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Structural Dynamics (Melville, N.Y.)

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https://www.readbyqxmd.com/read/28428974/perspective-a-toolbox-for-protein-structure-determination-in-physiological-environment-through-oriented-2d-ordered-site-specific-immobilization
#1
M Altissimo, M Kiskinova, R Mincigrucci, L Vaccari, C Guarnaccia, C Masciovecchio
Revealing the structure of complex biological macromolecules, such as proteins, is an essential step for understanding the chemical mechanisms that determine the diversity of their functions. Synchrotron based X-ray crystallography and cryo-electron microscopy have made major contributions in determining thousands of protein structures even from micro-sized crystals. They suffer from some limitations that have not been overcome, such as radiation damage, the natural inability to crystallize a number of proteins, and experimental conditions for structure determination that are incompatible with the physiological environment...
July 2017: Structural Dynamics (Melville, N.Y.)
https://www.readbyqxmd.com/read/28428973/compression-of-high-density-0-16-pc-electron-bunches-through-high-field-gradients-for-ultrafast-single-shot-electron-diffraction-the-compact-rf-gun
#2
Hazem Daoud, Klaus Floettmann, R J Dwayne Miller
We present an RF gun design for single shot ultrafast electron diffraction experiments that can produce sub-100 fs high-charge electron bunches in the 130 keV energy range. Our simulations show that our proposed half-cell RF cavity is capable of producing 137 keV, 27 fs rms (60 fs FWHM), 10(6) electron bunches with an rms spot size of 276 μm and a transverse coherence length of 2.0 nm. The required operation power is 9.2 kW, significantly lower than conventional rf cavity designs and a key design feature...
July 2017: Structural Dynamics (Melville, N.Y.)
https://www.readbyqxmd.com/read/28405593/molecular-couplings-and-energy-exchange-between-dna-and-water-mapped-by-femtosecond-infrared-spectroscopy-of-backbone-vibrations
#3
Yingliang Liu, Biswajit Guchhait, Torsten Siebert, Benjamin P Fingerhut, Thomas Elsaesser
Molecular couplings between DNA and water together with the accompanying processes of energy exchange are mapped via the ultrafast response of DNA backbone vibrations after OH stretch excitation of the water shell. Native salmon testes DNA is studied in femtosecond pump-probe experiments under conditions of full hydration and at a reduced hydration level with two water layers around the double helix. Independent of their local hydration patterns, all backbone vibrations in the frequency range from 940 to 1120 cm(-1) display a quasi-instantaneous reshaping of the spectral envelopes of their fundamental absorption bands upon excitation of the water shell...
July 2017: Structural Dynamics (Melville, N.Y.)
https://www.readbyqxmd.com/read/28405592/angle-resolved-photoemission-spectroscopy-of-liquid-water-at-29-5%C3%A2-ev
#4
Junichi Nishitani, Christopher W West, Toshinori Suzuki
Angle-resolved photoemission spectroscopy of liquid water was performed using extreme ultraviolet radiation at 29.5 eV and a time-of-flight photoelectron spectrometer. SiC/Mg coated mirrors were employed to select the single-order 19th harmonic from laser high harmonics, which provided a constant photon flux for different laser polarizations. The instrument was tested by measuring photoemission anisotropy for rare gases and water molecules and applied to a microjet of an aqueous NaI solution. The solute concentration was adjusted to eliminate an electric field gradient around the microjet...
July 2017: Structural Dynamics (Melville, N.Y.)
https://www.readbyqxmd.com/read/28405591/svd-aided-pseudo-principal-component-analysis-a-new-method-to-speed-up-and-improve-determination-of-the-optimum-kinetic-model-from-time-resolved-data
#5
Key Young Oang, Cheolhee Yang, Srinivasan Muniyappan, Jeongho Kim, Hyotcherl Ihee
Determination of the optimum kinetic model is an essential prerequisite for characterizing dynamics and mechanism of a reaction. Here, we propose a simple method, termed as singular value decomposition-aided pseudo principal-component analysis (SAPPA), to facilitate determination of the optimum kinetic model from time-resolved data by bypassing any need to examine candidate kinetic models. We demonstrate the wide applicability of SAPPA by examining three different sets of experimental time-resolved data and show that SAPPA can efficiently determine the optimum kinetic model...
