used menaquinone/demethylmenaquinone (MQ/DMQ) to couple hydrogen oxidation to fumarate reduction. HybA was essential for electron transfer from Hyd-2 to MQ/DMQ. H2 evolution catalyzed by Hyd-2 during fermentation of glycerol in the presence of Casamino Acids or in a fumarate reductase-negative strain growing with glycerol-fumarate was also shown to be dependent on both HybA and MQ/DMQ. The uncoupler carbonyl cyanide m-chlorophenylhydrazone (CCCP) inhibited Hyd-2-dependent H2 evolution from glycerol, indicating the requirement for a proton gradient. In contrast, CCCP failed to inhibit H2-coupled fumarate reduction. Although a Hyd-2 enzyme lacking HybA could not catalyze Hyd-2-dependent H2 oxidation or H2 evolution in whole cells, reversible H2-dependent reduction of viologen dyes still occurred. Finally, hydrogen-dependent dye reduction by Hyd-2 was reversibly inhibited in extracts derived from cells grown in H2 evolution mode. Our findings suggest that Hyd-2 switches between H2-consuming and H2-producing modes in response to the redox status of the quinone pool. Hyd-2-dependent H2 evolution from glycerol requires reverse electron transport. PMID:25368299

Pinske, Constanze; Jaroschinsky, Monique; Linek, Sabine; Kelly, Ciarán L; Sargent, Frank; Sawers, R Gary

2015-01-15

186

X-ray crystallographic and EPR spectroscopic analysis of HydG, a maturase in [FeFe]-hydrogenase H-cluster assembly.  

PubMed

Hydrogenases use complex metal cofactors to catalyze the reversible formation of hydrogen. In [FeFe]-hydrogenases, the H-cluster cofactor includes a diiron subcluster containing azadithiolate, three CO, and two CN(-) ligands. During the assembly of the H cluster, the radical S-adenosyl methionine (SAM) enzyme HydG lyses the substrate tyrosine to yield the diatomic ligands. These diatomic products form an enzyme-bound Fe(CO)x(CN)y synthon that serves as a precursor for eventual H-cluster assembly. To further elucidate the mechanism of this complex reaction, we report the crystal structure and EPR analysis of HydG. At one end of the HydG (??)8 triosephosphate isomerase (TIM) barrel, a canonical [4Fe-4S] cluster binds SAM in close proximity to the proposed tyrosine binding site. At the opposite end of the active-site cavity, the structure reveals the auxiliary Fe-S cluster in two states: one monomer contains a [4Fe-5S] cluster, and the other monomer contains a [5Fe-5S] cluster consisting of a [4Fe-4S] cubane bridged by a ?2-sulfide ion to a mononuclear Fe(2+) center. This fifth iron is held in place by a single highly conserved protein-derived ligand: histidine 265. EPR analysis confirms the presence of the [5Fe-5S] cluster, which on incubation with cyanide, undergoes loss of the labile iron to yield a [4Fe-4S] cluster. We hypothesize that the labile iron of the [5Fe-5S] cluster is the site of Fe(CO)x(CN)y synthon formation and that the limited bonding between this iron and HydG may facilitate transfer of the intact synthon to its cognate acceptor for subsequent H-cluster assembly. PMID:25605932

Dinis, Pedro; Suess, Daniel L M; Fox, Stephen J; Harmer, Jenny E; Driesener, Rebecca C; De La Paz, Liliana; Swartz, James R; Essex, Jonathan W; Britt, R David; Roach, Peter L

2015-02-01

187

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

188

Replication ofBacteriophage SH133inthe Facultative Autotroph Hydrogenomonas facilis II.Bacteriophage Synthesis andHydrogenase Induction UnderStep-Up andStep-Down GrowthConditions  

Microsoft Academic Search

Autotrophically grown infected cells areabletoreplicate phageSH-133after beingswitched toa heterotrophic environment (step-up growth). Theeffect of step-down growth on phagereplication varies withthechoice oforganic sub- strate. Phagereplication andtheinduction ofcellular hydrogenase occur un- derstep-down growth fromacetate butnotpeptonebroth. Therequirement of a continued source ofenergy forphagereplication ineither heterotroph- ically or autotrophically grown cells couldbeuniquely demonstrated inthis phage-host systembythedeletion ofhydrogen fromthegrowth medium.

GARY M. ARON; CHRISTINEF. POOTJES

1973-01-01

189

An Innovative Cloning Platform Enables Large-Scale Production and Maturation of an Oxygen-Tolerant [NiFe]-Hydrogenase from Cupriavidus necator in Escherichia coli  

PubMed Central

Expression of multiple heterologous genes in a dedicated host is a prerequisite for approaches in synthetic biology, spanning from the production of recombinant multiprotein complexes to the transfer of tailor-made metabolic pathways. Such attempts are often exacerbated, due in most cases to a lack of proper directional, robust and readily accessible genetic tools. Here, we introduce an innovative system for cloning and expression of multiple genes in Escherichia coli BL21 (DE3). Using the novel methodology, genes are equipped with individual promoters and terminators and subsequently assembled. The resulting multiple gene cassettes may either be placed in one vector or alternatively distributed among a set of compatible plasmids. We demonstrate the effectiveness of the developed tool by production and maturation of the NAD+reducing soluble [NiFe]-hydrogenase (SH) from Cupriavidus necator H16 (formerly Ralstonia eutropha H16) in E. coli BL21Star™ (DE3). The SH (encoded in hoxFUYHI) was successfully matured by co-expression of a dedicated set of auxiliary genes, comprising seven hyp genes (hypC1D1E1A2B2F2X) along with hoxW, which encodes a specific endopeptidase. Deletion of genes involved in SH maturation reduced maturation efficiency substantially. Further addition of hoxN1, encoding a high-affinity nickel permease from C. necator, considerably increased maturation efficiency in E. coli. Carefully balanced growth conditions enabled hydrogenase production at high cell-densities, scoring mg·(Liter culture)?1 yields of purified functional SH. Specific activities of up to 7.2±1.15 U·mg?1 were obtained in cell-free extracts, which is in the range of the highest activities ever determined in C. necator extracts. The recombinant enzyme was isolated in equal purity and stability as previously achieved with the native form, yielding ultrapure preparations with anaerobic specific activities of up to 230 U·mg?1. Owing to the combinatorial power exhibited by the presented cloning platform, the system might represent an important step towards new routes in synthetic biology. PMID:23861944

Schiffels, Johannes; Pinkenburg, Olaf; Schelden, Maximilian; Aboulnaga, El-Hussiny A. A.; Baumann, Marcus E. M.; Selmer, Thorsten

2013-01-01

190

Molecular and biochemical characterization of two tungsten- and selenium-containing formate dehydrogenases from Eubacterium acidaminophilum that are associated with components of an iron-only hydrogenase.  

PubMed

Two gene clusters encoding similar formate dehydrogenases (FDH) were identified in Eubacterium acidaminophilum. Each cluster is composed of one gene coding for a catalytic subunit ( fdhA-I, fdhA-II) and one for an electron-transferring subunit ( fdhB-I, fdhB-II). Both fdhA genes contain a TGA codon for selenocysteine incorporation and the encoded proteins harbor five putative iron-sulfur clusters in their N-terminal region. Both FdhB subunits resemble the N-terminal region of FdhA on the amino acid level and contain five putative iron-sulfur clusters. Four genes thought to encode the subunits of an iron-only hydrogenase are located upstream of the FDH gene cluster I. By sequence comparison, HymA and HymB are predicted to contain one and four iron-sulfur clusters, respectively, the latter protein also binding sites for FMN and NAD(P). Thus, HymA and HymB seem to represent electron-transferring subunits, and HymC the putative catalytic subunit containing motifs for four iron-sulfur clusters and one H-cluster specific for Fe-only hydrogenases. HymD has six predicted transmembrane helices and might be an integral membrane protein. Viologen-dependent FDH activity was purified from serine-grown cells of E. acidaminophilum and the purified protein complex contained four subunits, FdhA and FdhB, encoded by FDH gene cluster II, and HymA and HymB, identified after determination of their N-terminal sequences. Thus, this complex might represent the most simple type of a formate hydrogen lyase. The purified formate dehydrogenase fraction contained iron, tungsten, a pterin cofactor, and zinc, but no molybdenum. FDH-II had a two-fold higher K(m) for formate (0.37 mM) than FDH-I and also catalyzed CO(2) reduction to formate. Reverse transcription (RT)-PCR pointed to increased expression of FDH-II in serine-grown cells, supporting the isolation of this FDH isoform. The fdhA-I gene was expressed as inactive protein in Escherichia coli. The in-frame UGA codon for selenocysteine incorporation was read in the heterologous system only as stop codon, although its potential SECIS element exhibited a quite high similarity to that of E. coli FDH. PMID:12560990

Graentzdoerffer, Andrea; Rauh, David; Pich, Andreas; Andreesen, Jan R

2003-01-01

191

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

192

High yield purification of a tagged cytoplasmic [NiFe]-hydrogenase and a catalytically-active nickel-free intermediate form.  

PubMed

The cytoplasmic [NiFe]-hydrogenase I (SHI) of the hyperthermophile Pyrococcus furiosus evolves hydrogen gas (H2) from NADPH. It has been previously used for biohydrogen production from sugars using a mixture of enzymes in an in vitro cell-free synthetic pathway. The theoretical yield (12 H2/glucose) is three times greater than microbial fermentation (4 H2/glucose), making the in vitro approach very promising for large scale biohydrogen production. Further development of this process at an industrial scale is limited by the availability of the H2-producing SHI. To overcome the obstacles of the complex biosynthetic and maturation pathway for the [NiFe] site of SHI, the four gene operon encoding the enzyme was overexpressed in P. furiosus and included a polyhistidine affinity tag. The one-step purification resulted in a 50-fold increase in yield compared to the four-step purification procedure for the native enzyme. A trimeric form was also identified that lacked the [NiFe]-catalytic subunit but catalyzed NADPH oxidation with a specific activity similar to that of the tetrameric form. The presence of an active trimeric intermediate confirms the proposed maturation pathway where, in the terminal step, the NiFe-containing catalytic subunit assembles with NADPH-oxidizing trimeric form to give the active holoenzyme. PMID:25462812

Chandrayan, Sanjeev K; Wu, Chang-Hao; McTernan, Patrick M; Adams, Michael W W

2015-03-01

193

Applications of X-ray absorption spectroscopy to biologically relevant metal-based chemistry  

NASA Astrophysics Data System (ADS)

Recent developments in the understanding of the biosynthesis of the active site of the nitrogenase enzyme, the structure of the iron centre of [Fe]-hydrogenase and the structure and biomimetic chemistry of the [FeFe] hydrogenase H-cluster as deduced by application of X-ray spectroscopy are reviewed. The techniques central to this work include X-ray absorption spectroscopy either in the form of extended X-ray absorption fine structure (EXAFS), X-ray absorption near-edge structure (XANES) and nuclear resonant vibrational spectroscopy (NRVS). Examples of the advances in the understanding of the chemistry of the system through integration of a range of spectroscopic and computational techniques with X-ray spectroscopy are highlighted. The critical role played by ab initio calculation of structural and spectroscopic properties of transition-metal compounds using density functional theory (DFT) is illustrated both by the calculation of nuclear resonance vibrational spectroscopy (NRVS) spectra and the structures and spectra of intermediates through the catalytic reactions of hydrogenase model compounds.

Best, Stephen P.; Cheah, Mun Hon

2010-02-01

194

E-pharmacophore and molecular dynamics study of flavonols and dihydroflavonols as inhibitors against DiHydroOrotate DeHydrogenase.  

PubMed

DiHydroOrotate DeHydrogenase [huDHODH] is a therapeutic target for Rheumatoid arthritis [RA]. Leflunomide [A771726] is a widely used synthetic inhibitor against huDHODH. We to find more efficient lead like compounds. A four featured E-Pharmacophore A1D4H6R7 was built based on the inhibitor A771726. This pharmacophore was validated by checking its ability to identify known highly active inhibitors of huDHODH and assigning higher fitness scores to them. A reverse validation was also performed where random 4 featured pharmacophores were built and its efficiency in identifying actives was compared with our E-Pharmacophore. Our Epharmacophore was very efficient, since it passed both validations by picking the known active molecules with high fitness scores. This validated E- pharmacophore was searched against the KEGG phytochemicals subset database. This search resulted in 18 molecules which were subjected to docking with huDHODH. The molecules with docking score greater than that of A771726 were selected. The docking results were further validated using MM/GBSA which gave similar ranking with high binding free energy values. The four molecules 6-Methoxytaxifolin, Rhamnetin, Rhamnazin and Pinoquercetin were taken for explicit 3ns simulation and it was observed that all four molecules had acceptable RMSD values and stable interactions. Thus our study, suggests four phytomolecules that might inhibit huDHODH more efficiently than A771726. Interestingly, some of the obtained hits have already been proven in vitro anti-inflammatory activity which confirms that, the developed E-pharmacophore can be used to identify novel small molecules against inflammatory target, huDHODH. PMID:24655039

Swaminathan, Priya; Kalva, Sukesh; Saleena, Lilly M

2014-01-01

195

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

196

Computer Modeling in Biotechnology  

NASA Astrophysics Data System (ADS)

Computational modeling can be a useful partner in biotechnology, in particular, in nanodevice engineering. Such modeling guides development through nanoscale views of biomolecules and devices not available through experimental imaging methods. We illustrate the role of computational modeling, mainly of molecular dynamics, through four case studies: development of silicon bionanodevices for single molecule electrical recording, development of carbon nano-tube-biomolecular systems as in vivo sensors, development of lipoprotein nanodiscs for assays of single membrane proteins, and engineering of oxygen tolerance into the enzyme hydrogenase for photosynthetic hydrogen gas production. The four case studies show how molecular dynamics approaches were adapted to the specific technical uses through (i) multi-scale extensions, (ii) fast quantum chemical force field evaluation, (iii) coarse graining, and (iv) novel sampling methods. The adapted molecular dynamics simulations provided key information on device behavior and revealed development opportunities, arguing that the "computational microscope" is an indispensable nanoengineering tool.

Aksimentiev, Aleksei; Brunner, Robert; Cohen, Jordi; Comer, Jeffrey; Cruz-Chu, Eduardo; Hardy, David; Rajan, Aruna; Shih, Amy; Sigalov, Grigori; Yin, Ying; Schulten, Klaus

197

Modulation of the electronic structure and the NiFe distance in heterobimetallic models for the active site in [NiFe]hydrogenase  

Microsoft Academic Search

Reaction of the mononuclear Ni(II) thiolate complexes [Ni(L)] [L, L1, H2L1, bis(2-mercaptoethyl)-1,2-dimercaptoethane; L2, H2L2, N,N'-dimethyl-N,N'-bis(2-mercaptoethyl)-bis(aminoethyl)sulfide] with [FeCp(CO)2I] gives the dithiolate-bridged heterobimetallic species, [Ni(L1)FeCp(CO)]PF6, 1, and [Ni(L2)FeCp]I, 2, respectively. Binding of a Fe(CO)3 fragment via reaction of square-planar [Ni(pdt)(dppe)] (dppe, 1,2-diphenylphosphinoethane; pdt2-, 1,3-propanedithiolate) with Fe3(CO)12 or [Fe(CO)3(BDA)] (BDA, benzylidene acetone) affords diamagnetic [(dppe)Ni(mu-pdt)Fe(CO)3], 3, in which the Ni(II) center is bound

Wenfeng Zhu; Andrew C. Marr; Qiang Wang; Frank Neese; Douglas J. E. Spencer; Alexander J. Blake; Paul A. Cooke; Claire Wilson; Martin Schröder; Jack Halpern

2005-01-01

198

Functionalization of robust Zr(iv)-based metal-organic framework films via a postsynthetic ligand exchange.  

PubMed

A facile and efficient fabrication approach for homogeneous, crack-free UiO-66 films with exceptionally high crystallinity and tunable thickness on a transparent and conductive glass substrate is reported. Two functionalized species, a catechol ligand and a Fe2 complex with structural resemblance to the active site of [FeFe] hydrogenase, were introduced into the MOF films via a postsynthetic exchange. Voltammetric studies show the [FeFe] complex in the thinner UiO-66 films (2-5 ?m) can be reduced electrochemically. PMID:25364799

Fei, Honghan; Pullen, Sonja; Wagner, Andreas; Ott, Sascha; Cohen, Seth M

2015-01-01

199

Structural and spectroscopic features of mixed valent Fe(II)Fe(I) complexes and factors related to the rotated configuration of diiron hydrogenase.  

PubMed

The compounds of this study have yielded to complementary structural, spectroscopic (Mössbauer, EPR/ENDOR, IR), and computational probes that illustrate the fine control of electronic and steric features that are involved in the two structural forms of (?-SRS)[Fe(CO)2PMe3]2(0,+) complexes. The installation of bridgehead bulk in the -SCH2CR2CH2S- dithiolate (R = Me, Et) model complexes produces 6-membered FeS2C3 cyclohexane-type rings that produce substantial distortions in Fe(I)Fe(I) precursors. Both the innocent (Fc(+)) and the noninnocent or incipient (NO(+)/CO exchange) oxidations result in complexes with inequivalent iron centers in contrast to the Fe(I)Fe(I) derivatives. In the Fe(II)Fe(I) complexes of S = 1/2, there is complete inversion of one square pyramid relative to the other with strong super hyperfine coupling to one PMe3 and weak SHFC to the other. Remarkably, diamagnetic complexes deriving from isoelectronic replacement of CO by NO(+), {(?-SRS)[Fe(CO)2PMe3] [Fe(CO)(NO)PMe3](+)}, are also rotated and exist in only one isomeric form with the -SCH2CR2CH2S- dithiolates, in contrast to R = H ( Olsen , M. T. ; Bruschi , M. ; De Gioia , L. ; Rauchfuss , T. B. ; Wilson , S. R. J. Am. Chem. Soc. 2008 , 130 , 12021 -12030 ). The results and redox levels determined from the extensive spectroscopic analyses have been corroborated by gas-phase DFT calculations, with the primary spin density either localized on the rotated iron in the case of the S = 1/2 compound, or delocalized over the {Fe(NO)} unit in the S = 0 complex. In the latter case, the nitrosyl has effectively shifted electron density from the Fe(I)Fe(I) bond, repositioning it onto the spin coupled Fe-N-O unit such that steric repulsion is sufficient to induce the rotated structure in the Fe(II)-{Fe(I)((•)NO)}(8) derivatives. PMID:22774845

Hsieh, Chung-Hung; Erdem, Ozlen F; Harman, Scott D; Singleton, Michael L; Reijerse, Edward; Lubitz, Wolfgang; Popescu, Codrina V; Reibenspies, Joseph H; Brothers, Scott M; Hall, Michael B; Darensbourg, Marcetta Y

2012-08-01

200

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

201

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

202

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

by palladium diphosphine indicate a four-step mechanism: oxidative addition of C6H5Br, migratory insertion of C6H5 to C2H 4, b-hydride transfer/olefin elimination of styrene product, and catalyst regeneration by removal of HBr. For the oxidative addition...

Surawatanawong, Panida

2010-07-14

203

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

204

Spin relaxation in antiferromagnetic Fe–Fe dimers slowed down by anisotropic DyIII ions  

PubMed Central

Summary By using Mössbauer spectroscopy in combination with susceptibility measurements it was possible to identify the supertransferred hyperfine field through the oxygen bridges between DyIII and FeIII in a {Fe4Dy2} coordination cluster. The presence of the dysprosium ions provides enough magnetic anisotropy to “block” the hyperfine field that is experienced by the iron nuclei. This has resulted in magnetic spectra with internal hyperfine fields of the iron nuclei of about 23 T. The set of data permitted us to conclude that the direction of the anisotropy in lanthanide nanosize molecular clusters is associated with the single ion and crystal field contributions and 57Fe Mössbauer spectroscopy may be informative with regard to the the anisotropy not only of the studied isotope, but also of elements interacting with this isotope. PMID:24367750

Klöwer, Frederik; Lan, Yanhua; Clérac, Rodolphe; Wolny, Juliusz A; Schünemann, Volker; Anson, Christopher E

2013-01-01

205

Numerical models of the thermomechanical evolution of planetesimals: Application to the acapulcoite-lodranite parent body  

NASA Astrophysics Data System (ADS)

The acapulcoite-lodranite meteorites are members of the primitive achondrite class. The observation of partial melting and resulting partial removal of Fe-FeS indicates that this meteorite group could be an important link between achondrite and iron meteorites, on the one hand, and chondrite meteorites, on the other. Thus, a better understanding of the thermomechanical evolution of the parent body of this meteorite group can help improve our understanding of the evolution of early planetesimals. Here, we use 2-D and 3-D finite-difference numerical models to determine the formation time, initial radius of the parent body of the acapulcoite-lodranite meteorites, and their formation depth inside the body by applying available geochronological, thermal, and textural constraints to our numerical data. Our results indicate that the best fit to the data can be obtained for a parent body with 25-65 km radius, which formed around 1.3 Ma after calcium-aluminum-rich inclusions. The 2-D and 3-D results considering various initial temperatures and the effect of porosity indicate possible formation depths of the acapulcoite-lodranite meteorites of 9-19 and 14-25 km, respectively. Our data also suggest that other meteorite classes could form at different depths inside the same parent body, supporting recently proposed models (Elkins-Tanton et al.

Golabek, Gregor J.; Bourdon, Bernard; Gerya, Taras V.

2014-06-01

206

Cluster molecular orbital description of the electronic structures of mixed-valence iron oxides and silicates  

USGS Publications Warehouse

A molecular orbital description, based on spin-unrestricted X??-scattered wave calculations, is given for the electronic structures of mixed valence iron oxides and silicates. The cluster calculations show that electron hopping and optical intervalence charge-transger result from weak FeFe bonding across shared edges of FeO6 coordination polyhedra. In agreement with Zener's double exchange model, FeFe bonding is found to stabilize ferromagnetic coupling between Fe2+ and Fe3+ cations. ?? 1986.

Sherman, D.M.

1986-01-01

207

[In Process Citation].  

