51
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Seddon EA, Clarke JA, Dunning DJ, Masciovecchio C, Milne CJ, Parmigiani F, Rugg D, Spence JCH, Thompson NR, Ueda K, Vinko SM, Wark JS, Wurth W. Short-wavelength free-electron laser sources and science: a review. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2017; 80:115901. [PMID: 29059048 DOI: 10.1088/1361-6633/aa7cca] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
This review is focused on free-electron lasers (FELs) in the hard to soft x-ray regime. The aim is to provide newcomers to the area with insights into: the basic physics of FELs, the qualities of the radiation they produce, the challenges of transmitting that radiation to end users and the diversity of current scientific applications. Initial consideration is given to FEL theory in order to provide the foundation for discussion of FEL output properties and the technical challenges of short-wavelength FELs. This is followed by an overview of existing x-ray FEL facilities, future facilities and FEL frontiers. To provide a context for information in the above sections, a detailed comparison of the photon pulse characteristics of FEL sources with those of other sources of high brightness x-rays is made. A brief summary of FEL beamline design and photon diagnostics then precedes an overview of FEL scientific applications. Recent highlights are covered in sections on structural biology, atomic and molecular physics, photochemistry, non-linear spectroscopy, shock physics, solid density plasmas. A short industrial perspective is also included to emphasise potential in this area.
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Affiliation(s)
- E A Seddon
- ASTeC, STFC Daresbury Laboratory, Sci-Tech Daresbury, Keckwick Lane, Daresbury, Cheshire, WA4 4AD, United Kingdom. The School of Physics and Astronomy and Photon Science Institute, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom. The Cockcroft Institute, Sci-Tech Daresbury, Keckwick Lane, Daresbury, Cheshire, WA4 4AD, United Kingdom
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Papp G, Felisaz F, Sorez C, Lopez-Marrero M, Janocha R, Manjasetty B, Gobbo A, Belrhali H, Bowler MW, Cipriani F. FlexED8: the first member of a fast and flexible sample-changer family for macromolecular crystallography. Acta Crystallogr D Struct Biol 2017; 73:841-851. [PMID: 28994413 PMCID: PMC5633909 DOI: 10.1107/s2059798317013596] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 09/22/2017] [Indexed: 11/23/2022] Open
Abstract
Automated sample changers are now standard equipment for modern macromolecular crystallography synchrotron beamlines. Nevertheless, most are only compatible with a single type of sample holder and puck. Recent work aimed at reducing sample-handling efforts and crystal-alignment times at beamlines has resulted in a new generation of compact and precise sample holders for cryocrystallography: miniSPINE and NewPin [see the companion paper by Papp et al. (2017, Acta Cryst., D73, 829-840)]. With full data collection now possible within seconds at most advanced beamlines, and future fourth-generation synchrotron sources promising to extract data in a few tens of milliseconds, the time taken to mount and centre a sample is rate-limiting. In this context, a versatile and fast sample changer, FlexED8, has been developed that is compatible with the highly successful SPINE sample holder and with the miniSPINE and NewPin sample holders. Based on a six-axis industrial robot, FlexED8 is equipped with a tool changer and includes a novel open sample-storage dewar with a built-in ice-filtering system. With seven versatile puck slots, it can hold up to 112 SPINE sample holders in uni-pucks, or 252 miniSPINE or NewPin sample holders, with 36 samples per puck. Additionally, a double gripper, compatible with the SPINE sample holders and uni-pucks, allows a reduction in the sample-exchange time from 40 s, the typical time with a standard single gripper, to less than 5 s. Computer vision-based sample-transfer monitoring, sophisticated error handling and automatic error-recovery procedures ensure high reliability. The FlexED8 sample changer has been successfully tested under real conditions on a beamline.
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Affiliation(s)
- Gergely Papp
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
| | - Franck Felisaz
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
| | - Clement Sorez
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
| | - Marcos Lopez-Marrero
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
| | - Robert Janocha
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
| | - Babu Manjasetty
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
| | - Alexandre Gobbo
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
| | - Hassan Belrhali
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
| | - Matthew W. Bowler
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
| | - Florent Cipriani
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
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53
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Rodriguez JA, Eisenberg DS, Gonen T. Taking the measure of MicroED. Curr Opin Struct Biol 2017; 46:79-86. [PMID: 28648726 PMCID: PMC5683914 DOI: 10.1016/j.sbi.2017.06.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 05/30/2017] [Accepted: 06/07/2017] [Indexed: 10/19/2022]
Abstract
It is now possible to routinely determine atomic resolution structures by electron cryo-microscopy (cryoEM), facilitated in part by the method known as micro electron-diffraction (MicroED). Since its initial demonstration in 2013, MicroED has helped determine a variety of protein structures ranging in molecular weight from a few hundred Daltons to several hundred thousand Daltons. Some of these structures were novel while others were previously known. The resolutions of structures obtained thus far by MicroED range from 3.2Å to 1.0Å, with most better than 2.5Å. Crystals of various sizes and shapes, with different space group symmetries, and with a range of solvent content have all been studied by MicroED. The wide range of crystals explored to date presents the community with a landscape of opportunity for structure determination from nano crystals. Here we summarize the lessons we have learned during the first few years of MicroED, and from our attempts at the first ab initio structure determined by the method. We re-evaluate theoretical considerations in choosing the appropriate crystals for MicroED and for extracting the most meaning out of measured data. With more laboratories worldwide adopting the technique, we speculate what the first decade might hold for MicroED.
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Affiliation(s)
- Jose A Rodriguez
- Department of Chemistry and Biochemistry, UCLA-DOE Institute, University of California, Los Angeles, Los Angeles, CA, USA.
| | - David S Eisenberg
- Department of Biological Chemistry and Department of Chemistry and Biochemistry, University of California Los Angeles (UCLA), Howard Hughes Medical Institute (HHMI), UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA 90095, USA
| | - Tamir Gonen
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA; Departments of Biological Chemistry and Physiology, David Geffen School of Medicine at University of California Los Angeles (UCLA), Los Angeles, CA 90095 USA.
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54
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Artz JH, Zadvornyy OA, Mulder DW, King PW, Peters JW. Structural Characterization of Poised States in the Oxygen Sensitive Hydrogenases and Nitrogenases. Methods Enzymol 2017; 595:213-259. [PMID: 28882202 DOI: 10.1016/bs.mie.2017.07.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The crystallization of FeS cluster-containing proteins has been challenging due to their oxygen sensitivity, and yet these enzymes are involved in many critical catalytic reactions. The last few years have seen a wealth of innovative experiments designed to elucidate not just structural but mechanistic insights into FeS cluster enzymes. Here, we focus on the crystallization of hydrogenases, which catalyze the reversible reduction of protons to hydrogen, and nitrogenases, which reduce dinitrogen to ammonia. A specific focus is given to the different experimental parameters and strategies that are used to trap distinct enzyme states, specifically, oxidants, reductants, and gas treatments. Other themes presented here include the recent use of Cryo-EM, and how coupling various spectroscopies to crystallization is opening up new approaches for structural and mechanistic analysis.
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Affiliation(s)
- Jacob H Artz
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - Oleg A Zadvornyy
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - David W Mulder
- National Renewable Energy Laboratory, Biosciences Center, Golden, CO, United States
| | - Paul W King
- National Renewable Energy Laboratory, Biosciences Center, Golden, CO, United States
| | - John W Peters
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States.
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55
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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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56
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Johansson LC, Stauch B, Ishchenko A, Cherezov V. A Bright Future for Serial Femtosecond Crystallography with XFELs. Trends Biochem Sci 2017; 42:749-762. [PMID: 28733116 DOI: 10.1016/j.tibs.2017.06.007] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 06/12/2017] [Accepted: 06/20/2017] [Indexed: 11/19/2022]
Abstract
X-ray free electron lasers (XFELs) have the potential to revolutionize macromolecular structural biology due to the unique combination of spatial coherence, extreme peak brilliance, and short duration of X-ray pulses. A recently emerged serial femtosecond (fs) crystallography (SFX) approach using XFEL radiation overcomes some of the biggest hurdles of traditional crystallography related to radiation damage through the diffraction-before-destruction principle. Intense fs XFEL pulses enable high-resolution room-temperature structure determination of difficult-to-crystallize biological macromolecules, while simultaneously opening a new era of time-resolved structural studies. Here, we review the latest developments in instrumentation, sample delivery, data analysis, crystallization methods, and applications of SFX to important biological questions, and conclude with brief insights into the bright future of structural biology using XFELs.
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Affiliation(s)
- Linda C Johansson
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089-3303, USA
| | - Benjamin Stauch
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089-3303, USA
| | - Andrii Ishchenko
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089-3303, USA
| | - Vadim Cherezov
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089-3303, USA.
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Crystal Growth of High-Quality Protein Crystals under the Presence of an Alternant Electric Field in Pulse-Wave Mode, and a Strong Magnetic Field with Radio Frequency Pulses Characterized by X-ray Diffraction. CRYSTALS 2017. [DOI: 10.3390/cryst7060179] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The first part of this research was devoted to investigating the effect of alternate current (AC) using four different types of wave modes (pulse-wave) at 2 Hz on the crystal growth of lysozyme in solution. The best results, in terms of size and crystal quality, were obtained when protein crystals were grown under the influence of electric fields in a very specific wave mode (“breathing” wave), giving the highest resolution up to 1.34 Å in X-ray diffraction analysis compared with controls and with those crystals grown in gel. In the second part, we evaluated the effect of a strong magnetic field of 16.5 Tesla combined with radiofrequency pulses of 0.43 μs on the crystal growth in gels of tetragonal hen egg white (HEW) lysozyme. The lysozyme crystals grown, both in solution applying breathing-wave and in gel under the influence of this strong magnetic field with pulses of radio frequencies, produced the larger-in-size crystals and the highest resolution structures. Data processing and refinement statistics are very good in terms of the resolution, mosaicity and Wilson B factor obtained for each crystal. Besides, electron density maps show well-defined and distinctly separated atoms at several selected tryptophan residues for the crystal grown using the “breathing wave pulses”.
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58
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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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59
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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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60
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Abstract
The intense X-ray pulses from free-electron lasers, of only femtoseconds duration, outrun most of the processes that lead to structural degradation in X-ray exposures of macromolecules. Using these sources it is therefore possible to increase the dose to macromolecular crystals by several orders of magnitude higher than usually tolerable in conventional measurements, allowing crystal size to be decreased dramatically in diffraction measurements and without the need to cool the sample. Such pulses lead to the eventual vaporization of the sample, which has required a measurement approach, called serial crystallography, of consolidating snapshot diffraction patterns of many individual crystals. This in turn has further separated the connection between dose and obtainable diffraction information, with the only requirement from a single pattern being that to give enough information to place it, in three-dimensional reciprocal space, in relation to other patterns. Millions of extremely weak patterns can be collected and combined in this way, requiring methods to rapidly replenish the sample into the beam while generating the lowest possible background . The method is suited to time-resolved measurements over timescales below 1 ps to several seconds, and opens new opportunities for phasing. Some straightforward considerations of achievable signal levels are discussed and compared with a wide variety of recent experiments carried out at XFEL, synchrotron, and even laboratory sources, to discuss the capabilities of these new approaches and give some perspectives on their further development.
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Affiliation(s)
- Henry N Chapman
- Center for Free-Electron Laser Science, DESY, Hamburg, 22607, Germany.
