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2. Mechanisms of inward transmembrane proton translocation

Author

Kovalev, Kirill, Tsybrov, Fedor, Alekseev, Alexey, Shevchenko, Vitaly, Soloviov, Dmytro, Siletsky, Sergey, Bourenkov, Gleb, Agthe, Michael, Nikolova, Marina, von Stetten, David, Astashkin, Roman, Bukhdruker, Sergey, Chizhov, Igor, Royant, Antoine, Kuzmin, Alexander, Gushchin, Ivan, Rosselli, Riccardo, Rodriguez-Valera, Francisco, Ilyinskiy, Nikolay, Rogachev, Andrey, Borshchevskiy, Valentin, Schneider, Thomas R., Bamberg, Ernst, and Gordeliy, Valentin

Published
2023
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3. Deamidation of the human eye lens protein γS-crystallin accelerates oxidative aging

Author

Norton-Baker, Brenna, Mehrabi, Pedram, Kwok, Ashley O, Roskamp, Kyle W, Rocha, Megan A, Sprague-Piercy, Marc A, von Stetten, David, Miller, RJ Dwayne, and Martin, Rachel W

Subjects
Biochemistry and Cell Biology, Biological Sciences, Aging, Eye Disease and Disorders of Vision, Cataract, Humans, Lens, Crystalline, Oxidation-Reduction, Oxidative Stress, gamma-Crystallins, X-ray crystallography, cataract, crystallin, deamidation, disulfide bonding, oxidation, post-translational modification, protein aggregation, protein stability, second virial coefficient, Chemical Sciences, Information and Computing Sciences, Biophysics, Biological sciences, Chemical sciences
Abstract

Cataract, a clouding of the eye lens from protein precipitation, affects millions of people every year. The lens proteins, the crystallins, show extensive post-translational modifications (PTMs) in cataractous lenses. The most common PTMs, deamidation and oxidation, promote crystallin aggregation; however, it is not clear precisely how these PTMs contribute to crystallin insolubilization. Here, we report six crystal structures of the lens protein γS-crystallin (γS): one of the wild-type and five of deamidated γS variants, from three to nine deamidation sites, after sample aging. The deamidation mutations do not change the overall fold of γS; however, increasing deamidation leads to accelerated disulfide-bond formation. Addition of deamidated sites progressively destabilized protein structure, and the deamidated variants display an increased propensity for aggregation. These results suggest that the deamidated variants are useful as models for accelerated aging; the structural changes observed provide support for redox activity of γS-crystallin in the lens.

Published
2022

10. Specific radiation damage is a lesser concern at room temperature

Author

Gotthard, Guillaume, Aumonier, Sylvain, de Sanctis, Daniele, Leonard, Gordon, von Stetten, David, Royant, Antoine, European Synchrotron Radiation Facility (ESRF), Institut de biologie structurale (IBS - UMR 5075 ), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), icOS (Cryobench), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)

Subjects
Quantitative Biology::Subcellular Processes, Quantitative Biology::Biomolecules, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Quantitative Biology::Molecular Networks, time-resolved crystallography, lcsh:Q, room-temperature macromolecular crystallography, specific radiation damage, lcsh:Science, cryocrystallography, Research Papers
Abstract

Both global and specific radiation damage have been investigated using three different proteins at cryogenic and room temperature. The large decoupling between global and specific radiation damage at cryogenic temperature appears to be practically abolished at room temperature, which has positive implications for time-resolved protein crystallography., Carrying out macromolecular crystallography (MX) experiments at cryogenic temperatures significantly slows the rate of global radiation damage, thus facilitating the solution of high-resolution crystal structures of macromolecules. However, cryo-MX experiments suffer from the early onset of so-called specific radiation damage that affects certain amino-acid residues and, in particular, the active sites of many proteins. Here, a series of MX experiments are described which suggest that specific and global radiation damage are much less decoupled at room temperature than they are at cryogenic temperatures. The results reported here demonstrate the interest in reviving the practice of collecting MX diffraction data at room temperature and allow structural biologists to favourably envisage the development of time-resolved MX experiments at synchrotron sources.

