membrane protein; 2D crystal; image processing; electron crystallography; maximum likelihood; single particle
Castaño-Díez Daniel, Kudryashev Mikhail, Stahlberg Henning (2016), Dynamo Catalogue: Geometrical tools and data management for particle picking in subtomogram averaging of cryo-electron tomograms., in Journal of structural biology
Sborgi Lorenzo, Rühl Sebastian, Mulvihill Estefania, Pipercevic Joka, Heilig Rosalie, Stahlberg Henning, Farady Christopher J, Müller Daniel J, Broz Petr, Hiller Sebastian (2016), GSDMD membrane pore formation constitutes the mechanism of pyroptotic cell death., in The EMBO journal
, 35(16), 1766-78.
Taylor Nicholas M I, Prokhorov Nikolai S, Guerrero-Ferreira Ricardo C, Shneider Mikhail M, Browning Christopher, Goldie Kenneth N, Stahlberg Henning, Leiman Petr G (2016), Structure of the T4 baseplate and its function in triggering sheath contraction., in Nature
, 533(7603), 346-52.
Ayciriex Sophie, Gerber Hermeto, Osuna Guillermo M Garcia, Chami Mohamed, Stahlberg Henning, Shevchenko Andrej, Fraering Patrick C (2016), The lipidome associated with the γ-secretase complex is required for its integrity and activity., in The Biochemical journal
, 473(3), 321-34.
Kudryashev Mikhail, Castaño-Díez Daniel, Deluz Cédric, Hassaine Gherici, Grasso Luigino, Graf-Meyer Alexandra, Vogel Horst, Stahlberg Henning (2016), The Structure of the Mouse Serotonin 5-HT3 Receptor in Lipid Vesicles., in Structure (London, England : 1993)
, 24(1), 165-70.
Stahlberg Henning, Biyani Nikhil, Engel Andreas (2015), 3D reconstruction of two-dimensional crystals., in Archives of biochemistry and biophysics
, 581, 68-77.
Marabini Roberto, Carragher Bridget, Chen Shaoxia, Chen James, Cheng Anchi, Downing Kenneth H, Frank Joachim, Grassucci Robert A, Bernard Heymann J, Jiang Wen, Jonic Slavica, Liao Hstau Y, Ludtke Steven J, Patwari Shail, Piotrowski Angela L, Quintana Adrian, Sorzano Carlos O S, Stahlberg Henning, Vargas Javier, Voss Neil R, Chiu Wah, Carazo Jose M (2015), CTF Challenge: Result summary., in Journal of structural biology
, 190(3), 348-59.
Scherer Sebastian, Kowal Julia, Chami Mohamed, Dandey Venkata, Arheit Marcel, Ringler Philippe, Stahlberg Henning (2014), 2dx_automator: implementation of a semiautomatic high-throughput high-resolution cryo-electron crystallography pipeline., in Journal of structural biology
, 186(2), 302-7.
McCoy Jason G, Rusinova Radda, Kim Dorothy M, Kowal Julia, Banerjee Sourabh, Jaramillo Cartagena Alexis, Thompson Ameer N, Kolmakova-Partensky Ludmila, Stahlberg Henning, Andersen Olaf S, Nimigean Crina M (2014), A KcsA/MloK1 chimeric ion channel has lipid-dependent ligand-binding energetics., in The Journal of biological chemistry
, 289(14), 9535-46.
Goldie Kenneth N, Abeyrathne Priyanka, Kebbel Fabian, Chami Mohamed, Ringler Philippe, Stahlberg Henning (2014), Cryo-electron microscopy of membrane proteins., in Methods in molecular biology (Clifton, N.J.)
, 1117, 325-41.
Kowal Julia, Chami Mohamed, Baumgartner Paul, Arheit Marcel, Chiu Po-Lin, Rangl Martina, Scheuring Simon, Schröder Gunnar F, Nimigean Crina M, Stahlberg Henning (2014), Ligand-induced structural changes in the cyclic nucleotide-modulated potassium channel MloK1., in Nature communications
, 5, 3106-3106.
Scherer Sebastian, Arheit Marcel, Kowal Julia, Zeng Xiangyan, Stahlberg Henning (2014), Single particle 3D reconstruction for 2D crystal images of membrane proteins., in Journal of structural biology
, 185(3), 267-77.
Kudryashev Misha, Aktoudianaki Aikaterini, Dedoglou Dimitrios, Stahlberg Henning, Tsiotis Georgios (2014), The ultrastructure of Chlorobaculum tepidum revealed by cryo-electron tomography., in Biochimica et biophysica acta
, 1837(10), 1635-42.
Hassaine Ghérici, Deluz Cédric, Grasso Luigino, Wyss Romain, Tol Menno B, Hovius Ruud, Graff Alexandra, Stahlberg Henning, Tomizaki Takashi, Desmyter Aline, Moreau Christophe, Li Xiao-Dan, Poitevin Frédéric, Vogel Horst, Nury Hugues (2014), X-ray structure of the mouse serotonin 5-HT3 receptor., in Nature
, 512(7514), 276-81.
