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    Wyświetlanie 1-9 z 9
    Tytuł:
    Correlation of refractive index based and THz streaking arrival time tools for a hard X-ray free-electron laser
    Autorzy:
    Knopp, Gregor
    Johnson, Philip J. M.
    Milne, Christopher
    Cirelli, Claudio
    Usov, Ivan
    Divall, Edwin
    Juranić, Pavle
    Szlachetko, Jakub
    Lemke, Henric
    Patthey, Luc
    Arrell, Christopher
    Błachucki, Wojciech
    Opis:
    To fully exploit ultra-short X-ray pulse durations routinely available at X-ray free-electron lasers to follow out-of-equilibrium dynamics, inherent arrival time fluctuations of the X-ray pulse with an external perturbing laser pulse need to be measured. In this work, two methods of arrival time measurement were compared to measure the arrival time jitter of hard X-ray pulses. The methods were photoelectron streaking by a THz field and a transient refractive index change of a semiconductor. The methods were validated by shot-to-shot correction of a pump–probe transient reflectivity measurement. An ultimate shot-to-shot full width at half-maximum error between the devices of 19.2 ± 0.1 fs was measured.
    Dostawca treści:
    Repozytorium Uniwersytetu Jagiellońskiego
    Artykuł
    Tytuł:
    Ultrafast energy transfer from photoexcited tryptophan to the haem in cytochrome c
    Autorzy:
    Menzi, Samuel
    Cirelli, Claudio
    Ingle, Rebecca A.
    Lima, Frederico A.
    Pamfilidis, Georgios
    Milne, Christopher J.
    Knopp, Gregor
    Rodriguez-Fernandez, Angel
    Rouxel, Jérémy
    Kinschel, Dominik
    Gawelda, Wojciech
    Kubicek, Katharina
    Arrell, Christopfer A.
    Khakhulin, Dmitry
    Johnson, Philip J. M.
    Chergui, Majed
    Szlachetko, Jakub
    Bressler, Christian
    Biednov, Mykola
    Bacellar, Camila
    Cannelli, Oliviero
    Mancini, Giulia F.
    Zhao, Yang
    Ozerov, Dmitry
    Opis:
    We report femtosecond Fe K-edge absorption (XAS) and nonresonant X-ray emission (XES) spectra of ferric cytochrome C (Cyt c) upon excitation of the haem (>300nm) or mixed excitation of the haem and tryptophan (<300 nm). The XAS and XES transients obtained in both excitation energy ranges show no evidence for electron transfer processes between photoexcited tryptophan (Trp) and the haem, but rather an ultrafast energy transfer, in agreement with previous ultrafast optical fluorescence and transient absorption studies. The reported (J. Phys. Chem. B 2011, 115 (46), 13723−13730) decay times of Trp fluorescence in ferrous (∼350 fs) and ferric (∼700 fs) Cyt c are among the shortest ever reported for Trp in a protein. The observed time scales cannot be rationalized in terms of Förster or Dexter energy transfer mechanisms and call for a more thorough theoretical investigation.
    Dostawca treści:
    Repozytorium Uniwersytetu Jagiellońskiego
    Artykuł
    Tytuł:
    Structural effects of high laser power densities on an early bacteriorhodopsin photocycle intermediate
    Autorzy:
    Bertrand, Quentin
    Nogły, Przemysław
    Nass, Karol
    Iwata, So
    Schertler, Gebhard
    Tanaka, Rie
    Standfuss, Jörg
    James, Daniel
    Brünle, Steffen
    Furrer, Antonia
    Weinert, Tobias
    Kepa, Michal
    Kekilli, Demet
    Panneels, Valerie
    Börjesson, Per
    Ortolani, Giorgia
    Skopintsev, Petr
    Tanaka, Tomoyuki
    Huang, Chia-Ying
    Mous, Sandra
    Neutze, Richard
    Tono, Kensuke
    Johnson, Philip J. M.
