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  1. Article ; Online: Time-resolved cryogenic electron tomography for the study of transient cellular processes.

    Yoniles, Joseph / Summers, Jacob A / Zielinski, Kara A / Antolini, Cali / Panjalingam, Mayura / Lisova, Stella / Moss, Frank R / Perna, Maximus Aldo Di / Kupitz, Christopher / Hunter, Mark S / Pollack, Lois / Wakatsuki, Soichi / Dahlberg, Peter D

    Molecular biology of the cell

    2024  , Page(s) mbcE24010042

    Abstract: Cryogenic electron tomography (cryo-ET) is the highest resolution imaging technique applicable to the life sciences, enabling sub-nanometer visualization of specimens preserved in their near native states. The rapid plunge freezing process used to ... ...

    Abstract Cryogenic electron tomography (cryo-ET) is the highest resolution imaging technique applicable to the life sciences, enabling sub-nanometer visualization of specimens preserved in their near native states. The rapid plunge freezing process used to prepare samples lends itself to time-resolved studies, which researchers have pursued for
    Language English
    Publishing date 2024-05-08
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1098979-1
    ISSN 1939-4586 ; 1059-1524
    ISSN (online) 1939-4586
    ISSN 1059-1524
    DOI 10.1091/mbc.E24-01-0042
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  2. Article ; Online: Structural insights into functional properties of the oxidized form of cytochrome c oxidase.

    Ishigami, Izumi / Sierra, Raymond G / Su, Zhen / Peck, Ariana / Wang, Cong / Poitevin, Frederic / Lisova, Stella / Hayes, Brandon / Moss, Frank R / Boutet, Sébastien / Sublett, Robert E / Yoon, Chun Hong / Yeh, Syun-Ru / Rousseau, Denis L

    Nature communications

    2023  Volume 14, Issue 1, Page(s) 5752

    Abstract: Cytochrome c oxidase (CcO) is an essential enzyme in mitochondrial and bacterial respiration. It catalyzes the four-electron reduction of molecular oxygen to water and harnesses the chemical energy to translocate four protons across biological membranes. ...

    Abstract Cytochrome c oxidase (CcO) is an essential enzyme in mitochondrial and bacterial respiration. It catalyzes the four-electron reduction of molecular oxygen to water and harnesses the chemical energy to translocate four protons across biological membranes. The turnover of the CcO reaction involves an oxidative phase, in which the reduced enzyme (R) is oxidized to the metastable O
    MeSH term(s) Electron Transport Complex IV ; Protons ; Cell Membrane ; Crystallography, X-Ray ; Oxygen
    Chemical Substances Electron Transport Complex IV (EC 1.9.3.1) ; Protons ; Oxygen (S88TT14065)
    Language English
    Publishing date 2023-09-16
    Publishing country England
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-41533-x
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  3. Article: Structural basis for functional properties of cytochrome

    Ishigami, Izumi / Sierra, Raymond G / Su, Zhen / Peck, Ariana / Wang, Cong / Poitevin, Frederic / Lisova, Stella / Hayes, Brandon / Moss, Frank R / Boutet, Sébastien / Sublett, Robert E / Yoon, Chun Hong / Yeh, Syun-Ru / Rousseau, Denis L

    bioRxiv : the preprint server for biology

    2023  

    Abstract: ... ...

    Abstract Cytochrome
    Language English
    Publishing date 2023-03-22
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.03.20.530986
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  4. Article: RNA structures and dynamics with Å resolution revealed by x-ray free electron lasers.

    Zielinski, Kara A / Sui, Shuo / Pabit, Suzette A / Rivera, Daniel A / Wang, Tong / Hu, Qingyue / Kashipathy, Maithri M / Lisova, Stella / Schaffer, Chris B / Mariani, Valerio / Hunter, Mark S / Kupitz, Christopher / Moss, Frank R / Poitevin, Frédéric P / Grant, Thomas D / Pollack, Lois

    bioRxiv : the preprint server for biology

    2023  

    Abstract: RNA macromolecules, like proteins, fold to assume shapes that are intimately connected to their broadly recognized biological functions; however, because of their high charge and dynamic nature, RNA structures are far more challenging to determine. We ... ...