Published
2019

14. MXCuBE2 the dawn of MXCuBE Collaboration

Author

Oscarsson, Marcus, Beteva, Antonia, Flot, David, Gordon, Elspeth, Guijarro, Matias, Leonard, Gordon, McSweeney, Sean, Monaco, Stephanie, Mueller-Dieckmann, Christoph, Nanao, Max, Nurizzo, Didier, Popov, Alexander N., von Stetten, David, Svensson, Olof, Rey-Bakaikoa, Vicente, Chado, Idrissou, Chavas, Leonard M. G., Gadea, Laurent, Gourhant, Patrick, Isabet, Tatiana, Legrand, Pierre, Savko, Martin, Sirigu, Serena, Shepard, William, Thompson, Andrew, Mueller, Uwe, Nan, Jie, Eguiraun, Mikel, Bolmsten, Fredrick, Nardella, Alberto, Milàn-Otero, Antonio, Thunnissen, Marjolein, Hellmig, Michael, Kastner, Alexandra, Schmuckermaier, Lukas, Gerlach, Martin, Feiler, Christian, Weiss, Manfred S., Bowler, Matthew W., Gobbo, Alexandre, Papp, Gergely, Sinoir, Jeremy, McCarthy, Andrew A., Karpics, Ivars, Nikolova, Marina, Bourenkov, Gleb, Schneider, Thomas, Andreu, Jordi, Cuní, Guifré, Juanhuix, Judith, Boer, Roeland, Fogh, Rasmus, Keller, Peter, Flensburg, Claus, Paciorek, Wlodek, Vonrhein, Clemens, Bricogne, Gerard, and De Sanctis, Daniele

Subjects
synchrotron beamline control software, macromolecular crystallography, graphical user interface, ddc:550, Inhouse research on structure dynamics and function of matter, Research Papers, MXCuBE, software collaboration
Abstract

Journal of synchrotron radiation 26(2), 393 - 405 (2019). doi:10.1107/S1600577519001267, MXCuBE2 is the second-generation evolution of the MXCuBE beamline control software, initially developed and used at ESRF – the European Synchrotron. MXCuBE2 extends, in an intuitive graphical user interface (GUI), the functionalities and data collection methods available to users while keeping all previously available features and allowing for the straightforward incorporation of ongoing and future developments. MXCuBE2 introduces an extended abstraction layer that allows easy interfacing of any kind of macromolecular crystallography (MX) hardware component, whether this is a diffractometer, sample changer, detector or optical element. MXCuBE2 also works in strong synergy with the ISPyB Laboratory Information Management System, accessing the list of samples available for a particular experimental session and associating, either from instructions contained in ISPyB or from user input via the MXCuBE2 GUI, different data collection types to them. The development of MXCuBE2 forms the core of a fruitful collaboration which brings together several European synchrotrons and a software development factory and, as such, defines a new paradigm for the development of beamline control platforms for the European MX user community., Published by Wiley-Blackwell, [S.l.]

Published
2019

16. Tracking the route of molecular oxygen in O 2 -tolerant membrane-bound [NiFe] hydrogenase

Author

Kalms, Jacqueline, primary, Schmidt, Andrea, additional, Frielingsdorf, Stefan, additional, Utesch, Tillmann, additional, Gotthard, Guillaume, additional, von Stetten, David, additional, van der Linden, Peter, additional, Royant, Antoine, additional, Mroginski, Maria Andrea, additional, Carpentier, Philippe, additional, Lenz, Oliver, additional, and Scheerer, Patrick, additional

Published
2018
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18. Tracking the route of molecular oxygen in O2-tolerant membrane-bound [NiFe] hydrogenase.

