The Experts below are selected from a list of 6975 Experts worldwide ranked by ideXlab platform
Michele Parrinello - One of the best experts on this subject based on the ideXlab platform.
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interaction of short Chain Alkane thiols and thiolates with small gold clusters adsorption structures and energetics
Journal of Chemical Physics, 2001Co-Authors: Daniel Kruger, Roger Rousseau, Dominik Marx, Harald Fuchs, Michele ParrinelloAbstract:Gold–sulfur bonding is investigated theoretically using a variety of electronic structure methods, including the Becke–Perdew semilocal density functional, the B3LYP hybrid approach, the Hartree–Fock method, and the post Hartree–Fock approaches MP2 and QCISD(T). Particular emphasis is given to adsorption structure and energetics in the case of weak and strong interactions of this general type, using up to five gold atoms and up to three carbon atoms in the aliphatic Chain. It is found that all methods which take into account electron correlation, including the density functional methods, lead to quite similar structures. Concerning the energetics, the Becke–Perdew functional is found to overbind typically by about 5–15%. Quasiglobal structural relaxation based on ab initio simulated annealing clearly shows that the adsorption of thiolates onto gold clusters results in a dramatic distortion of the cluster framework. From a structural point of view the thiolate sulfur–gold bond has a distinctive directional...
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interaction of short Chain Alkane thiols and thiolates with small gold clusters adsorption structures and energetics
Journal of Chemical Physics, 2001Co-Authors: Daniel Kruger, Roger Rousseau, Dominik Marx, Harald Fuchs, Michele ParrinelloAbstract:Gold–sulfur bonding is investigated theoretically using a variety of electronic structure methods, including the Becke–Perdew semilocal density functional, the B3LYP hybrid approach, the Hartree–Fock method, and the post Hartree–Fock approaches MP2 and QCISD(T). Particular emphasis is given to adsorption structure and energetics in the case of weak and strong interactions of this general type, using up to five gold atoms and up to three carbon atoms in the aliphatic Chain. It is found that all methods which take into account electron correlation, including the density functional methods, lead to quite similar structures. Concerning the energetics, the Becke–Perdew functional is found to overbind typically by about 5–15%. Quasiglobal structural relaxation based on ab initio simulated annealing clearly shows that the adsorption of thiolates onto gold clusters results in a dramatic distortion of the cluster framework. From a structural point of view the thiolate sulfur–gold bond has a distinctive directional (covalent) character which results in a clear preference for Au–S–C bond angles in the range of 103.5° and 108.7°. In general, dissociation into open-shell species is preferred against the formation of the ionic closed-shell counterparts if the sulfur–gold bond is forced to break. However, neutral closed-shell products can be favored if fragmentation of the gold cluster is allowed for as a dissociation channel. Finally, it is demonstrated that using ethyl or n-propyl Chains instead of the methyl group leads to only small changes of the binding energies.
Lei Wang - One of the best experts on this subject based on the ideXlab platform.
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two novel metal independent long Chain alkyl alcohol dehydrogenases from geobacillus thermodenitrificans ng80 2
Microbiology, 2009Co-Authors: Xueqian Liu, Jing Zhang, Yanpeng Dong, Aixiang Zhang, Lei Wang, Lu FengAbstract:Two alkyl alcohol dehydrogenase (ADH) genes from the long-Chain Alkane-degrading strain Geobacillus thermodenitrificans NG80-2 were characterized in vitro. ADH1 and ADH2 were prepared heterologously in Escherichia coli as a homooctameric and a homodimeric protein, respectively. Both ADHs can oxidize a broad range of alkyl alcohols up to at least C30, as well as 1,3-propanediol and acetaldehyde. ADH1 also oxidizes glycerol, and ADH2 oxidizes isopropyl alcohol, isoamylol, acetone, octanal and decanal. The best substrate is ethanol for ADH1 and 1-octanol for ADH2. For both ADHs, the optimum assay condition is at 60 °C and pH 8.0, and both NAD and NADP can be used as the cofactor. Sequence analysis reveals that ADH1 and ADH2 belong to the Fe-containing/activated long-Chain ADHs. However, the two enzymes contain neither Fe nor other metals, and Fe is not required for the activity, suggesting a new type of ADH. The ADHs characterized here are potentially useful in crude oil bioremediation and other bioconversion processes.
