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Botha S, Fromme P. Review of serial femtosecond crystallography including the COVID-19 pandemic impact and future outlook. Structure 2023; 31:1306-1319. [PMID: 37898125 PMCID: PMC10842180 DOI: 10.1016/j.str.2023.10.005] [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: 07/18/2023] [Revised: 09/28/2023] [Accepted: 10/04/2023] [Indexed: 10/30/2023]
Abstract
Serial femtosecond crystallography (SFX) revolutionized macromolecular crystallography over the past decade by enabling the collection of X-ray diffraction data from nano- or micrometer sized crystals while outrunning structure-altering radiation damage effects at room temperature. The serial manner of data collection from millions of individual crystals coupled with the femtosecond duration of the ultrabright X-ray pulses enables time-resolved studies of macromolecules under near-physiological conditions to unprecedented temporal resolution. In 2020 the rapid spread of the coronavirus SARS-CoV-2 resulted in a global pandemic of coronavirus disease-2019. This led to a shift in how serial femtosecond experiments were performed, along with rapid funding and free electron laser beamtime availability dedicated to SARS-CoV-2-related studies. This review outlines the current state of SFX research, the milestones that were achieved, the impact of the global pandemic on this field as well as an outlook into exciting future directions.
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Affiliation(s)
- Sabine Botha
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; Department of Physics, Arizona State University, Tempe, AZ 85287-1504, USA.
| | - Petra Fromme
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA.
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2
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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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3
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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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4
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Yan X, Nie X, Tan Z, Liu P, Li X, Wang P, Shi H. A methanogenic protein facilitates the biosynthesis of the silver nanoparticles. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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5
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Martin-Garcia JM, Botha S, Hu H, Jernigan R, Castellví A, Lisova S, Gil F, Calisto B, Crespo I, Roy-Chowdhury S, Grieco A, Ketawala G, Weierstall U, Spence J, Fromme P, Zatsepin N, Boer DR, Carpena X. Serial macromolecular crystallography at ALBA Synchrotron Light Source. JOURNAL OF SYNCHROTRON RADIATION 2022; 29:896-907. [PMID: 35511023 PMCID: PMC9070724 DOI: 10.1107/s1600577522002508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 03/03/2022] [Indexed: 06/14/2023]
Abstract
The increase in successful adaptations of serial crystallography at synchrotron radiation sources continues. To date, the number of serial synchrotron crystallography (SSX) experiments has grown exponentially, with over 40 experiments reported so far. In this work, we report the first SSX experiments with viscous jets conducted at ALBA beamline BL13-XALOC. Small crystals (15-30 µm) of five soluble proteins (lysozyme, proteinase K, phycocyanin, insulin and α-spectrin-SH3 domain) were suspended in lipidic cubic phase (LCP) and delivered to the X-ray beam with a high-viscosity injector developed at Arizona State University. Complete data sets were collected from all proteins and their high-resolution structures determined. The high quality of the diffraction data collected from all five samples, and the lack of specific radiation damage in the structures obtained in this study, confirm that the current capabilities at the beamline enables atomic resolution determination of protein structures from microcrystals as small as 15 µm using viscous jets at room temperature. Thus, BL13-XALOC can provide a feasible alternative to X-ray free-electron lasers when determining snapshots of macromolecular structures.
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Affiliation(s)
- Jose M. Martin-Garcia
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Rocasolano, Spanish National Research Council (CSIC), Madrid, Spain
| | - Sabine Botha
- Department of Physics, Arizona State University, Tempe, AZ, USA
| | - Hao Hu
- Department of Physics, Arizona State University, Tempe, AZ, USA
| | - Rebecca Jernigan
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Albert Castellví
- Molecular Biology Institute of Barcelona, CSIC, Barcelona, Spain
| | - Stella Lisova
- Department of Physics, Arizona State University, Tempe, AZ, USA
| | - Fernando Gil
- ALBA Synchrotron, Cerdanyola del Vallès, Barcelona, Spain
| | | | - Isidro Crespo
- ALBA Synchrotron, Cerdanyola del Vallès, Barcelona, Spain
| | - Shatabdi Roy-Chowdhury
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Alice Grieco
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Rocasolano, Spanish National Research Council (CSIC), Madrid, Spain
| | - Gihan Ketawala
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Uwe Weierstall
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA
- Department of Physics, Arizona State University, Tempe, AZ, USA
| | - John Spence
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA
- Department of Physics, Arizona State University, Tempe, AZ, USA
| | - Petra Fromme
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Nadia Zatsepin
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA
- Department of Physics, Arizona State University, Tempe, AZ, USA
- ARC Centre of Excellence in Advance Molecular Physics, La Trobe Institute for Molecular ScienceImaging, Department of Chemistry and Physics, La Trobe University, Melbourne, Australia
| | | | - Xavi Carpena
- ALBA Synchrotron, Cerdanyola del Vallès, Barcelona, Spain
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6
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Nam KH. Hit and Indexing Rate in Serial Crystallography: Incomparable Statistics. Front Mol Biosci 2022; 9:858815. [PMID: 35402509 PMCID: PMC8990040 DOI: 10.3389/fmolb.2022.858815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 01/31/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Ki Hyun Nam
- Department of Life Science, Pohang University of Science and Technology, Pohang, South Korea
- POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, South Korea
- *Correspondence: Ki Hyun Nam,
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7
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Brenker J, Henzler K, Borca CN, Huthwelker T, Alan T. X-ray compatible microfluidics for in situ studies of chemical state, transport and reaction of light elements in an aqueous environment using synchrotron radiation. LAB ON A CHIP 2022; 22:1214-1230. [PMID: 35170605 DOI: 10.1039/d1lc00996f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
This paper presents an X-ray compatible microfluidic platform for in situ characterization of chemical reactions at synchrotron light sources. We demonstrate easy to implement techniques to probe reacting solutions as they first come into contact, and study the very first milliseconds of their reaction in real-time through X-ray absorption spectroscopy (XAS). The devices use polydimethylsiloxane (PDMS) microfluidic channels sandwiched between ultrathin, X-ray transparent silicon nitride observation windows and rigid substrates. The new approach has three key advantages: i) owing to the assembly techniques employed, the devices are suitable for both high energy and tender (1-5 keV) X-rays; ii) they can operate in a vacuum environment (a must for low energy X-rays) and iii) they are robust enough to survive a full 8 hour shift of continuous scanning with a micro-focused beam, providing higher spatial and thus greater time resolution than previous studies. The combination of these opens new opportunities for in situ studies. This has so far not been possible with Kapton or glass-based flow cells due to increased attenuation of the low energy beam passing through these materials. The devices provide a well-defined mixing region to collect spatial maps of spatially stable concentration profiles, and XAS point spectra to elucidate the chemical structure and characterize the chemical reactions. The versatility of the approach is demonstrated through in situ XAS measurements on the mixing of two reactants in a microfluidic laminar flow device, as well as a segmented droplet based system for time resolved analysis.
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Affiliation(s)
- Jason Brenker
- Department of Mechanical and Aerospace Engineering, Monash University, Clayton, Australia.
| | - Katja Henzler
- Paul Scherrer Institute, Swiss Light Source, Villigen, Switzerland.
| | - Camelia N Borca
- Paul Scherrer Institute, Swiss Light Source, Villigen, Switzerland.
| | | | - Tuncay Alan
- Department of Mechanical and Aerospace Engineering, Monash University, Clayton, Australia.
