1
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Mendez D, Holton JM, Lyubimov AY, Hollatz S, Mathews II, Cichosz A, Martirosyan V, Zeng T, Stofer R, Liu R, Song J, McPhillips S, Soltis M, Cohen AE. Deep residual networks for crystallography trained on synthetic data. Acta Crystallogr D Struct Biol 2024; 80:26-43. [PMID: 38164955 PMCID: PMC10833344 DOI: 10.1107/s2059798323010586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 12/12/2023] [Indexed: 01/03/2024] Open
Abstract
The use of artificial intelligence to process diffraction images is challenged by the need to assemble large and precisely designed training data sets. To address this, a codebase called Resonet was developed for synthesizing diffraction data and training residual neural networks on these data. Here, two per-pattern capabilities of Resonet are demonstrated: (i) interpretation of crystal resolution and (ii) identification of overlapping lattices. Resonet was tested across a compilation of diffraction images from synchrotron experiments and X-ray free-electron laser experiments. Crucially, these models readily execute on graphics processing units and can thus significantly outperform conventional algorithms. While Resonet is currently utilized to provide real-time feedback for macromolecular crystallography users at the Stanford Synchrotron Radiation Lightsource, its simple Python-based interface makes it easy to embed in other processing frameworks. This work highlights the utility of physics-based simulation for training deep neural networks and lays the groundwork for the development of additional models to enhance diffraction collection and analysis.
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Affiliation(s)
- Derek Mendez
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - James M. Holton
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Biochemistry and Biophysics, UC San Francisco, San Francisco, CA 94158, USA
| | - Artem Y. Lyubimov
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Sabine Hollatz
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Irimpan I. Mathews
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Aleksander Cichosz
- Department of Statistics and Applied Probability, UC Santa Barbara, Santa Barbara, CA 93106, USA
| | - Vardan Martirosyan
- Department of Mathematics, UC Santa Barbara, Santa Barbara, CA 93106, USA
| | - Teo Zeng
- Department of Statistics and Applied Probability, UC Santa Barbara, Santa Barbara, CA 93106, USA
| | - Ryan Stofer
- Department of Statistics and Applied Probability, UC Santa Barbara, Santa Barbara, CA 93106, USA
| | - Ruobin Liu
- Department of Statistics and Applied Probability, UC Santa Barbara, Santa Barbara, CA 93106, USA
| | - Jinhu Song
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Scott McPhillips
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Mike Soltis
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Aina E. Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
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2
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Pei X, Bhatt N, Wang H, Ando N, Meisburger SP. Introduction to diffuse scattering and data collection. Methods Enzymol 2023; 688:1-42. [PMID: 37748823 DOI: 10.1016/bs.mie.2023.07.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
A long-standing goal in X-ray crystallography has been to extract information about the collective motions of proteins from diffuse scattering: the weak, textured signal that is found in the background of diffraction images. In the past few years, the field of macromolecular diffuse scattering has seen dramatic progress, and many of the past challenges in measurement and interpretation are now considered tractable. However, the concept of diffuse scattering is still new to many researchers, and a general set of procedures needed to collect a high-quality dataset has never been described in detail. Here, we provide the first guidelines for performing diffuse scattering experiments, which can be performed at any macromolecular crystallography beamline that supports room-temperature studies with a direct detector. We begin with a brief introduction to the theory of diffuse scattering and then walk the reader through the decision-making processes involved in preparing for and conducting a successful diffuse scattering experiment. Finally, we define quality metrics and describe ways to assess data quality both at the beamline and at home. Data obtained in this way can be processed independently by crystallographic software and diffuse scattering software to produce both a crystal structure, which represents the average atomic coordinates, and a three-dimensional diffuse scattering map that can then be interpreted in terms of models for protein motions.
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Affiliation(s)
- Xiaokun Pei
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, United States
| | - Neti Bhatt
- Department of Physics, Cornell University, Ithaca, NY, United States
| | - Haoyue Wang
- Graduate Field of Biophysics, Cornell University, Ithaca, NY, United States
| | - Nozomi Ando
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, United States; Department of Physics, Cornell University, Ithaca, NY, United States; Graduate Field of Biophysics, Cornell University, Ithaca, NY, United States.
| | - Steve P Meisburger
- Cornell High Energy Synchrotron Source, Cornell University, Ithaca, NY, United States.
