1
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Arai T, Mio K, Onoda H, Chavas LMG, Umena Y, Sasaki YC. The Blinking of Small-Angle X-ray Scattering Reveals the Degradation Process of Protein Crystals at Microsecond Timescale. Int J Mol Sci 2023; 24:16640. [PMID: 38068964 PMCID: PMC10706227 DOI: 10.3390/ijms242316640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 11/21/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
X-ray crystallography has revolutionized our understanding of biological macromolecules by elucidating their three-dimensional structures. However, the use of X-rays in this technique raises concerns about potential damage to the protein crystals, which results in a quality degradation of the diffraction data even at very low temperatures. Since such damage can occur on the micro- to millisecond timescale, a development in its real-time measurement has been expected. Here, we introduce diffracted X-ray blinking (DXB), which was originally proposed as a method to analyze the intensity fluctuations of diffraction of crystalline particles, to small-angle X-ray scattering (SAXS) of a lysozyme single-crystal. This novel technique, called the small-angle X-ray blinking (SAXB) method, analyzes the fluctuation in SAXS intensity reflecting the domain fluctuation in the protein crystal caused by the X-ray irradiation, which could be correlated with the X-ray-induced damage on the crystal. There was no change in the protein crystal's domain dynamics between the first and second X-ray exposures at 95K, each of which lasted 0.7 s. On the other hand, its dynamics at 295K increased remarkably. The SAXB method further showed a dramatic increase in domain fluctuations with an increasing dose of X-ray radiation, indicating the significance of this method.
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Affiliation(s)
- Tatsuya Arai
- Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa 277-8561, Chiba, Japan;
- AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), 6-2-3 Kashiwanoha, Kashiwa 277-0882, Chiba, Japan;
| | - Kazuhiro Mio
- AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), 6-2-3 Kashiwanoha, Kashiwa 277-0882, Chiba, Japan;
| | - Hiroki Onoda
- Synchrotron Radiation Research Center, Nagoya University, Furo-Cho, Chikusa-Ku, Nagoya 464-8603, Aichi, Japan; (H.O.); (L.M.G.C.)
| | - Leonard M. G. Chavas
- Synchrotron Radiation Research Center, Nagoya University, Furo-Cho, Chikusa-Ku, Nagoya 464-8603, Aichi, Japan; (H.O.); (L.M.G.C.)
- Department of Applied Physics, Graduate School of Engineering, Nagoya University, Furo-Cho, Chikusa-Ku, Nagoya 464-8603, Aichi, Japan
| | - Yasufumi Umena
- Synchrotron Radiation Research Center, Nagoya University, Furo-Cho, Chikusa-Ku, Nagoya 464-8603, Aichi, Japan; (H.O.); (L.M.G.C.)
| | - Yuji C. Sasaki
- Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa 277-8561, Chiba, Japan;
- AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), 6-2-3 Kashiwanoha, Kashiwa 277-0882, Chiba, Japan;
- Center for Synchrotron Radiation Research, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho 679-5198, Hyogo, Japan
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2
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Bolinsson H, Söderberg C, Herranz-Trillo F, Wahlgren M, Nilsson L. Realizing the AF4-UV-SAXS on-line coupling on protein and antibodies using high flux synchrotron radiation at the CoSAXS beamline, MAX IV. Anal Bioanal Chem 2023; 415:6237-6246. [PMID: 37572213 PMCID: PMC10558385 DOI: 10.1007/s00216-023-04900-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/31/2023] [Accepted: 08/02/2023] [Indexed: 08/14/2023]
Abstract
In this paper, we demonstrate the coupling of synchrotron small angle X-ray scattering (SAXS) to asymmetrical flow-field flow fractionation (AF4) for protein characterization. To the best of our knowledge, this is the first time AF4 is successfully coupled to a synchrotron for on-line measurements on proteins. This coupling has potentially high impact, as it opens the possibility to characterize individual constituents of sensitive and/or complex samples, not suited for separation using other techniques, and for low electron density samples where high X-ray flux is required, e.g., biomolecules and biologics. AF4 fractionates complex samples in native or close to native environment, with low shear forces and system surface area. Many orders of magnitude in size can be fractionated in one measurement, without having to reconfigure the experimental setup. We report AF4 fractionations with correlated UV and statistically adequate SAXS data of bovine serum albumin and a monoclonal antibody and evaluate SAXS data recorded for the two protein systems.
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Affiliation(s)
- Hans Bolinsson
- Department of Food Technology, Engineering and Nutrition, Lund University, Lund, Sweden.
| | - Christopher Söderberg
- RISE Research Institutes of Sweden, Division Bioeconomy and Health, Chemical Process and Pharmaceutical Development, Lund, Sweden
| | | | - Marie Wahlgren
- Department of Food Technology, Engineering and Nutrition, Lund University, Lund, Sweden
| | - Lars Nilsson
- Department of Food Technology, Engineering and Nutrition, Lund University, Lund, Sweden
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3
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Thomä SLJ, Zobel M. Beam-induced redox chemistry in iron oxide nanoparticle dispersions at ESRF-EBS. JOURNAL OF SYNCHROTRON RADIATION 2023; 30:440-444. [PMID: 36891857 PMCID: PMC10000811 DOI: 10.1107/s1600577522011523] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 11/30/2022] [Indexed: 06/08/2023]
Abstract
The storage ring upgrade of the European Synchrotron Radiation Facility makes ESRF-EBS the most brilliant high-energy fourth-generation light source, enabling in situ studies with unprecedented time resolution. While radiation damage is commonly associated with degradation of organic matter such as ionic liquids or polymers in the synchrotron beam, this study clearly shows that highly brilliant X-ray beams readily induce structural changes and beam damage in inorganic matter, too. Here, the reduction of Fe3+ to Fe2+ in iron oxide nanoparticles by radicals in the brilliant ESRF-EBS beam, not observed before the upgrade, is reported. Radicals are created due to radiolysis of an EtOH-H2O mixture with low EtOH concentration (∼6 vol%). In light of extended irradiation times during insitu experiments in, for example, battery and catalysis research, beam-induced redox chemistry needs to be understood for proper interpretation of insitu data.
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Affiliation(s)
- Sabrina L. J. Thomä
- Institute of Crystallography, RWTH Aachen University, Jägerstraße 17–19, Aachen, 52066 Nordrhein-Westfalen, Germany
| | - Mirijam Zobel
- Institute of Crystallography, RWTH Aachen University, Jägerstraße 17–19, Aachen, 52066 Nordrhein-Westfalen, Germany
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4
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Hallier DC, Smales GJ, Seitz H, Hahn MB. Bio-SAXS of single-stranded DNA-binding proteins: radiation protection by the compatible solute ectoine. Phys Chem Chem Phys 2023; 25:5372-5382. [PMID: 36637121 DOI: 10.1039/d2cp05053f] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Small-angle X-ray scattering (SAXS) can be used for structural determination of biological macromolecules and polymers in their native states (e.g. liquid phase). This means that the structural changes of (bio-)polymers, such as proteins and DNA, can be monitored in situ to understand their sensitivity to changes in chemical environments. In an attempt to improve the reliability of such experiments, the reduction of radiation damage occurring from exposure to X-rays is required. One such method, is to use scavenger molecules to protect macromolecules against radicals produced during radiation exposure, such as reactive oxygen species (ROS). In this study we investigate the feasibility of applying the compatible solute, osmolyte and radiation protector Ectoine (THP(B)), as a scavenger molecule during SAXS measurements of the single-stranded DNA-binding protein Gene-V Protein (G5P/GVP). In this case, we monitor the radiation induced changes of G5P during bio-SAXS measurments and the resulting microscopic energy-damage relation was determined from microdosimetric calculations by Monte-Carlo based particle scattering simulations with TOPAS/Geant4 and a custom target-model. This resulted in a median-lethal energy deposit of pure G5P at 4 mg mL-1 of E1/2 = 7 ± 5 eV, whereas a threefold increase of energy-deposit was needed under the presence of Ectoine to reach the same level of damage. This indicates that Ectoine increases the possible exposure time before radiation-damage to G5P is observed. Furthermore, the dominant type of damage shifted from aggregation in pure solutions towards a fragmentation for solutions containing Ectoine as a cosolute. These results are interpreted in terms of indirect radiation damage by reactive secondary species, as well as post-irradiation effects, related to preferential-exclusion of the cosolute from the protein surface. Hence, Ectoine is shown to provide a non-disturbing way to improve structure-determination of proteins via bio-SAXS in future studies.
