Matching Items (206)
Description
Serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to enable the collection of single diffraction images before significant radiation damage to crystals sets in. Here we report the deposition of the XFEL data and provide further details on crystallization, XFEL data collection and analysis, structure determination, and the validation of the structural model. The rhodopsin-arrestin crystal structure solved with SFX represents the first near-atomic resolution structure of a GPCR-arrestin complex, provides structural insights into understanding of arrestin-mediated GPCR signaling, and demonstrates the great potential of this SFX-XFEL technology for accelerating crystal structure determination of challenging proteins and protein complexes.
ContributorsZhou, X. Edward (Author) / Gao, Xiang (Author) / Barty, Anton (Author) / Kang, Yanyong (Author) / He, Yuanzheng (Author) / Liu, Wei (Author) / Ishchenko, Andrii (Author) / White, Thomas A. (Author) / Yefanov, Oleksandr (Author) / Han, Gye Won (Author) / Xu, Qingping (Author) / de Waal, Parker W. (Author) / Suino-Powell, Kelly M. (Author) / Boutet, Sebastien (Author) / Williams, Garth J. (Author) / Wang, Meitian (Author) / Li, Dianfan (Author) / Caffrey, Martin (Author) / Chapman, Henry N. (Author) / Spence, John (Author) / Fromme, Petra (Author) / Weierstall, Uwe (Author) / Stevens, Raymond C. (Author) / Cherezov, Vadim (Author) / Melcher, Karsten (Author) / Xu, H. Eric (Author) / College of Liberal Arts and Sciences (Contributor) / School of Molecular Sciences (Contributor) / Biodesign Institute (Contributor) / Applied Structural Discovery (Contributor) / Department of Physics (Contributor)
Created2016-04-12
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 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
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 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
Description
Serial femtosecond crystallography (SFX) using X-ray free-electron laser sources is an emerging method with considerable potential for time-resolved pump-probe experiments. Here we present a lipidic cubic phase SFX structure of the light-driven proton pump bacteriorhodopsin (bR) to 2.3 Å resolution and a method to investigate protein dynamics with modest sample requirement. Time-resolved SFX (TR-SFX) with a pump-probe delay of 1 ms yields difference Fourier maps compatible with the dark to M state transition of bR. Importantly, the method is very sample efficient and reduces sample consumption to about 1 mg per collected time point. Accumulation of M intermediate within the crystal lattice is confirmed by time-resolved visible absorption spectroscopy. This study provides an important step towards characterizing the complete photocycle dynamics of retinal proteins and demonstrates the feasibility of a sample efficient viscous medium jet for TR-SFX.
ContributorsNogly, Przemyslaw (Author) / Panneels, Valerie (Author) / Nelson, Garrett (Author) / Gati, Cornelius (Author) / Kimura, Tetsunari (Author) / Milne, Christopher (Author) / Milathianaki, Despina (Author) / Kubo, Minoru (Author) / Wu, Wenting (Author) / Conrad, Chelsie (Author) / Coe, Jesse (Author) / Bean, Richard (Author) / Zhao, Yun (Author) / Bath, Petra (Author) / Dods, Robert (Author) / Harimoorthy, Rajiv (Author) / Beyerlein, Kenneth R. (Author) / Rheinberger, Jan (Author) / James, Daniel (Author) / Deponte, Daniel (Author) / Li, Chufeng (Author) / Sala, Leonardo (Author) / Williams, Garth J. (Author) / Hunter, Mark S. (Author) / Koglin, Jason E. (Author) / Berntsen, Peter (Author) / Nango, Eriko (Author) / Iwata, So (Author) / Chapman, Henry N. (Author) / Fromme, Petra (Author) / Frank, Matthias (Author) / Abela, Rafael (Author) / Boutet, Sebastien (Author) / Barty, Anton (Author) / White, Thomas A. (Author) / Weierstall, Uwe (Author) / Spence, John (Author) / Neutze, Richard (Author) / Schertler, Gebhard (Author) / Standfuss, Jorg (Author) / College of Liberal Arts and Sciences (Contributor) / Department of Physics (Contributor) / Department of Chemistry and Biochemistry (Contributor) / Biodesign Institute (Contributor) / Applied Structural Discovery (Contributor) / School of Molecular Sciences (Contributor)
Created2016-08-22
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 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
Description
This work presents a spectroscopic study of the thermally enhanced photoinduced electron emission from nitrogen-doped diamond films prepared on p-type silicon substrates. It has been shown that photon-enhanced thermionic emission (PETE) can substantially enhance thermionic emission intensity from a p-type semiconductor. An n-type diamond/p-type silicon structure was illuminated with 400–450 nm light, and the spectra of the emitted electrons showed a work function less than 2 eV and nearly an order of magnitude increase in emission intensity as the temperature was increased from ambient to ∼400 °C. Thermionic emission was negligible in this temperature range. The results are modeled in terms of contributions from PETE and direct photoelectron emission, and the large increase is consistent with a PETE component. The results indicate possible application in combined solar/thermal energy conversion devices.
