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Levenstein MA, Robertson K, Turner TD, Hunter L, O’Brien C, O’Shaughnessy C, Kulak AN, Le Magueres P, Wojciechowski J, Mykhaylyk OO, Kapur N, Meldrum FC. Serial small- and wide-angle X-ray scattering with laboratory sources. IUCRJ 2022; 9:538-543. [PMID: 36071805 PMCID: PMC9438489 DOI: 10.1107/s2052252522007631] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
Recent advances in X-ray instrumentation and sample injection systems have enabled serial crystallography of protein nanocrystals and the rapid structural analysis of dynamic processes. However, this progress has been restricted to large-scale X-ray free-electron laser (XFEL) and synchrotron facilities, which are often oversubscribed and have long waiting times. Here, we explore the potential of state-of-the-art laboratory X-ray systems to perform comparable analyses when coupled to micro- and millifluidic sample environments. Our results demonstrate that commercial small- and wide-angle X-ray scattering (SAXS/WAXS) instruments and X-ray diffractometers are ready to access samples and timescales (≳5 ms) relevant to many processes in materials science including the preparation of pharmaceuticals, nanoparticles and functional crystalline materials. Tests of different X-ray instruments highlighted the importance of the optical configuration and revealed that serial WAXS/XRD analysis of the investigated samples was only possible with the higher flux of a microfocus setup. We expect that these results will also stimulate similar developments for structural biology.
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Affiliation(s)
| | - Karen Robertson
- Department of Chemical and Environmental Engineering, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Thomas D. Turner
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, United Kingdom
| | - Liam Hunter
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, United Kingdom
| | - Cate O’Brien
- Soft Matter Analytical Laboratory, Department of Chemistry, The University of Sheffield, Brook Hill, Sheffield S3 7HF, United Kingdom
| | - Cedrick O’Shaughnessy
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, United Kingdom
| | - Alexander N. Kulak
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, United Kingdom
| | - Pierre Le Magueres
- Rigaku Americas Corporation, 9009 New Tails Drive, The Woodlands, TX 77381, USA
| | | | - Oleksandr O. Mykhaylyk
- Soft Matter Analytical Laboratory, Department of Chemistry, The University of Sheffield, Brook Hill, Sheffield S3 7HF, United Kingdom
| | - Nikil Kapur
- School of Mechanical Engineering, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, United Kingdom
| | - Fiona C. Meldrum
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, United Kingdom
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Levenstein MA, Kim YY, Hunter L, Anduix-Canto C, González Niño C, Day SJ, Li S, Marchant WJ, Lee PA, Tang CC, Burghammer M, Meldrum FC, Kapur N. Evaluation of microflow configurations for scale inhibition and serial X-ray diffraction analysis of crystallization processes. LAB ON A CHIP 2020; 20:2954-2964. [PMID: 32666988 DOI: 10.1039/d0lc00239a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The clean and reproducible conditions provided by microfluidic devices are ideal sample environments for in situ analyses of chemical and biochemical reactions and assembly processes. However, the small size of microchannels makes investigating the crystallization of poorly soluble materials on-chip challenging due to crystal nucleation and growth that result in channel fouling and blockage. Here, we demonstrate a reusable insert-based microfluidic platform for serial X-ray diffraction analysis and examine scale formation in response to continuous and segmented flow configurations across a range of temperatures. Under continuous flow, scale formation on the reactor walls begins almost immediately on mixing of the crystallizing species, which over time results in occlusion of the channel. Depletion of ions at the start of the channel results in reduced crystallization towards the end of the channel. Conversely, segmented flow can control crystallization, so it occurs entirely within the droplet. Consequently, the spatial location within the channel represents a temporal point in the crystallization process. Whilst each method can provide useful crystallographic information, time-resolved information is lost when reactor fouling occurs and changes the solution conditions with time. The flow within a single device can be manipulated to give a broad range of information addressing surface interaction or solution crystallization.
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Affiliation(s)
- Mark A Levenstein
- School of Mechanical Engineering, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK.
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Abstract
Oscillators are at the heart of optical lasers, providing stable, transform-limited pulses. Until now, laser oscillators have been available only in the infrared to visible and near-ultraviolet (UV) spectral region. In this paper, we present a study of an oscillator operating in the 5- to 12-keV photon-energy range. We show that, using the [Formula: see text] line of transition metal compounds as the gain medium, an X-ray free-electron laser as a periodic pump, and a Bragg crystal optical cavity, it is possible to build X-ray oscillators producing intense, fully coherent, transform-limited pulses. As an example, we consider the case of a copper nitrate gain medium generating ∼ 5 × [Formula: see text] photons per pulse with 37-fs pulse length and 48-meV spectral resolution at 8-keV photon energy. Our theoretical study and simulation of this system show that, because of the very large gain per pass, the oscillator saturates and reaches full coherence in four to six optical-cavity transits. We discuss the feasibility and design of the X-ray optical cavity and other parts of the oscillator needed for its realization, opening the way to extend X-ray-based research beyond current capabilities.
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Thompson MC, Yeates TO, Rodriguez JA. Advances in methods for atomic resolution macromolecular structure determination. F1000Res 2020; 9:F1000 Faculty Rev-667. [PMID: 32676184 PMCID: PMC7333361 DOI: 10.12688/f1000research.25097.1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/25/2020] [Indexed: 12/13/2022] Open
Abstract
Recent technical advances have dramatically increased the power and scope of structural biology. New developments in high-resolution cryo-electron microscopy, serial X-ray crystallography, and electron diffraction have been especially transformative. Here we highlight some of the latest advances and current challenges at the frontiers of atomic resolution methods for elucidating the structures and dynamical properties of macromolecules and their complexes.