    Abstract RNA macromolecules, like proteins, fold to assume shapes that are intimately connected to their broadly recognized biological functions; however, because of their high charge and dynamic nature, RNA structures are far more challenging to determine. We introduce an approach that exploits the high brilliance of x-ray free electron laser sources to reveal the formation and ready identification of Å scale features in structured and unstructured RNAs. New structural signatures of RNA secondary and tertiary structures are identified through wide angle solution scattering experiments. With millisecond time resolution, we observe an RNA fold from a dynamically varying single strand through a base paired intermediate to assume a triple helix conformation. While the backbone orchestrates the folding, the final structure is locked in by base stacking. In addition to understanding how RNA triplexes form and thereby function as dynamic signaling elements, this new method can vastly increase the rate of structure determination for these biologically essential, but mostly uncharacterized macromolecules.
    Language English
    Publishing date 2023-05-24
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.05.24.541763
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  5. Article ; Online: RNA structures and dynamics with Å resolution revealed by x-ray free-electron lasers.

    Zielinski, Kara A / Sui, Shuo / Pabit, Suzette A / Rivera, Daniel A / Wang, Tong / Hu, Qingyue / Kashipathy, Maithri M / Lisova, Stella / Schaffer, Chris B / Mariani, Valerio / Hunter, Mark S / Kupitz, Christopher / Moss, Frank R / Poitevin, Frédéric P / Grant, Thomas D / Pollack, Lois

    Science advances

    2023  Volume 9, Issue 39, Page(s) eadj3509

    Abstract: RNA macromolecules, like proteins, fold to assume shapes that are intimately connected to their broadly recognized biological functions; however, because of their high charge and dynamic nature, RNA structures are far more challenging to determine. We ... ...

    Abstract RNA macromolecules, like proteins, fold to assume shapes that are intimately connected to their broadly recognized biological functions; however, because of their high charge and dynamic nature, RNA structures are far more challenging to determine. We introduce an approach that exploits the high brilliance of x-ray free-electron laser sources to reveal the formation and ready identification of angstrom-scale features in structured and unstructured RNAs. Previously unrecognized structural signatures of RNA secondary and tertiary structures are identified through wide-angle solution scattering experiments. With millisecond time resolution, we observe an RNA fold from a dynamically varying single strand through a base-paired intermediate to assume a triple-helix conformation. While the backbone orchestrates the folding, the final structure is locked in by base stacking. This method may help to rapidly characterize and identify structural elements in nucleic acids in both equilibrium and time-resolved experiments.
    MeSH term(s) RNA ; Electrons ; Nucleic Acids ; Lasers
    Chemical Substances RNA (63231-63-0) ; Nucleic Acids
    Language English
    Publishing date 2023-09-27
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2810933-8
    ISSN 2375-2548 ; 2375-2548
    ISSN (online) 2375-2548
    ISSN 2375-2548
    DOI 10.1126/sciadv.adj3509
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  6. Article ; Online: A user-friendly plug-and-play cyclic olefin copolymer-based microfluidic chip for room-temperature, fixed-target serial crystallography.

    Liu, Zhongrui / Gu, Kevin K / Shelby, Megan L / Gilbile, Deepshika / Lyubimov, Artem Y / Russi, Silvia / Cohen, Aina E / Narayanasamy, Sankar Raju / Botha, Sabine / Kupitz, Christopher / Sierra, Raymond G / Poitevin, Fredric / Gilardi, Antonio / Lisova, Stella / Coleman, Matthew A / Frank, Matthias / Kuhl, Tonya L

    Acta crystallographica. Section D, Structural biology

    2023  Volume 79, Issue Pt 10, Page(s) 944–952

    Abstract: Over the past two decades, serial X-ray crystallography has enabled the structure determination of a wide range of proteins. With the advent of X-ray free-electron lasers (XFELs), ever-smaller crystals have yielded high-resolution diffraction and ... ...