July 2017: Structural Dynamics (Melville, N.Y.)
https://www.readbyqxmd.com/read/28396880/beating-darwin-bragg-losses-in-lab-based-ultrafast-x-ray-experiments
#6
Wilfred K Fullagar, Jens Uhlig, Ujjwal Mandal, Dharmalingam Kurunthu, Amal El Nahhas, Hideyuki Tatsuno, Alireza Honarfar, Fredrik Parnefjord Gustafsson, Villy Sundström, Mikko R J Palosaari, Kimmo M Kinnunen, Ilari J Maasilta, Luis Miaja-Avila, Galen C O'Neil, Young Il Joe, Daniel S Swetz, Joel N Ullom
The use of low temperature thermal detectors for avoiding Darwin-Bragg losses in lab-based ultrafast experiments has begun. An outline of the background of this new development is offered, showing the relevant history and initiative taken by this work.
July 2017: Structural Dynamics (Melville, N.Y.)
https://www.readbyqxmd.com/read/28396879/pulse-length-of-ultracold-electron-bunches-extracted-from-a-laser-cooled-gas
#7
J G H Franssen, T L I Frankort, E J D Vredenbregt, O J Luiten
We present measurements of the pulse length of ultracold electron bunches generated by near-threshold two-photon photoionization of a laser-cooled gas. The pulse length has been measured using a resonant 3 GHz deflecting cavity in TM110 mode. We have measured the pulse length in three ionization regimes. The first is direct two-photon photoionization using only a 480 nm femtosecond laser pulse, which results in short (∼15 ps) but hot (∼10(4 )K) electron bunches. The second regime is just-above-threshold femtosecond photoionization employing the combination of a continuous-wave 780 nm excitation laser and a tunable 480 nm femtosecond ionization laser which results in both ultracold (∼10 K) and ultrafast (∼25 ps) electron bunches...
July 2017: Structural Dynamics (Melville, N.Y.)
https://www.readbyqxmd.com/read/28396878/molecule-specific-interactions-of-diatomic-adsorbates-at-metal-liquid-interfaces
#8
Jan Philip Kraack, Andres Kaech, Peter Hamm
Ultrafast vibrational dynamics of small molecules on platinum (Pt) layers in water are investigated using 2D attenuated total reflectance IR spectroscopy. Isotope combinations of carbon monoxide and cyanide are used to elucidate inter-adsorbate and substrate-adsorbate interactions. Despite observed cross-peaks in the CO spectra, we conclude that the molecules are not vibrationally coupled. Rather, strong substrate-adsorbate interactions evoke rapid (∼2 ps) vibrational relaxation from the adsorbate into the Pt layer, leading to thermal cross-peaks...
July 2017: Structural Dynamics (Melville, N.Y.)
https://www.readbyqxmd.com/read/28345010/distortion-dependent-intersystem-crossing-a-femtosecond-time-resolved-photoelectron-spectroscopy-study-of-benzene-toluene-and-p-xylene
#9
Anne B Stephansen, Theis I Sølling
The competition between ultrafast intersystem crossing and internal conversion in benzene, toluene, and p-xylene is investigated with time-resolved photoelectron spectroscopy and quantum chemical calculations. By exciting to S2 out-of-plane symmetry breaking, distortions are activated at early times whereupon spin-forbidden intersystem crossing becomes (partly) allowed. Natural bond orbital analysis suggests that the pinnacle carbon atoms distorting from the aromatic plane change hybridization between the planar Franck-Condon geometry and the deformed (boat-shaped) S2 equilibrium geometry...
July 2017: Structural Dynamics (Melville, N.Y.)
https://www.readbyqxmd.com/read/28345009/optically-induced-lattice-deformations-electronic-structure-changes-and-enhanced-superconductivity-in-yba2cu3o6-48
#10
R Mankowsky, M Fechner, M Först, A von Hoegen, J Porras, T Loew, G L Dakovski, M Seaberg, S Möller, G Coslovich, B Keimer, S S Dhesi, A Cavalleri
Resonant optical excitation of apical oxygen vibrational modes in the normal state of underdoped YBa2Cu3O6+x induces a transient state with optical properties similar to those of the equilibrium superconducting state. Amongst these, a divergent imaginary conductivity and a plasma edge are transiently observed in the photo-stimulated state. Femtosecond hard x-ray diffraction experiments have been used in the past to identify the transient crystal structure in this non-equilibrium state. Here, we start from these crystallographic features and theoretically predict the corresponding electronic rearrangements that accompany these structural deformations...
July 2017: Structural Dynamics (Melville, N.Y.)
https://www.readbyqxmd.com/read/28191484/photoinduced-molecular-chirality-probed-by-ultrafast-resonant-x-ray-spectroscopy
#11
Jérémy R Rouxel, Markus Kowalewski, Shaul Mukamel
Recently developed circularly polarized X-ray light sources can probe the ultrafast chiral electronic and nuclear dynamics through spatially localized resonant core transitions. We present simulations of time-resolved circular dichroism signals given by the difference of left and right circularly polarized X-ray probe transmission following an excitation by a circularly polarized optical pump with the variable time delay. Application is made to formamide which is achiral in the ground state and assumes two chiral geometries upon optical excitation to the first valence excited state...