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Affiliation(s)
- Michael C. Thompson
- Department of Chemistry and Chemical Biology, University of California, Merced, CA, USA
| | - Todd O. Yeates
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA, USA
| | - Jose A. Rodriguez
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA, USA
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Abstract
The history of serial crystallography (SC) has its origins in the earliest attempts to merge data from several crystals. This preface provides an overview of some recent work, with a survey of the rapid advances made over the past decade in both sample delivery and data analysis.
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Logotheti S, Valmas A, Trampari S, Fili S, Saslis S, Spiliopoulou M, Beckers D, Degen T, Nénert G, Fitch AN, Karavassili F, Margiolaki I. Unit-cell response of tetragonal hen egg white lysozyme upon controlled relative humidity variation. J Appl Crystallogr 2019. [DOI: 10.1107/s1600576719009919] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Variation of relative humidity (rH) greatly affects the internal order of solvent-based protein crystals, and the rearrangement of molecules can be efficiently recorded in distinct diffraction patterns. This study focuses on this topic, reporting the effect of rH variation experiments on hen egg white lysozyme (HEWL) polycrystalline precipitates of tetragonal symmetry using X-ray powder diffraction (XRPD). In situ XRPD data were collected on HEWL specimens during dehydration and rehydration processes using laboratory instrumentation. A known polymorph [space group P43212, a = 79.07181 (1), c = 38.0776 (1) Å] was identified during gradual dehydration from 95 to 63% rH and vice versa. Pawley analysis of collected data sets and accurate extraction of unit-cell parameters indicated a characteristic evolution of the tetragonal axes with rH. In addition, there is a low humidity level below which samples do not retain their crystallinity. This work illustrates the accuracy of laboratory XRPD as a probe for time-resolved studies of proteins and in situ investigations of gradual structural modifications upon rH variation. These experiments provide essential information for improving production and post-production practices of microcrystalline protein-based pharmaceuticals.
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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: 31] [Impact Index Per Article: 4.4] [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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Spence JCH. XFELs for structure and dynamics in biology. IUCRJ 2017; 4:322-339. [PMID: 28875020 PMCID: PMC5571796 DOI: 10.1107/s2052252517005760] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 04/17/2017] [Indexed: 05/20/2023]
Abstract
The development and application of the free-electron X-ray laser (XFEL) to structure and dynamics in biology since its inception in 2009 are reviewed. The research opportunities which result from the ability to outrun most radiation-damage effects are outlined, and some grand challenges are suggested. By avoiding the need to cool samples to minimize damage, the XFEL has permitted atomic resolution imaging of molecular processes on the 100 fs timescale under near-physiological conditions and in the correct thermal bath in which molecular machines operate. Radiation damage, comparisons of XFEL and synchrotron work, single-particle diffraction, fast solution scattering, pump-probe studies on photosensitive proteins, mix-and-inject experiments, caged molecules, pH jump and other reaction-initiation methods, and the study of molecular machines are all discussed. Sample-delivery methods and data-analysis algorithms for the various modes, from serial femtosecond crystallo-graphy to fast solution scattering, fluctuation X-ray scattering, mixing jet experiments and single-particle diffraction, are also reviewed.
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Affiliation(s)
- J. C. H. Spence
- Department of Physics, Arizona State University, Tempe, AZ 85287-1504, USA
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Abstract
Serial crystallography was developed for the use at free-electron lasers but the approach has recently also been adapted to synchrotron sources. Here we discuss how the synergy between the two X-ray sources will facilitate a wide application of the technique in microcrystallography, room-temperature structure determination and time-resolved studies.
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Affiliation(s)
- Jörg Standfuss
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - John Spence
- Department of Physics, Arizona State University, Tempe, Arizona, USA
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Abstract
Serial crystallography at a synchrotron has been used to obtain time-resolved atomic resolution density maps of enzyme catalysis in copper nitrite reductase. Similar XFEL studies, intended to out-run radiation damage, will also soon appear.
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Affiliation(s)
- John Spence
- Physics, Arizona State University, Rural Rd, Tempe, 85287-1504, USA
| | - Eaton Lattman
- Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203-1101, USA
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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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Panneels V, Wu W, Tsai CJ, Nogly P, Rheinberger J, Jaeger K, Cicchetti G, Gati C, Kick LM, Sala L, Capitani G, Milne C, Padeste C, Pedrini B, Li XD, Standfuss J, Abela R, Schertler G. Time-resolved structural studies with serial crystallography: A new light on retinal proteins. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2015; 2:041718. [PMID: 26798817 PMCID: PMC4711639 DOI: 10.1063/1.4922774] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 06/03/2015] [Indexed: 05/19/2023]
Abstract
Structural information of the different conformational states of the two prototypical light-sensitive membrane proteins, bacteriorhodopsin and rhodopsin, has been obtained in the past by X-ray cryo-crystallography and cryo-electron microscopy. However, these methods do not allow for the structure determination of most intermediate conformations. Recently, the potential of X-Ray Free Electron Lasers (X-FELs) for tracking the dynamics of light-triggered processes by pump-probe serial femtosecond crystallography has been demonstrated using 3D-micron-sized crystals. In addition, X-FELs provide new opportunities for protein 2D-crystal diffraction, which would allow to observe the course of conformational changes of membrane proteins in a close-to-physiological lipid bilayer environment. Here, we describe the strategies towards structural dynamic studies of retinal proteins at room temperature, using injector or fixed-target based serial femtosecond crystallography at X-FELs. Thanks to recent progress especially in sample delivery methods, serial crystallography is now also feasible at synchrotron X-ray sources, thus expanding the possibilities for time-resolved structure determination.