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3
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Plapp BV, Gakhar L, Subramanian R. Dependence of crystallographic atomic displacement parameters on temperature (25-150 K) for complexes of horse liver alcohol dehydrogenase. Acta Crystallogr D Struct Biol 2022; 78:1221-1234. [PMID: 36189742 PMCID: PMC9527765 DOI: 10.1107/s2059798322008361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/22/2022] [Indexed: 11/19/2022] Open
Abstract
Enzymes catalyze reactions by binding and orienting substrates with dynamic interactions. Horse liver alcohol dehydrogenase catalyzes hydrogen transfer with quantum-mechanical tunneling that involves fast motions in the active site. The structures and B factors of ternary complexes of the enzyme with NAD+ and 2,3,4,5,6-pentafluorobenzyl alcohol or NAD+ and 2,2,2-trifluoroethanol were determined to 1.1-1.3 Å resolution below the `glassy transition' in order to extract information about the temperature-dependent harmonic motions, which are reflected in the crystallographic B factors. The refinement statistics and structures are essentially the same for each structure at all temperatures. The B factors were corrected for a small amount of radiation decay. The overall B factors for the complexes are similar (13-16 Å2) over the range 25-100 K, but increase somewhat at 150 K. Applying TLS refinement to remove the contribution of pseudo-rigid-body displacements of coenzyme binding and catalytic domains provided residual B factors of 7-10 Å2 for the overall complexes and of 5-10 Å2 for C4N of NAD+ and the methylene carbon of the alcohols. These residual B factors have a very small dependence on temperature and include local harmonic motions and apparently contributions from other sources. Structures at 100 K show complexes that are poised for hydrogen transfer, which involves atomic displacements of ∼0.3 Å and is compatible with the motions estimated from the residual B factors and molecular-dynamics simulations. At 298 K local conformational changes are also involved in catalysis, as enzymes with substitutions of amino acids in the substrate-binding site have similar positions of NAD+ and pentafluorobenzyl alcohol and similar residual B factors, but differ by tenfold in the rate constants for hydride transfer.
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Affiliation(s)
- Bryce V. Plapp
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA 52252, USA
| | - Lokesh Gakhar
- Protein and Crystallography Facility, Carver College of Medicine, The University of Iowa, Iowa City, IA 52252, USA
| | - Ramaswamy Subramanian
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA 52252, USA
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4
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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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5
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Quantifying and comparing radiation damage in the Protein Data Bank. Nat Commun 2022; 13:1314. [PMID: 35288575 PMCID: PMC8921271 DOI: 10.1038/s41467-022-28934-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 02/18/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractRadiation damage remains one of the major bottlenecks to accurate structure solution in protein crystallography. It can induce structural and chemical changes in protein crystals, and is hence an important consideration when assessing the quality and biological veracity of crystal structures in repositories like the Protein Data Bank (PDB). However, detection of radiation damage artefacts has traditionally proved very challenging. To address this, here we introduce the Bnet metric. Bnet summarises in a single value the extent of damage suffered by a crystal structure by comparing the B-factor values of damage-prone and non-damage-prone atoms in a similar local environment. After validating that Bnet successfully detects damage in 23 different crystal structures previously characterised as damaged, we calculate Bnet values for 93,978 PDB crystal structures. Our metric highlights a range of damage features, many of which would remain unidentified by the other summary statistics typically calculated for PDB structures.
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6
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Pan D, Fan J, Nie Z, Sun Z, Zhang J, Tong Y, He B, Song C, Kohmura Y, Yabashi M, Ishikawa T, Shen Y, Jiang H. Quantitative analysis of the effect of radiation on mitochondria structure using coherent diffraction imaging with a clustering algorithm. IUCRJ 2022; 9:223-230. [PMID: 35371506 PMCID: PMC8895015 DOI: 10.1107/s2052252521012963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 12/07/2021] [Indexed: 06/14/2023]
Abstract
Radiation damage and a low signal-to-noise ratio are the primary factors that limit spatial resolution in coherent diffraction imaging (CDI) of biomaterials using X-ray sources. Introduced here is a clustering algorithm named ConvRe based on deep learning, and it is applied to obtain accurate and consistent image reconstruction from noisy diffraction patterns of weakly scattering biomaterials. To investigate the impact of X-ray radiation on soft biomaterials, CDI experiments were performed on mitochondria from human embryonic kidney cells using synchrotron radiation. Benefiting from the new algorithm, structural changes in the mitochondria induced by X-ray radiation damage were quantitatively characterized and analysed at the nanoscale with different radiation doses. This work also provides a promising approach for improving the imaging quality of biomaterials with XFEL-based plane-wave CDI.