PubMed

The reduction of the Fe(II)Fe(II) complex [Fe2(CO)2{P(OMe)3}2(?(2)-IMe-CH2-IMe)(?-CO)(?-pdt)](2+) (2P(2+); pdt = S(CH2)3S), which is a synthetic model of the H cluster of the [FeFe] hydrogenases in its inactive state, has been investigated electrochemically and theoretically (by density functional theory, DFT) in order to determine the mechanisms, intermediates, and products of the related processes. The electrochemical reduction of 2P(2+) occurs according to an ECE-type reaction where the intervening chemical step is the loss of one P(OMe)3 ligand. This outcome, which is based on cyclic voltammetric experiments, is strongly supported by DFT calculations that provide additional information on the intermediates and the energetics of the reactions involved. The electrochemical reoxidation of the neutral product of the reduction follows an EEC process where the chemical step is the binding of P(OMe)3 to a dicationic intermediate. DFT calculations reveal that this intermediate has an unusual geometry wherein one of the two C-H bonds of a side methylene from the pdt group forms an agostic interaction with one Fe center. This interaction is crucial to stabilize the 32e(-) diferrous center and concomitantly to preserve Fe(II) from binding of weakly coordinating species. Nonetheless, it could be displaced by a relatively stronger electron donor such as H2, which could be relevant for the design of new oxidation catalysts. PMID:25496017

Chouffai, Dounia; Capon, Jean-François; De Gioia, Luca; Pétillon, François Y; Schollhammer, Philippe; Talarmin, Jean; Zampella, Giuseppe

2015-01-01

208

Modelling  

E-print Network

Modeling of technical machines became a standard technique since computer became powerful enough to handle the amount of data relevant to the specific system. Simulation of an existing physical device requires the knowledge of all relevant quantities. Electric fields given by the surrounding boundary as well as magnetic fields caused by coils or permanent magnets have to be known. Internal sources for both fields are sometimes taken into account, such as space charge forces or the internal magnetic field of a moving bunch of charged particles. Used solver routines are briefly described and some bench-marking is shown to estimate necessary computing times for different problems. Different types of charged particle sources will be shown together with a suitable model to describe the physical model. Electron guns are covered as well as different ion sources (volume ion sources, laser ion sources, Penning ion sources, electron resonance ion sources, and H$^-$-sources) together with some remarks on beam transport.

Spädtke, P

2013-01-01

209

ORIGINAL ARTICLE Hydrogenase-independent uptake and metabolism  

E-print Network

from cathodic electrons: Upon chemical inhibition of methanogenesis with 2-bromo-ethane sulfonate corrosion of elemental iron and mild steel by direct uptake of electrons and by the formation of an electrically conductive iron-sulfur-carbonate mineral, in addition to the accelerated corrosion caused

210

Hydrogen Production Using Hydrogenase-Containing Oxygenic Photosynthetic Organisms  

DOEpatents

A reversible physiological process provides for the temporal separation of oxygen evolution and hydrogen production in a microorganism, which includes the steps of growing a culture of the microorganism in medium under illuminated conditions to accumulate an endogenous substrate, depleting from the medium a nutrient selected from the group consisting of sulfur, iron, and/or manganese, sealing the culture from atmospheric oxygen, incubating the culture in light whereby a rate of light-induced oxygen production is equal to or less than a rate of respiration, and collecting an evolved gas. The process is particularly useful to accomplish a sustained photobiological hydrogen gas production in cultures of microorganisms, such as Chlamydomonas reinhardtii.

Melis, A.; Zhang, L.; Benemann, J. R.; Forestier, M.; Ghirardi, M.; Seibert, M.

2006-01-24

211

ORIGINAL ARTICLE [FeFe]-hydrogenase in Yellowstone National Park  

E-print Network

in contact with iron-bearing basalts (Apps and van de Kamp, 1993), through the reduction of water during), and through the radiolysis of water (Lin et al., 2005). Basalt-cata- lyzed H2 production occurs readily

212

Modeling  

NASA Technical Reports Server (NTRS)

A prediction of the future population of satellites, satellite fragments, and assorted spacecraft debris in Earth orbit can be reliably made only after three conditions are satisfied: (1) the size and spatial distributions of these Earth-orbiting objects are established at some present-day time; (2) the processes of orbital evolution, explosions, hypervelocity impact fragmentation, and atmospheric drag are understood; and (3) a reasonable traffic model for the future launch rate of Earth-orbiting objects is assumed. The theoretician will then take these three quantities as input data and will carry through the necessary mathematica and numerical analyses to project the present-day orbital population into the future.

Zook, H. A.

1985-01-01

213

Ion irradiation of Fe-Fe oxide core-shell nanocluster films: Effect of interface on stability of magnetic properties  

SciTech Connect

A cluster deposition method was used to produce films of loosely aggregated nanoclusters (NCs) of Fe core-Fe{sub 3}O{sub 4} shell or fully oxidized Fe{sub 3}O{sub 4}. Films of these NC on Si(100) or MgO(100)/Fe{sub 3}O{sub 4}(100) were irradiated to 10{sup 16} Si{sup 2+}/cm{sup 2} near room temperature using an ion accelerator. Ion irradiation creates structural change in the NC film with corresponding chemical and magnetic changes which depend on the initial oxidation state of the cluster. Films were characterized using magnetometry (hysteresis, first order reversal curves), microscopy (transmission electron, helium ion), and x-ray diffraction. In all cases, the particle sizes increased due to ion irradiation, and when a core of Fe is present, irradiation reduces the oxide shells to lower valent Fe species. These results show that ion irradiated behavior of the NC films depends strongly on the initial nanostructure and chemistry, but in general saturation magnetization decreases slightly.

McCloy, John S.; Jiang, Weilin; Droubay, Timothy C.; Varga, Tamas; Kovarik, Libor [Pacific Northwest National Laboratory, 902 Battelle Blvd., PO Box 999, Richland, Washington 99352 (United States)] [Pacific Northwest National Laboratory, 902 Battelle Blvd., PO Box 999, Richland, Washington 99352 (United States); Sundararajan, Jennifer A.; Kaur, Maninder; Qiang, You [Department of Physics, University of Idaho, Moscow, Idaho 83844 (United States)] [Department of Physics, University of Idaho, Moscow, Idaho 83844 (United States); Burks, Edward C.; Liu, Kai [Department of Physics, University of California, Davis, California 95616 (United States)] [Department of Physics, University of California, Davis, California 95616 (United States)

2013-08-28

214

Ion irradiation of Fe-Fe oxide core-shell nanocluster films: Effect of interface on stability of magnetic properties  

SciTech Connect

A cluster deposition method was used to produce films of loosely aggregated nanoclusters (NC) of Fe core-Fe3O4 shell or fully oxidized Fe3O4. Films of these NC on Si(100) or MgO(100)/Fe3O4(100) were irradiated to 1016 Si2+/cm2 near room temperature using an ion accelerator. Ion irradiation creates structural change in the NC film with corresponding chemical and magnetic changes which depend on the initial oxidation state of the cluster. Films were characterized using magnetometry (hysteresis, first order reversal curves), microscopy (transmission electron, helium ion), and x-ray diffraction. In all cases, the particle sizes increased due to ion irradiation, and when a core of Fe is present, irradiation reduces the oxide shells to lower valent Fe species. These results show that ion irradiated behavior of the nanocluster films depends strongly on the initial nanostructure and chemistry, but in general saturation magnetization decreases slightly.

McCloy, John S.; Jiang, Weilin; Droubay, Timothy C.; Varga, Tamas; Kovarik, Libor; Sundararajan, Jennifer A.; Kaur, Maninder; Qiang, You; Burks, Edward; Liu, Kai

2013-08-23

215

Toward a rigorous network of protein-protein interactions of the model sulfate reducer Desulfovibrio vulgaris Hildenborough  

SciTech Connect

Protein–protein interactions offer an insight into cellular processes beyond what may be obtained by the quantitative functional genomics tools of proteomics and transcriptomics. The aforementioned tools have been extensively applied to study E. coli and other aerobes and more recently to study the stress response behavior of Desulfovibrio 5 vulgaris Hildenborough, a model anaerobe and sulfate reducer. In this paper we present the first attempt to identify protein-protein interactions in an obligate anaerobic bacterium. We used suicide vector-assisted chromosomal modification of 12 open reading frames encoded by this sulfate reducer to append an eight amino acid affinity tag to the carboxy-terminus of the chosen proteins. Three biological replicates of the 10 ‘pulled-down’ proteins were separated and analyzed using liquid chromatography-mass spectrometry. Replicate agreement ranged between 35% and 69%. An interaction network among 12 bait and 90 prey proteins was reconstructed based on 134 bait-prey interactions computationally identified to be of high confidence. We discuss the biological significance of several unique metabolic features of D. vulgaris revealed by this protein-protein interaction data 15 and protein modifications that were observed. These include the distinct role of the putative carbon monoxide-induced hydrogenase, unique electron transfer routes associated with different oxidoreductases, and the possible role of methylation in regulating sulfate reduction.

Chhabra, S.R.; Joachimiak, M.P.; Petzold, C.J.; Zane, G.M.; Price, M.N.; Gaucher, S.; Reveco, S.A.; Fok, V.; Johanson, A.R.; Batth, T.S.; Singer, M.; Chandonia, J.M.; Joyner, D.; Hazen, T.C.; Arkin, A.P.; Wall, J.D.; Singh, A.K.; Keasling, J.D.

2011-05-01

216

Towards a rigorous network of protein-protein interactions of the model sulfate reducer Desulfovibrio vulgaris Hildenborough.  

PubMed

Protein-protein interactions offer an insight into cellular processes beyond what may be obtained by the quantitative functional genomics tools of proteomics and transcriptomics. The aforementioned tools have been extensively applied to study Escherichia coli and other aerobes and more recently to study the stress response behavior of Desulfovibrio vulgaris Hildenborough, a model obligate anaerobe and sulfate reducer and the subject of this study. Here we carried out affinity purification followed by mass spectrometry to reconstruct an interaction network among 12 chromosomally encoded bait and 90 prey proteins based on 134 bait-prey interactions identified to be of high confidence. Protein-protein interaction data are often plagued by the lack of adequate controls and replication analyses necessary to assess confidence in the results, including identification of potential false positives. We addressed these issues through the use of biological replication, exponentially modified protein abundance indices, results from an experimental negative control, and a statistical test to assign confidence to each putative interacting pair applicable to small interaction data studies. We discuss the biological significance of metabolic features of D. vulgaris revealed by these protein-protein interaction data and the observed protein modifications. These include the distinct role of the putative carbon monoxide-induced hydrogenase, unique electron transfer routes associated with different oxidoreductases, and the possible role of methylation in regulating sulfate reduction. PMID:21738675

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

2011-01-01

217

Genome Annotation Provides Insight into Carbon Monoxide and Hydrogen Metabolism in Rubrivivax gelatinosus.  

PubMed

We report here the sequencing and analysis of the genome of the purple non-sulfur photosynthetic bacterium Rubrivivax gelatinosus CBS. This microbe is a model for studies of its carboxydotrophic life style under anaerobic condition, based on its ability to utilize carbon monoxide (CO) as the sole carbon substrate and water as the electron acceptor, yielding CO2 and H2 as the end products. The CO-oxidation reaction is known to be catalyzed by two enzyme complexes, the CO dehydrogenase and hydrogenase. As expected, analysis of the genome of Rx. gelatinosus CBS reveals the presence of genes encoding both enzyme complexes. The CO-oxidation reaction is CO-inducible, which is consistent with the presence of two putative CO-sensing transcription factors in its genome. Genome analysis also reveals the presence of two additional hydrogenases, an uptake hydrogenase that liberates the electrons in H2 in support of cell growth, and a regulatory hydrogenase that senses H2 and relays the signal to a two-component system that ultimately controls synthesis of the uptake hydrogenase. The genome also contains two sets of hydrogenase maturation genes which are known to assemble the catalytic metallocluster of the hydrogenase NiFe active site. Collectively, the genome sequence and analysis information reveals the blueprint of an intricate network of signal transduction pathways and its underlying regulation that enables Rx. gelatinosus CBS to thrive on CO or H2 in support of cell growth. PMID:25479613

Wawrousek, Karen; Noble, Scott; Korlach, Jonas; Chen, Jin; Eckert, Carrie; Yu, Jianping; Maness, Pin-Ching

2014-01-01

218

Genome Annotation Provides Insight into Carbon Monoxide and Hydrogen Metabolism in Rubrivivax gelatinosus  

PubMed Central

We report here the sequencing and analysis of the genome of the purple non-sulfur photosynthetic bacterium Rubrivivax gelatinosus CBS. This microbe is a model for studies of its carboxydotrophic life style under anaerobic condition, based on its ability to utilize carbon monoxide (CO) as the sole carbon substrate and water as the electron acceptor, yielding CO2 and H2 as the end products. The CO-oxidation reaction is known to be catalyzed by two enzyme complexes, the CO dehydrogenase and hydrogenase. As expected, analysis of the genome of Rx. gelatinosus CBS reveals the presence of genes encoding both enzyme complexes. The CO-oxidation reaction is CO-inducible, which is consistent with the presence of two putative CO-sensing transcription factors in its genome. Genome analysis also reveals the presence of two additional hydrogenases, an uptake hydrogenase that liberates the electrons in H2 in support of cell growth, and a regulatory hydrogenase that senses H2 and relays the signal to a two-component system that ultimately controls synthesis of the uptake hydrogenase. The genome also contains two sets of hydrogenase maturation genes which are known to assemble the catalytic metallocluster of the hydrogenase NiFe active site. Collectively, the genome sequence and analysis information reveals the blueprint of an intricate network of signal transduction pathways and its underlying regulation that enables Rx. gelatinosus CBS to thrive on CO or H2 in support of cell growth. PMID:25479613

Wawrousek, Karen; Noble, Scott; Korlach, Jonas; Chen, Jin; Eckert, Carrie; Yu, Jianping; Maness, Pin-Ching

2014-01-01

219

Bioinspired Hydrogenase Models: The Mixed-Valence Triiron Complex [Fe3(CO)7(?-edt)2] and Phosphine Derivatives [Fe3(CO)7-x (PPh3) x (?-edt)2] (x = 1, 2) and [Fe3(CO)5(?(2)-diphosphine)(?-edt)2] as Proton Reduction Catalysts.  

PubMed

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

Rahaman, Ahibur; Ghosh, Shishir; Unwin, David G; Basak-Modi, Sucharita; Holt, Katherine B; Kabir, Shariff E; Nordlander, Ebbe; Richmond, Michael G; Hogarth, Graeme

2014-03-24

220

Modeling modeling.  

PubMed Central

Models are tools; they need to fit both the hand and the task. Presence or absence of a feature such as a pacemaker or a cascade is not in itself good. Or bad. Criteria for model evaluation involve benefit-cost ratios, with the numerator a function of the range of phenomena explained, goodness of fit, consistency with other nearby models, and intangibles such as beauty. The denominator is a function of complexity, the number of phenomena that must be ignored, and the effort necessary to incorporate the model into one's parlance. Neither part of the ratio can yet be evaluated for MTS, whose authors provide some cogent challenges to SET. PMID:10220934

Killeen, P R

1999-01-01

221

Engineering Synechocystis PCC6803 for Hydrogen Production: Influence on the Tolerance to Oxidative and Sugar Stresses  

PubMed Central

In the prospect of engineering cyanobacteria for the biological photoproduction of hydrogen, we have studied the hydrogen production machine in the model unicellular strain Synechocystis PCC6803 through gene deletion, and overexpression (constitutive or controlled by the growth temperature). We demonstrate that the hydrogenase-encoding hoxEFUYH operon is dispensable to standard photoautotrophic growth in absence of stress, and it operates in cell defense against oxidative (H2O2) and sugar (glucose and glycerol) stresses. Furthermore, we showed that the simultaneous over-production of the proteins HoxEFUYH and HypABCDE (assembly of hydrogenase), combined to an increase in nickel availability, led to an approximately 20-fold increase in the level of active hydrogenase. These novel results and mutants have major implications for those interested in hydrogenase, hydrogen production and redox metabolism, and their connections with environmental conditions. PMID:24586727

Ortega-Ramos, Marcia; Jittawuttipoka, Thichakorn; Saenkham, Panatda; Czarnecka-Kwasiborski, Aurelia; Bottin, Hervé; Cassier-Chauvat, Corinne; Chauvat, Franck

2014-01-01

222

Genome sequence of the model sulfate reducer Desulfovibrio gigas: a comparative analysis within the Desulfovibrio genus*  

PubMed Central

Desulfovibrio gigas is a model 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 hydrogenases 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

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

2014-01-01

223

Fe(III).ATP complexes. Models for ferritin and other polynuclear iron complexes with phosphate.  

PubMed

Polynuclear iron complexes of Fe(III) and phosphate occur in seawater and soils and in cells where the iron core of ferritin, the iron storage protein, contains up to 4500 Fe atoms in a complex with an average composition of (FeO.OH)8FeO.OPO3H2. Although phosphate influences the size of the ferritin core and thus the availability of stored iron, little is known about the nature of the Fe(III)-phosphate interaction. In the present study, Fe-phosphate interactions were analyzed in stable complexes of Fe(III).ATP which, in the polynuclear iron form, had phosphate at interior sites. Such Fe(III).ATP complexes are important not only as models but also because they may play a role in intracellular iron transport and in iron toxicity; the complexes were studied by extended x-ray absorption fine structure, EPR, NMR spectroscopy, and measurement of proton release. Mononuclear iron complexes exhibiting a g' = 4.3 EPR signal were formed at Fe:ATP ratios less than or equal to 1:3, and polynuclear iron complexes (Fe greater than or equal to 250, EPR silent at g' = 4.3) were formed at an Fe:ATP ratio of 4:1. No NMR signals due to ATP were observed when Fe was in excess (Fe:ATP = 4:1). Extended x-ray absorption fine structure analysis of the polynuclear Fe(III).ATP complex was able to distinguish an Fe-P distance at 3.27 A in addition to the octahedral O at 1.95 A and 4-5 Fe atoms at 3.36 A. The Fe-O and Fe-Fe distances are the same as in ferritin, and the Fe-P distance is analogous to that in another metal-ATP complex. An observable Fe-P environment in such a large polynuclear iron cluster as the Fe(III).ATP (4:1) complex indicates that the phosphate is distributed throughout rather than merely on the surface, in contrast to earlier models of chelate-stabilized iron clusters. Complexes of Fe(III) and ATP similar to those described here may form in vivo either as normal components of intracellular iron metabolism or during iron excess where the consequent alteration of free nucleotide triphosphate pools could contribute to the observed toxicity of iron. PMID:2989269

Mansour, A N; Thompson, C; Theil, E C; Chasteen, N D; Sayers, D E

1985-07-01

224

Modelling the thermal history of Vesta: time scale of accretion and differentiation.  

NASA Astrophysics Data System (ADS)

Vesta is the only known intact primordial asteroid in the Solar System showing an internal differentiated structure, as inferred by its spectral connection with HED meteorites (Keil et al. 2002, Scott 2007, Coradini et al. 2011). Recent results (Schiller et al. 2011) indicate a faster cooling of the interior of Vesta than previously thought. If confirmed, this would imply that the thermal history of Vesta diverges from the generally accepted picture (Ghosh & Mc Sween 1998). Using the thermal evolution code (Formisano et al. 2011) we developed, we are simulating several thermal and structural evolution scenarios of Vesta, by varying the delay ?td in the injection of 26Al in Vesta, which controls the strength of radiogenic sources. We consider a primordial Vesta as a sphere of radius 270 Km with the initial temperature fixed to 200 K. The initial composition is a homogeneous mixture of silicatic (77%) and metallic (23%) material. Our code solves contemporary the heat equation with the source term (i.e. the energy is supplied by the decay of 26Al, 60Fe ) and the equation for the mass transfer in a porous medium, by using a finite difference 1D method. When the melting temperature of Fe-FeS is reached, the percolation of the iron into the silicatic matrix takes place while, when the melting temperature of silicate is reached, the differentiation and subsequent core formation occur. Since our model does not take in account heat removal mechanisms other than the conduction and the irradiation at the surface, our results supply a reliable picture of the thermal history of Vesta up until the onset of the differentiation. When compared to the data provided by HED meteorites, our results suggest short accretion and differentiation times of Vesta respect to the condensation of CAIs. The scenarios characterized by ?td > 2 Ma show temperatures not reaching the melting temperature of silicate and for this reason they are incompatible with the basaltic magmatism suggest by HEDs (Keil et al. 2002, Bizzarro et al. 2005). In the scenarios with 1.5 Ma < ?td < 2 Ma, silicate melting occurs at about t = 6 Ma: this is incompatible with the crystallization ages of the oldest HEDs (Schiller et al 2011, Bizzarro et al. 2005). Finally, values of ?td < 1 Ma are the most compatible with the geologic history of Vesta as suggested by HEDs.

Formisano, M.; Federico, C.; Turrini, D.; Capaccioni, F.

