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  1. Article ; Online: Microstructure and crystal order during freezing of supercooled water drops.

    Kalita, Armin / Mrozek-McCourt, Maximillian / Kaldawi, Thomas F / Willmott, Philip R / Loh, N Duane / Marte, Sebastian / Sierra, Raymond G / Laksmono, Hartawan / Koglin, Jason E / Hayes, Matt J / Paul, Robert H / Guillet, Serge A H / Aquila, Andrew L / Liang, Mengning / Boutet, Sébastien / Stan, Claudiu A

    Nature

    2023  Volume 620, Issue 7974, Page(s) 557–561

    Abstract: Supercooled water droplets are widely used to study supercooled ... ...

    Abstract Supercooled water droplets are widely used to study supercooled water
    Language English
    Publishing date 2023-08-16
    Publishing country England
    Document type Journal Article
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/s41586-023-06283-2
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  2. Article ; Online: Optical constants of magnetron-sputtered boron carbide thin films from photoabsorption data in the range 30 to 770 eV.

    Soufli, Regina / Aquila, Andrew L / Salmassi, Farhad / Fernández-Perea, Mónica / Gullikson, Eric M

    Applied optics

    2008  Volume 47, Issue 25, Page(s) 4633–4639

    Abstract: This work discusses the experimental determination of the optical constants (refractive index) of DC-magnetron-sputtered boron carbide films in the 30-770 eV photon energy range. Transmittance measurements of three boron carbide films with thicknesses of ...

    Abstract This work discusses the experimental determination of the optical constants (refractive index) of DC-magnetron-sputtered boron carbide films in the 30-770 eV photon energy range. Transmittance measurements of three boron carbide films with thicknesses of 54.2, 79.0, and 112.5 nm were performed for this purpose. These are believed to be the first published experimental data for the refractive index of boron carbide films in the photon energy range above 160 eV and for the near-edge x-ray absorption fine structure regions around the boron K (188 eV), carbon K (284.2 eV), and oxygen K (543.1 eV) absorption edges. The density, composition, surface chemistry, and morphology of the films were also investigated using Rutherford backscattering, x-ray photoelectron spectroscopy, atomic force microscopy, scanning electron microscopy, and extreme ultraviolet reflectance measurements.
    Language English
    Publishing date 2008-04-16
    Publishing country United States
    Document type Journal Article
    ISSN 1539-4522
    ISSN (online) 1539-4522
    DOI 10.1364/ao.47.004633
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  3. Article ; Online: Negative Pressures and Spallation in Water Drops Subjected to Nanosecond Shock Waves.

    Stan, Claudiu A / Willmott, Philip R / Stone, Howard A / Koglin, Jason E / Liang, Mengning / Aquila, Andrew L / Robinson, Joseph S / Gumerlock, Karl L / Blaj, Gabriel / Sierra, Raymond G / Boutet, Sébastien / Guillet, Serge A H / Curtis, Robin H / Vetter, Sharon L / Loos, Henrik / Turner, James L / Decker, Franz-Josef

    The journal of physical chemistry letters

    2016  Volume 7, Issue 11, Page(s) 2055–2062

    Abstract: Most experimental studies of cavitation in liquid water at negative pressures reported cavitation at tensions significantly smaller than those expected for homogeneous nucleation, suggesting that achievable tensions are limited by heterogeneous ... ...

    Abstract Most experimental studies of cavitation in liquid water at negative pressures reported cavitation at tensions significantly smaller than those expected for homogeneous nucleation, suggesting that achievable tensions are limited by heterogeneous cavitation. We generated tension pulses with nanosecond rise times in water by reflecting cylindrical shock waves, produced by X-ray laser pulses, at the internal surface of drops of water. Depending on the X-ray pulse energy, a range of cavitation phenomena occurred, including the rupture and detachment, or spallation, of thin liquid layers at the surface of the drop. When spallation occurred, we evaluated that negative pressures below -100 MPa were reached in the drops. We model the negative pressures from shock reflection experiments using a nucleation-and-growth model that explains how rapid decompression could outrun heterogeneous cavitation in water, and enable the study of stretched water close to homogeneous cavitation pressures.
    Language English
    Publishing date 2016--02
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 1948-7185
    ISSN (online) 1948-7185
    DOI 10.1021/acs.jpclett.6b00687
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Se-SAD serial femtosecond crystallography datasets from selenobiotinyl-streptavidin.