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Affiliation(s)
- Dan Pan
- School of Physical Science and Technology and Center for Transformative Science, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, People’s Republic of China
| | - Jiadong Fan
- School of Physical Science and Technology and Center for Transformative Science, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, People’s Republic of China
| | - Zhenzhen Nie
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, People’s Republic of China
| | - Zhibin Sun
- School of Physical Science and Technology and Center for Transformative Science, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, People’s Republic of China
- Photon Science Division, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Jianhua Zhang
- School of Physical Science and Technology and Center for Transformative Science, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, People’s Republic of China
| | - Yajun Tong
- School of Physical Science and Technology and Center for Transformative Science, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, People’s Republic of China
| | - Bo He
- School of Physical Science and Technology and Center for Transformative Science, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, People’s Republic of China
| | - Changyong Song
- Department of Physics, Pohang University of Science and Technology, Pohang 37673, South Korea
| | - Yoshiki Kohmura
- SPring-8 Center, RIKEN, 1-1-1, Kouto, Sayo, Hyogo 679-5148, Japan
| | - Makina Yabashi
- SPring-8 Center, RIKEN, 1-1-1, Kouto, Sayo, Hyogo 679-5148, Japan
| | - Tetsuya Ishikawa
- SPring-8 Center, RIKEN, 1-1-1, Kouto, Sayo, Hyogo 679-5148, Japan
| | - Yuequan Shen
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, People’s Republic of China
| | - Huaidong Jiang
- School of Physical Science and Technology and Center for Transformative Science, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, People’s Republic of China
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7
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Suzuki R, Baba S, Mizuno N, Hasegawa K, Koizumi H, Kojima K, Kumasaka T, Tachibana M. Radiation-induced defects in protein crystals observed by X-ray topography. ACTA CRYSTALLOGRAPHICA SECTION D STRUCTURAL BIOLOGY 2022; 78:196-203. [DOI: 10.1107/s205979832101281x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 12/01/2021] [Indexed: 11/10/2022]
Abstract
The characterization of crystal defects induced by irradiation, such as X-rays, charged particles and neutrons, is important for understanding radiation damage and the associated generation of defects. Radiation damage to protein crystals has been measured using various methods. Until now, these methods have focused on decreased diffraction intensity, volume expansion of unit cells and specific damage to side chains. Here, the direct observation of specific crystal defects, such as dislocations, induced by X-ray irradiation of protein crystals at room temperature is reported. Dislocations are induced even by low absorbed doses of X-ray irradiation. This study revealed that for the same total absorbed dose, the formation of defects appears to critically depend on the dose rate. The relationship between dislocation energy and dose energy was analyzed based on dislocation theory associated with elasticity theory for crystalline materials. This demonstration of the crystal defects induced by X-ray irradiation could help to understand the underlying mechanisms of X-ray-induced radiation damage.
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8
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Parkhurst JM, Dumoux M, Basham M, Clare D, Siebert CA, Varslot T, Kirkland A, Naismith JH, Evans G. Parakeet: a digital twin software pipeline to assess the impact of experimental parameters on tomographic reconstructions for cryo-electron tomography. Open Biol 2021; 11:210160. [PMID: 34699732 PMCID: PMC8548082 DOI: 10.1098/rsob.210160] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
In cryo-electron tomography (cryo-ET) of biological samples, the quality of tomographic reconstructions can vary depending on the transmission electron microscope (TEM) instrument and data acquisition parameters. In this paper, we present Parakeet, a 'digital twin' software pipeline for the assessment of the impact of various TEM experiment parameters on the quality of three-dimensional tomographic reconstructions. The Parakeet digital twin is a digital model that can be used to optimize the performance and utilization of a physical instrument to enable in silico optimization of sample geometries, data acquisition schemes and instrument parameters. The digital twin performs virtual sample generation, TEM image simulation, and tilt series reconstruction and analysis within a convenient software framework. As well as being able to produce physically realistic simulated cryo-ET datasets to aid the development of tomographic reconstruction and subtomogram averaging programs, Parakeet aims to enable convenient assessment of the effects of different microscope parameters and data acquisition parameters on reconstruction quality. To illustrate the use of the software, we present the example of a quantitative analysis of missing wedge artefacts on simulated planar and cylindrical biological samples and discuss how data collection parameters can be modified for cylindrical samples where a full 180° tilt range might be measured.
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Affiliation(s)
- James M. Parkhurst
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK,Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Maud Dumoux
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Mark Basham
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK,Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Daniel Clare
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - C. Alistair Siebert
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Trond Varslot
- Thermo Fisher Scientific, Vlastimila Pecha, Brno, Czech Republic
| | - Angus Kirkland
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK,Electron Physical Science Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK,Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH, UK
| | - James H. Naismith
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK,Division of Structural Biology, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Gwyndaf Evans
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK,Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
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9
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Baba S, Matsuura H, Kawamura T, Sakai N, Nakamura Y, Kawano Y, Mizuno N, Kumasaka T, Yamamoto M, Hirata K. Guidelines for de novo phasing using multiple small-wedge data collection. JOURNAL OF SYNCHROTRON RADIATION 2021; 28:1284-1295. [PMID: 34475278 PMCID: PMC8415328 DOI: 10.1107/s1600577521008067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 08/05/2021] [Indexed: 05/30/2023]
Abstract
Intense micro-focus X-ray beamlines available at synchrotron facilities have achieved high-quality data collection even from the microcrystals of membrane proteins. The automatic data collection system developed at SPring-8, named ZOO, has contributed to many structure determinations of membrane proteins using small-wedge synchrotron crystallography (SWSX) datasets. The `small-wedge' (5-20°) datasets are collected from multiple crystals and then merged to obtain the final structure factors. To our knowledge, no systematic investigation on the dose dependence of data accuracy has so far been reported for SWSX, which is between `serial crystallography' and `rotation crystallography'. Thus, herein, we investigated the optimal dose conditions for experimental phasing with SWSX. Phase determination using anomalous scattering signals was found to be more difficult at higher doses. Furthermore, merging more homogeneous datasets grouped by hierarchical clustering with controlled doses mildly reduced the negative factors in data collection, such as `lack of signal' and `radiation damage'. In turn, as more datasets were merged, more probable phases could be obtained across a wider range of doses. Therefore, our findings show that it is essential to choose a lower dose than 10 MGy for de novo structure determination by SWSX. In particular, data collection using a dose of 5 MGy proved to be optimal in balancing the amount of signal available while reducing the amount of damage as much as possible.