2012-04-01

225

Involvement of NADH:Acceptor Oxidoreductase and Butyryl Coenzyme A Dehydrogenase in Reversed Electron Transport during Syntrophic Butyrate Oxidation by Syntrophomonas wolfei? †  

PubMed Central

Methanogenic oxidation of butyrate to acetate requires a tight cooperation between the syntrophically fermenting Syntrophomonas wolfei and the methanogen Methanospirillum hungatei, and a reversed electron transport system in S. wolfei was postulated to shift electrons from butyryl coenzyme A (butyryl-CoA) oxidation to the redox potential of NADH for H2 generation. The metabolic activity of butyrate-oxidizing S. wolfei cells was measured via production of formazan and acetate from butyrate, with 2,3,5-triphenyltetrazolium chloride as electron acceptor. This activity was inhibited by trifluoperazine (TPZ), an antitubercular agent known to inhibit NADH:menaquinone oxidoreductase. In cell extracts of S. wolfei, the oxidation of NADH could be measured with quinones, viologens, and tetrazolium dyes as electron acceptors, and also this activity was inhibited by TPZ. The TPZ-sensitive NADH:acceptor oxidoreductase activity appeared to be membrane associated but could be dissociated from the membrane as a soluble protein and was semipurified by anion-exchange chromatography. Recovered proteins were identified by peptide mass fingerprinting, which indicated the presence of an NADH:acceptor oxidoreductase as part of a three-component [FeFe] hydrogenase complex and a selenocysteine-containing formate dehydrogenase. Furthermore, purification of butyryl-CoA dehydrogenase (Bcd) activity and peptide mass fingerprinting revealed two Bcd proteins different from the Bcd subunit of the Bcd/electron-transfer flavoprotein complex (Bcd/EtfAB) predicted from the genome sequence of S. wolfei. The results suggest that syntrophic oxidation of butyrate in S. wolfei involves a membrane-associated TPZ-sensitive NADH:acceptor oxidoreductase as part of a hydrogenase complex similar to the recently discovered “bifurcating” hydrogenase in Thermotoga maritima and butyryl-CoA dehydrogenases that are different from Bcd of the Bcd/EtfAB complex. PMID:19648244

Müller, Nicolai; Schleheck, David; Schink, Bernhard

2009-01-01

226

Interruption of the cydB Locus in Brucella abortus Attenuates Intracellular Survival and Virulence in the Mouse Model of Infection  

PubMed Central

Brucellosis is characterized by abortion in ruminants and a protracted undulant fever in humans, which often results in severe pathological manifestations. Scant information exists about the molecular mechanisms employed by Brucella abortus to combat host defenses or to persist and replicate within host cells. Transposon (Tn5) mutagenesis of B. abortus and the subsequent screening of mutants for sensitivity to killing in murine macrophages and in the mouse model led to the identification of mutants which were severely attenuated for intracellular survival. One group of mutants was interrupted in cydB, a gene that is part of the cydAB operon encoding cytochrome bd oxidase, which catalyzes an alternate terminal electron transport step in bacterial respiration. The elevated affinity for molecular oxygen of this enzyme in Escherichia coli has suggested that it is involved in the protection of sensitive enzymatic activities such as those of hydrogenases and nitrogenases from damage. B. abortus cydB::Tn5 strains exhibited heightened sensitivity to the respiratory inhibitors zinc and azide, highly reactive oxygen species such as hydrogen peroxide, low pH, and attenuated virulence in the mouse model of infection. Virulence was restored by an intact copy of cydAB or by B. abortus genes encoding the oxidative radical-scavenging enzyme Cu/Zn superoxide dismutase or catalase. These results suggest a bifunctional role for the products of the cydAB operon, both in preventing the buildup of oxidative free radicals and in detoxifying the intracellular compartment, thus indicating the importance of these products in preventing intracellular destruction. Intracellular conditions that favor expression of the cydAB operon are under investigation and may be linked to the acid sensitivity also observed in this strain. PMID:11274104

Endley, Seema; McMurray, David; Ficht, Thomas A.

2001-01-01

227

Insights Into the P-To-Q Conversion in the Catalytic Cycle of Methane Monooxygenase From a Synthetic Model System  

SciTech Connect

For the catalytic cycle of soluble methane monooxygenase (sMMO), it has been proposed that cleavage of the O-O bond in the ({mu}-peroxo)diiron(III) intermediate P gives rise to the diiron(IV) intermediate Q with an Fe{sub 2}({mu}-O){sub 2} diamond core, which oxidizes methane to methanol. As a model for this conversion, ({mu}-oxo) diiron(III) complex 1 ([Fe{sup III}{sub 2}({mu}-O)({mu}-O{sub 2}H{sub 3})(L){sub 2}]{sup 3+}, L = tris(3,5-dimethyl-4-methoxypyridyl-2-methyl)amine) has been treated consecutively with one eq of H{sub 2}O{sub 2} and one eq of HClO{sub 4} to form 3 ([Fe{sup IV}{sub 2}({mu}-O){sub 2}(L){sub 2}]{sup 4+}). In the course of this reaction a new species, 2, can be observed before the protonation step; 2 gives rise to a cationic peak cluster by ESI-MS at m/z 1,399, corresponding to the [Fe{sub 2}O{sub 3}L{sub 2}H](OTf){sub 2}{sup +} ion in which 1 oxygen atom derives from 1 and the other two originate from H{sub 2}O{sub 2}. Moessbauer studies of 2 reveal the presence of two distinct, exchange coupled iron(IV) centers, and EXAFS fits indicate a short Fe-O bond at 1.66 {angstrom} and an Fe-Fe distance of 3.32 {angstrom}. Taken together, the spectroscopic data point to an HO-Fe{sup IV}-O-Fe{sup IV} = O core for 2. Protonation of 2 results in the loss of H{sub 2}O and the formation of 3. Isotope labeling experiments show that the [Fe{sup IV}{sub 2}({mu}-O){sub 2}] core of 3 can incorporate both oxygen atoms from H{sub 2}O{sub 2}. The reactions described here serve as the only biomimetic precedent for the conversion of intermediates P to Q in the sMMO reaction cycle and shed light on how a peroxodiiron(III) unit can transform into an [Fe{sup IV}{sub 2}({mu}-O){sub 2}] core.

Xue, G.; Fiedler, A.T.; Martinho, M.; Munck, E.; Que, L.; Jr.

2009-05-28

228

Experimental partitioning studies near the Fe-FeS eutectic, with an emphasis on elements important to iron meteorite chronologies (Pb, Ag, Pd, and Tl)  

NASA Astrophysics Data System (ADS)

Partitioning coefficients for metal/sulfide liquid, troilite/sulfide liquid, and schreibersite/sulfide liquid were determined for Ag, Au, Mo, Ni, Pd, and Tl (using EMPA and proton-induced X-ray microprobe and ion microprobe analyses) in order to understand the chronometer systems of iron meteorites. In general, the obtained schreibersite/metal and troilite/metal partition coefficients for 'compatible' elements were quite similar to those inferred from natural assemblages, reinforcing an earlier made conclusion that there is a class of elements for which experimental troilite/metal and schreibersite/metal partition coefficients approximate those inferred from natural samples. The consistency between experimental and natural assemblages, however, was not observed for Ag, Pb, and Tl, indicating that the abundances of these elements determined in 'metal' and 'troilite' separates from iron meteorites are influenced by trace minerals that concentrate incompatible elements.

Jones, J. H.; Hart, S. R.; Benjamin, T. M.

1993-01-01

229

Change in the magnetic properties of polycrystalline thin-film magnetite upon introduction of an iron sublayer  

NASA Astrophysics Data System (ADS)

The field dependences of the magnetic moment of polycrystalline magnetite films formed by pulsed laser deposition on a silicon substrate with the addition of an iron sublayer have been investigated. The influence of the sequence of layers Fe/Fe3O4 and Fe3O4/Fe on the magnetic characteristics of these structures has been analyzed. It has turned out that an increase in the saturation magnetization and the formation of a rectangular hysteresis loop with the coercive force acceptable for applications of thin-film magnetite as a hard magnetic electrode of the magnetic tunnel junction are observed only for the sequence of layers Fe/Fe3O4. The effect of the vacuum annealing temperature on the magnetic properties of polycrystalline samples of the Fe/Fe3O4 structure has been studied. It has been found that the best result is achieved at an annealing temperature of 500°C. The phenomenological model describing the magnetic properties of the polycrystalline two-layer magnetic structure Fe/Fe3O4 has been formulated. The results of numerical calculations have demonstrated that the introduction of only two phenomenological anisotropic interactions into the expression for the energy of the film provides a qualitative description of the observed experimental data in the form of hysteresis loops.

Anisimov, A. V.; Goikhman, A. Yu.; Kupriyanova, G. S.; Nevolin, V. N.; Popov, A. P.; Rodionova, V. V.

2012-06-01

230

Magnetic resonance and fluorescence studies on pyruvate hydrogenase complexes and their small molecular weight constituents  

Microsoft Academic Search

The articles presented in this thesis do not describe at first glance one well-defined subject. They are, however, in fact connected by one central theme: the study of large enzyme aggregates by molecular physical methods. Chosen was the pyruvate dehydrogenase complex (PDC) because of its physiological importance and because it is, perhaps therefore, one of the most studied multi-enzyme complexes.

H. J. Grande

1976-01-01

231

Chelate Control of Diiron(I) Dithiolates Relevant to the [Fe–Fe]-Hydrogenase Active Site  

PubMed Central

The reaction of Fe2(S2C2H4)(CO)6 with cis-Ph2PCH=CHPPh2 (dppv) yields Fe2(S2C2H4)(CO)4(dppv), 1(CO)4, wherein the dppv ligand is chelated to a single iron center. NMR analysis indicates that in 1(CO)4, the dppv ligand spans axial and basal coordination sites. In addition to the axial–basal isomer, the 1,3-propanedithiolate and azadithiolate derivatives exist as dibasal isomers. Density functional theory (DFT) calculations indicate that the axial–basal isomer is destabilized by nonbonding interactions between the dppv and the central NH or CH2 of the larger dithiolates. The Fe(CO)3 subunit in 1(CO)4 undergoes substitution with PMe3 and cyanide to afford 1(CO)3(PMe3) and (Et4N)[1(CN)(CO)3], respectively. Kinetic studies show that 1(CO)4 reacts faster with donor ligands than does its parent Fe2(S2C2H4)(CO)6. The rate of reaction of 1(CO)4 with PMe3 was first order in each reactant, k = 3.1 × 10? 4 M?1 s?1. The activation parameters for this substitution reaction, ?H‡ = 5.8(5) kcal/mol and ?S‡ = ?48(2) cal/deg·mol, indicate an associative pathway. DFT calculations suggest that, relative to Fe2(S2C2H4)(CO)6, the enhanced electrophilicity of 1(CO)4 arises from the stabilization of a “rotated” transition state, which is favored by the unsymmetrically disposed donor ligands. Oxidation of MeCN solutions of 1(CO)3(PMe3) with Cp2FePF6 yielded [Fe2(S2C2H4)(?-CO)(CO)2(dppv)(PMe3)(NCMe)](PF6)2. Reaction of this compound with PMe3 yielded [Fe2(S2C2H4)(?-CO)(CO)(dppv)(PMe3)2(NCMe)](PF6)2. PMID:17279743

Justice, Aaron K.; Zampella, Giuseppe; De Gioia, Luca; Rauchfuss, Thomas B.; van der Vlugt, Jarl Ivar; Wilson, Scott R.

2008-01-01

232

Classification of the uptake hydrogenase-positive (Hup+) bean rhizobia as Rhizobium tropici.  

PubMed Central

Phenotypic and genetic characterization indicated that Hup+ bean rhizobial strains are type IIA and type IIB Rhizobium tropici. The Hup+ strain USDA 2840, which did not cluster with either of the two types of R. tropici in a restriction fragment length polymorphism analysis, had electrophoretic patterns of PCR products generated with primers for repetitive extragenic palindromic and enterobacterial repetitive intergeneric consensus sequences similar to those of three reference strains of R. tropici type IIA. The Hup+ strain USDA 2738, which clustered with the reference strain of R. tropici IIB in a restriction fragment length polymorphism analysis, had electrophoretic patterns of PCR products generated with primers for repetitive extragenic palindromic and enterobacterial repetitive intergeneric consensus sequences more closely resembling those of the reference strains of R. tropici type IIA than those of type IIB. DNA amplification with the Y1 and Y2 primers to generate a portion of the 16S rDNA operon was useful to distinguish R. tropici type IIA strains from other bean rhizobial strains. The phylogenetic position of the type IIA strain of R. tropici USDA 2840, determined from the partial 16S rDNA sequence, indicated a more distant relationship with the type IIB strain of R. tropici CIAT899 than with the as yet unnamed rhizobial species of Leucaena leucocephala, TAL 1145. Therefore, we suggest that it may be appropriate either to separate R. tropici types IIA and IIB into two different species or to identify TAL 1145 to the species level as a third type of R. tropici. Images PMID:8135515

van Berkum, P; Navarro, R B; Vargas, A A

1994-01-01

233

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

Microsoft Academic Search

Not Available Bibtex entry for this abstract Preferred format for this abstract (see Preferences) Find Similar Abstracts: Use: Authors Title Return: Query Results Return items starting with number Query Form Database: Astronomy Physics arXiv e-prints

Gordon Ng; Curtis G. S. Tom; Angela S. Park; Lounis Zenad; Robert A. Ludwig; Malcolm James Horsburgh

2009-01-01

234

Iron EXAFS of Azotobacter vinelandii nitrogenase Mo-Fe and V-Fe proteins  

SciTech Connect

The structure of the iron sites of nitrogenase in dithionite-reduced and thionine-oxidized forms of the Mo-Fe and V-Fe proteins has been investigated using Fe K-edge X-ray absorption spectroscopy. For the dithionite-reduced Azotobacter vinelandii Mo-Fe protein, the dominant EXAFS Fourier transform peaks are assigned to Fe-S and Fe-Fe interactions at approximately 2.32 and 2.64 [angstrom], as expected for Fe-S clusters. An additional Fe-Mo component at 2.73 [angstrom] is required to completely fit the EXAFS in the 1-3-[angstrom] region. In the 3-5-[angstrom] region, a 3.8-[angstrom] Fe-Fe component is identified, with an amplitude corresponding to almost one long Fe-Fe interaction, averaged over all of the iron in the sample. Features that can be explained as Fe-S and Fe-Fe interactions at 4.3 and 4.7 [angstrom] are also observed. A similar pattern of Fe interactions is observed for the reduced A. vinelandii V-Fe protein, except that the short Fe-Mo interaction is no longer required. In both Mo-Fe and V-Fe proteins, the first coordination sphere Fe-S distances contract slightly upon thionine oxidation. The long-range Fe-S and Fe-Fe interactions are very close (within 0.1 [angstrom]) to corresponding distances in Fe[sub 6]S[sub 6] prismane clusters. If the amplitudes are adjusted by assuming that only 14 of 30 nitrogenase irons participate in the M center, then they are consistent with recently proposed crystallographic models. 43 refs., 7 figs., 2 tabs.

Chen, J. (Lawrence Berkeley Lab., CA (United States)); Christiansen, J.; George, S.J. (Univ. of California, Davis (United States)); Tittsworth, R.C.; Hales, B.J. (Louisiana State Univ., Baton Rouge (United States)); Concouvanis, D. (Univ. of Michigan, Ann Arbor (United States)); Cramer, S.P. (Lawrence Berkeley Lab., CA (United States) Univ. of California, Davis (United States))

1993-06-30

235

Flexibility of Syntrophic Enzyme Systems in Desulfovibrio Species Ensures Their Adaptation Capability to Environmental Changes  

PubMed Central

The mineralization of organic matter in anoxic environments relies on the cooperative activities of hydrogen producers and consumers obligately linked by interspecies metabolite exchange in syntrophic consortia that may include sulfate reducing species such as Desulfovibrio. To evaluate the metabolic flexibility of syntrophic Desulfovibrio to adapt to naturally fluctuating methanogenic environments, we studied Desulfovibrio alaskensis strain G20 grown in chemostats under respiratory and syntrophic conditions with alternative methanogenic partners, Methanococcus maripaludis and Methanospirillum hungatei, at different growth rates. Comparative whole-genome transcriptional analyses, complemented by G20 mutant strain growth experiments and physiological data, revealed a significant influence of both energy source availability (as controlled by dilution rate) and methanogen on the electron transfer systems, ratios of interspecies electron carriers, energy generating systems, and interspecies physical associations. A total of 68 genes were commonly differentially expressed under syntrophic versus respiratory lifestyle. Under low-energy (low-growth-rate) conditions, strain G20 further had the capacity to adapt to the metabolism of its methanogenic partners, as shown by its differing gene expression of enzymes involved in the direct metabolic interactions (e.g., periplasmic hydrogenases) and the ratio shift in electron carriers used for interspecies metabolite exchange (hydrogen/formate). A putative monomeric [Fe-Fe] hydrogenase and Hmc (high-molecular-weight-cytochrome c3) complex-linked reverse menaquinone (MQ) redox loop become increasingly important for the reoxidation of the lactate-/pyruvate oxidation-derived redox pair, DsrCred and Fdred, relative to the Qmo-MQ-Qrc (quinone-interacting membrane-bound oxidoreductase; quinone-reducing complex) loop. Together, these data underscore the high enzymatic and metabolic adaptive flexibility that likely sustains Desulfovibrio in naturally fluctuating methanogenic environments. PMID:23974031

Meyer, Birte; Kuehl, Jennifer V.; Deutschbauer, Adam M.; Arkin, Adam P.

2013-01-01

236

A Comparative Genomic Analysis of Energy Metabolism in Sulfate Reducing Bacteria and Archaea  

PubMed Central

The number of sequenced genomes of sulfate reducing organisms (SRO) has increased significantly in the recent years, providing an opportunity for a broader perspective into their energy metabolism. In this work we carried out a comparative survey of energy metabolism genes found in 25 available genomes of SRO. This analysis revealed a higher diversity of possible energy conserving pathways than classically considered to be present in these organisms, and permitted the identification of new proteins not known to be present in this group. The Deltaproteobacteria (and Thermodesulfovibrio yellowstonii) are characterized by a large number of cytochromes c and cytochrome c-associated membrane redox complexes, indicating that periplasmic electron transfer pathways are important in these bacteria. The Archaea and Clostridia groups contain practically no cytochromes c or associated membrane complexes. However, despite the absence of a periplasmic space, a few extracytoplasmic membrane redox proteins were detected in the Gram-positive bacteria. Several ion-translocating complexes were detected in SRO including H+-pyrophosphatases, complex I homologs, Rnf, and Ech/Coo hydrogenases. Furthermore, we found evidence that cytoplasmic electron bifurcating mechanisms, recently described for other anaerobes, are also likely to play an important role in energy metabolism of SRO. A number of cytoplasmic [NiFe] and [FeFe] hydrogenases, formate dehydrogenases, and heterodisulfide reductase-related proteins are likely candidates to be involved in energy coupling through electron bifurcation, from diverse electron donors such as H2, formate, pyruvate, NAD(P)H, ?-oxidation, and others. In conclusion, this analysis indicates that energy metabolism of SRO is far more versatile than previously considered, and that both chemiosmotic and flavin-based electron bifurcating mechanisms provide alternative strategies for energy conservation. PMID:21747791

Pereira, Inês A. Cardoso; Ramos, Ana Raquel; Grein, Fabian; Marques, Marta Coimbra; da Silva, Sofia Marques; Venceslau, Sofia Santos

2011-01-01

237

Synthesis, Purification, and Characterization of a [mu]-(1,3-Propanedithiolato)-Hexacarbonyldiiron  

ERIC Educational Resources Information Center

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 model for an iron-only hydro-genase. The project provides the students with experience of Schlenk line techniques, purification,…

Works, Carmen F.

2007-01-01

238

NUCLEAR MODELS  

Microsoft Academic Search

As an introduction to the discussion of nuclear models, the Bohr atomic ; model is described. The nuclear model analogous to this atomic model is then ; discussed. Because of the very narrow nuclear levels found by Fermi, the ; compound nucleus model was then proposed. This model was limited in the region ; of very high and very low

Beck

1956-01-01

239

MODEL DEVELOPMENT - DOSE MODELS  

EPA Science Inventory

Model 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...

240

Modeling Malaria  

NSDL National Science Digital Library

In this module, we develop models of the effects of malaria on various populations of humans and mosquitoes. After considering differential equations to model a system, we create a model using the systems modeling tool STELLA. Projects involve various refinements of the model.

Angela B. Shiflet

241

Ionospheric modeling  

Microsoft Academic Search

The purpose of this report is to familiarize a user of ionospheric models with the options presently available for ionospheric prediction and specification. Two types of ionospheric models are available: the numerical-phenomenological and theoretical models. From the numerical type, the ITS-78, IONCAP, and Bent models have been discussed. In the theoretical models the main concern is the number of parameters

B. S. Dandekar

1982-01-01

242

Fair Model  

NSDL National Science Digital Library

The Fair model web site includes a freely available United States macroeconomic econometric model and a multicounty econometric model. The models run on the Windows OS. Instructors can use the models to teach forecasting, run policy experiments, and evaluate historical episodes of macroeconomic behavior. The web site includes extensive documentation for both models. The simulation is for upper-division economics courses in macroeconomics or econometrics. The principle developer is Ray Fair at Yale University.

Blecha, Betty

243

The electron transfer from hydrogenase and formate dehydrogenase to polysulfide reductase in the membrane of Wolinella succinogenes  

Microsoft Academic Search

Freeze-thawing of the membrane fraction of Wolinella succinogenes with sonic liposomes containing vitamin K-1 gave an apparently homogeneous particle preparation. The specific electron transport activity based on membrane protein of these particles with polysulfide as acceptor and formate or H2 as donor decreased hyperbolically with the amount of liposomes fused to the membrane fraction, while the activities of formate dehydrogenase,

Aleksandra Jankielewicz; Oliver Klimmek; Achim Kröger

1995-01-01

244

Molecular hydrogen production by nitrogenase of Rhodobacter sphaeroides and by Fe-only hydrogenase of Rhodospirillum rubrum  

Microsoft Academic Search

The genes coding for two PII-like proteins, GlnB and GlnK, which play key roles in repressing the nitrogenase expression in the presence of ammonium ion, were interrupted from the chromosome of Rhodobacter sphaeroides. The glnB–glnK mutant exhibits the less ammonium ion-mediated repression for nitrogenase compared with its parental strain, which results in more H2 accumulation by the mutant under the

Eui-Jin Kim; Moon-Kyu Lee; Mi-Sun Kim; Jeong K. Lee

2008-01-01

245

Supermatrix models  

SciTech Connect

Radom matrix models based on an integral over supermatrices are proposed as a natural extension of bosonic matrix models. The subtle nature of superspace integration allows these models to have very different properties from the analogous bosonic models. 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 models. Another leads to an eigenvalue reduction which can be described by a two component plasma in one dimension. A stationary point of the model is described.

Yost, S.A.

1991-05-01

246

Effects of an intensive hog farming operation on groundwater in east Mediterranean (II): a study on K?, Na?, Cl ?, PO?³?-P, Ca²?, Mg²?, Fe³?/Fe²?, Mn²?, Cu²?, Zn²? and Ni²?.  