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Crystal structure of long-Chain Alkane monooxygenase (LadA) in complex with coenzyme FMN: unveiling the long-Chain Alkane hydroxylase
Journal of molecular biology, 2007Co-Authors: Xueqian Liu, Wei Wang, Lei Wang, Lu Feng, Wen Yang, Mark Bartlam, Zihe RaoAbstract:LadA, a long-Chain Alkane monooxygenase, utilizes a terminal oxidation pathway for the conversion of long-Chain Alkanes (up to at least C(36)) to corresponding primary alcohols in thermophilic bacillus Geobacillus thermodenitrificans NG80-2. Here, we report the first structure of the long-Chain Alkane hydroxylase, LadA, and its complex with the flavin mononucleotide (FMN) coenzyme. LadA is characterized as a new member of the SsuD subfamily of the bacterial luciferase family via a surprising structural relationship. The LadA:FMN binary complex structure and a LadA:FMN:Alkane model reveal a hydrophobic cavity that has dual roles: to provide a hydrogen-bond donor (His138) for catalysis and to create a solvent-free environment in which to stabilize the C4a-hydroperoxyflavin intermediate. Consequently, LadA should catalyze the conversion of long-Chain Alkanes via the acknowledged flavoprotein monooxygenase mechanism. This finding suggests that the ability of LadA to catalyze the degradation of long-Chain Alkanes is determined by the binding mode of the long-Chain Alkane substrates. The LadA structure opens a rational perspective to explore and alter the substrate binding site of LadA, with potential biotechnological applications in areas such as petroleum exploration and treatment of environmental oil pollution.
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genome and proteome of long Chain Alkane degrading geobacillus thermodenitrificans ng80 2 isolated from a deep subsurface oil reservoir
Proceedings of the National Academy of Sciences of the United States of America, 2007Co-Authors: Lu Feng, Wei Wang, Jiansong Cheng, Guang Zhao, Yun Tang, Xia Peng, Lei WangAbstract:The complete genome sequence of Geobacillus thermodenitrificans NG80-2, a thermophilic bacillus isolated from a deep oil reservoir in Northern China, consists of a 3,550,319-bp chromosome and a 57,693-bp plasmid. The genome reveals that NG80-2 is well equipped for adaptation into a wide variety of environmental niches, including oil reservoirs, by possessing genes for utilization of a broad range of energy sources, genes encoding various transporters for efficient nutrient uptake and detoxification, and genes for a flexible respiration system including an aerobic branch comprising five terminal oxidases and an anaerobic branch comprising a complete denitrification pathway for quick response to dissolved oxygen fluctuation. The identification of a nitrous oxide reductase gene has not been previously described in Gram-positive bacteria. The proteome further reveals the presence of a long-Chain Alkane degradation pathway; and the function of the key enzyme in the pathway, the long-Chain Alkane monooxygenase LadA, is confirmed by in vivo and in vitro experiments. The thermophilic soluble monomeric LadA is an ideal candidate for treatment of environmental oil pollutions and biosynthesis of complex molecules.
Daniel Kruger - One of the best experts on this subject based on the ideXlab platform.
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interaction of short Chain Alkane thiols and thiolates with small gold clusters adsorption structures and energetics
Journal of Chemical Physics, 2001Co-Authors: Daniel Kruger, Roger Rousseau, Dominik Marx, Harald Fuchs, Michele ParrinelloAbstract:Gold–sulfur bonding is investigated theoretically using a variety of electronic structure methods, including the Becke–Perdew semilocal density functional, the B3LYP hybrid approach, the Hartree–Fock method, and the post Hartree–Fock approaches MP2 and QCISD(T). Particular emphasis is given to adsorption structure and energetics in the case of weak and strong interactions of this general type, using up to five gold atoms and up to three carbon atoms in the aliphatic Chain. It is found that all methods which take into account electron correlation, including the density functional methods, lead to quite similar structures. Concerning the energetics, the Becke–Perdew functional is found to overbind typically by about 5–15%. Quasiglobal structural relaxation based on ab initio simulated annealing clearly shows that the adsorption of thiolates onto gold clusters results in a dramatic distortion of the cluster framework. From a structural point of view the thiolate sulfur–gold bond has a distinctive directional...
