51
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Lawrence JM, Orlans J, Evans G, Orville AM, Foadi J, Aller P. High-throughput in situ experimental phasing. Acta Crystallogr D Struct Biol 2020; 76:790-801. [PMID: 32744261 PMCID: PMC7397491 DOI: 10.1107/s2059798320009109] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 07/03/2020] [Indexed: 11/10/2022] Open
Abstract
In this article, a new approach to experimental phasing for macromolecular crystallography (MX) at synchrotrons is introduced and described for the first time. It makes use of automated robotics applied to a multi-crystal framework in which human intervention is reduced to a minimum. Hundreds of samples are automatically soaked in heavy-atom solutions, using a Labcyte Inc. Echo 550 Liquid Handler, in a highly controlled and optimized fashion in order to generate derivatized and isomorphous crystals. Partial data sets obtained on MX beamlines using an in situ setup for data collection are processed with the aim of producing good-quality anomalous signal leading to successful experimental phasing.
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Affiliation(s)
- Joshua M. Lawrence
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Julien Orlans
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- UMR0203, Biologie Fonctionnelle, Insectes et Interactions (BF2i); Institut National des Sciences Appliquées de Lyon (INSA Lyon); Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Lyon (Univ Lyon), F-69621 Villeurbanne, France
| | - Gwyndaf Evans
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Allen M. Orville
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
| | - James Foadi
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Pierre Aller
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
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52
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Pfanzagl V, Beale JH, Michlits H, Schmidt D, Gabler T, Obinger C, Djinović-Carugo K, Hofbauer S. X-ray-induced photoreduction of heme metal centers rapidly induces active-site perturbations in a protein-independent manner. J Biol Chem 2020; 295:13488-13501. [PMID: 32723869 DOI: 10.1074/jbc.ra120.014087] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/24/2020] [Indexed: 12/31/2022] Open
Abstract
Since the advent of protein crystallography, atomic-level macromolecular structures have provided a basis to understand biological function. Enzymologists use detailed structural insights on ligand coordination, interatomic distances, and positioning of catalytic amino acids to rationalize the underlying electronic reaction mechanisms. Often the proteins in question catalyze redox reactions using metal cofactors that are explicitly intertwined with their function. In these cases, the exact nature of the coordination sphere and the oxidation state of the metal is of utmost importance. Unfortunately, the redox-active nature of metal cofactors makes them especially susceptible to photoreduction, meaning that information obtained by photoreducing X-ray sources about the environment of the cofactor is the least trustworthy part of the structure. In this work we directly compare the kinetics of photoreduction of six different heme protein crystal species by X-ray radiation. We show that a dose of ∼40 kilograys already yields 50% ferrous iron in a heme protein crystal. We also demonstrate that the kinetics of photoreduction are completely independent from variables unique to the different samples tested. The photoreduction-induced structural rearrangements around the metal cofactors have to be considered when biochemical data of ferric proteins are rationalized by constraints derived from crystal structures of reduced enzymes.
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Affiliation(s)
- Vera Pfanzagl
- Department of Chemistry, Institute of Biochemistry, BOKU-University of Natural Resources and Life Sciences, Vienna, Austria.
| | | | - Hanna Michlits
- Department of Chemistry, Institute of Biochemistry, BOKU-University of Natural Resources and Life Sciences, Vienna, Austria
| | - Daniel Schmidt
- Department of Chemistry, Institute of Biochemistry, BOKU-University of Natural Resources and Life Sciences, Vienna, Austria
| | - Thomas Gabler
- Department of Chemistry, Institute of Biochemistry, BOKU-University of Natural Resources and Life Sciences, Vienna, Austria
| | - Christian Obinger
- Department of Chemistry, Institute of Biochemistry, BOKU-University of Natural Resources and Life Sciences, Vienna, Austria
| | - Kristina Djinović-Carugo
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna, Austria; Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Stefan Hofbauer
- Department of Chemistry, Institute of Biochemistry, BOKU-University of Natural Resources and Life Sciences, Vienna, Austria.