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Affiliation(s)
- Valérie Panneels
- Laboratory of Biomolecular Research, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Wenting Wu
- Laboratory of Biomolecular Research, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Ching-Ju Tsai
- Laboratory of Biomolecular Research, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Przemek Nogly
- Laboratory of Biomolecular Research, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Jan Rheinberger
- Laboratory of Biomolecular Research, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Kathrin Jaeger
- Laboratory of Biomolecular Research, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Gregor Cicchetti
- Laboratory of Biomolecular Research, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | | | - Leonhard M Kick
- Laboratory of Biomolecular Research, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Leonardo Sala
- Scientific Computing, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Guido Capitani
- Laboratory of Biomolecular Research, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Chris Milne
- SwissFEL Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Celestino Padeste
- Lab for Micro- and Nanotechnology, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Bill Pedrini
- SwissFEL Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Xiao-Dan Li
- Laboratory of Biomolecular Research, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Jörg Standfuss
- Laboratory of Biomolecular Research, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Rafael Abela
- SwissFEL Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
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15
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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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16
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Pande K, Schwander P, Schmidt M, Saldin DK. Deducing fast electron density changes in randomly orientated uncrystallized biomolecules in a pump-probe experiment. Philos Trans R Soc Lond B Biol Sci 2015; 369:20130332. [PMID: 24914159 PMCID: PMC4052868 DOI: 10.1098/rstb.2013.0332] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We propose a method for deducing time-resolved structural changes in uncrystallized biomolecules in solution. The method relies on measuring the angular correlations of the intensities, when averaged over a large number of diffraction patterns from randomly oriented biomolecules in solution in a liquid solvent. The experiment is somewhat like a pump–probe version of an experiment on small angle X-ray scattering, except that the data expected by the algorithm are not just the radial variation of the averaged intensities. The differences of these correlation functions as measured from a photoexcited and dark structure enable the direct calculation of the difference electron density with a knowledge of only the dark structure. We exploit a linear relation we derive between the difference in these correlation functions and the difference electron density, applicable for small structural changes.
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Affiliation(s)
- K Pande
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
| | - P Schwander
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
| | - M Schmidt
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
| | - D K Saldin
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
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17
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Stellato F, Oberthür D, Liang M, Bean R, Gati C, Yefanov O, Barty A, Burkhardt A, Fischer P, Galli L, Kirian RA, Meyer J, Panneerselvam S, Yoon CH, Chervinskii F, Speller E, White TA, Betzel C, Meents A, Chapman HN. Room-temperature macromolecular serial crystallography using synchrotron radiation. IUCRJ 2014; 1:204-12. [PMID: 25075341 PMCID: PMC4107920 DOI: 10.1107/s2052252514010070] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 05/05/2014] [Indexed: 05/18/2023]
Abstract
A new approach for collecting data from many hundreds of thousands of microcrystals using X-ray pulses from a free-electron laser has recently been developed. Referred to as serial crystallography, diffraction patterns are recorded at a constant rate as a suspension of protein crystals flows across the path of an X-ray beam. Events that by chance contain single-crystal diffraction patterns are retained, then indexed and merged to form a three-dimensional set of reflection intensities for structure determination. This approach relies upon several innovations: an intense X-ray beam; a fast detector system; a means to rapidly flow a suspension of crystals across the X-ray beam; and the computational infrastructure to process the large volume of data. Originally conceived for radiation-damage-free measurements with ultrafast X-ray pulses, the same methods can be employed with synchrotron radiation. As in powder diffraction, the averaging of thousands of observations per Bragg peak may improve the ratio of signal to noise of low-dose exposures. Here, it is shown that this paradigm can be implemented for room-temperature data collection using synchrotron radiation and exposure times of less than 3 ms. Using lysozyme microcrystals as a model system, over 40 000 single-crystal diffraction patterns were obtained and merged to produce a structural model that could be refined to 2.1 Å resolution. The resulting electron density is in excellent agreement with that obtained using standard X-ray data collection techniques. With further improvements the method is well suited for even shorter exposures at future and upgraded synchrotron radiation facilities that may deliver beams with 1000 times higher brightness than they currently produce.
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Affiliation(s)
- Francesco Stellato
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Dominik Oberthür
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg 22607, Germany
| | - Mengning Liang
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Richard Bean
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Cornelius Gati
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Oleksandr Yefanov
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Anton Barty
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
| | | | | | - Lorenzo Galli
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
- Department of Physics, University of Hamburg, Luruper Chaussee 149, Hamburg 22607, Germany
| | - Richard A. Kirian
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Jan Meyer
- Photon Science, DESY, Hamburg 22607, Germany
| | | | - Chun Hong Yoon
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
- European XFEL GmbH, Albert Einstein Ring 19, Hamburg 22761, Germany
| | - Fedor Chervinskii
- Moscow Institute of Physics and Technology, 141700 Moscow, Russian Federation
| | - Emily Speller
- Department of Physics, University of York, Heslington, York YO10 5DD, UK
| | - Thomas A. White
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Christian Betzel
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg 22607, Germany
- Center for Ultrafast Imaging, Luruper Chaussee 149, Hamburg 22761, Germany
| | - Alke Meents
- Photon Science, DESY, Hamburg 22607, Germany
| | - Henry N. Chapman
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
- Department of Physics, University of Hamburg, Luruper Chaussee 149, Hamburg 22607, Germany
- Center for Ultrafast Imaging, Luruper Chaussee 149, Hamburg 22761, Germany
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18
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Trebbin M, Krüger K, DePonte D, Roth SV, Chapman HN, Förster S. Microfluidic liquid jet system with compatibility for atmospheric and high-vacuum conditions. LAB ON A CHIP 2014; 14:1733-45. [PMID: 24671443 DOI: 10.1039/c3lc51363g] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
We present microfluidic chip based devices that produce liquid jets with micrometer diameters while operating at very low flow rates. The chip production is based on established soft-lithographical techniques employing a three-layer design protocol. This allows the exact, controlled and reproducible design of critical parts such as nozzles and the production of nozzle arrays. The microfluidic chips reproducibly generate liquid jets exiting at perfect right angles with diameters between 20 μm and 2 μm, and under special circumstances, even down to 0.9 μm. Jet diameter, jet length, and the domain of the jetting/dripping instability can be predicted and controlled based on the theory for liquid jets in the plate-orifice configuration described by Gañán-Calvo et al. Additionally, conditions under which the device produces highly reproducible monodisperse droplets at exact and predictable rates can be achieved. The devices operate under atmospheric and under vacuum conditions making them highly relevant for a wide range of applications, for example, for free-electron lasers. Further, the straightforward integration of additional features such as a jet-in-jet is demonstrated. This device design has the potential to integrate more features based on established microfluidic components and may become a standard device for small liquid jet production.
