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

Lieske, Julia; Cerv, Maximilian; Kreida, Stefan; Komadina, Dana; Fischer, Janine; Barthelmess, Miriam; Fischer, Pontus; Pakendorf, Tim; Yefanov, Oleksandr; Mariani, Valerio; Seine, Thomas; Ross, Breyan H.; Crosas, Eva; Lorbeer, Olga; Burkhardt, Anja; Lane, Thomas J.; Guenther, Sebastian; Bergtholdt, Julian; Schoen, Silvan; Törnroth-Horsefield, Susanna; Chapman, Henry N.; Meents, Alke

doi:10.1107/S2052252519007395

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

Journal Article · 18 June 2019 · IUCrJ

DOI: https://doi.org/10.1107/S2052252519007395 · OSTI ID:1617994

; Cerv, Maximilian; Kreida, Stefan; Komadina, Dana; Fischer, Janine; Barthelmess, Miriam; Fischer, Pontus; Pakendorf, Tim; Yefanov, Oleksandr;

; Seine, Thomas;

; Crosas, Eva; Lorbeer, Olga;

; Lane, Thomas J.; Guenther, Sebastian; Bergtholdt, Julian; Schoen, Silvan; Törnroth-Horsefield, Susanna more »

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.

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Research Organization:: SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States)

Sponsoring Organization:: USDOE; USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)

Grant/Contract Number:: AC02-76SF00515

OSTI ID:: 1617994

Journal Information:: IUCrJ, Journal Name: IUCrJ Journal Issue: 4 Vol. 6; ISSN 2052-2525; ISSN IUCRAJ

Publisher:: International Union of Crystallography (IUCr)Copyright Statement

Country of Publication:: United Kingdom

Language:: English

References (61)