Arheit Marcel, Castaño-Díez Daniel, Thierry Raphaël, Gipson Bryant R, Zeng Xiangyan, Stahlberg Henning (2013), Automation of image processing in electron crystallography., in Methods in molecular biology (Clifton, N.J.)
, 955, 313-30.
Arheit Marcel, Castaño-Díez Daniel, Thierry Raphaël, Gipson Bryant R, Zeng Xiangyan, Stahlberg Henning (2013), Image processing of 2D crystal images., in Methods in molecular biology (Clifton, N.J.)
, 955, 171-94.
Arheit Marcel, Castaño-Diéz Daniel, Thierry Raphaël, Abeyrathne Priyanka, Gipson Bryant R, Stahlberg Henning (2013), Merging of image data in electron crystallography., in Methods in molecular biology (Clifton, N.J.)
, 955, 195-209.
Degiacomi Matteo T, Iacovache Ioan, Pernot Lucile, Chami Mohamed, Kudryashev Misha, Stahlberg Henning, van der Goot F Gisou, Dal Peraro Matteo (2013), Molecular assembly of the aerolysin pore reveals a swirling membrane-insertion mechanism., in Nature chemical biology
, 9(10), 623-9.
Kebbel Fabian, Kurz Mareike, Arheit Marcel, Grütter Markus G, Stahlberg Henning (2013), Structure and substrate-induced conformational changes of the secondary citrate/sodium symporter CitS revealed by electron crystallography., in Structure (London, England : 1993)
, 21(7), 1243-50.
Kowal Julia, Chami Mohamed, Ringler Philippe, Müller Shirley A, Kudryashev Mikhail, Castaño-Díez Daniel, Amstutz Marlise, Cornelis Guy R, Stahlberg Henning, Engel Andreas (2013), Structure of the dodecameric Yersinia enterocolitica secretin YscC and its trypsin-resistant core., in Structure (London, England : 1993)
, 21(12), 2152-61.
Tol Menno B, Deluz Cédric, Hassaine Gherici, Graff Alexandra, Stahlberg Henning, Vogel Horst (2013), Thermal unfolding of a mammalian pentameric ligand-gated ion channel proceeds at consecutive, distinct steps., in The Journal of biological chemistry
, 288(8), 5756-69.
Kudryashev Mikhail, Stahlberg Henning, Castaño-Díez Daniel (2012), Assessing the benefits of focal pair cryo-electron tomography., in Journal of structural biology
, 178(2), 88-97.
Casuso Ignacio, Khao Jonathan, Chami Mohamed, Paul-Gilloteaux Perrine, Husain Mohamed, Duneau Jean-Pierre, Stahlberg Henning, Sturgis James N, Scheuring Simon (2012), Characterization of the motion of membrane proteins using high-speed atomic force microscopy., in Nature nanotechnology
, 7(8), 525-9.
Castaño-Díez Daniel, Kudryashev Mikhail, Arheit Marcel, Stahlberg Henning (2012), Dynamo: a flexible, user-friendly development tool for subtomogram averaging of cryo-EM data in high-performance computing environments., in Journal of structural biology
, 178(2), 139-51.
Kudryashev Mikhail, Castaño-Díez Daniel, Stahlberg Henning (2012), Limiting factors in single particle cryo electron tomography., in Computational and structural biotechnology journal
, 1, 201207002-201207002.
Kebbel Fabian, Kurz Mareike, Grütter Markus G, Stahlberg Henning (2012), Projection structure of the secondary citrate/sodium symporter CitS at 6 Å resolution by electron crystallography., in Journal of molecular biology
, 418(1-2), 117-26.
Membrane proteins are central to health and disease. Electron crystallography can deter-mine the high-resolution structure of membrane proteins from membrane-reconstituted and two-dimensionally crystallized protein. The Transmission Electron Microscope (TEM) is used to study membrane proteins in the lipid membrane environment, which is a powerful tool to study the structure and dynamic of membrane proteins, and of membrane protein complexes that still resist high-resolution 3D crystallization or large-quantity expression efforts.Two-dimensional membrane crystals are imaged by cryo-electron microscopy (cryo-EM). The high-resolution 3D membrane protein structure can then be reconstructed by computer im-age processing. Until recently, the only available software for that task was the MRC software (Crowther et al., 1996). Starting in 2003, my group has created a software system, called 2dx, which embeds the MRC software into a user-friendly graphical user interface, and in addition offers a multitude of additional functions that enable full automation of the processing task, user guidance, interactive documentation and help, and allows automated iterative refinement of the processing results. 2dx received good acceptance in and excellent feedback from the electron crystallography community, and we now count more than 240 external users (as of 1/15/2009).We here propose to extend the 2dx software by new algorithms, to increase resolution and speed of the membrane protein structure determination by electron crystallography, and to en-able high-resolution structure determination also from badly ordered 2D crystals. We will imple-ment a single-particle approach for 3D reconstructions from tilted 2D crystal images, and extend this by a maximum likelihood algorithm. We will develop a hybrid input output algorithm imple-mentation to improve the Z resolution of electron crystallography, and to reduce the need to record images of highly tilted 2D crystals. We will also modernize 2dx, by enabling cluster CPU and cluster GPU computing, and interface it with other systems like Eman2 and IPLT.