    Khusainov, Georgii
    Knopp, Gregor
    Owada, Shigeki
    Martiel, Isabelle
    Ozerov, Dmitry
    Milne, Christopher
    Dworkowski, Florian
    Nango, Eriko
    Cirelli, Claudio
    Opis:
    Time-resolved serial crystallography at X-ray Free Electron Lasers offers the opportunity to observe ultrafast photochemical reactions at the atomic level. The technique has yielded exciting molecular insights into various biological processes including light sensing and photochemical energy conversion. However, to achieve sufficient levels of activation within an optically dense crystal, high laser power densities are often used, which has led to an ongoing debate to which extent photodamage may compromise interpretation of the results. Here we compare time-resolved serial crystallographic data of the bacteriorhodopsin K-intermediate collected at laser power densities ranging from 0.04 to 2493 GW/cm2 and follow energy dissipation of the absorbed photons logarithmically from picoseconds to milliseconds. Although the effects of high laser power densities on the overall structure are small, in the upper excitation range we observe significant changes in retinal conformation and increased heating of the functionally critical counterion cluster. We compare light-activation within crystals to that in solution and discuss the impact of the observed changes on bacteriorhodopsin biology.
    Dostawca treści:
    Repozytorium Uniwersytetu Jagiellońskiego
    Artykuł
    Tytuł:
    Lipidic cubic phase injector is a viable crystal delivery system for time-resolved serial crystallography
    Autorzy:
    Nogły, Przemysław
    Kimura, Tetsunari
    Coe, Jesse
    Dods, Robert
    Iwata, So
    Schertler, Gebhard
    Harimoorthy, Rajiv
    Standfuss, Jörg
    Rheinberger, Jan
    James, Daniel
    Zhao, Yun
    Spence, John
    Frank, Matthias
    Hunter, Mark S.
    Sala, Leonardo
    Barty, Anton
    Wu, Wenting
    Beyerlein, Kenneth R.
    DePonte, Daniel
    Panneels, Valerie
    White, Thomas A.
    Conrad, Chelsie
    Milathianaki, Despina
    Kubo, Minoru
    Li, Chufeng
    Williams, Garth J.
    Båth, Petra
    Weierstall, Uwe
    Neutze, Richard
    Boutet, Sébastien
    Berntsen, Peter
    Gati, Cornelius
    Milne, Christopher
    Koglin, Jason E.
    Chapman, Henry N.
    Nelson, Garrett
    Abela, Rafael
    Fromme, Petra
    Nango, Eriko
    Bean, Richard
    Opis:
    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.
    Dostawca treści:
    Repozytorium Uniwersytetu Jagiellońskiego
    Artykuł
    Tytuł:
    Protocols for x-ray transient grating pump/optical probe experiments at x-ray free electron lasers
    Autorzy:
    Lima, Frederico
    Feurer, Thomas
    Biednov, Mykola
    Zalden, Peter
    Serrat, Carles
    Dhanalakshmi-Veeraraj, Mano R
    Mincigrucci, Riccardo
    Staub, Urs
    Madsen, Anders
    Vila-Comamala, Joan
    Knoll, Martin
    Bañares, Luis
    Cucini, Riccardo
    Chergui, Majed
    Torre, Renato
    Paltanin, Ettore
    Ardana-Lamas, Fernando
    Frankenberger, Paul
    Heder, Siti
    Khatu, Nupur N
    Rossi, Giorgio
    Masciovecchio, Claudio
    Szlachetko, Jakub
    Gessini, Alessandro
    Ferrari, Eugenio
    Maznev, Alexei A
    Cannizzo, Andrea
    Nelson, Keith A
    Carrara, Pietro
    Milne, Christopher
    Berndt, Nadia
    Bonetti, Stefano
    Beye, Martin
    Huang, Xinchao
    Bencivenga, Filippo
    Fainozzi, Danny
    Brioschi, Marta
    David, Christian
    Mamyrbayev, Talgat
    Scholz, Markus
    Xu, Han
    Gawelda, Wojciech M
    Bargheer, Matias
    Svetina, Cristian
    Engel, Robin Y.