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Affiliation(s)
- Dorothea C Hallier
- Universität Potsdam, Institut für Biochemie und Biologie, 14476 Potsdam, Germany.,Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses (IZI-BB), 14476 Potsdam, Germany.,Bundesanstalt für Materialforschung und -prüfung (BAM), 12205 Berlin, Germany.
| | - Glen J Smales
- Bundesanstalt für Materialforschung und -prüfung (BAM), 12205 Berlin, Germany.
| | - Harald Seitz
- Universität Potsdam, Institut für Biochemie und Biologie, 14476 Potsdam, Germany.,Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses (IZI-BB), 14476 Potsdam, Germany
| | - Marc Benjamin Hahn
- Bundesanstalt für Materialforschung und -prüfung (BAM), 12205 Berlin, Germany.
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5
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Reiser M, Girelli A, Ragulskaya A, Das S, Berkowicz S, Bin M, Ladd-Parada M, Filianina M, Poggemann HF, Begam N, Akhundzadeh MS, Timmermann S, Randolph L, Chushkin Y, Seydel T, Boesenberg U, Hallmann J, Möller J, Rodriguez-Fernandez A, Rosca R, Schaffer R, Scholz M, Shayduk R, Zozulya A, Madsen A, Schreiber F, Zhang F, Perakis F, Gutt C. Resolving molecular diffusion and aggregation of antibody proteins with megahertz X-ray free-electron laser pulses. Nat Commun 2022; 13:5528. [PMID: 36130930 PMCID: PMC9490738 DOI: 10.1038/s41467-022-33154-7] [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: 02/21/2022] [Accepted: 08/26/2022] [Indexed: 11/09/2022] Open
Abstract
X-ray free-electron lasers (XFELs) with megahertz repetition rate can provide novel insights into structural dynamics of biological macromolecule solutions. However, very high dose rates can lead to beam-induced dynamics and structural changes due to radiation damage. Here, we probe the dynamics of dense antibody protein (Ig-PEG) solutions using megahertz X-ray photon correlation spectroscopy (MHz-XPCS) at the European XFEL. By varying the total dose and dose rate, we identify a regime for measuring the motion of proteins in their first coordination shell, quantify XFEL-induced effects such as driven motion, and map out the extent of agglomeration dynamics. The results indicate that for average dose rates below 1.06 kGy μs-1 in a time window up to 10 μs, it is possible to capture the protein dynamics before the onset of beam induced aggregation. We refer to this approach as correlation before aggregation and demonstrate that MHz-XPCS bridges an important spatio-temporal gap in measurement techniques for biological samples.
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Affiliation(s)
- Mario Reiser
- Department of Physics, AlbaNova University Center, Stockholm University, SE-106 91, Stockholm, Sweden.
| | - Anita Girelli
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076, Tübingen, Germany
| | - Anastasia Ragulskaya
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076, Tübingen, Germany
| | - Sudipta Das
- Department of Physics, AlbaNova University Center, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Sharon Berkowicz
- Department of Physics, AlbaNova University Center, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Maddalena Bin
- Department of Physics, AlbaNova University Center, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Marjorie Ladd-Parada
- Department of Physics, AlbaNova University Center, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Mariia Filianina
- Department of Physics, AlbaNova University Center, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Hanna-Friederike Poggemann
- Department of Physics, AlbaNova University Center, Stockholm University, SE-106 91, Stockholm, Sweden.,Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076, Tübingen, Germany
| | - Nafisa Begam
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076, Tübingen, Germany
| | | | - Sonja Timmermann
- Department Physik, Universität Siegen, Walter-Flex-Strasse 3, 57072, Siegen, Germany
| | - Lisa Randolph
- Department Physik, Universität Siegen, Walter-Flex-Strasse 3, 57072, Siegen, Germany
| | - Yuriy Chushkin
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, CS 40220, 38043, Grenoble Cedex 9, France
| | - Tilo Seydel
- Institut Laue-Langevin, 71 Avenue des Martyrs, CS 20156, 38042, Grenoble Cedex 9, France
| | - Ulrike Boesenberg
- European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Jörg Hallmann
- European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Johannes Möller
- European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869, Schenefeld, Germany
| | | | - Robert Rosca
- European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Robert Schaffer
- European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Markus Scholz
- European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Roman Shayduk
- European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Alexey Zozulya
- European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Anders Madsen
- European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Frank Schreiber
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076, Tübingen, Germany
| | - Fajun Zhang
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076, Tübingen, Germany
| | - Fivos Perakis
- Department of Physics, AlbaNova University Center, Stockholm University, SE-106 91, Stockholm, Sweden.
| | - Christian Gutt
- Department Physik, Universität Siegen, Walter-Flex-Strasse 3, 57072, Siegen, Germany.
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6
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Childers KC, Peters SC, Lollar P, Spencer HT, Doering CB, Spiegel PC. SAXS analysis of the intrinsic tenase complex bound to a lipid nanodisc highlights intermolecular contacts between factors VIIIa/IXa. Blood Adv 2022; 6:3240-3254. [PMID: 35255502 PMCID: PMC9198903 DOI: 10.1182/bloodadvances.2021005874] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 02/27/2022] [Indexed: 11/20/2022] Open
Abstract
The intrinsic tenase (Xase) complex, formed by factors (f) VIIIa and fIXa, forms on activated platelet surfaces and catalyzes the activation of factor X to Xa, stimulating thrombin production in the blood coagulation cascade. The structural organization of the membrane-bound Xase complex remains largely unknown, hindering our understanding of the structural underpinnings that guide Xase complex assembly. Here, we aimed to characterize the Xase complex bound to a lipid nanodisc with biolayer interferometry (BLI), Michaelis-Menten kinetics, and small-angle X-ray scattering (SAXS). Using immobilized lipid nanodiscs, we measured binding rates and nanomolar affinities for fVIIIa, fIXa, and the Xase complex. Enzyme kinetic measurements demonstrated the assembly of an active enzyme complex in the presence of lipid nanodiscs. An ab initio molecular envelope of the nanodisc-bound Xase complex allowed us to computationally model fVIIIa and fIXa docked onto a flexible lipid membrane and identify protein-protein interactions. Our results highlight multiple points of contact between fVIIIa and fIXa, including a novel interaction with fIXa at the fVIIIa A1-A3 domain interface. Lastly, we identified hemophilia A/B-related mutations with varying severities at the fVIIIa/fIXa interface that may regulate Xase complex assembly. Together, our results support the use of SAXS as an emergent tool to investigate the membrane-bound Xase complex and illustrate how mutations at the fVIIIa/fIXa dimer interface may disrupt or stabilize the activated enzyme complex.
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Affiliation(s)
- Kenneth C Childers
- Department of Chemistry, Western Washington University, Bellingham, WA; and
| | - Shaun C Peters
- Department of Chemistry, Western Washington University, Bellingham, WA; and
| | - Pete Lollar
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Emory University, Atlanta, GA
| | - Harold Trent Spencer
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Emory University, Atlanta, GA
| | - Christopher B Doering
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Emory University, Atlanta, GA
| | - Paul C Spiegel
- Department of Chemistry, Western Washington University, Bellingham, WA; and
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7
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SEC-SAXS: Experimental set-up and software developments build up a powerful tool. Methods Enzymol 2022; 677:221-249. [DOI: 10.1016/bs.mie.2022.08.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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8
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Li F, Xu Q, Xia W, Zhang X, Zhao W, Zhou L, Zhong H, Peng W, Liu Z, Sun T. In situ small-angle X-ray scattering investigation of X-ray-induced gold nanoparticle synthesis without stabilizer. J Appl Crystallogr 2021. [DOI: 10.1107/s1600576721010207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The X-ray irradiation of gold salt aqueous solutions in the synthesis of gold nanoparticles (AuNPs) in the absence of any reducing agent or stabilizer is presented. The size, dispersion, number of particles, yield and morphology evolution during the radiolytic formation of AuNPs were followed simultaneously using in situ small-angle X-ray scattering. This study provides an insight into the overall kinetics and formation mechanisms at the initial stage of AuNP synthesis without reductants and stabilizers. The pH-dependent speciation of aqueous HAuCl4 and its influence on the synthesis, structure and properties of AuNPs were observed. The result sheds light on the key parameters required to obtain stable monomodal particles and the influence of the surface charge and reactivity of the chemical solution on the final particle size and shape.