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Affiliation(s)
- Martin Trebbin
- Physical Chemistry 1, University of Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany.
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Marmiroli B, Cacho-Nerin F, Sartori B, Pérez J, Amenitsch H. Thorough small-angle X-ray scattering analysis of the instability of liquid micro-jets in air. JOURNAL OF SYNCHROTRON RADIATION 2014; 21:193-202. [PMID: 24365936 DOI: 10.1107/s1600577513027951] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 10/11/2013] [Indexed: 06/03/2023]
Abstract
Liquid jets are of interest, both for their industrial relevance and for scientific applications (more important, in particular for X-rays, after the advent of free-electron lasers that require liquid jets as sample carrier). Instability mechanisms have been described theoretically and by numerical simulation, but confirmed by few experimental techniques. In fact, these are mainly based on cameras, which is limited by the imaging resolution, and on light scattering, which is hindered by absorption, reflection, Mie scattering and multiple scattering due to complex air/liquid interfaces during jet break-up. In this communication it is demonstrated that synchrotron small-angle X-ray scattering (SAXS) can give quantitative information on liquid jet dynamics at the nanoscale, by detecting time-dependent morphology and break-up length. Jets ejected from circular tubes of different diameters (100-450 µm) and speeds (0.7-21 m s(-1)) have been explored to cover the Rayleigh and first wind-induced regimes. Various solvents (water, ethanol, 2-propanol) and their mixtures have been examined. The determination of the liquid jet behaviour becomes essential, as it provides background data in subsequent studies of chemical and biological reactions using SAXS or X-ray diffraction based on synchrotron radiation and free-electron lasers.
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Affiliation(s)
- Benedetta Marmiroli
- Institute of Inorganic Chemistry, Graz University of Technology, Stremayrgasse 9/IV, Graz 8010, Austria
| | - Fernando Cacho-Nerin
- Institute of Inorganic Chemistry, Graz University of Technology, Stremayrgasse 9/IV, Graz 8010, Austria
| | - Barbara Sartori
- Institute of Inorganic Chemistry, Graz University of Technology, Stremayrgasse 9/IV, Graz 8010, Austria
| | - Javier Pérez
- Beamline SWING, Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, BP 48, 91192 Gif sur Yvette, France
| | - Heinz Amenitsch
- Institute of Inorganic Chemistry, Graz University of Technology, Stremayrgasse 9/IV, Graz 8010, Austria
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20
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Barends TRM, Foucar L, Shoeman RL, Bari S, Epp SW, Hartmann R, Hauser G, Huth M, Kieser C, Lomb L, Motomura K, Nagaya K, Schmidt C, Strecker R, Anielski D, Boll R, Erk B, Fukuzawa H, Hartmann E, Hatsui T, Holl P, Inubushi Y, Ishikawa T, Kassemeyer S, Kaiser C, Koeck F, Kunishima N, Kurka M, Rolles D, Rudek B, Rudenko A, Sato T, Schroeter CD, Soltau H, Strueder L, Tanaka T, Togashi T, Tono K, Ullrich J, Yase S, Wada SI, Yao M, Yabashi M, Ueda K, Schlichting I. Anomalous signal from S atoms in protein crystallographic data from an X-ray free-electron laser. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:838-42. [PMID: 23633593 DOI: 10.1107/s0907444913002448] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 01/24/2013] [Indexed: 11/10/2022]
Abstract
X-ray free-electron lasers (FELs) enable crystallographic data collection using extremely bright femtosecond pulses from microscopic crystals beyond the limitations of conventional radiation damage. This diffraction-before-destruction approach requires a new crystal for each FEL shot and, since the crystals cannot be rotated during the X-ray pulse, data collection requires averaging over many different crystals and a Monte Carlo integration of the diffraction intensities, making the accurate determination of structure factors challenging. To investigate whether sufficient accuracy can be attained for the measurement of anomalous signal, a large data set was collected from lysozyme microcrystals at the newly established `multi-purpose spectroscopy/imaging instrument' of the SPring-8 Ångstrom Compact Free-Electron Laser (SACLA) at RIKEN Harima. Anomalous difference density maps calculated from these data demonstrate that serial femtosecond crystallography using a free-electron laser is sufficiently accurate to measure even the very weak anomalous signal of naturally occurring S atoms in a protein at a photon energy of 7.3 keV.
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Affiliation(s)
- Thomas R M Barends
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany.