- Department of Physics, University of Hamburg, Hamburg, 22607, Germany.
- The Centre for Ultrafast Imaging, University of Hamburg, Hamburg, 22607, Germany.
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61
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Abstract
This chapter provides a review of different advanced methods that help to increase the success rate of a crystallization project, by producing larger and higher quality single crystals for determination of macromolecular structures by crystallographic methods. For this purpose, the chapter is divided into three parts. The first part deals with the fundamentals for understanding the crystallization process through different strategies based on physical and chemical approaches. The second part presents new approaches involved in more sophisticated methods not only for growing protein crystals but also for controlling the size and orientation of crystals through utilization of electromagnetic fields and other advanced techniques. The last section deals with three different aspects: the importance of microgravity, the use of ligands to stabilize proteins, and the use of microfluidics to obtain protein crystals. All these advanced methods will allow the readers to obtain suitable crystalline samples for high-resolution X-ray and neutron crystallography.
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Affiliation(s)
- Abel Moreno
- Instituto de Química, Universidad Nacional Autónoma de Mexico, Av. Universidad 3000, Cd.Mx., Mexico City, 04510, Mexico.
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62
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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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Abstract
AbstractIn 1912, Max von Laue and collaborators first observed diffraction spots from a millimeter-sized crystal of copper sulfate using an X-ray tube. Crystallography was born of this experiment, and since then, diffraction by both X-rays and electrons has revealed a myriad of inorganic and organic structures, including structures of complex protein assemblies. Advancements in X-ray sources have spurred a revolution in structure determination, facilitated by the development of new methods. This review explores some of the frontier methods that are shaping the future of X-ray diffraction, including coherent diffractive imaging, serial femtosecond X-ray crystallography and small-angle X-ray scattering. Collectively, these methods expand the current limits of structure determination in biological systems across multiple length and time scales.
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Lyubimov AY, Uervirojnangkoorn M, Zeldin OB, Zhou Q, Zhao M, Brewster AS, Michels-Clark T, Holton JM, Sauter NK, Weis WI, Brunger AT. Advances in X-ray free electron laser (XFEL) diffraction data processing applied to the crystal structure of the synaptotagmin-1 / SNARE complex. eLife 2016; 5. [PMID: 27731796 PMCID: PMC5094853 DOI: 10.7554/elife.18740] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Accepted: 10/11/2016] [Indexed: 12/03/2022] Open
Abstract
X-ray free electron lasers (XFELs) reduce the effects of radiation damage on macromolecular diffraction data and thereby extend the limiting resolution. Previously, we adapted classical post-refinement techniques to XFEL diffraction data to produce accurate diffraction data sets from a limited number of diffraction images (Uervirojnangkoorn et al., 2015), and went on to use these techniques to obtain a complete data set from crystals of the synaptotagmin-1 / SNARE complex and to determine the structure at 3.5 Å resolution (Zhou et al., 2015). Here, we describe new advances in our methods and present a reprocessed XFEL data set of the synaptotagmin-1 / SNARE complex. The reprocessing produced small improvements in electron density maps and the refined atomic model. The maps also contained more information than those of a lower resolution (4.1 Å) synchrotron data set. Processing a set of simulated XFEL diffraction images revealed that our methods yield accurate data and atomic models. DOI:http://dx.doi.org/10.7554/eLife.18740.001
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Affiliation(s)
- Artem Y Lyubimov
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Neurology and Neurological Science, Stanford University, Stanford, United States.,Structural Biology, Stanford University, Stanford, United States.,Photon Science, Stanford University, Stanford, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, United States
| | - Monarin Uervirojnangkoorn
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Neurology and Neurological Science, Stanford University, Stanford, United States.,Photon Science, Stanford University, Stanford, United States.,Structural Biology, Stanford University, Stanford, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, United States
| | - Oliver B Zeldin
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Neurology and Neurological Science, Stanford University, Stanford, United States.,Photon Science, Stanford University, Stanford, United States.,Structural Biology, Stanford University, Stanford, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, United States
| | - Qiangjun Zhou
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Neurology and Neurological Science, Stanford University, Stanford, United States.,Photon Science, Stanford University, Stanford, United States.,Structural Biology, Stanford University, Stanford, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, United States
| | - Minglei Zhao
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Neurology and Neurological Science, Stanford University, Stanford, United States.,Photon Science, Stanford University, Stanford, United States.,Structural Biology, Stanford University, Stanford, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, United States
| | - Aaron S Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Tara Michels-Clark
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - James M Holton
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States.,Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, United States.,Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Nicholas K Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - William I Weis
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Structural Biology, Stanford University, Stanford, United States.,Photon Science, Stanford University, Stanford, United States
| | - Axel T Brunger
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Neurology and Neurological Science, Stanford University, Stanford, United States.,Photon Science, Stanford University, Stanford, United States.,Structural Biology, Stanford University, Stanford, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, United States
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Perunicic VS, Hill CD, Hall LT, Hollenberg LCL. A quantum spin-probe molecular microscope. Nat Commun 2016; 7:12667. [PMID: 27725630 PMCID: PMC5062573 DOI: 10.1038/ncomms12667] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 07/21/2016] [Indexed: 01/09/2023] Open
Abstract
Imaging the atomic structure of a single biomolecule is an important challenge in the physical biosciences. Whilst existing techniques all rely on averaging over large ensembles of molecules, the single-molecule realm remains unsolved. Here we present a protocol for 3D magnetic resonance imaging of a single molecule using a quantum spin probe acting simultaneously as the magnetic resonance sensor and source of magnetic field gradient. Signals corresponding to specific regions of the molecule's nuclear spin density are encoded on the quantum state of the probe, which is used to produce a 3D image of the molecular structure. Quantum simulations of the protocol applied to the rapamycin molecule (C51H79NO13) show that the hydrogen and carbon substructure can be imaged at the angstrom level using current spin-probe technology. With prospects for scaling to large molecules and/or fast dynamic conformation mapping using spin labels, this method provides a realistic pathway for single-molecule microscopy. Single spin defects can allow high-resolution sensing of molecules under an applied magnetic field. Here, the authors propose a protocol for three-dimensional magnetic resonance imaging with angstrom-level resolution exploiting the dipolar field of a spin qubit, such as a diamond nitrogen-vacancy.
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Affiliation(s)
- V S Perunicic
- Centre for Quantum Computation and Communication Technology, School of Physics, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - C D Hill
- Centre for Quantum Computation and Communication Technology, School of Physics, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - L T Hall
- School of Physics, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - L C L Hollenberg
- Centre for Quantum Computation and Communication Technology, School of Physics, University of Melbourne, Melbourne, Victoria 3010, Australia.,School of Physics, University of Melbourne, Melbourne, Victoria 3010, Australia
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66
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Sui S, Wang Y, Kolewe KW, Srajer V, Henning R, Schiffman JD, Dimitrakopoulos C, Perry SL. Graphene-based microfluidics for serial crystallography. LAB ON A CHIP 2016; 16:3082-96. [PMID: 27241728 PMCID: PMC4970872 DOI: 10.1039/c6lc00451b] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Microfluidic strategies to enable the growth and subsequent serial crystallographic analysis of micro-crystals have the potential to facilitate both structural characterization and dynamic structural studies of protein targets that have been resistant to single-crystal strategies. However, adapting microfluidic crystallization platforms for micro-crystallography requires a dramatic decrease in the overall device thickness. We report a robust strategy for the straightforward incorporation of single-layer graphene into ultra-thin microfluidic devices. This architecture allows for a total material thickness of only ∼1 μm, facilitating on-chip X-ray diffraction analysis while creating a sample environment that is stable against significant water loss over several weeks. We demonstrate excellent signal-to-noise in our X-ray diffraction measurements using a 1.5 μs polychromatic X-ray exposure, and validate our approach via on-chip structure determination using hen egg white lysozyme (HEWL) as a model system. Although this work is focused on the use of graphene for protein crystallography, we anticipate that this technology should find utility in a wide range of both X-ray and other lab on a chip applications.
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Affiliation(s)
- Shuo Sui
- Department of Chemical Engineering, The University of Massachusetts Amherst, Amherst, MA 01003, USA.
| | - Yuxi Wang
- Department of Chemical Engineering, The University of Massachusetts Amherst, Amherst, MA 01003, USA.
| | - Kristopher W Kolewe
- Department of Chemical Engineering, The University of Massachusetts Amherst, Amherst, MA 01003, USA.
| | - Vukica Srajer
- BioCARS Center for Advanced Radiation Sources, The University of Chicago, Argonne, IL 60439, USA
| | - Robert Henning
- BioCARS Center for Advanced Radiation Sources, The University of Chicago, Argonne, IL 60439, USA
| | - Jessica D Schiffman
- Department of Chemical Engineering, The University of Massachusetts Amherst, Amherst, MA 01003, USA.
| | - Christos Dimitrakopoulos
- Department of Chemical Engineering, The University of Massachusetts Amherst, Amherst, MA 01003, USA.
| | - Sarah L Perry
- Department of Chemical Engineering, The University of Massachusetts Amherst, Amherst, MA 01003, USA.
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67
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Oghbaey S, Sarracini A, Ginn HM, Pare-Labrosse O, Kuo A, Marx A, Epp SW, Sherrell DA, Eger BT, Zhong Y, Loch R, Mariani V, Alonso-Mori R, Nelson S, Lemke HT, Owen RL, Pearson AR, Stuart DI, Ernst OP, Mueller-Werkmeister HM, Miller RJD. Fixed target combined with spectral mapping: approaching 100% hit rates for serial crystallography. Acta Crystallogr D Struct Biol 2016; 72:944-55. [PMID: 27487825 PMCID: PMC5937680 DOI: 10.1107/s2059798316010834] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 07/04/2016] [Indexed: 11/10/2022] Open
Abstract
The advent of ultrafast highly brilliant coherent X-ray free-electron laser sources has driven the development of novel structure-determination approaches for proteins, and promises visualization of protein dynamics on sub-picosecond timescales with full atomic resolution. Significant efforts are being applied to the development of sample-delivery systems that allow these unique sources to be most efficiently exploited for high-throughput serial femtosecond crystallography. Here, the next iteration of a fixed-target crystallography chip designed for rapid and reliable delivery of up to 11 259 protein crystals with high spatial precision is presented. An experimental scheme for predetermining the positions of crystals in the chip by means of in situ spectroscopy using a fiducial system for rapid, precise alignment and registration of the crystal positions is presented. This delivers unprecedented performance in serial crystallography experiments at room temperature under atmospheric pressure, giving a raw hit rate approaching 100% with an effective indexing rate of approximately 50%, increasing the efficiency of beam usage and allowing the method to be applied to systems where the number of crystals is limited.
