On-chip crystallization for serial crystallography experiments and on-chip ligand-binding studies

被引:42
作者
Lieske, Julia [1 ,2 ]
Cerv, Maximilian [2 ]
Kreida, Stefan [3 ]
Komadina, Dana [1 ]
Fischer, Janine [2 ]
Barthelmess, Miriam [1 ]
Fischer, Pontus [2 ]
Pakendorf, Tim [2 ]
Yefanov, Oleksandr [1 ]
Mariani, Valerio [1 ]
Seine, Thomas [1 ,4 ]
Ross, Breyan H. [1 ,5 ]
Crosas, Eva [2 ]
Lorbeer, Olga [2 ]
Burkhardt, Anja [2 ]
Lane, Thomas J. [6 ,7 ]
Guenther, Sebastian [2 ]
Bergtholdt, Julian [1 ]
Schoen, Silvan [2 ]
Tornroth-Horsefield, Susanna [3 ]
Chapman, Henry N. [1 ,8 ,9 ]
Meents, Alke [1 ,2 ]
机构
[1] Deutsch Elektronen Synchrotron DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany
[2] Deutsch Elektronen Synchrotron DESY, Photon Sci, Notkestr 85, D-22607 Hamburg, Germany
[3] Lund Univ, Dept Biochem & Struct Biol, Ctr Mol Prot Sci, Kemictr, S-22100 Lund, Sweden
[4] EMBL, Notkestr 85, D-22607 Hamburg, Germany
[5] Max Planck Inst Biochem, Klopferspitz 18, D-82152 Martinsried, Germany
[6] SLAC Natl Accelerator Lab, Biosci Div, Menlo Pk, CA 94025 USA
[7] SLAC Natl Accelerator Lab, Linac Coherent Light Source, Menlo Pk, CA 94025 USA
[8] Univ Hamburg, Dept Phys, Luruper Chaussee 149, D-22761 Hamburg, Germany
[9] Univ Hamburg, Ctr Ultrafast Imaging, Luruper Chaussee 149, D-22761 Hamburg, Germany
基金
瑞典研究理事会;
关键词
serial crystallography; silicon chip; fixed-target crystallography; in-situ diffraction; vapor diffusion; ligand binding; ligand soaking; drug discovery; protein structure; X-ray crystallography; PATTERNED SILICON CHIP; PROTEIN CRYSTALLIZATION; CRYSTAL-STRUCTURE; DIFFRACTION; KINASE; DRAK2; DEHYDROGENASE; FLAVOPROTEIN; GENERATION; HUMIDITY;
D O I
10.1107/S2052252519007395
中图分类号
O6 [化学];
学科分类号
0703 ;
摘要
Efficient and reliable sample delivery has remained one of the bottlenecks for serial crystallography experiments. Compared with other methods, fixed-target sample delivery offers the advantage of significantly reduced sample consumption and shorter data collection times owing to higher hit rates. Here, a new method of on-chip crystallization is reported which allows the efficient and reproducible growth of large numbers of protein crystals directly on micro-patterned silicon chips for in-situ serial crystallography experiments. Crystals are grown by sitting-drop vapor diffusion and previously established crystallization conditions can be directly applied. By reducing the number of crystal-handling steps, the method is particularly well suited for sensitive crystal systems. Excessive mother liquor can be efficiently removed from the crystals by blotting, and no sealing of the fixed-target sample holders is required to prevent the crystals from dehydrating. As a consequence, 'naked' crystals are obtained on the chip, resulting in very low background scattering levels and making the crystals highly accessible for external manipulation such as the application of ligand solutions. Serial diffraction experiments carried out at cryogenic temperatures at a synchrotron and at room temperature at an X-ray free-electron laser yielded high-quality X-ray structures of the human membrane protein aquaporin 2 and two new ligand-bound structures of thermolysin and the human kinase DRAK2. The results highlight the applicability of the method for future high-throughput on-chip screening of pharmaceutical compounds.
引用
收藏
页码:714 / 728
页数:15
相关论文
共 62 条
[1]   PHENIX: a comprehensive Python']Python-based system for macromolecular structure solution [J].
Adams, Paul D. ;
Afonine, Pavel V. ;
Bunkoczi, Gabor ;
Chen, Vincent B. ;
Davis, Ian W. ;
Echols, Nathaniel ;
Headd, Jeffrey J. ;
Hung, Li-Wei ;
Kapral, Gary J. ;
Grosse-Kunstleve, Ralf W. ;
McCoy, Airlie J. ;
Moriarty, Nigel W. ;
Oeffner, Robert ;
Read, Randy J. ;
Richardson, David C. ;
Richardson, Jane S. ;
Terwilliger, Thomas C. ;
Zwart, Peter H. .
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2010, 66 :213-221
[2]   Cheetah: software for high-throughput reduction and analysis of serial femtosecond X-ray diffraction data [J].
Barty, Anton ;
Kirian, Richard A. ;
Maia, Filipe R. N. C. ;
Hantke, Max ;
Yoon, Chun Hong ;
White, Thomas A. ;
Chapman, Henry .
JOURNAL OF APPLIED CRYSTALLOGRAPHY, 2014, 47 :1118-1131
[3]   Structure of a serine protease proteinase K from Tritirachium album limber at 0.98 Å resolution [J].
Betzel, C ;
Gourinath, S ;
Kumar, P ;
Kaur, P ;
Perbandt, M ;
Eschenburg, S ;
Singh, TP .
BIOCHEMISTRY, 2001, 40 (10) :3080-3088
[4]   Mix-and-diffuse serial synchrotron crystallography [J].
