Ethylbenzene dehydrogenase, a novel hydrocarbon-oxidizing molybdenum/iron-sulfur/heme enzyme

The initial enzyme of ethylbenzene metabolism in denitrifying Azoarcus strain EbN1, ethylbenzene dehydrogenase, was purified and characterized. The soluble periplasmic enzyme is the first known enzyme oxidizing a nonactivated hydrocarbon without molecular oxygen as cosubstrate. It is a novel molybdenum/iron-sulfur/heme protein of 155 kDa, which consists of three subunits (96, 43, and 23 kDa) in an αβγ structure. The N-terminal amino acid sequence of the α subunit is similar to that of other molybdenum proteins such as selenate reductase from the related speciesThauera selenatis. Ethylbenzene dehydrogenase is unique in that it oxidizes the hydrocarbon ethylbenzene, a compound without functional groups, to (S)-1-phenylethanol. Formation of the product was evident by coupling to an enantiomer-specific (S)-1-phenylethanol dehydrogenase from the same organism. The apparent K m of the enzyme for ethylbenzene is very low at <2 μm. Oxygen does not affect ethylbenzene dehydrogenase activity in extracts but inactivates the purified enzyme, if the heme b cofactor is in the reduced state. A variant of ethylbenzene dehydrogenase exhibiting significant activity also with the homolog n-propylbenzene was detected in a relatedAzoarcus strain (PbN1)

Electric Field Controlled, Pulsed Autoionization in Two Electron Wave Packets

In this paper, control of the evolution of a two electron wave packet through the application of a static electric field is demonstrated. Specifically, application of a small electric field is used to produce pulsed autoionization events, the timing of which can be controlled on a picosecond time scale. The technique is demonstrated by exciting calcium atoms using a short-pulsed laser to the 4p3/219d doubly excited state, which is energy degenerate with the 4p1/2nk stark states. Evolution of the resultant wave packet is monitored through the application of a second short laser pulse, which stimulates the atoms to emit a photon producing singly excited Rydberg states which are detected using field ionization

Short-pulse Laser-Induced Stabilization of Autoionizing States

Atoms in doubly excited states above the first ionization limit can decay via autoionization in which an electron is emitted leaving an ion, or by photoemission which leaves the atom in a singly excited state. In this paper, it is demonstrated that interaction between the atoms and a laser pulse that is short compared to the autoionization lifetime can lead to large enhancement of the photoemission process by stimulating the atoms to emit a photon. Since the resultant singly excited atoms do not autoionize, this process can be viewed as an enhancement of the stabilization of the doubly excited atoms against autoionization. A simple theoretical model is outlined that shows good agreement with the experimental results

Shakeoff Measurement of the L = 3 States of Barium

Isolated core excitation was used to produce low-energy continuum electrons in the l = 3 angular momentum state of barium. Data were taken over a region of energy that coincided with the energy of the 6p3/2nf doubly excited states. Analysis of the data using multichannel quantum defect theory allowed the measurement of the widths of the 6p3/2nf states and the energy-dependent phase of the continuum electronic wave functions due to interaction with the doubly excited states. The phase of the continuum electrons is shown to vary continuously with energy, due to the anomalously broad widths of the double excited states

Laser-Induced Stabilization of Autoionizing States

Stabilization of autoionizing states of barium by laser-induced, stimulated emission of light is demonstrated. Relative to purely flourescent stabilization, the data clearly show an enhancement of the stabilization process for laser pulses short compared to the flourescent lifetime of the autoionizing states. Shakeup spectra in which the principal quantum number of both electrons changes during the stimulated emission process are also clearly demonstrated

Direct Measurement of Oscillations between Degenerate Two-Electron Bound-State Configurations in a Rapidly Autoionizing System

In this paper we report a direct observation of the oscillation between bound-state configurations in a rapidly autoionizing system. Calcium atoms were excited to a pure 4p3/2nd two-electron configuration using a 500-fsec laser pulse. The initial 4p3/2nd doubly excited state is energy degenerate with the 4p1/2n\u27d states and several continuum channels. Because of the short-pulse excitation, the initial state of the atom is not an energy eigenstate, but a nonstationary wave packet. As a result, oscillations between the two bound configurations were produced. These oscillations were measured by scanning the timing of a second 500-fsec laser pulse tuned to drive the 4p1/2n\u27d ionic state back down to the 4sn\u27d singly excited configuration, which was subsequently detected using selective field ionization. A simple theoretical model was used to model the experimental results and produced good agreement with the data

Structure of HIV-1 quasi-species as early indicator for switches of co-receptor tropism

Deep sequencing is able to generate a complete picture of the retroviral quasi-species in a patient. We demonstrate that the unprecedented power of deep sequencing in conjunction with computational data analysis has great potential for clinical diagnostics and basic research. Specifically, we analyzed longitudinal deep sequencing data from patients in a study with Vicriviroc, a drug that blocks the HIV-1 co-receptor CCR5. Sequences covered the V3-loop of gp120, known to be the main determinant of co-receptor tropism. First, we evaluated this data with a computational model for the interpretation of V3-sequences with respect to tropism, and we found complete agreement with results from phenotypic assays. Thus, the method could be applied in cases where phenotypic assays fail. Second, computational analysis led to the discovery of a characteristic pattern in the quasi-species that foreshadows switches of co-receptor tropism. This analysis could help to unravel the mechanism of tropism switches, and to predict these switches weeks to months before they can be detected by a phenotypic assay

SNE: Signed Network Embedding

Several network embedding models have been developed for unsigned networks. However, these models based on skip-gram cannot be applied to signed networks because they can only deal with one type of link. In this paper, we present our signed network embedding model called SNE. Our SNE adopts the log-bilinear model, uses node representations of all nodes along a given path, and further incorporates two signed-type vectors to capture the positive or negative relationship of each edge along the path. We conduct two experiments, node classification and link prediction, on both directed and undirected signed networks and compare with four baselines including a matrix factorization method and three state-of-the-art unsigned network embedding models. The experimental results demonstrate the effectiveness of our signed network embedding.Comment: To appear in PAKDD 201

Structure of the membrane-bound formate hydrogenlyase complex from Escherichia coli

The prototypical hydrogen-producing enzyme, the membrane-bound formate hydrogenlyase (FHL) complex from Escherichia coli, links formate oxidation at a molybdopterin-containing formate dehydrogenase to proton reduction at a [NiFe] hydrogenase. It is of intense interest due to its ability to efficiently produce H2 during fermentation, its reversibility, allowing H2-dependent CO2 reduction, and its evolutionary link to respiratory complex I. FHL has been studied for over a century, but its atomic structure remains unknown. Here we report cryo-EM structures of FHL in its aerobically and anaerobically isolated forms at resolutions reaching 2.6 Å. This includes well-resolved density for conserved loops linking the soluble and membrane arms believed to be essential in coupling enzymatic turnover to ion translocation across the membrane in the complex I superfamily. We evaluate possible structural determinants of the bias toward hydrogen production over its oxidation and describe an unpredicted metal-binding site near the interface of FdhF and HycF subunits that may play a role in redox-dependent regulation of FdhF interaction with the complex