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Affiliation(s)
- Saeed Oghbaey
- Department of Physics & Chemistry, University of Toronto, 60 St. George Street, Toronto, Ontario, M5S 1A7, Canada
| | - Antoine Sarracini
- Department of Physics & Chemistry, University of Toronto, 60 St. George Street, Toronto, Ontario, M5S 1A7, Canada
| | - Helen M. Ginn
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, Oxfordshire, OX3 7BN, UK
- Diamond Light Source, Harwell & Innovation Campus, Didcot, Oxfordshire, OX11 ODE, UK
| | - Olivier Pare-Labrosse
- Department of Physics & Chemistry, University of Toronto, 60 St. George Street, Toronto, Ontario, M5S 1A7, Canada
| | - Anling Kuo
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada
| | - Alexander Marx
- Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, Hamburg, Germany
| | - Sascha W. Epp
- Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, Hamburg, Germany
| | - Darren A. Sherrell
- Diamond Light Source, Harwell & Innovation Campus, Didcot, Oxfordshire, OX11 ODE, UK
| | - Bryan T. Eger
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada
| | - Yinpeng Zhong
- Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, Hamburg, Germany
| | - Rolf Loch
- Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, Hamburg, Germany
| | - Valerio Mariani
- Center for Free-Electron Laser Science, Desy, 22607, Hamburg, Germany
| | - Roberto Alonso-Mori
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, 94025, USA
| | - Silke Nelson
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, 94025, USA
| | - Henrik T. Lemke
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, 94025, USA
| | - Robin L. Owen
- Diamond Light Source, Harwell & Innovation Campus, Didcot, Oxfordshire, OX11 ODE, UK
| | - Arwen R. Pearson
- Hamburg Centre for Ultrafast Imaging, University of Hamburg, Hamburg, Germany
| | - David I. Stuart
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, Oxfordshire, OX3 7BN, UK
- Diamond Light Source, Harwell & Innovation Campus, Didcot, Oxfordshire, OX11 ODE, UK
| | - Oliver P. Ernst
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada
| | - Henrike M. Mueller-Werkmeister
- Department of Physics & Chemistry, University of Toronto, 60 St. George Street, Toronto, Ontario, M5S 1A7, Canada
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada
- Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, Hamburg, Germany
| | - R. J. Dwayne Miller
- Department of Physics & Chemistry, University of Toronto, 60 St. George Street, Toronto, Ontario, M5S 1A7, Canada
- Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, Hamburg, Germany
- Hamburg Centre for Ultrafast Imaging, University of Hamburg, Hamburg, Germany
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68
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Hirata K, Foadi J, Evans G, Hasegawa K, Zeldin OB. Structural Biology with Microfocus Beamlines. ACTA ACUST UNITED AC 2016. [DOI: 10.1007/978-4-431-56030-2_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
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69
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Owen RL, Juanhuix J, Fuchs M. Current advances in synchrotron radiation instrumentation for MX experiments. Arch Biochem Biophys 2016; 602:21-31. [PMID: 27046341 PMCID: PMC5505570 DOI: 10.1016/j.abb.2016.03.021] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 03/16/2016] [Accepted: 03/21/2016] [Indexed: 11/15/2022]
Abstract
Following pioneering work 40 years ago, synchrotron beamlines dedicated to macromolecular crystallography (MX) have improved in almost every aspect as instrumentation has evolved. Beam sizes and crystal dimensions are now on the single micron scale while data can be collected from proteins with molecular weights over 10 MDa and from crystals with unit cell dimensions over 1000 Å. Furthermore it is possible to collect a complete data set in seconds, and obtain the resulting structure in minutes. The impact of MX synchrotron beamlines and their evolution is reflected in their scientific output, and MX is now the method of choice for a variety of aims from ligand binding to structure determination of membrane proteins, viruses and ribosomes, resulting in a much deeper understanding of the machinery of life. A main driving force of beamline evolution have been advances in almost every aspect of the instrumentation comprising a synchrotron beamline. In this review we aim to provide an overview of the current status of instrumentation at modern MX experiments. The most critical optical components are discussed, as are aspects of endstation design, sample delivery, visualisation and positioning, the sample environment, beam shaping, detectors and data acquisition and processing.
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Affiliation(s)
- Robin L Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK.
| | - Jordi Juanhuix
- Alba Synchrotron, Carrer de la llum 2-26, Cerdanyola, 08192, Spain.
| | - Martin Fuchs
- National Synchrotron Light Source II, Brookhaven National Lab, Upton, NY, 11973, USA.
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70
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Lyubimov AY, Uervirojnangkoorn M, Zeldin OB, Brewster AS, Murray TD, Sauter NK, Berger JM, Weis WI, Brunger AT. IOTA: integration optimization, triage and analysis tool for the processing of XFEL diffraction images. J Appl Crystallogr 2016; 49:1057-1064. [PMID: 27275148 PMCID: PMC4886991 DOI: 10.1107/s1600576716006683] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 04/19/2016] [Indexed: 01/25/2023] Open
Abstract
Serial femtosecond crystallography (SFX) uses an X-ray free-electron laser to extract diffraction data from crystals not amenable to conventional X-ray light sources owing to their small size or radiation sensitivity. However, a limitation of SFX is the high variability of the diffraction images that are obtained. As a result, it is often difficult to determine optimal indexing and integration parameters for the individual diffraction images. Presented here is a software package, called IOTA, which uses a grid-search technique to determine optimal spot-finding parameters that can in turn affect the success of indexing and the quality of integration on an image-by-image basis. Integration results can be filtered using a priori information about the Bravais lattice and unit-cell dimensions and analyzed for unit-cell isomorphism, facilitating an improvement in subsequent data-processing steps.
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Affiliation(s)
- Artem Y. Lyubimov
- Department of Molecular and Cellular Physiology, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Neurology and Neurological Science, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Photon Science, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Monarin Uervirojnangkoorn
- Department of Molecular and Cellular Physiology, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Neurology and Neurological Science, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Photon Science, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Oliver B. Zeldin
- Department of Molecular and Cellular Physiology, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Neurology and Neurological Science, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Photon Science, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Aaron S. Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Thomas D. Murray
- Biophysics Graduate Group, University of California, Berkeley, CA 94720, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nicholas K. Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - James M. Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - William I. Weis
- Department of Molecular and Cellular Physiology, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Photon Science, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
| | - Axel T. Brunger
- Department of Molecular and Cellular Physiology, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Neurology and Neurological Science, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Photon Science, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
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71
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Stevenson HP, Lin G, Barnes CO, Sutkeviciute I, Krzysiak T, Weiss SC, Reynolds S, Wu Y, Nagarajan V, Makhov AM, Lawrence R, Lamm E, Clark L, Gardella TJ, Hogue BG, Ogata CM, Ahn J, Gronenborn AM, Conway JF, Vilardaga JP, Cohen AE, Calero G. Transmission electron microscopy for the evaluation and optimization of crystal growth. Acta Crystallogr D Struct Biol 2016; 72:603-15. [PMID: 27139624 PMCID: PMC4854312 DOI: 10.1107/s2059798316001546] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 01/25/2016] [Indexed: 11/10/2022] Open
Abstract
The crystallization of protein samples remains the most significant challenge in structure determination by X-ray crystallography. Here, the effectiveness of transmission electron microscopy (TEM) analysis to aid in the crystallization of biological macromolecules is demonstrated. It was found that the presence of well ordered lattices with higher order Bragg spots, revealed by Fourier analysis of TEM images, is a good predictor of diffraction-quality crystals. Moreover, the use of TEM allowed (i) comparison of lattice quality among crystals from different conditions in crystallization screens; (ii) the detection of crystal pathologies that could contribute to poor X-ray diffraction, including crystal lattice defects, anisotropic diffraction and crystal contamination by heavy protein aggregates and nanocrystal nuclei; (iii) the qualitative estimation of crystal solvent content to explore the effect of lattice dehydration on diffraction and (iv) the selection of high-quality crystal fragments for microseeding experiments to generate reproducibly larger sized crystals. Applications to X-ray free-electron laser (XFEL) and micro-electron diffraction (microED) experiments are also discussed.
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Affiliation(s)
- Hilary P. Stevenson
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Guowu Lin
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Christopher O. Barnes
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Ieva Sutkeviciute
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, M240 Scaife Hall, 3550 Terrace Street, Pittsburgh, PA 15261, USA
| | - Troy Krzysiak
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Simon C. Weiss
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Shelley Reynolds
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Ying Wu
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | | | - Alexander M. Makhov
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Robert Lawrence
- School of Life Sciences, Arizona State University, PO Box 874501, Tempe, AZ 85287, USA
| | - Emily Lamm
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Lisa Clark
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Timothy J. Gardella
- Endocrine Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Brenda G. Hogue
- School of Life Sciences, Arizona State University, PO Box 874501, Tempe, AZ 85287, USA
| | - Craig M. Ogata
- Biosciences Division, Argonne National Laboratory, 9700 South Cass Ave, Lemont, IL 60439, USA
| | - Jinwoo Ahn
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Angela M. Gronenborn
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - James F. Conway
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Jean-Pierre Vilardaga
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, M240 Scaife Hall, 3550 Terrace Street, Pittsburgh, PA 15261, USA
| | - Aina E. Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Guillermo Calero
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
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72
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Martin-Garcia JM, Conrad CE, Coe J, Roy-Chowdhury S, Fromme P. Serial femtosecond crystallography: A revolution in structural biology. Arch Biochem Biophys 2016; 602:32-47. [PMID: 27143509 DOI: 10.1016/j.abb.2016.03.036] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 03/16/2016] [Accepted: 03/21/2016] [Indexed: 10/21/2022]
Abstract
Macromolecular crystallography at synchrotron sources has proven to be the most influential method within structural biology, producing thousands of structures since its inception. While its utility has been instrumental in progressing our knowledge of structures of molecules, it suffers from limitations such as the need for large, well-diffracting crystals, and radiation damage that can hamper native structural determination. The recent advent of X-ray free electron lasers (XFELs) and their implementation in the emerging field of serial femtosecond crystallography (SFX) has given rise to a remarkable expansion upon existing crystallographic constraints, allowing structural biologists access to previously restricted scientific territory. SFX relies on exceptionally brilliant, micro-focused X-ray pulses, which are femtoseconds in duration, to probe nano/micrometer sized crystals in a serial fashion. This results in data sets comprised of individual snapshots, each capturing Bragg diffraction of single crystals in random orientations prior to their subsequent destruction. Thus structural elucidation while avoiding radiation damage, even at room temperature, can now be achieved. This emerging field has cultivated new methods for nanocrystallogenesis, sample delivery, and data processing. Opportunities and challenges within SFX are reviewed herein.
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Affiliation(s)
- Jose M Martin-Garcia
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA; Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Chelsie E Conrad
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA; Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Jesse Coe
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA; Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Shatabdi Roy-Chowdhury
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA; Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Petra Fromme
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA; Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ 85287-7401, USA.
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73
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Russi S, Song J, McPhillips SE, Cohen AE. The Stanford Automated Mounter: pushing the limits of sample exchange at the SSRL macromolecular crystallography beamlines. J Appl Crystallogr 2016; 49:622-626. [PMID: 27047309 PMCID: PMC4815877 DOI: 10.1107/s1600576716000649] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 01/13/2016] [Indexed: 12/02/2022] Open
Abstract
The Stanford Automated Mounter System, a system for mounting and dismounting cryo-cooled crystals, has been upgraded to increase the throughput of samples on the macromolecular crystallography beamlines at the Stanford Synchrotron Radiation Lightsource. This upgrade speeds up robot maneuvers, reduces the heating/drying cycles, pre-fetches samples and adds an air-knife to remove frost from the gripper arms. Sample pin exchange during automated crystal quality screening now takes about 25 s, five times faster than before this upgrade.
