1
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Khorn PA, Luginina AP, Pospelov VA, Dashevsky DE, Khnykin AN, Moiseeva OV, Safronova NA, Belousov AS, Mishin AV, Borshchevsky VI. Rational Design of Drugs Targeting G-Protein-Coupled Receptors: A Structural Biology Perspective. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:747-764. [PMID: 38831510 DOI: 10.1134/s0006297924040138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 02/22/2024] [Accepted: 02/29/2024] [Indexed: 06/05/2024]
Abstract
G protein-coupled receptors (GPCRs) play a key role in the transduction of extracellular signals to cells and regulation of many biological processes, which makes these membrane proteins one of the most important targets for pharmacological agents. A significant increase in the number of resolved atomic structures of GPCRs has opened the possibility of developing pharmaceuticals targeting these receptors via structure-based drug design (SBDD). SBDD employs information on the structure of receptor-ligand complexes to search for selective ligands without the need for an extensive high-throughput experimental ligand screening and can significantly expand the chemical space for ligand search. In this review, we describe the process of deciphering GPCR structures using X-ray diffraction analysis and cryoelectron microscopy as an important stage in the rational design of drugs targeting this receptor class. Our main goal was to present modern developments and key features of experimental methods used in SBDD of GPCR-targeting agents to a wide range of specialists.
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Affiliation(s)
- Polina A Khorn
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Aleksandra P Luginina
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Vladimir A Pospelov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Dmitrii E Dashevsky
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Andrey N Khnykin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Olga V Moiseeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
- Scryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Nadezhda A Safronova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Anatolii S Belousov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Alexey V Mishin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.
| | - Valentin I Borshchevsky
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.
- Joint Institute for Nuclear Research, Frank Laboratory of Neutron Physics, Dubna, Moscow Region, 141980, Russia
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2
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Mendez D, Holton JM, Lyubimov AY, Hollatz S, Mathews II, Cichosz A, Martirosyan V, Zeng T, Stofer R, Liu R, Song J, McPhillips S, Soltis M, Cohen AE. Deep residual networks for crystallography trained on synthetic data. Acta Crystallogr D Struct Biol 2024; 80:26-43. [PMID: 38164955 PMCID: PMC10833344 DOI: 10.1107/s2059798323010586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 12/12/2023] [Indexed: 01/03/2024] Open
Abstract
The use of artificial intelligence to process diffraction images is challenged by the need to assemble large and precisely designed training data sets. To address this, a codebase called Resonet was developed for synthesizing diffraction data and training residual neural networks on these data. Here, two per-pattern capabilities of Resonet are demonstrated: (i) interpretation of crystal resolution and (ii) identification of overlapping lattices. Resonet was tested across a compilation of diffraction images from synchrotron experiments and X-ray free-electron laser experiments. Crucially, these models readily execute on graphics processing units and can thus significantly outperform conventional algorithms. While Resonet is currently utilized to provide real-time feedback for macromolecular crystallography users at the Stanford Synchrotron Radiation Lightsource, its simple Python-based interface makes it easy to embed in other processing frameworks. This work highlights the utility of physics-based simulation for training deep neural networks and lays the groundwork for the development of additional models to enhance diffraction collection and analysis.
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Affiliation(s)
- Derek Mendez
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - James M. Holton
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Biochemistry and Biophysics, UC San Francisco, San Francisco, CA 94158, USA
| | - Artem Y. Lyubimov
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Sabine Hollatz
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Irimpan I. Mathews
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Aleksander Cichosz
- Department of Statistics and Applied Probability, UC Santa Barbara, Santa Barbara, CA 93106, USA
| | - Vardan Martirosyan
- Department of Mathematics, UC Santa Barbara, Santa Barbara, CA 93106, USA
| | - Teo Zeng
- Department of Statistics and Applied Probability, UC Santa Barbara, Santa Barbara, CA 93106, USA
| | - Ryan Stofer
- Department of Statistics and Applied Probability, UC Santa Barbara, Santa Barbara, CA 93106, USA
| | - Ruobin Liu
- Department of Statistics and Applied Probability, UC Santa Barbara, Santa Barbara, CA 93106, USA
| | - Jinhu Song
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Scott McPhillips
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Mike Soltis
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Aina E. Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
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3
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Carrillo M, Mason TJ, Karpik A, Martiel I, Kepa MW, McAuley KE, Beale JH, Padeste C. Micro-structured polymer fixed targets for serial crystallography at synchrotrons and XFELs. IUCRJ 2023; 10:678-693. [PMID: 37727961 PMCID: PMC10619457 DOI: 10.1107/s2052252523007595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 08/31/2023] [Indexed: 09/21/2023]
Abstract
Fixed targets are a popular form of sample-delivery system used in serial crystallography at synchrotron and X-ray free-electron laser sources. They offer a wide range of sample-preparation options and are generally easy to use. The supports are typically made from silicon, quartz or polymer. Of these, currently, only silicon offers the ability to perform an aperture-aligned data collection where crystals are loaded into cavities in precise locations and sequentially rastered through, in step with the X-ray pulses. The polymer-based fixed targets have lacked the precision fabrication to enable this data-collection strategy and have been limited to directed-raster scans with crystals randomly distributed across the polymer surface. Here, the fabrication and first results from a new polymer-based fixed target, the micro-structured polymer fixed targets (MISP chips), are presented. MISP chips, like those made from silicon, have a precise array of cavities and fiducial markers. They consist of a structured polymer membrane and a stabilization frame. Crystals can be loaded into the cavities and the excess crystallization solution removed through apertures at their base. The fiducial markers allow for a rapid calculation of the aperture locations. The chips have a low X-ray background and, since they are optically transparent, also allow for an a priori analysis of crystal locations. This location mapping could, ultimately, optimize hit rates towards 100%. A black version of the MISP chip was produced to reduce light contamination for optical-pump/X-ray probe experiments. A study of the loading properties of the chips reveals that these types of fixed targets are best optimized for crystals of the order of 25 µm, but quality data can be collected from crystals as small as 5 µm. With the development of these chips, it has been proved that polymer-based fixed targets can be made with the precision required for aperture-alignment-based data-collection strategies. Further work can now be directed towards more cost-effective mass fabrication to make their use more sustainable for serial crystallography facilities and users.
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Affiliation(s)
- Melissa Carrillo
- Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen, Switzerland
- Department of Chemistry, University of Basel, Mattenstrasse 24a, 4002 Basel, Switzerland
- Swiss Nanoscience Institute, Klingelbergstrasse 82, 4056 Basel, Switzerland
| | - Thomas J. Mason
- Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Agnieszka Karpik
- Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen, Switzerland
- Institute of Polymer Nanotechnology (INKA), FHNW University of Applied Sciences and Arts Northwestern Switzerland, School of Engineering, Klosterzelgstrasse 2, 5210 Windisch, Switzerland
| | - Isabelle Martiel
- Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Michal W. Kepa
- Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | | | - John H. Beale
- Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Celestino Padeste
- Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen, Switzerland
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4
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Gu KK, Liu Z, Narayanasamy SR, Shelby ML, Chan N, Coleman MA, Frank M, Kuhl TL. All polymer microfluidic chips-A fixed target sample delivery workhorse for serial crystallography. BIOMICROFLUIDICS 2023; 17:051302. [PMID: 37840537 PMCID: PMC10576627 DOI: 10.1063/5.0167164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 09/27/2023] [Indexed: 10/17/2023]
Abstract
The development of x-ray free electron laser (XFEL) light sources and serial crystallography methodologies has led to a revolution in protein crystallography, enabling the determination of previously unobtainable protein structures and near-atomic resolution of otherwise poorly diffracting protein crystals. However, to utilize XFEL sources efficiently demands the continuous, rapid delivery of a large number of difficult-to-handle microcrystals to the x-ray beam. A recently developed fixed-target system, in which crystals of interest are enclosed within a sample holder, which is rastered through the x-ray beam, is discussed in detail in this Perspective. The fixed target is easy to use, maintains sample hydration, and can be readily modified to allow a broad range of sample types and different beamline requirements. Recent innovations demonstrate the potential of such microfluidic-based fixed targets to be an all-around "workhorse" for serial crystallography measurements. This Perspective will summarize recent advancements in microfluidic fixed targets for serial crystallography, examine needs for future development, and guide users in designing, choosing, and utilizing a fixed-target sample delivery device for their system.
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Affiliation(s)
- Kevin K. Gu
- Department of Chemical Engineering, University of California at Davis, Davis, California 95616, USA
| | - Zhongrui Liu
- Department of Chemical Engineering, University of California at Davis, Davis, California 95616, USA
| | - Sankar Raju Narayanasamy
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - Megan L. Shelby
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - Nicholas Chan
- Department of Chemical Engineering, University of California at Davis, Davis, California 95616, USA
| | | | | | - Tonya L. Kuhl
- Department of Chemical Engineering, University of California at Davis, Davis, California 95616, USA
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5
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Thompson MC. Combining temperature perturbations with X-ray crystallography to study dynamic macromolecules: A thorough discussion of experimental methods. Methods Enzymol 2023; 688:255-305. [PMID: 37748829 DOI: 10.1016/bs.mie.2023.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Temperature is an important state variable that governs the behavior of microscopic systems, yet crystallographers rarely exploit temperature changes to study the structure and dynamics of biological macromolecules. In fact, approximately 90% of crystal structures in the Protein Data Bank were determined under cryogenic conditions, because sample cryocooling makes crystals robust to X-ray radiation damage and facilitates data collection. On the other hand, cryocooling can introduce artifacts into macromolecular structures, and can suppress conformational dynamics that are critical for function. Fortunately, recent advances in X-ray detector technology, X-ray sources, and computational data processing algorithms make non-cryogenic X-ray crystallography easier and more broadly applicable than ever before. Without the reliance on cryocooling, high-resolution crystallography can be combined with various temperature perturbations to gain deep insight into the conformational landscapes of macromolecules. This Chapter reviews the historical reasons for the prevalence of cryocooling in macromolecular crystallography, and discusses its potential drawbacks. Next, the Chapter summarizes technological developments and methodologies that facilitate non-cryogenic crystallography experiments. Finally, the chapter discusses the theoretical underpinnings and practical aspects of multi-temperature and temperature-jump crystallography experiments, which are powerful tools for understanding the relationship between the structure, dynamics, and function of proteins and other biological macromolecules.
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Affiliation(s)
- Michael C Thompson
- Department of Chemistry and Biochemistry, University of California, Merced, Merced, CA, United States.
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6
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Shoeman RL, Hartmann E, Schlichting I. Growing and making nano- and microcrystals. Nat Protoc 2023; 18:854-882. [PMID: 36451055 DOI: 10.1038/s41596-022-00777-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 08/22/2022] [Indexed: 12/02/2022]
Abstract
Thanks to recent technological advances in X-ray and micro-electron diffraction and solid-state NMR, structural information can be obtained by using much smaller crystals. Thus, microcrystals have become a valuable commodity rather than a mere stepping stone toward obtaining macroscopic crystals. Microcrystals are particularly useful for structure determination using serial data collection approaches at synchrotrons and X-ray free-electron lasers. The latter's enormous peak brilliance and short X-ray pulse duration mean that structural information can be obtained before the effects of radiation damage are seen; these properties also facilitate time-resolved crystallography. To establish defined reaction initiation conditions, microcrystals with a desired and narrow size distribution are critical. Here, we describe milling and seeding techniques as well as filtration approaches for the reproducible and size-adjustable preparation of homogeneous nano- and microcrystals. Nanocrystals and crystal seeds can be obtained by milling using zirconium beads and the BeadBug homogenizer; fragmentation of large crystals yields micro- or nanocrystals by flowing crystals through stainless steel filters by using an HPLC pump. The approaches can be scaled to generate micro- to milliliter quantities of microcrystals, starting from macroscopic crystals. The procedure typically takes 3-5 d, including the time required to grow the microcrystals.