PubMed

The application of treated animal wastewater generated in concentrated animal feeding operations on surface soil (within farm borders) leads to degradation of groundwater. Effects of an intensive hog farming operation, located at a Mediterranean limestone soil coastal area, on groundwater were investigated. Treated animal wastewater was discharged on a small plot (~10.8 ha) with a geologic fault. Samples were taken from seven groundwater monitoring wells close to the farm. A significant increase of K(+), Na(+), Cl(-), PO4 (3-)-P, Ca(2+) and Mg(2+) concentrations was found in monitoring wells which are affected by the subsurface flow of groundwater. Concentrations of Fe(3+)/Fe(2+), Mn(2+), Cu(2+), Zn(2+) and Ni(2+) in all groundwater monitoring wells were extremely low. During the winter, significant increases in concentrations of K(+) and PO4 (3-)-P were noted and attributed to high precipitation, which assisted in the leaching of K and P to groundwater. PMID:25370904

Michalopoulos, Charalampos; Tzamtzis, Nikolaos; Liodakis, Stylianos

2014-12-01

247

Measurement and Calculation of Electrochemical Potentials in Hydrogenated High Temperature Water, including an Evaluation of the Yttria-Stabilized Zirconia/Iron-Iron Oxide (Fe/Fe3O4) Probe as Reference Electrode  

SciTech Connect

The importance of knowing the electrochemical corrosion potential (ECP, also referred to as E{sub con}) of nickel-base alloys in hydrogenated water is related to the need to understand the effects of dissolved (i.e., aqueous) hydrogen concentration ([H{sub 2}]) on primary water stress corrosion cracking (PWSCC). Also, the use of a reference electrode (RE) can improve test quality by heightening the ability to detect instances of out-of-specification or unexpected chemistry. Three methods are used to measure and calculate the ECP of nickel-based alloys in hydrogenated water containing {approx} 1 to 150 scc/kg H{sub 2} (0.1 to 13.6 ppm H{sub 2}) at 260 to 360 C. The three methods are referred to as the specimen/component method, the platinum (Pt) method, and the yttria-stabilized zirconia/iron-iron oxide (YSZ/Fe-Fe{sub 3}O{sub 4}) RE method. The specimen/component method relies upon the assumption that the specimen or component behaves as a hydrogen electrode, and its E{sub corr} is calculated using the Nernst equation. The present work shows that this method is valid for aqueous H{sub 2} levels {ge} {approx} 5 to 10 scc/kg H{sub 2}. The Pt method uses a voltage measurement between the specimen or component and a Pt electrode, with the Pt assumed to behave as a hydrogen electrode; this method is valid as long as the aqueous H{sub 2}level is known. The YSZ/Fe-Fe{sub 3}O{sub 4}, which represents a relatively new approach for measuring E{sub corr} in this environment, can be used even if the aqueous H{sub 2} level is unknown. The electrochemical performance of the YSZ/Fe-Fe{sub 3}O{sub 4} probe supports its viability as a RE for use in high temperature hydrogenated water. Recent design modifications incorporating a teflon sealant have improved the durability of this RE (however, some of the REs do still fail prematurely due to water in-leakage). The Pt method is judged to represent the best overall approach, though there are cases where the other methods are superior. For example, the specimen/component method provides the simplest approach for calculating the E{sub corr} of plant components, and the YSZ/Fe-Fe{sub 3}O{sub 4} RE method provides the best approach if the H{sub 2} level is unknown, or in off-nominal chemistry conditions. The present paper describes the use of these methods to determine the ECP of a specimen or component versus the ECP of the nickel/nickel oxide (Ni/NiO) phase transition, which is important since prior work has shown that this parameter (ECP-ECP{sub Ni/NiO}) can be used to assess aqueous H{sub 2} effects on PWSCC.

Steven A. Attanasio; David S. Morton; Mark A. Ando

2001-10-22

248

Nanocomposite Fe1-xO/Fe3O4, Fe/Fe1-xO thin films prepared by RF sputtering and revealed by magnetic coupling effects  

NASA Astrophysics Data System (ADS)

Magnetic and semi-conducting nanocomposite iron oxide thin films have been prepared under bias polarization, by radio-frequency sputtering of a magnetite target. The nature of the phases obtained in the thin films depends on the bias power density. The increase in power density, from 0 to 110 mW/cm2, allows the preparation of magnetite, magnetite/wustite and wustite/ ?-iron nanocomposites successively. Magnetic measurements at low temperature show exchange bias for two-phases films even though the minor phase is not detected by grazing angle X-ray diffraction. The exchange bias can reach very high values of about 4300 Oe. Electrical properties at room temperature are interpreted taking into account both the modifications of the film compactness, and the nature of the phases from which they are made.

Mauvernay, B.; Presmanes, L.; Bonningue, C.; Tailhades, Ph.

249

MODELS - 3  

EPA Science Inventory

Models-3 is a third generation air quality modeling 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 ...

250

Landscape Models  

NSDL National Science Digital Library

In this assignment students model different scenarios of landscape evolution using an on-line landscape evolution model. The assignment takes them through several situations involving changes in commonly modeled landscape variables like overland flow, faulting and uplift, erosivity, and drainage incision. At the end I have students devise a situation (of variables) that tests a hypothesis or the sensitivity of the model to changes in a variable. Designed for a geomorphology course Uses online and/or real-time data

Marchetti, David

251

Phoenix model  

EPA Science Inventory

Phoenix (formerly referred to as the Second Generation Model or SGM) is a global general equilibrium model designed to analyze energy-economy-climate related questions and policy implications in the medium- to long-term. This model disaggregates the global economy into 26 industr...

252

Animal models.  

PubMed

Epilepsy accounts for a significant portion of the dis-ease burden worldwide. Research in this field is fundamental and mandatory. Animal models 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 models are discussed,with major emphasis on the in vivo studies. Models 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 models have often helped to clarify these differences. In this chapter, developmental aspects have been emphasized.Electrical stimulation and chemical-induced models of seizures have been described first, as they represent the oldest and most common models. Among these models, kindling raised great interest, especially for the study of the epileptogenesis. Acquired focal models 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 models. To date, absence epilepsy is one of the most common and (often) benign forms of epilepsy. There are several models, including acute pharmacological models (PTZ, penicillin, THIP, GBL) and chronic models (GAERS, WAG/Rij). Although atypical absence seizures are less benign, thus needing more investigation, only two models 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 models is recent and fascinating. Different approaches have been used including genetic (Down syndrome,ARX mutation) and acquired (multiple hit, TTX, CRH,betamethasone-NMDA) models.An entire section has been dedicated to genetic models, from the older models obtained with spontaneous mutations (GEPRs) to the new engineered knockout, knocking, and transgenic models. Some of these models 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 model, and the progressive myoclonic epilepsy. The contribution of animal models 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

Coppola, Antonietta; Moshé, Solomon L

2012-01-01

253

Hydrological models are mediating models  

NASA Astrophysics Data System (ADS)

Despite the increasing role of models in hydrological research and decision-making processes, only few accounts of the nature and function of models exist in hydrology. Earlier considerations have traditionally been conducted while making a clear distinction between physically-based and conceptual models. A new philosophical account, primarily based on the fields of physics and economics, transcends classes of models and scientific disciplines by considering models as "mediators" between theory and observations. The core of this approach lies in identifying models as (1) being only partially dependent on theory and observations, (2) integrating non-deductive elements in their construction, and (3) carrying the role of instruments of scientific enquiry about both theory and the world. The applicability of this approach to hydrology is evaluated in the present article. Three widely used hydrological models, each showing a different degree of apparent physicality, are confronted to the main characteristics of the "mediating models" concept. We argue that irrespective of their kind, hydrological models depend on both theory and observations, rather than merely on one of these two domains. Their construction is additionally involving a large number of miscellaneous, external ingredients, such as past experiences, model objectives, knowledge and preferences of the modeller, as well as hardware and software resources. We show that hydrological models convey the role of instruments in scientific practice by mediating between theory and the world. It results from these considerations that the traditional distinction between physically-based and conceptual models is necessarily too simplistic and refers at best to the stage at which theory and observations are steering model construction. The large variety of ingredients involved in model construction would deserve closer attention, for being rarely explicitly presented in peer-reviewed literature. We believe that devoting more importance to identifying and communicating on the many factors involved in model development might increase transparency of model building.

Babel, L. V.; Karssenberg, D.

2013-08-01

254

Model Experiments and Model Descriptions  

NASA Technical Reports Server (NTRS)

The Second Workshop on Stratospheric Models 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 models 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 models as having a reliable prediction for future ozone behavior. This section is divided into two: model experiment and model descriptions. In the model experiment, participant were given the charge to design a number of experiments that would use observations to test whether models 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 model predicted responses of stratospheric ozone to perturbations. The specifications for the experiments were sent out to the modeling community in June 1997. Twenty eight modeling groups responded to the requests for input. The first part of this section discusses the different modeling group, along with the experiments performed. Part two of this section, gives brief descriptions of each model as provided by the individual modeling groups.

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

1999-01-01

255

Station Models  

NSDL National Science Digital Library

This project will allow users to become acquainted with station models that are found on weather maps. Students will study the various atmospheric variables that are depicted on a station model and then practice on an interactive station model program. Part 1 - Being able to read and interpret weather maps is a very important skill in meteorology. One of the most basic skills of predicting the weather is being able to interpret a station model of a given location. A station model is a bundle of information that ...

Ertl, Mr.

2007-11-03

256

Modeling & Simulation  

NSDL National Science Digital Library

Modeling & Simulation is a journal published by The Society for Modeling and Simulation International. The Society has made its 2004 Modeling and Simulation Resource Guide available free to download. The directory provides descriptions and contact information for the many modeling and simulation software packages currently available, as well as listings for various modeling 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.

257

Computer Models  

NSDL National Science Digital Library

This undergraduate meteorology tutorial from Texas A&M University focuses on computer models 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 models: the Eta Model, the Nested Grid model (NGM), the Rapid Update Cycle (RUC), and the Global Forecast System (GFS). Each model 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 models and to read model output.

Nielsen-Gammon, John

1996-01-01

258

ICRF modelling  

SciTech Connect

This lecture provides a survey of the methods used to model fast magnetosonic wave coupling, propagation, and absorption in tokamaks. The validity and limitations of three distinct types of modelling codes, which will be contrasted, include discrete models which utilize ray tracing techniques, approximate continuous field models based on a parabolic approximation of the wave equation, and full field models derived using finite difference techniques. Inclusion of mode conversion effects in these models 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 modelling codes. 52 refs., 15 figs.

Phillips, C.K.

1985-12-01

259

Turbulence modeling  

NASA Technical Reports Server (NTRS)

The performance of existing two-equation eddy viscosity models was examined. An effort was made to develop better models for near-wall turbulence using direct numerical simulations of plane channel and boundary layer flows. The asymptotic near-wall behavior of turbulence was used to examine the problems of current second order closure models and develop new models with the correct near-wall behavior. Rapid Distortion Theory was used to analytically study the effects of mean deformation on turbulence, obtain analytical solutions for the spectrum tensor, Reynolds stress tensor, anisotropy tensor and its invariants, which can be used in the turbulence model development. The potential of the renormalization group theory in turbulence modeling was studied, as well as compressible turbulent flows, and modeling of bypass transition.

Shih, Tsan-Hsing

1991-01-01

260

Metabolic deficiences revealed in the biotechnologically important model bacterium Escherichia coli BL21(DE3).  

PubMed

The Escherichia coli B strain BL21(DE3) has had a profound impact on biotechnology through its use in the production of recombinant proteins. Little is understood, however, regarding the physiology of this important E. coli strain. We show here that BL21(DE3) totally lacks activity of the four [NiFe]-hydrogenases, the three molybdenum- and selenium-containing formate dehydrogenases and molybdenum-dependent nitrate reductase. Nevertheless, all of the structural genes necessary for the synthesis of the respective anaerobic metalloenzymes are present in the genome. However, the genes encoding the high-affinity molybdate transport system and the molybdenum-responsive transcriptional regulator ModE are absent from the genome. Moreover, BL21(DE3) has a nonsense mutation in the gene encoding the global oxygen-responsive transcriptional regulator FNR. The activities of the two hydrogen-oxidizing hydrogenases, therefore, could be restored to BL21(DE3) by supplementing the growth medium with high concentrations of Ni²? (Ni²?-transport is FNR-dependent) or by introducing a wild-type copy of the fnr gene. Only combined addition of plasmid-encoded fnr and high concentrations of MoO?²? ions could restore hydrogen production to BL21(DE3); however, to only 25-30% of a K-12 wildtype. We could show that limited hydrogen production from the enzyme complex responsible for formate-dependent hydrogen evolution was due solely to reduced activity of the formate dehydrogenase (FDH-H), not the hydrogenase component. The activity of the FNR-dependent formate dehydrogenase, FDH-N, could not be restored, even when the fnr gene and MoO?²? were supplied; however, nitrate reductase activity could be recovered by combined addition of MoO?²? and the fnr gene. This suggested that a further component specific for biosynthesis or activity of formate dehydrogenases H and N was missing. Re-introduction of the gene encoding ModE could only partially restore the activities of both enzymes. Taken together these results demonstrate that BL21(DE3) has major defects in anaerobic metabolism, metal ion transport and metalloprotein biosynthesis. PMID:21826210

Pinske, Constanze; Bönn, Markus; Krüger, Sara; Lindenstrauss, Ute; Sawers, R Gary

2011-01-01

261

Functions and Models: Mathematical Models  

NSDL National Science Digital Library

Describe the process of mathematical modeling;Name and describe some methods of modeling;Classify a symbolically represented function as one of the elementary algebraic or transcendental functions;Appraise the suitability of different models for interpreting a given set of data.

Michael Freeze

262

Climate Models  

NASA Technical Reports Server (NTRS)

Climate models 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 modeling studies for a variety of geographic regions by an international roster of authors. The climate research community generally uses the rubric climate models 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 models are integrated over time in order to compute the temporal and spatial variations of these parameters. Model domains can be global or regional and the horizontal and vertical resolutions of the computational grid vary from model to model. Considering the entire climate system requires accounting for interactions between solar insolation, atmospheric, oceanic and continental processes, the latter including land hydrology and vegetation. Model simulations may concentrate on one or more of these components, but the most sophisticated models will estimate the mutual interactions of all of these environments. Advances in computer technology have prompted investments in more complex model 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 model performance. Extensive research is required to test and document any advantages gained by greater sophistication in model formulation. One purpose for publishing climate model research results is to present purported advances for evaluation by the scientific community.

Druyan, Leonard M.

2012-01-01

263

SCARP Model  

NSDL National Science Digital Library

SCARP is the first in a sequence of spreadsheet modeling exercises (SCARP2, LONGPRO, and GLACPRO). In this exercise, students use a simple arithmetic model (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 model. The purpose of the exercise, in addition to the simulation, is to develop basic skills in spreadsheeting and especially in graphical display.

Locke, Bill

264

Atmospheric Modeling  

Microsoft Academic Search

\\u000a Air quality models simulate the atmospheric concentrations and deposition fluxes to the Earth’s surface of air pollutants\\u000a by solving the mass conservation equations that represent the emissions, transport, dispersion, transformations and removal\\u000a of those air pollutants and associated chemical species. Contemporary air quality models can be grouped into two major categories:\\u000a (1) models that calculate the concentrations of air pollutants

Christian Seigneur; Robin Dennis

265

Floodplain Modeling  

NSDL National Science Digital Library

Students explore the impact of changing river volumes and different floodplain terrain in experimental trials with table top-sized riverbed models. The models are made using modeling clay in aluminum baking pans placed on a slight incline. Water added "upstream" at different flow rates and to different riverbed configurations simulates different potential flood conditions. Students study flood dynamics as they modify the riverbed with blockages or levees to simulate real-world scenarios.

Integrated Teaching And Learning Program

266

Cloud Modeling  

NASA Technical Reports Server (NTRS)

Numerical cloud models have been developed and applied extensively to study cloud-scale and mesoscale processes during the past four decades. The distinctive aspect of these cloud models is their ability to treat explicitly (or resolve) cloud-scale dynamics. This requires the cloud models to be formulated from the non-hydrostatic equations of motion that explicitly include the vertical acceleration terms since the vertical and horizontal scales of convection are similar. Such models are also necessary in order to allow gravity waves, such as those triggered by clouds, to be resolved explicitly. In contrast, the hydrostatic approximation, usually applied in global or regional models, does allow the presence of gravity waves. In addition, the availability of exponentially increasing computer capabilities has resulted in time integrations increasing from hours to days, domain grids boxes (points) increasing from less than 2000 to more than 2,500,000 grid points with 500 to 1000 m resolution, and 3-D models becoming increasingly prevalent. The cloud resolving model is now at a stage where it can provide reasonably accurate statistical information of the sub-grid, cloud-resolving processes poorly parameterized in climate models and numerical prediction models.

Tao, Wei-Kuo; Moncrieff, Mitchell; Einaud, Franco (Technical Monitor)

2001-01-01

267

Ventilation Model  

SciTech Connect

The purpose of the Ventilation Model is to simulate the heat transfer processes in and around waste emplacement drifts during periods of forced ventilation. The model evaluates the effects of emplacement drift ventilation on the thermal conditions in the emplacement drifts and surrounding rock mass, and calculates the heat removal by ventilation as a measure of the viability of ventilation to delay the onset of peak repository temperature and reduce its magnitude. The heat removal by ventilation is temporally and spatially dependent, and is expressed as the fraction of heat carried away by the ventilation air compared to the fraction of heat produced by radionuclide decay. One minus the heat removal is called the wall heat fraction, or the remaining amount of heat that is transferred via conduction to the surrounding rock mass. Downstream models, such as the ''Multiscale Thermohydrologic Model'' (BSC 2001), use the wall heat fractions as outputted from the Ventilation Model to initialize their post-closure analyses. The Ventilation Model report was initially developed to analyze the effects of preclosure continuous ventilation in the Engineered Barrier System (EBS) emplacement drifts, and to provide heat removal data to support EBS design. Revision 00 of the Ventilation Model included documentation of the modeling results from the ANSYS-based heat transfer model. The purposes of Revision 01 of the Ventilation Model are: (1) To validate the conceptual model for preclosure ventilation of emplacement drifts and verify its numerical application in accordance with new procedural requirements as outlined in AP-SIII-10Q, Models (Section 7.0). (2) To satisfy technical issues posed in KTI agreement RDTME 3.14 (Reamer and Williams 2001a). Specifically to demonstrate, with respect to the ANSYS ventilation model, the adequacy of the discretization (Section 6.2.3.1), and the downstream applicability of the model results (i.e. wall heat fractions) to initialize post-closure thermal models (Section 6.6). (3) To satisfy the remainder of KTI agreement TEF 2.07 (Reamer and Williams 2001b). Specifically to provide the results of post-test ANSYS modeling of the Atlas Facility forced convection tests (Section 7.1.2). This portion of the model report also serves as a validation exercise per AP-SIII.10Q, Models, for the ANSYS ventilation model. (4) To further satisfy KTI agreements RDTME 3.01 and 3.14 (Reamer and Williams 2001a) by providing the source documentation referred to in the KTI Letter Report, ''Effect of Forced Ventilation on Thermal-Hydrologic Conditions in the Engineered Barrier System and Near Field Environment'' (Williams 2002). Specifically to provide the results of the MULTIFLUX model which simulates the coupled processes of heat and mass transfer in and around waste emplacement drifts during periods of forced ventilation. This portion of the model report is presented as an Alternative Conceptual Model with a numerical application, and also provides corroborative results used for model validation purposes (Section 6.3 and 6.4).

V. Chipman

2002-10-05

268

Model Selection for Geostatistical Models  

SciTech Connect

We consider the problem of model selection for geospatial data. Spatial correlation is typically ignored in the selection of explanatory variables and this can influence model selection results. For example, the inclusion or exclusion of particular explanatory variables may not be apparent when spatial correlation is ignored. To address this problem, we consider the Akaike Information Criterion (AIC) as applied to a geostatistical model. We offer a heuristic derivation of the AIC in this context and provide simulation results that show that using AIC for a geostatistical model is superior to the often used approach of ignoring spatial correlation in the selection of explanatory variables. These ideas are further demonstrated via a model for lizard abundance. We also employ the principle of minimum description length (MDL) to variable selection for the geostatistical model. The effect of sampling design on the selection of explanatory covariates is also explored.

Hoeting, Jennifer A.; Davis, Richard A.; Merton, Andrew A.; Thompson, Sandra E.

2006-02-01

269

Daisyworld Model  

NSDL National Science Digital Library

The simulation exercise uses a STELLA-based model called Daisyworld to explore concepts associated with Earth's energy balance and climate change. Students examine the evolution of a simplified model 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.

Lovelock, James; Watson, Andrew; Bice, Dave; Dept. Of Geosciences, Penn S.

270

Minibeast Models  

NSDL National Science Digital Library

In this activity, learners create models of bugs. Learners use household materials like plastic cups and straws to create models of bugs like centipedes and spiders. The activity is covered in the first 5 pages of the document. There are also a number of related activities that introduce learners to the world of invertebrates.

The University of Plymouth

2012-06-26

271

Modeling Sunspots  

ERIC Educational Resources Information Center

Modeling in science has been studied by education researchers for decades and is now being applied broadly in school. It is among the scientific practices featured in the "Next Generation Science Standards" ("NGSS") (Achieve Inc. 2013). This article describes modeling activities in an extracurricular science club in a high…

Oh, Phil Seok; Oh, Sung Jin

2013-01-01

272

Scale Models  

NSDL National Science Digital Library

In this activity, learners explore the relative sizes and distances of objects in the solar system. Without being informed of the expected product, learners will make a Play-doh model of the Earth-Moon system, scaled to size and distance. The facilitator reveals the true identity of the system at the conclusion of the activity. During the construction phase, learners try to guess what members of the solar system their model represents. Each group receives different amounts of Play-doh, with each group assigned a color (red, blue, yellow, white). At the end, groups set up their models and inspect the models of other groups. They report patterns of scale that they notice; as the amount of Play-doh increases, for example, so do the size and distance of the model. This resource guide includes background information about the Earth to Moon ratio and solar eclipses.

McDonald Observatory

2011-01-01

273

What is a model? Why modelling?  

E-print Network

What is a model? Why modelling? Which models? What is a useful model? How done? Demo vowels Symposium on Phonetic Frontiers, Pékin : Chine (2008)" #12;What is a model? Why modelling? Which models? What is a useful model? How done? Demo vowels consonants Other uses speaker anatomy speaker strategy

Boyer, Edmond

274

Model Center  

NSDL National Science Digital Library

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 'model' organisms that are easy to keep and manipulate in the laboratory. Despite obvious differences, model organisms share with humans many key biochemical and physiological functions that have been conserved (maintained) by evolution. Each of the following model 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 model. Clicking on a geneâÃÂÃÂs name will take you to the National Center for Biological Information, where you can explore the latest relevant scientific literature.

