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Darmanin C, Babayekhorasani F, Formosa A, Spicer P, Abbey B. Polarisation and rheology characterisation of monoolein/water liquid crystal dynamical behaviour during high-viscosity injector extrusion. J Colloid Interface Sci 2024; 653:1123-1136. [PMID: 37783012 DOI: 10.1016/j.jcis.2023.09.093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 09/01/2023] [Accepted: 09/14/2023] [Indexed: 10/04/2023]
Abstract
HYPOTHESIS The use of monoolein/water mixtures in serial crystallography experiments using high-viscosity injectors (HVI) results in significant departures from equilibrium behaviour. This is expected to include changes in phase, viscosity, and associated flow behaviour. It should be possible to detect these changes, in-situ, using a combination of polarisation and rheology characterisation techniques. EXPERIMENTS A systematic study was performed using monoolein, varying the water content to create a range of mixtures. Injection induced phase changes within the HVI flow were established using real-time cross-polarization measurements. Dynamic flow characteristics and viscosity was characterized by particle tracking and rheology. FINDINGS HVI injection induces deformation and phase changes within monoolein (MO)/water mixtures which can be detected through variations in the transmitted intensity during in-situ polarisation studies. The heterogeneity of the extruded sample results in a highly viscous cubic phase in the central region of the stream and a less viscous lamellar-rich phase at the edges adjacent to the walls. The extent of these variations depends on sample composition and injection conditions. Shear-thinning behaviour and increasing heterogeneity in the vicinity of the capillary walls under dynamic flow conditions. This is the first report observing injection induced dynamical behaviour in MO/water mixtures under realistic flow conditions.
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Affiliation(s)
- Connie Darmanin
- La Trobe Institute for Molecular Science, Department of Mathematical and Physical Sciences, School of Computing Engineering and Mathematical Science, La Trobe University, Bundoora, VIC 3086, Australia.
| | - Firoozeh Babayekhorasani
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, NSW 2052, Australia; School of Chemical Engineering, University of New South Wales, Sydney, NSW 2052, Australia.
| | - Andrew Formosa
- La Trobe Institute for Molecular Science, Department of Mathematical and Physical Sciences, School of Computing Engineering and Mathematical Science, La Trobe University, Bundoora, VIC 3086, Australia.
| | - Patrick Spicer
- School of Chemical Engineering, University of New South Wales, Sydney, NSW 2052, Australia.
| | - Brian Abbey
- La Trobe Institute for Molecular Science, Department of Mathematical and Physical Sciences, School of Computing Engineering and Mathematical Science, La Trobe University, Bundoora, VIC 3086, Australia.
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2
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Hadian-Jazi M, Sadri A. A Python package based on robust statistical analysis for serial crystallography data processing. Acta Crystallogr D Struct Biol 2023; 79:820-829. [PMID: 37584428 PMCID: PMC10478633 DOI: 10.1107/s2059798323005855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 07/03/2023] [Indexed: 08/17/2023] Open
Abstract
The term robustness in statistics refers to methods that are generally insensitive to deviations from model assumptions. In other words, robust methods are able to preserve their accuracy even when the data do not perfectly fit the statistical models. Robust statistical analyses are particularly effective when analysing mixtures of probability distributions. Therefore, these methods enable the discretization of X-ray serial crystallography data into two probability distributions: a group comprising true data points (for example the background intensities) and another group comprising outliers (for example Bragg peaks or bad pixels on an X-ray detector). These characteristics of robust statistical analysis are beneficial for the ever-increasing volume of serial crystallography (SX) data sets produced at synchrotron and X-ray free-electron laser (XFEL) sources. The key advantage of the use of robust statistics for some applications in SX data analysis is that it requires minimal parameter tuning because of its insensitivity to the input parameters. In this paper, a software package called Robust Gaussian Fitting library (RGFlib) is introduced that is based on the concept of robust statistics. Two methods are presented based on the concept of robust statistics and RGFlib for two SX data-analysis tasks: (i) a robust peak-finding algorithm and (ii) an automated robust method to detect bad pixels on X-ray pixel detectors.
