Matching Items (173)
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Description
Diacylglycerol kinase catalyses the ATP-dependent conversion of diacylglycerol to phosphatidic acid in the plasma membrane of Escherichia coli. The small size of this integral membrane trimer, which has 121 residues per subunit, means that available protein must be used economically to craft three catalytic and substrate-binding sites centred about the

Diacylglycerol kinase catalyses the ATP-dependent conversion of diacylglycerol to phosphatidic acid in the plasma membrane of Escherichia coli. The small size of this integral membrane trimer, which has 121 residues per subunit, means that available protein must be used economically to craft three catalytic and substrate-binding sites centred about the membrane/cytosol interface. How nature has accomplished this extraordinary feat is revealed here in a crystal structure of the kinase captured as a ternary complex with bound lipid substrate and an ATP analogue. Residues, identified as essential for activity by mutagenesis, decorate the active site and are rationalized by the ternary structure. The γ-phosphate of the ATP analogue is positioned for direct transfer to the primary hydroxyl of the lipid whose acyl chain is in the membrane. A catalytic mechanism for this unique enzyme is proposed. The active site architecture shows clear evidence of having arisen by convergent evolution.
ContributorsLi, Dianfan (Author) / Stansfeld, Phillip J. (Author) / Sansom, Mark S. P. (Author) / Keogh, Aaron (Author) / Vogeley, Lutz (Author) / Howe, Nicole (Author) / Lyons, Joseph A. (Author) / Aragao, David (Author) / Fromme, Petra (Author) / Fromme, Raimund (Author) / Basu, Shibom (Author) / Grotjohann, Ingo (Author) / Kupitz, Christopher (Author) / Rendek, Kimberley (Author) / Weierstall, Uwe (Author) / Zatsepin, Nadia (Author) / Cherezov, Vadim (Author) / Liu, Wei (Author) / Bandaru, Sateesh (Author) / English, Niall J. (Author) / Gati, Cornelius (Author) / Barty, Anton (Author) / Yefanov, Oleksandr (Author) / Chapman, Henry N. (Author) / Diederichs, Kay (Author) / Messerschmidt, Marc (Author) / Boutet, Sebastien (Author) / Williams, Garth J. (Author) / Seibert, M. Marvin (Author) / Caffrey, Martin (Author) / College of Liberal Arts and Sciences (Contributor) / School of Molecular Sciences (Contributor) / Biodesign Institute (Contributor) / Applied Structural Discovery (Contributor) / Department of Physics (Contributor)
Created2015-12-17
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Description
Phytochromes are a family of photoreceptors that control light responses of plants, fungi and bacteria. A sequence of structural changes, which is not yet fully understood, leads to activation of an output domain. Time-resolved serial femtosecond crystallography (SFX) can potentially shine light on these conformational changes. Here we report the

Phytochromes are a family of photoreceptors that control light responses of plants, fungi and bacteria. A sequence of structural changes, which is not yet fully understood, leads to activation of an output domain. Time-resolved serial femtosecond crystallography (SFX) can potentially shine light on these conformational changes. Here we report the room temperature crystal structure of the chromophore-binding domains of the Deinococcus radiodurans phytochrome at 2.1 Å resolution. The structure was obtained by serial femtosecond X-ray crystallography from microcrystals at an X-ray free electron laser. We find overall good agreement compared to a crystal structure at 1.35 Å resolution derived from conventional crystallography at cryogenic temperatures, which we also report here. The thioether linkage between chromophore and protein is subject to positional ambiguity at the synchrotron, but is fully resolved with SFX. The study paves the way for time-resolved structural investigations of the phytochrome photocycle with time-resolved SFX.
ContributorsEdlund, Petra (Author) / Takala, Heikki (Author) / Claesson, Elin (Author) / Henry, Leocadie (Author) / Dods, Robert (Author) / Lehtivuori, Heli (Author) / Panman, Matthijs (Author) / Pande, Kanupriya (Author) / White, Thomas (Author) / Nakane, Takanori (Author) / Berntsson, Oskar (Author) / Gustavsson, Emil (Author) / Bath, Petra (Author) / Modi, Vaibhav (Author) / Roy Chowdhury, Shatabdi (Author) / Zook, James (Author) / Berntsen, Peter (Author) / Pandey, Suraj (Author) / Poudyal, Ishwor (Author) / Tenboer, Jason (Author) / Kupitz, Christopher (Author) / Barty, Anton (Author) / Fromme, Petra (Author) / Koralek, Jake D. (Author) / Tanaka, Tomoyuki (Author) / Spence, John (Author) / Liang, Mengning (Author) / Hunter, Mark S. (Author) / Boutet, Sebastien (Author) / Nango, Eriko (Author) / Moffat, Keith (Author) / Groenhof, Gerrit (Author) / Ihalainen, Janne (Author) / Stojkovic, Emina A. (Author) / Schmidt, Marius (Author) / Westenhoff, Sebastian (Author) / College of Liberal Arts and Sciences (Contributor) / School of Molecular Sciences (Contributor) / Biodesign Institute (Contributor) / Applied Structural Discovery (Contributor) / Department of Physics (Contributor)
Created2016-10-19
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Description