July 2017: Structural Dynamics (Melville, N.Y.)
https://www.readbyqxmd.com/read/28191483/shaped-cathodes-for-the-production-of-ultra-short-multi-electron-pulses
#12
Ariel Alcides Petruk, Kostyantyn Pichugin, Germán Sciaini
An electrostatic electron source design capable of producing sub-20 femtoseconds (rms) multi-electron pulses is presented. The photoelectron gun concept builds upon geometrical electric field enhancement at the cathode surface. Particle tracer simulations indicate the generation of extremely short bunches even beyond 40 cm of propagation. Comparisons with compact electron sources commonly used for femtosecond electron diffraction are made.
July 2017: Structural Dynamics (Melville, N.Y.)
https://www.readbyqxmd.com/read/28083543/a-general-method-for-baseline-removal-in-ultrafast-electron-powder-diffraction-data-using-the-dual-tree-complex-wavelet-transform
#13
Laurent P René de Cotret, Bradley J Siwick
The general problem of background subtraction in ultrafast electron powder diffraction (UEPD) is presented with a focus on the diffraction patterns obtained from materials of moderately complex structure which contain many overlapping peaks and effectively no scattering vector regions that can be considered exclusively background. We compare the performance of background subtraction algorithms based on discrete and dual-tree complex (DTCWT) wavelet transforms when applied to simulated UEPD data on the M1-R phase transition in VO2 with a time-varying background...
July 2017: Structural Dynamics (Melville, N.Y.)
https://www.readbyqxmd.com/read/28083542/structural-enzymology-using-x-ray-free-electron-lasers
#14
Christopher Kupitz, Jose L Olmos, Mark Holl, Lee Tremblay, Kanupriya Pande, Suraj Pandey, Dominik Oberthür, Mark Hunter, Mengning Liang, Andrew Aquila, Jason Tenboer, George Calvey, Andrea Katz, Yujie Chen, Max O Wiedorn, Juraj Knoska, Alke Meents, Valerio Majriani, Tyler Norwood, Ishwor Poudyal, Thomas Grant, Mitchell D Miller, Weijun Xu, Aleksandra Tolstikova, Andrew Morgan, Markus Metz, Jose M Martin-Garcia, James D Zook, Shatabdi Roy-Chowdhury, Jesse Coe, Nirupa Nagaratnam, Domingo Meza, Raimund Fromme, Shibom Basu, Matthias Frank, Thomas White, Anton Barty, Sasa Bajt, Oleksandr Yefanov, Henry N Chapman, Nadia Zatsepin, Garrett Nelson, Uwe Weierstall, John Spence, Peter Schwander, Lois Pollack, Petra Fromme, Abbas Ourmazd, George N Phillips, Marius Schmidt
Mix-and-inject serial crystallography (MISC) is a technique designed to image enzyme catalyzed reactions in which small protein crystals are mixed with a substrate just prior to being probed by an X-ray pulse. This approach offers several advantages over flow cell studies. It provides (i) room temperature structures at near atomic resolution, (ii) time resolution ranging from microseconds to seconds, and (iii) convenient reaction initiation. It outruns radiation damage by using femtosecond X-ray pulses allowing damage and chemistry to be separated...
July 2017: Structural Dynamics (Melville, N.Y.)
https://www.readbyqxmd.com/read/28083541/localized-holes-and-delocalized-electrons-in-photoexcited-inorganic-perovskites-watching-each-atomic-actor-by-picosecond-x-ray-absorption-spectroscopy
#15
Fabio G Santomauro, Jakob Grilj, Lars Mewes, Georgian Nedelcu, Sergii Yakunin, Thomas Rossi, Gloria Capano, André Al Haddad, James Budarz, Dominik Kinschel, Dario S Ferreira, Giacomo Rossi, Mario Gutierrez Tovar, Daniel Grolimund, Valerie Samson, Maarten Nachtegaal, Grigory Smolentsev, Maksym V Kovalenko, Majed Chergui
We report on an element-selective study of the fate of charge carriers in photoexcited inorganic CsPbBr3 and CsPb(ClBr)3 perovskite nanocrystals in toluene solutions using time-resolved X-ray absorption spectroscopy with 80 ps time resolution. Probing the Br K-edge, the Pb L3-edge, and the Cs L2-edge, we find that holes in the valence band are localized at Br atoms, forming small polarons, while electrons appear as delocalized in the conduction band. No signature of either electronic or structural changes is observed at the Cs L2-edge...