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7
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Zhao FZ, Wang ZJ, Xiao QJ, Yu L, Sun B, Hou Q, Chen LL, Liang H, Wu H, Guo WH, He JH, Wang QS, Yin DC. Microfluidic rotating-target device capable of three-degrees-of-freedom motion for efficient in situ serial synchrotron crystallography. JOURNAL OF SYNCHROTRON RADIATION 2023; 30:347-358. [PMID: 36891848 PMCID: PMC10000801 DOI: 10.1107/s1600577523000462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 01/17/2023] [Indexed: 06/18/2023]
Abstract
There is an increasing demand for simple and efficient sample delivery technology to match the rapid development of serial crystallography and its wide application in analyzing the structural dynamics of biological macromolecules. Here, a microfluidic rotating-target device is presented, capable of three-degrees-of-freedom motion, including two rotational degrees of freedom and one translational degree of freedom, for sample delivery. Lysozyme crystals were used as a test model with this device to collect serial synchrotron crystallography data and the device was found to be convenient and useful. This device enables in situ diffraction from crystals in a microfluidic channel without the need for crystal harvesting. The circular motion ensures that the delivery speed can be adjusted over a wide range, showing its good compatibility with different light sources. Moreover, the three-degrees-of-freedom motion guarantees the full utilization of crystals. Hence, sample consumption is greatly reduced, and only 0.1 mg of protein is consumed in collecting a complete dataset.
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Affiliation(s)
- Feng-Zhu Zhao
- School of Life Sciences, Northwestern Polytechnical University, Xi’an 710072, People’s Republic of China
- School of NCO, Army Medical University, Shijiazhuang 050081, People’s Republic of China
| | - Zhi-Jun Wang
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201800, People’s Republic of China
| | - Qing-Jie Xiao
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201800, People’s Republic of China
| | - Li Yu
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, People’s Republic of China
| | - Bo Sun
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201800, People’s Republic of China
| | - Qian Hou
- School of Materials Science and Engineering, Northwestern Polytechnical University, Xi’an 710072, People’s Republic of China
| | - Liang-Liang Chen
- School of Life Sciences, Northwestern Polytechnical University, Xi’an 710072, People’s Republic of China
| | - Huan Liang
- School of Life Sciences, Northwestern Polytechnical University, Xi’an 710072, People’s Republic of China
| | - Hai Wu
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, People’s Republic of China
| | - Wei-Hong Guo
- School of Life Sciences, Northwestern Polytechnical University, Xi’an 710072, People’s Republic of China
| | - Jian-Hua He
- The Institute for Advanced Studies, Wuhan University, Wuhan 430072, People’s Republic of China
| | - Qi-Sheng Wang
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201800, People’s Republic of China
| | - Da-Chuan Yin
- School of Life Sciences, Northwestern Polytechnical University, Xi’an 710072, People’s Republic of China
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8
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Simon PS, Makita H, Bogacz I, Fuller F, Bhowmick A, Hussein R, Ibrahim M, Zhang M, Chatterjee R, Cheah MH, Chernev P, Doyle MD, Brewster AS, Alonso-Mori R, Sauter NK, Bergmann U, Dobbek H, Zouni A, Messinger J, Kern J, Yachandra VK, Yano J. Capturing the sequence of events during the water oxidation reaction in photosynthesis using XFELs. FEBS Lett 2023; 597:30-37. [PMID: 36310373 PMCID: PMC9839502 DOI: 10.1002/1873-3468.14527] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 10/13/2022] [Accepted: 10/17/2022] [Indexed: 01/17/2023]
Abstract
Ever since the discovery that Mn was required for oxygen evolution in plants by Pirson in 1937 and the period-four oscillation in flash-induced oxygen evolution by Joliot and Kok in the 1970s, understanding of this process has advanced enormously using state-of-the-art methods. The most recent in this series of innovative techniques was the introduction of X-ray free-electron lasers (XFELs) a decade ago, which led to another quantum leap in the understanding in this field, by enabling operando X-ray structural and X-ray spectroscopy studies at room temperature. This review summarizes the current understanding of the structure of Photosystem II (PS II) and its catalytic centre, the Mn4 CaO5 complex, in the intermediate Si (i = 0-4)-states of the Kok cycle, obtained using XFELs.
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Affiliation(s)
- Philipp S Simon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Hiroki Makita
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Isabel Bogacz
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Franklin Fuller
- Pulse Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Asmit Bhowmick
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Rana Hussein
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Mohamed Ibrahim
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Miao Zhang
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mun Hon Cheah
- Molecular Biomimetics, Department of Chemistry - Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Petko Chernev
- Molecular Biomimetics, Department of Chemistry - Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Margaret D Doyle
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Aaron S Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Roberto Alonso-Mori
- LINAC Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Nicholas K Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Uwe Bergmann
- Department of Physics, University of Wisconsin-Madison, Madison, WI, USA
| | - Holger Dobbek
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Athina Zouni
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Johannes Messinger
- Molecular Biomimetics, Department of Chemistry - Ångström Laboratory, Uppsala University, Uppsala, Sweden
- Department of Chemistry, Umeå University, Umeå, Sweden
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Vittal K Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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9
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Thorne RE. Determining biomolecular structures near room temperature using X-ray crystallography: concepts, methods and future optimization. Acta Crystallogr D Struct Biol 2023; 79:78-94. [PMID: 36601809 PMCID: PMC9815097 DOI: 10.1107/s2059798322011652] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 12/04/2022] [Indexed: 01/05/2023] Open
Abstract
For roughly two decades, cryocrystallography has been the overwhelmingly dominant method for determining high-resolution biomolecular structures. Competition from single-particle cryo-electron microscopy and micro-electron diffraction, increased interest in functionally relevant information that may be missing or corrupted in structures determined at cryogenic temperature, and interest in time-resolved studies of the biomolecular response to chemical and optical stimuli have driven renewed interest in data collection at room temperature and, more generally, at temperatures from the protein-solvent glass transition near 200 K to ∼350 K. Fischer has recently reviewed practical methods for room-temperature data collection and analysis [Fischer (2021), Q. Rev. Biophys. 54, e1]. Here, the key advantages and physical principles of, and methods for, crystallographic data collection at noncryogenic temperatures and some factors relevant to interpreting the resulting data are discussed. For room-temperature data collection to realize its potential within the structural biology toolkit, streamlined and standardized methods for delivering crystals prepared in the home laboratory to the synchrotron and for automated handling and data collection, similar to those for cryocrystallography, should be implemented.
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Affiliation(s)
- Robert E. Thorne
- Physics Department, Cornell University, Ithaca, NY 14853, USA
- MiTeGen LLC, PO Box 3867, Ithaca, NY 14850, USA
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10
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Barends TR, Stauch B, Cherezov V, Schlichting I. Serial femtosecond crystallography. NATURE REVIEWS. METHODS PRIMERS 2022; 2:59. [PMID: 36643971 PMCID: PMC9833121 DOI: 10.1038/s43586-022-00141-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
With the advent of X-ray Free Electron Lasers (XFELs), new, high-throughput serial crystallography techniques for macromolecular structure determination have emerged. Serial femtosecond crystallography (SFX) and related methods provide possibilities beyond canonical, single-crystal rotation crystallography by mitigating radiation damage and allowing time-resolved studies with unprecedented temporal resolution. This primer aims to assist structural biology groups with little or no experience in serial crystallography planning and carrying out a successful SFX experiment. It discusses the background of serial crystallography and its possibilities. Microcrystal growth and characterization methods are discussed, alongside techniques for sample delivery and data processing. Moreover, it gives practical tips for preparing an experiment, what to consider and do during a beamtime and how to conduct the final data analysis. Finally, the Primer looks at various applications of SFX, including structure determination of membrane proteins, investigation of radiation damage-prone systems and time-resolved studies.
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Affiliation(s)
- Thomas R.M. Barends
- Department for Biological Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Benjamin Stauch
- Department of Chemistry, The Bridge Institute, University of Southern California, Los Angeles, CA, USA
| | - Vadim Cherezov
- Department of Chemistry, The Bridge Institute, University of Southern California, Los Angeles, CA, USA
| | - Ilme Schlichting
- Department for Biological Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany,
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11
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Gilbile D, Shelby ML, Lyubimov AY, Wierman JL, Monteiro DCF, Cohen AE, Russi S, Coleman MA, Frank M, Kuhl TL. Plug-and-play polymer microfluidic chips for hydrated, room temperature, fixed-target serial crystallography. LAB ON A CHIP 2021; 21:4831-4845. [PMID: 34821226 PMCID: PMC8915944 DOI: 10.1039/d1lc00810b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The practice of serial X-ray crystallography (SX) depends on efficient, continuous delivery of hydrated protein crystals while minimizing background scattering. Of the two major types of sample delivery devices, fixed-target devices offer several advantages over widely adopted jet injectors, including: lower sample consumption, clog-free delivery, and the ability to control on-chip crystal density to improve hit rates. Here we present our development of versatile, inexpensive, and robust polymer microfluidic chips for routine and reliable room temperature serial measurements at both synchrotrons and X-ray free electron lasers (XFELs). Our design includes highly X-ray-transparent enclosing thin film layers tuned to minimize scatter background, adaptable sample flow layers tuned to match crystal size, and a large sample area compatible with both raster scanning and rotation based serial data collection. The optically transparent chips can be used both for in situ protein crystallization (to eliminate crystal handling) or crystal slurry loading, with prepared samples stable for weeks in a humidified environment and for several hours in ambient conditions. Serial oscillation crystallography, using a multi-crystal rotational data collection approach, at a microfocus synchrotron beamline (SSRL, beamline 12-1) was used to benchmark the performance of the chips. High-resolution structures (1.3-2.7 Å) were collected from five different proteins - hen egg white lysozyme, thaumatin, bovine liver catalase, concanavalin-A (type VI), and SARS-CoV-2 nonstructural protein NSP5. Overall, our modular fabrication approach enables precise control over the cross-section of materials in the X-ray beam path and facilitates chip adaption to different sample and beamline requirements for user-friendly, straightforward diffraction measurements at room temperature.
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Affiliation(s)
- Deepshika Gilbile
- Department of Chemical Engineering, University of California at Davis, Davis, CA 95616, USA.
| | - Megan L Shelby
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Artem Y Lyubimov
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | | | - Diana C F Monteiro
- Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, New York 14203, USA
| | - Aina E Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Silvia Russi
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Matthew A Coleman
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
- Department of Radiation Oncology, School of Medicine, University of California at Davis, Sacramento, CA 95817, USA
| | - Matthias Frank
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California at Davis, Sacramento, CA 95817, USA
| | - Tonya L Kuhl
- Department of Chemical Engineering, University of California at Davis, Davis, CA 95616, USA.
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12
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Martiel I, Beale JH, Karpik A, Huang CY, Vera L, Olieric N, Wranik M, Tsai CJ, Mühle J, Aurelius O, John J, Högbom M, Wang M, Marsh M, Padeste C. Versatile microporous polymer-based supports for serial macromolecular crystallography. Acta Crystallogr D Struct Biol 2021; 77:1153-1167. [PMID: 34473086 PMCID: PMC8411977 DOI: 10.1107/s2059798321007324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 07/15/2021] [Indexed: 11/10/2022] Open
Abstract
Serial data collection has emerged as a major tool for data collection at state-of-the-art light sources, such as microfocus beamlines at synchrotrons and X-ray free-electron lasers. Challenging targets, characterized by small crystal sizes, weak diffraction and stringent dose limits, benefit most from these methods. Here, the use of a thin support made of a polymer-based membrane for performing serial data collection or screening experiments is demonstrated. It is shown that these supports are suitable for a wide range of protein crystals suspended in liquids. The supports have also proved to be applicable to challenging cases such as membrane proteins growing in the sponge phase. The sample-deposition method is simple and robust, as well as flexible and adaptable to a variety of cases. It results in an optimally thin specimen providing low background while maintaining minute amounts of mother liquor around the crystals. The 2 × 2 mm area enables the deposition of up to several microlitres of liquid. Imaging and visualization of the crystals are straightforward on the highly transparent membrane. Thanks to their affordable fabrication, these supports have the potential to become an attractive option for serial experiments at synchrotrons and free-electron lasers.