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Affiliation(s)
- Marjan Hadian-Jazi
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Victoria 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Melbourne, Victoria 3052, Australia
| | - Alireza Sadri
- School of Physics and Astronomy, Monash University, Clayton, Victoria 3800, Australia
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3
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Henkel A, Galchenkova M, Maracke J, Yefanov O, Klopprogge B, Hakanpää J, Mesters JR, Chapman HN, Oberthuer D. JINXED: just in time crystallization for easy structure determination of biological macromolecules. IUCRJ 2023; 10:253-260. [PMID: 36892542 PMCID: PMC10161778 DOI: 10.1107/s2052252523001653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 02/23/2023] [Indexed: 05/06/2023]
Abstract
Macromolecular crystallography is a well established method in the field of structural biology and has led to the majority of known protein structures to date. After focusing on static structures, the method is now under development towards the investigation of protein dynamics through time-resolved methods. These experiments often require multiple handling steps of the sensitive protein crystals, e.g. for ligand-soaking and cryo-protection. These handling steps can cause significant crystal damage, and hence reduce data quality. Furthermore, in time-resolved experiments based on serial crystallography, which use micrometre-sized crystals for short diffusion times of ligands, certain crystal morphologies with small solvent channels can prevent sufficient ligand diffusion. Described here is a method that combines protein crystallization and data collection in a novel one-step process. Corresponding experiments were successfully performed as a proof-of-principle using hen egg-white lysozyme and crystallization times of only a few seconds. This method, called JINXED (Just IN time Crystallization for Easy structure Determination), promises high-quality data due to the avoidance of crystal handling and has the potential to enable time-resolved experiments with crystals containing small solvent channels by adding potential ligands to the crystallization buffer, simulating traditional co-crystallization approaches.
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Affiliation(s)
- Alessandra Henkel
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Marina Galchenkova
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Julia Maracke
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Bjarne Klopprogge
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Johanna Hakanpää
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Jeroen R Mesters
- Institut für Biochemie, Universität zu Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Henry N Chapman
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Dominik Oberthuer
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
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4
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Lee K, Kim J, Baek S, Park J, Park S, Lee JL, Chung WK, Cho Y, Nam KH. Combination of an inject-and-transfer system for serial femtosecond crystallography. J Appl Crystallogr 2022; 55:813-822. [DOI: 10.1107/s1600576722005556] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 05/22/2022] [Indexed: 09/03/2023] Open
Abstract
Serial femtosecond crystallography (SFX) enables the determination of room-temperature crystal structures of macromolecules with minimized radiation damage and provides time-resolved molecular dynamics by pump–probe or mix-and-inject experiments. In SFX, a variety of sample delivery methods with unique advantages have been developed and applied. The combination of existing sample delivery methods can enable a new approach to SFX data collection that combines the advantages of the individual methods. This study introduces a combined inject-and-transfer system (BITS) method for sample delivery in SFX experiments: a hybrid injection and fixed-target scanning method. BITS allows for solution samples to be reliably deposited on ultraviolet ozone (UVO)-treated polyimide films, at a minimum flow rate of 0.5 nl min−1, in both vertical and horizontal scanning modes. To utilize BITS in SFX experiments, lysozyme crystal samples were embedded in a viscous lard medium and injected at flow rates of 50–100 nl min−1 through a syringe needle onto a UVO-treated polyimide film, which was mounted on a fixed-target scan stage. The crystal samples deposited on the film were raster scanned with an X-ray free electron laser using a motion stage in both horizontal and vertical directions. Using the BITS method, the room-temperature structure of lysozyme was successfully determined at a resolution of 2.1 Å, and thus BITS could be utilized in future SFX experiments.