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53
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Thompson MC, Yeates TO, Rodriguez JA. Advances in methods for atomic resolution macromolecular structure determination. F1000Res 2020; 9:F1000 Faculty Rev-667. [PMID: 32676184 PMCID: PMC7333361 DOI: 10.12688/f1000research.25097.1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/25/2020] [Indexed: 12/13/2022] Open
Abstract
Recent technical advances have dramatically increased the power and scope of structural biology. New developments in high-resolution cryo-electron microscopy, serial X-ray crystallography, and electron diffraction have been especially transformative. Here we highlight some of the latest advances and current challenges at the frontiers of atomic resolution methods for elucidating the structures and dynamical properties of macromolecules and their complexes.
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Affiliation(s)
- Michael C. Thompson
- Department of Chemistry and Chemical Biology, University of California, Merced, CA, USA
| | - Todd O. Yeates
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA, USA
| | - Jose A. Rodriguez
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA, USA
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54
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Polysaccharide-Based Injection Matrix for Serial Crystallography. Int J Mol Sci 2020; 21:ijms21093332. [PMID: 32397185 PMCID: PMC7247560 DOI: 10.3390/ijms21093332] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 05/02/2020] [Accepted: 05/05/2020] [Indexed: 12/21/2022] Open
Abstract
Serial crystallography (SX) provides an opportunity to observe the molecular dynamics of macromolecular structures at room temperature via pump-probe studies. The delivery of crystals embedded in a viscous medium via an injector or syringe is widely performed in synchrotrons or X-ray free-electron laser facilities with low repetition rates. Various viscous media have been developed; however, there are cases in which the delivery material undesirably interacts chemically or biologically with specific protein samples, or changes the stability of the injection stream, depending on the crystallization solution. Therefore, continued discovery and characterization of new delivery media is necessary for expanding future SX applications. Here, the preparation and characterization of new polysaccharide (wheat starch (WS) and alginate)-based sample delivery media are introduced for SX. Crystals embedded in a WS or alginate injection medium showed a stable injection stream at a flow rate of < 200 nL/min and low-level X-ray background scattering similar to other hydrogels. Using these media, serial millisecond crystallography (SMX) was performed, and the room temperature crystal structures of glucose isomerase and lysozyme were determined at 1.9–2.0 Å resolutions. WS and alginate will allow an expanded application of sample delivery media in SX experiments.
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55
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Mehrabi P, Müller-Werkmeister HM, Leimkohl JP, Schikora H, Ninkovic J, Krivokuca S, Andriček L, Epp SW, Sherrell D, Owen RL, Pearson AR, Tellkamp F, Schulz EC, Miller RJD. The HARE chip for efficient time-resolved serial synchrotron crystallography. JOURNAL OF SYNCHROTRON RADIATION 2020; 27:360-370. [PMID: 32153274 PMCID: PMC7064102 DOI: 10.1107/s1600577520000685] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 01/20/2020] [Indexed: 05/02/2023]
Abstract
Serial synchrotron crystallography (SSX) is an emerging technique for static and time-resolved protein structure determination. Using specifically patterned silicon chips for sample delivery, the `hit-and-return' (HARE) protocol allows for efficient time-resolved data collection. The specific pattern of the crystal wells in the HARE chip provides direct access to many discrete time points. HARE chips allow for optical excitation as well as on-chip mixing for reaction initiation, making a large number of protein systems amenable to time-resolved studies. Loading of protein microcrystals onto the HARE chip is streamlined by a novel vacuum loading platform that allows fine-tuning of suction strength while maintaining a humid environment to prevent crystal dehydration. To enable the widespread use of time-resolved serial synchrotron crystallography (TR-SSX), detailed technical descriptions of a set of accessories that facilitate TR-SSX workflows are provided.