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Affiliation(s)
- Isabelle Martiel
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - John H. Beale
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Agnieszka Karpik
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
- Institute of Polymer Nanotechnology (INKA), FHNW University of Applied Sciences and Arts Northwestern Switzerland, 5210 Windisch, Switzerland
| | - Chia-Ying Huang
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Laura Vera
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Natacha Olieric
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Maximilian Wranik
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Ching-Ju Tsai
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Jonas Mühle
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Oskar Aurelius
- Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden
- MAX IV Laboratory, Lund University, Fotongatan 2, 224 84 Lund, Sweden
| | - Juliane John
- Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden
| | - Meitian Wang
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - May Marsh
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Celestino Padeste
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
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13
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Liang M, Yu L, Wang Z, Zhou H, Zhang Y, Wang Q, He J. Novel combined crystallization plate for high-throughput crystal screening and in situ data collection at a crystallography beamline. Acta Crystallogr F Struct Biol Commun 2021; 77:319-327. [PMID: 34473109 PMCID: PMC8411933 DOI: 10.1107/s2053230x21008104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 08/06/2021] [Indexed: 11/10/2022] Open
Abstract
In situ microplates are small in size, crystal cultivation and operation are difficult, and the efficiency of crystal screening is relatively low. To solve this problem, a novel combined crystallization plate was designed for high-throughput crystal cultivation and in situ data collection. A frame was used to hold 48 in situ microplates, and the in situ microplates were sealed on one side with an ultralow background-scattering Kapton film. An automatic liquid handler (Mosquito) was used to add a liquid drop to the in situ microplates in the frame, and CrystalClear HD tape was used to seal the frame. A sealed frame holding 48 microplates was developed as a novel combined crystallization plate and was used for crystal cultivation under different conditions and in situ data collection at the synchrotron beamline. Moreover, individual microplates can be separated from the combined crystal plate and then fixed on a magnetic base or loaded onto a UniPuck for in situ data collection. Automatic grid scanning was used to locate crystals. The efficiency of the combined crystallization plate for crystal screening was verified. This method avoids the manual manipulation of crystals during crystal screening and diffraction data collection; therefore, the combined crystallization plate is suitable for large-scale screening of microcrystals.
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Affiliation(s)
- Miao Liang
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Li Yu
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Zhijun Wang
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, People’s Republic of China
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, People’s Republic of China
| | - Huan Zhou
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, People’s Republic of China
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, People’s Republic of China
| | - Yi Zhang
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, People’s Republic of China
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, People’s Republic of China
| | - Qisheng Wang
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, People’s Republic of China
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, People’s Republic of China
| | - Jianhua He
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, People’s Republic of China
- The Institute for Advanced Studies, Wuhan University, Wuhan 430072, People’s Republic of China
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14
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Sui S, Mulichak A, Kulathila R, McGee J, Filiatreault D, Saha S, Cohen A, Song J, Hung H, Selway J, Kirby C, Shrestha OK, Weihofen W, Fodor M, Xu M, Chopra R, Perry SL. A capillary-based microfluidic device enables primary high-throughput room-temperature crystallographic screening. J Appl Crystallogr 2021; 54:1034-1046. [PMID: 34429718 PMCID: PMC8366422 DOI: 10.1107/s1600576721004155] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 04/18/2021] [Indexed: 11/10/2022] Open
Abstract
A novel capillary-based microfluidic strategy to accelerate the process of small-molecule-compound screening by room-temperature X-ray crystallography using protein crystals is reported. The ultra-thin microfluidic devices are composed of a UV-curable polymer, patterned by cleanroom photolithography, and have nine capillary channels per chip. The chip was designed for ease of sample manipulation, sample stability and minimal X-ray background. 3D-printed frames and cassettes conforming to SBS standards are used to house the capillary chips, providing additional mechanical stability and compatibility with automated liquid- and sample-handling robotics. These devices enable an innovative in situ crystal-soaking screening workflow, akin to high-throughput compound screening, such that quantitative electron density maps sufficient to determine weak binding events are efficiently obtained. This work paves the way for adopting a room-temperature microfluidics-based sample delivery method at synchrotron sources to facilitate high-throughput protein-crystallography-based screening of compounds at high concentration with the aim of discovering novel binding events in an automated manner.
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Affiliation(s)
- Shuo Sui
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, MA, USA
| | - Anne Mulichak
- IMCA-CAT, Argonne National Laboratory, Lemont, IL, USA
| | | | - Joshua McGee
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, MA, USA
| | | | - Sarthak Saha
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, MA, USA
| | - Aina Cohen
- Macromolecular Crystallography Group, Stanford Synchrotron Radiation Lightsource, Menlo Park, CA, USA
| | - Jinhu Song
- Macromolecular Crystallography Group, Stanford Synchrotron Radiation Lightsource, Menlo Park, CA, USA
| | | | - Jonathan Selway
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Christina Kirby
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Om K. Shrestha
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Michelle Fodor
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Mei Xu
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Rajiv Chopra
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Sarah L. Perry
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, MA, USA
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15
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Lahey-Rudolph JM, Schönherr R, Barthelmess M, Fischer P, Seuring C, Wagner A, Meents A, Redecke L. Fixed-target serial femtosecond crystallography using in cellulo grown microcrystals. IUCRJ 2021; 8:665-677. [PMID: 34258014 PMCID: PMC8256716 DOI: 10.1107/s2052252521005297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 05/18/2021] [Indexed: 05/05/2023]
Abstract
The crystallization of recombinant proteins in living cells is an exciting new approach in structural biology. Recent success has highlighted the need for fast and efficient diffraction data collection, optimally directly exposing intact crystal-containing cells to the X-ray beam, thus protecting the in cellulo crystals from environmental challenges. Serial femtosecond crystallography (SFX) at free-electron lasers (XFELs) allows the collection of detectable diffraction even from tiny protein crystals, but requires very fast sample exchange to utilize each XFEL pulse. Here, an efficient approach is presented for high-resolution structure elucidation using serial femtosecond in cellulo diffraction of micometre-sized crystals of the protein HEX-1 from the fungus Neurospora crassa on a fixed target. Employing the fast and highly accurate Roadrunner II translation-stage system allowed efficient raster scanning of the pores of micro-patterned, single-crystalline silicon chips loaded with living, crystal-containing insect cells. Compared with liquid-jet and LCP injection systems, the increased hit rates of up to 30% and reduced background scattering enabled elucidation of the HEX-1 structure. Using diffraction data from only a single chip collected within 12 min at the Linac Coherent Light Source, a 1.8 Å resolution structure was obtained with significantly reduced sample consumption compared with previous SFX experiments using liquid-jet injection. This HEX-1 structure is almost superimposable with that previously determined using synchrotron radiation from single HEX-1 crystals grown by sitting-drop vapour diffusion, validating the approach. This study demonstrates that fixed-target SFX using micro-patterned silicon chips is ideally suited for efficient in cellulo diffraction data collection using living, crystal-containing cells, and offers huge potential for the straightforward structure elucidation of proteins that form intracellular crystals at both XFELs and synchrotron sources.
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Affiliation(s)
- J. Mia Lahey-Rudolph
- Institute of Biochemistry, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Robert Schönherr
- Institute of Biochemistry, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
- Photon Science, Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Miriam Barthelmess
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Pontus Fischer
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Carolin Seuring
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, 22671 Hamburg, Germany
| | - Armin Wagner
- Diamond Light Source, Diamond House DH2-52, Chilton, Didcot OX11 0DE, United Kingdom
| | - Alke Meents
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
- Photon Science, Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Lars Redecke
- Institute of Biochemistry, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
- Photon Science, Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
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16
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Illava G, Jayne R, Finke AD, Closs D, Zeng W, Milano SK, Huang Q, Kriksunov I, Sidorenko P, Wise FW, Zipfel WR, Apker BA, Thorne RE. Integrated sample-handling and mounting system for fixed-target serial synchrotron crystallography. Acta Crystallogr D Struct Biol 2021; 77:628-644. [PMID: 33950019 PMCID: PMC8098472 DOI: 10.1107/s2059798321001868] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 02/15/2021] [Indexed: 11/15/2022] Open
Abstract
Serial synchrotron crystallography (SSX) is enabling the efficient use of small crystals for structure-function studies of biomolecules and for drug discovery. An integrated SSX system has been developed comprising ultralow background-scatter sample holders suitable for room and cryogenic temperature crystallographic data collection, a sample-loading station and a humid `gloveless' glovebox. The sample holders incorporate thin-film supports with a variety of designs optimized for different crystal-loading challenges. These holders facilitate the dispersion of crystals and the removal of excess liquid, can be cooled at extremely high rates, generate little background scatter, allow data collection over >90° of oscillation without obstruction or the risk of generating saturating Bragg peaks, are compatible with existing infrastructure for high-throughput cryocrystallography and are reusable. The sample-loading station allows sample preparation and loading onto the support film, the application of time-varying suction for optimal removal of excess liquid, crystal repositioning and cryoprotection, and the application of sealing films for room-temperature data collection, all in a controlled-humidity environment. The humid glovebox allows microscope observation of the sample-loading station and crystallization trays while maintaining near-saturating humidities that further minimize the risks of sample dehydration and damage, and maximize working times. This integrated system addresses common problems in obtaining properly dispersed, properly hydrated and isomorphous microcrystals for fixed-orientation and oscillation data collection. Its ease of use, flexibility and optimized performance make it attractive not just for SSX but also for single-crystal and few-crystal data collection. Fundamental concepts that are important in achieving desired crystal distributions on a sample holder via time-varying suction-induced liquid flows are also discussed.
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Affiliation(s)
- Gabrielle Illava
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | | | | | - David Closs
- MiTeGen LLC, PO Box 3867, Ithaca, NY 14850, USA
| | - Wenjie Zeng
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Shawn K. Milano
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | | | | | - Pavel Sidorenko
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
| | - Frank W. Wise
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
| | - Warren R. Zipfel
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA
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17
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Abstract
X-ray crystallography enables detailed structural studies of proteins to understand and modulate their function. Conducting crystallographic experiments at cryogenic temperatures has practical benefits but potentially limits the identification of functionally important alternative protein conformations that can be revealed only at room temperature (RT). This review discusses practical aspects of preparing, acquiring, and analyzing X-ray crystallography data at RT to demystify preconceived impracticalities that freeze progress of routine RT data collection at synchrotron sources. Examples are presented as conceptual and experimental templates to enable the design of RT-inspired studies; they illustrate the diversity and utility of gaining novel insights into protein conformational landscapes. An integrative view of protein conformational dynamics enables opportunities to advance basic and biomedical research.
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18
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Dynamic Structural Biology Experiments at XFEL or Synchrotron Sources. Methods Mol Biol 2021; 2305:203-228. [PMID: 33950392 DOI: 10.1007/978-1-0716-1406-8_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Macromolecular crystallography (MX) leverages the methods of physics and the language of chemistry to reveal fundamental insights into biology. Often beautifully artistic images present MX results to support profound functional hypotheses that are vital to entire life science research community. Over the past several decades, synchrotrons around the world have been the workhorses for X-ray diffraction data collection at many highly automated beamlines. The newest tools include X-ray-free electron lasers (XFELs) located at facilities in the USA, Japan, Korea, Switzerland, and Germany that deliver about nine orders of magnitude higher brightness in discrete femtosecond long pulses. At each of these facilities, new serial femtosecond crystallography (SFX) strategies exploit slurries of micron-size crystals by rapidly delivering individual crystals into the XFEL X-ray interaction region, from which one diffraction pattern is collected per crystal before it is destroyed by the intense X-ray pulse. Relatively simple adaptions to SFX methods produce time-resolved data collection strategies wherein reactions are triggered by visible light illumination or by chemical diffusion/mixing. Thus, XFELs provide new opportunities for high temporal and spatial resolution studies of systems engaged in function at physiological temperature. In this chapter, we summarize various issues related to microcrystal slurry preparation, sample delivery into the X-ray interaction region, and some emerging strategies for time-resolved SFX data collection.
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19
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Ren Z, Wang C, Shin H, Bandara S, Kumarapperuma I, Ren MY, Kang W, Yang X. An automated platform for in situ serial crystallography at room temperature. IUCRJ 2020; 7:1009-1018. [PMID: 33209315 PMCID: PMC7642789 DOI: 10.1107/s2052252520011288] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 08/17/2020] [Indexed: 06/11/2023]
Abstract
Direct observation of functional motions in protein structures is highly desirable for understanding how these nanomachineries of life operate at the molecular level. Because cryogenic temperatures are non-physiological and may prohibit or even alter protein structural dynamics, it is necessary to develop robust X-ray diffraction methods that enable routine data collection at room temperature. We recently reported a crystal-on-crystal device to facilitate in situ diffraction of protein crystals at room temperature devoid of any sample manipulation. Here an automated serial crystallography platform based on this crystal-on-crystal technology is presented. A hardware and software prototype has been implemented, and protocols have been established that allow users to image, recognize and rank hundreds to thousands of protein crystals grown on a chip in optical scanning mode prior to serial introduction of these crystals to an X-ray beam in a programmable and high-throughput manner. This platform has been tested extensively using fragile protein crystals. We demonstrate that with affordable sample consumption, this in situ serial crystallography technology could give rise to room-temperature protein structures of higher resolution and superior map quality for those protein crystals that encounter difficulties during freezing. This serial data collection platform is compatible with both monochromatic oscillation and Laue methods for X-ray diffraction and presents a widely applicable approach for static and dynamic crystallographic studies at room temperature.