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8
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Nam KH. Beef tallow injection matrix for serial crystallography. Sci Rep 2022; 12:694. [PMID: 35027663 PMCID: PMC8758675 DOI: 10.1038/s41598-021-04714-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 12/29/2021] [Indexed: 12/22/2022] Open
Abstract
Serial crystallography (SX) enables the visualization of the time-resolved molecular dynamics of macromolecular structures at room temperature while minimizing radiation damage. In SX experiments, the delivery of a large number of crystals into an X-ray interaction point in a serial and stable manner is key. Sample delivery using viscous medium maintains the stable injection stream at low flow rates, markedly reducing sample consumption compared with that of a liquid jet injector and is widely applied in SX experiments with low repetition rates. As the sample properties and experimental environment can affect the stability of the injection stream of a viscous medium, it is important to develop sample delivery media with various characteristics to optimize the experimental environment. In this study, a beef tallow injection matrix possessing a higher melting temperature than previously reported fat-based shortening and lard media was introduced as a sample delivery medium and applied to SX. Beef tallow was prepared by heat treating fats from cattle, followed by the removal of soluble impurities from the extract by phase separation. Beef tallow exhibited a very stable injection stream at room temperature and a flow rate of < 10 nL/min. The room-temperature structures of lysozyme and glucose isomerase embedded in beef tallow were successfully determined at 1.55 and 1.60 Å, respectively. The background scattering of beef tallow was higher than that of previously reported fat-based shortening and lard media but negligible for data processing. In conclusion, the beef tallow matrix can be employed for sample delivery in SX experiments conducted at temperatures exceeding room temperature.
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Affiliation(s)
- Ki Hyun Nam
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Korea. .,POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Korea.
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9
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Abstract
Serial crystallography (SX) is an emerging technique to determine macromolecules at room temperature. SX with a pump–probe experiment provides the time-resolved dynamics of target molecules. SX has developed rapidly over the past decade as a technique that not only provides room-temperature structures with biomolecules, but also has the ability to time-resolve their molecular dynamics. The serial femtosecond crystallography (SFX) technique using an X-ray free electron laser (XFEL) has now been extended to serial synchrotron crystallography (SSX) using synchrotron X-rays. The development of a variety of sample delivery techniques and data processing programs is currently accelerating SX research, thereby increasing the research scope. In this editorial, I briefly review some of the experimental techniques that have contributed to advances in the field of SX research and recent major research achievements. This Special Issue will contribute to the field of SX research.
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10
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Schulz EC, Yorke BA, Pearson AR, Mehrabi P. Best practices for time-resolved serial synchrotron crystallography. Acta Crystallogr D Struct Biol 2022; 78:14-29. [PMID: 34981758 PMCID: PMC8725164 DOI: 10.1107/s2059798321011621] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 11/03/2021] [Indexed: 11/10/2022] Open
Abstract
With recent developments in X-ray sources, instrumentation and data-analysis tools, time-resolved crystallographic experiments, which were originally the preserve of a few expert groups, are becoming simpler and can be carried out at more radiation sources, and are thus increasingly accessible to a growing user base. However, these experiments are just that: discrete experiments, not just `data collections'. As such, careful planning and consideration of potential pitfalls is required to enable a successful experiment. Here, some of the key factors that should be considered during the planning and execution of a time-resolved structural study are outlined, with a particular focus on synchrotron-based experiments.
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Affiliation(s)
- Eike C. Schulz
- Institute for Nanostructure and Solid State Physics, Universität Hamburg, HARBOR, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Briony A. Yorke
- School of Chemistry and Bioscience, University of Bradford, Bradford BD7 1DP, United Kingdom
| | - Arwen R. Pearson
- Institute for Nanostructure and Solid State Physics, Universität Hamburg, HARBOR, Luruper Chaussee 149, 22761 Hamburg, Germany
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, HARBOR, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Pedram Mehrabi
- Institute for Nanostructure and Solid State Physics, Universität Hamburg, HARBOR, Luruper Chaussee 149, 22761 Hamburg, 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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Komorek P, Jachimska B, Brand I. Adsorption of lysozyme on gold surfaces in the presence of an external electric potential. Bioelectrochemistry 2021; 142:107946. [PMID: 34507162 DOI: 10.1016/j.bioelechem.2021.107946] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/30/2021] [Accepted: 08/29/2021] [Indexed: 10/20/2022]
Abstract
Adsorbed protein films consist of essential building blocks of many biotechnological and biomedical devices. The electrostatic potential may significantly modulate the protein behaviour on surfaces, affecting their structure and biological activity. In this study, lysozyme was used to investigate the effects of applied electric potentials on adsorption and the protein structure. The pH and the surface charge determine the amount and secondary structure of adsorbed lysozyme on a gold surface. In-situ measurements using polarization modulation infrared reflection absorption spectroscopy indicated that the concentration of both the adsorbed anions and the lysozyme led to conformational changes in the protein film, which was demonstrated by a greater amount of aggregated β-sheets in films fabricated at net positive charges of the Au electrode (Eads > Epzc). The changes in secondary structure involved two parallel processes. One comprised changes in the hydration/hydrogen-bond network at helices, leading to diverse helical structures: α-, 310- and/or π-helices. In the second process β-turns, β-sheets, and random coils displayed an ability to form aggregated β-sheet structures. The study illuminates the understanding of electrical potential-dependent changes involved in the protein misfolding process.
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Affiliation(s)
- Paulina Komorek
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Niezapominajek 8, 30-239 Cracow, Poland
| | - Barbara Jachimska
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Niezapominajek 8, 30-239 Cracow, Poland.
| | - Izabella Brand
- Department of Chemistry, University of Oldenburg, 26111 Oldenburg, Germany.
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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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14
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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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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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Polyimide mesh-based sample holder with irregular crystal mounting holes for fixed-target serial crystallography. Sci Rep 2021; 11:13115. [PMID: 34162965 PMCID: PMC8222285 DOI: 10.1038/s41598-021-92687-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 06/11/2021] [Indexed: 01/07/2023] Open
Abstract
The serial crystallography (SX) technique enables the determination of the room-temperature structure of a macromolecule while causing minimal radiation damage, as well as the visualization of the molecular dynamics by time-resolved studies. The fixed-target (FT) scanning approach is one method for SX sample delivery that minimizes sample consumption and minimizes physical damage to crystals during data collection. Settling of the crystals on the sample holder in random orientation is important for complete three dimensional data collection. To increase the random orientation of crystals on the sample holder, we developed a polyimide mesh-based sample holder with irregular crystal mounting holes for FT-SX. The polyimide mesh was fabricated using a picosecond laser. Each hole in the polyimide mesh has irregularly shaped holes because of laser thermal damage, which may cause more crystals to settle at random orientations compared to regular shaped sample holders. A crystal sample was spread onto a polyimide-mesh, and a polyimide film was added to both sides to prevent dehydration. Using this sample holder, FT-SX was performed at synchrotron and determined the room-temperature lysozyme structure at 1.65 Å. The polyimide mesh with irregularly shaped holes will allow for expanded applications in sample delivery for FT-SX experiments.