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Affiliation(s)
- Pedram Mehrabi
- Department for Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Henrike M. Müller-Werkmeister
- Department for Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
- Institute of Chemistry – Physical Chemistry, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam-Golm, Germany
| | - Jan-Philipp Leimkohl
- Scientific Support Unit Machine Physics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Hendrik Schikora
- Scientific Support Unit Machine Physics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Jelena Ninkovic
- Halbleiterlabor der Max-Planck-Gesellschaft, Otto-Hahn-Ring 6, D-81739 Munich, Germany
| | - Silvia Krivokuca
- Halbleiterlabor der Max-Planck-Gesellschaft, Otto-Hahn-Ring 6, D-81739 Munich, Germany
| | - Ladislav Andriček
- Halbleiterlabor der Max-Planck-Gesellschaft, Otto-Hahn-Ring 6, D-81739 Munich, Germany
| | - Sascha W. Epp
- Department for Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Darren Sherrell
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Robin L. Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Arwen R. Pearson
- Department of Physics, Universität Hamburg, Jungiusstrasse 9, 20355 Hamburg, Germany
| | - Friedjof Tellkamp
- Scientific Support Unit Machine Physics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Eike C. Schulz
- Department for Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - R. J. Dwayne Miller
- Department for Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Physics, Universität Hamburg, Jungiusstrasse 9, 20355 Hamburg, Germany
- Departments of Chemistry and Physics, University of Toronto, 80 St George Street, Toronto, Ontario M5S 3H6, Canada
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56
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Monteiro DCF, von Stetten D, Stohrer C, Sans M, Pearson AR, Santoni G, van der Linden P, Trebbin M. 3D-MiXD: 3D-printed X-ray-compatible microfluidic devices for rapid, low-consumption serial synchrotron crystallography data collection in flow. IUCRJ 2020; 7:207-219. [PMID: 32148849 PMCID: PMC7055382 DOI: 10.1107/s2052252519016865] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 12/17/2019] [Indexed: 05/24/2023]
Abstract
Serial crystallography has enabled the study of complex biological questions through the determination of biomolecular structures at room temperature using low X-ray doses. Furthermore, it has enabled the study of protein dynamics by the capture of atomically resolved and time-resolved molecular movies. However, the study of many biologically relevant targets is still severely hindered by high sample consumption and lengthy data-collection times. By combining serial synchrotron crystallography (SSX) with 3D printing, a new experimental platform has been created that tackles these challenges. An affordable 3D-printed, X-ray-compatible microfluidic device (3D-MiXD) is reported that allows data to be collected from protein microcrystals in a 3D flow with very high hit and indexing rates, while keeping the sample consumption low. The miniaturized 3D-MiXD can be rapidly installed into virtually any synchrotron beamline with only minimal adjustments. This efficient collection scheme in combination with its mixing geometry paves the way for recording molecular movies at synchrotrons by mixing-triggered millisecond time-resolved SSX.
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Affiliation(s)
- Diana C. F. Monteiro
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Hauptman–Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
| | - David von Stetten
- European Molecular Biology Laboratory, Notkestrasse 85, 22607 Hamburg, Germany
| | - Claudia Stohrer
- The Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, England
| | - Marta Sans
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Physics, Universität Hamburg, Jungiusstrasse 9, 20355 Hamburg, Germany
| | - Arwen R. Pearson
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Physics, Universität Hamburg, Jungiusstrasse 9, 20355 Hamburg, Germany
| | - Gianluca Santoni
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38043 Grenoble, France
| | - Peter van der Linden
- Partnership for Soft Condensed Matter, European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38043 Grenoble, France
| | - Martin Trebbin
- Hauptman–Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
- Department of Chemistry, The State University of New York at Buffalo, Natural Sciences Complex 760, Buffalo, NY 14260-3000, USA
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57
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Bücker R, Hogan-Lamarre P, Mehrabi P, Schulz EC, Bultema LA, Gevorkov Y, Brehm W, Yefanov O, Oberthür D, Kassier GH, Dwayne Miller RJ. Serial protein crystallography in an electron microscope. Nat Commun 2020; 11:996. [PMID: 32081905 PMCID: PMC7035385 DOI: 10.1038/s41467-020-14793-0] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 01/27/2020] [Indexed: 12/16/2022] Open
Abstract
Serial X-ray crystallography at free-electron lasers allows to solve biomolecular structures from sub-micron-sized crystals. However, beam time at these facilities is scarce, and involved sample delivery techniques are required. On the other hand, rotation electron diffraction (MicroED) has shown great potential as an alternative means for protein nano-crystallography. Here, we present a method for serial electron diffraction of protein nanocrystals combining the benefits of both approaches. In a scanning transmission electron microscope, crystals randomly dispersed on a sample grid are automatically mapped, and a diffraction pattern at fixed orientation is recorded from each at a high acquisition rate. Dose fractionation ensures minimal radiation damage effects. We demonstrate the method by solving the structure of granulovirus occlusion bodies and lysozyme to resolutions of 1.55 Å and 1.80 Å, respectively. Our method promises to provide rapid structure determination for many classes of materials with minimal sample consumption, using readily available instrumentation.
