1
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Thorne RE. Determining biomolecular structures near room temperature using X-ray crystallography: concepts, methods and future optimization. Acta Crystallogr D Struct Biol 2023; 79:78-94. [PMID: 36601809 PMCID: PMC9815097 DOI: 10.1107/s2059798322011652] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 12/04/2022] [Indexed: 01/05/2023] Open
Abstract
For roughly two decades, cryocrystallography has been the overwhelmingly dominant method for determining high-resolution biomolecular structures. Competition from single-particle cryo-electron microscopy and micro-electron diffraction, increased interest in functionally relevant information that may be missing or corrupted in structures determined at cryogenic temperature, and interest in time-resolved studies of the biomolecular response to chemical and optical stimuli have driven renewed interest in data collection at room temperature and, more generally, at temperatures from the protein-solvent glass transition near 200 K to ∼350 K. Fischer has recently reviewed practical methods for room-temperature data collection and analysis [Fischer (2021), Q. Rev. Biophys. 54, e1]. Here, the key advantages and physical principles of, and methods for, crystallographic data collection at noncryogenic temperatures and some factors relevant to interpreting the resulting data are discussed. For room-temperature data collection to realize its potential within the structural biology toolkit, streamlined and standardized methods for delivering crystals prepared in the home laboratory to the synchrotron and for automated handling and data collection, similar to those for cryocrystallography, should be implemented.
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Affiliation(s)
- Robert E. Thorne
- Physics Department, Cornell University, Ithaca, NY 14853, USA
- MiTeGen LLC, PO Box 3867, Ithaca, NY 14850, USA
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2
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Bellini D. A drug-discovery-oriented non-invasive protocol for protein crystal cryoprotection by dehydration, with application for crystallization screening. J Appl Crystallogr 2022; 55:370-379. [PMID: 35497658 PMCID: PMC8985602 DOI: 10.1107/s1600576722002382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 03/01/2022] [Indexed: 11/10/2022] Open
Abstract
In X-ray macromolecular crystallography, cryoprotection of crystals mounted on harvesting loops is achieved when the water in the sample solvent transitions to vitreous ice before crystalline ice forms. This is achieved by rapid cooling in liquid nitro-gen or propane. Protocols for protein crystal cryoprotection are based on either increasing the environmental pressure or reducing the water fraction in the solvent. This study presents a new protocol for cryoprotecting crystals. It is based on vapour diffusion dehydration of the crystal drop to reduce the water fraction in the solvent by adding a highly concentrated salt solution, 13 M potassium formate (KF13), directly to the reservoir. Several salt solutions were screened to identify KF13 as optimal. Cryoprotection using the KF13 protocol is non-invasive to the crystal, high throughput and easy to implement, can benefit diffraction resolution and ligand binding, and is very useful in cases with high redundancy such as drug-discovery projects which use very large compound or fragment libraries. An application of KF13 to discover new crystal hits from clear drops of equilibrated crystallization screening plates is also shown.
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Affiliation(s)
- Dom Bellini
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, Cambridgeshire CB2 0QH, United Kingdom
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3
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Barthel T, Huschmann FU, Wallacher D, Feiler CG, Klebe G, Weiss MS, Wollenhaupt J. Facilitated crystal handling using a simple device for evaporation reduction in microtiter plates. J Appl Crystallogr 2021; 54:376-382. [PMID: 33833659 PMCID: PMC7941301 DOI: 10.1107/s1600576720016477] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 12/20/2020] [Indexed: 12/20/2022] Open
Abstract
In the past two decades, most of the steps in a macromolecular crystallography experiment have undergone tremendous development with respect to speed, feasibility and increase of throughput. The part of the experimental workflow that is still a bottleneck, despite significant efforts, involves the manipulation and harvesting of the crystals for the diffraction experiment. Here, a novel low-cost device is presented that functions as a cover for 96-well crystallization plates. This device enables access to the individual experiments one at a time by its movable parts, while minimizing evaporation of all other experiments of the plate. In initial tests, drops of many typically used crystallization cocktails could be successfully protected for up to 6 h. Therefore, the manipulation and harvesting of crystals is straightforward for the experimenter, enabling significantly higher throughput. This is useful for many macromolecular crystallography experiments, especially multi-crystal screening campaigns.