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5
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Wells DJ, Berntsen P, Balaur E, Kewish CM, Adams P, Aquila A, Binns J, Boutet S, Broomhall H, Caleman C, Christofferson A, Conn CE, Dahlqvist C, Flueckiger L, Gian Roque F, Greaves TL, Hejazian M, Hunter M, Hadian Jazi M, Jönsson HO, Pathirannahalage SK, Kirian RA, Kozlov A, Kurta RP, Marman H, Mendez D, Morgan A, Nugent K, Oberthuer D, Quiney H, Reinhardt J, Saha S, Sellberg JA, Sierra R, Wiedorn M, Abbey B, Martin AV, Darmanin C. Observations of phase changes in monoolein during high viscous injection. JOURNAL OF SYNCHROTRON RADIATION 2022; 29:602-614. [PMID: 35510993 PMCID: PMC9070699 DOI: 10.1107/s1600577522001862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 02/17/2022] [Indexed: 06/14/2023]
Abstract
Serial crystallography of membrane proteins often employs high-viscosity injectors (HVIs) to deliver micrometre-sized crystals to the X-ray beam. Typically, the carrier medium is a lipidic cubic phase (LCP) media, which can also be used to nucleate and grow the crystals. However, despite the fact that the LCP is widely used with HVIs, the potential impact of the injection process on the LCP structure has not been reported and hence is not yet well understood. The self-assembled structure of the LCP can be affected by pressure, dehydration and temperature changes, all of which occur during continuous flow injection. These changes to the LCP structure may in turn impact the results of X-ray diffraction measurements from membrane protein crystals. To investigate the influence of HVIs on the structure of the LCP we conducted a study of the phase changes in monoolein/water and monoolein/buffer mixtures during continuous flow injection, at both atmospheric pressure and under vacuum. The reservoir pressure in the HVI was tracked to determine if there is any correlation with the phase behaviour of the LCP. The results indicated that, even though the reservoir pressure underwent (at times) significant variation, this did not appear to correlate with observed phase changes in the sample stream or correspond to shifts in the LCP lattice parameter. During vacuum injection, there was a three-way coexistence of the gyroid cubic phase, diamond cubic phase and lamellar phase. During injection at atmospheric pressure, the coexistence of a cubic phase and lamellar phase in the monoolein/water mixtures was also observed. The degree to which the lamellar phase is formed was found to be strongly dependent on the co-flowing gas conditions used to stabilize the LCP stream. A combination of laboratory-based optical polarization microscopy and simulation studies was used to investigate these observations.
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Affiliation(s)
- Daniel J. Wells
- La Trobe Institute for Molecular Science, Department of Mathematical and Physical Sciences, School of Computing Engineering and Mathematical Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Peter Berntsen
- La Trobe Institute for Molecular Science, Department of Mathematical and Physical Sciences, School of Computing Engineering and Mathematical Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Eugeniu Balaur
- La Trobe Institute for Molecular Science, Department of Mathematical and Physical Sciences, School of Computing Engineering and Mathematical Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Cameron M. Kewish
- Australian Synchrotron, Australian Nuclear Science and Technology Organisation, 800 Blackburn Road, Clayton, VIC 3168, Australia
- Department of Chemistry and Physics, School of Molecular Sciences, La Trobe University, Bundoora, VIC 3086, Australia
| | - Patrick Adams
- School of Science, RMIT University, Melbourne, VIC 3000, Australia
| | - Andrew Aquila
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Jack Binns
- School of Science, RMIT University, Melbourne, VIC 3000, Australia
| | - Sébastien Boutet
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Hayden Broomhall
- School of Science, RMIT University, Melbourne, VIC 3000, Australia
| | - Carl Caleman
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | | | | | - Caroline Dahlqvist
- Biomedical and X-ray Physics, Department of Applied Physics, AlbaNova University Center, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Leonie Flueckiger
- La Trobe Institute for Molecular Science, Department of Mathematical and Physical Sciences, School of Computing Engineering and Mathematical Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Francisco Gian Roque
- La Trobe Institute for Molecular Science, Department of Mathematical and Physical Sciences, School of Computing Engineering and Mathematical Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Tamar L. Greaves