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9
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Radajewski D, Hunter L, He X, Nahi O, Galloway JM, Meldrum FC. An innovative data processing method for studying nanoparticle formation in droplet microfluidics using X-rays scattering. LAB ON A CHIP 2021; 21:4498-4506. [PMID: 34671784 DOI: 10.1039/d1lc00545f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
X-ray scattering techniques provide a powerful means of characterizing the formation of nanoparticles in solution. Coupling these techniques to segmented-flow microfluidic devices that offer well-defined environments gives access to in situ time-resolved analysis, excellent reproducibility, and eliminates potential radiation damage. However, analysis of the resulting datasets can be extremely time-consuming, where these comprise frames corresponding to the droplets alone, the continuous phase alone, and to both at their interface. We here describe a robust, low-cost, and versatile droplet microfluidics device and use it to study the formation of magnetite nanoparticles with simultaneous synchrotron SAXS and WAXS. Lateral outlet capillaries facilitate the X-ray analysis and reaction times of between a few seconds and minutes can be accommodated. A two-step data processing method is then described that exploits the unique WAXS signatures of the droplets, continuous phase, and interfacial region to identify the frames corresponding to the droplets. These are then sorted, and the background scattering is subtracted using an automated frame-by-frame approach, allowing the signal from the nanoparticles to be isolated from the raw data. Modeling these data gives quantitative information about the evolution of the sizes and structures of the nanoparticles, in agreement with TEM observations. This versatile platform can be readily employed to study a wide range of dynamic processes in heterogeneous systems.
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Affiliation(s)
- Dimitri Radajewski
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK.
| | - Liam Hunter
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK.
| | - Xuefeng He
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK.
| | - Ouassef Nahi
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK.
| | - Johanna M Galloway
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK.
| | - Fiona C Meldrum
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK.
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10
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Stachowski TR, Snell ME, Snell EH. A SAXS-based approach to rationally evaluate radical scavengers - toward eliminating radiation damage in solution and crystallographic studies. JOURNAL OF SYNCHROTRON RADIATION 2021; 28:1309-1320. [PMID: 34475280 PMCID: PMC8415334 DOI: 10.1107/s1600577521004045] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 04/15/2021] [Indexed: 05/30/2023]
Abstract
X-ray-based techniques are a powerful tool in structural biology but the radiation-induced chemistry that results can be detrimental and may mask an accurate structural understanding. In the crystallographic case, cryocooling has been employed as a successful mitigation strategy but also has its limitations including the trapping of non-biological structural states. Crystallographic and solution studies performed at physiological temperatures can reveal otherwise hidden but relevant conformations, but are limited by their increased susceptibility to radiation damage. In this case, chemical additives that scavenge the species generated by radiation can mitigate damage but are not always successful and the mechanisms are often unclear. Using a protein designed to undergo a large-scale structural change from breakage of a disulfide bond, radiation damage can be monitored with small-angle X-ray scattering. Using this, we have quantitatively evaluated how three scavengers commonly used in crystallographic experiments - sodium nitrate, cysteine, and ascorbic acid - perform in solution at 10°C. Sodium nitrate was the most effective scavenger and completely inhibited fragmentation of the disulfide bond at a lower concentration (500 µM) compared with cysteine (∼5 mM) while ascorbic acid performed best at 5 mM but could only reduce fragmentation by ∼75% after a total accumulated dose of 792 Gy. The relative effectiveness of each scavenger matches their reported affinities for solvated electrons. Saturating concentrations of each scavenger shifted fragmentation from first order to a zeroth-order process, perhaps indicating the direct contribution of photoabsorption. The SAXS-based method can detect damage at X-ray doses far lower than those accessible crystallographically, thereby providing a detailed picture of scavenger processes. The solution results are also in close agreement with what is known about scavenger performance and mechanism in a crystallographic setting and suggest that a link can be made between the damage phenomenon in the two scenarios. Therefore, our engineered approach might provide a platform for more systematic and comprehensive screening of radioprotectants that can directly inform mitigation strategies for both solution and crystallographic experiments, while also clarifying fundamental radiation damage mechanisms.
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Affiliation(s)
- Timothy R. Stachowski
- Hauptman-Woodward Medical Research Institute, 700 Ellicott St, Buffalo, NY 14203, USA
- Cell Stress Biology, Roswell Park Comprehensive Cancer Center, 665 Elm Street, Buffalo, NY 14203, USA
| | - Mary E. Snell
- Hauptman-Woodward Medical Research Institute, 700 Ellicott St, Buffalo, NY 14203, USA
| | - Edward H. Snell
- Hauptman-Woodward Medical Research Institute, 700 Ellicott St, Buffalo, NY 14203, USA
- Materials Design and Innovation, State University at New York at Buffalo, 700 Ellicott St, Buffalo, NY 14203, USA
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11
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Kristensen LG, Holton JM, Rad B, Chen Y, Petzold CJ, Gupta S, Ralston CY. Hydroxyl radical mediated damage of proteins in low oxygen solution investigated using X-ray footprinting mass spectrometry. JOURNAL OF SYNCHROTRON RADIATION 2021; 28:1333-1342. [PMID: 34475282 PMCID: PMC8415330 DOI: 10.1107/s1600577521004744] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/04/2021] [Indexed: 05/12/2023]
Abstract
In the method of X-ray footprinting mass spectrometry (XFMS), proteins at micromolar concentration in solution are irradiated with a broadband X-ray source, and the resulting hydroxyl radical modifications are characterized using liquid chromatography mass spectrometry to determine sites of solvent accessibility. These data are used to infer structural changes in proteins upon interaction with other proteins, folding, or ligand binding. XFMS is typically performed under aerobic conditions; dissolved molecular oxygen in solution is necessary in many, if not all, the hydroxyl radical modifications that are generally reported. In this study we investigated the result of X-ray induced modifications to three different proteins under aerobic versus low oxygen conditions, and correlated the extent of damage with dose calculations. We observed a concentration-dependent protecting effect at higher protein concentration for a given X-ray dose. For the typical doses used in XFMS experiments there was minimal X-ray induced aggregation and fragmentation, but for higher doses we observed formation of covalent higher molecular weight oligomers, as well as fragmentation, which was affected by the amount of dissolved oxygen in solution. The higher molecular weight products in the form of dimers, trimers, and tetramers were present in all sample preparations, and, upon X-ray irradiation, these oligomers became non-reducible as seen in SDS-PAGE. The results provide an important contribution to the large body of X-ray radiation damage literature in structural biology research, and will specifically help inform the future planning of XFMS, and well as X-ray crystallography and small-angle X-ray scattering experiments.
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Affiliation(s)
- Line G Kristensen
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - James M Holton
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Behzad Rad
- Molecular Foundry Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Yan Chen
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Christopher J Petzold
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Sayan Gupta
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Corie Y Ralston
- Molecular Foundry Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
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12
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Lawrence Bright E, Giacobbe C, Wright JP. Beam heating from a fourth-generation synchrotron source. JOURNAL OF SYNCHROTRON RADIATION 2021; 28:1377-1385. [PMID: 34475286 PMCID: PMC8415326 DOI: 10.1107/s160057752100669x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 06/26/2021] [Indexed: 06/13/2023]
Abstract
The high levels of flux available at a fourth-generation synchrotron are shown to have significant beam heating effects for high-energy X-rays and radiation hard samples, leading to temperature increases of over 400 K with a monochromatic beam. These effects have been investigated at the ID11 beamline at the recently upgraded ESRF Extremely Brilliant Source, using thermal lattice expansion to perform in situ measurements of beam heating. Results showed significant increases in temperature for metal and ceria samples, which are compared with a lumped thermodynamic model, providing a tool for estimating beam heating effects. These temperature increases may have a drastic effect on samples and measurements, such as the rapid recrystallization of a copper wire shown here. These results demonstrate the importance of beam heating and provide information needed to consider, predict and mitigate these effects.
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Affiliation(s)
| | - Carlotta Giacobbe
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38040 Grenoble, France
| | - Jonathan P. Wright
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38040 Grenoble, France
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13
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Lurio LB, Thurston GM, Zhang Q, Narayanan S, Dufresne EM. Use of continuous sample translation to reduce radiation damage for XPCS studies of protein diffusion. JOURNAL OF SYNCHROTRON RADIATION 2021; 28:490-498. [PMID: 33650561 DOI: 10.1107/s1600577521000035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 01/02/2021] [Indexed: 06/12/2023]
Abstract
An experimental setup to measure X-ray photon correlation spectroscopy during continuous sample translation is presented and its effectiveness as a means to avoid sample damage in dynamics studies of protein diffusion is evaluated. X-ray damage from focused coherent synchrotron radiation remains below tolerable levels as long as the sample is translated through the beam sufficiently quickly. Here it is shown that it is possible to separate sample dynamics from the effects associated with the transit of the sample through the beam. By varying the sample translation rate, the damage threshold level, Dthresh = 1.8 kGy, for when beam damage begins to modify the dynamics under the conditions used, is also determined. Signal-to-noise ratios, Rsn ≥ 20, are obtained down to the shortest delay times of 20 µs. The applicability of this method of data collection to the next generation of multi-bend achromat synchrotron sources is discussed and it is shown that sub-microsecond dynamics should be obtainable on protein samples.