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Affiliation(s)
- Seiki Baba
- Protein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Hiroaki Matsuura
- Life Science Research Infrastructure Group, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-Cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Takashi Kawamura
- Protein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Naoki Sakai
- Life Science Research Infrastructure Group, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-Cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Yuki Nakamura
- Protein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Yoshiaki Kawano
- Life Science Research Infrastructure Group, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-Cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Nobuhiro Mizuno
- Protein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Takashi Kumasaka
- Protein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Masaki Yamamoto
- Life Science Research Infrastructure Group, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-Cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Kunio Hirata
- Life Science Research Infrastructure Group, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-Cho, Sayo-gun, Hyogo 679-5148, Japan
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10
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Abstract
The bedrock of drug discovery and a key tool for understanding cellular function and drug mechanisms of action is the structure determination of chemical compounds, peptides, and proteins. The development of new structure characterization tools, particularly those that fill critical gaps in existing methods, presents important steps forward for structural biology and drug discovery. The emergence of microcrystal electron diffraction (MicroED) expands the application of cryo-electron microscopy to include samples ranging from small molecules and membrane proteins to even large protein complexes using crystals that are one-billionth the size of those required for X-ray crystallography. This review outlines the conception, achievements, and exciting future trajectories for MicroED, an important addition to the existing biophysical toolkit.
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Affiliation(s)
- Xuelang Mu
- Howard Hughes Medical Institute, Department of Biological Chemistry, University of California, Los Angeles, California 90095, USA; .,Molecular Biology Institute, University of California, Los Angeles, California 90095, USA.,Howard Hughes Medical Institute, Department of Physiology, University of California, Los Angeles, California 90095, USA
| | - Cody Gillman
- Howard Hughes Medical Institute, Department of Biological Chemistry, University of California, Los Angeles, California 90095, USA; .,Molecular Biology Institute, University of California, Los Angeles, California 90095, USA.,Howard Hughes Medical Institute, Department of Physiology, University of California, Los Angeles, California 90095, USA
| | - Chi Nguyen
- Howard Hughes Medical Institute, Department of Biological Chemistry, University of California, Los Angeles, California 90095, USA;
| | - Tamir Gonen
- Howard Hughes Medical Institute, Department of Biological Chemistry, University of California, Los Angeles, California 90095, USA; .,Molecular Biology Institute, University of California, Los Angeles, California 90095, USA.,Howard Hughes Medical Institute, Department of Physiology, University of California, Los Angeles, California 90095, USA
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11
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Abstract
Microcrystal electron diffraction (MicroED) is a technique for structure determination that relies on the strong interaction of electrons with a minuscule, crystalline sample. While some of the electrons used to probe the crystal interact without altering the crystal, others deposit energy which changes the sample through a series of damage events. It follows that the sample cannot be observed without damaging it, and the frames obtained at the beginning of data collection reflect a crystal that differs from the one that yields the last frames of the dataset. Data acquisition at cryogenic temperatures has been found to reduce the rate of damage progression and is routinely used to increase the dose tolerance of the crystal, allowing more useful data to be obtained before the sample is destroyed. Low-dose data collection can further prolong the lifetime of the crystal, such that less damage is inflicted over the course of data acquisition. Ideally, lower doses increase the measurable volume of a single-crystal lattice by reducing the damage caused by probing electrons. However, the information that can be recovered from a diffraction image is directly related to the number of electrons used to probe the sample. The signal from a weakly exposed crystal runs the risk of being lost in the noise contributed by solvent, crystal disorder, and the electron detection process. This work focuses on obtaining the best possible data from a MicroED measurement, which requires considering several aspects such as sample, dose, and camera type.