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17
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Norton-Baker B, Mehrabi P, Boger J, Schönherr R, von Stetten D, Schikora H, Kwok AO, Martin RW, Miller RJD, Redecke L, Schulz EC. A simple vapor-diffusion method enables protein crystallization inside the HARE serial crystallography chip. Acta Crystallogr D Struct Biol 2021; 77:820-834. [PMID: 34076595 PMCID: PMC8171066 DOI: 10.1107/s2059798321003855] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 04/10/2021] [Indexed: 11/12/2022] Open
Abstract
Fixed-target serial crystallography has become an important method for the study of protein structure and dynamics at synchrotrons and X-ray free-electron lasers. However, sample homogeneity, consumption and the physical stress on samples remain major challenges for these high-throughput experiments, which depend on high-quality protein microcrystals. The batch crystallization procedures that are typically applied require time- and sample-intensive screening and optimization. Here, a simple protein crystallization method inside the features of the HARE serial crystallography chips is reported that circumvents batch crystallization and allows the direct transfer of canonical vapor-diffusion conditions to in-chip crystallization. Based on conventional hanging-drop vapor-diffusion experiments, the crystallization solution is distributed into the wells of the HARE chip and equilibrated against a reservoir with mother liquor. Using this simple method, high-quality microcrystals were generated with sufficient density for the structure determination of four different proteins. A new protein variant was crystallized using the protein concentrations encountered during canonical crystallization experiments, enabling structure determination from ∼55 µg of protein. Additionally, structure determination from intracellular crystals grown in insect cells cultured directly in the features of the HARE chips is demonstrated. In cellulo crystallization represents a comparatively unexplored space in crystallization, especially for proteins that are resistant to crystallization using conventional techniques, and eliminates any need for laborious protein purification. This in-chip technique avoids harvesting the sensitive crystals or any further physical handling of the crystal-containing cells. These proof-of-principle experiments indicate the potential of this method to become a simple alternative to batch crystallization approaches and also as a convenient extension to canonical crystallization screens.
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Affiliation(s)
- Brenna Norton-Baker
- Department for Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Chemistry, University of California, Irvine, CA 92697-2025, USA
| | - Pedram Mehrabi
- Department for Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, HARBOR, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Juliane Boger
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Robert Schönherr
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
- Photon Science, Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - David von Stetten
- European Molecular Biology Laboratory, Hamburg Unit c/o Deutsches Elektronen-Synchrotron, 22607 Hamburg, Germany
| | - Hendrik Schikora
- Scientific Support Unit Machine Physics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Ashley O. Kwok
- Department of Chemistry, University of California, Irvine, CA 92697-2025, USA
| | - Rachel W. Martin
- Department of Chemistry, University of California, Irvine, CA 92697-2025, USA
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, USA
| | - R. J. Dwayne Miller
- Department of Physics, Universität Hamburg, Jungiusstrasse 9, 20355 Hamburg, Germany
- Departments of Chemistry and Physics, University of Toronto, 80 St George Street, Toronto, ON M5S 3H6, Canada
| | - Lars Redecke
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
- Photon Science, Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Eike C. Schulz
- Department for Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, HARBOR, Luruper Chaussee 149, 22761 Hamburg, Germany
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18
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Protein Dynamics and Time Resolved Protein Crystallography at Synchrotron Radiation Sources: Past, Present and Future. CRYSTALS 2021. [DOI: 10.3390/cryst11050521] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The ultrabright and ultrashort pulses produced at X-ray free electron lasers (XFELs) has enabled studies of crystallized molecular machines at work under ‘native’ conditions at room temperature by the so-called time-resolved serial femtosecond crystallography (TR-SFX) technique. Since early TR-SFX experiments were conducted at XFELs, it has been largely reported in the literature that time-resolved X-ray experiments at synchrotrons are no longer feasible or are impractical due to the severe technical limitations of these radiation sources. The transfer of the serial crystallography approach to newest synchrotrons upgraded for higher flux density and with beamlines using sophisticated focusing optics, submicron beam diameters and fast low-noise photon-counting detectors offers a way to overcome these difficulties opening new and exciting possibilities. In fact, there is an increasing amount of publications reporting new findings in structural dynamics of protein macromolecules by using time resolved crystallography from microcrystals at synchrotron sources. This review gathers information to provide an overview of the recent work and the advances made in this filed in the past years, as well as outlines future perspectives at the next generation of synchrotron sources and the upcoming compact pulsed X-ray sources.
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19
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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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20
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Zhao FZ, Sun B, Yu L, Xiao QJ, Wang ZJ, Chen LL, Liang H, Wang QS, He JH, Yin DC. A novel sample delivery system based on circular motion for in situ serial synchrotron crystallography. LAB ON A CHIP 2020; 20:3888-3898. [PMID: 32966481 DOI: 10.1039/d0lc00443j] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
A sample delivery system is one of the key parts of serial crystallography. It is the main limiting factor affecting the application of serial crystallography. At present, although a variety of useful sample delivery systems have been developed for serial crystallography, it still remains the focus of the field to further improve the performance and efficiency of sample delivery. In existing sample delivery technologies, samples are usually delivered in linear motion. Here we show that the samples can also be delivered using circular motion, which is a novel motion mode never tested before. In this paper, we report a microfluidic rotating-target sample delivery device, which is characterized by the circular motion of the samples, and verify the performance of the device at a synchrotron radiation facility. The microfluidic rotating-target sample delivery device consists of two parts: a microfluidic sample plate and a motion control system. Sample delivery is realized by rotating the microfluidic sample plate containing in situ grown crystals. This device offers significant advantages, including a very wide adjustable range of delivery speed, low background noise, and low sample consumption. Using the microfluidic rotating-target device, we carried out in situ serial crystallography experiments with lysozyme and proteinase K as model samples at the Shanghai Synchrotron Radiation Facility, and performed structural determination based on the serial crystallographic data. The results showed that the designed device is fully compatible with the synchrotron radiation facility, and the structure determination of proteins is successful using the serial crystallographic data obtained with the device.
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Affiliation(s)
- Feng-Zhu Zhao
- School of Life Sciences, Northwestern Polytechnical University, Xi'an, China.
| | - Bo Sun
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China
| | - Li Yu
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China.
| | - Qing-Jie Xiao
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China. and State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Zhi-Jun Wang
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China
| | - Liang-Liang Chen
- School of Life Sciences, Northwestern Polytechnical University, Xi'an, China.
| | - Huan Liang
- School of Life Sciences, Northwestern Polytechnical University, Xi'an, China.
| | - Qi-Sheng Wang
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China
| | - Jian-Hua He
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China. and The Institute for Advanced Studies, Wuhan University, Wuhan, China
| | - Da-Chuan Yin
- School of Life Sciences, Northwestern Polytechnical University, Xi'an, China. and Shenzhen Research Institute, Northwestern Polytechnical University, Shenzhen, China
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21
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Fixed-Target Serial Synchrotron Crystallography Using Nylon Mesh and Enclosed Film-Based Sample Holder. CRYSTALS 2020. [DOI: 10.3390/cryst10090803] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Serial crystallography (SX) technique using synchrotron X-ray allows the visualization of room-temperature crystal structures with low-dose data collection as well as time-resolved molecular dynamics. In an SX experiment, delivery of numerous crystals for X-ray interaction, in a serial manner, is very important. Fixed-target scanning approach has the advantage of dramatically minimizing sample consumption as well as any physical damage to crystal sample, compared to other sample delivery methods. Here, we introduce the simple approach of fixed-target serial synchrotron crystallography (FT-SSX) using nylon mesh and enclosed film (NAM)-based sample holder. The NAM-based sample holder consisted of X-ray-transparent nylon-mesh and polyimide film, attached to a magnetic base. This sample holder was mounted to a goniometer head on macromolecular crystallography beamline, and translated along vertical and horizontal directions for raster scanning by the goniometer. Diffraction data were collected in two raster scanning approaches: (i) 100 ms X-ray exposure and 0.011° oscillation at each scan point and (ii) 500 ms X-ray exposure and 0.222° oscillation at each scan point. Using this approach, we determined the room-temperature crystal structures of lysozyme and glucose isomerase at 1.5–2.0 Å resolution. The sample holder produced negligible X-ray background scattering for data processing. Therefore, the new approach provided an opportunity to perform FT-SSX with high accessibility using macromolecular crystallography beamlines at synchrotron without any special equipment.