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21
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Sierra RG, Laksmono H, Kern J, Tran R, Hattne J, Alonso-Mori R, Lassalle-Kaiser B, Glöckner C, Hellmich J, Schafer DW, Echols N, Gildea RJ, Grosse-Kunstleve RW, Sellberg J, McQueen TA, Fry AR, Messerschmidt MM, Miahnahri A, Seibert MM, Hampton CY, Starodub D, Loh ND, Sokaras D, Weng TC, Zwart PH, Glatzel P, Milathianaki D, White WE, Adams PD, Williams GJ, Boutet S, Zouni A, Messinger J, Sauter NK, Bergmann U, Yano J, Yachandra VK, Bogan MJ. Nanoflow electrospinning serial femtosecond crystallography. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:1584-7. [PMID: 23090408 PMCID: PMC3478121 DOI: 10.1107/s0907444912038152] [Citation(s) in RCA: 153] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 09/05/2012] [Indexed: 11/10/2022]
Abstract
An electrospun liquid microjet has been developed that delivers protein microcrystal suspensions at flow rates of 0.14-3.1 µl min(-1) to perform serial femtosecond crystallography (SFX) studies with X-ray lasers. Thermolysin microcrystals flowed at 0.17 µl min(-1) and diffracted to beyond 4 Å resolution, producing 14,000 indexable diffraction patterns, or four per second, from 140 µg of protein. Nanoflow electrospinning extends SFX to biological samples that necessitate minimal sample consumption.
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Affiliation(s)
- Raymond G. Sierra
- PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Hartawan Laksmono
- PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Jan Kern
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Rosalie Tran
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Johan Hattne
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | | | - Carina Glöckner
- Max-Volmer-Laboratorium für Biophysikalische Chemie, Technische Universität Berlin, Strasse des 17 Juni 135, 10623 Berlin, Germany
| | - Julia Hellmich
- Max-Volmer-Laboratorium für Biophysikalische Chemie, Technische Universität Berlin, Strasse des 17 Juni 135, 10623 Berlin, Germany
| | - Donald W. Schafer
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Nathaniel Echols
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Richard J. Gildea
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - Jonas Sellberg
- SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
- Department of Physics, AlbaNova, Stockholm University, S-106 91 Stockholm, Sweden
| | - Trevor A. McQueen
- Department of Chemistry, Stanford University, Stanford, CA 94025, USA
| | - Alan R. Fry
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | | | - Alan Miahnahri
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - M. Marvin Seibert
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Christina Y. Hampton
- PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Dmitri Starodub
- PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - N. Duane Loh
- PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | | | - Tsu-Chien Weng
- SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Petrus H. Zwart
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Pieter Glatzel
- European Synchrotron Radiation Facility, Grenoble, France
| | | | - William E. White
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Paul D. Adams
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Garth J. Williams
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Sébastien Boutet
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Athina Zouni
- Max-Volmer-Laboratorium für Biophysikalische Chemie, Technische Universität Berlin, Strasse des 17 Juni 135, 10623 Berlin, Germany
| | - Johannes Messinger
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, Umeå, Sweden
| | - Nicholas K. Sauter
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Uwe Bergmann
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Junko Yano
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Vittal K. Yachandra
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Michael J. Bogan
- PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
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22
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Spence JCH, Weierstall U, Chapman HN. X-ray lasers for structural and dynamic biology. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2012; 75:102601. [PMID: 22975810 DOI: 10.1088/0034-4885/75/10/102601] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Research opportunities and techniques are reviewed for the application of hard x-ray pulsed free-electron lasers (XFEL) to structural biology. These include the imaging of protein nanocrystals, single particles such as viruses, pump--probe experiments for time-resolved nanocrystallography, and snapshot wide-angle x-ray scattering (WAXS) from molecules in solution. The use of femtosecond exposure times, rather than freezing of samples, as a means of minimizing radiation damage is shown to open up new opportunities for the molecular imaging of biochemical reactions at room temperature in solution. This is possible using a 'diffract-and-destroy' mode in which the incident pulse terminates before radiation damage begins. Methods for delivering hundreds of hydrated bioparticles per second (in random orientations) to a pulsed x-ray beam are described. New data analysis approaches are outlined for the correlated fluctuations in fast WAXS, for protein nanocrystals just a few molecules on a side, and for the continuous x-ray scattering from a single virus. Methods for determining the orientation of a molecule from its diffraction pattern are reviewed. Methods for the preparation of protein nanocrystals are also reviewed. New opportunities for solving the phase problem for XFEL data are outlined. A summary of the latest results is given, which now extend to atomic resolution for nanocrystals. Possibilities for time-resolved chemistry using fast WAXS (solution scattering) from mixtures is reviewed, toward the general goal of making molecular movies of biochemical processes.
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Affiliation(s)
- J C H Spence
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA.
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23
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Weierstall U, Spence JCH, Doak RB. Injector for scattering measurements on fully solvated biospecies. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2012; 83:035108. [PMID: 22462961 DOI: 10.1063/1.3693040] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
We describe a liquid jet injector system developed to deliver fully solvated microscopic target species into a probe beam under either vacuum or ambient conditions. The injector was designed specifically for x-ray scattering studies of biological nanospecies using x-ray free electron lasers and third generation synchrotrons, but is of interest to any application in which microscopic samples must be delivered in a fully solvated state and with microscopic precision. By utilizing a gas dynamic virtual nozzle (GDVN) to generate a sample-containing liquid jet of diameter ranging from 300 nm to 20 μm, the injector avoids the clogging problems associated in this size range with conventional Rayleigh jets. A differential pumping system incorporated into the injector shields the experimental chamber from the gas load of the GDVN, making the injector compatible with high vacuum systems. The injector houses a fiber-optically coupled pump laser to illuminate the jet for pump-probe experiments and a hermetically sealed microscope to observe the liquid jet for diagnostics and alignment during operation. This injector system has now been used during several experimental runs at the Linac Coherent Light Source. Recent refinements in GDVN design are also presented.