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Affiliation(s)
- Robert Bücker
- Max Planck Institute for the Structure and Dynamics of Matter, CFEL, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Pascal Hogan-Lamarre
- Max Planck Institute for the Structure and Dynamics of Matter, CFEL, Luruper Chaussee 149, 22761, Hamburg, Germany
- Departments of Chemistry and Physics, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada
| | - Pedram Mehrabi
- Max Planck Institute for the Structure and Dynamics of Matter, CFEL, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Eike C Schulz
- Max Planck Institute for the Structure and Dynamics of Matter, CFEL, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Lindsey A Bultema
- Max Planck Institute for the Structure and Dynamics of Matter, CFEL, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Yaroslav Gevorkov
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
- Institute of Vision Systems, Hamburg University of Technology, Harburger Schlossstrasse 20, 21079, Hamburg, Germany
| | - Wolfgang Brehm
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Dominik Oberthür
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Günther H Kassier
- Max Planck Institute for the Structure and Dynamics of Matter, CFEL, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - R J Dwayne Miller
- Max Planck Institute for the Structure and Dynamics of Matter, CFEL, Luruper Chaussee 149, 22761, Hamburg, Germany.
- Departments of Chemistry and Physics, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada.
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58
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Radiation damage and dose limits in serial synchrotron crystallography at cryo- and room temperatures. Proc Natl Acad Sci U S A 2020; 117:4142-4151. [PMID: 32047034 PMCID: PMC7049125 DOI: 10.1073/pnas.1821522117] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Macromolecular X-ray crystallography (MX) is the most prolific structure determination method in structural biology but is limited by radiation damage. To reduce damage progression, MX is usually carried out at cryogenic temperatures, sometimes blocking functionally important conformational heterogeneity. Lacking this shortcoming, room temperature MX has gained momentum with the recent advent of serial crystallography, whereby distribution of the X-ray dose over thousands of crystals mitigates damage. Here, an approach to serial crystallography is presented allowing visualization of specific damage to amino acids at room temperature and determination of a dose limit above which structural information from electron density maps decreases due to radiation damage. This limit provides important guidance for the growing number of synchrotron room temperature MX experiments. Radiation damage limits the accuracy of macromolecular structures in X-ray crystallography. Cryogenic (cryo-) cooling reduces the global radiation damage rate and, therefore, became the method of choice over the past decades. The recent advent of serial crystallography, which spreads the absorbed energy over many crystals, thereby reducing damage, has rendered room temperature (RT) data collection more practical and also extendable to microcrystals, both enabling and requiring the study of specific and global radiation damage at RT. Here, we performed sequential serial raster-scanning crystallography using a microfocused synchrotron beam that allowed for the collection of two series of 40 and 90 full datasets at 2- and 1.9-Å resolution at a dose rate of 40.3 MGy/s on hen egg white lysozyme (HEWL) crystals at RT and cryotemperature, respectively. The diffraction intensity halved its initial value at average doses (D1/2) of 0.57 and 15.3 MGy at RT and 100 K, respectively. Specific radiation damage at RT was observed at disulfide bonds but not at acidic residues, increasing and then apparently reversing, a peculiar behavior that can be modeled by accounting for differential diffraction intensity decay due to the nonuniform illumination by the X-ray beam. Specific damage to disulfide bonds is evident early on at RT and proceeds at a fivefold higher rate than global damage. The decay modeling suggests it is advisable not to exceed a dose of 0.38 MGy per dataset in static and time-resolved synchrotron crystallography experiments at RT. This rough yardstick might change for proteins other than HEWL and at resolutions other than 2 Å.