ContributorsSun, Tianyin (Author) / Koeck, Franz (Author) / Rezikyan, Aram (Author) / Treacy, Michael (Author) / Nemanich, Robert (Author) / College of Liberal Arts and Sciences (Contributor) / Department of Physics (Contributor)
Created2014-09-15
Description
The effects of surface pretreatment, dielectric growth, and post deposition annealing on interface electronic structure and polarization charge compensation of Ga- and N-face bulk GaN were investigated. The cleaning process consisted of an ex-situ wet chemical NH[subscript 4]OH treatment and an in-situ elevated temperature NH[subscript 3] plasma process to remove carbon contamination, reduce oxygen coverage, and potentially passivate N-vacancy related defects. After the cleaning process, carbon contamination decreased below the x-ray photoemission spectroscopy detection limit, and the oxygen coverage stabilized at ∼1 monolayer on both Ga- and N-face GaN. In addition, Ga- and N-face GaN had an upward band bending of 0.8 ± 0.1 eV and 0.6 ± 0.1 eV, respectively, which suggested the net charge of the surface states and polarization bound charge was similar on Ga- and N-face GaN. Furthermore, three dielectrics (HfO[subscript 2], Al[subscript 2]O[subscript 3], and SiO[subscript 2]) were prepared by plasma-enhanced atomic layer deposition on Ga- or N-face GaN and annealed in N[subscript 2] ambient to investigate the effect of the polarization charge on the interface electronic structure and band offsets. The respective valence band offsets of HfO[subscript 2], Al[subscript 2]O[subscript 3], and SiO[subscript 2] with respect to Ga- and N-face GaN were 1.4 ± 0.1, 2.0 ± 0.1, and 3.2 ± 0.1 eV, regardless of dielectric thickness. The corresponding conduction band offsets were 1.0 ± 0.1, 1.3 ± 0.1, and 2.3 ± 0.1 eV, respectively. Experimental band offset results were consistent with theoretical calculations based on the charge neutrality level model. The trend of band offsets for dielectric/GaN interfaces was related to the band gap and/or the electronic part of the dielectric constant. The effect of polarization charge on band offset was apparently screened by the dielectric-GaN interface states.
ContributorsYang, Jialing (Author) / Eller, Brianna S. (Author) / Nemanich, Robert (Author) / College of Liberal Arts and Sciences (Contributor) / Department of Physics (Contributor)
Created2014-09-28
Description
In this project we are analyzing the diamond-titanium interface as it applies to diamond-based diode devices, including alpha particle, proton, and neutron detectors. This is done through the fabrication of an O-terminated B-doped diamond sample with a 20 Å Ti / 10 Å Pt overlayer which was then annealed and examined via X-ray photoelectron spectroscopy (XPS). It was discovered that after annealing the sample at temperatures ranging from 400 C - 900 C that TiC was not formed at any point during this experiment. Possible reasons for this include a lack of sufficient titanium in order to form TiC and over oxygenating the diamond surface before the metal was deposited.
ContributorsJohnson, Holly (Author) / Zaniewski, Anna (Thesis director) / Nemanich, Robert (Committee member) / Department of Physics (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
The ASU Compact X-ray Free Electron Laser (CXFEL) is a first of its kind instrument that will illuminate the processes of life and allow scientists to create more effective treatments for disease. The dimensions of the linear accelerator (LINAC) cavities must remain stable during operation, for a change in the geometry alters the standing wave microwave energy resonance within the cavities and leads to reflected rather than coupled and useful microwave energy to electric field coupling. This disturbs the electron bunch acceleration dynamics critical to the ultimate generation of x-ray pulses. Cooling water must be supplied to the electron generating RF-GUN, and linear accelerator (LINAC) structures at unique flowrate and temperature setpoints that are specific to the operating mode of the CXFEL. Design specifications for the water supply to the RF-GUN and three LINACs and were made for the nominal operating mode, which adds a 3 kW heat load to the water. To maintain steady cavity dimensions, water must be supplied to each device under test at 30.0 ºC ± 0.06 ºC. The flowrate of water must be 3.5 GPM to the RF-GUN and 2.5 GPM to each of the three LINACs with ± 0.01 GPM flowrate resolution. The primary function of the Dedicated-Precision Thermal Trim Unit (D-PTTU) is to control the flowrate and temperature of water supply to each device under test. A simplified model of the system was developed to select valves that would meet our design specifications for flowrate and temperature control. After using this model for valve selection, a detailed system model was created to simulate relevant coupled-domain physics of the integrated system. The detailed system model was used to determine the critical sensitivities of the system and will be used to optimize the performance of the system in the future. Before the detailed system model can be verified and tuned with experiments, the sensors were calibrated in an ice-bath to ensure the sensors measure accurate and precise values. During initial testing, the D-PTTU was able to achieve ± 0.02 ºC temperature resolution, which exceeds the design specification by a factor of three.
ContributorsGardeck, Alex John (Author) / Holl, Mark (Thesis director) / Smith, Dean (Committee member) / Department of Physics (Contributor) / Mechanical and Aerospace Engineering Program (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
Similar to the real numbers, the p-adic fields are completions of the rational numbers. However, distance in this space is determined based on divisibility by a prime number, p, rather than by the traditional absolute value. This gives rise to a peculiar topology which offers significant simplifications for p-adic continuous functions and p-adic integration than is present in the real numbers. These simplifications may present significant advantages to modern physics – specifically in harmonic analysis, quantum mechanics, and string theory. This project discusses the construction of the p-adic numbers, elementary p-adic topology, p-adic continuous functions, introductory p-adic measure theory, the q-Volkenborn distribution, and applications of p-adic numbers to physics. We define q-Volkenborn integration and its connection to Bernoulli numbers.
ContributorsBurgueno, Alyssa Erin (Author) / Childress, Nancy (Thesis director) / Jones, John (Committee member) / School of Mathematical and Statistical Sciences (Contributor, Contributor, Contributor) / Department of Physics (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05