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Affiliation(s)
- Laurence B Lurio
- Department of Physics, Northern Illinois University, DeKalb, IL 60115, USA
| | - George M Thurston
- School of Physics and Astronomy, Rochester Institute of Technology, Rochester, NY 14623, USA
| | - Qingteng Zhang
- X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Suresh Narayanan
- X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Eric M Dufresne
- X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
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14
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Rai DK, Gillilan RE, Huang Q, Miller R, Ting E, Lazarev A, Tate MW, Gruner SM. High-pressure small-angle X-ray scattering cell for biological solutions and soft materials. J Appl Crystallogr 2021; 54:111-122. [PMID: 33841059 PMCID: PMC7941318 DOI: 10.1107/s1600576720014752] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 11/06/2020] [Indexed: 11/10/2022] Open
Abstract
Pressure is a fundamental thermodynamic parameter controlling the behavior of biological macromolecules. Pressure affects protein denaturation, kinetic parameters of enzymes, ligand binding, membrane permeability, ion trans-duction, expression of genetic information, viral infectivity, protein association and aggregation, and chemical processes. In many cases pressure alters the molecular shape. Small-angle X-ray scattering (SAXS) is a primary method to determine the shape and size of macromolecules. However, relatively few SAXS cells described in the literature are suitable for use at high pressures and with biological materials. Described here is a novel high-pressure SAXS sample cell that is suitable for general facility use by prioritization of ease of sample loading, temperature control, mechanical stability and X-ray background minimization. Cell operation at 14 keV is described, providing a q range of 0.01 < q < 0.7 Å-1, pressures of 0-400 MPa and an achievable temperature range of 0-80°C. The high-pressure SAXS cell has recently been commissioned on the ID7A beamline at the Cornell High Energy Synchrotron Source and is available to users on a peer-reviewed proposal basis.
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Affiliation(s)
- Durgesh K. Rai
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY 14853, USA
| | - Richard E. Gillilan
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY 14853, USA
| | - Qingqiu Huang
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY 14853, USA
| | - Robert Miller
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY 14853, USA
- Department of Chemistry, Cornell University, Ithaca, NY 14853, USA
| | - Edmund Ting
- Pressure BioSciences Inc., South Easton, MA 02375, USA
| | | | - Mark W. Tate
- Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY 14853, USA
| | - Sol M. Gruner
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY 14853, USA
- Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY 14853, USA
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15
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Stachowski TR, Snell ME, Snell EH. SAXS studies of X-ray induced disulfide bond damage: Engineering high-resolution insight from a low-resolution technique. PLoS One 2020; 15:e0239702. [PMID: 33201877 PMCID: PMC7671560 DOI: 10.1371/journal.pone.0239702] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 09/12/2020] [Indexed: 12/17/2022] Open
Abstract
A significant problem in biological X-ray crystallography is the radiation chemistry caused by the incident X-ray beam. This produces both global and site-specific damage. Site specific damage can misdirect the biological interpretation of the structural models produced. Cryo-cooling crystals has been successful in mitigating damage but not eliminating it altogether; however, cryo-cooling can be difficult in some cases and has also been shown to limit functionally relevant protein conformations. The doses used for X-ray crystallography are typically in the kilo-gray to mega-gray range. While disulfide bonds are among the most significantly affected species in proteins in the crystalline state at both cryogenic and higher temperatures, there is limited information on their response to low X-ray doses in solution, the details of which might inform biomedical applications of X-rays. In this work we engineered a protein that dimerizes through a susceptible disulfide bond to relate the radiation damage processes seen in cryo-cooled crystals to those closer to physiologic conditions. This approach enables a low-resolution technique, small angle X-ray scattering (SAXS), to detect and monitor a residue specific process. A dose dependent fragmentation of the engineered protein was seen that can be explained by a dimer to monomer transition through disulfide bond cleavage. This supports the crystallographically derived mechanism and demonstrates that results obtained crystallographically can be usefully extrapolated to physiologic conditions. Fragmentation was influenced by pH and the conformation of the dimer, providing information on mechanism and pointing to future routes for investigation and potential mitigation. The novel engineered protein approach to generate a large-scale change through a site-specific interaction represents a promising tool for advancing radiation damage studies under solution conditions.
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Affiliation(s)
- Timothy R. Stachowski
- Hauptman-Woodward Medical Research Institute, Buffalo, New York, United States of America
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, United States of America
| | - Mary E. Snell
- Hauptman-Woodward Medical Research Institute, Buffalo, New York, United States of America
| | - Edward H. Snell
- Hauptman-Woodward Medical Research Institute, Buffalo, New York, United States of America
- Department of Materials Design and Innovation, State University at New York at Buffalo, Buffalo, New York, United States of America
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16
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Castellví A, Pascual-Izarra C, Crosas E, Malfois M, Juanhuix J. Improving data quality and expanding BioSAXS experiments to low-molecular-weight and low-concentration protein samples. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2020; 76:971-981. [PMID: 33021499 DOI: 10.1107/s2059798320010700] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 08/03/2020] [Indexed: 11/10/2022]
Abstract
The addition of compounds to scavenge the radical species produced during biological small-angle X-ray scattering (BioSAXS) experiments is a common strategy to reduce the effects of radiation damage and produce better quality data. As almost half of the experiments leading to structures deposited in the SASBDB database used scavengers, finding potent scavengers would be advantageous for many experiments. Here, four compounds, three nucleosides and one nitrogenous base, are presented which can act as very effective radical-scavenging additives and increase the critical dose by up to 20 times without altering the stability or reducing the contrast of the tested protein solutions. The efficacy of these scavengers is higher than those commonly used in the field to date, as verified for lysozyme solutions at various concentrations from 7.0 to 0.5 mg ml-1. The compounds are also very efficient at mitigating radiation damage to four proteins with molecular weights ranging from 7 to 240 kDa and pH values from 3 to 8, with the extreme case being catalase at 6.7 mg ml-1, with a scavenging factor exceeding 100. These scavengers can therefore be instrumental in expanding BioSAXS to low-molecular-weight and low-concentration protein samples that were previously inaccessible owing to poor data quality. It is also demonstrated that an increase in the critical dose in standard BioSAXS experiments leads to an increment in the retrieved information, in particular at higher angles, and thus to higher resolution of the model.
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Affiliation(s)
- Albert Castellví
- Experiments Division, ALBA Synchrotron, Carrer de la Llum 2-26, Cerdanyola del Vallès, 08290 Barcelona, Spain
| | - Carlos Pascual-Izarra
- Experiments Division, ALBA Synchrotron, Carrer de la Llum 2-26, Cerdanyola del Vallès, 08290 Barcelona, Spain
| | - Eva Crosas
- DESY Photon Science, Notkestrasse 85, 08290 Hamburg, Germany
| | - Marc Malfois
- Experiments Division, ALBA Synchrotron, Carrer de la Llum 2-26, Cerdanyola del Vallès, 08290 Barcelona, Spain
| | - Judith Juanhuix
- Experiments Division, ALBA Synchrotron, Carrer de la Llum 2-26, Cerdanyola del Vallès, 08290 Barcelona, Spain
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17
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Martin EW, Hopkins JB, Mittag T. Small-angle X-ray scattering experiments of monodisperse intrinsically disordered protein samples close to the solubility limit. Methods Enzymol 2020; 646:185-222. [PMID: 33453925 PMCID: PMC8370720 DOI: 10.1016/bs.mie.2020.07.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The condensation of biomolecules into biomolecular condensates via liquid-liquid phase separation (LLPS) is a ubiquitous mechanism that drives cellular organization. To enable these functions, biomolecules have evolved to drive LLPS and facilitate partitioning into biomolecular condensates. Determining the molecular features of proteins that encode LLPS will provide critical insights into a plethora of biological processes. Problematically, probing biomolecular dense phases directly is often technologically difficult or impossible. By capitalizing on the symmetry between the conformational behavior of biomolecules in dilute solution and dense phases, it is possible to infer details critical to phase separation by precise measurements of the dilute phase thus circumventing complicated characterization of dense phases. The symmetry between dilute and dense phases is found in the size and shape of the conformational ensemble of a biomolecule-parameters that small-angle X-ray scattering (SAXS) is ideally suited to probe. Recent technological advances have made it possible to accurately characterize samples of intrinsically disordered protein regions at low enough concentration to avoid interference from intermolecular attraction, oligomerization or aggregation, all of which were previously roadblocks to characterizing self-assembling proteins. Herein, we describe the pitfalls inherent to measuring such samples, the experimental details required for circumventing these issues and analysis methods that place the results of SAXS measurements into the theoretical framework of LLPS.
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Affiliation(s)
- Erik W Martin
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Jesse B Hopkins
- The Biophysics Collaborative Access Team (BioCAT), Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL, United States
| | - Tanja Mittag
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, United States.