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22
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Lange T, Charton S, Bizien T, Testard F, Malloggi F. OSTE+ for in situ SAXS analysis with droplet microfluidic devices. LAB ON A CHIP 2020; 20:2990-3000. [PMID: 32696785 DOI: 10.1039/d0lc00454e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
In recent years, microfluidic-based sample preparation techniques have emerged as a powerful tool for measurements at large scale X-ray facilities. Most often the microfluidic device was a form of hybrid system, i.e. an assembly of different materials, because a simple, versatile and inexpensive microfabrication method, on the one hand, and X-ray compatibility, on the other hand, cannot generally be achieved by the same material. The arrival of a new polymer family based on off-stoichiometric thiol-ene-epoxy (OSTE+) has recently redistributed the cards. In this context, we studied the relevance and the compatibility of OSTE+ for small-angle X-ray scattering (SAXS) studies. The material was characterized regarding its X-ray properties (transmission coefficient, attenuation coefficient, scattering pattern and polymer aging under X-ray light) and their comparison with those of the usual polymers used in microfluidics and/or for synchrotron radiation experiments. We show that OSTE+ has a better SAXS signal than polyimide, the polymer of reference in the SAXS community. Then a detailed protocol to manufacture a suitably thin full OSTE+ chip (total thickness <500 μm) is described and the potency of full OSTE+ devices for in situ SAXS studies is highlighted in two case-studies: the characterization of gold nanoparticles and the precipitation of cerium oxalate particles, both in moving droplets. Additionally, a method to analyze the scattering signals from droplet and carrier phase in a segmented flow is proposed.
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Affiliation(s)
- Tobias Lange
- Université Paris-Saclay, CEA, CNRS, NIMBE, 91191 Gif-sur-Yvette Cedex, France.
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23
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Lee K, Lee D, Baek S, Park J, Lee SJ, Park S, Chung WK, Lee JL, Cho HS, Cho Y, Nam KH. Viscous-medium-based crystal support in a sample holder for fixed-target serial femtosecond crystallography. J Appl Crystallogr 2020. [DOI: 10.1107/s1600576720008663] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Serial femtosecond crystallography (SFX) enables the determination of the room-temperature crystal structure of macromolecules, as well as providing time-resolved molecular dynamics data in pump–probe experiments. Fixed-target SFX (FT-SFX) can minimize sample consumption and physical effects on crystals during sample delivery. In FT-SFX studies, having a sample holder that can stably fix crystal samples is one of the key elements required for efficient data collection. Hence, development of sample holders from new materials capable of supporting various crystal sizes and shapes may expand the applications of FT-SFX. Here, a viscous-media-based crystal support in a sample holder for FT-SFX is introduced. Crystal samples were embedded in viscous media, namely gelatin and agarose, which were enclosed in a polyimide film. In the vertically placed sample holder, 10–15%(w/v) viscous gelatin and 1–4%(w/v) agarose gel stably supported crystals between two polyimide films, thereby preventing the crystals from descending owing to gravity. Using this method, FT-SFX experiments were performed with glucose isomerase and lysozyme embedded in gelatin and agarose, respectively. The room-temperature crystal structures of glucose isomerase and lysozyme were successfully determined at 1.75 and 1.80 Å resolutions, respectively. The glucose isomerase and lysozyme diffraction analyses were not impeded by excessive background scattering from the viscous media. This method is useful for delivering crystal samples of various sizes and shapes in FT-SFX experiments.
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24
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Huang CY, Meier N, Caffrey M, Wang M, Olieric V. 3D-printed holders for in meso in situ fixed-target serial X-ray crystallography. J Appl Crystallogr 2020; 53:854-859. [PMID: 32684901 PMCID: PMC7312129 DOI: 10.1107/s1600576720002897] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 03/01/2020] [Indexed: 11/10/2022] Open
Abstract
The in meso in situ serial X-ray crystallography method was developed to ease the handling of small fragile crystals of membrane proteins and for rapid data collection on hundreds of microcrystals directly in the growth medium without the need for crystal harvesting. To facilitate mounting of these in situ samples on a goniometer at cryogenic or at room temperatures, two new 3D-printed holders have been developed. They provide for cubic and sponge phase sample stability in the X-ray beam and are compatible with sample-changing robots. The holders can accommodate a variety of window material types, as well as bespoke samples for diffraction screening and data collection at conventional macromolecular crystallography beamlines. They can be used for convenient post-crystallization treatments such as ligand and heavy-atom soaking. The design, assembly and application of the holders for in situ serial crystallography are described. Files for making the holders using a 3D printer are included as supporting information.
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Affiliation(s)
- Chia-Ying Huang
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen-PSI, 5232, Switzerland
| | - Nathalie Meier
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen-PSI, 5232, Switzerland
| | - Martin Caffrey
- Membrane Structural and Functional Biology Group, Trinity Biomedical Sciences Institute, Trinity College, Dublin 2, D02 R590, Ireland
| | - Meitian Wang
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen-PSI, 5232, Switzerland
| | - Vincent Olieric
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen-PSI, 5232, Switzerland
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25
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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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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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Beale JH, Bolton R, Marshall SA, Beale EV, Carr SB, Ebrahim A, Moreno-Chicano T, Hough MA, Worrall JAR, Tews I, Owen RL. Successful sample preparation for serial crystallography experiments. J Appl Crystallogr 2019; 52:1385-1396. [PMID: 31798361 PMCID: PMC6878878 DOI: 10.1107/s1600576719013517] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 10/02/2019] [Indexed: 11/10/2022] Open
Abstract
Serial crystallography, at both synchrotron and X-ray free-electron laser light sources, is becoming increasingly popular. However, the tools in the majority of crystallization laboratories are focused on producing large single crystals by vapour diffusion that fit the cryo-cooled paradigm of modern synchrotron crystallography. This paper presents several case studies and some ideas and strategies on how to perform the conversion from a single crystal grown by vapour diffusion to the many thousands of micro-crystals required for modern serial crystallography grown by batch crystallization. These case studies aim to show (i) how vapour diffusion conditions can be converted into batch by optimizing the length of time crystals take to appear; (ii) how an understanding of the crystallization phase diagram can act as a guide when designing batch crystallization protocols; and (iii) an accessible methodology when attempting to scale batch conditions to larger volumes. These methods are needed to minimize the sample preparation gap between standard rotation crystallography and dedicated serial laboratories, ultimately making serial crystallography more accessible to all crystallographers.