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Affiliation(s)
- Tatjana Barthel
- Helmholtz-Zentrum Berlin, Macromolecular Crystallography, Albert-Einstein-Straße 15, 12489 Berlin, Germany
- Freie Universität Berlin, Institute for Chemistry and Biochemistry, Structural Biochemistry Group, Takustraße 5, 14195 Berlin, Germany
| | - Franziska U. Huschmann
- Helmholtz-Zentrum Berlin, Macromolecular Crystallography, Albert-Einstein-Straße 15, 12489 Berlin, Germany
- Philipps-Universität Marburg, Institute of Pharmaceutical Chemistry, Drug Design Group, Marbacher Weg 6, 35032 Marburg, Germany
| | - Dirk Wallacher
- Helmholtz-Zentrum Berlin, Department Sample Environment, Hahn-Meitner-Platz 1, 14109 Berlin, Germany
| | - Christian G. Feiler
- Helmholtz-Zentrum Berlin, Macromolecular Crystallography, Albert-Einstein-Straße 15, 12489 Berlin, Germany
| | - Gerhard Klebe
- Philipps-Universität Marburg, Institute of Pharmaceutical Chemistry, Drug Design Group, Marbacher Weg 6, 35032 Marburg, Germany
| | - Manfred S. Weiss
- Helmholtz-Zentrum Berlin, Macromolecular Crystallography, Albert-Einstein-Straße 15, 12489 Berlin, Germany
| | - Jan Wollenhaupt
- Helmholtz-Zentrum Berlin, Macromolecular Crystallography, Albert-Einstein-Straße 15, 12489 Berlin, Germany
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4
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Wright ND, Collins P, Koekemoer L, Krojer T, Talon R, Nelson E, Ye M, Nowak R, Newman J, Ng JT, Mitrovich N, Wiggers H, von Delft F. The low-cost Shifter microscope stage transforms the speed and robustness of protein crystal harvesting. Acta Crystallogr D Struct Biol 2021; 77:62-74. [PMID: 33404526 PMCID: PMC7787106 DOI: 10.1107/s2059798320014114] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 10/22/2020] [Indexed: 12/05/2022] Open
Abstract
Despite the tremendous success of X-ray cryo-crystallography in recent decades, the transfer of crystals from the drops in which they are grown to diffractometer sample mounts remains a manual process in almost all laboratories. Here, the Shifter, a motorized, interactive microscope stage that transforms the entire crystal-mounting workflow from a rate-limiting manual activity to a controllable, high-throughput semi-automated process, is described. By combining the visual acuity and fine motor skills of humans with targeted hardware and software automation, it was possible to transform the speed and robustness of crystal mounting. Control software, triggered by the operator, manoeuvres crystallization plates beneath a clear protective cover, allowing the complete removal of film seals and thereby eliminating the tedium of repetitive seal cutting. The software, either upon request or working from an imported list, controls motors to position crystal drops under a hole in the cover for human mounting at a microscope. The software automatically captures experimental annotations for uploading to the user's data repository, removing the need for manual documentation. The Shifter facilitates mounting rates of 100-240 crystals per hour in a more controlled process than manual mounting, which greatly extends the lifetime of the drops and thus allows a dramatic increase in the number of crystals retrievable from any given drop without loss of X-ray diffraction quality. In 2015, the first in a series of three Shifter devices was deployed as part of the XChem fragment-screening facility at Diamond Light Source, where they have since facilitated the mounting of over 120 000 crystals. The Shifter was engineered to have a simple design, providing a device that could be readily commercialized and widely adopted owing to its low cost. The versatile hardware design allows use beyond fragment screening and protein crystallography.
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Affiliation(s)
- Nathan David Wright
- Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Patrick Collins
- I04-1, Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0QX, United Kingdom
| | - Lizbé Koekemoer
- Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Tobias Krojer
- Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Romain Talon
- Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
- I04-1, Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0QX, United Kingdom
| | - Elliot Nelson
- Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Mingda Ye
- Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Radosław Nowak
- Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Joseph Newman
- Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Jia Tsing Ng
- Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Nick Mitrovich
- Oxford Lab Technologies Ltd, Kemp House, 160 City Road, London EC1V 2N, United Kingdom
| | - Helton Wiggers
- Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Frank von Delft
- Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
- I04-1, Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0QX, United Kingdom
- Faculty of Science, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa
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5
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Krekic S, Zakar T, Gombos Z, Valkai S, Mero M, Zimányi L, Heiner Z, Dér A. Nonlinear Optical Investigation of Microbial Chromoproteins. FRONTIERS IN PLANT SCIENCE 2020; 11:547818. [PMID: 33193480 PMCID: PMC7609429 DOI: 10.3389/fpls.2020.547818] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 09/22/2020] [Indexed: 06/01/2023]
Abstract
Membrane-bound or cytosolic light-sensitive proteins, playing a crucial role in energy- and signal-transduction processes of various photosynthetic microorganisms, have been optimized for sensing or harvesting light by myriads of years of evolution. Upon absorption of a photon, they undergo a usually cyclic reaction series of conformations, and the accompanying spectro-kinetic events assign robust nonlinear optical (NLO) properties for these chromoproteins. During recent years, they have attracted a considerable interest among researchers of the applied optics community as well, where finding the appropriate NLO material for a particular application is a pivotal task. Potential applications have emerged in various branches of photonics, including optical information storage and processing, higher-harmonic and white-light continuum generation, or biosensorics. In our earlier work, we also raised the possibility of using chromoproteins, such as bacteriorhodopsin (bR), as building blocks for the active elements of integrated optical (IO) circuits, where several organic and inorganic photonic materials have been considered as active components, but so far none of them has been deemed ideal for the purpose. In the current study, we investigate the linear and NLO properties of biofilms made of photoactive yellow protein (PYP) and bR. The kinetics of the photoreactions are monitored by time-resolved absorption experiments, while the refractive index of the films and its light-induced changes are measured using the Optical Waveguide Lightmode Spectroscopy (OWLS) and Z-scan techniques, respectively. The nonlinear refractive index and the refractive index change of both protein films were determined in the green spectral range in a wide range of intensities and at various laser repetition rates. The nonlinear refractive index and refractive index change of PYP were compared to those of bR, with respect to photonics applications. Our results imply that the NLO properties of these proteins make them promising candidates for utilization in applied photonics, and they should be considered as valid alternatives for active components of IO circuits.