Beyerlein, Kenneth R. ;
Dierksmeyer, Dennis ;
Mariani, Valerio ;
Kuhn, Manuela ;
Sarrou, Iosifina ;
Ottaviano, Angelica ;
Awel, Salah ;
Knoska, Juraj ;
Fuglerud, Silje ;
Jonsson, Olof ;
Stern, Stephan ;
Wiedorn, Max O. ;
Yefanov, Oleksandr ;
Adriano, Luigi ;
Bean, Richard ;
Burkhardt, Anja ;
Fischer, Pontus ;
Heymann, Michael ;
Horke, Daniel A. ;
Jungnickel, Katharina E. J. ;
Kovaleva, Elena ;
Lorbeer, Olga ;
Metz, Markus ;
Meyer, Jan ;
Morgan, Andrew ;
Pande, Kanupriya ;
Panneerselvam, Saravanan ;
Seuring, Carolin ;
Tolstikova, Aleksandra ;
Lieske, Julia ;
Aplin, Steve ;
Roessle, Manfred ;
White, Thomas A. ;
Chapman, Henry N. ;
Meents, Alke ;
Oberthuer, Dominik .
IUCRJ, 2017, 4 :769-777
[5]   High-Resolution Protein Structure Determination by Serial Femtosecond Crystallography [J].
Boutet, Sebastien ;
Lomb, Lukas ;
Williams, Garth J. ;
Barends, Thomas R. M. ;
Aquila, Andrew ;
Doak, R. Bruce ;
Weierstall, Uwe ;
DePonte, Daniel P. ;
Steinbrener, Jan ;
Shoeman, Robert L. ;
Messerschmidt, Marc ;
Barty, Anton ;
White, Thomas A. ;
Kassemeyer, Stephan ;
Kirian, Richard A. ;
Seibert, M. Marvin ;
Montanez, Paul A. ;
Kenney, Chris ;
Herbst, Ryan ;
Hart, Philip ;
Pines, Jack ;
Haller, Gunther ;
Gruner, Sol M. ;
Philipp, Hugh T. ;
Tate, Mark W. ;
Hromalik, Marianne ;
Koerner, Lucas J. ;
van Bakel, Niels ;
Morse, John ;
Ghonsalves, Wilfred ;
Arnlund, David ;
Bogan, Michael J. ;
Caleman, Carl ;
Fromme, Raimund ;
Hampton, Christina Y. ;
Hunter, Mark S. ;
Johansson, Linda C. ;
Katona, Gergely ;
Kupitz, Christopher ;
Liang, Mengning ;
Martin, Andrew V. ;
Nass, Karol ;
Redecke, Lars ;
Stellato, Francesco ;
Timneanu, Nicusor ;
Wang, Dingjie ;
Zatsepin, Nadia A. ;
Schafer, Donald ;
Defever, James ;
Neutze, Richard .
SCIENCE, 2012, 337 (6092) :362-364
[6]   Status of the crystallography beamlines at PETRA III [J].
Burkhardt, Anja ;
Pakendorf, Tim ;
Reime, Bernd ;
Meyer, Jan ;
Fischer, Pontus ;
Stuebe, Nicolas ;
Panneerselvam, Saravanan ;
Lorbeer, Olga ;
Stachnik, Karolina ;
Warmer, Martin ;
Roedig, Philip ;
Goeries, Dennis ;
Meents, Alke .
EUROPEAN PHYSICAL JOURNAL PLUS, 2016, 131 (03) :1-9
[7]   Femtosecond X-ray protein nanocrystallography [J].
Chapman, Henry N. ;
Fromme, Petra ;
Barty, Anton ;
White, Thomas A. ;
Kirian, Richard A. ;
Aquila, Andrew ;
Hunter, Mark S. ;
Schulz, Joachim ;
DePonte, Daniel P. ;
Weierstall, Uwe ;
Doak, R. Bruce ;
Maia, Filipe R. N. C. ;
Martin, Andrew V. ;
Schlichting, Ilme ;
Lomb, Lukas ;
Coppola, Nicola ;
Shoeman, Robert L. ;
Epp, Sascha W. ;
Hartmann, Robert ;
Rolles, Daniel ;
Rudenko, Artem ;
Foucar, Lutz ;
Kimmel, Nils ;
Weidenspointner, Georg ;
Holl, Peter ;
Liang, Mengning ;
Barthelmess, Miriam ;
Caleman, Carl ;
Boutet, Sebastien ;
Bogan, Michael J. ;
Krzywinski, Jacek ;
Bostedt, Christoph ;
Bajt, Sasa ;
Gumprecht, Lars ;
Rudek, Benedikt ;
Erk, Benjamin ;
Schmidt, Carlo ;
Hoemke, Andre ;
Reich, Christian ;
Pietschner, Daniel ;
Strueder, Lothar ;
Hauser, Guenter ;
Gorke, Hubert ;
Ullrich, Joachim ;
Herrmann, Sven ;
Schaller, Gerhard ;
Schopper, Florian ;
Soltau, Heike ;
Kuehnel, Kai-Uwe ;
Messerschmidt, Marc .
NATURE, 2011, 470 (7332) :73-U81
[8]   Comparative studies of protein crystallization by vapour-diffusion and microbatch techniques [J].
Chayen, NE .
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 1998, 54 :8-15
[9]   Molecular Basis of the Death-Associated Protein Kinase-Calcium/Calmodulin Regulator Complex [J].
de Diego, Inaki ;
Kuper, Jochen ;
Bakalova, Neda ;
Kursula, Petri ;
Wilmanns, Matthias .
SCIENCE SIGNALING, 2010, 3 (106) :ra6
[10]   Approaches to automated protein crystal harvesting [J].
Deller, Marc C. ;
Rupp, Bernhard .
ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS, 2014, 70 :133-155