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Affiliation(s)
- John H. Beale
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Fermi Avenue, Didcot OX11 0DE, UK
| | - Rachel Bolton
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Fermi Avenue, Didcot OX11 0DE, UK
- Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Stephen A. Marshall
- Manchester Institute of Biotechnology, The University of Manchester, Princess Street, Manchester M1 7DN, UK
| | - Emma V. Beale
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Fermi Avenue, Didcot OX11 0DE, UK
| | - Stephen B. Carr
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, UK
| | - Ali Ebrahim
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Fermi Avenue, Didcot OX11 0DE, UK
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Tadeo Moreno-Chicano
- Institute de Biologie Structurale, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Michael A. Hough
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | | | - Ivo Tews
- Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Robin L. Owen
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Fermi Avenue, Didcot OX11 0DE, UK
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29
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Cheng R, Huang C, Hennig M, Nar H, Schnapp G. In situ
crystallography as an emerging method for structure solution of membrane proteins: the case of CCR2A. FEBS J 2019; 287:866-873. [DOI: 10.1111/febs.15098] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 09/10/2019] [Accepted: 10/15/2019] [Indexed: 12/27/2022]
Affiliation(s)
| | - Chia‐Ying Huang
- Swiss Light Source Paul Scherrer Institute Villigen Switzerland
| | | | - Herbert Nar
- Boehringer Ingelheim Pharma GmbH & Co. KG Biberach Germany
| | - Gisela Schnapp
- Boehringer Ingelheim Pharma GmbH & Co. KG Biberach Germany
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30
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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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31
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Echelmeier A, Kim D, Cruz Villarreal J, Coe J, Quintana S, Brehm G, Egatz-Gomez A, Nazari R, Sierra RG, Koglin JE, Batyuk A, Hunter MS, Boutet S, Zatsepin N, Kirian RA, Grant TD, Fromme P, Ros A. 3D printed droplet generation devices for serial femtosecond crystallography enabled by surface coating. J Appl Crystallogr 2019; 52:997-1008. [PMID: 31636518 DOI: 10.1107/s1600576719010343] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 07/19/2019] [Indexed: 11/10/2022] Open
Abstract
The role of surface wetting properties and their impact on the performance of 3D printed microfluidic droplet generation devices for serial femtosecond crystallography (SFX) are reported. SFX is a novel crystallography method enabling structure determination of proteins at room temperature with atomic resolution using X-ray free-electron lasers (XFELs). In SFX, protein crystals in their mother liquor are delivered and intersected with a pulsed X-ray beam using a liquid jet injector. Owing to the pulsed nature of the X-ray beam, liquid jets tend to waste the vast majority of injected crystals, which this work aims to overcome with the delivery of aqueous protein crystal suspension droplets segmented by an oil phase. For this purpose, 3D printed droplet generators that can be easily customized for a variety of XFEL measurements have been developed. The surface properties, in particular the wetting properties of the resist materials compatible with the employed two-photon printing technology, have so far not been characterized extensively, but are crucial for stable droplet generation. This work investigates experimentally the effectiveness and the long-term stability of three different surface treatments on photoresist films and glass as models for our 3D printed droplet generator and the fused silica capillaries employed in the other fluidic components of an SFX experiment. Finally, the droplet generation performance of an assembly consisting of the 3D printed device and fused silica capillaries is examined. Stable and reproducible droplet generation was achieved with a fluorinated surface coating which also allowed for robust downstream droplet delivery. Experimental XFEL diffraction data of crystals formed from the large membrane protein complex photosystem I demonstrate the full compatibility of the new injection method with very fragile membrane protein crystals and show that successful droplet generation of crystal-laden aqueous droplets intersected by an oil phase correlates with increased crystal hit rates.
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Affiliation(s)
- Austin Echelmeier
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Daihyun Kim
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Jorvani Cruz Villarreal
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Jesse Coe
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Sebastian Quintana
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Gerrit Brehm
- Institute for X-ray Physics, University of Göttingen, Göttingen, Germany
| | - Ana Egatz-Gomez
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Reza Nazari
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA.,Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Raymond G Sierra
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Jason E Koglin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Alexander Batyuk
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Nadia Zatsepin
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA.,Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Richard A Kirian
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA.,Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Thomas D Grant
- Hauptman-Woodward Institute, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, Buffalo, New York, USA
| | - Petra Fromme
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Alexandra Ros
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
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32
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Lieske J, Cerv M, Kreida S, Komadina D, Fischer J, Barthelmess M, Fischer P, Pakendorf T, Yefanov O, Mariani V, Seine T, Ross BH, Crosas E, Lorbeer O, Burkhardt A, Lane TJ, Guenther S, Bergtholdt J, Schoen S, Törnroth-Horsefield S, Chapman HN, Meents A. On-chip crystallization for serial crystallography experiments and on-chip ligand-binding studies. IUCRJ 2019; 6:714-728. [PMID: 31316815 PMCID: PMC6608620 DOI: 10.1107/s2052252519007395] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 05/21/2019] [Indexed: 05/18/2023]
Abstract
Efficient and reliable sample delivery has remained one of the bottlenecks for serial crystallography experiments. Compared with other methods, fixed-target sample delivery offers the advantage of significantly reduced sample consumption and shorter data collection times owing to higher hit rates. Here, a new method of on-chip crystallization is reported which allows the efficient and reproducible growth of large numbers of protein crystals directly on micro-patterned silicon chips for in-situ serial crystallography experiments. Crystals are grown by sitting-drop vapor diffusion and previously established crystallization conditions can be directly applied. By reducing the number of crystal-handling steps, the method is particularly well suited for sensitive crystal systems. Excessive mother liquor can be efficiently removed from the crystals by blotting, and no sealing of the fixed-target sample holders is required to prevent the crystals from dehydrating. As a consequence, 'naked' crystals are obtained on the chip, resulting in very low background scattering levels and making the crystals highly accessible for external manipulation such as the application of ligand solutions. Serial diffraction experiments carried out at cryogenic temperatures at a synchrotron and at room temperature at an X-ray free-electron laser yielded high-quality X-ray structures of the human membrane protein aquaporin 2 and two new ligand-bound structures of thermolysin and the human kinase DRAK2. The results highlight the applicability of the method for future high-throughput on-chip screening of pharmaceutical compounds.
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Affiliation(s)
- Julia Lieske
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Maximilian Cerv
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Stefan Kreida
- Center for Molecular Protein Science, Department of Biochemistry and Structural Biology, Lund University, Kemicentrum, 221 00 Lund, Sweden
| | - Dana Komadina
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Janine Fischer
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Miriam Barthelmess
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Pontus Fischer
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Tim Pakendorf
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Valerio Mariani
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Thomas Seine
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- EMBL, Notkestrasse 85, 22607 Hamburg, Germany
| | - Breyan H. Ross
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Eva Crosas
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Olga Lorbeer
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Anja Burkhardt
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Thomas J. Lane
- Bioscience Division and Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Sebastian Guenther
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Julian Bergtholdt
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Silvan Schoen
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Susanna Törnroth-Horsefield
- Center for Molecular Protein Science, Department of Biochemistry and Structural Biology, Lund University, Kemicentrum, 221 00 Lund, Sweden
| | - Henry N. Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Centre for Ultrafast Imaging, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Alke Meents
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
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33
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Echelmeier A, Sonker M, Ros A. Microfluidic sample delivery for serial crystallography using XFELs. Anal Bioanal Chem 2019; 411:6535-6547. [PMID: 31250066 DOI: 10.1007/s00216-019-01977-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/23/2019] [Accepted: 06/12/2019] [Indexed: 12/18/2022]
Abstract
Serial femtosecond crystallography (SFX) with X-ray free electron lasers (XFELs) is an emerging field for structural biology. One of its major impacts lies in the ability to reveal the structure of complex proteins previously inaccessible with synchrotron-based crystallography techniques and allowing time-resolved studies from femtoseconds to seconds. The nature of this serial technique requires new approaches for crystallization, data analysis, and sample delivery. With continued advancements in microfabrication techniques, various developments have been reported in the past decade for innovative and efficient microfluidic sample delivery for crystallography experiments using XFELs. This article summarizes the recent developments in microfluidic sample delivery with liquid injection and fixed-target approaches, which allow exciting new research with XFELs. Graphical abstract.