2009-04-14

275

Energy Models  

EPA Science Inventory

Energy models 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...

276

Supernova models  

SciTech Connect

Recent progress in understanding the observed properties of type I supernovae as a consequence of the thermonuclear detonation of white dwarf stars and the ensuing decay of the Ni-56 produced therein is reviewed. The expected nucleosynthesis and gamma-line spectra for this model of type I explosions and a model for type II explosions are presented. Finally, a qualitatively new approach to the problem of massive star death and type II supernovae based upon a combination of rotation and thermonuclear burning is discussed. While the theoretical results of existing models are predicated upon the assumption of a successful core bounce calculation and the neglect of such two-dimensional effects as rotation and magnetic fields the new model suggests an entirely different scenario in which a considerable portion of the energy carried by an equatorially ejected blob is deposited in the red giant envelope overlying the mantle of the star.

Woosley, S.E. (California, University, Santa Cruz; California, University, Livermore, CA); Weaver, T.A. (California, University, Livermore, CA)

1981-12-29

277

Modeling Quality Information within Business Process Models  

E-print Network

Modeling Quality Information within Business Process Models Robert Heinrich, Alexander Kappe. Business process models are a useful means to document information about structure and behavior literature and tool survey on modeling quality information within business process models. Keywords: Business

Paech, Barbara

278

Device modeling  

NASA Technical Reports Server (NTRS)

A summary report is given of the activities of the device modeling workshop which was held as a part of the Space Photovoltaic Research and Technology Conference at the Lewis Research Center, October 7 to 9, 1986. The purpose of this workshop was to access the status of solar cell device modeling to see if it is meeting present and future needs of the photovoltaic community.

Schwartz, Richard

1987-01-01

279

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 modeling of pair distribution function data and implications for magnetic order  

SciTech Connect

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 Fe--Fe nearest neighbor pairs than in a random distribution. Reverse Monte Carlo modeling of the pair distribution function data has provided the Fe--O, Mn--O, and Cr--O bond length distributions and information on the coordination numbers of the Fe, Mn, and Cr cations. In 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 modeling 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.

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)

2013-02-15

280

Mechanistic models  

SciTech Connect

Several models and theories are reviewed that incorporate the idea of radiation-induced lesions (repairable and/or irreparable) that can be related to molecular lesions in the DNA molecule. Usually the DNA double-strand or chromatin break is suggested as the critical lesion. In the models, the shoulder on the low-LET survival curve is hypothesized as being due to one (or more) of the following three mechanisms: (1) ``interaction`` of lesions produced by statistically independent particle tracks; (2) nonlinear (i.e., linear-quadratic) increase in the yield of initial lesions, and (3) saturation of repair processes at high dose. Comparisons are made between the various approaches. Several significant advances in model development are discussed; in particular, a description of the matrix formulation of the Markov versions of the RMR and LPL models is given. The more advanced theories have incorporated statistical fluctuations in various aspects of the energy-loss and lesion-formation process. An important direction is the inclusion of physical and chemical processes into the formulations by incorporating relevant track structure theory (Monte Carlo track simulations) and chemical reactions of radiation-induced radicals. At the biological end, identification of repair genes and how they operate as well as a better understanding of how DNA misjoinings lead to lethal chromosome aberrations are needed for appropriate inclusion into the theories. More effort is necessary to model the complex end point of radiation-induced carcinogenesis.

Curtis, S.B.

1990-09-01

281

Mechanistic models  

SciTech Connect

Several models and theories are reviewed that incorporate the idea of radiation-induced lesions (repairable and/or irreparable) that can be related to molecular lesions in the DNA molecule. Usually the DNA double-strand or chromatin break is suggested as the critical lesion. In the models, the shoulder on the low-LET survival curve is hypothesized as being due to one (or more) of the following three mechanisms: (1) interaction'' of lesions produced by statistically independent particle tracks; (2) nonlinear (i.e., linear-quadratic) increase in the yield of initial lesions, and (3) saturation of repair processes at high dose. Comparisons are made between the various approaches. Several significant advances in model development are discussed; in particular, a description of the matrix formulation of the Markov versions of the RMR and LPL models is given. The more advanced theories have incorporated statistical fluctuations in various aspects of the energy-loss and lesion-formation process. An important direction is the inclusion of physical and chemical processes into the formulations by incorporating relevant track structure theory (Monte Carlo track simulations) and chemical reactions of radiation-induced radicals. At the biological end, identification of repair genes and how they operate as well as a better understanding of how DNA misjoinings lead to lethal chromosome aberrations are needed for appropriate inclusion into the theories. More effort is necessary to model the complex end point of radiation-induced carcinogenesis.

Curtis, S.B.

1990-09-01

282

Gnomon Model  

NSDL National Science Digital Library

The EJS Gnomon model 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 model was created using the Easy Java Simulations (Ejs) modeling 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 models. Additional Ejs models for astronomy are available. They can be found by searching ComPADRE for Open Source Physics, OSP, or Ejs.

Timberlake, Todd

2009-08-19

283

Modeling reality  

NASA Technical Reports Server (NTRS)

Although powerful computers have allowed complex physical and manmade hardware systems to be modeled successfully, we have encountered persistent problems with the reliability of computer models 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 models 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.

Denning, Peter J.

1990-01-01

284

Modelling osteomyelitis  

PubMed Central

Background This work focuses on the computational modelling 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 models. 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 model of osteoporosis and of osteomyelitis. Our models could be seen as a hybrid ODE and probabilistic verification modelling 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 modeling 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

2012-01-01

285

Supernova models  

SciTech Connect

Recent progress in understanding the observed properties of Type I supernovae as a consequence of the thermonuclear detonation of white dwarf stars and the ensuing decay of the /sup 56/Ni produced therein is reviewed. Within the context of this model for Type I explosions and the 1978 model for Type II explosions, the expected nucleosynthesis and gamma-line spectra from both kinds of supernovae are presented. Finally, a qualitatively new approach to the problem of massive star death and Type II supernovae based upon a combination of rotation and thermonuclear burning is discussed.

Woosley, S.E.; Weaver, T.A.

1980-01-01

286

Marshmallow Models  

NSDL National Science Digital Library

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 models they want.

Science, Lawrence H.

2010-01-01

287

Ensemble Models  

EPA Science Inventory

Ensemble forecasting has been used for operational numerical weather prediction in the United States and Europe since the early 1990s. An ensemble of weather or climate forecasts is used to characterize the two main sources of uncertainty in computer models of physical systems: ...

288

Why model?  

PubMed Central

Next generation sequencing technologies are bringing about a renaissance of mining approaches. A comprehensive picture of the genetic landscape of an individual patient will be useful, for example, to identify groups of patients that do or do not respond to certain therapies. The high expectations may however not be satisfied if the number of patient groups with similar characteristics is going to be very large. I therefore doubt that mining sequence data will give us an understanding of why and when therapies work. For understanding the mechanisms underlying diseases, an alternative approach is to model small networks in quantitative mechanistic detail, to elucidate the role of gene and proteins in dynamically changing the functioning of cells. Here an obvious critique is that these models consider too few components, compared to what might be relevant for any particular cell function. I show here that mining approaches and dynamical systems theory are two ends of a spectrum of methodologies to choose from. Drawing upon personal experience in numerous interdisciplinary collaborations, I provide guidance on how to model by discussing the question “Why model?” PMID:24478728

Wolkenhauer, Olaf

2013-01-01

289

Modeling Muscles  

ERIC Educational Resources Information Center

Teaching the anatomy of the muscle system to high school students can be challenging. Students often learn about muscle anatomy by memorizing information from textbooks or by observing plastic, inflexible models. Although these mediums help students learn about muscle placement, the mediums do not facilitate understanding regarding integration of…

Goodwyn, Lauren; Salm, Sarah

2007-01-01

290

Groundwater Model  

NSDL National Science Digital Library

In this activity, students build a model 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.

291

Modeling Convection  

ERIC Educational Resources Information Center

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 model prior to instruction on these topics may facilitate students' understanding of processes that are largely…

Ebert, James R.; Elliott, Nancy A.; Hurteau, Laura; Schulz, Amanda

2004-01-01

292

Urban Modelling  

Microsoft Academic Search

Urban models are computer-based simulations used for testing theories about spatial location and interaction between land uses and related activities. They also provide digital environments for testing the consequences of physical planning policies on the future form of cities. As computers, software and data have become richer, and as our conception of the way complex systems such as cities grow

Michael Batty; Rob Kitchin; Nigel Thrift

293

Daisyworld Model  

NSDL National Science Digital Library

The Daisyworld model created by Andrew Watson and James Lovelock (1983, Tellus, v. 35B, p. 284-289) is a wonderful example of a self-regulating system incorporating positive and negative feedbacks. The model consists of a planet on which black and white daisies are growing. The growth of these daisies is governed by a parabolic shaped growth function regulated by planetary temperature and is set to zero for temperatures less than 5 ºC or greater than 40 ºC and optimized at 22.5 ºC. The model explores the effect of a steadily increasing solar luminosity on the growth of daisies and the resulting planetary temperature. The growth function for the daisies allows them to modulate the planet's temperature for many years, warming it early on as black daisies grow, and cooling it later as white daisies grow. Eventually, the solar luminosity increases beyond the daisies' capability to modulate the temperature and they die out, leading to a rapid rise in the planetary temperature. Students read Watson and Lovelock's original paper, and then use STELLA to create their own Daisyworld model with which they can experiment. Experiments include changing the albedos of the daisies, changing their death rates, and changing the rate at which energy is conducted from one part of the planet to another. In all cases, students keep track of daisy populations and of planetary temperature over time.

Menking, Kirsten

294

Atmospheric Modeling  

EPA Science Inventory

Although air quality models have been applied historically to address issues specific to ambient air quality standards (i.e., one criteria pollutant at a time) or welfare (e.g.. acid deposition or visibility impairment). they are inherently multipollutant based. Therefore. in pri...

295

ATMOSPHERIC MODELING: MODEL AND ACCURACY  

EPA Science Inventory

The development of models 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...

296

Linear Models  

NSDL National Science Digital Library

This site uses linear models 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.

Frank Wattenberg

1997-01-01

297

Geometric Models  

NSDL National Science Digital Library

Created by Kyle Siegrist of the University of Alabama-Huntsville, this is an online, interactive lesson on geometric models. 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.

Siegrist, Kyle

298

10. MOVABLE BED SEDIMENTATION MODELS. DOGTOOTH BEND MODEL (MODEL SCALE: ...  

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

10. MOVABLE BED SEDIMENTATION MODELS. DOGTOOTH BEND MODEL (MODEL SCALE: 1' = 400' HORIZONTAL, 1' = 100' VERTICAL), AND GREENVILLE BRIDGE MODEL (MODEL SCALE: 1' = 360' HORIZONTAL, 1' = 100' VERTICAL). - Waterways Experiment Station, Hydraulics Laboratory, Halls Ferry Road, 2 miles south of I-20, Vicksburg, Warren County, MS

299

Eratosthenes Model  

NSDL National Science Digital Library

The Eratosthenes model displays the shadows cast by two gnomons (sticks) at different locations on Earth. For one gnomon, Sun is directly overhead (as would be the case if the gnomon was on the Tropic of Cancer at the summer solstice). The other gnomon is due north of the first gnomon. The sizes of the gnomons are greatly exaggerated for visibility. This simulation can be used to help illustrate how Eratosthenes was able to measure the diameter of Earth using the shadows cast by two gnomons, one situated due north of the other, on a day when the southerly gnomon cast no shadow at all. The distance between the two gnomons (along Earth's surface) can be adjusted. The length of the shadow is given, and this length can be used to determine the angle between the gnomon lines and from that the circumference (and diameter, radius, etc) of Earth. Earth can be hidden to give a better view of the relevant geometry. Eratosthenes model is distributed as a ready-to-run (compiled) Java archive. Double clicking the ejs_astronomy_Eratosthenes.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 plot and selecting "Open EJS Model" from the pop-up menu item.

Timberlake, Todd

2010-01-03

300

Modeling biomembranes.  

SciTech Connect

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 models of biomembranes. Molecular dynamics (MD) simulations and classical density functional theory (DFT) calculations using these models 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 models 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.

Plimpton, Steven James; Heffernan, Julieanne; Sasaki, Darryl Yoshio; Frischknecht, Amalie Lucile; Stevens, Mark Jackson; Frink, Laura J. Douglas

2005-11-01

301

General Model Independent Normal Model Correlated Normal Model Conclusion Sequential Bayesian Ranking and Selection with  

E-print Network

General Model Independent Normal Model Correlated Normal Model Conclusion Sequential Bayesian;General Model Independent Normal Model Correlated Normal Model Conclusion Example, Time 0 #12;General Model Independent Normal Model Correlated Normal Model Conclusion Example, Time 1 #12;General Model

Keinan, Alon

302

Molecular Modeling  

NASA Astrophysics Data System (ADS)

Molecular modeling 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 modeling 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. Typical molecular modeling exercise: finding conformation energies. Molecular Modeling 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. 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 Modeling Exercises and Experiments: Mission Statement We are seeking in this JCE Internet feature column to publish molecular modeling 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 modeling software programs (e.g. HyperChem, Spartan, CAChe, PC Model). Exercises that are specific to a particular modeling program are acceptable, but those usable with any modeling program are preferred. Ideally the exercises/experiments will be of the type where the "correct"answer is not obvious so

Holmes, Jon L.

1999-06-01

303

Atomic Models, Nagaoka's Saturnian Model  

Microsoft Academic Search

In late 1903, Hantaro Nagaoka (1865–1950) developed the earliest published quasi-planetary model 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

Klaus Hentschel

304

Biomimetic modelling.  

PubMed Central

Biomimetics is seen as a path from biology to engineering. The only path from engineering to biology in current use is the application of engineering concepts and models to biological systems. However, there is another pathway: the verification of biological mechanisms by manufacture, leading to an iterative process between biology and engineering in which the new understanding that the engineering implementation of a biological system can bring is fed back into biology, allowing a more complete and certain understanding and the possibility of further revelations for application in engineering. This is a pathway as yet unformalized, and one that offers the possibility that engineers can also be scientists. PMID:14561351

Vincent, Julian F V

2003-01-01

305

Fraction Models  

NSDL National Science Digital Library

This interactive activity allows users the ability to explore different representations for fractions and how they are equivalent to mixed numbers, decimals, and percentages. Users adjust the numerator (up to 100) and the denominator (1 to 25) in order to see a visual representation of the fraction. The visual representation can be seen as a length, area, region, or set model. Users also have the ability to keep track of the equivalent forms of fractions in a table. Instructions and exploration questions are given.

2011-01-01

306

The Role of Charge Changing Cross-Sections in Cosmic Ray Propagation  

NASA Astrophysics Data System (ADS)

Variations of cosmic ray nuclear abundance at the top of the atmosphere is studied using different available partial cross-sections e.g. semi empirical formulations of Tsao et al., Garrard et al. and theoretical formulation of Wilson et al., based on the abrasion-ablation model. The Andersand Ebihara solar abundance is taken as a standard source spectrum in a Monte Carlo simulation of cosmic ray propagation through ISM. A Comparative study of the sub Fe/Fe ratios obtained using different cross-sections has been made.

Basu, Basudhara

307

Constructing NARMAX models using ARMAX models  

Microsoft Academic Search

This paper outlines how it is possible to decompose a complex non-linear modelling problem into a set of simpler linear modelling problems. Local ARMAX models valid within certain operating regimes are interpolated to construct a global NARMAX (non-linear NARMAX) model. Knowledge of the system behaviour in terms of operating regimes is the primary basis for building such models, hence it

TOR A. JOHANSEN; BJARNE A. FOSS

1993-01-01

308

Pre-Modeling Ensures Accurate Solid Models  

ERIC Educational Resources Information Center

Successful solid modeling 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 modeled. The solid-modeling process is faster and less prone to modeling errors when the design tree is a simple and geometrically logical definition of the modeled object. Few high…

Gow, George

2010-01-01

309

Comparisons of debris environment model breakup models  

Microsoft Academic Search

This paper presents a comparison of current spacecraft breakup models used in orbital (space) debris computational environment models. The breakup models to be compared come from the NASA EVOLVE (Evolutionary) model long term debris model, the IMPACT code developed by Aerospace Corp., and the Fragmentation Algorithms for Satellite Targets (FAST) developed by Kaman Sciences. The comparison will show the methodologies

F. Jonas; K. Yates; R. Evans

1993-01-01

310

Modelling intonational structure using hidden markov models  

E-print Network

A method is introduced for using hidden Markov models (HMMs) to model intonational structure. HMMs are probabilistic and can capture the variability in structure which previous finite state network models lack. We show ...

Wright, Helen; Taylor, Paul A

1997-01-01

311

Analytic Modeling Birth-Death Model  

E-print Network

Analytic Modeling Birth-Death Model 1 A Review -Random Variables · A variable representing on Exponential Distribution 11 Birth-Death Model 12 #12;Birth-Death Model · Queuing system with a single service State Dependent Arrival Rate 14 #12;State Dependent Service Rate 15 Definition of Birth-Death Process 16

Shihada, Basem

312

I&C Modeling in SPAR Models  

SciTech Connect

The Standardized Plant Analysis Risk (SPAR) models for the U.S. commercial nuclear power plants currently have very limited instrumentation and control (I&C) modeling [1]. Most of the I&C components in the operating plant SPAR models are related to the reactor protection system. This was identified as a finding during the industry peer review of SPAR models. While the Emergency Safeguard Features (ESF) actuation and control system was incorporated into the Peach Bottom Unit 2 SPAR model in a recent effort [2], various approaches to expend resources for detailed I&C modeling in other SPAR models are investigated.

John A. Schroeder

2012-06-01

313

Comparative Protein Structure Modeling Using Modeller  

PubMed Central

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 modeling can sometimes provide a useful 3-D model for a protein that is related to at least one known protein structure. Comparative modeling 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, model building, and model evaluation. This unit describes how to calculate comparative models using the program MODELLER and discusses all four steps of comparative modeling, frequently observed errors, and some applications. Modeling lactate dehydrogenase from Trichomonas vaginalis (TvLDH) is described as an example. The download and installation of the MODELLER software is also described. PMID:18428767

Eswar, Narayanan; Marti-Renom, Marc A.; Madhusudhan, M.S.; Eramian, David; Shen, Min-yi; Pieper, Ursula

2014-01-01

314

Loglinear Rasch model tests  

Microsoft Academic Search

Existing statistical tests for the fit of the Rasch model have been criticized, because they are only sensitive to specific violations of its assumptions. Contingency table methods using loglinear models have been used to test various psychometric models. In this paper, the assumptions of the Rasch model are discussed and the Rasch model is reformulated as a quasi-independence model. The

Hendrikus Kelderman

1984-01-01

315

Hydrogen use by bacterial enteric pathogens.  

E-print Network

??Uptake-type hydrogenases catalyze the oxidation of molecular hydrogen in an energy-conserving manner. Many prokaryotes use these hydrogenases in their central metabolism. It has been recently… (more)

Zbell, Andrea Lynn

2008-01-01

316

Comparisons of debris environment model breakup models  

NASA Astrophysics Data System (ADS)

This paper presents a comparison of current spacecraft breakup models used in orbital (space) debris computational environment models. The breakup models to be compared come from the NASA EVOLVE (Evolutionary) model long term debris model, the IMPACT code developed by Aerospace Corp., and the Fragmentation Algorithms for Satellite Targets (FAST) developed by Kaman Sciences. The comparison will show the methodologies and results obtained for each model such as mass versus fragment number distributions. Implications for debris cloud formation will be discussed in terms of the environments produced. No attempt is made to recommend any one model over the other as each were designed and employed for specific purposes in the environment models they are part of or contribute to. The comparisons are intended to provide researchers both quantitative and qualitative information on the models for use in their own research activities.

Jonas, F.; Yates, K.; Evans, R.

1993-01-01

317

Uncertainty Modeling Via Frequency Domain Model Validation  

NASA Technical Reports Server (NTRS)

Abstract The majority of literature on robust control assumes that a design model is available and that the uncertainty model bounds the actual variations about the nominal model. However, methods for generating accurate design models have not received as much attention in the literature. The influence of the level of accuracy of the uncertainty model on closed loop performance has received even less attention. The research reported herein is an initial step in applying and extending the concept of model validation to the problem of obtaining practical uncertainty models for robust control analysis and design applications. An extension of model validation called 'sequential validation' is presented and applied to a simple spring-mass-damper system to establish the feasibility of the approach and demonstrate the benefits of the new developments.

Waszak, Martin R.; Andrisani, Dominick, II

1999-01-01

318

Development and Partial Characterization of Nearly Isogenic Pea Lines (Pisum sativum L.) that Alter Uptake Hydrogenase Activity in Symbiotic Rhizobium1  

PubMed Central

Some Rhizobium bacteria have H2-uptake (Hup) systems that oxidize H2 evolved from nitrogenase in leguminous root nodules. Pea (Pisum sativum L.) cultivars `JI1205' and `Alaska' produce high Hup (Hup++) and moderate Hup (Hup+) phenotypes, respectively, in Rhizobium leguminosarum 128C53. The physiological significance and biochemical basis of this host plant genetic effect are unknown. The purpose of this investigation was to advance basic Hup studies by developing nearly isogenic lines of peas that alter Hup phenotypes in R. leguminosarum strains containing hup genes. Eight pairs of nearly isogenic pea lines that produce Hup++ and Hup+ phenotypes in R. leguminosarum 128C53 were identified in 173 F2-derived F6 families produced from crosses between JI1205 and Alaska. Tests with the pea isolines and three strains of hup-containing R. leguminosarum showed that the isolines altered Hup activity significantly (P ? 0.05) in 19 of 24 symbiotic combinations. Analyses of Hup phenotypes in F6 families, the F1 population, and two backcrosses suggested involvement of a single genetic locus. Three of the eight pairs of isolines were identified as being suitable for physiological studies, because the two lines in each pair showed similar growth, N assimilation, and flowering traits under nonsymbiotic conditions. Tests of those lines under N2-dependent conditions with isogenic Hup+ and negligible Hup (Hup?) mutants of R. leguminosarum 128C53 showed that, in symbioses with Hup+ rhizobia, two out of three Hup++ pea lines decreased N2 fixation relative to Hup+ peas. In one of those cases, however, the Hup++ plant line also decreased fixation by Hup? rhizobia. When results were averaged across all rhizobia tested, Hup+ pea isolines had 8.2% higher dry weight (P ? 0.05) and fixed 12.6% more N2 (P ? 0.05) than Hup++ isolines. Pea lines described here may help identify host plant factors that influence rhizobial Hup activity and should assist in clarifying how Hup systems influence other physiological processes. PMID:16667415

Phillips, Donald A.; Kapulnik, Yoram; Bedmar, Eulogio J.; Joseph, Cecillia M.