    Opis:
    Transient grating spectroscopy is a specialized application of the four-wave-mixing methodology and constitutes a versatile technique for investigating the dynamics of vibrational, magnetic and electronic degrees of freedom of matter in a background-free fashion. Recent developments in free-electron laser sources have enabled the extension of this technique into the extreme ultraviolet range. Ongoing efforts to expand transient grating spectroscopy into the x-ray regime promise numerous advantages: (1) substantial penetration depths that allow for probing bulk material properties, (2) element specificity via specific core-excited states, and (3) short wavelengths that allow for excitation gratings with higher momentum transfer and improved spatial resolution. In this study, we comprehensively outline the procedures for conducting x-ray transient grating pump/optical probe experiment. The process encompasses the design and alignment of the experimental setup, as well as the subsequent steps involved in data acquisition and analysis. This paper is intended as a comprehensive guide for researchers interested in implementing x-ray transient grating spectroscopy, providing valuable insights into the intricacies of the experimental workflow required for this novel technique. Furthermore, we discuss the potential for extending this methodology to an x-ray pump/x-ray probe scheme, envisioning a future direction that holds promise for enhancing the capabilities and scope of x-ray transient grating spectroscopy, opening new opportunities for studying ultrafast processes with unprecedented temporal and spatial resolutions.
    Dostawca treści:
    Repozytorium Uniwersytetu Jagiellońskiego
    Artykuł
    Tytuł:
    Ultrafast structural changes direct the first molecular events of vision
    Autorzy:
    Mühle, Jonas
    Kabanova, Victoria
    Tsai, Ching-Ju
    Cirelli, Claudio
    Skopintsev, Petr
    James, Daniel
    Sen, Saumik
    Diethelm, Azeglio D.
    Deupi, Xavier
    Panneels, Valerie
    Martiel, Isabelle
    Iwata, So
    Milne, Christopher J.
    Wach, Anna
    Guixà-González, Ramon
    Kekilli, Demet
    Glover, Hannah
    Knopp, Gregor
    Brünle, Steffen
    Mous, Sandra
    Boutet, Sébastien
    Standfuss, Jörg
    Tanaka, Rie
    Ortolani, Giorgia
    Sarabi, Daniel
    Gotthard, Guillaume
    Joti, Yasumasa
    Johnson, Philip J. M.
    Tono, Kensuke
    Rodrigues, Matthew J.
    Casadei, Cecilia M.
    Båth, Petra
    Furrer, Antonia
    Nogły, Przemysław
    Weinert, Tobias
    Neutze, Richard
    Nango, Eriko
    Varma, Niranjan
    Schertler, Gebhard
    Ma, Pikyee
    Bacellar, Camila
    Nass, Karol
    Gruhl, Thomas
    Lesca, Elena
    Tejero, Oliver
    Dworkowski, Florian
    Ozerov, Dmitry
    Owada, Shigeki
    Pamula, Filip
    Gashi, Dardan
    Opis:
    Vision is initiated by the rhodopsin family of light-sensitive G protein-coupled receptors (GPCRs)1. A photon is absorbed by the 11-cis retinal chromophore of rhodopsin, which isomerizes within 200 femtoseconds to the all-trans conformation2, thereby initiating the cellular signal transduction processes that ultimately lead to vision. However, the intramolecular mechanism by which the photoactivated retinal induces the activation events inside rhodopsin remains experimentally unclear. Here we use ultrafast time-resolved crystallography at room temperature to determine how an isomerized twisted all-trans retinal stores the photon energy that is required to initiate the protein conformational changes associated with the formation of the G protein-binding signalling state. The distorted retinal at a 1-ps time delay after photoactivation has pulled away from half of its numerous interactions with its binding pocket, and the excess of the photon energy is released through an anisotropic protein breathing motion in the direction of the extracellular space. Notably, the very early structural motions in the protein side chains of rhodopsin appear in regions that are involved in later stages of the conserved class A GPCR activation mechanism. Our study sheds light on the earliest stages of vision in vertebrates and points to fundamental aspects of the molecular mechanisms of agonist-mediated GPCR activation.
    Dostawca treści:
    Repozytorium Uniwersytetu Jagiellońskiego
    Artykuł
      Wyświetlanie 1-9 z 9

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