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Affiliation(s)
- Austin Echelmeier
- School of Molecular Sciences, Arizona State University, Box 871604, Tempe, AZ, 85287-1604, USA.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Box 875001, Tempe, AZ, 85287-7401, USA
| | - Mukul Sonker
- School of Molecular Sciences, Arizona State University, Box 871604, Tempe, AZ, 85287-1604, USA.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Box 875001, Tempe, AZ, 85287-7401, USA
| | - Alexandra Ros
- School of Molecular Sciences, Arizona State University, Box 871604, Tempe, AZ, 85287-1604, USA. .,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Box 875001, Tempe, AZ, 85287-7401, USA.
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34
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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: 36] [Impact Index Per Article: 7.2] [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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35
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Martin-Garcia JM, Zhu L, Mendez D, Lee MY, Chun E, Li C, Hu H, Subramanian G, Kissick D, Ogata C, Henning R, Ishchenko A, Dobson Z, Zhang S, Weierstall U, Spence JCH, Fromme P, Zatsepin NA, Fischetti RF, Cherezov V, Liu W. High-viscosity injector-based pink-beam serial crystallography of microcrystals at a synchrotron radiation source. IUCRJ 2019; 6:412-425. [PMID: 31098022 PMCID: PMC6503920 DOI: 10.1107/s205225251900263x] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 02/20/2019] [Indexed: 05/29/2023]
Abstract
Since the first successful serial crystallography (SX) experiment at a synchrotron radiation source, the popularity of this approach has continued to grow showing that third-generation synchrotrons can be viable alternatives to scarce X-ray free-electron laser sources. Synchrotron radiation flux may be increased ∼100 times by a moderate increase in the bandwidth ('pink beam' conditions) at some cost to data analysis complexity. Here, we report the first high-viscosity injector-based pink-beam SX experiments. The structures of proteinase K (PK) and A2A adenosine receptor (A2AAR) were determined to resolutions of 1.8 and 4.2 Å using 4 and 24 consecutive 100 ps X-ray pulse exposures, respectively. Strong PK data were processed using existing Laue approaches, while weaker A2AAR data required an alternative data-processing strategy. This demonstration of the feasibility presents new opportunities for time-resolved experiments with microcrystals to study structural changes in real time at pink-beam synchrotron beamlines worldwide.
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Affiliation(s)
- Jose M. Martin-Garcia
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA
| | - Lan Zhu
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA
| | - Derek Mendez
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, 550 East Tyler Drive, Tempe, AZ 85287, USA
| | - Ming-Yue Lee
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA
| | - Eugene Chun
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA
| | - Chufeng Li
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, 550 East Tyler Drive, Tempe, AZ 85287, USA
| | - Hao Hu
- Department of Physics, Arizona State University, 550 East Tyler Drive, Tempe, AZ 85287, USA
| | - Ganesh Subramanian
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, 550 East Tyler Drive, Tempe, AZ 85287, USA
| | - David Kissick
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Ave, Lemont, IL 90439, USA
| | - Craig Ogata
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Ave, Lemont, IL 90439, USA
| | - Robert Henning
- Center for Advanced Radiation Sources, The University of Chicago, Argonne National Laboratory, 9700 South Cass Ave, Lemont, IL 90439, USA
| | - Andrii Ishchenko
- Department of Chemistry, Bridge Institute, University of Southern California, 1002 Childs Way, Los Angeles, CA 90089, USA
| | - Zachary Dobson
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA
| | - Shangji Zhang
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA
| | - Uwe Weierstall
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, 550 East Tyler Drive, Tempe, AZ 85287, USA
| | - John C. H. Spence
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, 550 East Tyler Drive, Tempe, AZ 85287, USA
| | - Petra Fromme
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA
| | - Nadia A. Zatsepin
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, 550 East Tyler Drive, Tempe, AZ 85287, USA
| | - Robert F. Fischetti
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Ave, Lemont, IL 90439, USA
| | - Vadim Cherezov
- Department of Chemistry, Bridge Institute, University of Southern California, 1002 Childs Way, Los Angeles, CA 90089, USA
| | - Wei Liu
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA
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36
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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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Wierman JL, Paré-Labrosse O, Sarracini A, Besaw JE, Cook MJ, Oghbaey S, Daoud H, Mehrabi P, Kriksunov I, Kuo A, Schuller DJ, Smith S, Ernst OP, Szebenyi DME, Gruner SM, Miller RJD, Finke AD. Fixed-target serial oscillation crystallography at room temperature. IUCRJ 2019; 6:305-316. [PMID: 30867928 PMCID: PMC6400179 DOI: 10.1107/s2052252519001453] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Accepted: 01/25/2019] [Indexed: 05/18/2023]
Abstract
A fixed-target approach to high-throughput room-temperature serial synchrotron crystallography with oscillation is described. Patterned silicon chips with microwells provide high crystal-loading density with an extremely high hit rate. The microfocus, undulator-fed beamline at CHESS, which has compound refractive optics and a fast-framing detector, was built and optimized for this experiment. The high-throughput oscillation method described here collects 1-5° of data per crystal at room temperature with fast (10° s-1) oscillation rates and translation times, giving a crystal-data collection rate of 2.5 Hz. Partial datasets collected by the oscillation method at a storage-ring source provide more complete data per crystal than still images, dramatically lowering the total number of crystals needed for a complete dataset suitable for structure solution and refinement - up to two orders of magnitude fewer being required. Thus, this method is particularly well suited to instances where crystal quantities are low. It is demonstrated, through comparison of first and last oscillation images of two systems, that dose and the effects of radiation damage can be minimized through fast rotation and low angular sweeps for each crystal.