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18
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Schewa S, Schroer MA, Zickmantel T, Song YH, Blanchet CE, Gruzinov AY, Katona G, Svergun DI, Roessle M. A THz transparent 3D printed microfluidic cell for small angle x-ray scattering. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2020; 91:084101. [PMID: 32872894 DOI: 10.1063/5.0004706] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 07/09/2020] [Indexed: 06/11/2023]
Abstract
Excitation frequencies in the terahertz (THz) range are expected to lead to functionally relevant domain movements within the biological macromolecules such as proteins. The possibility of examining such movements in an aqueous environment is particularly valuable since here proteins are not deprived of any motional degrees of freedom. Small angle x-ray scattering (SAXS) is a powerful method to study the structure and domain movements of proteins in solution. Here, we present a microfluidic cell for SAXS experiments, which is also transparent for THz radiation. Specifically, cell dimensions and material were optimized for both radiation sources. In addition, the polystyrene cell can be 3D printed and easily assembled. We demonstrate the practicality of our design for SAXS measurements on several proteins in solution.
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Affiliation(s)
- S Schewa
- University of Applied Sciences Lübeck, Mönkhofer Weg 239, 23562 Lübeck, Germany
| | - M A Schroer
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - T Zickmantel
- Physics Institute, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Y-H Song
- Physics Institute, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - C E Blanchet
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - A Yu Gruzinov
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - G Katona
- Department of Chemistry and Molecular Biology, University of Gothenburg, 41390 Gothenburg, Sweden
| | - D I Svergun
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - M Roessle
- University of Applied Sciences Lübeck, Mönkhofer Weg 239, 23562 Lübeck, Germany
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19
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Yang L, Antonelli S, Chodankar S, Byrnes J, Lazo E, Qian K. Solution scattering at the Life Science X-ray Scattering (LiX) beamline. JOURNAL OF SYNCHROTRON RADIATION 2020; 27:804-812. [PMID: 32381785 PMCID: PMC7206542 DOI: 10.1107/s1600577520002362] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 02/19/2020] [Indexed: 05/03/2023]
Abstract
This work reports the instrumentation and software implementation at the Life Science X-ray Scattering (LiX) beamline at NSLS-II in support of biomolecular solution scattering. For automated static measurements, samples are stored in PCR tubes and grouped in 18-position sample holders. Unattended operations are enabled using a six-axis robot that exchanges sample holders between a storage box and a sample handler, transporting samples from the PCR tubes to the X-ray beam for scattering measurements. The storage box has a capacity of 20 sample holders. At full capacity, the measurements on all samples last for ∼9 h. For in-line size-exclusion chromatography, the beamline-control software coordinates with a commercial high-performance liquid chromatography (HPLC) system to measure multiple samples in batch mode. The beamline can switch between static and HPLC measurements instantaneously. In all measurements, the scattering data span a wide q-range of typically 0.006-3.2 Å-1. Functionalities in the Python package py4xs have been developed to support automated data processing, including azimuthal averaging, merging data from multiple detectors, buffer scattering subtraction, data storage in HDF5 format and exporting the final data in a three-column text format that is acceptable by most data analysis tools. These functionalities have been integrated into graphical user interfaces that run in Jupyter notebooks, with hooks for external data analysis software.
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Affiliation(s)
- Lin Yang
- NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | | | | | - James Byrnes
- NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Edwin Lazo
- NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Kun Qian
- NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
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20
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Delhommel F, Gabel F, Sattler M. Current approaches for integrating solution NMR spectroscopy and small-angle scattering to study the structure and dynamics of biomolecular complexes. J Mol Biol 2020; 432:2890-2912. [DOI: 10.1016/j.jmb.2020.03.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 02/27/2020] [Accepted: 03/10/2020] [Indexed: 01/24/2023]
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21
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Unzueta U, Roldán M, Pesarrodona M, Benitez R, Sánchez-Chardi A, Conchillo-Solé O, Mangues R, Villaverde A, Vázquez E. Self-assembling as regular nanoparticles dramatically minimizes photobleaching of tumour-targeted GFP. Acta Biomater 2020; 103:272-280. [PMID: 31812843 DOI: 10.1016/j.actbio.2019.12.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 11/29/2019] [Accepted: 12/03/2019] [Indexed: 11/25/2022]
Abstract
Fluorescent proteins are useful imaging and theranostic agents, but their potential superiority over alternative dyes is weakened by substantial photobleaching under irradiation. Enhancing protein photostability has been attempted through diverse strategies, with irregular results and limited applicability. In this context, we wondered if the controlled oligomerization of Green Fluorescent Protein (GFP) as nanoscale supramolecular complexes could stabilize the fluorophore through the newly formed protein-protein contacts, and thus, enhance its global photostability. For that, we have here analyzed the photobleaching profile of several GFP versions, engineered to self-assemble as tumour-homing nanoparticles with different targeting, size and structural stability. This has been done under prolonged irradiation in confocal laser scanning microscopy and by small-angle X-ray scattering. The results show that the oligomerization of GFP at the nanoscale enhances, by more than seven-fold, the stability of fluorescence emission. Interestingly, GFP nanoparticles are much more resistant to X-ray damage than the building block counterparts, indicating that the gained photostability is linked to enhanced structural resistance to radiation. Therefore, the controlled oligomerization of self-assembling fluorescent proteins as protein nanoparticles is a simple, versatile and powerful method to enhance their photostability for uses in precision imaging and therapy. STATEMENT OF SIGNIFICANCE: Fluorescent protein assembly into regular and highly symmetric nanoscale structures has been identified to confer enhanced structural stability against radiation stresses dramatically reducing their photobleaching. Being this the main bottleneck in the use of fluorescent proteins for imaging and theranostics, this protein architecture engineering principle appears as a powerful method to enhance their photostability for a broad applicability in precision imaging, drug delivery and theranostics.
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22
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23
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Stachowski T, Grant TD, Snell EH. Structural consequences of transforming growth factor beta-1 activation from near-therapeutic X-ray doses. JOURNAL OF SYNCHROTRON RADIATION 2019; 26:967-979. [PMID: 31274418 PMCID: PMC6613122 DOI: 10.1107/s1600577519005113] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 04/14/2019] [Indexed: 05/24/2023]
Abstract
Dissociation of transforming growth factor beta-1 (TGFβ-1) from the inhibitory protein latency-associated peptide (LAP) can occur from low doses of X-ray irradiation of the LAP-TGFβ-1 complex, resulting in the activation of TGFβ-1, and can have health-related consequences. Using the tools and knowledge developed in the study of radiation damage in the crystallographic setting, small-angle X-ray scattering (SAXS) and complementary techniques suggest an activation process that is initiated but not driven by the initial X-ray exposure. LAP is revealed to be extended when not bound to TGFβ-1 and has a different structural conformation compared to the bound state. These studies pave the way for the structural understanding of systems impacted at therapeutic X-ray doses and show the potential impact of radiation damage studies beyond their original intent.
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Affiliation(s)
- Timothy Stachowski
- Hauptman–Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
- Cell Stress Biology, Roswell Park Comprehensive Cancer Center, 665 Elm Street, Buffalo, NY 14203, USA
| | - Thomas D. Grant
- Hauptman–Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, 700 Ellicott Street, Buffalo, NY 14203, USA
| | - Edward H. Snell
- Hauptman–Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
- Materials Design and Innovation, State University of New York at Buffalo, 700 Ellicott Street, Buffalo, NY 14203, USA
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24
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Taube M, Pietralik Z, Szymanska A, Szutkowski K, Clemens D, Grubb A, Kozak M. The domain swapping of human cystatin C induced by synchrotron radiation. Sci Rep 2019; 9:8548. [PMID: 31189973 PMCID: PMC6561922 DOI: 10.1038/s41598-019-44811-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 05/13/2019] [Indexed: 02/04/2023] Open
Abstract
Domain swapping is observed for many proteins with flexible conformations. This phenomenon is often associated with the development of conformational diseases. Importantly, domain swapping has been observed for human cystatin C (HCC), a protein capable of forming amyloid deposits in brain arteries. In this study, the ability of short exposure to high-intensity X-ray radiation to induce domain swapping in solutions of several HCC variants (wild-type HCC and V57G, V57D, V57N, V57P, and L68V mutants) was determined. The study was conducted using time-resolved small-angle X-ray scattering (TR-SAXS) synchrotron radiation. The protein samples were also analysed using small-angle neutron scattering and NMR diffusometry. Exposing HCC to synchrotron radiation (over 50 ms) led to a gradual increase in the dimeric fraction, and for exposures longer than 150 ms, the oligomer fraction was dominant. In contrast, the non-irradiated protein solutions, apart from the V57P variant, were predominantly monomeric (e.g., V57G) or in monomer/dimer equilibrium. This work might represent the first observation of domain swapping induced by high-intensity X-rays.