Locating interaction sites on proteins: The crystal structure of thermolysin soaked in 2% to 100% isopropanol English, Andrew C.; Done, Sarah H.; Caves, Leo S. D. Proteins: Structure, Function, and Genetics, Vol. 37, Issue 4 https://doi.org/10.1002/(SICI)1097-0134(19991201)37:4<628::AID-PROT13>3.0.CO;2-G	journal	December 1999
Structural analysis of zinc substitutions in the active site of thermolysin Holland, Debra R.; Hausrath, Andrew C.; Juers, Doug Protein Science, Vol. 4, Issue 10 https://doi.org/10.1002/pro.5560041001	journal	October 1995
DRAK2 Participates in a Negative Feedback Loop to Control TGF-β/Smads Signaling by Binding to Type I TGF-β Receptor Yang, Kyung-Min; Kim, Wonjoo; Bae, Eunjin Cell Reports, Vol. 2, Issue 5 https://doi.org/10.1016/j.celrep.2012.09.028	journal	November 2012
A PEF/Y Substrate Recognition and Signature Motif Plays a Critical Role in DAPK-Related Kinase Activity Temmerman, Koen; de Diego, Iñaki; Pogenberg, Vivian Chemistry & Biology, Vol. 21, Issue 2 https://doi.org/10.1016/j.chembiol.2013.12.008	journal	February 2014
High-Throughput Crystallography: Reliable and Efficient Identification of Fragment Hits Schiebel, Johannes; Krimmer, Stefan G.; Röwer, Karine Structure, Vol. 24, Issue 8 https://doi.org/10.1016/j.str.2016.06.010	journal	August 2016
Derivatization of Proteinase K with Heavy Atoms Enhances Its Thermal Stability Yazawa, Kenjiro; Sugahara, Michihiro; Yutani, Katsuhide ACS Catalysis, Vol. 6, Issue 5 https://doi.org/10.1021/acscatal.6b00100	journal	April 2016
Structure of a Serine Protease Proteinase K from Tritirachium album limber at 0.98 Å Resolution ^† Betzel, Christian; Gourinath, S.; Kumar, Pravindra Biochemistry, Vol. 40, Issue 10 https://doi.org/10.1021/bi002538n	journal	March 2001
Generation of Size-Controlled, Submicrometer Protein Crystals Falkner, Joshua C.; Al-Somali, Ali M.; Jamison, Jennifer A. Chemistry of Materials, Vol. 17, Issue 10 https://doi.org/10.1021/cm047924w	journal	May 2005
Femtosecond X-ray protein nanocrystallography Chapman, Henry N.; Fromme, Petra; Barty, Anton Nature, Vol. 470, Issue 7332, p. 73-77 https://doi.org/10.1038/nature09750	journal	February 2011
Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallography Stagno, J. R.; Liu, Y.; Bhandari, Y. R. Nature, Vol. 541, Issue 7636 https://doi.org/10.1038/nature20599	journal	November 2016
Lipidic cubic phase injector is a viable crystal delivery system for time-resolved serial crystallography Nogly, Przemyslaw; Panneels, Valerie; Nelson, Garrett Nature Communications, Vol. 7, Issue 1 https://doi.org/10.1038/ncomms12314	journal	August 2016
Lipidic cubic phase injector facilitates membrane protein serial femtosecond crystallography Weierstall, Uwe; James, Daniel; Wang, Chong Nature Communications, Vol. 5, Issue 1 https://doi.org/10.1038/ncomms4309	journal	February 2014
High-speed fixed-target serial virus crystallography Roedig, Philip; Ginn, Helen M.; Pakendorf, Tim Nature Methods, Vol. 14, Issue 8 https://doi.org/10.1038/nmeth.4335	journal	June 2017
Pink-beam serial crystallography Meents, A.; Wiedorn, M. O.; Srajer, V. Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/s41467-017-01417-3	journal	November 2017
Regulation of the apoptosis-inducing kinase DRAK2 by cyclooxygenase-2 in colorectal cancer Doherty, G. A.; Byrne, S. M.; Austin, S. C. British Journal of Cancer, Vol. 101, Issue 3 https://doi.org/10.1038/sj.bjc.6605144	journal	July 2009
Fixed-target protein serial microcrystallography with an x-ray free electron laser Hunter, Mark S.; Segelke, Brent; Messerschmidt, Marc Scientific Reports, Vol. 4, Issue 1 https://doi.org/10.1038/srep06026	journal	August 2014
A micro-patterned silicon chip as sample holder for macromolecular crystallography experiments with minimal background scattering Roedig, P.; Vartiainen, I.; Duman, R. Scientific Reports, Vol. 5, Issue 1 https://doi.org/10.1038/srep10451	journal	May 2015
Double-flow focused liquid injector for efficient serial femtosecond crystallography Oberthuer, Dominik; Knoška, Juraj; Wiedorn, Max O. Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/srep44628	journal	March 2017
Crystal-on-crystal chips for in situ serial diffraction at room temperature Ren, Zhong; Ayhan, Medine; Bandara, Sepalika Lab on a Chip, Vol. 18, Issue 15 https://doi.org/10.1039/C8LC00489G	journal	January 2018
Enzyme transient state kinetics in crystal and solution from the perspective of a time-resolved crystallographer Schmidt, Marius; Saldin, Dilano K. Structural Dynamics, Vol. 1, Issue 2 https://doi.org/10.1063/1.4869472	journal	March 2014
Structural enzymology using X-ray free electron lasers Kupitz, Christopher; Olmos, Jose L.; Holl, Mark Structural Dynamics, Vol. 4, Issue 4 https://doi.org/10.1063/1.4972069	journal	December 2016
X-ray structure of human aquaporin 2 and its implications for nephrogenic diabetes insipidus and trafficking Frick, A.; Eriksson, U. K.; de Mattia, F. Proceedings of the National Academy of Sciences, Vol. 111, Issue 17 https://doi.org/10.1073/pnas.1321406111	journal	April 2014