- School of Science, RMIT University, Melbourne, VIC 3000, Australia
| | - Majid Hejazian
- La Trobe Institute for Molecular Science, Department of Mathematical and Physical Sciences, School of Computing Engineering and Mathematical Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Mark Hunter
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Marjan Hadian Jazi
- La Trobe Institute for Molecular Science, Department of Mathematical and Physical Sciences, School of Computing Engineering and Mathematical Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - H. Olof Jönsson
- Biomedical and X-ray Physics, Department of Applied Physics, AlbaNova University Center, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | | | - Richard A. Kirian
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Alex Kozlov
- ARC Centre of Excellence for Advanced Molecular Imaging, The University of Melbourne, Parkville, VIC 3010, Australia
| | | | - Hugh Marman
- La Trobe Institute for Molecular Science, Department of Mathematical and Physical Sciences, School of Computing Engineering and Mathematical Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Derek Mendez
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Andrew Morgan
- ARC Centre of Excellence for Advanced Molecular Imaging, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Keith Nugent
- Research School of Physics, The Australian National University, Acton, ACT, Australia
| | - Dominik Oberthuer
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Harry Quiney
- ARC Centre of Excellence for Advanced Molecular Imaging, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Juliane Reinhardt
- Australian Synchrotron, Australian Nuclear Science and Technology Organisation, 800 Blackburn Road, Clayton, VIC 3168, Australia
| | - Saumitra Saha
- ARC Centre of Excellence for Advanced Molecular Imaging, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Jonas A. Sellberg
- Biomedical and X-ray Physics, Department of Applied Physics, AlbaNova University Center, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Raymond Sierra
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Max Wiedorn
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Brian Abbey
- La Trobe Institute for Molecular Science, Department of Mathematical and Physical Sciences, School of Computing Engineering and Mathematical Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Andrew V. Martin
- School of Science, RMIT University, Melbourne, VIC 3000, Australia
| | - Connie Darmanin
- La Trobe Institute for Molecular Science, Department of Mathematical and Physical Sciences, School of Computing Engineering and Mathematical Science, La Trobe University, Bundoora, VIC 3086, Australia
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6
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Berntsen P, Darmanin C, Balaur E, Flueckiger L, Kozlov A, Roque FG, Adams P, Binns J, Wells D, Hadian Jazi M, Saha S, Hawley A, Ryan T, Mudie S, Kirby N, Abbey B, Martin AV. Stability, flow alignment and a phase transition of the lipidic cubic phase during continuous flow injection. J Colloid Interface Sci 2022; 611:588-598. [PMID: 34973655 DOI: 10.1016/j.jcis.2021.12.110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 11/30/2021] [Accepted: 12/16/2021] [Indexed: 10/19/2022]
Abstract
Continuous flow injection is a key technology for serial crystallography measurements of protein crystals suspended in the lipidic cubic phase (LCP). To date, there has been little discussion in the literature regarding the impact of the injection process itself on the structure of the lipidic phase. This is despite the fact that the phase of the injection matrix is critical for the flow properties of the stream and potentially for sample stability. Here we report small-angle X-ray scattering measurements of a monoolein:water mixture during continuous delivery using a high viscosity injector. We observe both an alignment and modification of the LCP as a direct result of the injection process. The orientation of the cubic lattice with respect to the beam was estimated based on the anisotropy of the diffraction pattern and does not correspond to a single low order zone axis. The solvent fraction was also observed to impact the stability of the cubic phase during injection. In addition, depending on the distance traveled by the lipid after exiting the needle, the phase is observed to transition from a pure diamond phase (Pn3m) to a mixture containing both gyriod (Ia3d) and lamellar (Lα) phases. Finite element modelling of the observed phase behaviour during injection indicates that the pressure exerted on the lipid stream during extrusion accounts for the variations in the phase composition of the monoolein:water mixture.