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Affiliation(s)
- Michal Taube
- Department of Macromolecular Physics, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 2, 61-614, Poznań, Poland
- Joint Laboratory for SAXS Studies, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 2, 61-614, Poznań, Poland
| | - Zuzanna Pietralik
- Department of Macromolecular Physics, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 2, 61-614, Poznań, Poland
| | - Aneta Szymanska
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Kosma Szutkowski
- Department of Macromolecular Physics, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 2, 61-614, Poznań, Poland
- NanoBioMedical Centre at Adam Mickiewicz University in Poznań, Wszechnicy Piastowskiej 3, 61-614, Poznań, Poland
| | - Daniel Clemens
- Helmholtz-Zentrum Berlin für Materialien und Energie Lise-Meitner-Campus Hahn-Meitner-Platz 1, 14109, Berlin, Germany
| | - Anders Grubb
- Department of Clinical Chemistry, Lund University Hospital, S-22185, Lund, Sweden
| | - Maciej Kozak
- Department of Macromolecular Physics, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 2, 61-614, Poznań, Poland.
- Joint Laboratory for SAXS Studies, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 2, 61-614, Poznań, Poland.
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25
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Tajima H, Penttilä PA, Imai T, Yamamoto K, Yuguchi Y. Observation of in vitro cellulose synthesis by bacterial cellulose synthase with time-resolved small angle X-ray scattering. Int J Biol Macromol 2019; 130:765-777. [PMID: 30831170 DOI: 10.1016/j.ijbiomac.2019.02.167] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 02/25/2019] [Accepted: 02/28/2019] [Indexed: 10/27/2022]
Abstract
Cellulose synthase is the enzyme that produces cellulose in the living organisms like plant, and has two functions: polymerizing glucose residues (polymerization) and assembling these polymerized molecules into a crystalline microfibril with a "cellulose I" crystallographic structure (crystallization). Many studies, however, have shown that an in vitro reaction of cellulose synthase produces aggregates of a non-native crystallographic structure "cellulose II", despite the remaining polymerizing activity. This is partial denaturation or loss of crystallization function in cellulose synthase, which needs to be resolved to reconstitute its native activity. To this end, we aimed to clarify the process of cellulose II formation by bacterial cellulose synthase in vitro, using in situ small angle X-ray scattering (SAXS). An increase in scattering specific to synthesis was observed around two distinct regions of q (0.2-0.4 nm-1 and <0.1 nm-1) by time-resolved SAXS measurement. The scattering at higher q-region appears prior to lower-q scattering at beginning of the reaction, indicating the existence of smaller primitive aggregations at the initiation stage. This study demonstrates the use of in situ SAXS measurement to decipher the dynamics of biosynthesized cellulose chains, which is a remarkable example of polymer assembly in ambient conditions.
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Affiliation(s)
- Hirotaka Tajima
- Research Institute for Sustainable Humanosphere (RISH), Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Paavo A Penttilä
- Research Institute for Sustainable Humanosphere (RISH), Kyoto University, Uji, Kyoto 611-0011, Japan; Science Division/Large-Scale Structures Group, Institut Laue-Langevin (ILL), 71 avenue des Martyrs, 38042 Grenoble, France
| | - Tomoya Imai
- Research Institute for Sustainable Humanosphere (RISH), Kyoto University, Uji, Kyoto 611-0011, Japan.
| | - Kyoko Yamamoto
- Faculty of Engineering, Osaka Electro-Communication University, 18-8 Hatsucho, Neyagawa, Osaka 572-8530, Japan
| | - Yoshiaki Yuguchi
- Faculty of Engineering, Osaka Electro-Communication University, 18-8 Hatsucho, Neyagawa, Osaka 572-8530, Japan.
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26
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Efficacy of aldose reductase inhibitors is affected by oxidative stress induced under X-ray irradiation. Sci Rep 2019; 9:3177. [PMID: 30816220 PMCID: PMC6395642 DOI: 10.1038/s41598-019-39722-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 01/29/2019] [Indexed: 01/01/2023] Open
Abstract
Human aldose reductase (hAR, AKR1B1) has been explored as drug target since the 1980s for its implication in diabetic complications. An activated form of hAR was found in cells from diabetic patients, showing a reduced sensitivity to inhibitors in clinical trials, which may prevent its pharmacological use. Here we report the conversion of native hAR to its activated form by X-ray irradiation simulating oxidative stress conditions. Upon irradiation, the enzyme activity increases moderately and the potency of several hAR inhibitors decay before global protein radiation damage appears. The catalytic behavior of activated hAR is also reproduced as the KM increases dramatically while the kcat is not much affected. Consistently, the catalytic tetrad is not showing any modification. The only catalytically-relevant structural difference observed is the conversion of residue Cys298 to serine and alanine. A mechanism involving electron capture is suggested for the hAR activation. We propose that hAR inhibitors should not be designed against the native protein but against the activated form as obtained from X-ray irradiation. Furthermore, since the reactive species produced under irradiation conditions are the same as those produced under oxidative stress, the described irradiation method can be applied to other relevant proteins under oxidative stress environments.
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27
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Barteau KP, Ma K, Kohle FF, Gardinier TC, Beaucage PA, Gillilan RE, Wiesner U. Quantitative Measure of the Size Dispersity in Ultrasmall Fluorescent Organic-Inorganic Hybrid Core-Shell Silica Nanoparticles by Small-angle X-ray Scattering. CHEMISTRY OF MATERIALS : A PUBLICATION OF THE AMERICAN CHEMICAL SOCIETY 2019; 31:643-657. [PMID: 30886456 PMCID: PMC6420223 DOI: 10.1021/acs.chemmater.8b04369] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Small-angle X-ray scattering (SAXS) was performed on dispersions of ultrasmall (d < 10 nm) fluorescent organic-inorganic hybrid core-shell silica nanoparticles synthesized in aqueous solutions (C' dots) by using an oscillating flow cell to overcome beam induced particle degradation. Form factor analysis and fitting was used to determine the size and size dispersity of the internal silica core containing covalently encapsulated fluorophores. The structure of the organic poly(ethylene glycol) (PEG) shell was modelled as a monodisperse corona containing concentrated and semi-dilute regimes of decaying density and as a simple polydisperse shell to determine the bounds of dispersity in the overall hybrid particle. C' dots containing single growth step silica cores have dispersities of 0.19-0.21; growth of additional silica shells onto the core produces a thin, dense silica layer, and increases the dispersity to 0.22-0.23. Comparison to FCS and DLS measures of size shows good agreement with SAXS measured and modelled sizes and size dispersities. Finally, comparison of a set of same sized and purified particles demonstrates that SAXS is sensitive to the skewness of the gel permeation chromatography elugrams of the original as-made materials. These and other insights provided by quantitative SAXS assessments may become useful for generation of robust nanoparticle design criteria necessary for their successful and safe use, for example in nanomedicine and oncology applications.
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Affiliation(s)
- Katherine P. Barteau
- Department of Materials Science & Engineering, Cornell High Energy Synchrotron Source, Cornell University, Ithaca, NY 14853, United States
| | - Kai Ma
- Department of Materials Science & Engineering, Cornell High Energy Synchrotron Source, Cornell University, Ithaca, NY 14853, United States
| | - Ferdinand F.E. Kohle
- Department of Chemistry and Chemical Biology, Cornell High Energy Synchrotron Source, Cornell University, Ithaca, NY 14853, United States
| | - Thomas C. Gardinier
- Department of Materials Science & Engineering, Cornell High Energy Synchrotron Source, Cornell University, Ithaca, NY 14853, United States
| | - Peter A. Beaucage
- Department of Materials Science & Engineering, Cornell High Energy Synchrotron Source, Cornell University, Ithaca, NY 14853, United States
| | | | - Ulrich Wiesner
- Department of Materials Science & Engineering, Cornell High Energy Synchrotron Source, Cornell University, Ithaca, NY 14853, United States
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28
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Ye D, Le TP, Kuei B, Zhu C, Zwart PH, Wang C, Gomez ED, Gomez EW. Resonant Soft X-Ray Scattering Provides Protein Structure with Chemical Specificity. Structure 2018; 26:1513-1521.e3. [PMID: 30220541 PMCID: PMC8224816 DOI: 10.1016/j.str.2018.07.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 05/26/2018] [Accepted: 07/26/2018] [Indexed: 01/08/2023]
Abstract
We introduce resonant soft X-ray scattering (RSoXS) as an approach to study the structure of proteins and other biological molecules in solution. Scattering contrast calculations suggest that RSoXS has comparable or even higher sensitivity than hard X-ray scattering because of contrast generated at the absorption edges of constituent elements, such as carbon and oxygen. Here, we demonstrate that working near the carbon edge reveals the envelope function of bovine serum albumin, using scattering volumes of 10-5 μL that are multiple orders of magnitude lower than traditional scattering experiments. Furthermore, tuning the X-ray energy within the carbon absorption edge provides different signatures of the size and shape of the protein by revealing the density of different types of bonding motifs within the protein. The combination of chemical specificity, smaller sample size, and enhanced X-ray contrast will propel RSoXS as a complementary tool to existing techniques for the study of biomolecular structure.