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12
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Membrane protein crystallography in the era of modern structural biology. Biochem Soc Trans 2020; 48:2505-2524. [DOI: 10.1042/bst20200066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 02/07/2023]
Abstract
The aim of structural biology has been always the study of biological macromolecules structures and their mechanistic behaviour at molecular level. To achieve its goal, multiple biophysical methods and approaches have become part of the structural biology toolbox. Considered as one of the pillars of structural biology, X-ray crystallography has been the most successful method for solving three-dimensional protein structures at atomic level to date. It is however limited by the success in obtaining well-ordered protein crystals that diffract at high resolution. This is especially true for challenging targets such as membrane proteins (MPs). Understanding structure-function relationships of MPs at the biochemical level is vital for medicine and drug discovery as they play critical roles in many cellular processes. Though difficult, structure determination of MPs by X-ray crystallography has significantly improved in the last two decades, mainly due to many relevant technological and methodological developments. Today, numerous MP crystal structures have been solved, revealing many of their mechanisms of action. Yet the field of structural biology has also been through significant technological breakthroughs in recent years, particularly in the fields of single particle electron microscopy (cryo-EM) and X-ray free electron lasers (XFELs). Here we summarise the most important advancements in the field of MP crystallography and the significance of these developments in the present era of modern structural biology.
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13
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Nguyen C, Gonen T. Beyond protein structure determination with MicroED. Curr Opin Struct Biol 2020; 64:51-58. [PMID: 32610218 PMCID: PMC7321661 DOI: 10.1016/j.sbi.2020.05.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/22/2020] [Accepted: 05/22/2020] [Indexed: 12/14/2022]
Abstract
Microcrystal electron diffraction (MicroED) was first coined and developed in 2013 at the Janelia Research Campus as a new modality in electron cryomicroscopy (cryoEM). Since then, MicroED has not only made important contributions in pushing the resolution limits of cryoEM protein structure characterization but also of peptides, small-organic and inorganic molecules, and natural-products that have resisted structure determination by other methods. This review showcases important recent developments in MicroED, highlighting the importance of the technique in fields of studies beyond protein structure determination where MicroED is beginning to have paradigm shifting roles.
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Affiliation(s)
- Chi Nguyen
- Department of Biological Chemistry, University of California Los Angeles, 615 Charles E Young Drive South, Los Angeles, CA90095, United States
| | - Tamir Gonen
- Department of Biological Chemistry, University of California Los Angeles, 615 Charles E Young Drive South, Los Angeles, CA90095, United States; Department of Physiology, University of California Los Angeles, 615 Charles E Young Drive South, Los Angeles, CA90095, United States; Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA90095, United States.
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14
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Bhattacharyya R, Dhar J, Ghosh Dastidar S, Chakrabarti P, Weiss MS. The susceptibility of disulfide bonds towards radiation damage may be explained by S⋯O interactions. IUCRJ 2020; 7:825-834. [PMID: 32939274 PMCID: PMC7467163 DOI: 10.1107/s2052252520008520] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 06/25/2020] [Indexed: 05/30/2023]
Abstract
Radiation-induced damage to protein crystals during X-ray diffraction data collection is a major impediment to obtaining accurate structural information on macromolecules. Some of the specific impairments that are inflicted upon highly brilliant X-ray irradiation are metal-ion reduction, disulfide-bond cleavage and a loss of the integrity of the carboxyl groups of acidic residues. With respect to disulfide-bond reduction, previous results have indicated that not all disulfide bridges are equally susceptible to damage. A careful analysis of the chemical environment of disulfide bonds in the structures of elastase, lysozyme, acetylcholinesterase and other proteins suggests that S-S bonds which engage in a close contact with a carbonyl O atom along the extension of the S-S bond vector are more susceptible to reduction than the others. Such an arrangement predisposes electron transfer to occur from the O atom to the disulfide bond, leading to its reduction. The interaction between a nucleophile and an electrophile, akin to hydrogen bonding, stabilizes protein structures, but it also provides a pathway of electron transfer to the S-S bond, leading to its reduction during exposure of the protein crystal to an intense X-ray beam. An otherwise stabilizing interaction can thus be the cause of destabilization under the condition of radiation exposure.
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Affiliation(s)
- Rajasri Bhattacharyya
- Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700 054, India
| | - Jesmita Dhar
- Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700 054, India
| | - Shubhra Ghosh Dastidar
- Division of Bioinformatics, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700 054, India
| | - Pinak Chakrabarti
- Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700 054, India
| | - Manfred S. Weiss
- Macromolecular Crystallography (HZB-MX), Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, D-12489 Berlin, Germany
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15
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Atakisi H, Conger L, Moreau DW, Thorne RE. Resolution and dose dependence of radiation damage in biomolecular systems. IUCRJ 2019; 6:1040-1053. [PMID: 31709060 PMCID: PMC6830208 DOI: 10.1107/s2052252519008777] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 06/19/2019] [Indexed: 05/30/2023]
Abstract
The local Fourier-space relation between diffracted intensity I, diffraction wavevector q and dose D, , is key to probing and understanding radiation damage by X-rays and energetic particles in both diffraction and imaging experiments. The models used in protein crystallography for the last 50 years provide good fits to experimental I(q) versus nominal dose data, but have unclear physical significance. More recently, a fit to diffraction and imaging experiments suggested that the maximum tolerable dose varies as q -1 or linearly with resolution. Here, it is shown that crystallographic data have been strongly perturbed by the effects of spatially nonuniform crystal irradiation and diffraction during data collection. Reanalysis shows that these data are consistent with a purely exponential local dose dependence, = I 0(q)exp[-D/D e(q)], where D e(q) ∝ q α with α ≃ 1.7. A physics-based model for radiation damage, in which damage events occurring at random locations within a sample each cause energy deposition and blurring of the electron density within a small volume, predicts this exponential variation with dose for all q values and a decay exponent α ≃ 2 in two and three dimensions, roughly consistent with both diffraction and imaging experiments over more than two orders of magnitude in resolution. The B-factor model used to account for radiation damage in crystallographic scaling programs is consistent with α = 2, but may not accurately capture the dose dependencies of structure factors under typical nonuniform illumination conditions. The strong q dependence of radiation-induced diffraction decays implies that the previously proposed 20-30 MGy dose limit for protein crystallography should be replaced by a resolution-dependent dose limit that, for atomic resolution data sets, will be much smaller. The results suggest that the physics underlying basic experimental trends in radiation damage at T ≃ 100 K is straightforward and universal. Deviations of the local I(q, D) from strictly exponential behavior may provide mechanistic insights, especially into the radiation-damage processes responsible for the greatly increased radiation sensitivity observed at T ≃ 300 K.