    Abstract Over the past two decades, serial X-ray crystallography has enabled the structure determination of a wide range of proteins. With the advent of X-ray free-electron lasers (XFELs), ever-smaller crystals have yielded high-resolution diffraction and structure determination. A crucial need to continue advancement is the efficient delivery of fragile and micrometre-sized crystals to the X-ray beam intersection. This paper presents an improved design of an all-polymer microfluidic `chip' for room-temperature fixed-target serial crystallography that can be tailored to broadly meet the needs of users at either synchrotron or XFEL light sources. The chips are designed to be customized around different types of crystals and offer users a friendly, quick, convenient, ultra-low-cost and robust sample-delivery platform. Compared with the previous iteration of the chip [Gilbile et al. (2021), Lab Chip, 21, 4831-4845], the new design eliminates cleanroom fabrication. It has a larger imaging area to volume, while maintaining crystal hydration stability for both in situ crystallization or direct crystal slurry loading. Crystals of two model proteins, lysozyme and thaumatin, were used to validate the effectiveness of the design at both synchrotron (lysozyme and thaumatin) and XFEL (lysozyme only) facilities, yielding complete data sets with resolutions of 1.42, 1.48 and 1.70 Å, respectively. Overall, the improved chip design, ease of fabrication and high modifiability create a powerful, all-around sample-delivery tool that structural biologists can quickly adopt, especially in cases of limited sample volume and small, fragile crystals.
    MeSH term(s) Crystallography ; Muramidase/chemistry ; Cycloparaffins ; Microfluidics/methods ; Temperature ; Equipment Design ; Crystallography, X-Ray ; Proteins ; Polymers
    Chemical Substances Muramidase (EC 3.2.1.17) ; Cycloparaffins ; Proteins ; Polymers
    Language English
    Publishing date 2023-09-25
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2968623-4
    ISSN 2059-7983 ; 0907-4449
    ISSN (online) 2059-7983
    ISSN 0907-4449
    DOI 10.1107/S2059798323007027
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  7. Article ; Online: Serial macromolecular crystallography at ALBA Synchrotron Light Source. Erratum.

    Martin-Garcia, Jose M / Botha, Sabine / Hu, Hao / Jernigan, Rebecca / Castellví, Albert / Lisova, Stella / Gil, Fernando / Calisto, Barbara / Crespo, Isidro / Roy-Chowdhury, Shatabdi / Grieco, Alice / Ketawala, Gihan / Weierstall, Uwe / Spence, John / Fromme, Petra / Zatsepin, Nadia / Boer, Dirk Roeland / Carpena, Xavi

    Journal of synchrotron radiation

    2022  Volume 29, Issue Pt 4, Page(s) 1130

    Abstract: A revised version of Table 2 of Martin-Garcia et al. [J. Synchrotron Rad. (2022). 29, 896-907] is provided. ...

    Abstract A revised version of Table 2 of Martin-Garcia et al. [J. Synchrotron Rad. (2022). 29, 896-907] is provided.
    Language English
    Publishing date 2022-05-16
    Publishing country United States
    Document type Published Erratum
    ZDB-ID 2021413-3
    ISSN 1600-5775 ; 0909-0495
    ISSN (online) 1600-5775
    ISSN 0909-0495
    DOI 10.1107/S1600577522005185
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  8. Article ; Online: Serial macromolecular crystallography at ALBA Synchrotron Light Source.

    Martin-Garcia, Jose M / Botha, Sabine / Hu, Hao / Jernigan, Rebecca / Castellví, Albert / Lisova, Stella / Gil, Fernando / Calisto, Barbara / Crespo, Isidro / Roy-Chowdhury, Shatabdi / Grieco, Alice / Ketawala, Gihan / Weierstall, Uwe / Spence, John / Fromme, Petra / Zatsepin, Nadia / Boer, Dirk Roeland / Carpena, Xavi

    Journal of synchrotron radiation

    2022  Volume 29, Issue Pt 3, Page(s) 896–907

    Abstract: The increase in successful adaptations of serial crystallography at synchrotron radiation sources continues. To date, the number of serial synchrotron crystallography (SSX) experiments has grown exponentially, with over 40 experiments reported so far. In ...

    Abstract The increase in successful adaptations of serial crystallography at synchrotron radiation sources continues. To date, the number of serial synchrotron crystallography (SSX) experiments has grown exponentially, with over 40 experiments reported so far. In this work, we report the first SSX experiments with viscous jets conducted at ALBA beamline BL13-XALOC. Small crystals (15-30 µm) of five soluble proteins (lysozyme, proteinase K, phycocyanin, insulin and α-spectrin-SH3 domain) were suspended in lipidic cubic phase (LCP) and delivered to the X-ray beam with a high-viscosity injector developed at Arizona State University. Complete data sets were collected from all proteins and their high-resolution structures determined. The high quality of the diffraction data collected from all five samples, and the lack of specific radiation damage in the structures obtained in this study, confirm that the current capabilities at the beamline enables atomic resolution determination of protein structures from microcrystals as small as 15 µm using viscous jets at room temperature. Thus, BL13-XALOC can provide a feasible alternative to X-ray free-electron lasers when determining snapshots of macromolecular structures.
    MeSH term(s) Crystallography, X-Ray ; Humans ; Lasers ; Macromolecular Substances ; Proteins ; Synchrotrons ; Viscosity
    Chemical Substances Macromolecular Substances ; Proteins
    Language English
    Publishing date 2022-04-04
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2021413-3
    ISSN 1600-5775 ; 0909-0495
    ISSN (online) 1600-5775
    ISSN 0909-0495
    DOI 10.1107/S1600577522002508
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  9. Article ; Online: Changes in an enzyme ensemble during catalysis observed by high-resolution XFEL crystallography.