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Affiliation(s)
- Zhong Ren
- Department of Chemistry, University of Illinois at Chicago, 845 W Taylor St, Chicago, IL 60607, USA
- Renz Research, Inc., Westmont, IL 60559, USA
| | - Cong Wang
- Department of Chemistry, University of Illinois at Chicago, 845 W Taylor St, Chicago, IL 60607, USA
| | - Heewhan Shin
- Department of Chemistry, University of Illinois at Chicago, 845 W Taylor St, Chicago, IL 60607, USA
| | - Sepalika Bandara
- Department of Chemistry, University of Illinois at Chicago, 845 W Taylor St, Chicago, IL 60607, USA
| | - Indika Kumarapperuma
- Department of Chemistry, University of Illinois at Chicago, 845 W Taylor St, Chicago, IL 60607, USA
| | - Michael Y. Ren
- A. James Clark School of Engineering, University of Maryland, College Park, MD 20742, USA
| | - Weijia Kang
- Department of Chemistry, University of Illinois at Chicago, 845 W Taylor St, Chicago, IL 60607, USA
| | - Xiaojing Yang
- Department of Chemistry, University of Illinois at Chicago, 845 W Taylor St, Chicago, IL 60607, USA
- Department of Ophthalmology and Vision Sciences, University of Illinois at Chicago, 845 W Taylor St, Chicago, IL 60607, USA
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20
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Thompson MC, Yeates TO, Rodriguez JA. Advances in methods for atomic resolution macromolecular structure determination. F1000Res 2020; 9:F1000 Faculty Rev-667. [PMID: 32676184 PMCID: PMC7333361 DOI: 10.12688/f1000research.25097.1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/25/2020] [Indexed: 12/13/2022] Open
Abstract
Recent technical advances have dramatically increased the power and scope of structural biology. New developments in high-resolution cryo-electron microscopy, serial X-ray crystallography, and electron diffraction have been especially transformative. Here we highlight some of the latest advances and current challenges at the frontiers of atomic resolution methods for elucidating the structures and dynamical properties of macromolecules and their complexes.
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Affiliation(s)
- Michael C. Thompson
- Department of Chemistry and Chemical Biology, University of California, Merced, CA, USA
| | - Todd O. Yeates
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA, USA
| | - Jose A. Rodriguez
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA, USA
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21
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Fontecilla-Camps JC, Bricogne G. Jean-Luc Ferrer (1964–2020): structural biologist, beamline instrumentation innovator and entrepreneur. Acta Crystallogr D Struct Biol 2020. [DOI: 10.1107/s2059798320007081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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22
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Abstract
The advent of the X-ray free electron laser (XFEL) in the last decade created the discipline of serial crystallography but also the challenge of how crystal samples are delivered to X-ray. Early sample delivery methods demonstrated the proof-of-concept for serial crystallography and XFEL but were beset with challenges of high sample consumption, jet clogging and low data collection efficiency. The potential of XFEL and serial crystallography as the next frontier of structural solution by X-ray for small and weakly diffracting crystals and provision of ultra-fast time-resolved structural data spawned a huge amount of scientific interest and innovation. To utilize the full potential of XFEL and broaden its applicability to a larger variety of biological samples, researchers are challenged to develop better sample delivery methods. Thus, sample delivery is one of the key areas of research and development in the serial crystallography scientific community. Sample delivery currently falls into three main systems: jet-based methods, fixed-target chips, and drop-on-demand. Huge strides have since been made in reducing sample consumption and improving data collection efficiency, thus enabling the use of XFEL for many biological systems to provide high-resolution, radiation damage-free structural data as well as time-resolved dynamics studies. This review summarizes the current main strategies in sample delivery and their respective pros and cons, as well as some future direction.
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23
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Wolff AM, Young ID, Sierra RG, Brewster AS, Martynowycz MW, Nango E, Sugahara M, Nakane T, Ito K, Aquila A, Bhowmick A, Biel JT, Carbajo S, Cohen AE, Cortez S, Gonzalez A, Hino T, Im D, Koralek JD, Kubo M, Lazarou TS, Nomura T, Owada S, Samelson AJ, Tanaka T, Tanaka R, Thompson EM, van den Bedem H, Woldeyes RA, Yumoto F, Zhao W, Tono K, Boutet S, Iwata S, Gonen T, Sauter NK, Fraser JS, Thompson MC. Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals. IUCRJ 2020; 7:306-323. [PMID: 32148858 PMCID: PMC7055375 DOI: 10.1107/s205225252000072x] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 01/21/2020] [Indexed: 06/10/2023]
Abstract
Innovative new crystallographic methods are facilitating structural studies from ever smaller crystals of biological macromolecules. In particular, serial X-ray crystallography and microcrystal electron diffraction (MicroED) have emerged as useful methods for obtaining structural information from crystals on the nanometre to micrometre scale. Despite the utility of these methods, their implementation can often be difficult, as they present many challenges that are not encountered in traditional macromolecular crystallography experiments. Here, XFEL serial crystallography experiments and MicroED experiments using batch-grown microcrystals of the enzyme cyclophilin A are described. The results provide a roadmap for researchers hoping to design macromolecular microcrystallography experiments, and they highlight the strengths and weaknesses of the two methods. Specifically, we focus on how the different physical conditions imposed by the sample-preparation and delivery methods required for each type of experiment affect the crystal structure of the enzyme.
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Affiliation(s)
- Alexander M. Wolff
- Graduate Program in Biophysics, University of California, San Francisco, San Francisco, California, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Iris D. Young
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Raymond G. Sierra
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Aaron S. Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Michael W. Martynowycz
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, California, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, California, USA
| | - Eriko Nango
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Michihiro Sugahara
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Takanori Nakane
- Department of Biological Science, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Kazutaka Ito
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
- Laboratory for Drug Discovery, Pharmaceuticals Research Center, Asahi Kasei Pharma Corporation, 632-1 Mifuku, Izunokuni-shi, Shizuoka 410-2321, Japan
| | - Andrew Aquila
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Asmit Bhowmick
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Justin T. Biel
- Graduate Program in Biophysics, University of California, San Francisco, San Francisco, California, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Sergio Carbajo
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Aina E. Cohen
- SSRL, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Saul Cortez
- Department of Biology, San Francisco State University, San Francisco, California, USA
| | - Ana Gonzalez
- SSRL, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Tomoya Hino
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, 4-101 Koyama-cho, Minami, Tottori 680-8552, Japan
- Center for Research on Green Sustainable Chemistry, Tottori University, Tottori, Japan
| | - Dohyun Im
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Jake D. Koralek
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Minoru Kubo
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Graduate School of Life Science, University of Hyogo, Ako-gun, Hyogo 678-1297, Japan
| | | | - Takashi Nomura
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Shigeki Owada
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Avi J. Samelson
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, California, USA
| | - Tomoyuki Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Rie Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Erin M. Thompson
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
- Graduate Program in Chemistry and Chemical Biology, University of California, San Francisco, San Francisco, California, USA
| | - Henry van den Bedem
- Bioscience Department, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Rahel A. Woldeyes
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
- Graduate Program in Chemistry and Chemical Biology, University of California, San Francisco, San Francisco, California, USA
| | - Fumiaki Yumoto
- Structural Biology Research Center, Institute of Materials Structure Science, KEK/High Energy Accelerator Research Organization, Tsukuba, Ibaraki 305-0034, Japan
| | - Wei Zhao
- Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Kensuke Tono
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Sebastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - So Iwata
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Tamir Gonen
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, California, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, California, USA
- Department of Physiology, University of California, Los Angeles, Los Angeles, California, USA
| | - Nicholas K. Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - James S. Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Michael C. Thompson
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
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24
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Monteiro DCF, von Stetten D, Stohrer C, Sans M, Pearson AR, Santoni G, van der Linden P, Trebbin M. 3D-MiXD: 3D-printed X-ray-compatible microfluidic devices for rapid, low-consumption serial synchrotron crystallography data collection in flow. IUCRJ 2020; 7:207-219. [PMID: 32148849 PMCID: PMC7055382 DOI: 10.1107/s2052252519016865] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 12/17/2019] [Indexed: 05/24/2023]
Abstract
Serial crystallography has enabled the study of complex biological questions through the determination of biomolecular structures at room temperature using low X-ray doses. Furthermore, it has enabled the study of protein dynamics by the capture of atomically resolved and time-resolved molecular movies. However, the study of many biologically relevant targets is still severely hindered by high sample consumption and lengthy data-collection times. By combining serial synchrotron crystallography (SSX) with 3D printing, a new experimental platform has been created that tackles these challenges. An affordable 3D-printed, X-ray-compatible microfluidic device (3D-MiXD) is reported that allows data to be collected from protein microcrystals in a 3D flow with very high hit and indexing rates, while keeping the sample consumption low. The miniaturized 3D-MiXD can be rapidly installed into virtually any synchrotron beamline with only minimal adjustments. This efficient collection scheme in combination with its mixing geometry paves the way for recording molecular movies at synchrotrons by mixing-triggered millisecond time-resolved SSX.
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Affiliation(s)
- Diana C. F. Monteiro
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Hauptman–Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
| | - David von Stetten
- European Molecular Biology Laboratory, Notkestrasse 85, 22607 Hamburg, Germany
| | - Claudia Stohrer
- The Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, England
| | - Marta Sans
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Physics, Universität Hamburg, Jungiusstrasse 9, 20355 Hamburg, Germany
| | - Arwen R. Pearson
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Physics, Universität Hamburg, Jungiusstrasse 9, 20355 Hamburg, Germany
| | - Gianluca Santoni
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38043 Grenoble, France
| | - Peter van der Linden
- Partnership for Soft Condensed Matter, European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38043 Grenoble, France
| | - Martin Trebbin
- Hauptman–Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
- Department of Chemistry, The State University of New York at Buffalo, Natural Sciences Complex 760, Buffalo, NY 14260-3000, USA
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25
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Brenker JC, Devendran C, Neild A, Alan T. On-demand sample injection: combining acoustic actuation with a tear-drop shaped nozzle to generate droplets with precise spatial and temporal control. LAB ON A CHIP 2020; 20:253-265. [PMID: 31854405 DOI: 10.1039/c9lc00837c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
An on-demand droplet injection method for controlled delivery of nanolitre-volume liquid samples to scientific instruments for subsequent analysis is presented. We employ pulsed focussed surface acoustic waves (SAW) to eject droplets from an enclosed microfluidic channel into an open environment. The 3D position of individual droplets and their time of arrival can be precisely controlled to within 61 μs in a 500 μm square target region 40 μm wide. The continuous ejection rate of 16 000 droplets per second can be tuned to produce pulsed trains of droplets from 0 up to 357 Hz. The main benefit of this technique is its ease of integration with complex microfluidic processing steps, such as droplet merging, sorting, and encapsulation, prior to sample delivery. With its ability to precisely deliver a small quantity of fluid to a pre-defined location this technology is applicable in X-ray based molecular studies, including the rapidly expanding field of X-ray free electron lasers. Fabrication procedures for this device, the underlying forcing mechanism, the role of nozzle design, and demonstration of the performance in both continuous and on-demand modes are reported.
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Affiliation(s)
- Jason C Brenker
- Laboratory for Micro Systems, Department of Mechanical and Aerospace, Engineering, Monash University, Clayton, Victoria 3800, Australia.
| | - Citsabehsan Devendran
- Laboratory for Micro Systems, Department of Mechanical and Aerospace, Engineering, Monash University, Clayton, Victoria 3800, Australia.
| | - Adrian Neild
- Laboratory for Micro Systems, Department of Mechanical and Aerospace, Engineering, Monash University, Clayton, Victoria 3800, Australia.
| | - Tuncay Alan
- Laboratory for Micro Systems, Department of Mechanical and Aerospace, Engineering, Monash University, Clayton, Victoria 3800, Australia.