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Affiliation(s)
- Hakan Atakisi
- Physics Department, Cornell University, Ithaca, NY 14853, USA
| | | | - David W. Moreau
- Physics Department, Cornell University, Ithaca, NY 14853, USA
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16
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Taberman H, Bury CS, van der Woerd MJ, Snell EH, Garman EF. Structural knowledge or X-ray damage? A case study on xylose isomerase illustrating both. JOURNAL OF SYNCHROTRON RADIATION 2019; 26:931-944. [PMID: 31274415 PMCID: PMC6613113 DOI: 10.1107/s1600577519005599] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Accepted: 04/23/2019] [Indexed: 05/29/2023]
Abstract
Xylose isomerase (XI) is an industrially important metalloprotein studied for decades. Its reaction mechanism has been postulated to involve movement of the catalytic metal cofactor to several different conformations. Here, a dose-dependent approach was used to investigate the radiation damage effects on XI and their potential influence on the reaction mechanism interpreted from the X-ray derived structures. Radiation damage is still one of the major challenges for X-ray diffraction experiments and causes both global and site-specific damage. In this study, consecutive high-resolution data sets from a single XI crystal from the same wedge were collected at 100 K and the progression of radiation damage was tracked over increasing dose (0.13-3.88 MGy). The catalytic metal and its surrounding amino acid environment experience a build-up of free radicals, and the results show radiation-damage-induced structural perturbations ranging from an absolute metal positional shift to specific residue motions in the active site. The apparent metal movement is an artefact of global damage and the resulting unit-cell expansion, but residue motion appears to be driven by the dose. Understanding and identifying radiation-induced damage is an important factor in accurately interpreting the biological conclusions being drawn.
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Affiliation(s)
- Helena Taberman
- Macromolecular Crystallography (HZB-MX), Helmholtz-Zentrum Berlin, Albert-Einstein Straße 15, 12489 Berlin, Germany
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Charles S. Bury
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Mark J. van der Woerd
- Department of Enterprise Technology Services, 2001 Capitol Avenue, Cheyenne, WY 82001, USA
| | - Edward H. Snell
- Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
- Materials Design and Innovation, State University of New York at Buffalo, 700 Ellicott Street, Buffalo, NY 14203, USA
| | - Elspeth F. Garman
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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17
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Bugris V, Harmat V, Ferenc G, Brockhauser S, Carmichael I, Garman EF. Radiation-damage investigation of a DNA 16-mer. JOURNAL OF SYNCHROTRON RADIATION 2019; 26:998-1009. [PMID: 31274421 DOI: 10.1107/s160057751900763x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 05/25/2019] [Indexed: 06/09/2023]
Abstract
In macromolecular crystallography, a great deal of effort has been invested in understanding radiation-damage progression. While the sensitivity of protein crystals has been well characterized, crystals of DNA and of DNA-protein complexes have not thus far been studied as thoroughly. Here, a systematic investigation of radiation damage to a crystal of a DNA 16-mer diffracting to 1.8 Å resolution and held at 100 K, up to an absorbed dose of 45 MGy, is reported. The RIDL (Radiation-Induced Density Loss) automated computational tool was used for electron-density analysis. Both the global and specific damage to the DNA crystal as a function of dose were monitored, following careful calibration of the X-ray flux and beam profile. The DNA crystal was found to be fairly radiation insensitive to both global and specific damage, with half of the initial diffraction intensity being lost at an absorbed average diffraction-weighted dose, D1/2, of 19 MGy, compared with 9 MGy for chicken egg-white lysozyme crystals under the same beam conditions but at the higher resolution of 1.4 Å. The coefficient of sensitivity of the DNA crystal was 0.014 Å2 MGy-1, which is similar to that observed for proteins. These results imply that the significantly greater radiation hardness of DNA and RNA compared with protein observed in a DNA-protein complex and an RNA-protein complex could be due to scavenging action by the protein, thereby protecting the DNA and RNA in these studies. In terms of specific damage, the regions of DNA that were found to be sensitive were those associated with some of the bound calcium ions sequestered from the crystallization buffer. In contrast, moieties farther from these sites showed only small changes even at higher doses.