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Affiliation(s)
- Silvia Russi
- Stanford Synchrotron Radiation Lightsource / SLAC National Accelerator Laboratory, 2575 Sand Hill Road, MS 99, Menlo Park, California 94025, USA
| | - Jinhu Song
- Stanford Synchrotron Radiation Lightsource / SLAC National Accelerator Laboratory, 2575 Sand Hill Road, MS 99, Menlo Park, California 94025, USA
| | - Scott E. McPhillips
- Stanford Synchrotron Radiation Lightsource / SLAC National Accelerator Laboratory, 2575 Sand Hill Road, MS 99, Menlo Park, California 94025, USA
| | - Aina E. Cohen
- Stanford Synchrotron Radiation Lightsource / SLAC National Accelerator Laboratory, 2575 Sand Hill Road, MS 99, Menlo Park, California 94025, USA
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74
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Zander U, Hoffmann G, Cornaciu I, Marquette JP, Papp G, Landret C, Seroul G, Sinoir J, Röwer M, Felisaz F, Rodriguez-Puente S, Mariaule V, Murphy P, Mathieu M, Cipriani F, Márquez JA. Automated harvesting and processing of protein crystals through laser photoablation. Acta Crystallogr D Struct Biol 2016; 72:454-66. [PMID: 27050125 PMCID: PMC4822559 DOI: 10.1107/s2059798316000954] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 01/16/2016] [Indexed: 01/10/2023] Open
Abstract
Currently, macromolecular crystallography projects often require the use of highly automated facilities for crystallization and X-ray data collection. However, crystal harvesting and processing largely depend on manual operations. Here, a series of new methods are presented based on the use of a low X-ray-background film as a crystallization support and a photoablation laser that enable the automation of major operations required for the preparation of crystals for X-ray diffraction experiments. In this approach, the controlled removal of the mother liquor before crystal mounting simplifies the cryocooling process, in many cases eliminating the use of cryoprotectant agents, while crystal-soaking experiments are performed through diffusion, precluding the need for repeated sample-recovery and transfer operations. Moreover, the high-precision laser enables new mounting strategies that are not accessible through other methods. This approach bridges an important gap in automation and can contribute to expanding the capabilities of modern macromolecular crystallography facilities.
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Affiliation(s)
- Ulrich Zander
- Grenoble Outstation, European Molecular Biology Laboratory; Unit of Virus Host-Cell Interactions (UMI 3265), University Grenoble Alpes–EMBL–CNRS, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Guillaume Hoffmann
- Grenoble Outstation, European Molecular Biology Laboratory; Unit of Virus Host-Cell Interactions (UMI 3265), University Grenoble Alpes–EMBL–CNRS, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Irina Cornaciu
- Grenoble Outstation, European Molecular Biology Laboratory; Unit of Virus Host-Cell Interactions (UMI 3265), University Grenoble Alpes–EMBL–CNRS, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Jean-Pierre Marquette
- Structure Design Informatics and Structural Biology, Sanofi, 13 Quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Gergely Papp
- Grenoble Outstation, European Molecular Biology Laboratory; Unit of Virus Host-Cell Interactions (UMI 3265), University Grenoble Alpes–EMBL–CNRS, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Christophe Landret
- Grenoble Outstation, European Molecular Biology Laboratory; Unit of Virus Host-Cell Interactions (UMI 3265), University Grenoble Alpes–EMBL–CNRS, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Gaël Seroul
- Grenoble Outstation, European Molecular Biology Laboratory; Unit of Virus Host-Cell Interactions (UMI 3265), University Grenoble Alpes–EMBL–CNRS, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Jérémy Sinoir
- Grenoble Outstation, European Molecular Biology Laboratory; Unit of Virus Host-Cell Interactions (UMI 3265), University Grenoble Alpes–EMBL–CNRS, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Martin Röwer
- Grenoble Outstation, European Molecular Biology Laboratory; Unit of Virus Host-Cell Interactions (UMI 3265), University Grenoble Alpes–EMBL–CNRS, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Frank Felisaz
- Grenoble Outstation, European Molecular Biology Laboratory; Unit of Virus Host-Cell Interactions (UMI 3265), University Grenoble Alpes–EMBL–CNRS, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Sonia Rodriguez-Puente
- Grenoble Outstation, European Molecular Biology Laboratory; Unit of Virus Host-Cell Interactions (UMI 3265), University Grenoble Alpes–EMBL–CNRS, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Vincent Mariaule
- Grenoble Outstation, European Molecular Biology Laboratory; Unit of Virus Host-Cell Interactions (UMI 3265), University Grenoble Alpes–EMBL–CNRS, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Peter Murphy
- Grenoble Outstation, European Molecular Biology Laboratory; Unit of Virus Host-Cell Interactions (UMI 3265), University Grenoble Alpes–EMBL–CNRS, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Magali Mathieu
- Structure Design Informatics and Structural Biology, Sanofi, 13 Quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Florent Cipriani
- Grenoble Outstation, European Molecular Biology Laboratory; Unit of Virus Host-Cell Interactions (UMI 3265), University Grenoble Alpes–EMBL–CNRS, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - José Antonio Márquez
- Grenoble Outstation, European Molecular Biology Laboratory; Unit of Virus Host-Cell Interactions (UMI 3265), University Grenoble Alpes–EMBL–CNRS, 71 Avenue des Martyrs, 38042 Grenoble, France
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75
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Rose JP, Wang BC. SAD phasing: History, current impact and future opportunities. Arch Biochem Biophys 2016; 602:80-94. [PMID: 27036852 DOI: 10.1016/j.abb.2016.03.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 03/17/2016] [Accepted: 03/19/2016] [Indexed: 01/17/2023]
Abstract
Single wavelength anomalous diffraction (SAD) can trace its beginnings to the early 1950s. Researchers at the time recognized that SAD offers some unique features that might be advantageous for crystallographic phasing, despite the fact that at that time recording accurate SAD data was problematic. In this review we will follow the trail from those early days, highlighting key advances in the field and interpreting them in terms on how they stimulated continued phasing development that produced the theoretical foundation for the routine macromolecular structure determination by SAD today. The technological advances over the past three decades in both hardware and software, which played a significant role in making SAD phasing a 'first choice method', will also be described.
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Affiliation(s)
- John P Rose
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA.
| | - Bi-Cheng Wang
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA.
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76
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Roessler CG, Agarwal R, Allaire M, Alonso-Mori R, Andi B, Bachega JFR, Bommer M, Brewster AS, Browne MC, Chatterjee R, Cho E, Cohen AE, Cowan M, Datwani S, Davidson VL, Defever J, Eaton B, Ellson R, Feng Y, Ghislain LP, Glownia JM, Han G, Hattne J, Hellmich J, Héroux A, Ibrahim M, Kern J, Kuczewski A, Lemke HT, Liu P, Majlof L, McClintock WM, Myers S, Nelsen S, Olechno J, Orville AM, Sauter NK, Soares AS, Soltis SM, Song H, Stearns RG, Tran R, Tsai Y, Uervirojnangkoorn M, Wilmot CM, Yachandra V, Yano J, Yukl ET, Zhu D, Zouni A. Acoustic Injectors for Drop-On-Demand Serial Femtosecond Crystallography. Structure 2016; 24:631-640. [PMID: 26996959 DOI: 10.1016/j.str.2016.02.007] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 09/25/2015] [Accepted: 02/17/2016] [Indexed: 02/01/2023]
Abstract
X-ray free-electron lasers (XFELs) provide very intense X-ray pulses suitable for macromolecular crystallography. Each X-ray pulse typically lasts for tens of femtoseconds and the interval between pulses is many orders of magnitude longer. Here we describe two novel acoustic injection systems that use focused sound waves to eject picoliter to nanoliter crystal-containing droplets out of microplates and into the X-ray pulse from which diffraction data are collected. The on-demand droplet delivery is synchronized to the XFEL pulse scheme, resulting in X-ray pulses intersecting up to 88% of the droplets. We tested several types of samples in a range of crystallization conditions, wherein the overall crystal hit ratio (e.g., fraction of images with observable diffraction patterns) is a function of the microcrystal slurry concentration. We report crystal structures from lysozyme, thermolysin, and stachydrine demethylase (Stc2). Additional samples were screened to demonstrate that these methods can be applied to rare samples.
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Affiliation(s)
- Christian G Roessler
- Photon Sciences Division, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Rakhi Agarwal
- Biosciences Department, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Marc Allaire
- Photon Sciences Division, Brookhaven National Laboratory, Upton, NY 11973-5000, USA.
| | - Roberto Alonso-Mori
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Babak Andi
- Photon Sciences Division, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - José F R Bachega
- Centro de Biotecnologia Molecular Estrutural, Instituto de Física de São Carlos, Universidade de São Paulo, Caixa Postal 369, São Carlos, CEP: 13560-970, Brazil
| | - Martin Bommer
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany
| | - Aaron S Brewster
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8177, USA
| | - Michael C Browne
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Ruchira Chatterjee
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8177, USA
| | - Eunsun Cho
- Department of Chemistry, Boston University, Boston, MA 02215-2521, USA
| | - Aina E Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Matthew Cowan
- Photon Sciences Division, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | | | - Victor L Davidson
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32816-2364, USA
| | - Jim Defever
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | | | | | - Yiping Feng
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | | | - James M Glownia
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Guangye Han
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8177, USA
| | - Johan Hattne
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8177, USA
| | - Julia Hellmich
- Max-Volmer-Laboratorium für Biophysikalische Chemie, Technische Universität, D-10623 Berlin, Germany; Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany
| | - Annie Héroux
- Photon Sciences Division, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Mohamed Ibrahim
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany
| | - Jan Kern
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8177, USA; Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Anthony Kuczewski
- Photon Sciences Division, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Henrik T Lemke
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Pinghua Liu
- Department of Chemistry, Boston University, Boston, MA 02215-2521, USA
| | | | | | - Stuart Myers
- Photon Sciences Division, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Silke Nelsen
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | | | - Allen M Orville
- Photon Sciences Division, Brookhaven National Laboratory, Upton, NY 11973-5000, USA; Biosciences Department, Brookhaven National Laboratory, Upton, NY 11973-5000, USA.
| | - Nicholas K Sauter
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8177, USA
| | - Alexei S Soares
- Photon Sciences Division, Brookhaven National Laboratory, Upton, NY 11973-5000, USA.
| | - S Michael Soltis
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Heng Song
- Department of Chemistry, Boston University, Boston, MA 02215-2521, USA
| | | | - Rosalie Tran
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8177, USA
| | - Yingssu Tsai
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA; Department of Chemistry, Stanford University, Stanford, CA 94305-4401, USA
| | | | - Carrie M Wilmot
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Vittal Yachandra
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8177, USA
| | - Junko Yano
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8177, USA
| | - Erik T Yukl
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Diling Zhu
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Athina Zouni
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany
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77
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Dynamic structures in DNA damage responses & cancer. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2016; 117:129-133. [PMID: 25934179 DOI: 10.1016/j.pbiomolbio.2015.04.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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78
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Boutet S, Cohen A, Wakatsuki S. The New Macromolecular Femtosecond Crystallography (MFX) Instrument at LCLS. SYNCHROTRON RADIATION NEWS 2016; 29:23-28. [PMID: 28736484 PMCID: PMC5519296 DOI: 10.1080/08940886.2016.1124681] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Aina Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Soichi Wakatsuki
- Bioscience Division, SLAC National Accelerator Laboratory, Menlo Park, California, USA
- Structural Biology, School of Medicine, Stanford University, Stanford, California, USA
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79
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Crystal structure of the pristine peroxidase ferryl center and its relevance to proton-coupled electron transfer. Proc Natl Acad Sci U S A 2016; 113:1226-31. [PMID: 26787871 DOI: 10.1073/pnas.1521664113] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The reaction of peroxides with peroxidases oxidizes the heme iron from Fe(III) to Fe(IV)=O and a porphyrin or aromatic side chain to a cationic radical. X-ray-generated hydrated electrons rapidly reduce Fe(IV), thereby requiring very short exposures using many crystals, and, even then, some reduction cannot be avoided. The new generation of X-ray free electron lasers capable of generating intense X-rays on the tenths of femtosecond time scale enables structure determination with no reduction or X-ray damage. Here, we report the 1.5-Å crystal structure of cytochrome c peroxidase (CCP) compound I (CmpI) using data obtained with the Stanford Linear Coherent Light Source (LCLS). This structure is consistent with previous structures. Of particular importance is the active site water structure that can mediate the proton transfer reactions required for both CmpI formation and reduction of Fe(IV)=O to Fe(III)-OH. The structures indicate that a water molecule is ideally positioned to shuttle protons between an iron-linked oxygen and the active site catalytic His. We therefore have carried out both computational and kinetic studies to probe the reduction of Fe(IV)=O. Kinetic solvent isotope experiments show that the transfer of a single proton is critical in the peroxidase rate-limiting step, which is very likely the proton-coupled reduction of Fe(IV)=O to Fe(III)-OH. We also find that the pKa of the catalytic His substantially increases in CmpI, indicating that this active site His is the source of the proton required in the reduction of Fe(IV)=O to Fe(IV)-OH.