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Affiliation(s)
- Dan Ye
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Thinh P Le
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Brooke Kuei
- Department of Materials Science and Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Chenhui Zhu
- Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Peter H Zwart
- Berkeley Center for Structural Biology, Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA; The Center for Advanced Mathematics for Energy Research Applications, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Cheng Wang
- Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
| | - Enrique D Gomez
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA; Department of Materials Science and Engineering, The Pennsylvania State University, University Park, PA 16802, USA; Materials Research Institute, The Pennsylvania State University, University Park, PA 16802, USA.
| | - Esther W Gomez
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA; Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA.
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29
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Lehmkühler F, Valerio J, Sheyfer D, Roseker W, Schroer MA, Fischer B, Tono K, Yabashi M, Ishikawa T, Grübel G. Dynamics of soft nanoparticle suspensions at hard X-ray FEL sources below the radiation-damage threshold. IUCRJ 2018; 5:801-807. [PMID: 30443363 PMCID: PMC6211528 DOI: 10.1107/s2052252518013696] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 09/26/2018] [Indexed: 05/20/2023]
Abstract
The application of X-ray photon correlation spectroscopy (XPCS) at free-electron laser (FEL) facilities enables, for the first time, the study of dynamics on a (sub-)nanometre scale in an unreached time range between femtoseconds and seconds. For soft-matter materials, radiation damage is a major limitation when going beyond single-shot applications. Here, an XPCS study is presented at a hard X-ray FEL on radiation-sensitive polymeric poly(N-isopropylacrylamide) (PNIPAM) nanoparticles. The dynamics of aqueous suspensions of densely packed silica-PNIPAM core-shell particles and a PNIPAM nanogel below the radiation-damage threshold are determined. The XPCS data indicate non-diffusive behaviour, suggesting ballistic and stress-dominated heterogeneous particle motions. These results demonstrate the feasibility of XPCS experiments on radiation-sensitive soft-matter materials at FEL sources and pave the way for future applications at MHz repetition rates as well as ultrafast modes using split-pulse devices.
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Affiliation(s)
- Felix Lehmkühler
- Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Joana Valerio
- Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Dina Sheyfer
- Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Wojciech Roseker
- Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Martin A. Schroer
- Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Birgit Fischer
- Institute of Physical Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Makina Yabashi
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Tetsuya Ishikawa
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Gerhard Grübel
- Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
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30
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Dyett B, Zychowski L, Bao L, Meikle TG, Peng S, Yu H, Li M, Strachan J, Kirby N, Logan A, Conn CE, Zhang X. Crystallization of Femtoliter Surface Droplet Arrays Revealed by Synchrotron Small-Angle X-ray Scattering. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:9470-9476. [PMID: 30021434 DOI: 10.1021/acs.langmuir.8b01252] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The crystallization of oil droplets is critical in the processing and storage of lipid-based food and pharmaceutical products. Arrays of femtoliter droplets on a surface offer a unique opportunity to study surfactant-free colloidlike systems. In this work, the crystal growth process in these confined droplets was followed by cooling a model lipid (trimyristin) from a liquid state utilizing synchrotron small-angle X-ray scattering (SAXS). The measurements by SAXS demonstrated a reduced crystallization rate and a greater degree of supercooling required to trigger lipid crystallization in droplets compared to those of bulk lipids. These results suggest that surface droplets crystallize in a stochastic manner. Interestingly, the crystallization rate is slower for larger femtoliter droplets, which may be explained by the onset of crystallization from the three-phase contact line. The larger surface nanodroplets exhibit a smaller ratio of droplet volume to the length of three-phase contact line and hence a slower crystallization rate.
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Affiliation(s)
| | - Lisa Zychowski
- CSIRO Agriculture and Food , Werribee , Victoria 3030 , Australia
| | | | | | | | | | | | | | - Nigel Kirby
- Australian Synchrotron , 800 Blackburn Road , Clayton , Victoria 3169 , Australia
| | - Amy Logan
- CSIRO Agriculture and Food , Werribee , Victoria 3030 , Australia
| | | | - Xuehua Zhang
- Department of Chemical and Materials Engineering , University of Alberta , Edmonton , T6G1H9 Alberta , Canada
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31
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Wang C, Lin Y, Bougie D, Gillilan RE. Predicting data quality in biological X-ray solution scattering. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:727-738. [PMID: 30082508 DOI: 10.1107/s2059798318005004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 03/27/2018] [Indexed: 11/10/2022]
Abstract
Biological small-angle X-ray solution scattering (BioSAXS) is now widely used to gain information on biomolecules in the solution state. Often, however, it is not obvious in advance whether a particular sample will scatter strongly enough to give useful data to draw conclusions under practically achievable solution conditions. Conformational changes that appear to be large may not always produce scattering curves that are distinguishable from each other at realistic concentrations and exposure times. Emerging technologies such as time-resolved SAXS (TR-SAXS) pose additional challenges owing to small beams and short sample path lengths. Beamline optics vary in brilliance and degree of background scatter, and major upgrades and improvements to sources promise to expand the reach of these methods. Computations are developed to estimate BioSAXS sample intensity at a more detailed level than previous approaches, taking into account flux, energy, sample thickness, window material, instrumental background, detector efficiency, solution conditions and other parameters. The results are validated with calibrated experiments using standard proteins on four different beamlines with various fluxes, energies and configurations. The ability of BioSAXS to statistically distinguish a variety of conformational movements under continuous-flow time-resolved conditions is then computed on a set of matched structure pairs drawn from the Database of Macromolecular Motions (http://molmovdb.org). The feasibility of experiments is ranked according to sample consumption, a quantity that varies by over two orders of magnitude for the set of structures. In addition to photon flux, the calculations suggest that window scattering and choice of wavelength are also important factors given the short sample path lengths common in such setups.
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Affiliation(s)
- Chenzheng Wang
- DellEMC Shanghai COE, Shanghai 200433, People's Republic of China
| | - Yuexia Lin
- Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Devin Bougie
- CLASSE (Cornell Laboratory for Accelerator-based ScienceS and Education), Cornell University, Ithaca, NY 14853, USA
| | - Richard E Gillilan
- MacCHESS (Macromolecular Diffraction Facility at CHESS), Cornell University, Ithaca, NY 14853, USA
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32
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Schroer MA, Blanchet CE, Gruzinov AY, Gräwert MA, Brennich ME, Hajizadeh NR, Jeffries CM, Svergun DI. Smaller capillaries improve the small-angle X-ray scattering signal and sample consumption for biomacromolecular solutions. JOURNAL OF SYNCHROTRON RADIATION 2018; 25:1113-1122. [PMID: 29979172 PMCID: PMC6038601 DOI: 10.1107/s1600577518007907] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 05/28/2018] [Indexed: 05/20/2023]
Abstract
Radiation damage by intense X-ray beams at modern synchrotron facilities is one of the major complications for biological small-angle X-ray scattering (SAXS) investigations of macromolecules in solution. To limit the damage, samples are typically measured under a laminar flow through a cell (typically a capillary) such that fresh solution is continuously exposed to the beam during measurement. The diameter of the capillary that optimizes the scattering-to-absorption ratio at a given X-ray wavelength can be calculated a priori based on fundamental physical properties. However, these well established scattering and absorption principles do not take into account the radiation susceptibility of the sample or the often very limited amounts of precious biological material available for an experiment. Here it is shown that, for biological solution SAXS, capillaries with smaller diameters than those calculated from simple scattering/absorption criteria allow for a better utilization of the available volumes of radiation-sensitive samples. This is demonstrated by comparing two capillary diameters di (di = 1.7 mm, close to optimal for 10 keV; and di = 0.9 mm, which is nominally sub-optimal) applied to study different protein solutions at various flow rates. The use of the smaller capillaries ultimately allows one to collect higher-quality SAXS data from the limited amounts of purified biological macromolecules.