DRAKs, Novel Serine/Threonine Kinases Related to Death-associated Protein Kinase That Trigger Apoptosis Sanjo, Hideki; Kawai, Taro; Akira, Shizuo Journal of Biological Chemistry, Vol. 273, Issue 44 https://doi.org/10.1074/jbc.273.44.29066	journal	October 1998
Binding of Flavin Adenine Dinucleotide to Molybdenum-containing Carbon Monoxide Dehydrogenase from Oligotropha carboxidovorans : STRUCTURAL AND FUNCTIONAL ANALYSIS OF A CARBON MONOXIDE DEHYDROGENASE SPECIES IN WHICH THE NATIVE FLAVOPROTEIN HAS BEEN REPLACED BY ITS RECOMBINANT COUNTERPART PRODUCED IN Gremer, Lothar; Kellner, Sabine; Dobbek, Holger Journal of Biological Chemistry, Vol. 275, Issue 3 https://doi.org/10.1074/jbc.275.3.1864	journal	January 2000
Gas dynamic virtual nozzle for generation of microscopic droplet streams DePonte, D. P.; Weierstall, U.; Schmidt, K. Journal of Physics D: Applied Physics, Vol. 41, Issue 19, Article No. 195505 https://doi.org/10.1088/0022-3727/41/19/195505	journal	September 2008
Drak2 is not required for tumor surveillance and suppression Edwards, Benjamin A.; Harris, Tarsha L.; Floersh, Helen International Immunology, Vol. 27, Issue 3 https://doi.org/10.1093/intimm/dxu146	journal	January 2015
Microcrystallization techniques for serial femtosecond crystallography using photosystem II from Thermosynechococcus elongatus as a model system Kupitz, Christopher; Grotjohann, Ingo; Conrad, Chelsie E. Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 369, Issue 1647 https://doi.org/10.1098/rstb.2013.0316	journal	July 2014
Mapping the continuous reciprocal space intensity distribution of X-ray serial crystallography Yefanov, Oleksandr; Gati, Cornelius; Bourenkov, Gleb Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 369, Issue 1647 https://doi.org/10.1098/rstb.2013.0333	journal	July 2014
Liquid sample delivery techniques for serial femtosecond crystallography Weierstall, Uwe Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 369, Issue 1647 https://doi.org/10.1098/rstb.2013.0337	journal	July 2014
Phaser crystallographic software McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D. Journal of Applied Crystallography, Vol. 40, Issue 4 https://doi.org/10.1107/S0021889807021206	journal	July 2007
ANODE : anomalous and heavy-atom density calculation Thorn, Andrea; Sheldrick, George M. Journal of Applied Crystallography, Vol. 44, Issue 6 https://doi.org/10.1107/S0021889811041768	journal	November 2011
CrystFEL : a software suite for snapshot serial crystallography White, Thomas A.; Kirian, Richard A.; Martin, Andrew V. Journal of Applied Crystallography, Vol. 45, Issue 2 https://doi.org/10.1107/S0021889812002312	journal	March 2012
Improving diffraction by humidity control: a novel device compatible with X-ray beamlines Sanchez-Weatherby, Juan; Bowler, Matthew W.; Huet, Julien Acta Crystallographica Section D Biological Crystallography, Vol. 65, Issue 12 https://doi.org/10.1107/S0907444909037822	journal	November 2009
XDS Kabsch, Wolfgang Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2 https://doi.org/10.1107/S0907444909047337	journal	January 2010
PHENIX: a comprehensive Python-based system for macromolecular structure solution Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221 https://doi.org/10.1107/S0907444909052925	journal	January 2010
Features and development of Coot Emsley, P.; Lohkamp, B.; Scott, W. G. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/S0907444910007493	journal	March 2010
Crystallography on a chip Zarrine-Afsar, Arash; Barends, Thomas R. M.; Müller, Christina Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 3 https://doi.org/10.1107/S0907444911055296	journal	February 2012
Clustering procedures for the optimal selection of data sets from multiple crystals in macromolecular crystallography Foadi, James; Aller, Pierre; Alguel, Yilmaz Acta Crystallographica Section D Biological Crystallography, Vol. 69, Issue 8 https://doi.org/10.1107/S0907444913012274	journal	July 2013
Comparative Studies of Protein Crystallization by Vapour-Diffusion and Microbatch Techniques Chayen, Naomi E. Acta Crystallographica Section D Biological Crystallography, Vol. 54, Issue 1 https://doi.org/10.1107/S0907444997005374	journal	January 1998
Acoustic methods for high-throughput protein crystal mounting at next-generation macromolecular crystallographic beamlines Roessler, Christian G.; Kuczewski, Anthony; Stearns, Richard Journal of Synchrotron Radiation, Vol. 20, Issue 5 https://doi.org/10.1107/S0909049513020372	journal	August 2013
Hitting the target: fragment screening with acoustic in situ co-crystallization of proteins plus fragment libraries on pin-mounted data-collection micromeshes Yin, Xingyu; Scalia, Alexander; Leroy, Ludmila Acta Crystallographica Section D Biological Crystallography, Vol. 70, Issue 5 https://doi.org/10.1107/S1399004713034603	journal	April 2014
A high-transparency, micro-patternable chip for X-ray diffraction analysis of microcrystals under native growth conditions Murray, Thomas D.; Lyubimov, Artem Y.; Ogata, Craig M. Acta Crystallographica Section D Biological Crystallography, Vol. 71, Issue 10 https://doi.org/10.1107/S1399004715015011	journal	September 2015