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80
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Baxter EL, Aguila L, Alonso-Mori R, Barnes CO, Bonagura CA, Brehmer W, Brunger AT, Calero G, Caradoc-Davies TT, Chatterjee R, Degrado WF, Fraser JS, Ibrahim M, Kern J, Kobilka BK, Kruse AC, Larsson KM, Lemke HT, Lyubimov AY, Manglik A, McPhillips SE, Norgren E, Pang SS, Soltis SM, Song J, Thomaston J, Tsai Y, Weis WI, Woldeyes RA, Yachandra V, Yano J, Zouni A, Cohen AE. High-density grids for efficient data collection from multiple crystals. Acta Crystallogr D Struct Biol 2016; 72:2-11. [PMID: 26894529 PMCID: PMC4756618 DOI: 10.1107/s2059798315020847] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 11/03/2015] [Indexed: 03/01/2023] Open
Abstract
Higher throughput methods to mount and collect data from multiple small and radiation-sensitive crystals are important to support challenging structural investigations using microfocus synchrotron beamlines. Furthermore, efficient sample-delivery methods are essential to carry out productive femtosecond crystallography experiments at X-ray free-electron laser (XFEL) sources such as the Linac Coherent Light Source (LCLS). To address these needs, a high-density sample grid useful as a scaffold for both crystal growth and diffraction data collection has been developed and utilized for efficient goniometer-based sample delivery at synchrotron and XFEL sources. A single grid contains 75 mounting ports and fits inside an SSRL cassette or uni-puck storage container. The use of grids with an SSRL cassette expands the cassette capacity up to 7200 samples. Grids may also be covered with a polymer film or sleeve for efficient room-temperature data collection from multiple samples. New automated routines have been incorporated into the Blu-Ice/DCSS experimental control system to support grids, including semi-automated grid alignment, fully automated positioning of grid ports, rastering and automated data collection. Specialized tools have been developed to support crystallization experiments on grids, including a universal adaptor, which allows grids to be filled by commercial liquid-handling robots, as well as incubation chambers, which support vapor-diffusion and lipidic cubic phase crystallization experiments. Experiments in which crystals were loaded into grids or grown on grids using liquid-handling robots and incubation chambers are described. Crystals were screened at LCLS-XPP and SSRL BL12-2 at room temperature and cryogenic temperatures.
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Affiliation(s)
- Elizabeth L. Baxter
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Laura Aguila
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Roberto Alonso-Mori
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Christopher O. Barnes
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | | | - Winnie Brehmer
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Axel T. Brunger
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Guillermo Calero
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Tom T. Caradoc-Davies
- The ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, Victoria 3800, Australia
- Australian Synchrotron, 800 Blackburn Road, Clayton, Melbourne, Victoria 3168, Australia
| | - Ruchira Chatterjee
- Physical Bioscences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - William F. Degrado
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - James S. Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
| | - Mohamed Ibrahim
- Institut für Biologie, Humboldt-Universität zu Berlin, 10099 Berlin, Germany
| | - Jan Kern
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
- Physical Bioscences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Brian K. Kobilka
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
| | - Andrew C. Kruse
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
| | - Karl M. Larsson
- Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Heinrik T. Lemke
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Artem Y. Lyubimov
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Aashish Manglik
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
| | - Scott E. McPhillips
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Erik Norgren
- Art Robbins Instruments, Sunnyvale, CA 94089, USA
| | - Siew S. Pang
- The ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, Victoria 3800, Australia
| | - S. M. Soltis
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Jinhu Song
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Jessica Thomaston
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Yingssu Tsai
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - William I. Weis
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
| | - Rahel A. Woldeyes
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
| | - Vittal Yachandra
- Physical Bioscences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Junko Yano
- Physical Bioscences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Athina Zouni
- Institut für Biologie, Humboldt-Universität zu Berlin, 10099 Berlin, Germany
| | - Aina E. Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
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81
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82
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Affiliation(s)
- Elspeth F. Garman
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, Oxford, UK
| | - Martin Weik
- University Grenoble Alpes, Grenoble, France
- CNRS, IBS, Grenoble, France
- CEA, IBS, Grenoble, France
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83
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Yefanov O, Mariani V, Gati C, White TA, Chapman HN, Barty A. Accurate determination of segmented X-ray detector geometry. OPTICS EXPRESS 2015; 23:28459-70. [PMID: 26561117 PMCID: PMC4646514 DOI: 10.1364/oe.23.028459] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 09/18/2015] [Accepted: 10/09/2015] [Indexed: 05/21/2023]
Abstract
Recent advances in X-ray detector technology have resulted in the introduction of segmented detectors composed of many small detector modules tiled together to cover a large detection area. Due to mechanical tolerances and the desire to be able to change the module layout to suit the needs of different experiments, the pixels on each module might not align perfectly on a regular grid. Several detectors are designed to permit detector sub-regions (or modules) to be moved relative to each other for different experiments. Accurate determination of the location of detector elements relative to the beam-sample interaction point is critical for many types of experiment, including X-ray crystallography, coherent diffractive imaging (CDI), small angle X-ray scattering (SAXS) and spectroscopy. For detectors with moveable modules, the relative positions of pixels are no longer fixed, necessitating the development of a simple procedure to calibrate detector geometry after reconfiguration. We describe a simple and robust method for determining the geometry of segmented X-ray detectors using measurements obtained by serial crystallography. By comparing the location of observed Bragg peaks to the spot locations predicted from the crystal indexing procedure, the position, rotation and distance of each module relative to the interaction region can be refined. We show that the refined detector geometry greatly improves the results of experiments.
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Affiliation(s)
- 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
| | - Cornelius Gati
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Thomas A. White
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - 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, 22607 Hamburg, Germany
- Centre for Ultrafast Imaging, Luruper Chaussee 149, 22607 Hamburg, Germany
| | - Anton Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
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84
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Sherrell DA, Foster AJ, Hudson L, Nutter B, O’Hea J, Nelson S, Paré-Labrosse O, Oghbaey S, Miller RJD, Owen RL. A modular and compact portable mini-endstation for high-precision, high-speed fixed target serial crystallography at FEL and synchrotron sources. JOURNAL OF SYNCHROTRON RADIATION 2015; 22:1372-8. [PMID: 26524301 PMCID: PMC4629865 DOI: 10.1107/s1600577515016938] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 09/10/2015] [Indexed: 05/18/2023]
Abstract
The design and implementation of a compact and portable sample alignment system suitable for use at both synchrotron and free-electron laser (FEL) sources and its performance are described. The system provides the ability to quickly and reliably deliver large numbers of samples using the minimum amount of sample possible, through positioning of fixed target arrays into the X-ray beam. The combination of high-precision stages, high-quality sample viewing, a fast controller and a software layer overcome many of the challenges associated with sample alignment. A straightforward interface that minimizes setup and sample changeover time as well as simplifying communication with the stages during the experiment is also described, together with an intuitive naming convention for defining, tracking and locating sample positions. The setup allows the precise delivery of samples in predefined locations to a specific position in space and time, reliably and simply.
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Affiliation(s)
- Darren A. Sherrell
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 ODE, UK
| | - Andrew J. Foster
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 ODE, UK
| | - Lee Hudson
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 ODE, UK
| | - Brian Nutter
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 ODE, UK
| | - James O’Hea
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 ODE, UK
| | - Silke Nelson
- LCLS, SLAC National Laboratory, Menlo Park, CA 94025, USA
| | - Olivier Paré-Labrosse
- Department of Chemistry and Physics, University of Toronto, 80 St George St, Toronto, ON M5S 1A8, Canada
| | - Saeed Oghbaey
- Department of Chemistry and Physics, University of Toronto, 80 St George St, Toronto, ON M5S 1A8, Canada
| | - R. J. Dwayne Miller
- Department of Chemistry and Physics, University of Toronto, 80 St George St, Toronto, ON M5S 1A8, Canada
- The Max Planck Institute for the Structure and Dynamics of Matter, and Hamburg Centre for Ultrafast Imaging, CFEL Building 99, Luruper Chaussee 149, Hamburg 22761, Germany
| | - Robin L. Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 ODE, UK
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85
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Murray TD, Lyubimov AY, Ogata CM, Vo H, Uervirojnangkoorn M, Brunger AT, Berger JM. A high-transparency, micro-patternable chip for X-ray diffraction analysis of microcrystals under native growth conditions. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:1987-97. [PMID: 26457423 PMCID: PMC4601365 DOI: 10.1107/s1399004715015011] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 08/11/2015] [Indexed: 11/14/2022]
Abstract
Microcrystals present a significant impediment to the determination of macromolecular structures by X-ray diffraction methods. Although microfocus synchrotron beamlines and X-ray free-electron lasers (XFELs) can enable the collection of interpretable diffraction data from microcrystals, there is a need for efficient methods of harvesting small volumes (<2 µl) of microcrystals grown under common laboratory formats and delivering them to an X-ray beam source under native growth conditions. One approach that shows promise in overcoming the challenges intrinsic to microcrystal analysis is to pair so-called `fixed-target' sample-delivery devices with microbeam-based X-ray diffraction methods. However, to record weak diffraction patterns it is necessary to fabricate devices from X-ray-transparent materials that minimize background scattering. Presented here is the design of a new micro-diffraction device consisting of three layers fabricated from silicon nitride, photoresist and polyimide film. The chip features low X-ray scattering and X-ray absorption properties, and uses a customizable blend of hydrophobic and hydrophilic surface patterns to help localize microcrystals to defined regions. Microcrystals in their native growth conditions can be loaded into the chips with a standard pipette, allowing data collection at room temperature. Diffraction data collected from hen egg-white lysozyme microcrystals (10-15 µm) loaded into the chips yielded a complete, high-resolution (<1.6 Å) data set sufficient to determine a high-quality structure by molecular replacement. The features of the chip allow the rapid and user-friendly analysis of microcrystals grown under virtually any laboratory format at microfocus synchrotron beamlines and XFELs.