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Affiliation(s)
- Szilvia Krekic
- Institute of Biophysics, Biological Research Centre, Szeged, Hungary
- Doctoral School of Multidisciplinary Medical Sciences, University of Szeged, Szeged, Hungary
| | - Tomás Zakar
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
| | - Zoltán Gombos
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
| | - Sándor Valkai
- Institute of Biophysics, Biological Research Centre, Szeged, Hungary
| | - Mark Mero
- Max Born Institute for Nonlinear Optics and Short Pulse Spectroscopy, Berlin, Germany
| | - László Zimányi
- Institute of Biophysics, Biological Research Centre, Szeged, Hungary
| | - Zsuzsanna Heiner
- School of Analytical Sciences Adlershof, Humboldt-Universität zu Berlin, Berlin, Germany
| | - András Dér
- Institute of Biophysics, Biological Research Centre, Szeged, Hungary
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6
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Aumonier S, Santoni G, Gotthard G, von Stetten D, Leonard GA, Royant A. Millisecond time-resolved serial oscillation crystallography of a blue-light photoreceptor at a synchrotron. IUCRJ 2020; 7:728-736. [PMID: 32695419 PMCID: PMC7340269 DOI: 10.1107/s2052252520007411] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 06/03/2020] [Indexed: 05/23/2023]
Abstract
The recent development of serial crystallography has popularized time-resolved crystallography as a technique to determine the structure of protein-reaction intermediate states. However, most approaches rely on the availability of thousands to millions of microcrystals. A method is reported here, using monochromatic synchrotron radiation, for the room-temperature collection, processing and merging of X-ray oscillation diffraction data from <100 samples in order to observe the build up of a photoreaction intermediate species. Using this method, we monitored with a time resolution of 63 ms how the population of a blue-light photoreceptor domain in a crystal progressively photoconverts from the dark to the light state. The series of resulting snapshots allows us to visualize in detail the gradual rearrangement of both the protein and chromophore during this process.
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Affiliation(s)
- Sylvain Aumonier
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble Cedex 9, 38043, France
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, 71 avenue des Martyrs, Grenoble Cedex 9, 38044, France
| | - Gianluca Santoni
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble Cedex 9, 38043, France
| | - Guillaume Gotthard
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble Cedex 9, 38043, France
| | - David von Stetten
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble Cedex 9, 38043, France
| | - Gordon A. Leonard
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble Cedex 9, 38043, France
| | - Antoine Royant
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble Cedex 9, 38043, France
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, 71 avenue des Martyrs, Grenoble Cedex 9, 38044, France
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7
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Naschberger A, Juyoux P, von Velsen J, Rupp B, Bowler MW. Controlled dehydration, structural flexibility and gadolinium MRI contrast compound binding in the human plasma glycoprotein afamin. Acta Crystallogr D Struct Biol 2019; 75:1071-1083. [PMID: 31793901 PMCID: PMC6889915 DOI: 10.1107/s2059798319013500] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 10/02/2019] [Indexed: 01/29/2023] Open
Abstract
Afamin, which is a human blood plasma glycoprotein, a putative multifunctional transporter of hydrophobic molecules and a marker for metabolic syndrome, poses multiple challenges for crystallographic structure determination, both practically and in analysis of the models. Several hundred crystals were analysed, and an unusual variability in cell volume and difficulty in solving the structure despite an ∼34% sequence identity with nonglycosylated human serum albumin indicated that the molecule exhibits variable and context-sensitive packing, despite the simplified glycosylation in insect cell-expressed recombinant afamin. Controlled dehydration of the crystals was able to stabilize the orthorhombic crystal form, reducing the number of molecules in the asymmetric unit from the monoclinic form and changing the conformational state of the protein. An iterative strategy using fully automatic experiments available on MASSIF-1 was used to quickly determine the optimal protocol to achieve the phase transition, which should be readily applicable to many types of sample. The study also highlights the drawback of using a single crystallographic structure model for computational modelling purposes given that the conformational state of the binding sites and the electron density in the binding site, which is likely to result from PEGs, greatly varies between models. This also holds for the analysis of nonspecific low-affinity ligands, where often a variety of fragments with similar uncertainty can be modelled, inviting interpretative bias. As a promiscuous transporter, afamin also seems to bind gadoteridol, a magnetic resonance imaging contrast compound, in at least two sites. One pair of gadoteridol molecules is located near the human albumin Sudlow site, and a second gadoteridol molecule is located at an intermolecular site in proximity to domain IA. The data from the co-crystals support modern metrics of data quality in the context of the information that can be gleaned from data sets that would be abandoned on classical measures.