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Affiliation(s)
- U Weierstall
- Department of Physics, Arizona State University, Tempe, Arizona 85287-1504, USA
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24
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Hunter MS, Fromme P. Toward structure determination using membrane-protein nanocrystals and microcrystals. Methods 2011; 55:387-404. [PMID: 22197730 DOI: 10.1016/j.ymeth.2011.12.006] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Revised: 12/03/2011] [Accepted: 12/14/2011] [Indexed: 02/05/2023] Open
Abstract
Membrane proteins are very important for all living cells, being involved in respiration, photosynthesis, cellular uptake and signal transduction, amongst other vital functions. However, less than 300 unique membrane protein structures have been determined to date, often due to difficulties associated with the growth of sufficiently large and well-ordered crystals. This work has been focused on showing the first proof of concept for using membrane protein nanocrystals and microcrystals for high-resolution structure determination. Upon determining that crystals of the membrane protein Photosystem I, which is the largest and most complex membrane protein crystallized to date, exist with only 100 unit cells with sizes of less than 200 nm on an edge, work was done to develop a technique that could exploit the growth of the Photosystem I nanocrystals and microcrystals. Femtosecond X-ray protein nanocrystallography was developed for use at the first high-energy X-ray free electron laser, the LCLS at SLAC National Accelerator Laboratory, in which a liquid jet brought fully-hydrated Photosystem I nanocrystals into the interaction region of the pulsed X-ray source. Diffraction patterns were recorded from millions of individual PSI nanocrystals and data from thousands of different, randomly oriented crystallites were integrated using Monte Carlo integration of the peak intensities. The short pulses (∼70fs) provided by the LCLS allowed the possibility to collect the diffraction data before the onset of radiation damage, exploiting the diffract-before-destroy principle. During the initial experiments at the AMO beamline using 6.9-Å wavelength, Bragg peaks were recorded to 8.5-Å resolution, and an electron-density map was determined that did not show any effects of X-ray-induced radiation damage [94]. Many additional techniques still need to be developed to explore the femtosecond nanocrystallography technique for experimental phasing and time-resolved X-ray crystallography experiments. The first proof-of-principle results for the femtosecond nanocrystallography technique indicate the incredible potential of the technique to offer a new route to the structure determination of membrane proteins.
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Affiliation(s)
- Mark S Hunter
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA.
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25
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Saldin DK, Poon HC, Schwander P, Uddin M, Schmidt M. Reconstructing an icosahedral virus from single-particle diffraction experiments. OPTICS EXPRESS 2011; 19:17318-35. [PMID: 21935096 DOI: 10.1364/oe.19.017318] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The first experimental data from single-particle scattering experiments from free electron lasers (FELs) are now becoming available. The first such experiments are being performed on relatively large objects such as viruses, which produce relatively low-resolution, low-noise diffraction patterns in so-called "diffract-and-destroy" experiments. We describe a very simple test on the angular correlations of measured diffraction data to determine if the scattering is from an icosahedral particle. If this is confirmed, the efficient algorithm proposed can then combine diffraction data from multiple shots of particles in random unknown orientations to generate a full 3D image of the icosahedral particle. We demonstrate this with a simulation for the satellite tobacco necrosis virus (STNV), the atomic coordinates of whose asymmetric unit is given in Protein Data Bank entry 2BUK.
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Affiliation(s)
- D K Saldin
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53201, USA.
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26
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Santucci SC, Cojoc D, Amenitsch H, Marmiroli B, Sartori B, Burghammer M, Schoeder S, DiCola E, Reynolds M, Riekel C. Optical tweezers for synchrotron radiation probing of trapped biological and soft matter objects in aqueous environments. Anal Chem 2011; 83:4863-70. [PMID: 21542583 DOI: 10.1021/ac200515x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Investigations of single fragile objects manipulated by optical forces with high brilliance X-ray beams may initiate the development of new research fields such as protein crystallography in an aqueous environment. We have developed a dedicated optical tweezers setup with a compact, portable, and versatile geometry for the customary manipulation of objects for synchrotron radiation applications. Objects of a few micrometers up to a few tens of micrometers size can be trapped for extended periods of time. The selection and positioning of single objects out of a batch of many can be performed semi-automatically by software routines. The performance of the setup has been tested by wide-angle and small-angle X-ray scattering experiments on single optically trapped starch granules, using a synchrotron radiation microbeam. We demonstrate here for the first time the feasibility of microdiffraction on optically trapped protein crystals. Starch granules and insulin crystals were repeatedly raster-scanned at about 50 ms exposure/raster-point up to the complete loss of the structural order. Radiation damage in starch granules results in the appearance of low-angle scattering due to the breakdown of the polysaccharide matrix. For insulin crystals, order along the densely packed [110] direction is preferentially maintained until complete loss of long-range order.
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Affiliation(s)
- Silvia C Santucci
- European Synchrotron Radiation Facility, B.P. 220, F-38043 Grenoble Cedex, France.
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27
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Hunter MS, DePonte DP, Shapiro DA, Kirian RA, Wang X, Starodub D, Marchesini S, Weierstall U, Doak RB, Spence JCH, Fromme P. X-ray diffraction from membrane protein nanocrystals. Biophys J 2011; 100:198-206. [PMID: 21190672 DOI: 10.1016/j.bpj.2010.10.049] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Revised: 10/02/2010] [Accepted: 10/13/2010] [Indexed: 11/25/2022] Open
Abstract
Membrane proteins constitute > 30% of the proteins in an average cell, and yet the number of currently known structures of unique membrane proteins is < 300. To develop new concepts for membrane protein structure determination, we have explored the serial nanocrystallography method, in which fully hydrated protein nanocrystals are delivered to an x-ray beam within a liquid jet at room temperature. As a model system, we have collected x-ray powder diffraction data from the integral membrane protein Photosystem I, which consists of 36 subunits and 381 cofactors. Data were collected from crystals ranging in size from 100 nm to 2 μm. The results demonstrate that there are membrane protein crystals that contain < 100 unit cells (200 total molecules) and that 3D crystals of membrane proteins, which contain < 200 molecules, may be suitable for structural investigation. Serial nanocrystallography overcomes the problem of x-ray damage, which is currently one of the major limitations for x-ray structure determination of small crystals. By combining serial nanocrystallography with x-ray free-electron laser sources in the future, it may be possible to produce molecular-resolution electron-density maps using membrane protein crystals that contain only a few hundred or thousand unit cells.