X-ray free electron lasers are used in measuring diffraction patterns from nanocrystals in the 'diffract-before-destroy' mode by outrunning radiation damage. The finite-sized nanocrystals provide an opportunity to recover intensity between Bragg spots by removing the modulating function that depends on crystal shape, i.e. the transform of the crystal shape. This

X-ray free electron lasers are used in measuring diffraction patterns from nanocrystals in the 'diffract-before-destroy' mode by outrunning radiation damage. The finite-sized nanocrystals provide an opportunity to recover intensity between Bragg spots by removing the modulating function that depends on crystal shape, i.e. the transform of the crystal shape. This shape-transform dividing-out scheme for solving the phase problem has been tested using simulated examples with cubic crystals. It provides a phasing method which does not require atomic resolution data, chemical modification to the sample, or modelling based on the protein databases. It is common to find multiple structural units (e.g. molecules, in symmetry-related positions) within a single unit cell, therefore incomplete unit cells (e.g. one additional molecule) can be observed at surface layers of crystals. In this work, the effects of such incomplete unit cells on the 'dividing-out' phasing algorithm are investigated using 2D crystals within the projection approximation. It is found that the incomplete unit cells do not hinder the recovery of the scattering pattern from a single unit cell (after dividing out the shape transforms from data merged from many nanocrystals of different sizes), assuming that certain unit-cell types are preferred. The results also suggest that the dynamic range of the data is a critical issue to be resolved in order to apply the shape transform method practically.

ContributorsLiu, Haiguang (Author) / Zatsepin, Nadia (Author) / Spence, John (Author) / College of Liberal Arts and Sciences (Contributor) / Department of Physics (Contributor)
Created2014-01-01
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Description
A major conceptual step forward in understanding the logical architecture of living systems was advanced by von Neumann with his universal constructor, a physical device capable of self-reproduction. A necessary condition for a universal constructor to exist is that the laws of physics permit physical universality, such that any transformation

A major conceptual step forward in understanding the logical architecture of living systems was advanced by von Neumann with his universal constructor, a physical device capable of self-reproduction. A necessary condition for a universal constructor to exist is that the laws of physics permit physical universality, such that any transformation (consistent with the laws of physics and availability of resources) can be caused to occur. While physical universality has been demonstrated in simple cellular automata models, so far these have not displayed a requisite feature of life—namely open-ended evolution—the explanation of which was also a prime motivator in von Neumann’s formulation of a universal constructor. Current examples of physical universality rely on reversible dynamical laws, whereas it is well-known that living processes are dissipative. Here we show that physical universality and open-ended dynamics should both be possible in irreversible dynamical systems if one entertains the possibility of state-dependent laws. We demonstrate with simple toy models how the accessibility of state space can yield open-ended trajectories, defined as trajectories that do not repeat within the expected Poincaré recurrence time and are not reproducible by an isolated system. We discuss implications for physical universality, or an approximation to it, as a foundational framework for developing a physics for life.
Created2017-09-01
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Description
X-ray free-electron lasers (XFELs) provide new opportunities for structure determination of biomolecules, viruses and nanomaterials. With unprecedented peak brilliance and ultra-short pulse duration, XFELs can tolerate higher X-ray doses by exploiting the femtosecond-scale exposure time, and can thus go beyond the resolution limits achieved with conventional X-ray diffraction imaging techniques.

X-ray free-electron lasers (XFELs) provide new opportunities for structure determination of biomolecules, viruses and nanomaterials. With unprecedented peak brilliance and ultra-short pulse duration, XFELs can tolerate higher X-ray doses by exploiting the femtosecond-scale exposure time, and can thus go beyond the resolution limits achieved with conventional X-ray diffraction imaging techniques. Using XFELs, it is possible to collect scattering information from single particles at high resolution, however particle heterogeneity and unknown orientations complicate data merging in three-dimensional space. Using the Linac Coherent Light Source (LCLS), synthetic inorganic nanocrystals with a core–shell architecture were used as a model system for proof-of-principle coherent diffractive single-particle imaging experiments. To deal with the heterogeneity of the core–shell particles, new computational methods have been developed to extract the particle size and orientation from the scattering data to assist data merging. The size distribution agrees with that obtained by electron microscopy and the merged data support a model with a core–shell architecture.
ContributorsLi, Xuanxuan (Author) / Spence, John (Author) / Hogue, Brenda (Author) / Liu, Haiguang (Author) / College of Liberal Arts and Sciences (Contributor) / Department of Physics (Contributor) / Biodesign Institute (Contributor) / Applied Structural Discovery (Contributor)
Created2017-08-27
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Description