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Affiliation(s)
- Andreas Naschberger
- Department of Genetic Epidemiology, Medical University Innsbruck, Schöpfstrasse 41, A-6020 Innsbruck, Austria
| | - Pauline Juyoux
- Grenoble Outstation, European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Jill von Velsen
- Grenoble Outstation, European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Bernhard Rupp
- Department of Genetic Epidemiology, Medical University Innsbruck, Schöpfstrasse 41, A-6020 Innsbruck, Austria
- C.V.M.O., k. k. Hofkristallamt, 991 Audrey Place, Vista, California, USA
| | - Matthew W. Bowler
- Grenoble Outstation, European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France
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8
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Lieske J, Cerv M, Kreida S, Komadina D, Fischer J, Barthelmess M, Fischer P, Pakendorf T, Yefanov O, Mariani V, Seine T, Ross BH, Crosas E, Lorbeer O, Burkhardt A, Lane TJ, Guenther S, Bergtholdt J, Schoen S, Törnroth-Horsefield S, Chapman HN, Meents A. On-chip crystallization for serial crystallography experiments and on-chip ligand-binding studies. IUCRJ 2019; 6:714-728. [PMID: 31316815 PMCID: PMC6608620 DOI: 10.1107/s2052252519007395] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 05/21/2019] [Indexed: 05/18/2023]
Abstract
Efficient and reliable sample delivery has remained one of the bottlenecks for serial crystallography experiments. Compared with other methods, fixed-target sample delivery offers the advantage of significantly reduced sample consumption and shorter data collection times owing to higher hit rates. Here, a new method of on-chip crystallization is reported which allows the efficient and reproducible growth of large numbers of protein crystals directly on micro-patterned silicon chips for in-situ serial crystallography experiments. Crystals are grown by sitting-drop vapor diffusion and previously established crystallization conditions can be directly applied. By reducing the number of crystal-handling steps, the method is particularly well suited for sensitive crystal systems. Excessive mother liquor can be efficiently removed from the crystals by blotting, and no sealing of the fixed-target sample holders is required to prevent the crystals from dehydrating. As a consequence, 'naked' crystals are obtained on the chip, resulting in very low background scattering levels and making the crystals highly accessible for external manipulation such as the application of ligand solutions. Serial diffraction experiments carried out at cryogenic temperatures at a synchrotron and at room temperature at an X-ray free-electron laser yielded high-quality X-ray structures of the human membrane protein aquaporin 2 and two new ligand-bound structures of thermolysin and the human kinase DRAK2. The results highlight the applicability of the method for future high-throughput on-chip screening of pharmaceutical compounds.
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Affiliation(s)
- Julia Lieske
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Maximilian Cerv
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Stefan Kreida
- Center for Molecular Protein Science, Department of Biochemistry and Structural Biology, Lund University, Kemicentrum, 221 00 Lund, Sweden
| | - Dana Komadina
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Janine Fischer
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Miriam Barthelmess
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Pontus Fischer
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Tim Pakendorf
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Valerio Mariani
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Thomas Seine
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- EMBL, Notkestrasse 85, 22607 Hamburg, Germany
| | - Breyan H. Ross
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Eva Crosas
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Olga Lorbeer
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Anja Burkhardt
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Thomas J. Lane
- Bioscience Division and Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Sebastian Guenther
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Julian Bergtholdt
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Silvan Schoen
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Susanna Törnroth-Horsefield
- Center for Molecular Protein Science, Department of Biochemistry and Structural Biology, Lund University, Kemicentrum, 221 00 Lund, Sweden
| | - Henry N. Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Centre for Ultrafast Imaging, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Alke Meents
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
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9
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Li W, Liu W, Wen W, Liu H, Liu M, Zhou C, Luo B. The liquid crystalline order, rheology and their correlation in chitin whiskers suspensions. Carbohydr Polym 2019; 209:92-100. [DOI: 10.1016/j.carbpol.2019.01.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 12/19/2018] [Accepted: 01/02/2019] [Indexed: 10/27/2022]
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10
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Bommer M, Coates L, Dau H, Zouni A, Dobbek H. Protein crystallization and initial neutron diffraction studies of the photosystem II subunit PsbO. Acta Crystallogr F Struct Biol Commun 2017; 73:525-531. [PMID: 28876232 PMCID: PMC5619745 DOI: 10.1107/s2053230x17012171] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 08/22/2017] [Indexed: 11/10/2022] Open
Abstract
The PsbO protein of photosystem II stabilizes the active-site manganese cluster and is thought to act as a proton antenna. To enable neutron diffraction studies, crystals of the β-barrel core of PsbO were grown in capillaries. The crystals were optimized by screening additives in a counter-diffusion setup in which the protein and reservoir solutions were separated by a 1% agarose plug. Crystals were cross-linked with glutaraldehyde. Initial neutron diffraction data were collected from a 0.25 mm3 crystal at room temperature using the MaNDi single-crystal diffractometer at the Spallation Neutron Source, Oak Ridge National Laboratory.