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26
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Huang CY, Olieric V, Caffrey M, Wang M. In Meso In Situ Serial X-Ray Crystallography (IMISX): A Protocol for Membrane Protein Structure Determination at the Swiss Light Source. Methods Mol Biol 2020; 2127:293-319. [PMID: 32112330 DOI: 10.1007/978-1-0716-0373-4_20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The lipid cubic phases (LCP) have enabled the determination of many important high-resolution structures of membrane proteins such as G-protein-coupled receptors, photosensitive proteins, enzymes, channels, and transporters. However, harvesting the crystals from the glass or plastic plates in which crystals grow is challenging. The in meso in situ serial X-ray crystallography (IMISX) method uses thin plastic windowed plates that minimize LCP crystal manipulation. The method, which is compatible with high-throughput in situ measurements, allows systematic diffraction screening and rapid data collection from hundreds of microcrystals in in meso crystallization wells without direct crystal harvesting. In this chapter, we describe an IMISX protocol for in situ serial X-ray data collection of LCP-grown crystals at both cryogenic and room temperatures which includes the crystallization setup, sample delivery, automated serial diffraction data collection, and experimental phasing. We also detail how the IMISX method was applied successfully for the structure determination of two novel targets-the undecaprenyl-pyrophosphate phosphatase BacA and the chemokine G-protein-coupled receptor CCR2A.
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Affiliation(s)
- Chia-Ying Huang
- Swiss Light Source, Paul Scherrer Institut, Forschungsstrasse 111, Villigen-PSI, 5232, Switzerland.
| | - Vincent Olieric
- Swiss Light Source, Paul Scherrer Institut, Forschungsstrasse 111, Villigen-PSI, 5232, Switzerland
| | - Martin Caffrey
- Membrane Structural and Functional Biology (MS&FB) Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland
| | - Meitian Wang
- Swiss Light Source, Paul Scherrer Institut, Forschungsstrasse 111, Villigen-PSI, 5232, Switzerland
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27
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Shelby ML, Gilbile D, Grant TD, Seuring C, Segelke BW, He W, Evans AC, Pakendorf T, Fischer P, Hunter MS, Batyuk A, Barthelmess M, Meents A, Coleman MA, Kuhl TL, Frank M. A fixed-target platform for serial femtosecond crystallography in a hydrated environment. IUCRJ 2020; 7:30-41. [PMID: 31949902 PMCID: PMC6949605 DOI: 10.1107/s2052252519014003] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 10/15/2019] [Indexed: 05/19/2023]
Abstract
For serial femtosecond crystallography at X-ray free-electron lasers, which entails collection of single-pulse diffraction patterns from a constantly refreshed supply of microcrystalline sample, delivery of the sample into the X-ray beam path while maintaining low background remains a technical challenge for some experiments, especially where this methodology is applied to relatively low-ordered samples or those difficult to purify and crystallize in large quantities. This work demonstrates a scheme to encapsulate biological samples using polymer thin films and graphene to maintain sample hydration in vacuum conditions. The encapsulated sample is delivered into the X-ray beam on fixed targets for rapid scanning using the Roadrunner fixed-target system towards a long-term goal of low-background measurements on weakly diffracting samples. As a proof of principle, we used microcrystals of the 24 kDa rapid encystment protein (REP24) to provide a benchmark for polymer/graphene sandwich performance. The REP24 microcrystal unit cell obtained from our sandwiched in-vacuum sample was consistent with previously established unit-cell parameters and with those measured by us without encapsulation in humidified helium, indicating that the platform is robust against evaporative losses. While significant scattering from water was observed because of the sample-deposition method, the polymer/graphene sandwich itself was shown to contribute minimally to background scattering.
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Affiliation(s)
- M. L. Shelby
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - D. Gilbile
- University of California at Davis, California, USA
| | - T. D. Grant
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, Hauptman-Woodward Institute, SUNY University at Buffalo, Buffalo, New York, USA
| | - C. Seuring
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Hamburg, Germany
| | - B. W. Segelke
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - W. He
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - A. C. Evans
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
- University of California at Davis, California, USA
| | - T. Pakendorf
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Hamburg, Germany
| | - P. Fischer
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Hamburg, Germany
| | - M. S. Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - A. Batyuk
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - M. Barthelmess
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Hamburg, Germany
| | - A. Meents
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Hamburg, Germany
| | - M. A. Coleman
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
- University of California at Davis, California, USA
| | - T. L. Kuhl
- University of California at Davis, California, USA
| | - M. Frank
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
- University of California at Davis, California, USA
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28
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Zhao F, Zhang B, Yan E, Sun B, Wang Z, He J, Yin D. A guide to sample delivery systems for serial crystallography. FEBS J 2019; 286:4402-4417. [DOI: 10.1111/febs.15099] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Revised: 09/26/2019] [Accepted: 10/15/2019] [Indexed: 01/07/2023]
Affiliation(s)
- Feng‐Zhu Zhao
- School of Life Sciences Northwestern Polytechnical University Xi'an China
| | - Bin Zhang
- School of Life Sciences Northwestern Polytechnical University Xi'an China
| | - Er‐Kai Yan
- School of Life Sciences Northwestern Polytechnical University Xi'an China
| | - Bo Sun
- Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai China
| | - Zhi‐Jun Wang
- Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai China
| | - Jian‐Hua He
- Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai China
| | - Da‐Chuan Yin
- School of Life Sciences Northwestern Polytechnical University Xi'an China
- Shenzhen Research Institute Northwestern Polytechnical University Shenzhen China
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29
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Nylon mesh-based sample holder for fixed-target serial femtosecond crystallography. Sci Rep 2019; 9:6971. [PMID: 31061502 PMCID: PMC6502819 DOI: 10.1038/s41598-019-43485-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 04/25/2019] [Indexed: 11/08/2022] Open
Abstract
Fixed-target serial femtosecond crystallography (FT-SFX) was an important advance in crystallography by dramatically reducing sample consumption, while maintaining the benefits of SFX for obtaining crystal structures at room temperature without radiation damage. Despite a number of advantages, preparation of a sample holder for the sample delivery in FT-SFX with the use of many crystals in a single mount at ambient temperature is challenging as it can be complicated and costly, and thus, development of an efficient sample holder is essential. In this study, we introduced a nylon mesh-based sample holder enclosed by a polyimide film. This sample holder can be rapidly manufactured using a commercially available nylon mesh with pores of a desired size at a low cost without challenging technology. Furthermore, this simple device is highly efficient in data acquisition. We performed FT-SFX using a nylon mesh-based sample holder and collected over 130,000 images on a single sample holder using a 30 Hz X-ray pulse for 1.2 h. We determined the crystal structures of lysozyme and glucose isomerase using the nylon mesh at 1.65 and 1.75 Å, respectively. The nylon mesh exposed to X-rays produced very low levels of background scattering at 3.75 and 4.30 Å, which are negligible for data analysis. Our method provides a simple and rapid but highly efficient way to deliver samples for FT-SFX.
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30
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Basu S, Olieric V, Leonarski F, Matsugaki N, Kawano Y, Takashi T, Huang CY, Yamada Y, Vera L, Olieric N, Basquin J, Wojdyla JA, Bunk O, Diederichs K, Yamamoto M, Wang M. Long-wavelength native-SAD phasing: opportunities and challenges. IUCRJ 2019; 6:373-386. [PMID: 31098019 PMCID: PMC6503925 DOI: 10.1107/s2052252519002756] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 02/22/2019] [Indexed: 05/04/2023]
Abstract
Native single-wavelength anomalous dispersion (SAD) is an attractive experimental phasing technique as it exploits weak anomalous signals from intrinsic light scatterers (Z < 20). The anomalous signal of sulfur in particular, is enhanced at long wavelengths, however the absorption of diffracted X-rays owing to the crystal, the sample support and air affects the recorded intensities. Thereby, the optimal measurable anomalous signals primarily depend on the counterplay of the absorption and the anomalous scattering factor at a given X-ray wavelength. Here, the benefit of using a wavelength of 2.7 over 1.9 Å is demonstrated for native-SAD phasing on a 266 kDa multiprotein-ligand tubulin complex (T2R-TTL) and is applied in the structure determination of an 86 kDa helicase Sen1 protein at beamline BL-1A of the KEK Photon Factory, Japan. Furthermore, X-ray absorption at long wavelengths was controlled by shaping a lysozyme crystal into spheres of defined thicknesses using a deep-UV laser, and a systematic comparison between wavelengths of 2.7 and 3.3 Å is reported for native SAD. The potential of laser-shaping technology and other challenges for an optimized native-SAD experiment at wavelengths >3 Å are discussed.
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Affiliation(s)
- Shibom Basu
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
| | - Vincent Olieric
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
| | - Filip Leonarski
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
| | - Naohiro Matsugaki
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, Tsukuba, 305-0801, Japan
| | - Yoshiaki Kawano
- Advanced Photon Technology Division, RIKEN SPring-8 Center, Hyogo 679-5148, Japan
| | - Tomizaki Takashi
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
| | - Chia-Ying Huang
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
| | - Yusuke Yamada
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, Tsukuba, 305-0801, Japan
| | - Laura Vera
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
| | - Natacha Olieric
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institut, Villigen, PSI 5232, Switzerland
| | - Jerome Basquin
- Department of Biochemistry, Max Planck Institute of Biochemistry, Munich, Germany
| | - Justyna A. Wojdyla
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
| | - Oliver Bunk
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
| | - Kay Diederichs
- Department of Biology, University of Konstanz, Konstanz, 78457, Germany
| | - Masaki Yamamoto
- Advanced Photon Technology Division, RIKEN SPring-8 Center, Hyogo 679-5148, Japan
| | - Meitian Wang
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
- Correspondence e-mail:
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31
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The crystal structure of dGTPase reveals the molecular basis of dGTP selectivity. Proc Natl Acad Sci U S A 2019; 116:9333-9339. [PMID: 31019074 PMCID: PMC6511015 DOI: 10.1073/pnas.1814999116] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
While cellular dNTPases display broad activity toward dNTPs (e.g., SAMHD1), Escherichia coli (Ec)-dGTPase is the only known enzyme that specifically hydrolyzes dGTP. Here, we present methods for highly efficient, fixed-target X-ray free-electron laser data collection, which is broadly applicable to multiple crystal systems including RNA polymerase II complexes, and the free Ec-dGTPase enzyme. Structures of free and bound Ec-dGTPase shed light on the mechanisms of dGTP selectivity, highlighted by a dynamic active site where conformational changes are coupled to dGTP binding. Moreover, despite no sequence homology between Ec-dGTPase and SAMHD1, both enzymes share similar active-site architectures; however, dGTPase residues at the end of the substrate-binding pocket provide dGTP specificity, while a 7-Å cleft separates SAMHD1 residues from dNTP. Deoxynucleotide triphosphohydrolases (dNTPases) play a critical role in cellular survival and DNA replication through the proper maintenance of cellular dNTP pools. While the vast majority of these enzymes display broad activity toward canonical dNTPs, such as the dNTPase SAMHD1 that blocks reverse transcription of retroviruses in macrophages by maintaining dNTP pools at low levels, Escherichia coli (Ec)-dGTPase is the only known enzyme that specifically hydrolyzes dGTP. However, the mechanism behind dGTP selectivity is unclear. Here we present the free-, ligand (dGTP)- and inhibitor (GTP)-bound structures of hexameric Ec-dGTPase, including an X-ray free-electron laser structure of the free Ec-dGTPase enzyme to 3.2 Å. To obtain this structure, we developed a method that applied UV-fluorescence microscopy, video analysis, and highly automated goniometer-based instrumentation to map and rapidly position individual crystals randomly located on fixed target holders, resulting in the highest indexing rates observed for a serial femtosecond crystallography experiment. Our structures show a highly dynamic active site where conformational changes are coupled to substrate (dGTP), but not inhibitor binding, since GTP locks dGTPase in its apo- form. Moreover, despite no sequence homology, Ec-dGTPase and SAMHD1 share similar active-site and HD motif architectures; however, Ec-dGTPase residues at the end of the substrate-binding pocket mimic Watson–Crick interactions providing guanine base specificity, while a 7-Å cleft separates SAMHD1 residues from dNTP bases, abolishing nucleotide-type discrimination. Furthermore, the structures shed light on the mechanism by which long distance binding (25 Å) of single-stranded DNA in an allosteric site primes the active site by conformationally “opening” a tyrosine gate allowing enhanced substrate binding.