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Affiliation(s)
- Peter Berntsen
- ARC Centre of Excellence for Advanced Molecular Imaging, La Trobe University, Bundoora 3086, VIC, Australia
| | - Connie Darmanin
- ARC Centre of Excellence for Advanced Molecular Imaging, La Trobe University, Bundoora 3086, VIC, Australia.
| | - Eugeniu Balaur
- ARC Centre of Excellence for Advanced Molecular Imaging, La Trobe University, Bundoora 3086, VIC, Australia
| | - Leonie Flueckiger
- ARC Centre of Excellence for Advanced Molecular Imaging, La Trobe University, Bundoora 3086, VIC, Australia
| | - Alex Kozlov
- ARC Centre of Excellence for Advanced Molecular Imaging, The University of Melbourne, Parkville 3010, VIC, Australia
| | - Francisco G Roque
- ARC Centre of Excellence for Advanced Molecular Imaging, La Trobe University, Bundoora 3086, VIC, Australia
| | - Patrick Adams
- School of Science, RMIT University, Melbourne 3000 Australia
| | - Jack Binns
- School of Science, RMIT University, Melbourne 3000 Australia
| | - Daniel Wells
- ARC Centre of Excellence for Advanced Molecular Imaging, La Trobe University, Bundoora 3086, VIC, Australia
| | - Marjan Hadian Jazi
- ARC Centre of Excellence for Advanced Molecular Imaging, La Trobe University, Bundoora 3086, VIC, Australia
| | - Saumitra Saha
- ARC Centre of Excellence for Advanced Molecular Imaging, The University of Melbourne, Parkville 3010, VIC, Australia
| | - Adrian Hawley
- The Australian Nuclear Science Technology Organisation, The Australian Synchrotron, Clayton, Vic, Australia
| | - Tim Ryan
- The Australian Nuclear Science Technology Organisation, The Australian Synchrotron, Clayton, Vic, Australia
| | - Stephen Mudie
- The Australian Nuclear Science Technology Organisation, The Australian Synchrotron, Clayton, Vic, Australia
| | - Nigel Kirby
- The Australian Nuclear Science Technology Organisation, The Australian Synchrotron, Clayton, Vic, Australia
| | - Brian Abbey
- ARC Centre of Excellence for Advanced Molecular Imaging, La Trobe University, Bundoora 3086, VIC, Australia
| | - Andrew V Martin
- School of Science, RMIT University, Melbourne 3000 Australia.
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7
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Nam KH. Beef tallow injection matrix for serial crystallography. Sci Rep 2022; 12:694. [PMID: 35027663 PMCID: PMC8758675 DOI: 10.1038/s41598-021-04714-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 12/29/2021] [Indexed: 12/22/2022] Open
Abstract
Serial crystallography (SX) enables the visualization of the time-resolved molecular dynamics of macromolecular structures at room temperature while minimizing radiation damage. In SX experiments, the delivery of a large number of crystals into an X-ray interaction point in a serial and stable manner is key. Sample delivery using viscous medium maintains the stable injection stream at low flow rates, markedly reducing sample consumption compared with that of a liquid jet injector and is widely applied in SX experiments with low repetition rates. As the sample properties and experimental environment can affect the stability of the injection stream of a viscous medium, it is important to develop sample delivery media with various characteristics to optimize the experimental environment. In this study, a beef tallow injection matrix possessing a higher melting temperature than previously reported fat-based shortening and lard media was introduced as a sample delivery medium and applied to SX. Beef tallow was prepared by heat treating fats from cattle, followed by the removal of soluble impurities from the extract by phase separation. Beef tallow exhibited a very stable injection stream at room temperature and a flow rate of < 10 nL/min. The room-temperature structures of lysozyme and glucose isomerase embedded in beef tallow were successfully determined at 1.55 and 1.60 Å, respectively. The background scattering of beef tallow was higher than that of previously reported fat-based shortening and lard media but negligible for data processing. In conclusion, the beef tallow matrix can be employed for sample delivery in SX experiments conducted at temperatures exceeding room temperature.
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Affiliation(s)
- Ki Hyun Nam
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Korea. .,POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Korea.