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Affiliation(s)
- M S Hunter
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona, USA
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28
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Spence JCH, Kirian RA, Wang X, Weierstall U, Schmidt KE, White T, Barty A, Chapman HN, Marchesini S, Holton J. Phasing of coherent femtosecond X-ray diffraction from size-varying nanocrystals. OPTICS EXPRESS 2011; 19:2866-73. [PMID: 21369108 DOI: 10.1364/oe.19.002866] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The scattering between Bragg reflections from nanocrystals is used to aid solution of the phase problem. We describe a method for reconstructing the charge density of a typical molecule within a single unit cell, if sufficiently finely-sampled "snap-shot" diffraction data (as provided a free-electron X-ray laser) are available from many nanocrystals of different sizes lying in random orientations. By using information on the particle-size distribution within the patterns, this digital method succeeds, using all the data, without knowledge of the distribution of particle size or requiring atomic-resolution data.
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Affiliation(s)
- John C H Spence
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA.
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29
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Caleman C, Huldt G, Maia FRNC, Ortiz C, Parak FG, Hajdu J, van der Spoel D, Chapman HN, Timneanu N. On the feasibility of nanocrystal imaging using intense and ultrashort X-ray pulses. ACS NANO 2011; 5:139-46. [PMID: 21138321 DOI: 10.1021/nn1020693] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Structural studies of biological macromolecules are severely limited by radiation damage. Traditional crystallography curbs the effects of damage by spreading damage over many copies of the molecule of interest in the crystal. X-ray lasers offer an additional opportunity for limiting damage by out-running damage processes with ultrashort and very intense X-ray pulses. Such pulses may allow the imaging of single molecules, clusters, or nanoparticles. Coherent flash imaging will also open up new avenues for structural studies on nano- and microcrystalline substances. This paper addresses the theoretical potentials and limitations of nanocrystallography with extremely intense coherent X-ray pulses. We use urea nanocrystals as a model for generic biological substances and simulate the primary and secondary ionization dynamics in the crystalline sample. The results establish conditions for ultrafast single-shot nanocrystallography diffraction experiments as a function of X-ray fluence, pulse duration, and the size of nanocrystals. Nanocrystallography using ultrafast X-ray pulses has the potential to open up a new route in protein crystallography to solve atomic structures of many systems that remain inaccessible using conventional X-ray sources.
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Affiliation(s)
- Carl Caleman
- Physik Department E17, Technische Universität München, James-Franck-Strasse, DE-85748 Garching, Germany
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30
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van Oudheusden T, Pasmans PLEM, van der Geer SB, de Loos MJ, van der Wiel MJ, Luiten OJ. Compression of subrelativistic space-charge-dominated electron bunches for single-shot femtosecond electron diffraction. PHYSICAL REVIEW LETTERS 2010; 105:264801. [PMID: 21231672 DOI: 10.1103/physrevlett.105.264801] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2010] [Indexed: 05/09/2023]
Abstract
We demonstrate the compression of 95 keV, space-charge-dominated electron bunches to sub-100 fs durations. These bunches have sufficient charge (200 fC) and are of sufficient quality to capture a diffraction pattern with a single shot, which we demonstrate by a diffraction experiment on a polycrystalline gold foil. Compression is realized by means of velocity bunching by inverting the positive space-charge-induced velocity chirp. This inversion is induced by the oscillatory longitudinal electric field of a 3 GHz radio-frequency cavity. The arrival time jitter is measured to be 80 fs.
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Affiliation(s)
- T van Oudheusden
- Department of Applied Physics, Eindhoven University of Technology, Eindhoven, The Netherlands
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31
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Deponte DP, McKeown JT, Weierstall U, Doak RB, Spence JCH. Towards ETEM serial crystallography: Electron diffraction from liquid jets. Ultramicroscopy 2010; 111:824-7. [PMID: 21146302 DOI: 10.1016/j.ultramic.2010.11.036] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2010] [Revised: 11/19/2010] [Accepted: 11/24/2010] [Indexed: 11/30/2022]
Abstract
A sufficiently thin column of liquid was produced to permit penetration with a 200 keV electron beam as evidenced by the observation of diffraction rings due to the intermolecular spacing of the liquid samples. For liquid thickness below 800 nm, the diffraction rings became visible above the inelastic background. Studies were carried out in the environmental chamber of a transmission electron microscope using water and isopropanol.
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Affiliation(s)
- D P Deponte
- Department of Physics and Astronomy, Arizona State University, Tempe, AZ 85287, USA.
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32
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Kirian RA, Wang X, Weierstall U, Schmidt KE, Spence JCH, Hunter M, Fromme P, White T, Chapman HN, Holton J. Femtosecond protein nanocrystallography-data analysis methods. OPTICS EXPRESS 2010; 18:5713-23. [PMID: 20389587 PMCID: PMC4038330 DOI: 10.1364/oe.18.005713] [Citation(s) in RCA: 117] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
X-ray diffraction patterns may be obtained from individual submicron protein nanocrystals using a femtosecond pulse from a free-electron X-ray laser. Many "single-shot" patterns are read out every second from a stream of nanocrystals lying in random orientations. The short pulse terminates before significant atomic (or electronic) motion commences, minimizing radiation damage. Simulated patterns for Photosystem I nanocrystals are used to develop a method for recovering structure factors from tens of thousands of snapshot patterns from nanocrystals varying in size, shape and orientation. We determine the number of shots needed for a required accuracy in structure factor measurement and resolution, and investigate the convergence of our Monte-Carlo integration method.