Thermionic energy conversion, a process that allows direct transformation of thermal to electrical energy, presents a means of efficient electrical power generation as the hot and cold side of the corresponding heat engine are separated by a vacuum gap. Conversion efficiencies approaching those of the Carnot cycle are possible if

Thermionic energy conversion, a process that allows direct transformation of thermal to electrical energy, presents a means of efficient electrical power generation as the hot and cold side of the corresponding heat engine are separated by a vacuum gap. Conversion efficiencies approaching those of the Carnot cycle are possible if material parameters of the active elements at the converter, i.e., electron emitter or cathode and collector or anode, are optimized for operation in the desired temperature range.

These parameters can be defined through the law of Richardson–Dushman that quantifies the ability of a material to release an electron current at a certain temperature as a function of the emission barrier or work function and the emission or Richardson constant. Engineering materials to defined parameter values presents the key challenge in constructing practical thermionic converters. The elevated temperature regime of operation presents a constraint that eliminates most semiconductors and identifies diamond, a wide band-gap semiconductor, as a suitable thermionic material through its unique material properties. For its surface, a configuration can be established, the negative electron affinity, that shifts the vacuum level below the conduction band minimum eliminating the surface barrier for electron emission.

In addition, its ability to accept impurities as donor states allows materials engineering to control the work function and the emission constant. Single-crystal diamond electrodes with nitrogen levels at 1.7 eV and phosphorus levels at 0.6 eV were prepared by plasma-enhanced chemical vapor deposition where the work function was controlled from 2.88 to 0.67 eV, one of the lowest thermionic work functions reported. This work function range was achieved through control of the doping concentration where a relation to the amount of band bending emerged. Upward band bending that contributed to the work function was attributed to surface states where lower doped homoepitaxial films exhibited a surface state density of ∼3 × 10[superscript 11] cm[superscript −2]. With these optimized doped diamond electrodes, highly efficient thermionic converters are feasible with a Schottky barrier at the diamond collector contact mitigated through operation at elevated temperatures.

ContributorsKoeck, Franz (Author) / Nemanich, Robert (Author) / College of Liberal Arts and Sciences (Contributor) / Department of Physics (Contributor)
Created2017-12-06
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Description
Diamond is considered as an ideal material for high field and high power devices due to its high breakdown field, high lightly doped carrier mobility, and high thermal conductivity. The modeling and simulation of diamond devices are therefore important to predict the performances of diamond based devices. In this context,

Diamond is considered as an ideal material for high field and high power devices due to its high breakdown field, high lightly doped carrier mobility, and high thermal conductivity. The modeling and simulation of diamond devices are therefore important to predict the performances of diamond based devices. In this context, we use Silvaco[superscript ®] Atlas, a drift-diffusion based commercial software, to model diamond based power devices. The models used in Atlas were modified to account for both variable range and nearest neighbor hopping transport in the impurity bands associated with high activation energies for boron doped and phosphorus doped diamond. The models were fit to experimentally reported resistivity data over a wide range of doping concentrations and temperatures. We compare to recent data on depleted diamond Schottky PIN diodes demonstrating low turn-on voltages and high reverse breakdown voltages, which could be useful for high power rectifying applications due to the low turn-on voltage enabling high forward current densities. Three dimensional simulations of the depleted Schottky PIN diamond devices were performed and the results are verified with experimental data at different operating temperatures.
Created2016-06-08
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Description
The invention of the laser in the 1950 s for visible light and microwaves, and the slow but steady recognition of its manifold uses, is a truly remarkable story in the history of science. But the severe λ[superscript 3] dependence of the ratio of stimulated (mostly coherent) to spontaneous (incoherent) emission