    Yoon, Chun Hong / DeMirci, Hasan / Sierra, Raymond G / Dao, E Han / Ahmadi, Radman / Aksit, Fulya / Aquila, Andrew L / Batyuk, Alexander / Ciftci, Halilibrahim / Guillet, Serge / Hayes, Matt J / Hayes, Brandon / Lane, Thomas J / Liang, Meng / Lundström, Ulf / Koglin, Jason E / Mgbam, Paul / Rao, Yashas / Rendahl, Theodore /
    Rodriguez, Evan / Zhang, Lindsey / Wakatsuki, Soichi / Boutet, Sébastien / Holton, James M / Hunter, Mark S

    Scientific data

    2017  Volume 4, Page(s) 170055

    Abstract: We provide a detailed description of selenobiotinyl-streptavidin (Se-B SA) co-crystal datasets recorded using the Coherent X-ray Imaging (CXI) instrument at the Linac Coherent Light Source (LCLS) for selenium single-wavelength anomalous diffraction (Se- ... ...

    Abstract We provide a detailed description of selenobiotinyl-streptavidin (Se-B SA) co-crystal datasets recorded using the Coherent X-ray Imaging (CXI) instrument at the Linac Coherent Light Source (LCLS) for selenium single-wavelength anomalous diffraction (Se-SAD) structure determination. Se-B SA was chosen as the model system for its high affinity between biotin and streptavidin where the sulfur atom in the biotin molecule (C
    Language English
    Publishing date 2017--25
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2775191-0
    ISSN 2052-4463 ; 2052-4463
    ISSN (online) 2052-4463
    ISSN 2052-4463
    DOI 10.1038/sdata.2017.55
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  5. Article ; Online: Rational Control of Off-State Heterogeneity in a Photoswitchable Fluorescent Protein Provides Switching Contrast Enhancement**

    Adam, Virgile / Hadjidemetriou, Kyprianos / Jensen, Nickels / Shoeman, Robert L. / Woodhouse, Joyce / Aquila, Andrew L. / Banneville, Anne-Sophie / Barends, Thomas Reinier M. / Bezchastnov, Victor G. / Boutet, Sébastien / Byrdin, Martin / Cammarata, Marco / Carbajo, Sergio / Eleni Christou, Nina / Coquelle, Nicolas / Mora, Eugenio de la / El-Khatib, Mariam / Moreno-Chicano, Tadeo / Bruce Doak, R. /
    Fieschi, Franck / Foucar, Lutz M. / Glushonkov, Oleksandr / Gorel, Alexander / Grünbein, Marie Luise / Hilpert, Mario / Hunter, Mark S. / Kloos, Marco / Koglin, Jason E. / Lane, Thomas J. / Liang, Mengning / Mantovanelli, Angela / Nass, Karol / Nass Kovács, Gabriela / Owada, Shigeki / Roome, Christopher M. / Schirò, Giorgio / Seaberg, Matthew D. / Stricker, Miriam / Thépaut, Michel / Tono, Kensuke / Ueda, Kiyoshi / Uriarte, Lucas Martinez / You, Daehyun / Zala, Ninon / Domratcheva, Tatiana / Jakobs, Stefan / Sliwa, Michel / Schlichting, Ilme / Colletier, Jacques Philippe / Bourgeois, Dominique / Weik, Martin

    2022  

    Abstract: Reversibly photoswitchable fluorescent proteins are essential markers for advanced biological imaging, and optimization of their photophysical properties underlies improved performance and novel applications. Here we establish a link between ... ...