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32
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Monteiro DCF, Vakili M, Harich J, Sztucki M, Meier SM, Horrell S, Josts I, Trebbin M. A microfluidic flow-focusing device for low sample consumption serial synchrotron crystallography experiments in liquid flow. JOURNAL OF SYNCHROTRON RADIATION 2019; 26:406-412. [PMID: 30855249 DOI: 10.1107/s1600577519000304] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 01/07/2019] [Indexed: 06/09/2023]
Abstract
Serial synchrotron crystallography allows low X-ray dose, room-temperature crystal structures of proteins to be determined from a population of microcrystals. Protein production and crystallization is a non-trivial procedure and it is essential to have X-ray-compatible sample environments that keep sample consumption low and the crystals in their native environment. This article presents a fast and optimized manufacturing route to metal-polyimide microfluidic flow-focusing devices which allow for the collection of X-ray diffraction data in flow. The flow-focusing conditions allow for sample consumption to be significantly decreased, while also opening up the possibility of more complex experiments such as rapid mixing for time-resolved serial crystallography. This high-repetition-rate experiment allows for full datasets to be obtained quickly (∼1 h) from crystal slurries in liquid flow. The X-ray compatible microfluidic chips are easily manufacturable, reliable and durable and require sample-flow rates on the order of only 30 µl h-1.
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Affiliation(s)
- Diana C F Monteiro
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, Hamburg 22761, Germany
| | - Mohammad Vakili
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, Hamburg 22761, Germany
| | - Jessica Harich
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, Hamburg 22761, Germany
| | - Michael Sztucki
- ESRF, European Synchrotron Radiation Facility, 71 Avenue des Martyrs, Grenoble CS 40220, France
| | - Susanne M Meier
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, Hamburg 22761, Germany
| | - Sam Horrell
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, Hamburg 22761, Germany
| | - Inokentijs Josts
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, Hamburg 22761, Germany
| | - Martin Trebbin
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, Hamburg 22761, Germany
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33
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Martiel I, Müller-Werkmeister HM, Cohen AE. Strategies for sample delivery for femtosecond crystallography. Acta Crystallogr D Struct Biol 2019; 75:160-177. [PMID: 30821705 PMCID: PMC6400256 DOI: 10.1107/s2059798318017953] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 12/19/2018] [Indexed: 11/11/2022] Open
Abstract
Highly efficient data-collection methods are required for successful macromolecular crystallography (MX) experiments at X-ray free-electron lasers (XFELs). XFEL beamtime is scarce, and the high peak brightness of each XFEL pulse destroys the exposed crystal volume. It is therefore necessary to combine diffraction images from a large number of crystals (hundreds to hundreds of thousands) to obtain a final data set, bringing about sample-refreshment challenges that have previously been unknown to the MX synchrotron community. In view of this experimental complexity, a number of sample delivery methods have emerged, each with specific requirements, drawbacks and advantages. To provide useful selection criteria for future experiments, this review summarizes the currently available sample delivery methods, emphasising the basic principles and the specific sample requirements. Two main approaches to sample delivery are first covered: (i) injector methods with liquid or viscous media and (ii) fixed-target methods using large crystals or using microcrystals inside multi-crystal holders or chips. Additionally, hybrid methods such as acoustic droplet ejection and crystal extraction are covered, which combine the advantages of both fixed-target and injector approaches.
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Affiliation(s)
- Isabelle Martiel
- Swiss Light Source, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Henrike M. Müller-Werkmeister
- Institute of Chemistry – Physical Chemistry, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam-Golm, Germany
| | - Aina E. Cohen
- Stanford Synchrotron Radiation Lightsource, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
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Keedy DA. Journey to the center of the protein: allostery from multitemperature multiconformer X-ray crystallography. Acta Crystallogr D Struct Biol 2019; 75:123-137. [PMID: 30821702 PMCID: PMC6400254 DOI: 10.1107/s2059798318017941] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 12/19/2018] [Indexed: 02/08/2023] Open
Abstract
Proteins inherently fluctuate between conformations to perform functions in the cell. For example, they sample product-binding, transition-state-stabilizing and product-release states during catalysis, and they integrate signals from remote regions of the structure for allosteric regulation. However, there is a lack of understanding of how these dynamic processes occur at the basic atomic level. This gap can be at least partially addressed by combining variable-temperature (instead of traditional cryogenic temperature) X-ray crystallography with algorithms for modeling alternative conformations based on electron-density maps, in an approach called multitemperature multiconformer X-ray crystallography (MMX). Here, the use of MMX to reveal alternative conformations at different sites in a protein structure and to estimate the degree of energetic coupling between them is discussed. These insights can suggest testable hypotheses about allosteric mechanisms. Temperature is an easily manipulated experimental parameter, so the MMX approach is widely applicable to any protein that yields well diffracting crystals. Moreover, the general principles of MMX are extensible to other perturbations such as pH, pressure, ligand concentration etc. Future work will explore strategies for leveraging X-ray data across such perturbation series to more quantitatively measure how different parts of a protein structure are coupled to each other, and the consequences thereof for allostery and other aspects of protein function.
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Affiliation(s)
- Daniel A. Keedy
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, USA
- Department of Chemistry and Biochemistry, City College of New York, New York, USA
- PhD Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York, New York, USA
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Grünbein ML, Nass Kovacs G. Sample delivery for serial crystallography at free-electron lasers and synchrotrons. Acta Crystallogr D Struct Biol 2019; 75:178-191. [PMID: 30821706 PMCID: PMC6400261 DOI: 10.1107/s205979831801567x] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 11/05/2018] [Indexed: 12/21/2022] Open
Abstract
The high peak brilliance and femtosecond pulse duration of X-ray free-electron lasers (XFELs) provide new scientific opportunities for experiments in physics, chemistry and biology. In structural biology, one of the major applications is serial femtosecond crystallography. The intense XFEL pulse results in the destruction of any exposed microcrystal, making serial data collection mandatory. This requires a high-throughput serial approach to sample delivery. To this end, a number of such sample-delivery techniques have been developed, some of which have been ported to synchrotron sources, where they allow convenient low-dose data collection at room temperature. Here, the current sample-delivery techniques used at XFEL and synchrotron sources are reviewed, with an emphasis on liquid injection and high-viscosity extrusion, including their application for time-resolved experiments. The challenges associated with sample delivery at megahertz repetition-rate XFELs are also outlined.
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Affiliation(s)
- Marie Luise Grünbein
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Gabriela Nass Kovacs
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
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Basu S, Kaminski JW, Panepucci E, Huang CY, Warshamanage R, Wang M, Wojdyla JA. Automated data collection and real-time data analysis suite for serial synchrotron crystallography. JOURNAL OF SYNCHROTRON RADIATION 2019; 26:244-252. [PMID: 30655492 PMCID: PMC6337882 DOI: 10.1107/s1600577518016570] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 11/21/2018] [Indexed: 05/03/2023]
Abstract
At the Swiss Light Source macromolecular crystallography (MX) beamlines the collection of serial synchrotron crystallography (SSX) diffraction data is facilitated by the recent DA+ data acquisition and analysis software developments. The SSX suite allows easy, efficient and high-throughput measurements on a large number of crystals. The fast continuous diffraction-based two-dimensional grid scan method allows initial location of microcrystals. The CY+ GUI utility enables efficient assessment of a grid scan's analysis output and subsequent collection of multiple wedges of data (so-called minisets) from automatically selected positions in a serial and automated way. The automated data processing (adp) routines adapted to the SSX data collection mode provide near real time analysis for data in both CBF and HDF5 formats. The automatic data merging (adm) is the latest extension of the DA+ data analysis software routines. It utilizes the sxdm (SSX data merging) package, which provides automatic online scaling and merging of minisets and allows identification of a minisets subset resulting in the best quality of the final merged data. The results of both adp and adm are sent to the MX MongoDB database and displayed in the web-based tracker, which provides the user with on-the-fly feedback about the experiment.
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Affiliation(s)
- Shibom Basu
- Swiss Light Source, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Jakub W. Kaminski
- Swiss Light Source, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Ezequiel Panepucci
- Swiss Light Source, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Chia-Ying Huang
- Swiss Light Source, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | | | - Meitian Wang
- Swiss Light Source, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
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Samara YN, Brennan HM, McCarthy L, Bollard MT, Laspina D, Wlodek JM, Campos SL, Natarajan R, Gofron K, McSweeney S, Soares AS, Leroy L. Using sound pulses to solve the crystal-harvesting bottleneck. Acta Crystallogr D Struct Biol 2018; 74:986-999. [PMID: 30289409 PMCID: PMC6173054 DOI: 10.1107/s2059798318011506] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 08/14/2018] [Indexed: 01/16/2023] Open
Abstract
Crystal harvesting has proven to be difficult to automate and remains the rate-limiting step for many structure-determination and high-throughput screening projects. This has resulted in crystals being prepared more rapidly than they can be harvested for X-ray data collection. Fourth-generation synchrotrons will support extraordinarily rapid rates of data acquisition, putting further pressure on the crystal-harvesting bottleneck. Here, a simple solution is reported in which crystals can be acoustically harvested from slightly modified MiTeGen In Situ-1 crystallization plates. This technique uses an acoustic pulse to eject each crystal out of its crystallization well, through a short air column and onto a micro-mesh (improving on previous work, which required separately grown crystals to be transferred before harvesting). Crystals can be individually harvested or can be serially combined with a chemical library such as a fragment library.
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Affiliation(s)
- Yasmin N. Samara
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- Universidade Federal de Santa Maria, 97105-900 Santa Maria-RS, Brazil
| | - Haley M. Brennan
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- Department of Biology, College of William and Mary, Williamsburg, VA 23187, USA
| | - Liam McCarthy
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- Department of Biology, Stony Brook University, New York, NY 11794-5215, USA
| | - Mary T. Bollard
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- Department of Biology, York College of Pennsylvania, York, PA 17403, USA
| | - Denise Laspina
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- Department of Biology, Stony Brook University, New York, NY 11794-5215, USA
| | - Jakub M. Wlodek
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- Department of Computer Science, Stony Brook University, New York, NY 11794-5215, USA
| | - Stefanie L. Campos
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- Department of Clinical Nutrition, Stony Brook University, New York, NY 11794-5215, USA
| | - Ramya Natarajan
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Kazimierz Gofron
- Energy Sciences Directorate, NSLS II, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Sean McSweeney
- Energy Sciences Directorate, NSLS II, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Alexei S. Soares
- Energy Sciences Directorate, NSLS II, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Ludmila Leroy
- Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte-MG, Brazil
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Doak RB, Nass Kovacs G, Gorel A, Foucar L, Barends TRM, Grünbein ML, Hilpert M, Kloos M, Roome CM, Shoeman RL, Stricker M, Tono K, You D, Ueda K, Sherrell DA, Owen RL, Schlichting I. Crystallography on a chip - without the chip: sheet-on-sheet sandwich. Acta Crystallogr D Struct Biol 2018; 74:1000-1007. [PMID: 30289410 PMCID: PMC6173051 DOI: 10.1107/s2059798318011634] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 08/16/2018] [Indexed: 11/29/2022] Open
Abstract
Crystallography chips are fixed-target supports consisting of a film (for example Kapton) or wafer (for example silicon) that is processed using semiconductor-microfabrication techniques to yield an array of wells or through-holes in which single microcrystals can be lodged for raster-scan probing. Although relatively expensive to fabricate, chips offer an efficient means of high-throughput sample presentation for serial diffraction data collection at synchrotron or X-ray free-electron laser (XFEL) sources. Truly efficient loading of a chip (one microcrystal per well and no wastage during loading) is nonetheless challenging. The wells or holes must match the microcrystal size of interest, requiring that a large stock of chips be maintained. Raster scanning requires special mechanical drives to step the chip rapidly and with micrometre precision from well to well. Here, a `chip-less' adaptation is described that essentially eliminates the challenges of loading and precision scanning, albeit with increased, yet still relatively frugal, sample usage. The device consists simply of two sheets of Mylar with the crystal solution sandwiched between them. This sheet-on-sheet (SOS) sandwich structure has been employed for serial femtosecond crystallography data collection with micrometre-sized crystals at an XFEL. The approach is also well suited to time-resolved pump-probe experiments, in particular for long time delays. The SOS sandwich enables measurements under XFEL beam conditions that would damage conventional chips, as documented here. The SOS sheets hermetically seal the sample, avoiding desiccation of the sample provided that the X-ray beam does not puncture the sheets. This is the case with a synchrotron beam but not with an XFEL beam. In the latter case, desiccation, setting radially outwards from each punched hole, sets lower limits on the speed and line spacing of the raster scan. It is shown that these constraints are easily accommodated.