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interaction of short Chain Alkane thiols and thiolates with small gold clusters adsorption structures and energetics
Journal of Chemical Physics, 2001Co-Authors: Daniel Kruger, Roger Rousseau, Dominik Marx, Harald Fuchs, Michele ParrinelloAbstract:Gold–sulfur bonding is investigated theoretically using a variety of electronic structure methods, including the Becke–Perdew semilocal density functional, the B3LYP hybrid approach, the Hartree–Fock method, and the post Hartree–Fock approaches MP2 and QCISD(T). Particular emphasis is given to adsorption structure and energetics in the case of weak and strong interactions of this general type, using up to five gold atoms and up to three carbon atoms in the aliphatic Chain. It is found that all methods which take into account electron correlation, including the density functional methods, lead to quite similar structures. Concerning the energetics, the Becke–Perdew functional is found to overbind typically by about 5–15%. Quasiglobal structural relaxation based on ab initio simulated annealing clearly shows that the adsorption of thiolates onto gold clusters results in a dramatic distortion of the cluster framework. From a structural point of view the thiolate sulfur–gold bond has a distinctive directional (covalent) character which results in a clear preference for Au–S–C bond angles in the range of 103.5° and 108.7°. In general, dissociation into open-shell species is preferred against the formation of the ionic closed-shell counterparts if the sulfur–gold bond is forced to break. However, neutral closed-shell products can be favored if fragmentation of the gold cluster is allowed for as a dissociation channel. Finally, it is demonstrated that using ethyl or n-propyl Chains instead of the methyl group leads to only small changes of the binding energies.
Lu Feng - One of the best experts on this subject based on the ideXlab platform.
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two novel metal independent long Chain alkyl alcohol dehydrogenases from geobacillus thermodenitrificans ng80 2
Microbiology, 2009Co-Authors: Xueqian Liu, Jing Zhang, Yanpeng Dong, Aixiang Zhang, Lei Wang, Lu FengAbstract:Two alkyl alcohol dehydrogenase (ADH) genes from the long-Chain Alkane-degrading strain Geobacillus thermodenitrificans NG80-2 were characterized in vitro. ADH1 and ADH2 were prepared heterologously in Escherichia coli as a homooctameric and a homodimeric protein, respectively. Both ADHs can oxidize a broad range of alkyl alcohols up to at least C30, as well as 1,3-propanediol and acetaldehyde. ADH1 also oxidizes glycerol, and ADH2 oxidizes isopropyl alcohol, isoamylol, acetone, octanal and decanal. The best substrate is ethanol for ADH1 and 1-octanol for ADH2. For both ADHs, the optimum assay condition is at 60 °C and pH 8.0, and both NAD and NADP can be used as the cofactor. Sequence analysis reveals that ADH1 and ADH2 belong to the Fe-containing/activated long-Chain ADHs. However, the two enzymes contain neither Fe nor other metals, and Fe is not required for the activity, suggesting a new type of ADH. The ADHs characterized here are potentially useful in crude oil bioremediation and other bioconversion processes.
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Crystal structure of long-Chain Alkane monooxygenase (LadA) in complex with coenzyme FMN: unveiling the long-Chain Alkane hydroxylase
Journal of molecular biology, 2007Co-Authors: Xueqian Liu, Wei Wang, Lei Wang, Lu Feng, Wen Yang, Mark Bartlam, Zihe RaoAbstract:LadA, a long-Chain Alkane monooxygenase, utilizes a terminal oxidation pathway for the conversion of long-Chain Alkanes (up to at least C(36)) to corresponding primary alcohols in thermophilic bacillus Geobacillus thermodenitrificans NG80-2. Here, we report the first structure of the long-Chain Alkane hydroxylase, LadA, and its complex with the flavin mononucleotide (FMN) coenzyme. LadA is characterized as a new member of the SsuD subfamily of the bacterial luciferase family via a surprising structural relationship. The LadA:FMN binary complex structure and a LadA:FMN:Alkane model reveal a hydrophobic cavity that has dual roles: to provide a hydrogen-bond donor (His138) for catalysis and to create a solvent-free environment in which to stabilize the C4a-hydroperoxyflavin intermediate. Consequently, LadA should catalyze the conversion of long-Chain Alkanes via the acknowledged flavoprotein monooxygenase mechanism. This finding suggests that the ability of LadA to catalyze the degradation of long-Chain Alkanes is determined by the binding mode of the long-Chain Alkane substrates. The LadA structure opens a rational perspective to explore and alter the substrate binding site of LadA, with potential biotechnological applications in areas such as petroleum exploration and treatment of environmental oil pollution.