    Abstract Reversibly photoswitchable fluorescent proteins are essential markers for advanced biological imaging, and optimization of their photophysical properties underlies improved performance and novel applications. Here we establish a link between photoswitching contrast, one of the key parameters that dictate the achievable resolution in nanoscopy applications, and chromophore conformation in the non-fluorescent state of rsEGFP2, a widely employed label in REversible Saturable OpticaL Fluorescence Transitions (RESOLFT) microscopy. Upon illumination, the cis chromophore of rsEGFP2 isomerizes to two distinct off-state conformations, trans1 and trans2, located on either side of the V151 side chain. Reducing or enlarging the side chain at this position (V151A and V151L variants) leads to single off-state conformations that exhibit higher and lower switching contrast, respectively, compared to the rsEGFP2 parent. The combination of structural information obtained by serial femtosecond crystallography with high-level quantum chemical calculations and with spectroscopic and photophysical data determined in vitro suggests that the changes in switching contrast arise from blue- and red-shifts of the absorption bands associated to trans1 and trans2, respectively. Thus, due to elimination of trans2, the V151A variants of rsEGFP2 and its superfolding variant rsFolder2 display a more than two-fold higher switching contrast than their respective parent proteins, both in vitro and in E. coli cells. The application of the rsFolder2-V151A variant is demonstrated in RESOLFT nanoscopy. Our study rationalizes the connection between structural and photophysical chromophore properties and suggests a means to rationally improve fluorescent proteins for nanoscopy applications.

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    Keywords nanoscopy ; photoswitchable fluorescent proteins ; quantum chemistry ; serial femtosecond crystallography ; switching contrast
    Subject code 670
    Language English
    Publishing country de
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Selenium single-wavelength anomalous diffraction de novo phasing using an X-ray-free electron laser.

    Hunter, Mark S / Yoon, Chun Hong / DeMirci, Hasan / Sierra, Raymond G / Dao, E Han / Ahmadi, Radman / Aksit, Fulya / Aquila, Andrew L / Ciftci, Halilibrahim / Guillet, Serge / Hayes, Matt J / Lane, Thomas J / Liang, Meng / Lundström, Ulf / Koglin, Jason E / Mgbam, Paul / Rao, Yashas / Zhang, Lindsey / Wakatsuki, Soichi /
    Holton, James M / Boutet, Sébastien

    Nature communications

    2016  Volume 7, Page(s) 13388

    Abstract: Structural information about biological macromolecules near the atomic scale provides important insight into the functions of these molecules. To date, X-ray crystallography has been the predominant method used for macromolecular structure determination. ...

    Abstract Structural information about biological macromolecules near the atomic scale provides important insight into the functions of these molecules. To date, X-ray crystallography has been the predominant method used for macromolecular structure determination. However, challenges exist when solving structures with X-rays, including the phase problem and radiation damage. X-ray-free electron lasers (X-ray FELs) have enabled collection of diffraction information before the onset of radiation damage, yet the majority of structures solved at X-ray FELs have been phased using external information via molecular replacement. De novo phasing at X-ray FELs has proven challenging due in part to per-pulse variations in intensity and wavelength. Here we report the solution of a selenobiotinyl-streptavidin structure using phases obtained by the anomalous diffraction of selenium measured at a single wavelength (Se-SAD) at the Linac Coherent Light Source. Our results demonstrate Se-SAD, routinely employed at synchrotrons for novel structure determination, is now possible at X-ray FELs.
    MeSH term(s) Bacterial Proteins/chemistry ; Bacterial Proteins/ultrastructure ; Biotin/analogs & derivatives ; Biotin/chemistry ; Crystallography, X-Ray/instrumentation ; Crystallography, X-Ray/methods ; Electrons ; Feasibility Studies ; Lasers ; Models, Molecular ; Protein Conformation ; Selenium/chemistry
    Chemical Substances Bacterial Proteins ; selenobiotinyl streptavidin ; Biotin (6SO6U10H04) ; Selenium (H6241UJ22B)
    Language English
    Publishing date 2016-11-04
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 2041-1723
    ISSN (online) 2041-1723
    DOI 10.1038/ncomms13388
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Serial time-resolved crystallography of photosystem II using a femtosecond X-ray laser.