Author

Kalms, Jacqueline, Schmidt, Andrea, Frielingsdorf, Stefan, Utesch, Tillmann, Gotthard, Guillaume, von Stetten, David, van der Linden, Peter, Royant, Antoine, Mroginski, Maria Andrea, Carpentier, Philippe, Lenz, Oliver, and Scheerer, Patrick

Subjects
HYDROGENASE, RALSTONIA eutropha, CATALYTIC reduction, METALLOPROTEINS, X-ray crystallography
Abstract

[NiFe] hydrogenases catalyze the reversible splitting of H2 into protons and electrons at a deeply buried active site. The catalytic center can be accessed by gas molecules through a hydrophobic tunnel network. While most [NiFe] hydrogenases are inactivated by O2, a small subgroup, including the membrane-bound [NiFe] hydrogenase (MBH) of Ralstonia eutropha, is able to overcome aerobic inactivation by catalytic reduction of O2 to water. This O2tolerance relies on a special [4Fe3S] cluster that is capable of releasing two electrons upon O2 attack. Here, the O2 accessibility of the MBH gas tunnel network has been probed experimentally using a "soak-and-freeze" derivatization method, accompanied by protein X-ray crystallography and computational studies. This combined approach revealed several sites of O2molecules within a hydrophobic tunnel network leading, via two tunnel entrances, to the catalytic center of MBH. The corresponding site occupancies were related to the O2 concentrations used for MBH crystal derivatization. The examination of the O2-derivatized data furthermore uncovered two unexpected structural alterations at the [4Fe3S] cluster, which might be related to the O2tolerance of the enzyme. [ABSTRACT FROM AUTHOR]

Published
2018
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19. Conformational heterogeneity of the Pfr chromophore in plant and cyanobacterial phytochromes

Author

Velazquez Escobar, Francisco, primary, von Stetten, David, additional, Günther-Lütkens, Mina, additional, Keidel, Anke, additional, Michael, Norbert, additional, Lamparter, Tilman, additional, Essen, Lars-Oliver, additional, Hughes, Jon, additional, Gärtner, Wolfgang, additional, Yang, Yang, additional, Heyne, Karsten, additional, Mroginski, Maria A., additional, and Hildebrandt, Peter, additional

Published
2015
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22. Crystal structure of a common GPCR-binding interface for G protein and arrestin

Author

Szczepek, Michal, primary, Beyrière, Florent, additional, Hofmann, Klaus Peter, additional, Elgeti, Matthias, additional, Kazmin, Roman, additional, Rose, Alexander, additional, Bartl, Franz J., additional, von Stetten, David, additional, Heck, Martin, additional, Sommer, Martha E., additional, Hildebrand, Peter W., additional, and Scheerer, Patrick, additional

Published
2014
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24. Structure of the Biliverdin Cofactor in the Pfr State of Bathy and Prototypical Phytochromes

Author

Salewski, Johannes, primary, Escobar, Francisco Velazquez, additional, Kaminski, Steve, additional, von Stetten, David, additional, Keidel, Anke, additional, Rippers, Yvonne, additional, Michael, Norbert, additional, Scheerer, Patrick, additional, Piwowarski, Patrick, additional, Bartl, Franz, additional, Frankenberg-Dinkel, Nicole, additional, Ringsdorf, Simone, additional, Gärtner, Wolfgang, additional, Lamparter, Tilman, additional, Mroginski, Maria Andrea, additional, and Hildebrandt, Peter, additional

Published
2013
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29. Cyanochromes Are Blue/Green Light Photoreversible Photoreceptors Defined by a Stable Double Cysteine Linkage to a Phycoviolobilin-type Chromophore

Author

Ulijasz, Andrew T., primary, Cornilescu, Gabriel, additional, von Stetten, David, additional, Cornilescu, Claudia, additional, Velazquez Escobar, Francisco, additional, Zhang, Junrui, additional, Stankey, Robert J., additional, Rivera, Mario, additional, Hildebrandt, Peter, additional, and Vierstra, Richard D., additional

Published
2009
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30. Chromophore Structure of Cyanobacterial Phytochrome Cph1 in the Pr State: Reconciling Structural and Spectroscopic Data by QM/MM Calculations