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Affiliation(s)
| | - Olivier Paré-Labrosse
- Departments of Chemistry and Physics, University of Toronto, Toronto, ON Canada
- Max Planck Institute for the Structure and Dynamics of Matter, Hamburg, Germany
| | - Antoine Sarracini
- Departments of Chemistry and Physics, University of Toronto, Toronto, ON Canada
| | - Jessica E. Besaw
- Departments of Chemistry and Physics, University of Toronto, Toronto, ON Canada
| | | | - Saeed Oghbaey
- Departments of Chemistry and Physics, University of Toronto, Toronto, ON Canada
| | - Hazem Daoud
- Departments of Chemistry and Physics, University of Toronto, Toronto, ON Canada
| | - Pedram Mehrabi
- Max Planck Institute for the Structure and Dynamics of Matter, Hamburg, Germany
| | | | - Anling Kuo
- Departments of Biochemistry and Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - Scott Smith
- MacCHESS, Cornell University, Ithaca, NY 14853, USA
| | - Oliver P. Ernst
- Departments of Biochemistry and Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - Sol M. Gruner
- MacCHESS, Cornell University, Ithaca, NY 14853, USA
- Department of Physics, Cornell University, Ithaca, NY 14853, USA
- Kavli Institute for Nanoscale Science, Cornell University, Ithaca, NY 14853, USA
| | - R. J. Dwayne Miller
- Departments of Chemistry and Physics, University of Toronto, Toronto, ON Canada
- Max Planck Institute for the Structure and Dynamics of Matter, Hamburg, Germany
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Hirata K, Yamashita K, Ueno G, Kawano Y, Hasegawa K, Kumasaka T, Yamamoto M. ZOO: an automatic data-collection system for high-throughput structure analysis in protein microcrystallography. Acta Crystallogr D Struct Biol 2019; 75:138-150. [PMID: 30821703 PMCID: PMC6400253 DOI: 10.1107/s2059798318017795] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 12/17/2018] [Indexed: 11/10/2022] Open
Abstract
Owing to the development of brilliant microfocus beamlines, rapid-readout detectors and sample changers, protein microcrystallography is rapidly becoming a popular technique for accessing structural information from complex biological samples. However, the method is time-consuming and labor-intensive and requires technical expertise to obtain high-resolution protein crystal structures. At SPring-8, an automated data-collection system named ZOO has been developed. This system enables faster data collection, facilitates advanced data-collection and data-processing techniques, and permits the collection of higher quality data. In this paper, the key features of the functionality put in place on the SPring-8 microbeam beamline BL32XU are described and the major advantages of this system are outlined. The ZOO system will be a major driving force in the evolution of the macromolecular crystallography beamlines at SPring-8.
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Affiliation(s)
- Kunio Hirata
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Japan Science and Technology Agency, Precursory Research for Embryonic Science and Technology (PRESTO), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | | | - Go Ueno
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Yoshiaki Kawano
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Kazuya Hasegawa
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo 679-5198, Hyogo, Japan
| | - Takashi Kumasaka
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo 679-5198, Hyogo, Japan
| | - Masaki Yamamoto
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
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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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40
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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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41
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Raskar T, Koh CY, Niebling S, Kini RM, Hosur MV. X-ray crystallographic analysis of time-dependent binding of guanidine hydrochloride to HEWL: First steps during protein unfolding. Int J Biol Macromol 2018; 122:903-913. [PMID: 30412756 DOI: 10.1016/j.ijbiomac.2018.11.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 10/24/2018] [Accepted: 11/05/2018] [Indexed: 01/02/2023]
Abstract
Time-dependent binding of guanidine hydrochloride (GuHCl) to hen egg-white lysozyme (HEWL), and effects of this binding on the protein structure have been investigated by solving X-ray structures of crystalline complexes. The complexes have been prepared by soaking, for different periods of time, native lysozyme crystals in solutions containing 2.5M GuHCl. In the refined structures, the number of water molecules in the protein's first solvent shell has progressively decreased from 152 to 115, showing protein's preference for guanidinium over water. Guanidinium ions preferentially hydrogen bond with the backbone carbonyl oxygen atoms. In their van der Waals interactions, they do not show any preference for apolar residues. Guanidinium ions have replaced water molecules that form cages around exposed hydrophobic residues. Guanidinium binding has decreased the average length of water-water hydrogen bond by 0.1Å. The hydrogen bonds between main chain atoms have been weakened by GuHCl, and this may be the reason for increased potency of GuHCl compared to urea. Guanidinium binding destabilizes the β-domain by causing loss of hydrogen bonds involving Asn 59 side chain. Interestingly, this loss is almost identical to that observed in structures of amyloidogenic variants of human lysozyme. Compounds preventing this loss could be anti-amyloidogenic.
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Affiliation(s)
- Tushar Raskar
- Ultrafast Molecular Dynamics Group, Centre for Hybrid Nanostructures (ChyN), University of Hamburg, Germany
| | - Cho Yeow Koh
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Stephan Niebling
- Ultrafast Molecular Dynamics Group, Centre for Hybrid Nanostructures (ChyN), University of Hamburg, Germany
| | - R M Kini
- Department of Biological Sciences, National University of Singapore, Singapore
| | - M V Hosur
- National Institute of Advanced Studies, IISc campus, Bengaluru 560012, India.
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42
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Trantidou T, Friddin MS, Gan KB, Han L, Bolognesi G, Brooks NJ, Ces O. Mask-Free Laser Lithography for Rapid and Low-Cost Microfluidic Device Fabrication. Anal Chem 2018; 90:13915-13921. [DOI: 10.1021/acs.analchem.8b03169] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Tatiana Trantidou
- Department of Chemistry, Imperial College London, 80 Wood Lane, London W12 0BZ, U.K
- Institute of Chemical Biology, Imperial College London, 80 Wood Lane, London W12 0BZ, U.K
| | - Mark S. Friddin
- Department of Chemistry, Imperial College London, 80 Wood Lane, London W12 0BZ, U.K
- Institute of Chemical Biology, Imperial College London, 80 Wood Lane, London W12 0BZ, U.K
| | - Kin B. Gan
- Department of Chemistry, Imperial College London, 80 Wood Lane, London W12 0BZ, U.K
| | - Luyao Han
- Department of Chemistry, Imperial College London, 80 Wood Lane, London W12 0BZ, U.K
| | - Guido Bolognesi
- Department of Chemical Engineering, Loughborough University, Loughborough LE11 3TU, U.K
| | - Nicholas J. Brooks
- Department of Chemistry, Imperial College London, 80 Wood Lane, London W12 0BZ, U.K
- Institute of Chemical Biology, Imperial College London, 80 Wood Lane, London W12 0BZ, U.K
| | - Oscar Ces
- Department of Chemistry, Imperial College London, 80 Wood Lane, London W12 0BZ, U.K
- Institute of Chemical Biology, Imperial College London, 80 Wood Lane, London W12 0BZ, U.K
- FABRICELL, Imperial College, London SW7 2AZ, U.K
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43
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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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44
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Moringo NA, Shen H, Tauzin LJ, Wang W, Bishop LDC, Landes CF. Variable Lysozyme Transport Dynamics on Oxidatively Functionalized Polystyrene Films. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:10818-10828. [PMID: 28937222 DOI: 10.1021/acs.langmuir.7b02641] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Tuning protein adsorption dynamics at polymeric interfaces is of great interest to many biomedical and material applications. Functionalization of polymer surfaces is a common method to introduce application-specific surface chemistries to a polymer interface. In this work, single-molecule fluorescence microscopy is utilized to determine the adsorption dynamics of lysozyme, a well-studied antibacterial protein, at the interface of polystyrene oxidized via UV exposure and oxygen plasma and functionalized by ligand grafting to produce varying degrees of surface hydrophilicity, surface roughness, and induced oxygen content. Single-molecule tracking indicates lysozyme loading capacities, and surface mobility at the polymer interface is hindered as a result of all functionalization techniques. Adsorption dynamics of lysozyme depend on the extent and the specificity of the oxygen functionalities introduced to the polystyrene surface. Hindered adsorption and mobility are dominated by hydrophobic effects attributed to water hydration layer formation at the functionalized polystyrene surfaces.