    Smith, Nathan / Dasgupta, Medhanjali / Wych, David C / Dolamore, Cole / Sierra, Raymond G / Lisova, Stella / Marchany-Rivera, Darya / Cohen, Aina E / Boutet, Sébastien / Hunter, Mark S / Kupitz, Christopher / Poitevin, Frédéric / Moss, Frank R / Mittan-Moreau, David W / Brewster, Aaron S / Sauter, Nicholas K / Young, Iris D / Wolff, Alexander M / Tiwari, Virendra K /
    Kumar, Nivesh / Berkowitz, David B / Hadt, Ryan G / Thompson, Michael C / Follmer, Alec H / Wall, Michael E / Wilson, Mark A

    Science advances

    2024  Volume 10, Issue 13, Page(s) eadk7201

    Abstract: Enzymes populate ensembles of structures necessary for catalysis that are difficult to experimentally characterize. We use time-resolved mix-and-inject serial crystallography at an x-ray free electron laser to observe catalysis in a designed mutant ... ...

    Abstract Enzymes populate ensembles of structures necessary for catalysis that are difficult to experimentally characterize. We use time-resolved mix-and-inject serial crystallography at an x-ray free electron laser to observe catalysis in a designed mutant isocyanide hydratase (ICH) enzyme that enhances sampling of important minor conformations. The active site exists in a mixture of conformations, and formation of the thioimidate intermediate selects for catalytically competent substates. The influence of cysteine ionization on the ICH ensemble is validated by determining structures of the enzyme at multiple pH values. Large molecular dynamics simulations in crystallo and time-resolved electron density maps show that Asp
    MeSH term(s) Crystallography, X-Ray ; Proteins/chemistry ; Catalysis ; Molecular Dynamics Simulation ; Protein Conformation ; Hydrolases
    Chemical Substances Proteins ; Hydrolases (EC 3.-)
    Language English
    Publishing date 2024-03-27
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2810933-8
    ISSN 2375-2548 ; 2375-2548
    ISSN (online) 2375-2548
    ISSN 2375-2548
    DOI 10.1126/sciadv.adk7201
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  10. Article: Heterogeneity in the M. tuberculosis β-Lactamase Inhibition by Sulbactam.

    Schmidt, Marius / Malla, Tek Narsingh / Zielinski, Kara / Aldama, Luis / Bajt, Sasa / Feliz, Denisse / Hayes, Brandon / Hunter, Mark / Kupitz, Christopher / Lisova, Stella / Knoska, Juraj / Martin-Garcia, Jose / Mariani, Valerio / Pandey, Suraj / Poudyal, Ishwor / Sierra, Raymond / Tolstikova, Alexandra / Yefanov, Oleksandr / Yoon, Ching Hong /
    Ourmazd, Abbas / Fromme, Petra / Schwander, Peter / Barty, Anton / Chapman, Henry / Stojković, Emina / Batyuk, Alexander / Boutet, Sébastien / Phillips, George / Pollack, Lois

    Research square

    2023  

    Abstract: For decades, researchers have been determined to elucidate essential enzymatic functions on the atomic lengths scale by tracing atomic positions in real time. Our work builds on new possibilities unleashed by mix-and-inject serial crystallography (MISC) ...

    Abstract For decades, researchers have been determined to elucidate essential enzymatic functions on the atomic lengths scale by tracing atomic positions in real time. Our work builds on new possibilities unleashed by mix-and-inject serial crystallography (MISC)
    Language English
    Publishing date 2023-01-10
    Publishing country United States
    Document type Preprint
    DOI 10.21203/rs.3.rs-2334665/v1
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