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Affiliation(s)
- Valéria Bugris
- X-ray Crystallography Laboratory, Biological Research Centre, HAC-BRC, Temesvári krt. 62, Szeged 6726, Hungary
| | - Veronika Harmat
- X-ray Crystallography Laboratory, Biological Research Centre, HAC-BRC, Temesvári krt. 62, Szeged 6726, Hungary
| | - Györgyi Ferenc
- Nucleic Acid Synthesis Laboratory, Biological Research Centre, HAC-BRC, Temesvári krt. 62, Szeged 6726, Hungary
| | - Sándor Brockhauser
- X-ray Crystallography Laboratory, Biological Research Centre, HAC-BRC, Temesvári krt. 62, Szeged 6726, Hungary
| | - Ian Carmichael
- Notre Dame Radiation Laboratory, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Elspeth F Garman
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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18
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Berejnov V, Rubinstein B, Melo LGA, Hitchcock AP. First-principles X-ray absorption dose calculation for time-dependent mass and optical density. JOURNAL OF SYNCHROTRON RADIATION 2018; 25:833-847. [PMID: 29714195 DOI: 10.1107/s1600577518002655] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 02/13/2018] [Indexed: 06/08/2023]
Abstract
A dose integral of time-dependent X-ray absorption under conditions of variable photon energy and changing sample mass is derived from first principles starting with the Beer-Lambert (BL) absorption model. For a given photon energy the BL dose integral D(e, t) reduces to the product of an effective time integral T(t) and a dose rate R(e). Two approximations of the time-dependent optical density, i.e. exponential A(t) = c + aexp(-bt) for first-order kinetics and hyperbolic A(t) = c + a/(b + t) for second-order kinetics, were considered for BL dose evaluation. For both models three methods of evaluating the effective time integral are considered: analytical integration, approximation by a function, and calculation of the asymptotic behaviour at large times. Data for poly(methyl methacrylate) and perfluorosulfonic acid polymers measured by scanning transmission soft X-ray microscopy were used to test the BL dose calculation. It was found that a previous method to calculate time-dependent dose underestimates the dose in mass loss situations, depending on the applied exposure time. All these methods here show that the BL dose is proportional to the exposure time D(e, t) ≃ K(e)t.
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Affiliation(s)
- Viatcheslav Berejnov
- Automotive Fuel Cell Cooperation Corporation, 9000 Glenlyon Parkway, Burnaby, BC, Canada V5J 5J8
| | - Boris Rubinstein
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
| | - Lis G A Melo
- Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON, Canada L8S 4M1
| | - Adam P Hitchcock
- Brockhouse Institute for Materials Research, McMaster University, 1280 Main Street West, Hamilton, ON, Canada L8S 4M1
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19
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Hattne J, Shi D, Glynn C, Zee CT, Gallagher-Jones M, Martynowycz MW, Rodriguez JA, Gonen T. Analysis of Global and Site-Specific Radiation Damage in Cryo-EM. Structure 2018; 26:759-766.e4. [PMID: 29706530 DOI: 10.1016/j.str.2018.03.021] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 02/01/2018] [Accepted: 03/30/2018] [Indexed: 11/20/2022]
Abstract
Micro-crystal electron diffraction (MicroED) combines the efficiency of electron scattering with diffraction to allow structure determination from nano-sized crystalline samples in cryoelectron microscopy (cryo-EM). It has been used to solve structures of a diverse set of biomolecules and materials, in some cases to sub-atomic resolution. However, little is known about the damaging effects of the electron beam on samples during such measurements. We assess global and site-specific damage from electron radiation on nanocrystals of proteinase K and of a prion hepta-peptide and find that the dynamics of electron-induced damage follow well-established trends observed in X-ray crystallography. Metal ions are perturbed, disulfide bonds are broken, and acidic side chains are decarboxylated while the diffracted intensities decay exponentially with increasing exposure. A better understanding of radiation damage in MicroED improves our assessment and processing of all types of cryo-EM data.
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Affiliation(s)
- Johan Hattne
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles CA 90095, USA; Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Dan Shi
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Calina Glynn
- Department of Chemistry and Biochemistry, UCLA-DOE Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Chih-Te Zee
- Department of Chemistry and Biochemistry, UCLA-DOE Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Marcus Gallagher-Jones
- Department of Chemistry and Biochemistry, UCLA-DOE Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Michael W Martynowycz
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles CA 90095, USA; Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Jose A Rodriguez
- Department of Chemistry and Biochemistry, UCLA-DOE Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Tamir Gonen
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles CA 90095, USA; Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA; Departments of Physiology and Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles CA 90095, USA.