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Affiliation(s)
- Thomas D. Murray
- Biophysics Graduate Group, University of California, Berkeley, CA 94720, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Artem Y. Lyubimov
- Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, Structural Biology and Photon Science, and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Craig M. Ogata
- GM/CA@APS, X-Ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Huy Vo
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Monarin Uervirojnangkoorn
- Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, Structural Biology and Photon Science, and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Axel T. Brunger
- Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, Structural Biology and Photon Science, and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - James M. Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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86
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Keedy DA, Kenner LR, Warkentin M, Woldeyes RA, Hopkins JB, Thompson MC, Brewster AS, Van Benschoten AH, Baxter EL, Uervirojnangkoorn M, McPhillips SE, Song J, Alonso-Mori R, Holton JM, Weis WI, Brunger AT, Soltis SM, Lemke H, Gonzalez A, Sauter NK, Cohen AE, van den Bedem H, Thorne RE, Fraser JS. Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography. eLife 2015; 4. [PMID: 26422513 PMCID: PMC4721965 DOI: 10.7554/elife.07574] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 09/29/2015] [Indexed: 12/14/2022] Open
Abstract
Determining the interconverting conformations of dynamic proteins in atomic detail is a major challenge for structural biology. Conformational heterogeneity in the active site of the dynamic enzyme cyclophilin A (CypA) has been previously linked to its catalytic function, but the extent to which the different conformations of these residues are correlated is unclear. Here we compare the conformational ensembles of CypA by multitemperature synchrotron crystallography and fixed-target X-ray free-electron laser (XFEL) crystallography. The diffraction-before-destruction nature of XFEL experiments provides a radiation-damage-free view of the functionally important alternative conformations of CypA, confirming earlier synchrotron-based results. We monitored the temperature dependences of these alternative conformations with eight synchrotron datasets spanning 100-310 K. Multiconformer models show that many alternative conformations in CypA are populated only at 240 K and above, yet others remain populated or become populated at 180 K and below. These results point to a complex evolution of conformational heterogeneity between 180-–240 K that involves both thermal deactivation and solvent-driven arrest of protein motions in the crystal. The lack of a single shared conformational response to temperature within the dynamic active-site network provides evidence for a conformation shuffling model, in which exchange between rotamer states of a large aromatic ring in the middle of the network shifts the conformational ensemble for the other residues in the network. Together, our multitemperature analyses and XFEL data motivate a new generation of temperature- and time-resolved experiments to structurally characterize the dynamic underpinnings of protein function. DOI:http://dx.doi.org/10.7554/eLife.07574.001 Proteins are the workhorses of the cell. The shape that a protein molecule adopts enables it to carry out its role. However, a protein’s shape, or 'conformation', is not static. Instead, a protein can shift between different conformations. This is particularly true for enzymes – the proteins that catalyze chemical reactions. The region of an enzyme where the chemical reaction happens, known as the active site, often has to change its conformation to allow catalysis to proceed. Changes in temperature can also make a protein shift between alternative conformations. Understanding how a protein shifts between conformations gives insight into how it works. A common method for studying protein conformation is X-ray crystallography. This technique uses a beam of X-rays to figure out where the atoms of the protein are inside a crystal made of millions of copies of that protein. At room temperature or biological temperature, X-rays can rapidly damage the protein. Because of this, most crystal structures are determined at very low temperatures to minimize damage. But cooling to low temperatures changes the conformations that the protein adopts, and usually causes fewer conformations to be present. Keedy, Kenner, Warkentin, Woldeyes et al. have used X-ray crystallography from a very low temperature (-173°C or 100 K) to above room temperature (up to 27°C or 300 K) to explore the alternative conformations of an enzyme called cyclophilin A. These alternative conformations include those that have previously been linked to this enzyme’s activity. Starting at a low temperature, parts of the enzyme were seen to shift from having a single conformation to many conformations above a threshold temperature. Unexpectedly, different parts of the enzyme have different threshold temperatures, suggesting that there isn’t a single transition across the whole protein. Instead, it appears the way a protein’s conformation changes in response to temperature is more complex than was previously realized. This result suggests that conformations in different parts of a protein are coupled to each other in complex ways. Keedy, Kenner, Warkentin, Woldeyes et al. then performed X-ray crystallography at room temperature using an X-ray free-electron laser (XFEL). This technique can capture the protein’s structure before radiation damage occurs, and confirmed that the alternative conformations observed were not affected by radiation damage. The combination of X-ray crystallography at multiple temperatures, new analysis methods for identifying and measuring alternative conformations, and XFEL crystallography should help future studies to characterize conformational changes in other proteins. DOI:http://dx.doi.org/10.7554/eLife.07574.002
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Affiliation(s)
- Daniel A Keedy
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
| | - Lillian R Kenner
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
| | | | - Rahel A Woldeyes
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
| | - Jesse B Hopkins
- Department of Physics, Cornell University, Ithaca, United States
| | - Michael C Thompson
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
| | - Aaron S Brewster
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Andrew H Van Benschoten
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
| | - Elizabeth L Baxter
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, United States
| | - Monarin Uervirojnangkoorn
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, United States
| | - Scott E McPhillips
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, United States
| | - Jinhu Song
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, United States
| | - Roberto Alonso-Mori
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, United States
| | - James M Holton
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States.,Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, United States.,Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - William I Weis
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Department of Structural Biology, Stanford University, Stanford, United States.,Department of Photon Science, SLAC National Accelerator Laboratory, Menlo Park, United States
| | - Axel T Brunger
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, United States.,Department of Structural Biology, Stanford University, Stanford, United States.,Department of Photon Science, SLAC National Accelerator Laboratory, Menlo Park, United States
| | - S Michael Soltis
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, United States
| | - Henrik Lemke
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, United States
| | - Ana Gonzalez
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, United States
| | - Nicholas K Sauter
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Aina E Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, United States
| | - Henry van den Bedem
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, United States
| | - Robert E Thorne
- Department of Physics, Cornell University, Ithaca, United States
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
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87
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Zhou Q, Lai Y, Bacaj T, Zhao M, Lyubimov AY, Uervirojnangkoorn M, Zeldin OB, Brewster AS, Sauter NK, Cohen AE, Soltis SM, Alonso-Mori R, Chollet M, Lemke HT, Pfuetzner RA, Choi UB, Weis WI, Diao J, Südhof TC, Brunger AT. Architecture of the synaptotagmin-SNARE machinery for neuronal exocytosis. Nature 2015; 525:62-7. [PMID: 26280336 PMCID: PMC4607316 DOI: 10.1038/nature14975] [Citation(s) in RCA: 219] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 07/27/2015] [Indexed: 02/07/2023]
Abstract
Synaptotagmin-1 and neuronal SNARE proteins have central roles in evoked synchronous neurotransmitter release; however, it is unknown how they cooperate to trigger synaptic vesicle fusion. Here we report atomic-resolution crystal structures of Ca(2+)- and Mg(2+)-bound complexes between synaptotagmin-1 and the neuronal SNARE complex, one of which was determined with diffraction data from an X-ray free-electron laser, leading to an atomic-resolution structure with accurate rotamer assignments for many side chains. The structures reveal several interfaces, including a large, specific, Ca(2+)-independent and conserved interface. Tests of this interface by mutagenesis suggest that it is essential for Ca(2+)-triggered neurotransmitter release in mouse hippocampal neuronal synapses and for Ca(2+)-triggered vesicle fusion in a reconstituted system. We propose that this interface forms before Ca(2+) triggering, moves en bloc as Ca(2+) influx promotes the interactions between synaptotagmin-1 and the plasma membrane, and consequently remodels the membrane to promote fusion, possibly in conjunction with other interfaces.
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Affiliation(s)
- Qiangjun Zhou
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
- Departments of Neurology and Neurological Sciences, Photon Science, and Structural Biology, Stanford University, Stanford, California 94305, USA
| | - Ying Lai
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
- Departments of Neurology and Neurological Sciences, Photon Science, and Structural Biology, Stanford University, Stanford, California 94305, USA
| | - Taulant Bacaj
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
| | - Minglei Zhao
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
- Departments of Neurology and Neurological Sciences, Photon Science, and Structural Biology, Stanford University, Stanford, California 94305, USA
| | - Artem Y Lyubimov
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
- Departments of Neurology and Neurological Sciences, Photon Science, and Structural Biology, Stanford University, Stanford, California 94305, USA
| | - Monarin Uervirojnangkoorn
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
- Departments of Neurology and Neurological Sciences, Photon Science, and Structural Biology, Stanford University, Stanford, California 94305, USA
| | - Oliver B Zeldin
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
- Departments of Neurology and Neurological Sciences, Photon Science, and Structural Biology, Stanford University, Stanford, California 94305, USA
| | - Aaron S Brewster
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Nicholas K Sauter
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Aina E Cohen
- SLAC National Accelerator Laboratory, Stanford, California 94305, USA
| | - S Michael Soltis
- SLAC National Accelerator Laboratory, Stanford, California 94305, USA
| | | | - Matthieu Chollet
- SLAC National Accelerator Laboratory, Stanford, California 94305, USA
| | - Henrik T Lemke
- SLAC National Accelerator Laboratory, Stanford, California 94305, USA
| | - Richard A Pfuetzner
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
- Departments of Neurology and Neurological Sciences, Photon Science, and Structural Biology, Stanford University, Stanford, California 94305, USA
| | - Ucheor B Choi
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
- Departments of Neurology and Neurological Sciences, Photon Science, and Structural Biology, Stanford University, Stanford, California 94305, USA
| | - William I Weis
- Departments of Structural Biology, Molecular and Cellular Physiology, and Photon Science, Stanford University, Stanford, California 94305, USA
| | - Jiajie Diao
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
- Departments of Neurology and Neurological Sciences, Photon Science, and Structural Biology, Stanford University, Stanford, California 94305, USA
| | - Thomas C Südhof
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
| | - Axel T Brunger
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
- Departments of Neurology and Neurological Sciences, Photon Science, and Structural Biology, Stanford University, Stanford, California 94305, USA
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88
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Kern J, Yachandra VK, Yano J. Metalloprotein structures at ambient conditions and in real-time: biological crystallography and spectroscopy using X-ray free electron lasers. Curr Opin Struct Biol 2015; 34:87-98. [PMID: 26342144 DOI: 10.1016/j.sbi.2015.07.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 07/23/2015] [Accepted: 07/24/2015] [Indexed: 10/23/2022]
Abstract
Although the structure of enzymes and the chemistry at the catalytic sites have been studied intensively, an understanding of the atomic-scale chemistry requires a new approach beyond steady state X-ray crystallography and X-ray spectroscopy at cryogenic temperatures. Following the dynamic changes in the geometric and electronic structure of metallo-enzymes at ambient conditions, while overcoming the severe X-ray-induced changes to the redox active catalytic center, is key for deriving reaction mechanisms. Such studies become possible by the intense and ultra-short femtosecond (fs) X-ray pulses from an X-ray free electron laser (XFEL) by acquiring a signal before the sample is destroyed. This review describes the recent and pioneering uses of XFELs to study the protein structure and dynamics of metallo-enzymes using crystallography and scattering, as well as the chemical structure and dynamics of the catalytic complexes (charge, spin, and covalency) using spectroscopy during the reaction to understand the electron-transfer processes and elucidate the mechanism.