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8
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Hadian-Jazi M, Sadri A, Barty A, Yefanov O, Galchenkova M, Oberthuer D, Komadina D, Brehm W, Kirkwood H, Mills G, de Wijn R, Letrun R, Kloos M, Vakili M, Gelisio L, Darmanin C, Mancuso AP, Chapman HN, Abbey B. Data reduction for serial crystallography using a robust peak finder. J Appl Crystallogr 2021; 54:1360-1378. [PMID: 34667447 PMCID: PMC8493619 DOI: 10.1107/s1600576721007317] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 07/14/2021] [Indexed: 11/23/2022] Open
Abstract
A peak-finding algorithm for serial crystallography (SX) data analysis based on the principle of 'robust statistics' has been developed. Methods which are statistically robust are generally more insensitive to any departures from model assumptions and are particularly effective when analysing mixtures of probability distributions. For example, these methods enable the discretization of data into a group comprising inliers (i.e. the background noise) and another group comprising outliers (i.e. Bragg peaks). Our robust statistics algorithm has two key advantages, which are demonstrated through testing using multiple SX data sets. First, it is relatively insensitive to the exact value of the input parameters and hence requires minimal optimization. This is critical for the algorithm to be able to run unsupervised, allowing for automated selection or 'vetoing' of SX diffraction data. Secondly, the processing of individual diffraction patterns can be easily parallelized. This means that it can analyse data from multiple detector modules simultaneously, making it ideally suited to real-time data processing. These characteristics mean that the robust peak finder (RPF) algorithm will be particularly beneficial for the new class of MHz X-ray free-electron laser sources, which generate large amounts of data in a short period of time.
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Affiliation(s)
- Marjan Hadian-Jazi
- ARC Centre of Excellence in Advanced Molecular Imaging, La Trobe Institute for Molecular Sciences, La Trobe University, Melbourne, Australia
- Australian Nuclear Science and Technology Organisation (ANSTO), Australia
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Alireza Sadri
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Anton Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Marina Galchenkova
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Dominik Oberthuer
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Dana Komadina
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Wolfgang Brehm
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | | | - Grant Mills
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | - Romain Letrun
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Marco Kloos
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | - Luca Gelisio
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Connie Darmanin
- ARC Centre of Excellence in Advanced Molecular Imaging, La Trobe Institute for Molecular Sciences, La Trobe University, Melbourne, Australia
| | - Adrian P. Mancuso
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Henry N. Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Brian Abbey
- ARC Centre of Excellence in Advanced Molecular Imaging, La Trobe Institute for Molecular Sciences, La Trobe University, Melbourne, Australia
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9
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Analysis of Multi-Hit Crystals in Serial Synchrotron Crystallography Experiments Using High-Viscosity Injectors. CRYSTALS 2021. [DOI: 10.3390/cryst11010049] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Serial Synchrotron Crystallography (SSX) is rapidly emerging as a promising technique for collecting data for time-resolved structural studies or for performing room temperature micro-crystallography measurements using micro-focused beamlines. SSX is often performed using high frame rate detectors in combination with continuous sample scanning or high-viscosity or liquid jet injectors. When performed using ultra-bright X-ray Free Electron Laser (XFEL) sources serial crystallography typically involves a process known as ’diffract-and-destroy’ where each crystal is measured just once before it is destroyed by the intense XFEL pulse. In SSX, however, particularly when using high-viscosity injectors (HVIs) such as Lipidico, the crystal can be intercepted multiple times by the X-ray beam prior to exiting the interaction region. This has a number of important consequences for SSX including whether these multiple-hits can be incorporated into the data analysis or whether they need to be excluded due to the potential impact of radiation damage. Here, we investigate the occurrence and characteristics of multiple hits on single crystals using SSX with lipidico. SSX data are collected from crystals as they tumble within a high viscous stream of silicone grease flowing through a micro-focused X-ray beam. We confirmed that, using the Eiger 16M, we are able to collect up to 42 frames of data from the same single crystal prior to it leaving the X-ray interaction region. The frequency and occurrence of multiple hits may be controlled by varying the sample flow rate and X-ray beam size. Calculations of the absorbed dose confirm that these crystals are likely to undergo radiation damage but that nonetheless incorporating multiple hits into damage-free data should lead to a significant reduction in the number of crystals required for structural analysis when compared to just looking at a single diffraction pattern from each crystal.