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Affiliation(s)
- R. Bruce Doak
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Gabriela Nass Kovacs
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Alexander Gorel
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Lutz Foucar
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Thomas R. M. Barends
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Marie Luise Grünbein
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Mario Hilpert
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Marco Kloos
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Christopher M. Roome
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Robert L. Shoeman
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Miriam Stricker
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute (JASRI), 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Daehyun You
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
| | - Kiyoshi Ueda
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
| | - Darren A. Sherrell
- Diamond Light Source, Harwell Science and Innovation Campus, Fermi Avenue, Didcot OX11 0DE, England
| | - Robin L. Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Fermi Avenue, Didcot OX11 0DE, England
| | - Ilme Schlichting
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
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Ren Z, Ayhan M, Bandara S, Bowatte K, Kumarapperuma I, Gunawardana S, Shin H, Wang C, Zeng X, Yang X. Crystal-on-crystal chips for in situ serial diffraction at room temperature. LAB ON A CHIP 2018; 18:2246-2256. [PMID: 29952383 PMCID: PMC6057835 DOI: 10.1039/c8lc00489g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Recent developments in serial crystallography at X-ray free electron lasers (XFELs) and synchrotrons have been driven by two scientific goals in structural biology - first, static structure determination from nano or microcrystals of membrane proteins and large complexes that are difficult for conventional cryocrystallography, and second, direct observations of transient structural species in biochemical reactions at near atomic resolution. Since room-temperature diffraction experiments naturally demand a large quantity of purified protein, sample economy is critically important for all steps of serial crystallography from crystallization, crystal delivery to data collection. Here we report the development and applications of "crystal-on-crystal" devices to facilitate large-scale in situ serial diffraction experiments on protein crystals of all sizes - large, small, or microscopic. We show that the monocrystalline quartz as a substrate material prevents vapor loss during crystallization and significantly reduces background X-ray scattering. These devices can be readily adopted at XFEL and synchrotron beamlines, which enable efficient delivery of hundreds to millions of crystals to the X-ray beam, with an overall protein consumption per dataset comparable to that of cryocrystallography.
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Affiliation(s)
- Zhong Ren
- Department of Chemistry, The University of Illinois at Chicago, Chicago, IL 60607, USA
- Renz Research, Inc., Westmont, IL 60559, USA
- Corresponding authors: and
| | - Medine Ayhan
- Department of Chemistry, The University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Sepalika Bandara
- Department of Chemistry, The University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Kalinga Bowatte
- Department of Chemistry, The University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Indika Kumarapperuma
- Department of Chemistry, The University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Semini Gunawardana
- Department of Chemistry, The University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Heewhan Shin
- Department of Chemistry, The University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Cong Wang
- Department of Chemistry, The University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Xiaoli Zeng
- Department of Chemistry, The University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Xiaojing Yang
- Department of Chemistry, The University of Illinois at Chicago, Chicago, IL 60607, USA
- Department of Ophthalmology and Vision Sciences, The University of Illinois at Chicago, Chicago, IL 60607, USA
- Corresponding authors: and
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40
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A Graphene-Based Microfluidic Platform for Electrocrystallization and In Situ X-ray Diffraction. CRYSTALS 2018. [DOI: 10.3390/cryst8020076] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Here, we describe a novel microfluidic platform for use in electrocrystallization experiments. The device incorporates ultra-thin graphene-based films as electrodes and as X-ray transparent windows to enable in situ X-ray diffraction analysis. Furthermore, large-area graphene films serve as a gas barrier, creating a stable sample environment over time. We characterize different methods for fabricating graphene electrodes, and validate the electrical capabilities of our device through the use of methyl viologen, a redox-sensitive dye. Proof-of-concept electrocrystallization experiments using an internal electric field at constant potential were performed using hen egg-white lysozyme (HEWL) as a model system. We observed faster nucleation and crystal growth, as well as a higher signal-to-noise for diffraction data obtained from crystals prepared in the presence of an applied electric field. Although this work is focused on the electrocrystallization of proteins for structural biology, we anticipate that this technology should also find utility in a broad range of both X-ray technologies and other applications of microfluidic technology.
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Yamamoto M, Hirata K, Yamashita K, Hasegawa K, Ueno G, Ago H, Kumasaka T. Protein microcrystallography using synchrotron radiation. IUCRJ 2017; 4:529-539. [PMID: 28989710 PMCID: PMC5619846 DOI: 10.1107/s2052252517008193] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 06/02/2017] [Indexed: 05/21/2023]
Abstract
The progress in X-ray microbeam applications using synchrotron radiation is beneficial to structure determination from macromolecular microcrystals such as small in meso crystals. However, the high intensity of microbeams causes severe radiation damage, which worsens both the statistical quality of diffraction data and their resolution, and in the worst cases results in the failure of structure determination. Even in the event of successful structure determination, site-specific damage can lead to the misinterpretation of structural features. In order to overcome this issue, technological developments in sample handling and delivery, data-collection strategy and data processing have been made. For a few crystals with dimensions of the order of 10 µm, an elegant two-step scanning strategy works well. For smaller samples, the development of a novel method to analyze multiple isomorphous microcrystals was motivated by the success of serial femtosecond crystallography with X-ray free-electron lasers. This method overcame the radiation-dose limit in diffraction data collection by using a sufficient number of crystals. Here, important technologies and the future prospects for microcrystallography are discussed.
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Affiliation(s)
- Masaki Yamamoto
- Advanced Photon Technology Division, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Kunio Hirata
- Advanced Photon Technology Division, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Keitaro Yamashita
- Advanced Photon Technology Division, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Kazuya Hasegawa
- Advanced Photon Technology Division, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Protein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Go Ueno
- Advanced Photon Technology Division, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Hideo Ago
- Advanced Photon Technology Division, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Takashi Kumasaka
- Advanced Photon Technology Division, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Protein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
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42
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XFEL structures of the influenza M2 proton channel: Room temperature water networks and insights into proton conduction. Proc Natl Acad Sci U S A 2017; 114:13357-13362. [PMID: 28835537 DOI: 10.1073/pnas.1705624114] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The M2 proton channel of influenza A is a drug target that is essential for the reproduction of the flu virus. It is also a model system for the study of selective, unidirectional proton transport across a membrane. Ordered water molecules arranged in "wires" inside the channel pore have been proposed to play a role in both the conduction of protons to the four gating His37 residues and the stabilization of multiple positive charges within the channel. To visualize the solvent in the pore of the channel at room temperature while minimizing the effects of radiation damage, data were collected to a resolution of 1.4 Å using an X-ray free-electron laser (XFEL) at three different pH conditions: pH 5.5, pH 6.5, and pH 8.0. Data were collected on the Inwardopen state, which is an intermediate that accumulates at high protonation of the His37 tetrad. At pH 5.5, a continuous hydrogen-bonded network of water molecules spans the vertical length of the channel, consistent with a Grotthuss mechanism model for proton transport to the His37 tetrad. This ordered solvent at pH 5.5 could act to stabilize the positive charges that build up on the gating His37 tetrad during the proton conduction cycle. The number of ordered pore waters decreases at pH 6.5 and 8.0, where the Inwardopen state is less stable. These studies provide a graphical view of the response of water to a change in charge within a restricted channel environment.
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Roedig P, Ginn HM, Pakendorf T, Sutton G, Harlos K, Walter TS, Meyer J, Fischer P, Duman R, Vartiainen I, Reime B, Warmer M, Brewster AS, Young ID, Michels-Clark T, Sauter NK, Kotecha A, Kelly J, Rowlands DJ, Sikorsky M, Nelson S, Damiani DS, Alonso-Mori R, Ren J, Fry EE, David C, Stuart DI, Wagner A, Meents A. High-speed fixed-target serial virus crystallography. Nat Methods 2017; 14:805-810. [PMID: 28628129 PMCID: PMC5588887 DOI: 10.1038/nmeth.4335] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 05/15/2017] [Indexed: 12/19/2022]
Abstract
We report a method for serial X-ray crystallography at X-ray free-electron lasers (XFELs), which allows for full use of the current 120-Hz repetition rate of the Linear Coherent Light Source (LCLS). Using a micropatterned silicon chip in combination with the high-speed Roadrunner goniometer for sample delivery, we were able to determine the crystal structures of the picornavirus bovine enterovirus 2 (BEV2) and the cytoplasmic polyhedrosis virus type 18 polyhedrin, with total data collection times of less than 14 and 10 min, respectively. Our method requires only micrograms of sample and should therefore broaden the applicability of serial femtosecond crystallography to challenging projects for which only limited sample amounts are available. By synchronizing the sample exchange to the XFEL repetition rate, our method allows for most efficient use of the limited beam time available at XFELs and should enable a substantial increase in sample throughput at these facilities.
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Affiliation(s)
- Philip Roedig
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Helen M. Ginn
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Diamond Light Source Limited, Harwell Science & Innovation Campus, Didcot, United Kingdom
| | - Tim Pakendorf
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Geoff Sutton
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Karl Harlos
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Thomas S. Walter
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Jan Meyer
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Pontus Fischer
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Ramona Duman
- Diamond Light Source Limited, Harwell Science & Innovation Campus, Didcot, United Kingdom
| | - Ismo Vartiainen
- Institute of Photonics, University of Eastern Finland, Joensuu, Finland
| | - Bernd Reime
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Martin Warmer
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Aaron S. Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Iris D. Young
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Tara Michels-Clark
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Nicholas K. Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Abhay Kotecha
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - James Kelly
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
- The Pirbright Institute, Pirbright, United Kingdom
| | - David J. Rowlands
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Marcin Sikorsky
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Silke Nelson
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Daniel S. Damiani
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Roberto Alonso-Mori
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Jingshan Ren
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Elizabeth E. Fry
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | | | - David I. Stuart
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Diamond Light Source Limited, Harwell Science & Innovation Campus, Didcot, United Kingdom
| | - Armin Wagner
- Diamond Light Source Limited, Harwell Science & Innovation Campus, Didcot, United Kingdom
| | - Alke Meents
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
- Center for Free Electron Laser Science (CFEL), Hamburg, Germany
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44
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Johansson LC, Stauch B, Ishchenko A, Cherezov V. A Bright Future for Serial Femtosecond Crystallography with XFELs. Trends Biochem Sci 2017; 42:749-762. [PMID: 28733116 DOI: 10.1016/j.tibs.2017.06.007] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 06/12/2017] [Accepted: 06/20/2017] [Indexed: 11/19/2022]
Abstract
X-ray free electron lasers (XFELs) have the potential to revolutionize macromolecular structural biology due to the unique combination of spatial coherence, extreme peak brilliance, and short duration of X-ray pulses. A recently emerged serial femtosecond (fs) crystallography (SFX) approach using XFEL radiation overcomes some of the biggest hurdles of traditional crystallography related to radiation damage through the diffraction-before-destruction principle. Intense fs XFEL pulses enable high-resolution room-temperature structure determination of difficult-to-crystallize biological macromolecules, while simultaneously opening a new era of time-resolved structural studies. Here, we review the latest developments in instrumentation, sample delivery, data analysis, crystallization methods, and applications of SFX to important biological questions, and conclude with brief insights into the bright future of structural biology using XFELs.
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Affiliation(s)
- Linda C Johansson
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089-3303, USA
| | - Benjamin Stauch
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089-3303, USA
| | - Andrii Ishchenko
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089-3303, USA
| | - Vadim Cherezov
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089-3303, USA.