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59
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Lučić M, Chaplin AK, Moreno-Chicano T, Dworkowski FSN, Wilson MT, Svistunenko DA, Hough MA, Worrall JAR. A subtle structural change in the distal haem pocket has a remarkable effect on tuning hydrogen peroxide reactivity in dye decolourising peroxidases fromStreptomyces lividans. Dalton Trans 2020; 49:1620-1636. [DOI: 10.1039/c9dt04583j] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A subtle positional shift of the distal haem pocket aspartate in two dye decolourising peroxidase homologs has a remarkable effect on their reactivity with H2O2.
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Affiliation(s)
- Marina Lučić
- School of Life Sciences
- University of Essex
- Colchester
- UK
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60
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Shelby ML, Gilbile D, Grant TD, Seuring C, Segelke BW, He W, Evans AC, Pakendorf T, Fischer P, Hunter MS, Batyuk A, Barthelmess M, Meents A, Coleman MA, Kuhl TL, Frank M. A fixed-target platform for serial femtosecond crystallography in a hydrated environment. IUCRJ 2020; 7:30-41. [PMID: 31949902 PMCID: PMC6949605 DOI: 10.1107/s2052252519014003] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 10/15/2019] [Indexed: 05/19/2023]
Abstract
For serial femtosecond crystallography at X-ray free-electron lasers, which entails collection of single-pulse diffraction patterns from a constantly refreshed supply of microcrystalline sample, delivery of the sample into the X-ray beam path while maintaining low background remains a technical challenge for some experiments, especially where this methodology is applied to relatively low-ordered samples or those difficult to purify and crystallize in large quantities. This work demonstrates a scheme to encapsulate biological samples using polymer thin films and graphene to maintain sample hydration in vacuum conditions. The encapsulated sample is delivered into the X-ray beam on fixed targets for rapid scanning using the Roadrunner fixed-target system towards a long-term goal of low-background measurements on weakly diffracting samples. As a proof of principle, we used microcrystals of the 24 kDa rapid encystment protein (REP24) to provide a benchmark for polymer/graphene sandwich performance. The REP24 microcrystal unit cell obtained from our sandwiched in-vacuum sample was consistent with previously established unit-cell parameters and with those measured by us without encapsulation in humidified helium, indicating that the platform is robust against evaporative losses. While significant scattering from water was observed because of the sample-deposition method, the polymer/graphene sandwich itself was shown to contribute minimally to background scattering.