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Affiliation(s)
- Martin Bommer
- Institut für Biologie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
| | - Leighton Coates
- Biology and Soft Matter Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Holger Dau
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Athina Zouni
- Institut für Biologie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
| | - Holger Dobbek
- Institut für Biologie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
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11
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Roedig P, Ginn HM, Pakendorf T, Sutton G, Harlos K, Walter TS, Meyer J, Fischer P, Duman R, Vartiainen I, Reime B, Warmer M, Brewster AS, Young ID, Michels-Clark T, Sauter NK, Kotecha A, Kelly J, Rowlands DJ, Sikorsky M, Nelson S, Damiani DS, Alonso-Mori R, Ren J, Fry EE, David C, Stuart DI, Wagner A, Meents A. High-speed fixed-target serial virus crystallography. Nat Methods 2017; 14:805-810. [PMID: 28628129 PMCID: PMC5588887 DOI: 10.1038/nmeth.4335] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 05/15/2017] [Indexed: 12/19/2022]
Abstract
We report a method for serial X-ray crystallography at X-ray free-electron lasers (XFELs), which allows for full use of the current 120-Hz repetition rate of the Linear Coherent Light Source (LCLS). Using a micropatterned silicon chip in combination with the high-speed Roadrunner goniometer for sample delivery, we were able to determine the crystal structures of the picornavirus bovine enterovirus 2 (BEV2) and the cytoplasmic polyhedrosis virus type 18 polyhedrin, with total data collection times of less than 14 and 10 min, respectively. Our method requires only micrograms of sample and should therefore broaden the applicability of serial femtosecond crystallography to challenging projects for which only limited sample amounts are available. By synchronizing the sample exchange to the XFEL repetition rate, our method allows for most efficient use of the limited beam time available at XFELs and should enable a substantial increase in sample throughput at these facilities.
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Affiliation(s)
- Philip Roedig
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Helen M. Ginn
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Diamond Light Source Limited, Harwell Science & Innovation Campus, Didcot, United Kingdom
| | - Tim Pakendorf
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Geoff Sutton
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Karl Harlos
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Thomas S. Walter
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Jan Meyer
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Pontus Fischer
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Ramona Duman
- Diamond Light Source Limited, Harwell Science & Innovation Campus, Didcot, United Kingdom
| | - Ismo Vartiainen
- Institute of Photonics, University of Eastern Finland, Joensuu, Finland
| | - Bernd Reime
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Martin Warmer
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Aaron S. Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Iris D. Young
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Tara Michels-Clark
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Nicholas K. Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Abhay Kotecha
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - James Kelly
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
- The Pirbright Institute, Pirbright, United Kingdom
| | - David J. Rowlands
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Marcin Sikorsky
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Silke Nelson
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Daniel S. Damiani
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Roberto Alonso-Mori
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Jingshan Ren
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Elizabeth E. Fry
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | | | - David I. Stuart
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Diamond Light Source Limited, Harwell Science & Innovation Campus, Didcot, United Kingdom
| | - Armin Wagner
- Diamond Light Source Limited, Harwell Science & Innovation Campus, Didcot, United Kingdom
| | - Alke Meents
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
- Center for Free Electron Laser Science (CFEL), Hamburg, Germany
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12
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Abstract
Cellular potassium import systems play a fundamental role in osmoregulation, pH homeostasis and membrane potential in all domains of life. In bacteria, the kdp operon encodes a four subunit potassium pump that maintains intracellular homeostasis as well as cell shape and turgor under conditions where potassium is limiting1. This membrane complex, called KdpFABC, has one channel-like subunit (KdpA) belonging to the Superfamily of Potassium Transporters and another pump-like subunit (KdpB) belonging to the Superfamily of P-type ATPases. Although there is considerable structural and functional information about members from both superfamilies, the mechanism by which uphill potassium transport through KdpA is coupled with ATP hydrolysis by KdpB remains poorly understood. Here we report the 2.9 Å X-ray structure of the complete Escherichia coli KdpFABC complex with a potassium ion within the selectivity filter of KdpA as well as a water molecule at a canonical cation site in the transmembrane domain of KdpB. The structure also reveals two structural elements that appear to mediate the coupling between these two subunits. Specifically, a protein-embedded tunnel runs between these potassium and water sites and a helix controlling the cytoplasmic gate of KdpA is linked to the phosphorylation domain of KdpB. Based on these observations, we propose an unprecedented mechanism that repurposes protein channel architecture for active transport across biomembranes.