Cheetah : software for high-throughput reduction and analysis of serial femtosecond X-ray diffraction data Barty, Anton; Kirian, Richard A.; Maia, Filipe R. N. C. Journal of Applied Crystallography, Vol. 47, Issue 3 https://doi.org/10.1107/S1600576714007626	journal	May 2014
Recent developments in CrystFEL White, Thomas A.; Mariani, Valerio; Brehm, Wolfgang Journal of Applied Crystallography, Vol. 49, Issue 2 https://doi.org/10.1107/S1600576716004751	journal	March 2016
Room-temperature macromolecular crystallography using a micro-patterned silicon chip with minimal background scattering Roedig, Philip; Duman, Ramona; Sanchez-Weatherby, Juan Journal of Applied Crystallography, Vol. 49, Issue 3 https://doi.org/10.1107/S1600576716006348	journal	May 2016
OnDA : online data analysis and feedback for serial X-ray imaging Mariani, Valerio; Morgan, Andrew; Yoon, Chun Hong Journal of Applied Crystallography, Vol. 49, Issue 3 https://doi.org/10.1107/S1600576716007469	journal	May 2016
Direct protein crystallization on ultrathin membranes for diffraction measurements at X-ray free-electron lasers Opara, Nadia; Martiel, Isabelle; Arnold, Stefan A. Journal of Applied Crystallography, Vol. 50, Issue 3 https://doi.org/10.1107/S1600576717005799	journal	June 2017
Solvent minimization induces preferential orientation and crystal clustering in serial micro-crystallography on micro-meshes, in situ plates and on a movable crystal conveyor belt Soares, Alexei S.; Mullen, Jeffrey D.; Parekh, Ruchi M. Journal of Synchrotron Radiation, Vol. 21, Issue 6 https://doi.org/10.1107/S1600577514017731	journal	October 2014
Measurement of the equilibrium relative humidity for common precipitant concentrations: facilitating controlled dehydration experiments Wheeler, Matthew J.; Russi, Silvia; Bowler, Michael G. Acta Crystallographica Section F Structural Biology and Crystallization Communications, Vol. 68, Issue 1 https://doi.org/10.1107/S1744309111054029	journal	December 2011
Room-temperature macromolecular serial crystallography using synchrotron radiation Stellato, Francesco; Oberthür, Dominik; Liang, Mengning IUCrJ, Vol. 1, Issue 4, p. 204-212 https://doi.org/10.1107/S2052252514010070	journal	May 2014
Serial femtosecond crystallography of soluble proteins in lipidic cubic phase Fromme, Raimund; Ishchenko, Andrii; Metz, Markus IUCrJ, Vol. 2, Issue 5, p. 545-551 https://doi.org/10.1107/S2052252515013160	journal	August 2015
Mix-and-diffuse serial synchrotron crystallography Beyerlein, Kenneth R.; Dierksmeyer, Dennis; Mariani, Valerio IUCrJ, Vol. 4, Issue 6 https://doi.org/10.1107/S2052252517013124	journal	October 2017
1 kHz fixed-target serial crystallography using a multilayer monochromator and an integrating pixel detector Tolstikova, A.; Levantino, M.; Yefanov, O. IUCrJ, Vol. 6, Issue 5 https://doi.org/10.1107/S205225251900914X	journal	August 2019
Approaches to automated protein crystal harvesting Deller, Marc C.; Rupp, Bernhard Acta Crystallographica Section F Structural Biology Communications, Vol. 70, Issue 2 https://doi.org/10.1107/S2053230X14000387	journal	January 2014
Batch crystallization of rhodopsin for structural dynamics using an X-ray free-electron laser Wu, Wenting; Nogly, Przemyslaw; Rheinberger, Jan Acta Crystallographica Section F Structural Biology Communications, Vol. 71, Issue 7 https://doi.org/10.1107/S2053230X15009966	journal	June 2015
Using sound pulses to solve the crystal-harvesting bottleneck Samara, Yasmin N.; Brennan, Haley M.; McCarthy, Liam Acta Crystallographica Section D Structural Biology, Vol. 74, Issue 10 https://doi.org/10.1107/S2059798318011506	journal	October 2018
High-Resolution Protein Structure Determination by Serial Femtosecond Crystallography Boutet, S.; Lomb, L.; Williams, G. J. Science, Vol. 337, Issue 6092 https://doi.org/10.1126/science.1217737	journal	May 2012
Femtosecond structural dynamics drives the trans/cis isomerization in photoactive yellow protein Pande, K.; Hutchison, C. D. M.; Groenhof, G. Science, Vol. 352, Issue 6286 https://doi.org/10.1126/science.aad5081	journal	May 2016
Molecular Basis of the Death-Associated Protein Kinase-Calcium/Calmodulin Regulator Complex de Diego, I.; Kuper, J.; Bakalova, N. Science Signaling, Vol. 3, Issue 106 https://doi.org/10.1126/scisignal.2000552	journal	January 2010
Status of the crystallography beamlines at PETRA III Burkhardt, Anja; Pakendorf, Tim; Reime, Bernd The European Physical Journal Plus, Vol. 131, Issue 3 https://doi.org/10.1140/epjp/i2016-16056-0	journal	March 2016
Drak2 Does Not Regulate TGF-β Signaling in T Cells Harris, Tarsha L.; McGargill, Maureen A. PLOS ONE, Vol. 10, Issue 5 https://doi.org/10.1371/journal.pone.0123650	journal	May 2015

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37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
59 BASIC BIOLOGICAL SCIENCES
X-ray crystallography
drug discovery
fixed-target crystallography
in-situ diffraction
ligand binding
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protein structure
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silicon chip
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Title: On-chip crystallization for serial crystallography experiments and on-chip ligand-binding studies

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