Author

Mroginski, Maria Andrea, primary, von Stetten, David, additional, Escobar, Francisco Velazquez, additional, Strauss, Holger M., additional, Kaminski, Steve, additional, Scheerer, Patrick, additional, Günther, Mina, additional, Murgida, Daniel H., additional, Schmieder, Peter, additional, Bongards, Christian, additional, Gärtner, Wolfgang, additional, Mailliet, Jo, additional, Hughes, Jon, additional, Essen, Lars-Oliver, additional, and Hildebrandt, Peter, additional

Published
2009
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33. Mutational Analysis of Deinococcus radiodurans Bacteriophytochrome Reveals Key Amino Acids Necessary for the Photochromicity and Proton Exchange Cycle of Phytochromes

Author

Wagner, Jeremiah R., primary, Zhang, Junrui, additional, von Stetten, David, additional, Günther, Mina, additional, Murgida, Daniel H., additional, Mroginski, Maria Andrea, additional, Walker, Joseph M., additional, Forest, Katrina T., additional, Hildebrandt, Peter, additional, and Vierstra, Richard D., additional

Published
2008
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37. Structure of the chromophore binding pocket in the Pr state of plant phytochrome phyA.

Author

Mroginski MA, Kaminski S, von Stetten D, Ringsdorf S, Gärtner W, Essen LO, and Hildebrandt P

Subjects
Bacterial Proteins chemistry, Hydrogen Bonding, Molecular Dynamics Simulation, Photoreceptors, Microbial, Phycobilins chemistry, Phycocyanin chemistry, Phytochrome chemistry, Protein Binding, Protein Kinases chemistry, Protein Structure, Tertiary, Quantum Theory, Spectrum Analysis, Raman, Phytochrome A chemistry
Abstract

A homology structural model was generated for plant phytochrome phyA utilizing the crystal structure of the sensory module of cyanobacterial phytochrome Cph1 (Cph1Δ2). As chromophores, either the native phytochromobilin cofactor (PΦB) or phycocyanobilin (PCB), the natural cofactor in Cph1, was incorporated. These homology models were further optimized by molecular dynamics (MD) simulations revealing a satisfying overall agreement with the crystal structure of Cph1Δ2. Notable differences in the PΦB adduct of phyA result from a restructuring of the small helical segment α(7) that leads to displacements of a few amino acids away from the cofactor. This repositioning of residues also include aspartate 218 such that, instead of its carbonyl function as in Cph1Δ2, an additional water molecule forms hydrogen bonds with the ring B and C NH groups. To validate the phyA structural model in the chromophore binding pocket, Raman spectra of the cofactor were calculated by means of the quantum mechanics/molecular mechanics (QM/MM) hybrid methodology and compared with the experimental resonance Raman (RR) spectra. The satisfactory overall agreement between calculated and experimental spectra is taken as an indication for the good quality of the structural model. Moreover, the methine bridge stretching modes and the effects of isotopic labeling at selected positions of the chromophore are very well reproduced to allow confirming even details of the methine bridge geometry as predicted by the homology model. Specifically, it is demonstrated that the experimental RR spectra are consistent with a torsional angle of ring D with respect to ring C that is distinctly higher for phyA-PCB (45°) and phyA-PΦB (42°) than for Cph1Δ2 (30°). Raman spectra calculated from different points of the MD trajectory display variations of the mode frequencies and intensities reflecting the structural fluctuations from snapshot to snapshot. The snapshot spectrum of the lowest energy structure and the sum of all snapshot spectra afford an equally good description of the experimental data. Particularly large variations between the snapshots are noted for the N-H in-plane bending mode of the pyrrole rings B and C, which reflect alterations of the hydrogen bond interactions brought about by fluctuations of water molecules in the cofactor cavity. This overestimation of the water molecule mobility is a consequence of the deficiency of the current QM/MM methodology that, due to the lack of appropriate protein force fields, cannot adequately account for the electrostatics in the cofactor pocket.

Published
2011
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