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Affiliation(s)
- Ching-Shin Huang
- Molecular Biophysics Graduate Program, New York University School of Medicine, Skirball Institute, 540 First Avenue, New York, New York 10016, USA
| | - Bjørn Panyella Pedersen
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000 Aarhus C, Denmark.,Aarhus Institute of Advanced Studies, Aarhus University, Høegh-Guldbergs Gade 6B, DK-8000 Aarhus C, Denmark
| | - David L Stokes
- Department of Cell Biology, New York University School of Medicine, Skirball Institute, 540 First Avenue, New York, New York 10016, USA
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13
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Bowler MG, Bowler DR, Bowler MW. Raoult's law revisited: accurately predicting equilibrium relative humidity points for humidity control experiments. J Appl Crystallogr 2017; 50:631-638. [PMID: 28381983 PMCID: PMC5377353 DOI: 10.1107/s1600576717003636] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 03/07/2017] [Indexed: 11/16/2022] Open
Abstract
The humidity surrounding a sample is an important variable in scientific experiments. Biological samples in particular require not just a humid atmosphere but often a relative humidity (RH) that is in equilibrium with a stabilizing solution required to maintain the sample in the same state during measurements. The controlled dehydration of macromolecular crystals can lead to significant increases in crystal order, leading to higher diffraction quality. Devices that can accurately control the humidity surrounding crystals while monitoring diffraction have led to this technique being increasingly adopted, as the experiments become easier and more reproducible. Matching the RH to the mother liquor is the first step in allowing the stable mounting of a crystal. In previous work [Wheeler, Russi, Bowler & Bowler (2012). Acta Cryst. F68, 111-114], the equilibrium RHs were measured for a range of concentrations of the most commonly used precipitants in macromolecular crystallography and it was shown how these related to Raoult's law for the equilibrium vapour pressure of water above a solution. However, a discrepancy between the measured values and those predicted by theory could not be explained. Here, a more precise humidity control device has been used to determine equilibrium RH points. The new results are in agreement with Raoult's law. A simple argument in statistical mechanics is also presented, demonstrating that the equilibrium vapour pressure of a solvent is proportional to its mole fraction in an ideal solution: Raoult's law. The same argument can be extended to the case where the solvent and solute molecules are of different sizes, as is the case with polymers. The results provide a framework for the correct maintenance of the RH surrounding a sample.
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Affiliation(s)
- Michael G. Bowler
- Department of Physics, University of Oxford, Keble Road, Oxford OX1 3RH, UK
| | - David R. Bowler
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, UK
| | - Matthew W. Bowler
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, CS 90181, Grenoble F-38042, France
- Unit for Virus Host Cell Interactions, Université Grenoble Alpes–EMBL–CNRS, 71 avenue des Martyrs, CS 90181, Grenoble F-38042, France
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14
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Lobley CMC, Sandy J, Sanchez-Weatherby J, Mazzorana M, Krojer T, Nowak RP, Sorensen TL. A generic protocol for protein crystal dehydration using the HC1b humidity controller. Acta Crystallogr D Struct Biol 2016; 72:629-40. [PMID: 27139626 PMCID: PMC4854313 DOI: 10.1107/s2059798316003065] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 02/21/2016] [Indexed: 11/11/2022] Open
Abstract
Dehydration may change the crystal lattice and affect the mosaicity, resolution and quality of X-ray diffraction data. A dehydrating environment can be generated around a crystal in several ways with various degrees of precision and complexity. This study uses a high-precision crystal humidifier/dehumidifier to provide an airstream of known relative humidity in which the crystals are mounted: a precise yet hassle-free approach to altering crystal hydration. A protocol is introduced to assess the impact of crystal dehydration systematically applied to nine experimental crystal systems. In one case, that of glucose isomerase, dehydration triggering a change of space group from I222 to P21212 was observed. This observation is supported by an extended study of the behaviour of the glucose isomerase crystal structure during crystal dehydration.
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Affiliation(s)
- Carina M. C. Lobley
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - James Sandy
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | | | - Marco Mazzorana
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Tobias Krojer
- Structural Genomics Consortium, University of Oxford, Roosevelt Drive, Headington, Oxford OX3 7DQ, England
| | - Radosław P. Nowak
- Structural Genomics Consortium, University of Oxford, Roosevelt Drive, Headington, Oxford OX3 7DQ, England
| | - Thomas L. Sorensen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
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15
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Sanchez-Weatherby J, Moraes I. Crystal Dehydration in Membrane Protein Crystallography. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 922:73-89. [PMID: 27553236 PMCID: PMC6126552 DOI: 10.1007/978-3-319-35072-1_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Crystal dehydration has been successfully implemented to facilitate the structural solution of a number of soluble and membrane protein structures over the years. This chapter will present the currently available tools to undertake controlled crystal dehydration, focusing on some successful membrane protein cases. Also discussed here will be some practical considerations regarding membrane protein crystals and the relationship between different techniques in order to help researchers to select the most suitable technique for their projects.