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Affiliation(s)
- Richard A. Kirian
- Department of Physics, Arizona State University, Tempe, Arizona 85287 USA
| | - Xiaoyu Wang
- Department of Physics, Arizona State University, Tempe, Arizona 85287 USA
| | - Uwe Weierstall
- Department of Physics, Arizona State University, Tempe, Arizona 85287 USA
| | - Kevin E. Schmidt
- Department of Physics, Arizona State University, Tempe, Arizona 85287 USA
| | - John C. H. Spence
- Department of Physics, Arizona State University, Tempe, Arizona 85287 USA
| | - Mark Hunter
- Department of Biochemistry, Arizona State Unviversity, Tempe, Arizona 85287 USA
| | - Petra Fromme
- Department of Biochemistry, Arizona State Unviversity, Tempe, Arizona 85287 USA
| | - Thomas White
- Center for Free Electron Laser Science DESY University of Hamburg, Notkestrasse 85, 22607, Hamburg, Germany
| | - Henry N. Chapman
- Center for Free Electron Laser Science DESY University of Hamburg, Notkestrasse 85, 22607, Hamburg, Germany
- University of Hamburg, Luruper Chaussee 149, Hamburg 22761, Germany
| | - James Holton
- Advanced Light Source, Lawrence Berkeley Laboratory, Berkeley, California 94720 USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158 USA
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33
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Howells MR, Beetz T, Chapman HN, Cui C, Holton JM, Jacobsen CJ, Kirz J, Lima E, Marchesini S, Miao H, Sayre D, Shapiro DA, Spence JCH, Starodub D. An assessment of the resolution limitation due to radiation-damage in x-ray diffraction microscopy. JOURNAL OF ELECTRON SPECTROSCOPY AND RELATED PHENOMENA 2009; 170:4-12. [PMID: 20463854 PMCID: PMC2867487 DOI: 10.1016/j.elspec.2008.10.008] [Citation(s) in RCA: 134] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
X-ray diffraction microscopy (XDM) is a new form of x-ray imaging that is being practiced at several third-generation synchrotron-radiation x-ray facilities. Nine years have elapsed since the technique was first introduced and it has made rapid progress in demonstrating high-resolution three-dimensional imaging and promises few-nm resolution with much larger samples than can be imaged in the transmission electron microscope. Both life- and materials-science applications of XDM are intended, and it is expected that the principal limitation to resolution will be radiation damage for life science and the coherent power of available x-ray sources for material science. In this paper we address the question of the role of radiation damage. We use a statistical analysis based on the so-called "dose fractionation theorem" of Hegerl and Hoppe to calculate the dose needed to make an image of a single life-science sample by XDM with a given resolution. We find that for simply-shaped objects the needed dose scales with the inverse fourth power of the resolution and present experimental evidence to support this finding. To determine the maximum tolerable dose we have assembled a number of data taken from the literature plus some measurements of our own which cover ranges of resolution that are not well covered otherwise. The conclusion of this study is that, based on the natural contrast between protein and water and "Rose-criterion" image quality, one should be able to image a frozen-hydrated biological sample using XDM at a resolution of about 10 nm.
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Affiliation(s)
- M. R. Howells
- Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720 USA
| | - T. Beetz
- Department of Physics, State University of New York, Stony Brook, NY 11794, USA
| | - H. N. Chapman
- Lawrence Livermore National Laboratory, 7000 East Ave., Livermore, CA 94550, USA
| | - C. Cui
- Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720 USA
| | - J. M. Holton
- Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720 USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158-2330, USA
| | - C. J. Jacobsen
- Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720 USA
- Department of Physics, State University of New York, Stony Brook, NY 11794, USA
| | - J. Kirz
- Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720 USA
- Department of Physics, State University of New York, Stony Brook, NY 11794, USA
| | - E. Lima
- Department of Physics, State University of New York, Stony Brook, NY 11794, USA
| | - S. Marchesini
- Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720 USA
| | - H. Miao
- Department of Physics, State University of New York, Stony Brook, NY 11794, USA
| | - D. Sayre
- Department of Physics, State University of New York, Stony Brook, NY 11794, USA
| | - D. A. Shapiro
- Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720 USA
| | - J. C. H. Spence
- Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720 USA
- Department of Physics and Astronomy, Arizona State University, Tempe, AZ 85287-1504, USA
| | - D. Starodub
- Department of Physics and Astronomy, Arizona State University, Tempe, AZ 85287-1504, USA
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34
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DePonte DP, Doak RB, Hunter M, Liu Z, Weierstall U, Spence JCH. SEM imaging of liquid jets. Micron 2008; 40:507-9. [PMID: 19246201 DOI: 10.1016/j.micron.2008.12.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2008] [Revised: 12/10/2008] [Accepted: 12/22/2008] [Indexed: 11/26/2022]
Abstract
We present a technique for the study of liquid jets in an environmental scanning electron microscope (ESEM). By using a two-fluid stream consisting of a water inner core and a co-flowing outer gas sheath, we are able to produce liquid streams of sufficiently low flow rate to be compatible with ESEM vacuum requirements. We have recorded ESEM images of water jets down to 700 nm diameter. Details of the jet structure, such as the point of jet breakup and size and shape of the jet cone, can be measured with ESEM to far greater accuracy than with optical microscopy. ESEM imaging of liquid jets offers a valuable research tool for the study of aerosol production, combustion processes, ink-jet generation, and many other attributes of micro- and nanojet systems.
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Affiliation(s)
- Daniel P DePonte
- Department of Physics, Arizona State University, Tempe, AZ 85287, United States.
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