1990-01-01

319

Oxygen limitation modulates pH regulation of catabolism and hydrogenases, multidrug transporters, and envelope composition in Escherichia coli K-12  

Microsoft Academic Search

Background  InEscherichia coli, pH regulates genes for amino-acid and sugar catabolism, electron transport, oxidative stress, periplasmic and envelope proteins.\\u000a Many pH-dependent genes are co-regulated by anaerobiosis, but the overall intersection of pH stress and oxygen limitation\\u000a has not been investigated.\\u000a \\u000a \\u000a \\u000a \\u000a Results  The pH dependence of gene expression was analyzed in oxygen-limited cultures ofE. coli K-12 strain W3110.E. coli K-12 strain W3110 was

Everett T Hayes; Jessica C Wilks; Piero Sanfilippo; Elizabeth Yohannes; Daniel P Tate; Brian D Jones; Michael D Radmacher; Sandra S BonDurant; Joan L Slonczewski

2006-01-01

320

Genetic Diversity of Hydrogen-Producing Bacteria in an Acidophilic Ethanol-H2-Coproducing System, Analyzed Using the [Fe]-Hydrogenase Gene? †  

PubMed Central

Hydrogen gas (H2) produced by bacterial fermentation of biomass can be a sustainable energy source. The ability to produce H2 gas during anaerobic fermentation was previously thought to be restricted to a few species within the genera Clostridium and Enterobacter. This work reports genomic evidence for the presence of novel H2-producing bacteria (HPB) in acidophilic ethanol-H2-coproducing communities that were enriched using molasses wastewater. The majority of the enriched dominant populations in the acidophilic ethanol-H2-coproducing system were affiliated with low-G+C-content gram-positive bacteria, Bacteroidetes, and Actinobacteria, based on the 16S rRNA gene. However, PCR primers designed to specifically target bacterial hydA yielded 17 unique hydA sequences whose amino acid sequences differed from those of known HPB. The putative ethanol-H2-coproducing bacteria comprised 11 novel phylotypes closely related to Ethanoligenens harbinense, Clostridium thermocellum, and Clostridium saccharoperbutylacetonicum. Furthermore, analysis of the alcohol dehydrogenase isoenzyme also pointed to an E. harbinense-like organism, which is known to have a high conversion rate of carbohydrate to H2 and ethanol. We also found six novel HPB that were associated with lactate-, propionate-, and butyrate-oxidizing bacteria in the acidophilic H2-producing sludge. Thus, the microbial ecology of mesophilic and acidophilic H2 fermentation involves many other bacteria in addition to Clostridium and Enterobacter. PMID:18156331

Xing, Defeng; Ren, Nanqi; Rittmann, Bruce E.

2008-01-01

321

Comparison of laser models  

NASA Technical Reports Server (NTRS)

Progress on the comparison of laser models is reported. Equations for an oscillatory model and a nonoscillatory model for the simulation of iodine laser operation are solved. Reaction rate coefficients used in both models are listed. Currently there are four models for the simulation of iodine laser operation are solved. Reaction rate coefficients used in both models are listed. Currently there are four models for the simulation of an iodine laser. They are: (1) a time dependent model; (2) a quasi-steady state model; (3) a noncompressible model; and (4) a compressible flow laser model. Current research is being directed toward: (1) parameter studies using the compressible flow laser model; (2) development of a two-pass amplifier model; and (3) solving a system of equations describing operation of the high powered iodine MOPA (master oscillator power amplifier).

Heinbockel, John H.

1989-01-01

322

Model Mapping in MDA  

Microsoft Academic Search

In this paper we propose a general model of Model Mapping, one of the key features in MDA. We recall the fundamental relationships between system, model ,a ndformalism. Then mapping of models described in the same formalism (direct) or in different formalisms (indirect) is discussed. As an example, a Constraint Checker (CC) is presented. This application takes an UML model

Guy CAPLAT; Jean Louis SOURROUILLE

323

"Bohr's Atomic Model."  

ERIC Educational Resources Information Center

"Bohr's Atomic Model" is a small interactive multimedia program that introduces the viewer to a simplified model of the atom. This interactive simulation lets students build an atom using an atomic construction set. The underlying design methodology for "Bohr's Atomic Model" is model-centered instruction, which means the central model of the…

Willden, Jeff

2001-01-01

324

Multilevel Model Prediction  

ERIC Educational Resources Information Center

Multilevel models are proven tools in social research for modeling complex, hierarchical systems. In multilevel modeling, statistical inference is based largely on quantification of random variables. This paper distinguishes among three types of random variables in multilevel modeling--model disturbances, random coefficients, and future response…

Frees, Edward W.; Kim, Jee-Seon

2006-01-01

325

Discrete, Amorphous Physical Models  

Microsoft Academic Search

Discrete models of physical phenomena are an attractive alternative to continuous models such as partial differential equations. In discrete models, such as cellular automata, space is treated as having finitely many locations per unit volume, and physical processes are modelled by rules that depend on a small number of nearby locations. Such models depend critically on a regular (crystalline) lattice,

Erik Rauch

2003-01-01

326

A shock-metamorphic model for silicate darkening and compositionally variable plagioclase in CK and ordinary chondrites  

SciTech Connect

Silicate darkening in ordinary chondrites (OC) is caused by tiny grains of metallic Fe-Ni and troilite occurring mainly within curvilinear trails that traverse silicate interiors and decorate or, in some cases, cut across silicate grain boundaries. Highly shocked OC tend to have greater degrees of silicate darkening than lightly shocked OC; this indicates that silicate darkening is probably a result of shock metamorphism. The low Fe-FeS eutectic temperature (988C) renders metal and troilite susceptible to melting and mobilization during shock heating. Unshocked OC tend to have plagioclase with uniform compositions; shocked OC tend to have plagioclase with more variable (albeit still stoichiometric) compositions. The low impedance of plagioclase to shock compression makes it particularly susceptible to melting and mobilization; this is consistent with the molten appearance of plagioclase in highly shocked OC (e.g., Rose City and Paragould). CK chondrites also have compositionally variable plagioclase. The common association of silicate darkening with compositionally variable plagioclase is consistent with the hypothesis that both are products of shock metamorphism. Some CK and OC chondrites exhibit light shock effects in olivine that are consistent with equilibrium peak shock pressures that are too low to account for the silicate darkening or opaque shock veins in these meteorites. Therefore, the olivine in these chondrites may have been annealed after intense shock produced these effects. A few CK chondrites that contain olivine with undulose or mosaic extinction (e.g., LEW87009 and EET83311) may have been shocked again, after annealing.

Rubin, A.E. (Univ. of California, Los Angeles (United States))

1992-04-01

327

Bohr model as an algebraic collective model  

SciTech Connect

Developments and applications are presented of an algebraic version of Bohr's collective model. Illustrative examples show that fully converged calculations can be performed quickly and easily for a large range of Hamiltonians. As a result, the Bohr model becomes an effective tool in the analysis of experimental data. The examples are chosen both to confirm the reliability of the algebraic collective model and to show the diversity of results that can be obtained by its use. The focus of the paper is to facilitate identification of the limitations of the Bohr model with a view to developing more realistic, computationally tractable models.

Rowe, D. J.; Welsh, T. A.; Caprio, M. A. [Department of Physics, University of Toronto, Toronto, Ontario M5S 1A7 (Canada); Department of Physics, University of Notre Dame, Notre Dame, Indiana 46556-5670 (United States)

2009-05-15

328

Solicited abstract: Global hydrological modeling and models  

NASA Astrophysics Data System (ADS)

The origins of rainfall-runoff modeling in the broad sense can be found in the middle of the 19th century arising in response to three types of engineering problems: (1) urban sewer design, (2) land reclamation drainage systems design, and (3) reservoir spillway design. Since then numerous empirical, conceptual and physically-based models are developed including event based models using unit hydrograph concept, Nash's linear reservoir models, HBV model, TOPMODEL, SHE model, etc. From the late 1980s, the evolution of global and continental-scale hydrology has placed new demands on hydrologic modellers. The macro-scale hydrological (global and regional scale) models were developed on the basis of the following motivations (Arenll, 1999). First, for a variety of operational and planning purposes, water resource managers responsible for large regions need to estimate the spatial variability of resources over large areas, at a spatial resolution finer than can be provided by observed data alone. Second, hydrologists and water managers are interested in the effects of land-use and climate variability and change over a large geographic domain. Third, there is an increasing need of using hydrologic models as a base to estimate point and non-point sources of pollution loading to streams. Fourth, hydrologists and atmospheric modellers have perceived weaknesses in the representation of hydrological processes in regional and global climate models, and developed global hydrological models to overcome the weaknesses of global climate models. Considerable progress in the development and application of global hydrological models has been achieved to date, however, large uncertainties still exist considering the model structure including large scale flow routing, parameterization, input data, etc. This presentation will focus on the global hydrological models, and the discussion includes (1) types of global hydrological models, (2) procedure of global hydrological model development, (3) state-of-the-art of existing global hydrological models, and (4) challenges. Acknowledgment: Thanks to Lebing Gong, Elin Widén-Nilsson, and Sven Halldin of Uppsala University for the team work in global hydrological models.

Xu, Chong-Yu

2010-05-01

329

Mathematics and Statistics Models  

NSDL National Science Digital Library

Developed by Bob MacKay, Clark College. What are Mathematical and Statistical Models These types of models are obviously related, but there are also real differences between them. Mathematical Models: grow out of ...

330

Composite Linear Models  

Cancer.gov

Statistical Software Composite Linear Models (Written by Stuart G. Baker) The composite linear models software is a matrix approach to compute maximum likelihood estimates and asymptotic standard errors for models for incomplete multinomial data. It

331

Educating with Aircraft Models  

ERIC Educational Resources Information Center

Described is utilization of aircraft models, model aircraft clubs, and model aircraft magazines to promote student interest in aerospace education. The addresses for clubs and magazines are included. (SL)

Steele, Hobie

1976-01-01

332

Modeling Natural Selection  

NSDL National Science Digital Library

In their research, scientists generate, test, and modify scientific models. These models can be shared with others and demonstrate a scientist's understanding of how the natural world works. Similarly, students can generate and modify models to gain a bet

Lotter, Christine; Bogiages, Christopher A.

2011-02-01

333

American Modeling Teachers Association  

NSDL National Science Digital Library

This is the web site home for the American Modeling Teachers Association, and organization run by and for teachers who use modeling instruction in their classroom. Modeling instruction organizes science content around a small number of of scientific models, and uses a structured inquiry approach to teaching science content and skills. This web site includes information about the Association, Modeling workshops, and discussions regarding science education. Members of the AMTA have access to Modeling teaching resources.

2013-03-20

334

Morphable Models of Faces  

Microsoft Academic Search

\\u000a In this chapter, we present the Morphable Model, a three-dimensional (3D) representation that enables the accurate modeling\\u000a of any illumination and pose as well as the separation of these variations from the rest (identity and expression). The Morphable\\u000a Model is a generative model consisting of a linear 3D shape and appearance model plus an imaging model, which maps the 3D

Reinhard Knothe; Brian Amberg; Sami Romdhani; Volker Blanz; Thomas Vetter

335

Orbital Debris Modeling  

NASA Technical Reports Server (NTRS)

Presentation outlne: (1) The NASA Orbital Debris (OD) Engineering Model -- A mathematical model capable of predicting OD impact risks for the ISS and other critical space assets (2) The NASA OD Evolutionary Model -- A physical model capable of predicting future debris environment based on user-specified scenarios (3) The NASA Standard Satellite Breakup Model -- A model describing the outcome of a satellite breakup (explosion or collision)

Liou, J. C.

2012-01-01

336

Geologic Framework Model Analysis Model Report  

SciTech Connect

The purpose of this report is to document the Geologic Framework Model (GFM), Version 3.1 (GFM3.1) with regard to data input, modeling methods, assumptions, uncertainties, limitations, and validation of the model results, qualification status of the model, and the differences between Version 3.1 and previous versions. The GFM represents a three-dimensional interpretation of the stratigraphy and structural features of the location of the potential Yucca Mountain radioactive waste repository. The GFM encompasses an area of 65 square miles (170 square kilometers) and a volume of 185 cubic miles (771 cubic kilometers). The boundaries of the GFM were chosen to encompass the most widely distributed set of exploratory boreholes (the Water Table or WT series) and to provide a geologic framework over the area of interest for hydrologic flow and radionuclide transport modeling through the unsaturated zone (UZ). The depth of the model is constrained by the inferred depth of the Tertiary-Paleozoic unconformity. The GFM was constructed from geologic map and borehole data. Additional information from measured stratigraphy sections, gravity profiles, and seismic profiles was also considered. This interim change notice (ICN) was prepared in accordance with the Technical Work Plan for the Integrated Site Model Process Model Report Revision 01 (CRWMS M&O 2000). The constraints, caveats, and limitations associated with this model are discussed in the appropriate text sections that follow. The GFM is one component of the Integrated Site Model (ISM) (Figure l), which has been developed to provide a consistent volumetric portrayal of the rock layers, rock properties, and mineralogy of the Yucca Mountain site. The ISM consists of three components: (1) Geologic Framework Model (GFM); (2) Rock Properties Model (RPM); and (3) Mineralogic Model (MM). The ISM merges the detailed project stratigraphy into model stratigraphic units that are most useful for the primary downstream models and the repository design. These downstream models include the hydrologic flow models and the radionuclide transport models. All the models and the repository design, in turn, will be incorporated into the Total System Performance Assessment (TSPA) of the potential radioactive waste repository block and vicinity to determine the suitability of Yucca Mountain as a host for the repository. The interrelationship of the three components of the ISM and their interface with downstream uses are illustrated in Figure 2.

R. Clayton

2000-12-19

337

Hierarchical control models for multimodal process modeling.  

PubMed

The multimodal and hierarchical structure characteristics of a system make process modeling quite difficult. In this paper, we present a hierarchical control model (HCM) for hierarchically multimodal processing. From multiple streams, a control layer extracts the inherent group process that denotes the evolution of the system and controls the evolution of every modality. HCMs model the influences of the group on modalities and represent the hierarchical structure of the system by a multilayer network. To estimate the state order of the model, we also present a new information criterion that corrects the preference of traditional criteria for more complex models and proves the rationality of HCMs. Comparisons with other models on multiagent activity recognition show that HCMs are reliable and efficient. PMID:19342349

Zhang, Weidong; Chen, Feng; Xu, Wenli

2009-10-01

338

ROCK PROPERTIES MODEL ANALYSIS MODEL REPORT  

SciTech Connect

The purpose of this Analysis and Model Report (AMR) is to document Rock Properties Model (RPM) 3.1 with regard to input data, model methods, assumptions, uncertainties and limitations of model results, and qualification status of the model. The report also documents the differences between the current and previous versions and validation of the model. The rock properties models are intended principally for use as input to numerical physical-process modeling, such as of ground-water flow and/or radionuclide transport. The constraints, caveats, and limitations associated with this model are discussed in the appropriate text sections that follow. This work was conducted in accordance with the following planning documents: WA-0344, ''3-D Rock Properties Modeling for FY 1998'' (SNL 1997, WA-0358), ''3-D Rock Properties Modeling for FY 1999'' (SNL 1999), and the technical development plan, Rock Properties Model Version 3.1, (CRWMS M&O 1999c). The Interim Change Notice (ICNs), ICN 02 and ICN 03, of this AMR were prepared as part of activities being conducted under the Technical Work Plan, TWP-NBS-GS-000003, ''Technical Work Plan for the Integrated Site Model, Process Model Report, Revision 01'' (CRWMS M&O 2000b). The purpose of ICN 03 is to record changes in data input status due to data qualification and verification activities. These work plans describe the scope, objectives, tasks, methodology, and implementing procedures for model construction. The constraints, caveats, and limitations associated with this model are discussed in the appropriate text sections that follow. The work scope for this activity consists of the following: (1) Conversion of the input data (laboratory measured porosity data, x-ray diffraction mineralogy, petrophysical calculations of bound water, and petrophysical calculations of porosity) for each borehole into stratigraphic coordinates; (2) Re-sampling and merging of data sets; (3) Development of geostatistical simulations of porosity; (4) Generation of derivative property models via linear coregionalization with porosity; (5) Post-processing of the simulated models to impart desired secondary geologic attributes and to create summary and uncertainty models; and (6) Conversion of the models into real-world coordinates. The conversion to real world coordinates is performed as part of the integration of the RPM into the Integrated Site Model (ISM) 3.1; this activity is not part of the current analysis. The ISM provides a consistent volumetric portrayal of the rock layers, rock properties, and mineralogy of the Yucca Mountain site and consists of three components: (1) Geologic Framework Model (GFM); (2) RPM, which is the subject of this AMR; and (3) Mineralogic Model. The interrelationship of the three components of the ISM and their interface with downstream uses are illustrated in Figure 1. Figure 2 shows the geographic boundaries of the RPM and other component models of the ISM.

Clinton Lum

2002-02-04

339

Strategic Thinking of Modeling Method and Modeling  

Microsoft Academic Search

Three-dimensional computer software have much to accomplish in the current application areas because they all have powerful modeling and simulation and recycling functions of real scenes. Today the most well-known and widely used 3D software should be 3DSMAX software, which is widely used in construction, decoration, video advertising and other areas. It offers us many modeling functions and various modeling

Guobin Peng; Runhong Peng

2010-01-01

340

Business Modelling Is Not Process Modelling  

Microsoft Academic Search

Innovative e-business projects start with a design of the e-business model. We often encounter the view, in research as well as industry practice, that an e-business model is similar to a business process model, and so can be specified using UML activity diagrams or Petri nets. In this paper, we explain why this is a misunderstanding. The root cause is

Jaap Gordijn; Hans Akkermans; Hans Van Vliet

2000-01-01

341

Network epistemology Discrete models  

E-print Network

Network epistemology Discrete models Continuous models Social Structure and Social Influence A study in network epistemology Kevin J.S. Zollman Social Dynamics Seminar Kevin J.S. Zollman Social Structure and Social Influence #12;Network epistemology Discrete models Continuous models Network

Zollman, Kevin

342

Relevance based language models  

Microsoft Academic Search

We explore the relation between classical probabilistic models of information retrieval and the emerging language modeling approaches. It has long been recognized that the primary obstacle to effective performance of classical models is the need to estimate arelevance model: probabilities of words in the relevant class. We propose a novel technique for estimating these probabilities using the query alone. We

Victor Lavrenko; W. Bruce Croft

2001-01-01

343

AIDS Epidemiological models  

NASA Astrophysics Data System (ADS)

The aim of this paper is to present mathematical modelling 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 models are based in part on the models suggested in the field of th AIDS mathematical modelling as reported by ISHAM [6].

Rahmani, Fouad Lazhar

2010-11-01

344

Fire Model Matrix  

NSDL National Science Digital Library

The Fire Model Matrix is an on-line resource that presents four fire community models in a matrix that facilitates the exploration of the characteristics of each model. As part of the Advanced Fire Weather Forecasters Course, this matrix is meant to sensitize forecasters to the use of weather data in these fire models to forecast potential fire activity.

2014-09-14

345

Generative Models of Disfluency  

ERIC Educational Resources Information Center

This thesis describes a generative model for representing disfluent phenomena in human speech. This model makes use of observed syntactic structure present in disfluent speech, and uses a right-corner transform on syntax trees to model this structure in a very natural way. Specifically, the phenomenon of speech repair is modeled by explicitly…

Miller, Timothy A.

2010-01-01

346

New 3D model for dynamics modeling  

NASA Astrophysics Data System (ADS)

The wrist articulation represents one of the most complex mechanical systems of the human body. It is composed of eight bones rolling and sliding along their surface and along the faces of the five metacarpals of the hand and the two bones of the arm. The wrist dynamics are however fundamental for the hand movement, but it is so complex that it still remains incompletely explored. This work is a part of a new concept of computer-assisted surgery, which consists in developing computer models to perfect surgery acts by predicting their consequences. The modeling of the wrist dynamics are based first on the static model of its bones in three dimensions. This 3D model must optimise the collision detection procedure which is the necessary step to estimate the physical contact constraints. As many other possible computer vision models do not fit with enough precision to this problem, a new 3D model has been developed thanks to the median axis of the digital distance map of the bones reconstructed volume. The collision detection procedure is then simplified for contacts are detected between spheres. The experiment of this original 3D dynamic model products realistic computer animation images of solids in contact. It is now necessary to detect ligaments on digital medical images and to model them in order to complete a wrist model.

Perez, Alain

1994-05-01

347

Nearshore Wave Modeling  

NSDL National Science Digital Library

Ocean waves near shore impact public safety, commerce, navigation, and, of course recreation. Predicting these waves has driven efforts to model them for more than two decades. This module introduces forecasters to different nearshore wave models, including phase-resolving and 1- and 2-dimensional spectral models. It describes the processes that wave models simulate, the assumptions they make, the initial and boundary conditions required to run the models, and potential sources of error in model forecasts. While focusing on SWAN, the module also examines the Navy Standard surf Model and Bouss-2D.

Comet

2009-05-19

348

Calibrated Properties Model  

SciTech Connect

The purpose of this Analysis/Model Report (AMR) is to document the Calibrated Properties Model that provides calibrated parameter sets for unsaturated zone (UZ) flow and transport process models for the Yucca Mountain Site Characterization Project (YMP). This work was performed in accordance with the AMR Development Plan for U0035 Calibrated Properties Model REV00 (CRWMS M&O 1999c). These calibrated property sets include matrix and fracture parameters for the UZ Flow and Transport Model (UZ Model), drift seepage models, drift-scale and mountain-scale coupled-processes models, and Total System Performance Assessment (TSPA) models as well as Performance Assessment (PA) and other participating national laboratories and government agencies. These process models provide the necessary framework to test conceptual hypotheses of flow and transport at different scales and predict flow and transport behavior under a variety of climatic and thermal-loading conditions.