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Affiliation(s)
| | - Isabel Moraes
- Membrane Protein Laboratory, Diamond Light Source/Imperial College London, Harwell Campus, Didcot, Oxfordshire UK
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16
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Preparation, Crystallization, and Structure Determination of Chromatin Enzyme/Nucleosome Complexes. Methods Enzymol 2016; 573:43-65. [PMID: 27372748 DOI: 10.1016/bs.mie.2016.01.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
Structural studies of chromatin complexes composed of chromatin factors or enzymes bound to the nucleosome have been constrained by the ability to produce high-quality complexes in the amounts appropriate for biophysical studies and by the difficulty of crystallizing these complexes. We describe here procedures and approaches to prepare chromatin complexes, to crystallize chromatin complexes, and to improve diffraction properties through postcrystallization soaks. Special attention is paid to evaluating the quality of the purified chromatin complexes as well as assessing the presence of the chromatin protein or enzyme in crystals. The methods described for preparing and purifying chromatin complexes should be applicable to biochemical, biophysical, and other structural approaches including cryoelectron microscopy.
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17
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Mazzorana M, Sanchez-Weatherby J, Sandy J, Lobley CMC, Sorensen T. An evaluation of adhesive sample holders for advanced crystallographic experiments. ACTA ACUST UNITED AC 2014; 70:2390-400. [PMID: 25195752 PMCID: PMC4157448 DOI: 10.1107/s1399004714014370] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 06/18/2014] [Indexed: 05/28/2023]
Abstract
The hydration state of macromolecular crystals often affects their overall order and, ultimately, the quality of the X-ray diffraction pattern that they produce. Post-crystallization techniques that alter the solvent content of a crystal may induce rearrangement within the three-dimensional array making up the crystal, possibly resulting in more ordered packing. The hydration state of a crystal can be manipulated by exposing it to a stream of air at controlled relative humidity in which the crystal can equilibrate. This approach provides a way of exploring crystal hydration space to assess the diffraction capabilities of existing crystals. A key requirement of these experiments is to expose the crystal directly to the dehydrating environment by having the minimum amount of residual mother liquor around it. This is usually achieved by placing the crystal on a flat porous support (Kapton mesh) and removing excess liquid by wicking. Here, an alternative approach is considered whereby crystals are harvested using adhesives that capture naked crystals directly from their crystallization drop, reducing the process to a one-step procedure. The impact of using adhesives to ease the harvesting of different types of crystals is presented together with their contribution to background scattering and their usefulness in dehydration experiments. It is concluded that adhesive supports represent a valuable tool for mounting macromolecular crystals to be used in humidity-controlled experiments and to improve signal-to-noise ratios in diffraction experiments, and how they can protect crystals from modifications in the sample environment is discussed.
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Affiliation(s)
- Marco Mazzorana
- Diamond Light Source, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, England
| | - Juan Sanchez-Weatherby
- Diamond Light Source, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, England
| | - James Sandy
- Diamond Light Source, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, England
| | - Carina M C Lobley
- Diamond Light Source, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, England
| | - Thomas Sorensen
- Diamond Light Source, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, England
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18
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Farley C, Burks G, Siegert T, Juers DH. Improved reproducibility of unit-cell parameters in macromolecular cryocrystallography by limiting dehydration during crystal mounting. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:2111-24. [PMID: 25084331 PMCID: PMC4118824 DOI: 10.1107/s1399004714012310] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Accepted: 05/27/2014] [Indexed: 11/18/2022]
Abstract
In macromolecular cryocrystallography unit-cell parameters can have low reproducibility, limiting the effectiveness of combining data sets from multiple crystals and inhibiting the development of defined repeatable cooling protocols. Here, potential sources of unit-cell variation are investigated and crystal dehydration during loop-mounting is found to be an important factor. The amount of water lost by the unit cell depends on the crystal size, the loop size, the ambient relative humidity and the transfer distance to the cooling medium. To limit water loss during crystal mounting, a threefold strategy has been implemented. Firstly, crystal manipulations are performed in a humid environment similar to the humidity of the crystal-growth or soaking solution. Secondly, the looped crystal is transferred to a vial containing a small amount of the crystal soaking solution. Upon loop transfer, the vial is sealed, which allows transport of the crystal at its equilibrated humidity. Thirdly, the crystal loop is directly mounted from the vial into the cold gas stream. This strategy minimizes the exposure of the crystal to relatively low humidity ambient air, improves the reproducibility of low-temperature unit-cell parameters and offers some new approaches to crystal handling and cryoprotection.