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Affiliation(s)
- Martin A. Schroer
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Clement E. Blanchet
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Andrey Yu. Gruzinov
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Melissa A. Gräwert
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Martha E. Brennich
- European Molecular Biology Laboratory (EMBL), Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Nelly R. Hajizadeh
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Cy M. Jeffries
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
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33
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Recent developments in small-angle X-ray scattering and hybrid method approaches for biomacromolecular solutions. Emerg Top Life Sci 2018; 2:69-79. [PMID: 33525782 DOI: 10.1042/etls20170138] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 02/01/2018] [Accepted: 02/05/2018] [Indexed: 01/05/2023]
Abstract
Small-angle X-ray scattering (SAXS) has become a streamline method to characterize biological macromolecules, from small peptides to supramolecular complexes, in near-native solutions. Modern SAXS requires limited amounts of purified material, without the need for labelling, crystallization, or freezing. Dedicated beamlines at modern synchrotron sources yield high-quality data within or below several milliseconds of exposure time and are highly automated, allowing for rapid structural screening under different solutions and ambient conditions but also for time-resolved studies of biological processes. The advanced data analysis methods allow one to meaningfully interpret the scattering data from monodisperse systems, from transient complexes as well as flexible and heterogeneous systems in terms of structural models. Especially powerful are hybrid approaches utilizing SAXS with high-resolution structural techniques, but also with biochemical, biophysical, and computational methods. Here, we review the recent developments in the experimental SAXS practice and in analysis methods with a specific focus on the joint use of SAXS with complementary methods.
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34
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Sedlak SM, Bruetzel LK, Lipfert J. Quantitative evaluation of statistical errors in small-angle X-ray scattering measurements. J Appl Crystallogr 2017; 50:621-630. [PMID: 28381982 PMCID: PMC5377352 DOI: 10.1107/s1600576717003077] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 02/23/2017] [Indexed: 12/12/2022] Open
Abstract
A model is presented for the errors in small-angle X-ray scattering profiles that takes into account the physics of the measurement process. The model agrees quantitatively with the variations observed in experimental measurements and provides a straightforward prescription to add realistic errors to simulated scattering profiles. A new model is proposed for the measurement errors incurred in typical small-angle X-ray scattering (SAXS) experiments, which takes into account the setup geometry and physics of the measurement process. The model accurately captures the experimentally determined errors from a large range of synchrotron and in-house anode-based measurements. Its most general formulation gives for the variance of the buffer-subtracted SAXS intensity σ2(q) = [I(q) + const.]/(kq), where I(q) is the scattering intensity as a function of the momentum transfer q; k and const. are fitting parameters that are characteristic of the experimental setup. The model gives a concrete procedure for calculating realistic measurement errors for simulated SAXS profiles. In addition, the results provide guidelines for optimizing SAXS measurements, which are in line with established procedures for SAXS experiments, and enable a quantitative evaluation of measurement errors.
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Affiliation(s)
- Steffen M Sedlak
- Department of Physics, Nanosystems Initiative Munich, and Center for NanoScience, LMU Munich , Amalienstrasse 54, Munich, 80799, Germany
| | - Linda K Bruetzel
- Department of Physics, Nanosystems Initiative Munich, and Center for NanoScience, LMU Munich , Amalienstrasse 54, Munich, 80799, Germany
| | - Jan Lipfert
- Department of Physics, Nanosystems Initiative Munich, and Center for NanoScience, LMU Munich , Amalienstrasse 54, Munich, 80799, Germany
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35
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Brooks-Bartlett JC, Batters RA, Bury CS, Lowe ED, Ginn HM, Round A, Garman EF. Development of tools to automate quantitative analysis of radiation damage in SAXS experiments. JOURNAL OF SYNCHROTRON RADIATION 2017; 24:63-72. [PMID: 28009547 PMCID: PMC5182020 DOI: 10.1107/s1600577516015083] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 09/23/2016] [Indexed: 05/09/2023]
Abstract
Biological small-angle X-ray scattering (SAXS) is an increasingly popular technique used to obtain nanoscale structural information on macromolecules in solution. However, radiation damage to the samples limits the amount of useful data that can be collected from a single sample. In contrast to the extensive analytical resources available for macromolecular crystallography (MX), there are relatively few tools to quantitate radiation damage for SAXS, some of which require a significant level of manual characterization, with the potential of leading to conflicting results from different studies. Here, computational tools have been developed to automate and standardize radiation damage analysis for SAXS data. RADDOSE-3D, a dose calculation software utility originally written for MX experiments, has been extended to account for the cylindrical geometry of the capillary tube, the liquid composition of the sample and the attenuation of the beam by the capillary material to allow doses to be calculated for many SAXS experiments. Furthermore, a library has been written to visualize and explore the pairwise similarity of frames. The calculated dose for the frame at which three subsequent frames are determined to be dissimilar is defined as the radiation damage onset threshold (RDOT). Analysis of RDOTs has been used to compare the efficacy of radioprotectant compounds to extend the useful lifetime of SAXS samples. Comparison of the RDOTs shows that, for radioprotectant compounds at 5 and 10 mM concentration, glycerol is the most effective compound. However, at 1 and 2 mM concentrations, dithiothreitol (DTT) appears to be most effective. Our newly developed visualization library contains methods that highlight the unusual radiation damage results given by SAXS data collected using higher concentrations of DTT: these observations should pave the way to the development of more sophisticated frame merging strategies.
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Affiliation(s)
| | | | - Charles S. Bury
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Edward D. Lowe
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Helen Mary Ginn
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Adam Round
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, CS 90181, 38042 Grenoble, France
- SPB/SFX European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Faculty of Natural Sciences, Keele University, Staffordshire ST5 5BG, UK
| | - Elspeth F. Garman
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
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36
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Pérez J, Vachette P. A Successful Combination: Coupling SE-HPLC with SAXS. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1009:183-199. [PMID: 29218560 DOI: 10.1007/978-981-10-6038-0_11] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A monodispersed and ideal solution is a central (unique?) requirement of SAXS to allow one to extract structural information from the recorded pattern. On-line Size Exclusion Chromatography (SEC) marked a major breakthrough, separating particles present in solution according to their size. Identical frames under an elution peak can be averaged and further processed free from contamination. However, this is not always straightforward, separation is often incomplete and software have been developed to deconvolve the contributions from the different species (molecules or oligomeric forms) within the sample. In this chapter, we present the general workflow of a SEC-SAXS experiment. We present recent instrumental and data analysis improvements that have improved the quality of recorded data, extended its potential and turn it into a mainstream approach. We describe into some details two specific applications of SEC-SAXS that provide more than just separating associated forms from the particle of interest.
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Affiliation(s)
- Javier Pérez
- Synchrotron Soleil, L'Orme des Merisiers, Saint-Aubin BP48, 91192, Gif-sur-Yvette Cedex, France.
| | - Patrice Vachette
- Institut de Biologie Intégrative de la Cellule, UMR 9198, Université Paris-Sud, 91405, Orsay Cedex, France
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37
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Kirby N, Cowieson N, Hawley AM, Mudie ST, McGillivray DJ, Kusel M, Samardzic-Boban V, Ryan TM. Improved radiation dose efficiency in solution SAXS using a sheath flow sample environment. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2016; 72:1254-1266. [PMID: 27917826 PMCID: PMC5137223 DOI: 10.1107/s2059798316017174] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 10/25/2016] [Indexed: 12/24/2022]
Abstract
Coflow is a new method for delivering radiation-sensitive biological and other solution-based samples to high-brightness X-ray beamlines that exploits laminar flow to ameliorate radiation-damage limitations and provides a host of practical improvements associated with these types of experiments. Radiation damage is a major limitation to synchrotron small-angle X-ray scattering analysis of biomacromolecules. Flowing the sample during exposure helps to reduce the problem, but its effectiveness in the laminar-flow regime is limited by slow flow velocity at the walls of sample cells. To overcome this limitation, the coflow method was developed, where the sample flows through the centre of its cell surrounded by a flow of matched buffer. The method permits an order-of-magnitude increase of X-ray incident flux before sample damage, improves measurement statistics and maintains low sample concentration limits. The method also efficiently handles sample volumes of a few microlitres, can increase sample throughput, is intrinsically resistant to capillary fouling by sample and is suited to static samples and size-exclusion chromatography applications. The method unlocks further potential of third-generation synchrotron beamlines to facilitate new and challenging applications in solution scattering.
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Affiliation(s)
- Nigel Kirby
- SAXS/WAXS, Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Nathan Cowieson
- B21 SAXS, Diamond Light Source Ltd, Hartwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Adrian M Hawley
- SAXS/WAXS, Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Stephen T Mudie
- SAXS/WAXS, Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Duncan J McGillivray
- School of Chemical Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Michael Kusel
- Kusel Design, 6 Hambleton Street, Albert Park, Victoria 3206, Australia
| | - Vesna Samardzic-Boban
- SAXS/WAXS, Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Timothy M Ryan
- SAXS/WAXS, Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia
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