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Pearson AR, Mehrabi P. Serial synchrotron crystallography for time-resolved structural biology. Curr Opin Struct Biol 2020; 65:168-174. [PMID: 32846363 DOI: 10.1016/j.sbi.2020.06.019] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 06/26/2020] [Accepted: 06/26/2020] [Indexed: 10/23/2022]
Abstract
The current state-of-the-art experiments in time-resolved structural biology are undoubtedly the recent extremely impressive results that are emerging from XFEL-based experiments. However, there is a large range of macromolecular systems where the biological interest is predominantly in the slower dynamics (μs-s), that produce well diffracting microcrystals, and for which synchrotron-based experiments are extremely well suited. The combination of microfocus X-ray beams and the development of a range of sample delivery platforms has now made routine millisecond time-resolved experiments at microfocus macromolecular crystallography beamlines a real possibility and is driving development of dedicated endstations for time-resolved serial synchrotron crystallography.
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Affiliation(s)
- Arwen R Pearson
- Institute for Nanostructure and Solid State Physics, Hamburg Centre for Ultrafast Imaging, Universität Hamburg, CFEL, Luruper Chaussee 149, Hamburg 22761, Germany.
| | - Pedram Mehrabi
- Max Planck Institute for the Structure and Dynamics of Matter, CFEL, Luruper Chaussee 149, Hamburg 22761, Germany
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Nam KH. Lard Injection Matrix for Serial Crystallography. Int J Mol Sci 2020; 21:ijms21175977. [PMID: 32825186 PMCID: PMC7504126 DOI: 10.3390/ijms21175977] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 08/17/2020] [Accepted: 08/18/2020] [Indexed: 02/08/2023] Open
Abstract
Serial crystallography (SX) using X-ray free electron laser or synchrotron X-ray allows for the determination of structures, at room temperature, with reduced radiation damage. Moreover, it allows for the study of structural dynamics of macromolecules using a time-resolved pump-probe, as well as mix-and-inject experiments. Delivering a crystal sample using a viscous medium decreases sample consumption by lowering the flow rate while being extruded from the injector or syringe as compared to a liquid jet injector. Since the environment of crystal samples varies, continuous development of the delivery medium is important for extended SX applications. Herein, I report the preparation and characterization of a lard-based sample delivery medium for SX. This material was obtained using heat treatment, and then the soluble impurities were removed through phase separation. The lard injection medium was highly stable and could be injected via a syringe needle extruded at room temperature with a flow rate < 200 nL/min. Serial millisecond crystallography experiments were performed using lard, and the room temperature structures of lysozyme and glucose isomerase embedded in lard at 1.75 and 1.80 Å, respectively, were determined. The lard medium showed X-ray background scattering similar or relatively lower than shortenings and lipidic cubic phase; therefore, it can be used as sample delivery medium in SX experiments.
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Affiliation(s)
- Ki Hyun Nam
- Department of Life Science, Pohang University of Science and Technology, Pohang 37673, Korea
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Lee K, Lee D, Baek S, Park J, Lee SJ, Park S, Chung WK, Lee JL, Cho HS, Cho Y, Nam KH. Viscous-medium-based crystal support in a sample holder for fixed-target serial femtosecond crystallography. J Appl Crystallogr 2020. [DOI: 10.1107/s1600576720008663] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Serial femtosecond crystallography (SFX) enables the determination of the room-temperature crystal structure of macromolecules, as well as providing time-resolved molecular dynamics data in pump–probe experiments. Fixed-target SFX (FT-SFX) can minimize sample consumption and physical effects on crystals during sample delivery. In FT-SFX studies, having a sample holder that can stably fix crystal samples is one of the key elements required for efficient data collection. Hence, development of sample holders from new materials capable of supporting various crystal sizes and shapes may expand the applications of FT-SFX. Here, a viscous-media-based crystal support in a sample holder for FT-SFX is introduced. Crystal samples were embedded in viscous media, namely gelatin and agarose, which were enclosed in a polyimide film. In the vertically placed sample holder, 10–15%(w/v) viscous gelatin and 1–4%(w/v) agarose gel stably supported crystals between two polyimide films, thereby preventing the crystals from descending owing to gravity. Using this method, FT-SFX experiments were performed with glucose isomerase and lysozyme embedded in gelatin and agarose, respectively. The room-temperature crystal structures of glucose isomerase and lysozyme were successfully determined at 1.75 and 1.80 Å resolutions, respectively. The glucose isomerase and lysozyme diffraction analyses were not impeded by excessive background scattering from the viscous media. This method is useful for delivering crystal samples of various sizes and shapes in FT-SFX experiments.