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Affiliation(s)
- Christopher Farley
- Department of Physics, Whitman College, 345 Boyer Avenue, Walla Walla, WA 99362, USA
| | - Geoffry Burks
- Program in Biochemistry, Biophysics and Molecular Biology, Whitman College, 345 Boyer Avenue, Walla Walla, WA 99362, USA
| | - Thomas Siegert
- Program in Biochemistry, Biophysics and Molecular Biology, Whitman College, 345 Boyer Avenue, Walla Walla, WA 99362, USA
| | - Douglas H. Juers
- Department of Physics, Whitman College, 345 Boyer Avenue, Walla Walla, WA 99362, USA
- Program in Biochemistry, Biophysics and Molecular Biology, Whitman College, 345 Boyer Avenue, Walla Walla, WA 99362, USA
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19
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Bowler MG, Bowler MW. Measurement of the intrinsic variability within protein crystals: implications for sample-evaluation and data-collection strategies. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2013; 70:127-32. [PMID: 24419635 DOI: 10.1107/s2053230x13032007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 11/22/2013] [Indexed: 11/10/2022]
Abstract
The advent of micro-focused X-ray beams has led to the development of a number of advanced methods of sample evaluation and data collection. In particular, multiple-position data-collection and helical oscillation strategies are now becoming commonplace in order to alleviate the problems associated with radiation damage. However, intra-crystal and inter-crystal variation means that it is not always obvious on which crystals or on which region or regions of a crystal these protocols should be performed. For the automation of this process for large-scale screening, and to provide an indication of the best strategy for data collection, a metric of crystal variability could be useful. Here, measures of the intrinsic variability within protein crystals are presented and their implications for optimal data-collection strategies are discussed.
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Affiliation(s)
- Michael G Bowler
- Department of Physics, University of Oxford, Keble Road, Oxford OX1 3RH, England
| | - Matthew W Bowler
- European Molecular Biology Laboratory, Grenoble Outstation, 6 Rue Jules Horowitz, 38042 Grenoble, France
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20
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Douangamath A, Aller P, Lukacik P, Sanchez-Weatherby J, Moraes I, Brandao-Neto J. Using high-throughputin situplate screening to evaluate the effect of dehydration on protein crystals. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:920-3. [DOI: 10.1107/s0907444913002412] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Accepted: 01/23/2013] [Indexed: 11/10/2022]
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21
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22
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von Stetten D, Batot GO, Noirclerc-Savoye M, Royant A. Alteration of fluorescent protein spectroscopic properties upon cryoprotection. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:1578-83. [DOI: 10.1107/s0907444912037900] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 09/04/2012] [Indexed: 05/26/2023]
Abstract
Cryoprotection of a protein crystal by addition of small-molecule compounds may sometimes affect the structure of its active site. The spectroscopic and structural effects of the two cryoprotectants glycerol and ethylene glycol on the cyan fluorescent protein Cerulean were investigated. While glycerol had almost no noticeable effect, ethylene glycol was shown to induce a systematic red shift of the UV–vis absorption and fluorescence emission spectra. Additionally, ethylene glycol molecules were shown to enter the core of the protein, with one of them binding in close vicinity to the chromophore, which provides a sound explanation for the observed spectroscopic changes. These results highlight the need to systematically record spectroscopic data on crystals of light-absorbing proteins and reinforce the notion that fluorescent proteins must not been seen as rigid structures.
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23
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Increasing the X-ray diffraction power of protein crystals by dehydration: the case of bovine serum albumin and a survey of literature data. Int J Mol Sci 2012; 13:3782-3800. [PMID: 22489183 PMCID: PMC3317743 DOI: 10.3390/ijms13033782] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Revised: 03/07/2012] [Accepted: 03/08/2012] [Indexed: 12/19/2022] Open
Abstract
Serum albumin is one of the most widely studied proteins. It is the most abundant protein in plasma with a typical concentration of 5 g/100 mL and the principal transporter of fatty acids in plasma. While the crystal structures of human serum albumin (HSA) free and in complex with fatty acids, hemin, and local anesthetics have been characterized, no crystallographic models are available on bovine serum albumin (BSA), presumably because of the poor diffraction power of existing hexagonal BSA crystals. Here, the crystallization and diffraction data of a new BSA crystal form, obtained by the hanging drop method using MPEG 5K as precipitating agent, are presented. The crystals belong to space group C2, with unit-cell parameters a = 216.45 Å, b = 44.72 Å, c = 140.18 Å, β = 114.5°. Dehydration was found to increase the diffraction limit of BSA crystals from ~8 Å to 3.2 Å, probably by improving the packing of protein molecules in the crystal lattice. These results, together with a survey of more than 60 successful cases of protein crystal dehydration, confirm that it can be a useful procedure to be used in initial screening as a method of improving the diffraction limits of existing crystals.
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