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Affiliation(s)
- M. L. Shelby
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - D. Gilbile
- University of California at Davis, California, USA
| | - T. D. Grant
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, Hauptman-Woodward Institute, SUNY University at Buffalo, Buffalo, New York, USA
| | - C. Seuring
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Hamburg, Germany
| | - B. W. Segelke
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - W. He
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - A. C. Evans
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
- University of California at Davis, California, USA
| | - T. Pakendorf
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Hamburg, Germany
| | - P. Fischer
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Hamburg, Germany
| | - M. S. Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - A. Batyuk
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - M. Barthelmess
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Hamburg, Germany
| | - A. Meents
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Hamburg, Germany
| | - M. A. Coleman
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
- University of California at Davis, California, USA
| | - T. L. Kuhl
- University of California at Davis, California, USA
| | - M. Frank
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
- University of California at Davis, California, USA
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61
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Moreno-Chicano T, Ebrahim A, Axford D, Appleby MV, Beale JH, Chaplin AK, Duyvesteyn HME, Ghiladi RA, Owada S, Sherrell DA, Strange RW, Sugimoto H, Tono K, Worrall JAR, Owen RL, Hough MA. High-throughput structures of protein-ligand complexes at room temperature using serial femtosecond crystallography. IUCRJ 2019; 6:1074-1085. [PMID: 31709063 PMCID: PMC6830213 DOI: 10.1107/s2052252519011655] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 08/21/2019] [Indexed: 05/09/2023]
Abstract
High-throughput X-ray crystal structures of protein-ligand complexes are critical to pharmaceutical drug development. However, cryocooling of crystals and X-ray radiation damage may distort the observed ligand binding. Serial femtosecond crystallography (SFX) using X-ray free-electron lasers (XFELs) can produce radiation-damage-free room-temperature structures. Ligand-binding studies using SFX have received only modest attention, partly owing to limited beamtime availability and the large quantity of sample that is required per structure determination. Here, a high-throughput approach to determine room-temperature damage-free structures with excellent sample and time efficiency is demonstrated, allowing complexes to be characterized rapidly and without prohibitive sample requirements. This yields high-quality difference density maps allowing unambiguous ligand placement. Crucially, it is demonstrated that ligands similar in size or smaller than those used in fragment-based drug design may be clearly identified in data sets obtained from <1000 diffraction images. This efficiency in both sample and XFEL beamtime opens the door to true high-throughput screening of protein-ligand complexes using SFX.
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Affiliation(s)
- Tadeo Moreno-Chicano
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
| | - Ali Ebrahim
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Danny Axford
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Martin V. Appleby
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - John H. Beale
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Amanda K. Chaplin
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
| | - Helen M. E. Duyvesteyn
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
- Division of Structural Biology (STRUBI), University of Oxford, The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford OX3 7BN, England
| | - Reza A. Ghiladi
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, USA
| | - Shigeki Owada
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Darren A. Sherrell
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Richard W. Strange
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
| | | | - Kensuke Tono
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Jonathan A. R. Worrall
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
| | - Robin L. Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Michael A. Hough
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
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Garman EF, Weik M. X-ray radiation damage to biological samples: recent progress. JOURNAL OF SYNCHROTRON RADIATION 2019; 26:907-911. [PMID: 31274412 DOI: 10.1107/s1600577519009408] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 06/30/2019] [Indexed: 05/20/2023]
Abstract
With the continuing development of beamlines for macromolecular crystallography (MX) over the last few years providing ever higher X-ray flux densities, it has become even more important to be aware of the effects of radiation damage on the resulting structures. Nine papers in this issue cover a range of aspects related to the physics and chemistry of the manifestations of this damage, as observed in both MX and small-angle X-ray scattering (SAXS) on crystals, solutions and tissue samples. The reports include measurements of the heating caused by X-ray irradiation in ruby microcrystals, low-dose experiments examining damage rates as a function of incident X-ray energy up to 30 keV on a metallo-enzyme using a CdTe detector of high quantum efficiency as well as a theoretical analysis of the gains predicted in diffraction efficiency using these detectors, a SAXS examination of low-dose radiation exposure effects on the dissociation of a protein complex related to human health, theoretical calculations describing radiation chemistry pathways which aim to explain the specific structural damage widely observed in proteins, investigation of radiation-induced damage effects in a DNA crystal, a case study on a metallo-enzyme where structural movements thought to be mechanism related might actually be radiation-damage-induced changes, and finally a review describing what X-ray radiation-induced cysteine modifications can teach us about protein dynamics and catalysis. These papers, along with some other relevant literature published since the last Journal of Synchrotron Radiation Radiation Damage special issue in 2017, are briefly summarized below.
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Affiliation(s)
- Elspeth F Garman
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Martin Weik
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044 Grenoble, France
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