July 2017: Structural Dynamics (Melville, N.Y.)
https://www.readbyqxmd.com/read/27872875/a-comparison-of-the-innate-flexibilities-of-six-chains-in-f1-atpase-with-identical-secondary-and-tertiary-folds-3-active-enzymes-and-3-structural-proteins
#16
Monique M Tirion
The α and β subunits comprising the hexameric assembly of F1-ATPase share a high degree of structural identity, though low primary identity. Each subunit binds nucleotide in similar pockets, yet only β subunits are catalytically active. Why? We re-examine their internal symmetry axes and observe interesting differences. Dividing each chain into an N-terminal head region, a C-terminal foot region, and a central torso, we observe (1) that while the foot and head regions in all chains obtain high and similar mobility, the torsos obtain different mobility profiles, with the β subunits exhibiting a higher motility compared to the α subunits, a trend supported by the crystallographic B-factors...
July 2017: Structural Dynamics (Melville, N.Y.)
https://www.readbyqxmd.com/read/28345008/insights-into-the-mechanism-of-membrane-pyrophosphatases-by-combining-experiment-and-computer-simulation
#17
Nita R Shah, Craig Wilkinson, Steven P D Harborne, Ainoleena Turku, Kun-Mou Li, Yuh-Ju Sun, Sarah Harris, Adrian Goldman
Membrane-integral pyrophosphatases (mPPases) couple the hydrolysis of pyrophosphate (PPi) to the pumping of Na(+), H(+), or both these ions across a membrane. Recently solved structures of the Na(+)-pumping Thermotoga maritima mPPase (TmPPase) and H(+)-pumping Vigna radiata mPPase revealed the basis of ion selectivity between these enzymes and provided evidence for the mechanisms of substrate hydrolysis and ion-pumping. Our atomistic molecular dynamics (MD) simulations of TmPPase demonstrate that loop 5-6 is mobile in the absence of the substrate or substrate-analogue bound to the active site, explaining the lack of electron density for this loop in resting state structures...
May 2017: Structural Dynamics (Melville, N.Y.)
https://www.readbyqxmd.com/read/28345007/partial-occupancy-binders-identified-by-the-pan-dataset-density-analysis-method-offer-new-chemical-opportunities-and-reveal-cryptic-binding-sites
#18
Nicholas M Pearce, Anthony R Bradley, Tobias Krojer, Brian D Marsden, Charlotte M Deane, Frank von Delft
Crystallographic fragment screening uses low molecular weight compounds to probe the protein surface and although individual protein-fragment interactions are high quality, fragments commonly bind at low occupancy, historically making identification difficult. However, our new Pan-Dataset Density Analysis method readily identifies binders missed by conventional analysis: for fragment screening data of lysine-specific demethylase 4D (KDM4D), the hit rate increased from 0.9% to 10.6%. Previously unidentified fragments reveal multiple binding sites and demonstrate: the versatility of crystallographic fragment screening; that surprisingly large conformational changes are possible in crystals; and that low crystallographic occupancy does not by itself reflect a protein-ligand complex's significance...
May 2017: Structural Dynamics (Melville, N.Y.)
https://www.readbyqxmd.com/read/28289692/augmenting-the-anisotropic-network-model-with-torsional-potentials-improves-path-performance-enabling-detailed-comparison-with-experimental-rate-data
#19
Srinivas Niranj Chandrasekaran, Charles W Carter
PATH algorithms for identifying conformational transition states provide computational parameters-time to the transition state, conformational free energy differences, and transition state activation energies-for comparison to experimental data and can be carried out sufficiently rapidly to use in the "high throughput" mode. These advantages are especially useful for interpreting results from combinatorial mutagenesis experiments. This report updates the previously published algorithm with enhancements that improve correlations between PATH convergence parameters derived from virtual variant structures generated by RosettaBackrub and previously published kinetic data for a complete, four-way combinatorial mutagenesis of a conformational switch in Tryptophanyl-tRNA synthetase...
May 2017: Structural Dynamics (Melville, N.Y.)
https://www.readbyqxmd.com/read/28191482/a-short-history-of-structure-based-research-on-the-photocycle-of-photoactive-yellow-protein
#20
REVIEW
Marius Schmidt
The goals of time-resolved macromolecular crystallography are to extract the molecular structures of the reaction intermediates and the reaction dynamics from time-resolved X-ray data alone. To develop the techniques of time-resolved crystallography, biomolecules with special properties are required. The Photoactive Yellow Protein is the most sparkling of these.
May 2017: Structural Dynamics (Melville, N.Y.)
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