C.F. Ahlers, H.H. Liu

2001-12-18

349

Calibrated Properties Model  

SciTech Connect

The purpose of this Analysis/Model Report (AMR) is to document the Calibrated Properties Model that provides calibrated parameter sets for unsaturated zone (UZ) flow and transport process models for the Yucca Mountain Site Characterization Project (YMP). This work was performed in accordance with the ''AMR Development Plan for U0035 Calibrated Properties Model REV00. These calibrated property sets include matrix and fracture parameters for the UZ Flow and Transport Model (UZ Model), drift seepage models, drift-scale and mountain-scale coupled-processes models, and Total System Performance Assessment (TSPA) models as well as Performance Assessment (PA) and other participating national laboratories and government agencies. These process models provide the necessary framework to test conceptual hypotheses of flow and transport at different scales and predict flow and transport behavior under a variety of climatic and thermal-loading conditions.

C. Ahlers; H. Liu

2000-03-12

350

Gas Kick Mechanistic Model  

E-print Network

. The model is being simulated using Excel and Visual Basic for Applications (VBA). There are specific input Excel sheets through which the program creates profiles, simulated data and charts in specific output sheets. The calculations are performed in VBA... Santos model and mechanistic model ............................. 31 Fig. 16 - Comparison between Choe two phase model and mechanistic model .............. 31 vi LIST OF TABLES Page Table 1 – Input data for wellbore geometry, mud flow and bit...

Zubairy, Raheel

2014-04-18

351

Standard Information Models  

Microsoft Academic Search

In this chapter, the base Information Model of OPC UA is introduced. This model provides the foundation for OPC UA information\\u000a modeling and is always used as foundation to define additional Information Models. We will also look at the extensions of\\u000a this model defined by the OPC UA specification. Those extensions are used to define a standard way to represent

Wolfgang Mahnke; Stefan-Helmut Leitner

352

WASP TRANSPORT MODELING AND WASP ECOLOGICAL MODELING  

EPA Science Inventory

A combination of lectures, demonstrations, and hands-on excercises will be used to introduce pollutant transport modeling with the U.S. EPA's general water quality model, WASP (Water Quality Analysis Simulation Program). WASP features include a user-friendly Windows-based interfa...

353

Analytic Modeling Queuing Models with Single  

E-print Network

Analytic Modeling Queuing Models with Single Service Facility 1 Characteristics of a Service Facility · Number of servers · Queuing discipline ­ default is FCFS · Number of queuing spaces (or buffers ­ elapsed time from arrival to departure · Waiting time ­ time spent in queue · Number of customers

Shihada, Basem

354

Bohr model as an algebraic collective model  

Microsoft Academic Search

Developments and applications are presented of an algebraic version of Bohr's collective model. Illustrative examples show that fully converged calculations can be performed quickly and easily for a large range of Hamiltonians. As a result, the Bohr model becomes an effective tool in the analysis of experimental data. The examples are chosen both to confirm the reliability of the algebraic

D. J. Rowe; T. A. Welsh; M. A. Caprio

2009-01-01

355

MODELS AND HISTORY OF MODELING Hermann Schichl  

E-print Network

a mathematical model solar system with circles epicircles predict movement moon, and planets. The model accurate of mathematics independently application. Thales brought knowledge from Egypt, predicted solar eclipse philosophers Aristotle, Eudoxos, and many more added pieces, and years following Thales, geometry mathematics

Schichl, Hermann

356

1. Quark model 1 1. QUARK MODEL  

E-print Network

1. Quark model 1 1. QUARK MODEL Revised December 2005 by C. Amsler (University of Z¨urich), T. DeGrand (University of Colorado, Boulder) and B. Krusche (University of Basel). 1.1. Quantum numbers of the quarks Quarks are strongly interacting fermions with spin 1/2 and, by convention, positive parity

Krusche, Bernd

357

14. Quark model 1 14. QUARK MODEL  

E-print Network

14. Quark model 1 14. QUARK MODEL Revised August 2011 by C. Amsler (University of Z¨urich), T. DeGrand (University of Colorado, Boulder), and B. Krusche (University of Basel). 14.1. Quantum numbers of the quarks and its constituents are a set of fermions, the quarks, and gauge bosons, the gluons. Strongly interacting

358

14. Quark model 1 14. QUARK MODEL  

E-print Network

14. Quark model 1 14. QUARK MODEL Revised December 2005 by C. Amsler (University of Z¨urich), T. DeGrand (University of Colorado, Boulder) and B. Krusche (University of Basel). 14.1. Quantum numbers of the quarks Quarks are strongly interacting fermions with spin 1/2 and, by convention, positive parity

Krusche, Bernd

359

14. Quark model 1 14. QUARK MODEL  

E-print Network

14. Quark model 1 14. QUARK MODEL Revised September 2009 by C. Amsler (University of Z¨urich), T numbers of the quarks Quarks are strongly interacting fermions with spin 1/2 and, by convention, positive parity. Antiquarks have negative parity. Quarks have the additive baryon number 1/3, antiquarks -1

360

Business Model Innovation: A Process Model  

Microsoft Academic Search

What is business model innovation? A business model is much more than a description of a particular product or service. In addition to describing the offering itself, it lays out the value proposition behind it (i.e., how it creates value for a defined set of customers). It also describes the capabilities and resources needed to execute that value proposition and

Jeanne Liedtka

361

Models and their benefits. Models + Data  

E-print Network

of individual histories 3. hypothesis testing 4. parameter estimation #12;Haploid Model Diploid Model Wright;10 Alleles'Ancestry for 15 generations #12;Mean, E(X2) = 2N. Ex.: 2N = 20.000, Generation time 30 years, E(X2

Goldschmidt, Christina

362

What is a model? Mathematical modelling Examples Conclusions What is Mathematical Modelling?  

E-print Network

What is a model? Mathematical modelling Examples Conclusions What is Mathematical Modelling? John 21, 2014 What is a Model? 1/33 #12;What is a model? Mathematical modelling Examples Conclusions Outline 1 What is a model? Disciplinary differences 2 Mathematical modelling Definition Quotes Modelling

Stockie, John

363

jModelTest: phylogenetic model averaging.  

PubMed

jModelTest is a new program for the statistical selection of models of nucleotide substitution based on "Phyml" (Guindon and Gascuel 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 52:696-704.). It implements 5 different selection strategies, including "hierarchical and dynamical likelihood ratio tests," the "Akaike information criterion," the "Bayesian information criterion," and a "decision-theoretic performance-based" approach. This program also calculates the relative importance and model-averaged estimates of substitution parameters, including a model-averaged estimate of the phylogeny. jModelTest is written in Java and runs under Mac OSX, Windows, and Unix systems with a Java Runtime Environment installed. The program, including documentation, can be freely downloaded from the software section at http://darwin.uvigo.es. PMID:18397919

Posada, David

2008-07-01

364

Trapped Radiation Model Uncertainties: Model-Data and Model-Model Comparisons  

NASA Astrophysics Data System (ADS)

The standard AP8 and AE8 models for predicting trapped proton and electron environments have been compared with several sets of flight data to evaluate model uncertainties. Model comparisons are made with flux and dose measurements made on various U.S. low-Earth orbit satellites (APEX, CRRES, DMSP, LDEF, NOAA) and Space Shuttle flights, on Russian satellites (Photon-8, Cosmos-1887, Cosmos-2044), and on the Russian Mir Space Station. This report gives the details of the model-data comparisons-summary results in terms of empirical model uncertainty factors that can be applied for spacecraft design applications are given in a combination report. The results of model-model comparisons are also presented from standard AP8 and AE8 model predictions compared with the European Space Agency versions of AP8 and AE8 and with Russian-trapped radiation models.

Armstrong, T. W.; Colborn, B. L.

2000-03-01

365

Trapped Radiation Model Uncertainties: Model-Data and Model-Model Comparisons  

NASA Astrophysics Data System (ADS)

The standard AP8 and AE8 models for predicting trapped proton and electron environments have been compared with several sets of flight data to evaluate model uncertainties. Model comparisons are made with flux and dose measurements made on various U.S. low-Earth orbit satellites (APEX, CRRES, DMSP. LDEF, NOAA) and Space Shuttle flights, on Russian satellites (Photon-8, Cosmos-1887, Cosmos-2044), and on the Russian Mir space station. This report gives the details of the model-data comparisons -- summary results in terms of empirical model uncertainty factors that can be applied for spacecraft design applications are given in a companion report. The results of model-model comparisons are also presented from standard AP8 and AE8 model predictions compared with the European Space Agency versions of AP8 and AE8 and with Russian trapped radiation models.

Armstrong, T. W.; Colborn, B. L.

2000-02-01

366

Trapped Radiation Model Uncertainties: Model-Data and Model-Model Comparisons  

NASA Technical Reports Server (NTRS)

The standard AP8 and AE8 models for predicting trapped proton and electron environments have been compared with several sets of flight data to evaluate model uncertainties. Model comparisons are made with flux and dose measurements made on various U.S. low-Earth orbit satellites (APEX, CRRES, DMSP, LDEF, NOAA) and Space Shuttle flights, on Russian satellites (Photon-8, Cosmos-1887, Cosmos-2044), and on the Russian Mir Space Station. This report gives the details of the model-data comparisons-summary results in terms of empirical model uncertainty factors that can be applied for spacecraft design applications are given in a combination report. The results of model-model comparisons are also presented from standard AP8 and AE8 model predictions compared with the European Space Agency versions of AP8 and AE8 and with Russian-trapped radiation models.

Armstrong, T. W.; Colborn, B. L.

2000-01-01

367

Pharmacokinetics: philosophy of modeling.  

PubMed

Generally speaking, there are two extremes of scientific personality types: sharpeners and levelers. Sharpeners, highly attuned to system differences and nuances, and always alert to distinctions, try hard to let nothing slip by them unnoticed. Levelers, on the other hand, attempt to submerge system differences, reveal uniform patterns, and condense disparate elements. This paper is one leveler's attempt to address the following philosophical questions confronting pharmacokinetic modelers: (1) What is the nature of reality? (2) What is a model? (3) Why do we model? (4) What are the different types of models? (5) How do we model? (6) What are the properties and characteristics of models? (7) How do we evaluate models? (8) What are some of the tricks and traps of modeling? And (9), what are some of the psychological characteristics of modelers? PMID:1555495

Boxenbaum, H

1992-01-01

368

Practical Marginalized Multilevel Models.  

PubMed

Clustered data analysis is characterized by the need to describe both systematic variation in a mean model and cluster-dependent random variation in an association model. Marginalized multilevel models embrace the robustness and interpretations of a marginal mean model, while retaining the likelihood inference capabilities and flexible dependence structures of a conditional association model. Although there has been increasing recognition of the attractiveness of marginalized multilevel models, there has been a gap in their practical application arising from a lack of readily available estimation procedures. We extend the marginalized multilevel model to allow for nonlinear functions in both the mean and association aspects. We then formulate marginal models through conditional specifications to facilitate estimation with mixed model computational solutions already in place. We illustrate the MMM and approximate MMM approaches on a cerebrovascular deficiency crossover trial using SAS and an epidemiological study on race and visual impairment using R. Datasets, SAS and R code are included as supplemental materials. PMID:24357884

Griswold, Michael E; Swihart, Bruce J; Caffo, Brian S; Zeger, Scott L

2013-01-01

369

All models are wrong.  

PubMed

As the field of phylogeography has continued to move in the model-based direction, researchers continue struggling to construct useful models for inference. These models must be both simple enough to be tractable yet contain enough of the complexity of the natural world to make meaningful inference. Beyond constructing such models for inference, researchers explore model space and test competing models with the data on hand, with the goal of improving the understanding of the natural world and the processes underlying natural biological communities. Approximate Bayesian computation (ABC) has increased in recent popularity as a tool for evaluating alternative historical demographic models given population genetic samples. As a thorough demonstration, Pelletier & Carstens (2014) use ABC to test 143 phylogeographic submodels given geographically widespread genetic samples from the salamander species Plethodon idahoensis (Carstens et al. 2014) and, in so doing, demonstrate how the results of the ABC model choice procedure are dependent on the model set one chooses to evaluate. PMID:24931159

Hickerson, Michael J

2014-06-01

370

Marine Modeling and Analysis  

NSDL National Science Digital Library

The Marine Modeling and Analysis Branch (MMAB) of the Environmental Modeling Center is responsible for the development of improved numerical weather and marine prediction modeling systems. These models provide analysis and real-time forecast guidance on marine meteorological, oceanographic, and cryospheric parameters over the global oceans and coastal areas of the US. This site provides access to MMAB modeling tools for ocean waves (including an interactive presentation,) sea ice, marine meteorology, sea surface temperature and more. The site also features a mailing list, bibliography of publications, and information about modeling products still in the experimental and development phases.

National Centers For Environmental Prediction, National O.

371

Reliability model generator  

NASA Technical Reports Server (NTRS)

An improved method and system for automatically generating reliability models for use with a reliability evaluation tool is described. The reliability model generator of the present invention includes means for storing a plurality of low level reliability models which represent the reliability characteristics for low level system components. In addition, the present invention includes means for defining the interconnection of the low level reliability models via a system architecture description. In accordance with the principles of the present invention, a reliability model for the entire system is automatically generated by aggregating the low level reliability models based on the system architecture description.

McMann, Catherine M. (Inventor); Cohen, Gerald C. (Inventor)

1991-01-01

372

The Dgp Model Revisited  

NASA Astrophysics Data System (ADS)

In this paper, we study the model proposed by Dvali, Gabadadze and Porrati (the DGP model), which produces solutions with cosmic acceleration even in the absence of a cosmological constant. The model is fitted to the recent SNLS data using the minimum ?2 test, and an analytical method is used to marginalize over the nuisance parameters h and M. The result suggests that the DPG model does not fit the SNLS data much better than the ?CDM model, and further observations are needed to better distinguish the two models.

Ng, Kah Fee; Ng, Shao Chin Cindy

2014-04-01

373

Inflation models and observation  

E-print Network

We consider small-field models which invoke the usual framework for the effective field theory, and large-field models which go beyond that. Present and future possibilities for discriminating between the models are assessed, on the assumption that the primordial curvature perturbation is generated during inflation. With PLANCK data, the theoretical and observational uncertainties on the spectral index will be comparable, providing useful discrimination between small-field models. Further discrimination between models may come later through the tensor fraction, the running of the spectral index and non-gaussianity. The prediction for the trispectrum in a generic multi-field inflation model is given for the first time.

Laila Alabidi; David Lyth

2005-12-01

374

Energy-consumption modelling  

SciTech Connect

A highly sophisticated and accurate approach is described to compute on an hourly or daily basis the energy consumption for space heating by individual buildings, urban sectors, and whole cities. The need for models and specifically weather-sensitive models, composite models, and space-heating models are discussed. Development of the Colorado State University Model, based on heat-transfer equations and on a heuristic, adaptive, self-organizing computation learning approach, is described. Results of modeling energy consumption by the city of Minneapolis and Cheyenne are given. Some data on energy consumption in individual buildings are included.

Reiter, E.R.

1980-01-01

375

Modeling volatility using state space models.  

PubMed

In time series problems, noise can be divided into two categories: dynamic noise which drives the process, and observational noise which is added in the measurement process, but does not influence future values of the system. In this framework, we show that empirical volatilities (the squared relative returns of prices) exhibit a significant amount of observational noise. To model and predict their time evolution adequately, we estimate state space models that explicitly include observational noise. We obtain relaxation times for shocks in the logarithm of volatility ranging from three weeks (for foreign exchange) to three to five months (for stock indices). In most cases, a two-dimensional hidden state is required to yield residuals that are consistent with white noise. We compare these results with ordinary autoregressive models (without a hidden state) and find that autoregressive models underestimate the relaxation times by about two orders of magnitude since they do not distinguish between observational and dynamic noise. This new interpretation of the dynamics of volatility in terms of relaxators in a state space model carries over to stochastic volatility models and to GARCH models, and is useful for several problems in finance, including risk management and the pricing of derivative securities. Data sets used: Olsen & Associates high frequency DEM/USD foreign exchange rates (8 years). Nikkei 225 index (40 years). Dow Jones Industrial Average (25 years). PMID:9730016

Timmer, J; Weigend, A S

1997-08-01

376

Reducing Model Systematic Error through Super Modelling  

NASA Astrophysics Data System (ADS)

Numerical models are key tools in the projection of the future climate change. However, state-of-the-art general circulation models (GCMs) exhibit significant systematic errors and large uncertainty exists in future climate projections, because of limitations in parameterization schemes and numerical formulations. The general approach to tackle uncertainty is to use an ensemble of several different GCMs. However, ensemble results may smear out major variability, such as the ENSO. Here we take a novel approach and build a super model (i.e., an optimal combination of several models): We coupled two atmospheric GCMs (AGCM) with one ocean GCM (OGCM). The two AGCMs receive identical boundary conditions from the OGCM, while the OGCM is driven by a weighted flux combination from the AGCMs. The atmospheric models differed in their convection scheme and climate-related parameters. As climate models show large sensitivity to convection schemes and parameterization, this approach may be a good basis for constructing a super model. We performed experiments with a small set of manually chosen coefficients and also with a learning algorithm to adjust the coefficients. The coupling strategy is able to synchronize atmospheric variability of the two AGCMs in the tropics, particularly over the western equatorial Pacific, and produce reasonable climate variability. Different coupling weights were shown to alter the simulated mean climate state. Some improvements were found that suggest a refined strategy for choosing weighting coefficients could lead to even better performance.

Shen, Mao-Lin; Keenlyside, Noel; Selten, Frank; Duane, Gregory; Wiegerinck, Wim; Hiemstra, Paul

2013-04-01

377

Develop a Model Component  

NASA Technical Reports Server (NTRS)

During my internship at NASA, I was a model developer for Ground Support Equipment (GSE). The purpose of a model developer is to develop and unit test model component libraries (fluid, electrical, gas, etc.). The models are designed to simulate software for GSE (Ground Special Power, Crew Access Arm, Cryo, Fire and Leak Detection System, Environmental Control System (ECS), etc. .) before they are implemented into hardware. These models support verifying local control and remote software for End-Item Software Under Test (SUT). The model simulates the physical behavior (function, state, limits and 110) of each end-item and it's dependencies as defined in the Subsystem Interface Table, Software Requirements & Design Specification (SRDS), Ground Integrated Schematic (GIS), and System Mechanical Schematic.(SMS). The software of each specific model component is simulated through MATLAB's Simulink program. The intensiv model development life cycle is a.s follows: Identify source documents; identify model scope; update schedule; preliminary design review; develop model requirements; update model.. scope; update schedule; detailed design review; create/modify library component; implement library components reference; implement subsystem components; develop a test script; run the test script; develop users guide; send model out for peer review; the model is sent out for verifictionlvalidation; if there is empirical data, a validation data package is generated; if there is not empirical data, a verification package is generated; the test results are then reviewed; and finally, the user. requests accreditation, and a statement of accreditation is prepared. Once each component model is reviewed and approved, they are intertwined together into one integrated model. This integrated model is then tested itself, through a test script and autotest, so that it can be concluded that all models work conjointly, for a single purpose. The component I was assigned, specifically, was a fluid component, a discrete pressure switch. The switch takes a fluid pressure input, and if the pressure is greater than a designated cutoff pressure, the switch would stop fluid flow.

Ensey, Tyler S.

2013-01-01

378

Volumetric particle modeling  

E-print Network

This dissertation presents a robust method of modeling objects and forces for computer animation. Within this method objects and forces are represented as particles. As in most modeling systems, the movement of objects is driven by physically based...

Dingle, Brent Michael

2007-09-17

379

Monte Carlo Modeling  

NSDL National Science Digital Library

Monte Carlo modeling refers to the solution of mathematical problems with the use of random numbers. This can include both function integration and the modeling of stochastic phenomena using random processes.

David Joiner

380

X-33 RCS model  

NASA Technical Reports Server (NTRS)

Model support system and instumentation cabling of the 1% scale X-33 reaction control system model. Installed in the Unitary Plan Wind Tunnel for supersonic testing. In building 1251, test section #2.

1998-01-01

381

Communication system modeling  

NASA Technical Reports Server (NTRS)

This report presents the results of work on communications systems modeling and covers three different areas of modeling. The first of these deals with the modeling of signals in communication systems in the frequency domain and the calculation of spectra for various modulations. These techniques are applied in determining the frequency spectra produced by a unified carrier system, the down-link portion of the Command and Communications System (CCS). The second modeling area covers the modeling of portions of a communication system on a block basis. A detailed analysis and modeling effort based on control theory is presented along with its application to modeling of the automatic frequency control system of an FM transmitter. A third topic discussed is a method for approximate modeling of stiff systems using state variable techniques.

Holland, L. D.; Walsh, J. R., Jr.; Wetherington, R. D.

1971-01-01

382

SEDIMENT GEOCHEMICAL MODEL  

EPA Science Inventory

Until recently, sediment geochemical models (diagenetic models) have been only able to explain sedimentary flux and concentration profiles for a few simplified geochemical cycles (e.g., nitrogen, carbon and sulfur). However with advances in numerical methods, increased accuracy ...

383

Modeling Instruction Program  

NSDL National Science Digital Library

Arizona State University's modeling instruction and software development research. This approach to reform of curriculum design and teaching methodology has been guided by a Modeling Theory of Physics Instruction.

Hestenes, David

2003-10-10

384

Content models with attitude  

E-print Network

We present a probabilistic topic model for jointly identifying properties and attributes of social media review snippets. Our model simultaneously learns a set of properties of a product and captures aggregate user sentiments ...

Sauper, Christina Joan

385

TMDL RUSLE MODEL  

EPA Science Inventory

We developed a simplified spreadsheet modeling approach for characterizing and prioritizing sources of sediment loadings from watersheds in the United States. A simplified modeling approach was developed to evaluate sediment loadings from watersheds and selected land segments. ...