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Affiliation(s)
- Nicholas A Moringo
- Department of Chemistry, ‡Department of Electrical and Computer Engineering, and §Smalley-Curl Institute, Rice University , Houston, Texas 77251, United States
| | - Hao Shen
- Department of Chemistry, ‡Department of Electrical and Computer Engineering, and §Smalley-Curl Institute, Rice University , Houston, Texas 77251, United States
| | - Lawrence J Tauzin
- Department of Chemistry, ‡Department of Electrical and Computer Engineering, and §Smalley-Curl Institute, Rice University , Houston, Texas 77251, United States
| | - Wenxiao Wang
- Department of Chemistry, ‡Department of Electrical and Computer Engineering, and §Smalley-Curl Institute, Rice University , Houston, Texas 77251, United States
| | - Logan D C Bishop
- Department of Chemistry, ‡Department of Electrical and Computer Engineering, and §Smalley-Curl Institute, Rice University , Houston, Texas 77251, United States
| | - Christy F Landes
- Department of Chemistry, ‡Department of Electrical and Computer Engineering, and §Smalley-Curl Institute, Rice University , Houston, Texas 77251, United States
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45
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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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Martin-Garcia JM, Conrad CE, Nelson G, Stander N, Zatsepin NA, Zook J, Zhu L, Geiger J, Chun E, Kissick D, Hilgart MC, Ogata C, Ishchenko A, Nagaratnam N, Roy-Chowdhury S, Coe J, Subramanian G, Schaffer A, James D, Ketwala G, Venugopalan N, Xu S, Corcoran S, Ferguson D, Weierstall U, Spence JCH, Cherezov V, Fromme P, Fischetti RF, Liu W. Serial millisecond crystallography of membrane and soluble protein microcrystals using synchrotron radiation. IUCRJ 2017; 4:439-454. [PMID: 28875031 PMCID: PMC5571807 DOI: 10.1107/s205225251700570x] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 04/13/2017] [Indexed: 05/17/2023]
Abstract
Crystal structure determination of biological macromolecules using the novel technique of serial femtosecond crystallography (SFX) is severely limited by the scarcity of X-ray free-electron laser (XFEL) sources. However, recent and future upgrades render microfocus beamlines at synchrotron-radiation sources suitable for room-temperature serial crystallography data collection also. Owing to the longer exposure times that are needed at synchrotrons, serial data collection is termed serial millisecond crystallography (SMX). As a result, the number of SMX experiments is growing rapidly, with a dozen experiments reported so far. Here, the first high-viscosity injector-based SMX experiments carried out at a US synchrotron source, the Advanced Photon Source (APS), are reported. Microcrystals (5-20 µm) of a wide variety of proteins, including lysozyme, thaumatin, phycocyanin, the human A2A adenosine receptor (A2AAR), the soluble fragment of the membrane lipoprotein Flpp3 and proteinase K, were screened. Crystals suspended in lipidic cubic phase (LCP) or a high-molecular-weight poly(ethylene oxide) (PEO; molecular weight 8 000 000) were delivered to the beam using a high-viscosity injector. In-house data-reduction (hit-finding) software developed at APS as well as the SFX data-reduction and analysis software suites Cheetah and CrystFEL enabled efficient on-site SMX data monitoring, reduction and processing. Complete data sets were collected for A2AAR, phycocyanin, Flpp3, proteinase K and lysozyme, and the structures of A2AAR, phycocyanin, proteinase K and lysozyme were determined at 3.2, 3.1, 2.65 and 2.05 Å resolution, respectively. The data demonstrate the feasibility of serial millisecond crystallography from 5-20 µm crystals using a high-viscosity injector at APS. The resolution of the crystal structures obtained in this study was dictated by the current flux density and crystal size, but upcoming developments in beamline optics and the planned APS-U upgrade will increase the intensity by two orders of magnitude. These developments will enable structure determination from smaller and/or weakly diffracting microcrystals.
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Affiliation(s)
- Jose M. Martin-Garcia
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Chelsie E. Conrad
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Garrett Nelson
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, PO Box 871504, Tempe, AZ 85287, USA
| | - Natasha Stander
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, PO Box 871504, Tempe, AZ 85287, USA
| | - Nadia A. Zatsepin
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, PO Box 871504, Tempe, AZ 85287, USA
| | - James Zook
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Lan Zhu
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - James Geiger
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Eugene Chun
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - David Kissick
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
| | - Mark C. Hilgart
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
| | - Craig Ogata
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
| | - Andrii Ishchenko
- Department of Chemistry, Bridge Institute, University of Southern California, 3430 South Vermont Avenue, MC 3303, Los Angeles, CA 90089, USA
| | - Nirupa Nagaratnam
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Shatabdi Roy-Chowdhury
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Jesse Coe
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Ganesh Subramanian
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, PO Box 871504, Tempe, AZ 85287, USA
| | - Alexander Schaffer
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Daniel James
- Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Gihan Ketwala
- Department of Physics, Arizona State University, PO Box 871504, Tempe, AZ 85287, USA
| | - Nagarajan Venugopalan
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
| | - Shenglan Xu
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
| | - Stephen Corcoran
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
| | - Dale Ferguson
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
| | - Uwe Weierstall
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, PO Box 871504, Tempe, AZ 85287, USA
| | - John C. H. Spence
- Department of Physics, Arizona State University, PO Box 871504, Tempe, AZ 85287, USA
| | - Vadim Cherezov
- Department of Chemistry, Bridge Institute, University of Southern California, 3430 South Vermont Avenue, MC 3303, Los Angeles, CA 90089, USA
| | - Petra Fromme
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Robert F. Fischetti
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
| | - Wei Liu
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
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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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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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49
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Owen RL, Axford D, Sherrell DA, Kuo A, Ernst OP, Schulz EC, Miller RJD, Mueller-Werkmeister HM. Low-dose fixed-target serial synchrotron crystallography. Acta Crystallogr D Struct Biol 2017; 73:373-378. [PMID: 28375148 PMCID: PMC5379936 DOI: 10.1107/s2059798317002996] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 02/22/2017] [Indexed: 11/10/2022] Open
Abstract
The development of serial crystallography has been driven by the sample requirements imposed by X-ray free-electron lasers. Serial techniques are now being exploited at synchrotrons. Using a fixed-target approach to high-throughput serial sampling, it is demonstrated that high-quality data can be collected from myoglobin crystals, allowing room-temperature, low-dose structure determination. The combination of fixed-target arrays and a fast, accurate translation system allows high-throughput serial data collection at high hit rates and with low sample consumption.
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Affiliation(s)
- Robin L. Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Danny Axford
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Darren A. Sherrell
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Anling Kuo
- Department of Biochemistry, University of Toronto, King’s College Circle, Toronto, Ontario M5S 1A8, Canada
| | - Oliver P. Ernst
- Department of Biochemistry, University of Toronto, King’s College Circle, Toronto, Ontario M5S 1A8, Canada
- Department of Molecular Genetics, University of Toronto, King’s College Circle, Toronto, Ontario M5S 1A8, Canada
| | - Eike C. Schulz
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - R. J. Dwayne Miller
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
- Departments of Chemistry and Physics, University of Toronto, King’s College Circle, Toronto, Ontario M5S 1A8, Canada
| | - Henrike M. Mueller-Werkmeister
- Department of Biochemistry, University of Toronto, King’s College Circle, Toronto, Ontario M5S 1A8, Canada
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
- Departments of Chemistry and Physics, University of Toronto, King’s College Circle, Toronto, Ontario M5S 1A8, Canada
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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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