The invention of the laser in the 1950 s for visible light and microwaves, and the slow but steady recognition of its manifold uses, is a truly remarkable story in the history of science. But the severe λ[superscript 3] dependence of the ratio of stimulated (mostly coherent) to spontaneous (incoherent) emission meant that efforts to build an X-ray laser seemed hopeless for decades. As so often happens in the history of science, the breakthrough eventually occurred at the interface of several fields – synchrotron science (and especially their insertion devices), laser physics, and work on microwave tubes for radar, emerging from the second world war. Synchrotrons themselves were an outgrowth of the particle accelerators of nuclear physics, whose X-ray radiation was considered a nuisance. All of this culminated recently in the construction of the first hard-X-ray laser, the US Department of Energy's Linac Coherent Light Source (LCLS), at their SLAC laboratory near Stanford. The first X-ray lasing occurred in that two-mile long tunnel on April 21, 2009, at about 2 kV, in an all-or-nothing moment of intense excitement, as theoretical predictions proved spot-on. The new laser principle needed for hard-X-ray lasing, the free-electron laser (FEL), was first demonstrated in the infra-red region at Stanford in 1975 in John Madey's group, following earlier theoretical work by Motz and Phillips on microwave tubes. Other FELs soon followed, in the microwave and visible region, leading to the LCLS. The XFEL method provides brief pulses of X-ray laser radiation by the SASE (self-amplified spontaneous emission) process, using a resonant undulator driven by a LINAC electron accelerator. Each LCLS pulse, of 10 fs duration (repeated 120 times a second) contains about 10[superscript 12] hard-X-ray photons, about the same number that a synchrotron might generate in a second.
ContributorsSpence, John (Author) / College of Liberal Arts and Sciences (Contributor) / Department of Physics (Contributor)
Created2014-04-30
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Description
X-ray diffraction patterns from two-dimensional (2-D) protein crystals obtained using femtosecond X-ray pulses from an X-ray free-electron laser (XFEL) are presented. To date, it has not been possible to acquire transmission X-ray diffraction patterns from individual 2-D protein crystals due to radiation damage. However, the intense and ultrafast pulses generated

X-ray diffraction patterns from two-dimensional (2-D) protein crystals obtained using femtosecond X-ray pulses from an X-ray free-electron laser (XFEL) are presented. To date, it has not been possible to acquire transmission X-ray diffraction patterns from individual 2-D protein crystals due to radiation damage. However, the intense and ultrafast pulses generated by an XFEL permit a new method of collecting diffraction data before the sample is destroyed. Utilizing a diffract-before-destroy approach at the Linac Coherent Light Source, Bragg diffraction was acquired to better than 8.5 Å resolution for two different 2-D protein crystal samples each less than 10 nm thick and maintained at room temperature. These proof-of-principle results show promise for structural analysis of both soluble and membrane proteins arranged as 2-D crystals without requiring cryogenic conditions or the formation of three-dimensional crystals.
ContributorsFrank, Matthias (Author) / Carlson, David B. (Author) / Hunter, Mark S. (Author) / Williams, Garth J. (Author) / Messerschmidt, Marc (Author) / Zatsepin, Nadia (Author) / Barty, Anton (Author) / Benner, W. Henry (Author) / Chu, Kaiqin (Author) / Graf, Alexander T. (Author) / Hau-Riege, Stefan P. (Author) / Kirian, Richard A. (Author) / Padeste, Celestino (Author) / Pardini, Tommaso (Author) / Pedrini, Bill (Author) / Segelke, Brent (Author) / Seibert, M. Marvin (Author) / Spence, John (Author) / Tsai, Ching-Ju (Author) / Lane, Stephen M. (Author) / Li, Xiao-Dan (Author) / Schertler, Gebhard (Author) / Boutet, Sebastien (Author) / Coleman, Matthew (Author) / Evans, James E. (Author) / College of Liberal Arts and Sciences (Contributor) / Department of Physics (Contributor)
Created2014-02-28
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Description
GaN-based devices are currently limited by reliability issues such as gate leakage and current collapse, where the mechanisms responsible for degradation are closely related to the electronic surface state configuration. Therefore, understanding the electronic surface state configuration of GaN-based materials will help improve device performance. Since GaN has an inherent

GaN-based devices are currently limited by reliability issues such as gate leakage and current collapse, where the mechanisms responsible for degradation are closely related to the electronic surface state configuration. Therefore, understanding the electronic surface state configuration of GaN-based materials will help improve device performance. Since GaN has an inherent polarization, these materials are also subject to a bound polarization charge, which influences the electronic state configuration. In this study, the surface band bending of N-face GaN, Ga-face GaN, and Ga-face AlGaN was measured with x-ray photoemission spectroscopy after various cleaning steps to investigate the effects of the polarization. Despite the different surface bound charge on these materials, similar band bending was observed regardless of the magnitude or direction of the charge. Specifically, the band bending varied from −0.1 eV to 0.9 eV on these samples, which supported the models of a Fermi level pinning state at ∼0.4 eV to 0.8 eV below the conduction band. Based on available literature, we suggest this pinning state is indirectly evident of a nitrogen vacancy or gallium-dangling bond.
ContributorsEller, Brianna S. (Author) / Yang, Jialing (Author) / Nemanich, Robert (Author) / College of Liberal Arts and Sciences (Contributor) / Department of Physics (Contributor)
Created2014-12-01