386

Bounding Species Distribution Models  

NASA Technical Reports Server (NTRS)

Species distribution models are increasing in popularity for mapping suitable habitat for species of management concern. Many investigators now recognize that extrapolations of these models with geographic information systems (GIS) might be sensitive to the environmental bounds of the data used in their development, yet there is no recommended best practice for "clamping" model extrapolations. We relied on two commonly used modeling approaches: classification and regression tree (CART) and maximum entropy (Maxent) models, and we tested a simple alteration of the model extrapolations, bounding extrapolations to the maximum and minimum values of primary environmental predictors, to provide a more realistic map of suitable habitat of hybridized Africanized honey bees in the southwestern United States. Findings suggest that multiple models of bounding, and the most conservative bounding of species distribution models, like those presented here, should probably replace the unbounded or loosely bounded techniques currently used [Current Zoology 57 (5): 642-647, 2011].

Stohlgren, Thomas J.; Jarnevich, Cahterine S.; Morisette, Jeffrey T.; Esaias, Wayne E.

2011-01-01

387

Supersymmetry and model building  

SciTech Connect

An introductory review of supersymmetry and supersymmetric model building is presented. The topics discussed include, a brief introduction to the formalism of supersymmetry, the gauge hierarchy problem, the minimal supersymmetric standard model and supersymmetric grand unified theories.

Raby, S.

1986-06-01

388

Protein solubility modeling  

NASA Technical Reports Server (NTRS)

A thermodynamic framework (UNIQUAC model with temperature dependent parameters) is applied to model the salt-induced protein crystallization equilibrium, i.e., protein solubility. The framework introduces a term for the solubility product describing protein transfer between the liquid and solid phase and a term for the solution behavior describing deviation from ideal solution. Protein solubility is modeled as a function of salt concentration and temperature for a four-component system consisting of a protein, pseudo solvent (water and buffer), cation, and anion (salt). Two different systems, lysozyme with sodium chloride and concanavalin A with ammonium sulfate, are investigated. Comparison of the modeled and experimental protein solubility data results in an average root mean square deviation of 5.8%, demonstrating that the model closely follows the experimental behavior. Model calculations and model parameters are reviewed to examine the model and protein crystallization process. Copyright 1999 John Wiley & Sons, Inc.

Agena, S. M.; Pusey, M. L.; Bogle, I. D.

1999-01-01

389

How Mesoscale Models Work  

NSDL National Science Digital Library

The goal of this training module is to help you increase your understanding of how mesoscale models work. Such understanding, in turn, can help you more efficiently and accurately evaluate model-generated forecast products.

COMET

2002-04-22

390

Visualization of Model Output  

NSDL National Science Digital Library

Visualization of output from mathematical or statistical models is one of the best ways to introduce introductory geoscience students to the results and behavior of sophisticated models. Example of good sites ...

391

Of Molecules and Models.  

ERIC Educational Resources Information Center

Presents an activity in which models help students visualize both the DNA process and transcription. After constructing DNA, RNA messenger, and RNA transfer molecules; students model cells, protein synthesis, codons, and RNA movement. (MDH)

Brinner, Bonnie

1992-01-01

392

Melanoma Risk Prediction Models  

Cancer.gov

The following risk prediction models are intended primarily for research use and have been peer-reviewed, meaning the methodology and results of these models have been evaluated by qualified scientists and clinicians and published in scientific and medical journals.

393

Exposure Analysis Modeling System  

EPA Science Inventory

The Exposure Analysis Modeling System (EXAMS) is an interactive software application for formulating aquatic ecosystem models and evaluating the fate, transport, and exposure concentrations of synthetic organic chemicals including pesticides, industrial materials, and leachates f...

394

Modeling Thermospheric Neutral Density.  

E-print Network

??Satellite drag prediction requires determination of thermospheric neutral density. The NCAR Thermosphere-Ionosphere-Electrodynamics General Circulation Model (TIEGCM) and the global-mean Thermosphere-Ionosphere-Mesosphere-Electrodynamics General Circulation Model (TIMEGCM) were… (more)

Qian, Liying

2007-01-01

395

ISIS Camera Model Design  

NASA Astrophysics Data System (ADS)

The Integrated Software for Imagers and Spectromters (ISIS) provides camera model support for a variety of past and current NASA missions. Adding new camera models to ISIS has become easier due to object-oriented design.

Anderson, J. A.

2008-03-01

396

Osteoporotic fracture models.  

PubMed

Animal models are widely used to investigate the pathogenesis of osteoporosis and for the clinical testing of anti-resorptive drugs. However, osteoporotic fracture models designed to investigate novel ways to treat fractures of osteoporotic bone must fulfil requirements distinct from those of pharmacological testing. Bone strength and toughness, implant fixation and osteointegration and fracture repair are of particular interest. Osteoporotic models should reflect the underlying clinical scenario be that primary type 1 (post-menopausal) osteoporosis, primary type 2 (senile) osteoporosis or secondary osteoporosis. In each scenario, small and large animal models have been developed. While rodent models facilitate the study of fractures in strains specifically established to facilitate understanding of the pathologic basis of disease, concerns remain about the relevance of small animal fracture models to the human situation. There is currently no all-encompassing model, and the choice of species and model must be individualized to the scientific question being addressed. PMID:25388154

Simpson, A Hamish; Murray, Iain R

2015-02-01

397

The Model Builders  

NASA Technical Reports Server (NTRS)

This video explores the world of modeling at the NASA Johnson Space Center. Artisans create models, large and small, to help scientists and engineers make final design modifications before building more costly prototypes.

1991-01-01

398

METEOROLOGICAL AND TRANSPORT MODELING  

EPA Science Inventory

Advanced air quality simulation models, such as CMAQ, as well as other transport and dispersion models, require accurate and detailed meteorology fields. These meteorology fields include primary 3-dimensional dynamical and thermodynamical variables (e.g., winds, temperature, mo...

399

Faraday Loop Model  

NSDL National Science Digital Library

The EJS Faraday Loop Model shows a conducting loop in a time-dependent constant magnetic field. The model is initially incomplete and students must complete the model by adding the appropriate equations. If Ejs is installed, right-clicking within the plot and selecting âOpen Ejs Modelâ from the pop-up menu item allows for editing of the model. The Faraday Loop model was created using the Easy Java Simulations (Ejs) modeling tool. It is distributed as a ready-to-run (compiled) Java archive. Double clicking the ejs_em_FaradayLoop.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 models. Additional Ejs models are available. They can be found by searching ComPADRE for Open Source Physics, OSP, or Ejs.

Cox, Anne

2009-06-26

400

MODELING EARTHQUAKE DYNAMICS  

E-print Network

Abstract. In this paper, we investigate questions arising in [89]. Pseudo causal models connecting magnitudes and waiting times are consider, through generalized regression. We do use conditional model (magnitude given previous waiting time,

Arthur Charpentier; Marilou Durand; Mathieu Boudreault; A. Charpentier; M. Durand; M. Boudreault

2013-01-01

401

Generalized Additive Models  

Microsoft Academic Search

Likelihood-based regression models such as the normal linear regression model and the linear logistic model, assume a linear (or some other parametric) form for the covariates $X_1, X_2, \\\\cdots, X_p$. We introduce the class of generalized additive models which replaces the linear form $\\\\sum \\\\beta_jX_j$ by a sum of smooth functions $\\\\sum s_j(X_j)$. The $s_j(\\\\cdot)$'s are unspecified functions that are

Trevor Hastie; Robert Tibshirani

1986-01-01

402

Introduction to Ocean Models  

NSDL National Science Digital Library

Oceans cover over 70% of the surface of the earth, yet many details of their workings are not fully understood. To better understand and forecast the state of the ocean, we rely on numerical ocean models. Ocean models combine observations and physics to predict the ocean temperature, salinity, and currents at any time and any place across the ocean basins. This module will discuss what goes into numerical ocean models, including model physics, coordinate systems, parameterization, initialization, and boundary conditions.

Comet

2007-08-06

403

State-Space Models  

Microsoft Academic Search

\\u000a A very general model that seems to subsume a whole class of special cases of interest in much the same way that linear regression\\u000a does is the state-space model or the dynamic linear model, which was introduced in Kalman (1960) and Kalman and Bucy (1961).\\u000a Although the model was originally introduced as a method primarily for use in aerospace-related research,

Robert H. Shumway; David S. Stoffer

404

Interconnected air spring model  

Microsoft Academic Search

This article considers the mathematical modelling of the spring force of three interconnected rolling diaphragm type air springs used on a 40-ton tri-axle semi-trailer. The aim of the air spring model is to obtain a validated mathematical model that can be used in full vehicle multi-body dynamic simulations. The model considers the flow effects in the pipes connecting the three

Cor-Jacques Kat; Pieter Schalk Els

2009-01-01

405

Aerosol Modeling for the Global Model Initiative  

NASA Technical Reports Server (NTRS)

The goal of this project is to develop an aerosol module to be used within the framework of the Global Modeling Initiative (GMI). The model development work will be preformed jointly by the University of Michigan and AER, using existing aerosol models at the two institutions as starting points. The GMI aerosol model will be tested, evaluated against observations, and then applied to assessment of the effects of aircraft sulfur emissions as needed by the NASA Subsonic Assessment in 2001. The work includes the following tasks: 1. Implementation of the sulfur cycle within GMI, including sources, sinks, and aqueous conversion of sulfur. Aerosol modules will be added as they are developed and the GMI schedule permits. 2. Addition of aerosol types other than sulfate particles, including dust, soot, organic carbon, and black carbon. 3. Development of new and more efficient parameterizations for treating sulfate aerosol nucleation, condensation, and coagulation among different particle sizes and types.

Weisenstein, Debra K.; Ko, Malcolm K. W.

2001-01-01

406

3 Human vs. model 2 Salience model  

E-print Network

4 Contour model Robert J. Peters (1), T. Nathan Mundhenk (2), Laurent Itti (2), and Christof Koch (1 Winner-take-all Inhibition of return Attended location adapted from Itti&Koch (2001), Nat. Rev. Neurosci

Peters, Rob

407

Sources of Model Error  

NSDL National Science Digital Library

This undergraduate meteorology tutorial from Texas A&M University describes the common sources of weather forecasting computer model error, ways to identify model error, and how to correct a forecast for some simple types of error. Model sensitivity to parameterization and topography are covered.

Nielsen-Gammon, John

1996-01-01

408

Generic sonar Model  

Microsoft Academic Search

The Generic Sonar Model is a computer program designed to provide sonar system developers with a comprehensive modeling capability for evaluating the performance of sonar systems and investigating the ocean environment in which they operate. The model provides features not presently available in any single computer program. These permit cost\\/accuracy trade-offs for specific applications, and interfacing the results with generalized

H. Weinberg

1982-01-01

409

Lightning Return Stroke Models  

Microsoft Academic Search

We test the two most commonly used lightning return stroke models, Bruce-Golde and trammission line, against subsequent stroke electric and magnetic field wave forms measured simultaneously at near and distant stations and show that these models are inadequate to describe the experimental data. We then propose a new return stroke model that is physically plausible and that yields good approximations

Y. T. Lin; M. A. Uman; R. B. Standler

1980-01-01

410

Bioeconomic and market models  

Microsoft Academic Search

5 Abstract: The United States has a century of experience with the development of models that describe markets for forest products and trends in resource conditions. In the last four decades, increasing rigor in policy debates has stimulated the development of models to support policy analysis. Increasingly, research has evolved (often relying on computer-based models) to increase understanding of consumer

Richard Haynes; Darius Adams; Peter Ince; John Mills; Ralph Alig

411

An Eddifying Parsons Model  

E-print Network

The time-mean effects of eddies are studied in a model based on the Parsons–Veronis–Huang–Flierl models of the wind-driven gyre. Much of the analysis used for the steady solutions carries over if the model is cast in terms ...

Ferrari, Raffaele

412

Phenomenological models of baryon  

E-print Network

In this paper, I present almost my works performed during my time at VNU. I was interested in the composite Skyrme model proposed by H. Y. Cheung and F. Gursey. The expanding for this model based on results obtained from the original Skyrme model given by T. H. R. Skyrme in 1961 was general and interesting.

Do Quoc Tuan

2008-07-12

413

A Model Chemistry Class.  

ERIC Educational Resources Information Center

Described is an activity which uses a 96-well reaction plate and soda straws to construct a model of the periodic table of the elements. The model illustrates the ionization energies of the various elements. Construction of the model and related concepts are discussed. (CW)

Summerlin, Lee; Borgford, Christie

1989-01-01

414

Bicycles, motorcycles, and models  

Microsoft Academic Search

The development of bicycles and motorcycles since the first patented running machine, or draisine, in 1817 is described. Bicycle modeling and control were also discussed. These models include: derivatives or simplifications of Whipple's bicycle dynamics model in which the lateral motion constraints at the road contact are nonholonomic, requiring special techniques to form correct equations of motion; and the Timoshenko-Young

DAVID J. N. LIMEBEER; ROBIN S. SHARP

2006-01-01

415

The Constructivist Learning Model  

NSDL National Science Digital Library

Much cognitive science research has been used to support a new model of learning. This most promising new model is called the Constructivist Learning Model (CLM). Russell Yeany (University of Georgia) has called CLM the most exciting idea of the past 50 y

Robert E. Yager

2000-01-01

416

HETEROGENEOUS MODELING AND  

E-print Network

PTOLEMY II HETEROGENEOUS CONCURRENT MODELING AND DESIGN IN JAVA Edited by: Christopher Hylands of California at Berkeley http://ptolemy.eecs.berkeley.edu Document Version 2.0.1 for use with Ptolemy II 2 Concurrent Modeling and Design Contents Part 1: Using Ptolemy II 1. Introduction 1-1 1.1.Modeling and Design

417

Reasoning and Formal Modelling  

E-print Network

Reasoning and Formal Modelling for Forensic Science Lecture 10 Prof. Dr. Benedikt L¨owe Reasoning and Formal Modelling for Forensic Science Lecture 10 Prof. Dr. Benedikt L¨owe 2nd Semester 2010/11 #12;Reasoning and Formal Modelling for Forensic Science Lecture 10 Prof. Dr. Benedikt L¨owe A reminder from

Löwe, Benedikt

418

Reasoning and Formal Modelling  

E-print Network

Reasoning and Formal Modelling for Forensic Science Lecture 6 Prof. Dr. Benedikt L¨owe Reasoning and Formal Modelling for Forensic Science Lecture 6 Prof. Dr. Benedikt L¨owe 2nd Semester 2010/11 #12;Reasoning and Formal Modelling for Forensic Science Lecture 6 Prof. Dr. Benedikt L¨owe Reminder: Controlled

Löwe, Benedikt

419

Reasoning and Formal Modelling  

E-print Network

Reasoning and Formal Modelling for Forensic Science Lecture 5 Prof. Dr. Benedikt L¨owe Reasoning and Formal Modelling for Forensic Science Lecture 5 Prof. Dr. Benedikt L¨owe 2nd Semester 2010/11 #12;Reasoning and Formal Modelling for Forensic Science Lecture 5 Prof. Dr. Benedikt L¨owe Reminder: Controlled

Löwe, Benedikt

420

Reasoning and Formal Modelling  

E-print Network

Reasoning and Formal Modelling for Forensic Science Lecture 12 Prof. Dr. Benedikt L¨owe Reasoning and Formal Modelling for Forensic Science Lecture 12 Prof. Dr. Benedikt L¨owe 2nd Semester 2010/11 #12;Reasoning and Formal Modelling for Forensic Science Lecture 12 Prof. Dr. Benedikt L¨owe Plan for today. #12

Löwe, Benedikt

421

Reasoning and Formal Modelling  

E-print Network

Reasoning and Formal Modelling for Forensic Science Lecture 9 Prof. Dr. Benedikt L¨owe Reasoning and Formal Modelling for Forensic Science Lecture 9 Prof. Dr. Benedikt L¨owe 2nd Semester 2010/11 #12;Reasoning and Formal Modelling for Forensic Science Lecture 9 Prof. Dr. Benedikt L¨owe Argumentation Schemes

Löwe, Benedikt

422

Reasoning and Formal Modelling  

E-print Network

Reasoning and Formal Modelling for Forensic Science Lecture 4 Prof. Dr. Benedikt L¨owe Reasoning and Formal Modelling for Forensic Science Lecture 4 Prof. Dr. Benedikt L¨owe 2nd Semester 2010/11 #12;Reasoning and Formal Modelling for Forensic Science Lecture 4 Prof. Dr. Benedikt L¨owe Where are we right

Löwe, Benedikt

423

Reasoning and Formal Modelling  

E-print Network

Reasoning and Formal Modelling for Forensic Science Lecture 7 Prof. Dr. Benedikt L¨owe Reasoning and Formal Modelling for Forensic Science Lecture 7 Prof. Dr. Benedikt L¨owe 2nd Semester 2010/11 #12;Reasoning and Formal Modelling for Forensic Science Lecture 7 Prof. Dr. Benedikt L¨owe Reminder: logica

Löwe, Benedikt

424

Reasoning and Formal Modelling  

E-print Network

Reasoning and Formal Modelling for Forensic Science Lecture 3 Prof. Dr. Benedikt L¨owe Reasoning and Formal Modelling for Forensic Science Lecture 3 Prof. Dr. Benedikt L¨owe 2nd Semester 2010/11 #12;Reasoning and Formal Modelling for Forensic Science Lecture 3 Prof. Dr. Benedikt L¨owe Binary connectives

Löwe, Benedikt

425

IR DIAL performance modeling  

SciTech Connect

We are developing a DIAL performance model for CALIOPE at LLNL. The intent of the model is to provide quick and interactive parameter sensitivity calculations with immediate graphical output. A brief overview of the features of the performance model is given, along with an example of performance calculations for a non-CALIOPE application.

Sharlemann, E.T.

1994-07-01

426

Modeling the calcite Lysocline  

Microsoft Academic Search

A numerical model of calcite dissolution in contact with sediment pore water is used to predict the depth and shape of the calcite lysocline in the deep sea. Model results are compared with lysocline data from 13 regions in the Atlantic, Pacific, and Indian Oceans. The model lysocline shape is sensitive to the calcite dissolution rate constant, the calcite, organic

David Archer

1991-01-01

427

Crushed Salt Constitutive Model  

SciTech Connect

The constitutive model used to describe the deformation of crushed salt is presented in this report. Two mechanisms -- dislocation creep and grain boundary diffusional pressure solution -- are combined to form the basis for the constitutive model governing the deformation of crushed salt. The constitutive model is generalized to represent three-dimensional states of stress. Upon complete consolidation, the crushed-salt model reproduces the Multimechanism Deformation (M-D) model typically used for the Waste Isolation Pilot Plant (WIPP) host geological formation salt. New shear consolidation tests are combined with an existing database that includes hydrostatic consolidation and shear consolidation tests conducted on WIPP and southeastern New Mexico salt. Nonlinear least-squares model fitting to the database produced two sets of material parameter values for the model -- one for the shear consolidation tests and one for a combination of the shear and hydrostatic consolidation tests. Using the parameter values determined from the fitted database, the constitutive model is validated against constant strain-rate tests. Shaft seal problems are analyzed to demonstrate model-predicted consolidation of the shaft seal crushed-salt component. Based on the fitting statistics, the ability of the model to predict the test data, and the ability of the model to predict load paths and test data outside of the fitted database, the model appears to capture the creep consolidation behavior of crushed salt reasonably well.

Callahan, G.D.

1999-02-01

428

'Rational' Turbulence Models?  

NASA Astrophysics Data System (ADS)

A procedure to construct turbulence models is outlined beginning with the simplest case, a model for weak time-dependent perturbations of homogeneous isotropic turbulence, and ending with some models for inhomogeneous turbulence. The approach combines features of Yoshizawa's two-scale direct interaction approximation and the Hilbert expansion of kinetic theory.

Rubinstein, Robert; Woodruff, Stephen L.

429

Global Timber Model (GTM)  

EPA Science Inventory

GTM is an economic model capable of examining global forestry land-use, management, and trade responses to policies. In responding to a policy, the model captures afforestation, forest management, and avoided deforestation behavior. The model estimates harvests in industrial fore...

430

Modeling Hybrid Genetic Algorithms  

Microsoft Academic Search

This paper looks at how one form of hybrid genetic algorithm can be modeledin the context of the existing models for the simple genetic algorithm; it shouldbe possible to model the integration of other types of local search with geneticalgorithms using the same basic approach. A secondary goal of this paper is toreview the existing models for finite and infinite

Darrell Whitley

1995-01-01

431

Tests of Rating Models  

ERIC Educational Resources Information Center

The study reports empirical tests of Anderson's, Haubensak's, Helson's, and Parducci's rating models when two end anchors are used for rating. The results show that these models cannot predict the judgment effect called here the Dai Pra effect. It is shown that an extension of Anderson's model is consistent with this effect. The results confirm…

Masin, Sergio Cesare; Busetto, Martina

2010-01-01

432

The Model Neuron  

NSDL National Science Digital Library

In this activity, learners create a model of a neuron by using colored clay or play dough. Learners use diagrams to build the model and then label the parts on a piece of paper. This resource guide includes extension ideas like using fruit or candy instead of clay. See the "Modeling the Nervous System" page for a recipe for play dough.

2012-06-26

433

New Dual Quark Models  

Microsoft Academic Search

On the basis of new representations of the projective group, we construct some new dual quark models whose spin and internal symmetry are not multiplicative. One model is a factorized theory of exotic states with broken exchange degeneracy, ninth mesons being optional. The exotic states are suppressed three units below the Pomeranchon. In another model, with spin-orbit coupling and curved

K. Bardakci; M. B. Halpern

1971-01-01

434

Rock Properties Model  

SciTech Connect

The purpose of this model report is to document the Rock Properties Model version 3.1 with regard to input data, model methods, assumptions, uncertainties and limitations of model results, and qualification status of the model. The report also documents the differences between the current and previous versions and validation of the model. The rock properties model provides mean matrix and lithophysae porosity, and the cross-correlated mean bulk density as direct input to the ''Saturated Zone Flow and Transport Model Abstraction'', MDL-NBS-HS-000021, REV 02 (BSC 2004 [DIRS 170042]). The constraints, caveats, and limitations associated with this model are discussed in Section 6.6 and 8.2. Model validation accomplished by corroboration with data not cited as direct input is discussed in Section 7. The revision of this model report was performed as part of activities being conducted under the ''Technical Work Plan for: The Integrated Site Model, Revision 05'' (BSC 2004 [DIRS 169635]). The purpose of this revision is to bring the report up to current procedural requirements and address the Regulatory Integration Team evaluation comments. The work plan describes the scope, objectives, tasks, methodology, and procedures for this process.

C. Lum

2004-09-16

435