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45
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Crystal Growth of High-Quality Protein Crystals under the Presence of an Alternant Electric Field in Pulse-Wave Mode, and a Strong Magnetic Field with Radio Frequency Pulses Characterized by X-ray Diffraction. CRYSTALS 2017. [DOI: 10.3390/cryst7060179] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The first part of this research was devoted to investigating the effect of alternate current (AC) using four different types of wave modes (pulse-wave) at 2 Hz on the crystal growth of lysozyme in solution. The best results, in terms of size and crystal quality, were obtained when protein crystals were grown under the influence of electric fields in a very specific wave mode (“breathing” wave), giving the highest resolution up to 1.34 Å in X-ray diffraction analysis compared with controls and with those crystals grown in gel. In the second part, we evaluated the effect of a strong magnetic field of 16.5 Tesla combined with radiofrequency pulses of 0.43 μs on the crystal growth in gels of tetragonal hen egg white (HEW) lysozyme. The lysozyme crystals grown, both in solution applying breathing-wave and in gel under the influence of this strong magnetic field with pulses of radio frequencies, produced the larger-in-size crystals and the highest resolution structures. Data processing and refinement statistics are very good in terms of the resolution, mosaicity and Wilson B factor obtained for each crystal. Besides, electron density maps show well-defined and distinctly separated atoms at several selected tryptophan residues for the crystal grown using the “breathing wave pulses”.
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46
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Locating and Visualizing Crystals for X-Ray Diffraction Experiments. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2017; 1607:143-164. [PMID: 28573572 DOI: 10.1007/978-1-4939-7000-1_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Macromolecular crystallography has advanced from using macroscopic crystals, which might be >1 mm on a side, to crystals that are essentially invisible to the naked eye, or even under a standard laboratory microscope. As crystallography requires recognizing crystals when they are produced, and then placing them in an X-ray, electron, or neutron beam, this provides challenges, particularly in the case of advanced X-ray sources, where beams have very small cross sections and crystals may be vanishingly small. Methods for visualizing crystals are reviewed here, and examples of different types of cases are presented, including: standard crystals, crystals grown in mesophase, in situ crystallography, and crystals grown for X-ray Free Electron Laser or Micro Electron Diffraction experiments. As most techniques have limitations, it is desirable to have a range of complementary techniques available to identify and locate crystals. Ideally, a given technique should not cause sample damage, but sometimes it is necessary to use techniques where damage can only be minimized. For extreme circumstances, the act of probing location may be coincident with collecting X-ray diffraction data. Future challenges and directions are also discussed.
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47
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Opara N, Martiel I, Arnold SA, Braun T, Stahlberg H, Makita M, David C, Padeste C. Direct protein crystallization on ultrathin membranes for diffraction measurements at X-ray free-electron lasers. J Appl Crystallogr 2017. [DOI: 10.1107/s1600576717005799] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
A new era of protein crystallography started when X-ray free-electron lasers (XFELs) came into operation, as these provide an intense source of X-rays that facilitates data collection in the `diffract-before-destroy' regime. In typical experiments, crystals sequentially delivered to the beam are exposed to X-rays and destroyed. Therefore, the novel approach of serial crystallography requires thousands of nearly identical samples. Currently applied sample-delivery methods, in particular liquid jets or drop-on-demand systems, suffer from significant sample consumption of the precious crystalline material. Direct protein microcrystal growth by the vapour diffusion technique inside arrays of nanolitre-sized wells is a method specifically tailored to crystallography at XFELs. The wells, with X-ray transparent Si3N4windows as bottoms, are fabricated in silicon chips. Their reduced dimensions can significantly decrease protein specimen consumption. Arrays provide crystalline samples positioned in an ordered way without the need to handle fragile crystals. The nucleation process inside these microfabricated cavities was optimized to provide high membrane coverage and a quasi-random crystal distribution. Tight sealing of the chips and protection of the crystals from dehydration were achieved, as confirmed by diffraction experiments at a protein crystallography beamline. Finally, the test samples were shown to be suitable for time-resolved measurements at an XFEL at femtosecond resolution.
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48
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Fuller FD, Gul S, Chatterjee R, Burgie ES, Young ID, Lebrette H, Srinivas V, Brewster AS, Michels-Clark T, Clinger JA, Andi B, Ibrahim M, Pastor E, de Lichtenberg C, Hussein R, Pollock CJ, Zhang M, Stan CA, Kroll T, Fransson T, Weninger C, Kubin M, Aller P, Lassalle L, Bräuer P, Miller MD, Amin M, Koroidov S, Roessler CG, Allaire M, Sierra RG, Docker PT, Glownia JM, Nelson S, Koglin JE, Zhu D, Chollet M, Song S, Lemke H, Liang M, Sokaras D, Alonso-Mori R, Zouni A, Messinger J, Bergmann U, Boal AK, Bollinger JM, Krebs C, Högbom M, Phillips GN, Vierstra RD, Sauter NK, Orville AM, Kern J, Yachandra VK, Yano J. Drop-on-demand sample delivery for studying biocatalysts in action at X-ray free-electron lasers. Nat Methods 2017; 14:443-449. [PMID: 28250468 PMCID: PMC5376230 DOI: 10.1038/nmeth.4195] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 01/18/2017] [Indexed: 12/22/2022]
Abstract
X-ray crystallography at X-ray free-electron laser sources is a powerful method for studying macromolecules at biologically relevant temperatures. Moreover, when combined with complementary techniques like X-ray emission spectroscopy, both global structures and chemical properties of metalloenzymes can be obtained concurrently, providing insights into the interplay between the protein structure and dynamics and the chemistry at an active site. The implementation of such a multimodal approach can be compromised by conflicting requirements to optimize each individual method. In particular, the method used for sample delivery greatly affects the data quality. We present here a robust way of delivering controlled sample amounts on demand using acoustic droplet ejection coupled with a conveyor belt drive that is optimized for crystallography and spectroscopy measurements of photochemical and chemical reactions over a wide range of time scales. Studies with photosystem II, the phytochrome photoreceptor, and ribonucleotide reductase R2 illustrate the power and versatility of this method.
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Affiliation(s)
- Franklin D. Fuller
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Sheraz Gul
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ernest S. Burgie
- Department of Biology, Washington University in St. Louis, St.
Louis, Missouri 63130, USA
| | - Iris D. Young
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Hugo Lebrette
- Department of Biochemistry and Biophysics, Stockholm University,
SE-106 91 Stockholm, Sweden
| | - Vivek Srinivas
- Department of Biochemistry and Biophysics, Stockholm University,
SE-106 91 Stockholm, Sweden
| | - Aaron S. Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Tara Michels-Clark
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - Babak Andi
- National Synchrotron Light Source II, Brookhaven National
Laboratory, Upton, NY, 11973, USA
| | - Mohamed Ibrahim
- Institut für Biologie, Humboldt-Universität zu
Berlin, D-10099 Berlin, Germany
| | - Ernest Pastor
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Casper de Lichtenberg
- Institutionen för Kemi, Kemiskt Biologiskt Centrum,
Umeå Universitet, SE 90187 Umeå, Sweden
| | - Rana Hussein
- Institut für Biologie, Humboldt-Universität zu
Berlin, D-10099 Berlin, Germany
| | - Christopher J. Pollock
- Department of Chemistry, The Pennsylvania State University,
University Park, PA 16802, USA
| | - Miao Zhang
- Institut für Biologie, Humboldt-Universität zu
Berlin, D-10099 Berlin, Germany
| | - Claudiu A. Stan
- Stanford PULSE Institute, SLAC National Accelerator Laboratory,
Menlo Park, CA 94025, USA
| | - Thomas Kroll
- SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025,
USA
| | - Thomas Fransson
- Stanford PULSE Institute, SLAC National Accelerator Laboratory,
Menlo Park, CA 94025, USA
| | - Clemens Weninger
- Stanford PULSE Institute, SLAC National Accelerator Laboratory,
Menlo Park, CA 94025, USA
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025,
USA
| | - Markus Kubin
- Institute for Methods and Instrumentation on Synchrotron Radiation
Research, Helmholtz Zentrum Berlin für Materialien und Energie GmbH, 12489
Berlin, Germany
| | - Pierre Aller
- Diamond Light Source Ltd, Harwell Science and Innovation Campus,
Didcot, OX110DE, UK
| | - Louise Lassalle
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Philipp Bräuer
- Diamond Light Source Ltd, Harwell Science and Innovation Campus,
Didcot, OX110DE, UK
- Department of Biochemistry, University of Oxford, South Parks Road,
Oxford OX1 3QU, UK
| | | | - Muhamed Amin
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Sergey Koroidov
- Institutionen för Kemi, Kemiskt Biologiskt Centrum,
Umeå Universitet, SE 90187 Umeå, Sweden
- Stanford PULSE Institute, SLAC National Accelerator Laboratory,
Menlo Park, CA 94025, USA
| | - Christian G. Roessler
- National Synchrotron Light Source II, Brookhaven National
Laboratory, Upton, NY, 11973, USA
| | - Marc Allaire
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Raymond G. Sierra
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025,
USA
| | - Peter T. Docker
- Diamond Light Source Ltd, Harwell Science and Innovation Campus,
Didcot, OX110DE, UK
| | - James M. Glownia
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025,
USA
| | - Silke Nelson
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025,
USA
| | - Jason E. Koglin
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025,
USA
| | - Diling Zhu
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025,
USA
| | - Matthieu Chollet
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025,
USA
| | - Sanghoon Song
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025,
USA
| | - Henrik Lemke
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025,
USA
| | - Mengning Liang
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025,
USA
| | | | | | - Athina Zouni
- Institut für Biologie, Humboldt-Universität zu
Berlin, D-10099 Berlin, Germany
| | - Johannes Messinger
- Institutionen för Kemi, Kemiskt Biologiskt Centrum,
Umeå Universitet, SE 90187 Umeå, Sweden
- Department of Chemistry – Ångström,
Molecular Biomimetics, Uppsala University, SE 75120 Uppsala, Sweden
| | - Uwe Bergmann
- Stanford PULSE Institute, SLAC National Accelerator Laboratory,
Menlo Park, CA 94025, USA
| | - Amie K. Boal
- Department of Chemistry, The Pennsylvania State University,
University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania
State University, University Park, PA 16802, USA
| | - J. Martin Bollinger
- Department of Chemistry, The Pennsylvania State University,
University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania
State University, University Park, PA 16802, USA
| | - Carsten Krebs
- Department of Chemistry, The Pennsylvania State University,
University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania
State University, University Park, PA 16802, USA
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University,
SE-106 91 Stockholm, Sweden
- Department of Chemistry, Stanford University, Stanford, CA 94305,
USA
| | - George N. Phillips
- Department of BioSciences, Rice Univ. Houston, TX 77005, USA
- Department of Chemistry, Rice Univ. Houston, TX 77005, USA
| | - Richard D. Vierstra
- Department of Biology, Washington University in St. Louis, St.
Louis, Missouri 63130, USA
| | - Nicholas K. Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Allen M. Orville
- Diamond Light Source Ltd, Harwell Science and Innovation Campus,
Didcot, OX110DE, UK
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025,
USA
| | - Vittal K. Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
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49
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Abstract
This chapter provides a review of different advanced methods that help to increase the success rate of a crystallization project, by producing larger and higher quality single crystals for determination of macromolecular structures by crystallographic methods. For this purpose, the chapter is divided into three parts. The first part deals with the fundamentals for understanding the crystallization process through different strategies based on physical and chemical approaches. The second part presents new approaches involved in more sophisticated methods not only for growing protein crystals but also for controlling the size and orientation of crystals through utilization of electromagnetic fields and other advanced techniques. The last section deals with three different aspects: the importance of microgravity, the use of ligands to stabilize proteins, and the use of microfluidics to obtain protein crystals. All these advanced methods will allow the readers to obtain suitable crystalline samples for high-resolution X-ray and neutron crystallography.
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Affiliation(s)
- Abel Moreno
- Instituto de Química, Universidad Nacional Autónoma de Mexico, Av. Universidad 3000, Cd.Mx., Mexico City, 04510, Mexico.
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50
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Abstract
Prompted by methodological advances in measurements with X-ray free electron lasers, it was realized in the last two years that traditional (or conventional) methods for data collection from crystals of macromolecular specimens can be complemented by synchrotron measurements on microcrystals that would individually not suffice for a complete data set. Measuring, processing, and merging many partial data sets of this kind requires new techniques which have since been implemented at several third-generation synchrotron facilities, and are described here. Among these, we particularly focus on the possibility of in situ measurements combined with in meso crystal preparations and data analysis with the XDS package and auxiliary programs.
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Affiliation(s)
- Kay Diederichs
- Department of Biology, Universität Konstanz, Box 647, D-78457, Konstanz, Germany.
| | - Meitian Wang
- Swiss Light Source, Paul Scherrer Institute, CH-5232, Villigen, Switzerland
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