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Pump-Probe Time-Resolved Serial Femtosecond Crystallography at X-Ray Free Electron Lasers. CRYSTALS 2020. [DOI: 10.3390/cryst10070628] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
With time-resolved crystallography (TRX), it is possible to follow the reaction dynamics in biological macromolecules by investigating the structure of transient states along the reaction coordinate. X-ray free electron lasers (XFELs) have enabled TRX experiments on previously uncharted femtosecond timescales. Here, we review the recent developments, opportunities, and challenges of pump-probe TRX at XFELs.
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Polysaccharide-Based Injection Matrix for Serial Crystallography. Int J Mol Sci 2020; 21:ijms21093332. [PMID: 32397185 PMCID: PMC7247560 DOI: 10.3390/ijms21093332] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 05/02/2020] [Accepted: 05/05/2020] [Indexed: 12/21/2022] Open
Abstract
Serial crystallography (SX) provides an opportunity to observe the molecular dynamics of macromolecular structures at room temperature via pump-probe studies. The delivery of crystals embedded in a viscous medium via an injector or syringe is widely performed in synchrotrons or X-ray free-electron laser facilities with low repetition rates. Various viscous media have been developed; however, there are cases in which the delivery material undesirably interacts chemically or biologically with specific protein samples, or changes the stability of the injection stream, depending on the crystallization solution. Therefore, continued discovery and characterization of new delivery media is necessary for expanding future SX applications. Here, the preparation and characterization of new polysaccharide (wheat starch (WS) and alginate)-based sample delivery media are introduced for SX. Crystals embedded in a WS or alginate injection medium showed a stable injection stream at a flow rate of < 200 nL/min and low-level X-ray background scattering similar to other hydrogels. Using these media, serial millisecond crystallography (SMX) was performed, and the room temperature crystal structures of glucose isomerase and lysozyme were determined at 1.9–2.0 Å resolutions. WS and alginate will allow an expanded application of sample delivery media in SX experiments.
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Nam KH. Shortening injection matrix for serial crystallography. Sci Rep 2020; 10:107. [PMID: 31919476 PMCID: PMC6952439 DOI: 10.1038/s41598-019-56135-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 12/06/2019] [Indexed: 11/11/2022] Open
Abstract
Serial crystallography allows crystal structures to be determined at room temperature through the steady delivery of crystals to the X-ray interaction point. Viscous delivery media are advantageous because they afford efficient sample delivery from an injector or syringe at a low flow rate. Hydrophobic delivery media, such as lipidic cubic phase (LCP) or grease, provide a stable injection stream and are widely used. The development of new hydrophobic delivery materials can expand opportunities for future SX studies with various samples. Here, I introduce fat-based shortening as a delivery medium for SX experiments. This material is commercially available at low cost and is straightforward to handle because its phase (i.e., solid or liquid) can be controlled by temperature. Shortening was extruded from a syringe needle in a stable injection stream even below 200 nl/min. X-ray exposed shortening produced several background scattering rings, which have similar or lower intensities than those of LCP and contribute negligibly to data processing. Serial millisecond crystallography was performed using two shortening delivery media, and the room temperature crystal structures of lysozyme and glucose isomerase were successfully determined at resolutions of 1.5–2.0 Å. Therefore, shortening can be used as a sample delivery medium in SX experiments.
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Affiliation(s)
- Ki Hyun Nam
- Division of Biotechnology, Korea University, Seoul, Republic of Korea. .,Institute of Life Science and Natural Resources, Korea University, Seoul, Republic of Korea. .,Department of Life Science, Pohang University of Science and Technology, Pohang, Republic of Korea.
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