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Affiliation(s)
- Jan Kern
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
| | - Vittal K Yachandra
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Junko Yano
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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89
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Dao EH, Sierra RG, Laksmono H, Lemke HT, Alonso-Mori R, Coey A, Larsen K, Baxter EL, Cohen AE, Soltis SM, DeMirci H. Goniometer-based femtosecond X-ray diffraction of mutant 30S ribosomal subunit crystals. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2015; 2:041706. [PMID: 26798805 PMCID: PMC4711619 DOI: 10.1063/1.4919407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 04/20/2015] [Indexed: 06/05/2023]
Abstract
In this work, we collected radiation-damage-free data from a set of cryo-cooled crystals for a novel 30S ribosomal subunit mutant using goniometer-based femtosecond crystallography. Crystal quality assessment for these samples was conducted at the X-ray Pump Probe end-station of the Linac Coherent Light Source (LCLS) using recently introduced goniometer-based instrumentation. These 30S subunit crystals were genetically engineered to omit a 26-residue protein, Thx, which is present in the wild-type Thermus thermophilus 30S ribosomal subunit. We are primarily interested in elucidating the contribution of this ribosomal protein to the overall 30S subunit structure. To assess the viability of this study, femtosecond X-ray diffraction patterns from these crystals were recorded at the LCLS during a protein crystal screening beam time. During our data collection, we successfully observed diffraction from these difficult-to-grow 30S ribosomal subunit crystals. Most of our crystals were found to diffract to low resolution, while one crystal diffracted to 3.2 Å resolution. These data suggest the feasibility of pursuing high-resolution data collection as well as the need to improve sample preparation and handling in order to collect a complete radiation-damage-free data set using an X-ray Free Electron Laser.
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Affiliation(s)
- E Han Dao
- Stanford PULSE Institute, SLAC National Accelerator Laboratory , Menlo Park, California 94025, USA
| | - Raymond G Sierra
- Stanford PULSE Institute, SLAC National Accelerator Laboratory , Menlo Park, California 94025, USA
| | - Hartawan Laksmono
- Stanford PULSE Institute, SLAC National Accelerator Laboratory , Menlo Park, California 94025, USA
| | - Henrik T Lemke
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory , Menlo Park, California 94025, USA
| | - Roberto Alonso-Mori
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory , Menlo Park, California 94025, USA
| | - Aaron Coey
- Biophysics Program, Stanford University School of Medicine , Stanford, California 94305, USA
| | - Kevin Larsen
- Biophysics Program, Stanford University School of Medicine , Stanford, California 94305, USA
| | - Elizabeth L Baxter
- Stanford Synchrotron Radiation Lightsource (SSRL), SLAC National Accelerator Laboratory , Menlo Park, California 94025, USA
| | - Aina E Cohen
- Stanford Synchrotron Radiation Lightsource (SSRL), SLAC National Accelerator Laboratory , Menlo Park, California 94025, USA
| | - S Michael Soltis
- Stanford Synchrotron Radiation Lightsource (SSRL), SLAC National Accelerator Laboratory , Menlo Park, California 94025, USA
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90
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Rodriguez JA. Accessible atomic structures from sub-micron protein crystals. Acta Crystallogr A Found Adv 2015; 71:351-2. [DOI: 10.1107/s2053273315012206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 06/26/2015] [Indexed: 11/10/2022] Open
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91
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Luft JR, Wolfley JR, Franks EC, Lauricella AM, Gualtieri EJ, Snell EH, Xiao R, Everett JK, Montelione GT. The detection and subsequent volume optimization of biological nanocrystals. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2015; 2:041710. [PMID: 26798809 PMCID: PMC4711624 DOI: 10.1063/1.4921199] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 05/05/2015] [Indexed: 06/05/2023]
Abstract
Identifying and then optimizing initial crystallization conditions is a prerequisite for macromolecular structure determination by crystallography. Improved technologies enable data collection on crystals that are difficult if not impossible to detect using visible imaging. The application of second-order nonlinear imaging of chiral crystals and ultraviolet two-photon excited fluorescence detection is shown to be applicable in a high-throughput manner to rapidly verify the presence of nanocrystals in crystallization screening conditions. It is noted that the nanocrystals are rarely seen without also producing microcrystals from other chemical conditions. A crystal volume optimization method is described and associated with a phase diagram for crystallization.
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Affiliation(s)
| | - Jennifer R Wolfley
- Hauptman-Woodward Medical Research Institute , 700 Ellicott Street, Buffalo, New York 14203, USA
| | - Eleanor Cook Franks
- Hauptman-Woodward Medical Research Institute , 700 Ellicott Street, Buffalo, New York 14203, USA
| | - Angela M Lauricella
- Hauptman-Woodward Medical Research Institute , 700 Ellicott Street, Buffalo, New York 14203, USA
| | - Ellen J Gualtieri
- Formulatrix, Inc. , 10 DeAngelo Drive, Bedford, Massachusetts 01730, USA
| | | | - Rong Xiao
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, and Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey , 679 Hoes Lane, Piscataway, New Jersey 08854-8021, USA
| | - John K Everett
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, and Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey , 679 Hoes Lane, Piscataway, New Jersey 08854-8021, USA
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92
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Chavas LMG, Gumprecht L, Chapman HN. Possibilities for serial femtosecond crystallography sample delivery at future light sources. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2015; 2:041709. [PMID: 26798808 PMCID: PMC4711622 DOI: 10.1063/1.4921220] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 05/06/2015] [Indexed: 05/23/2023]
Abstract
Serial femtosecond crystallography (SFX) uses X-ray pulses from free-electron laser (FEL) sources that can outrun radiation damage and thereby overcome long-standing limits in the structure determination of macromolecular crystals. Intense X-ray FEL pulses of sufficiently short duration allow the collection of damage-free data at room temperature and give the opportunity to study irreversible time-resolved events. SFX may open the way to determine the structure of biological molecules that fail to crystallize readily into large well-diffracting crystals. Taking advantage of FELs with high pulse repetition rates could lead to short measurement times of just minutes. Automated delivery of sample suspensions for SFX experiments could potentially give rise to a much higher rate of obtaining complete measurements than at today's third generation synchrotron radiation facilities, as no crystal alignment or complex robotic motions are required. This capability will also open up extensive time-resolved structural studies. New challenges arise from the resulting high rate of data collection, and in providing reliable sample delivery. Various developments for fully automated high-throughput SFX experiments are being considered for evaluation, including new implementations for a reliable yet flexible sample environment setup. Here, we review the different methods developed so far that best achieve sample delivery for X-ray FEL experiments and present some considerations towards the goal of high-throughput structure determination with X-ray FELs.
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Affiliation(s)
- L M G Chavas
- Center for Free-Electron Laser Science, DESY , Notkestraße 85, 22607 Hamburg, Germany
| | - L Gumprecht
- Center for Free-Electron Laser Science, DESY , Notkestraße 85, 22607 Hamburg, Germany
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93
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Huang CY, Olieric V, Ma P, Panepucci E, Diederichs K, Wang M, Caffrey M. In meso in situ serial X-ray crystallography of soluble and membrane proteins. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:1238-56. [PMID: 26057665 PMCID: PMC4461204 DOI: 10.1107/s1399004715005210] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 03/13/2015] [Indexed: 11/21/2022]
Abstract
The lipid cubic phase (LCP) continues to grow in popularity as a medium in which to generate crystals of membrane (and soluble) proteins for high-resolution X-ray crystallographic structure determination. To date, the PDB includes 227 records attributed to the LCP or in meso method. Among the listings are some of the highest profile membrane proteins, including the β2-adrenoreceptor-Gs protein complex that figured in the award of the 2012 Nobel Prize in Chemistry to Lefkowitz and Kobilka. The most successful in meso protocol to date uses glass sandwich crystallization plates. Despite their many advantages, glass plates are challenging to harvest crystals from. However, performing in situ X-ray diffraction measurements with these plates is not practical. Here, an alternative approach is described that provides many of the advantages of glass plates and is compatible with high-throughput in situ measurements. The novel in meso in situ serial crystallography (IMISX) method introduced here has been demonstrated with AlgE and PepT (alginate and peptide transporters, respectively) as model integral membrane proteins and with lysozyme as a test soluble protein. Structures were solved by molecular replacement and by experimental phasing using bromine SAD and native sulfur SAD methods to resolutions ranging from 1.8 to 2.8 Å using single-digit microgram quantities of protein. That sulfur SAD phasing worked is testament to the exceptional quality of the IMISX diffraction data. The IMISX method is compatible with readily available, inexpensive materials and equipment, is simple to implement and is compatible with high-throughput in situ serial data collection at macromolecular crystallography synchrotron beamlines worldwide. Because of its simplicity and effectiveness, the IMISX approach is likely to supplant existing in meso crystallization protocols. It should prove particularly attractive in the area of ligand screening for drug discovery and development.
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Affiliation(s)
- Chia-Ying Huang
- Membrane Structural and Functional Biology Group, Schools of Medicine and Biochemistry and Immunology, Trinity College, Dublin, Ireland
| | - Vincent Olieric
- Swiss Light Source, Paul Scherrer Institute, CH-5232 Villigen, Switzerland
| | - Pikyee Ma
- Membrane Structural and Functional Biology Group, Schools of Medicine and Biochemistry and Immunology, Trinity College, Dublin, Ireland
| | - Ezequiel Panepucci
- Swiss Light Source, Paul Scherrer Institute, CH-5232 Villigen, Switzerland
| | - Kay Diederichs
- Fachbereich Biologie, Universität Konstanz, M647, D-78457 Konstanz, Germany
| | - Meitian Wang
- Swiss Light Source, Paul Scherrer Institute, CH-5232 Villigen, Switzerland
| | - Martin Caffrey
- Membrane Structural and Functional Biology Group, Schools of Medicine and Biochemistry and Immunology, Trinity College, Dublin, Ireland
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94
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Teplitsky E, Joshi K, Ericson DL, Scalia A, Mullen JD, Sweet RM, Soares AS. High throughput screening using acoustic droplet ejection to combine protein crystals and chemical libraries on crystallization plates at high density. J Struct Biol 2015; 191:49-58. [PMID: 26027487 DOI: 10.1016/j.jsb.2015.05.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 05/21/2015] [Accepted: 05/27/2015] [Indexed: 11/30/2022]
Abstract
We describe a high throughput method for screening up to 1728 distinct chemicals with protein crystals on a single microplate. Acoustic droplet ejection (ADE) was used to co-position 2.5nL of protein, precipitant, and chemicals on a MiTeGen in situ-1 crystallization plate™ for screening by co-crystallization or soaking. ADE-transferred droplets follow a precise trajectory which allows all components to be transferred through small apertures in the microplate lid. The apertures were large enough for 2.5nL droplets to pass through them, but small enough so that they did not disrupt the internal environment created by the mother liquor. Using this system, thermolysin and trypsin crystals were efficiently screened for binding to a heavy-metal mini-library. Fluorescence and X-ray diffraction were used to confirm that each chemical in the heavy-metal library was correctly paired with the intended protein crystal. A fragment mini-library was screened to observe two known lysozyme ligands using both co-crystallization and soaking. A similar approach was used to identify multiple, novel thaumatin binding sites for ascorbic acid. This technology pushes towards a faster, automated, and more flexible strategy for high throughput screening of chemical libraries (such as fragment libraries) using as little as 2.5nL of each component.