-
genome and proteome of long Chain Alkane degrading geobacillus thermodenitrificans ng80 2 isolated from a deep subsurface oil reservoir
Proceedings of the National Academy of Sciences of the United States of America, 2007Co-Authors: Lu Feng, Wei Wang, Jiansong Cheng, Guang Zhao, Yun Tang, Xia Peng, Lei WangAbstract:The complete genome sequence of Geobacillus thermodenitrificans NG80-2, a thermophilic bacillus isolated from a deep oil reservoir in Northern China, consists of a 3,550,319-bp chromosome and a 57,693-bp plasmid. The genome reveals that NG80-2 is well equipped for adaptation into a wide variety of environmental niches, including oil reservoirs, by possessing genes for utilization of a broad range of energy sources, genes encoding various transporters for efficient nutrient uptake and detoxification, and genes for a flexible respiration system including an aerobic branch comprising five terminal oxidases and an anaerobic branch comprising a complete denitrification pathway for quick response to dissolved oxygen fluctuation. The identification of a nitrous oxide reductase gene has not been previously described in Gram-positive bacteria. The proteome further reveals the presence of a long-Chain Alkane degradation pathway; and the function of the key enzyme in the pathway, the long-Chain Alkane monooxygenase LadA, is confirmed by in vivo and in vitro experiments. The thermophilic soluble monomeric LadA is an ideal candidate for treatment of environmental oil pollutions and biosynthesis of complex molecules.
Harald Fuchs - One of the best experts on this subject based on the ideXlab platform.
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interaction of short Chain Alkane thiols and thiolates with small gold clusters adsorption structures and energetics
Journal of Chemical Physics, 2001Co-Authors: Daniel Kruger, Roger Rousseau, Dominik Marx, Harald Fuchs, Michele ParrinelloAbstract:Gold–sulfur bonding is investigated theoretically using a variety of electronic structure methods, including the Becke–Perdew semilocal density functional, the B3LYP hybrid approach, the Hartree–Fock method, and the post Hartree–Fock approaches MP2 and QCISD(T). Particular emphasis is given to adsorption structure and energetics in the case of weak and strong interactions of this general type, using up to five gold atoms and up to three carbon atoms in the aliphatic Chain. It is found that all methods which take into account electron correlation, including the density functional methods, lead to quite similar structures. Concerning the energetics, the Becke–Perdew functional is found to overbind typically by about 5–15%. Quasiglobal structural relaxation based on ab initio simulated annealing clearly shows that the adsorption of thiolates onto gold clusters results in a dramatic distortion of the cluster framework. From a structural point of view the thiolate sulfur–gold bond has a distinctive directional...
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interaction of short Chain Alkane thiols and thiolates with small gold clusters adsorption structures and energetics
Journal of Chemical Physics, 2001Co-Authors: Daniel Kruger, Roger Rousseau, Dominik Marx, Harald Fuchs, Michele ParrinelloAbstract:Gold–sulfur bonding is investigated theoretically using a variety of electronic structure methods, including the Becke–Perdew semilocal density functional, the B3LYP hybrid approach, the Hartree–Fock method, and the post Hartree–Fock approaches MP2 and QCISD(T). Particular emphasis is given to adsorption structure and energetics in the case of weak and strong interactions of this general type, using up to five gold atoms and up to three carbon atoms in the aliphatic Chain. It is found that all methods which take into account electron correlation, including the density functional methods, lead to quite similar structures. Concerning the energetics, the Becke–Perdew functional is found to overbind typically by about 5–15%. Quasiglobal structural relaxation based on ab initio simulated annealing clearly shows that the adsorption of thiolates onto gold clusters results in a dramatic distortion of the cluster framework. From a structural point of view the thiolate sulfur–gold bond has a distinctive directional (covalent) character which results in a clear preference for Au–S–C bond angles in the range of 103.5° and 108.7°. In general, dissociation into open-shell species is preferred against the formation of the ionic closed-shell counterparts if the sulfur–gold bond is forced to break. However, neutral closed-shell products can be favored if fragmentation of the gold cluster is allowed for as a dissociation channel. Finally, it is demonstrated that using ethyl or n-propyl Chains instead of the methyl group leads to only small changes of the binding energies.