    Kupitz, Christopher / Basu, Shibom / Grotjohann, Ingo / Fromme, Raimund / Zatsepin, Nadia A / Rendek, Kimberly N / Hunter, Mark S / Shoeman, Robert L / White, Thomas A / Wang, Dingjie / James, Daniel / Yang, Jay-How / Cobb, Danielle E / Reeder, Brenda / Sierra, Raymond G / Liu, Haiguang / Barty, Anton / Aquila, Andrew L / Deponte, Daniel /
    Kirian, Richard A / Bari, Sadia / Bergkamp, Jesse J / Beyerlein, Kenneth R / Bogan, Michael J / Caleman, Carl / Chao, Tzu-Chiao / Conrad, Chelsie E / Davis, Katherine M / Fleckenstein, Holger / Galli, Lorenzo / Hau-Riege, Stefan P / Kassemeyer, Stephan / Laksmono, Hartawan / Liang, Mengning / Lomb, Lukas / Marchesini, Stefano / Martin, Andrew V / Messerschmidt, Marc / Milathianaki, Despina / Nass, Karol / Ros, Alexandra / Roy-Chowdhury, Shatabdi / Schmidt, Kevin / Seibert, Marvin / Steinbrener, Jan / Stellato, Francesco / Yan, Lifen / Yoon, Chunhong / Moore, Thomas A / Moore, Ana L / Pushkar, Yulia / Williams, Garth J / Boutet, Sébastien / Doak, R Bruce / Weierstall, Uwe / Frank, Matthias / Chapman, Henry N / Spence, John C H / Fromme, Petra

    Nature

    2014  Volume 513, Issue 7517, Page(s) 261–265

    Abstract: Photosynthesis, a process catalysed by plants, algae and cyanobacteria converts sunlight to energy thus sustaining all higher life on Earth. Two large membrane protein complexes, photosystem I and II (PSI and PSII), act in series to catalyse the light- ... ...

    Abstract Photosynthesis, a process catalysed by plants, algae and cyanobacteria converts sunlight to energy thus sustaining all higher life on Earth. Two large membrane protein complexes, photosystem I and II (PSI and PSII), act in series to catalyse the light-driven reactions in photosynthesis. PSII catalyses the light-driven water splitting process, which maintains the Earth's oxygenic atmosphere. In this process, the oxygen-evolving complex (OEC) of PSII cycles through five states, S0 to S4, in which four electrons are sequentially extracted from the OEC in four light-driven charge-separation events. Here we describe time resolved experiments on PSII nano/microcrystals from Thermosynechococcus elongatus performed with the recently developed technique of serial femtosecond crystallography. Structures have been determined from PSII in the dark S1 state and after double laser excitation (putative S3 state) at 5 and 5.5 Å resolution, respectively. The results provide evidence that PSII undergoes significant conformational changes at the electron acceptor side and at the Mn4CaO5 core of the OEC. These include an elongation of the metal cluster, accompanied by changes in the protein environment, which could allow for binding of the second substrate water molecule between the more distant protruding Mn (referred to as the 'dangler' Mn) and the Mn3CaOx cubane in the S2 to S3 transition, as predicted by spectroscopic and computational studies. This work shows the great potential for time-resolved serial femtosecond crystallography for investigation of catalytic processes in biomolecules.
    MeSH term(s) Crystallography, X-Ray ; Cyanobacteria/chemistry ; Models, Molecular ; Photosystem II Protein Complex/chemistry ; Protein Structure, Tertiary
    Chemical Substances Photosystem II Protein Complex
    Language English
    Publishing date 2014-07-09
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/nature13453
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