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Affiliation(s)
- Ella Teplitsky
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA; Department of Biochemistry and Cell Biology, Stony Brook University, NY 11794-5215, USA
| | - Karan Joshi
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA; Department of Electronics and Electrical Communication Engineering, PEC University of Technology, Chandigarh, India
| | - Daniel L Ericson
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA; Department of Biomedical Engineering, University at Buffalo, SUNY, 12 Capen Hall, Buffalo, NY 14260, USA
| | - Alexander Scalia
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA; Department of Biological Sciences, 4400 Vestal Parkway East, Binghamton University, NY 13902, USA
| | - Jeffrey D Mullen
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA; Physics Department, University of Oregon, Eugene, OR 97403-1274, USA
| | - Robert M Sweet
- Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Alexei S Soares
- Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY 11973-5000, USA.
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95
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Coquelle N, Brewster AS, Kapp U, Shilova A, Weinhausen B, Burghammer M, Colletier JP. Raster-scanning serial protein crystallography using micro- and nano-focused synchrotron beams. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:1184-96. [PMID: 25945583 PMCID: PMC4427202 DOI: 10.1107/s1399004715004514] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 03/04/2015] [Indexed: 01/30/2023]
Abstract
High-resolution structural information was obtained from lysozyme microcrystals (20 µm in the largest dimension) using raster-scanning serial protein crystallography on micro- and nano-focused beamlines at the ESRF. Data were collected at room temperature (RT) from crystals sandwiched between two silicon nitride wafers, thereby preventing their drying, while limiting background scattering and sample consumption. In order to identify crystal hits, new multi-processing and GUI-driven Python-based pre-analysis software was developed, named NanoPeakCell, that was able to read data from a variety of crystallographic image formats. Further data processing was carried out using CrystFEL, and the resultant structures were refined to 1.7 Å resolution. The data demonstrate the feasibility of RT raster-scanning serial micro- and nano-protein crystallography at synchrotrons and validate it as an alternative approach for the collection of high-resolution structural data from micro-sized crystals. Advantages of the proposed approach are its thriftiness, its handling-free nature, the reduced amount of sample required, the adjustable hit rate, the high indexing rate and the minimization of background scattering.
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Affiliation(s)
- Nicolas Coquelle
- Université Grenoble Alpes, IBS, 38044 Grenoble, France
- CNRS, IBS, 38044 Grenoble, France
- CEA, IBS, 38044 Grenoble, France
| | - Aaron S. Brewster
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ulrike Kapp
- European Synchrotron Radiation Facility, BP 220, 38043 Grenoble, France
| | - Anastasya Shilova
- European Synchrotron Radiation Facility, BP 220, 38043 Grenoble, France
| | - Britta Weinhausen
- European Synchrotron Radiation Facility, BP 220, 38043 Grenoble, France
| | - Manfred Burghammer
- European Synchrotron Radiation Facility, BP 220, 38043 Grenoble, France
- Department of Analytical Chemistry, Ghent University, Ghent B-9000, Belgium
| | - Jacques-Philippe Colletier
- Université Grenoble Alpes, IBS, 38044 Grenoble, France
- CNRS, IBS, 38044 Grenoble, France
- CEA, IBS, 38044 Grenoble, France
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96
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Lyubimov AY, Murray TD, Koehl A, Araci IE, Uervirojnangkoorn M, Zeldin OB, Cohen AE, Soltis SM, Baxter EL, Brewster AS, Sauter NK, Brunger AT, Berger JM. Capture and X-ray diffraction studies of protein microcrystals in a microfluidic trap array. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:928-40. [PMID: 25849403 PMCID: PMC4388268 DOI: 10.1107/s1399004715002308] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 02/03/2015] [Indexed: 11/10/2022]
Abstract
X-ray free-electron lasers (XFELs) promise to enable the collection of interpretable diffraction data from samples that are refractory to data collection at synchrotron sources. At present, however, more efficient sample-delivery methods that minimize the consumption of microcrystalline material are needed to allow the application of XFEL sources to a wide range of challenging structural targets of biological importance. Here, a microfluidic chip is presented in which microcrystals can be captured at fixed, addressable points in a trap array from a small volume (<10 µl) of a pre-existing slurry grown off-chip. The device can be mounted on a standard goniostat for conducting diffraction experiments at room temperature without the need for flash-cooling. Proof-of-principle tests with a model system (hen egg-white lysozyme) demonstrated the high efficiency of the microfluidic approach for crystal harvesting, permitting the collection of sufficient data from only 265 single-crystal still images to permit determination and refinement of the structure of the protein. This work shows that microfluidic capture devices can be readily used to facilitate data collection from protein microcrystals grown in traditional laboratory formats, enabling analysis when cryopreservation is problematic or when only small numbers of crystals are available. Such microfluidic capture devices may also be useful for data collection at synchrotron sources.
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Affiliation(s)
- Artem Y. Lyubimov
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
- Department of Neurology and Neurological Science, Stanford University, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
- Department of Photon Science, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Thomas D. Murray
- Biophysics Graduate Group, University of California, Berkeley, CA 94720, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Antoine Koehl
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
| | - Ismail Emre Araci
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Monarin Uervirojnangkoorn
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
- Department of Neurology and Neurological Science, Stanford University, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
- Department of Photon Science, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Oliver B. Zeldin
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
- Department of Neurology and Neurological Science, Stanford University, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
- Department of Photon Science, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Aina E. Cohen
- SLAC National Accelerator Laboratory, Stanford, CA 94305, USA
| | | | | | - Aaron S. Brewster
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Nicholas K. Sauter
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Axel T. Brunger
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
- Department of Neurology and Neurological Science, Stanford University, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
- Department of Photon Science, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - James M. Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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97
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Uervirojnangkoorn M, Zeldin OB, Lyubimov AY, Hattne J, Brewster AS, Sauter NK, Brunger AT, Weis WI. Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals. eLife 2015; 4. [PMID: 25781634 PMCID: PMC4397907 DOI: 10.7554/elife.05421] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 03/16/2015] [Indexed: 02/02/2023] Open
Abstract
There is considerable potential for X-ray free electron lasers (XFELs) to enable determination of macromolecular crystal structures that are difficult to solve using current synchrotron sources. Prior XFEL studies often involved the collection of thousands to millions of diffraction images, in part due to limitations of data processing methods. We implemented a data processing system based on classical post-refinement techniques, adapted to specific properties of XFEL diffraction data. When applied to XFEL data from three different proteins collected using various sample delivery systems and XFEL beam parameters, our method improved the quality of the diffraction data as well as the resulting refined atomic models and electron density maps. Moreover, the number of observations for a reflection necessary to assemble an accurate data set could be reduced to a few observations. These developments will help expand the applicability of XFEL crystallography to challenging biological systems, including cases where sample is limited.
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Affiliation(s)
| | - Oliver B Zeldin
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States
| | - Artem Y Lyubimov
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States
| | | | - Aaron S Brewster
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Nicholas K Sauter
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Axel T Brunger
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States
| | - William I Weis
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States
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98
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Garman EF, Weik M. Radiation damage to macromolecules: kill or cure? JOURNAL OF SYNCHROTRON RADIATION 2015; 22:195-200. [PMID: 25723921 DOI: 10.1107/s160057751500380x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 02/23/2015] [Indexed: 05/07/2023]
Abstract
Radiation damage induced by X-ray beams during macromolecular diffraction experiments remains an issue of concern in structural biology. While advances in our understanding of this phenomenon, driven in part by a series of workshops in this area, undoubtedly have been and are still being made, there are still questions to be answered. Eight papers in this volume give a flavour of ongoing investigations, addressing various issues. These range over: a proposed new metric derived from atomic B-factors for identifying potentially damaged amino acid residues, a study of the relative damage susceptibility of protein and DNA in a DNA/protein complex, a report of an indication of specific radiation damage to a protein determined from data collected using an X-ray free-electron laser (FEL), an account of the challenges in FEL raw diffraction data analysis, an exploration of the possibilities of using radiation damage induced phasing to solve structures using FELs, simulations of radiation damage as a function of FEL temporal pulse profiles, results on the influence of radiation damage during scanning X-ray diffraction measurements and, lastly, consideration of strategies for minimizing radiation damage during SAXS experiments. In this short introduction, these contributions are briefly placed in the context of other current work on radiation damage in the field.
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Affiliation(s)
- Elspeth F Garman
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Martin Weik
- Université Grenoble Alpes, IBS, F-38044 Grenoble, France
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99
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Schlichting I. Serial femtosecond crystallography: the first five years. IUCRJ 2015; 2:246-55. [PMID: 25866661 PMCID: PMC4392417 DOI: 10.1107/s205225251402702x] [Citation(s) in RCA: 225] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 12/09/2014] [Indexed: 05/18/2023]
Abstract
Protein crystallography using synchrotron radiation sources has had a tremendous impact on biology, having yielded the structures of thousands of proteins and given detailed insight into their mechanisms. However, the technique is limited by the requirement for macroscopic crystals, which can be difficult to obtain, as well as by the often severe radiation damage caused in diffraction experiments, in particular when using tiny crystals. To slow radiation damage, data collection is typically performed at cryogenic temperatures. With the advent of free-electron lasers (FELs) capable of delivering extremely intense femtosecond X-ray pulses, this situation appears to be remedied, allowing the structure determination of undamaged macromolecules using either macroscopic or microscopic crystals. The latter are exposed to the FEL beam in random orientations and their diffraction data are collected at cryogenic or room temperature in a serial fashion, since each crystal is destroyed upon a single exposure. The new approaches required for crystal growth and delivery, and for diffraction data analysis, including de novo phasing, are reviewed. The opportunities and challenges of SFX are described, including applications such as time-resolved measurements and the analysis of radiation damage-prone systems.
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Affiliation(s)
- Ilme Schlichting
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstraße 29, Heidelberg 69120, Germany
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100
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Sauter NK. XFEL diffraction: developing processing methods to optimize data quality. JOURNAL OF SYNCHROTRON RADIATION 2015; 22:239-48. [PMID: 25723925 PMCID: PMC4344359 DOI: 10.1107/s1600577514028203] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Accepted: 12/29/2014] [Indexed: 05/17/2023]
Abstract
Serial crystallography, using either femtosecond X-ray pulses from free-electron laser sources or short synchrotron-radiation exposures, has the potential to reveal metalloprotein structural details while minimizing damage processes. However, deriving a self-consistent set of Bragg intensities from numerous still-crystal exposures remains a difficult problem, with optimal protocols likely to be quite different from those well established for rotation photography. Here several data processing issues unique to serial crystallography are examined. It is found that the limiting resolution differs for each shot, an effect that is likely to be due to both the sample heterogeneity and pulse-to-pulse variation in experimental conditions. Shots with lower resolution limits produce lower-quality models for predicting Bragg spot positions during the integration step. Also, still shots by their nature record only partial measurements of the Bragg intensity. An approximate model that corrects to the full-spot equivalent (with the simplifying assumption that the X-rays are monochromatic) brings the distribution of intensities closer to that expected from an ideal crystal, and improves the sharpness of anomalous difference Fourier peaks indicating metal positions.
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Affiliation(s)
- Nicholas K. Sauter
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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