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20
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Abstract
Radiation damage still remains a major limitation and challenge in macromolecular X-ray crystallography. Some of the high-intensity radiation used for diffraction data collection experiments is absorbed by the crystals, generating free radicals. These give rise to radiation damage even at cryotemperatures (~100 K), which can lead to incorrect biological conclusions being drawn from the resulting structure, or even prevent structure solution entirely. Investigation of mitigation strategies and the effects caused by radiation damage has been extensive over the past fifteen years. Here, recent understanding of the physical and chemical phenomena of radiation damage is described, along with the global effects inflicted on the collected data and the specific effects observed in the solved structure. Furthermore, this review aims to summarise the progress made in radiation damage studies in macromolecular crystallography from the experimentalist’s point of view and to give an introduction to the current literature.
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21
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Borek D, Bromberg R, Hattne J, Otwinowski Z. Real-space analysis of radiation-induced specific changes with independent component analysis. JOURNAL OF SYNCHROTRON RADIATION 2018; 25:451-467. [PMID: 29488925 PMCID: PMC5829680 DOI: 10.1107/s1600577517018148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 12/19/2017] [Indexed: 05/06/2023]
Abstract
A method of analysis is presented that allows for the separation of specific radiation-induced changes into distinct components in real space. The method relies on independent component analysis (ICA) and can be effectively applied to electron density maps and other types of maps, provided that they can be represented as sets of numbers on a grid. Here, for glucose isomerase crystals, ICA was used in a proof-of-concept analysis to separate temperature-dependent and temperature-independent components of specific radiation-induced changes for data sets acquired from multiple crystals across multiple temperatures. ICA identified two components, with the temperature-independent component being responsible for the majority of specific radiation-induced changes at temperatures below 130 K. The patterns of specific temperature-independent radiation-induced changes suggest a contribution from the tunnelling of electron holes as a possible explanation. In the second case, where a group of 22 data sets was collected on a single thaumatin crystal, ICA was used in another type of analysis to separate specific radiation-induced effects happening on different exposure-level scales. Here, ICA identified two components of specific radiation-induced changes that likely result from radiation-induced chemical reactions progressing with different rates at different locations in the structure. In addition, ICA unexpectedly identified the radiation-damage state corresponding to reduced disulfide bridges rather than the zero-dose extrapolated state as the highest contrast structure. The application of ICA to the analysis of specific radiation-induced changes in real space and the data pre-processing for ICA that relies on singular value decomposition, which was used previously in data space to validate a two-component physical model of X-ray radiation-induced changes, are discussed in detail. This work lays a foundation for a better understanding of protein-specific radiation chemistries and provides a framework for analysing effects of specific radiation damage in crystallographic and cryo-EM experiments.
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Affiliation(s)
- Dominika Borek
- Department of Biophysics, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Raquel Bromberg
- Department of Biophysics, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Johan Hattne
- Department of Biophysics, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Zbyszek Otwinowski
- Department of Biophysics, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
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22
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Bury CS, Brooks-Bartlett JC, Walsh SP, Garman EF. Estimate your dose: RADDOSE-3D. Protein Sci 2017; 27:217-228. [PMID: 28921782 DOI: 10.1002/pro.3302] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 09/10/2017] [Accepted: 09/11/2017] [Indexed: 12/22/2022]
Abstract
We present the current status of RADDOSE-3D, a software tool allowing the estimation of the dose absorbed in a macromolecular crystallography diffraction experiment. The code allows a temporal and spatial dose contour map to be calculated for a crystal of any geometry and size as it is rotated in an X-ray beam, and gives several summary dose values: among them diffraction weighted dose. This allows experimenters to plan data collections which will minimize radiation damage effects by spreading the absorbed dose more homogeneously, and thus to optimize the use of their crystals. It also allows quantitative comparisons between different radiation damage studies, giving a universal "x-axis" against which to plot various metrics.
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Affiliation(s)
- Charles S Bury
- Department of Biochemistry, South Parks Road, Oxford, OX1 3QU, United Kingdom
| | | | - Steven P Walsh
- Department of Biochemistry, South Parks Road, Oxford, OX1 3QU, United Kingdom
| | - Elspeth F Garman
- Department of Biochemistry, South Parks Road, Oxford, OX1 3QU, United Kingdom
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23
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Yamamoto M, Hirata K, Yamashita K, Hasegawa K, Ueno G, Ago H, Kumasaka T. Protein microcrystallography using synchrotron radiation. IUCRJ 2017; 4:529-539. [PMID: 28989710 PMCID: PMC5619846 DOI: 10.1107/s2052252517008193] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 06/02/2017] [Indexed: 05/21/2023]
Abstract
The progress in X-ray microbeam applications using synchrotron radiation is beneficial to structure determination from macromolecular microcrystals such as small in meso crystals. However, the high intensity of microbeams causes severe radiation damage, which worsens both the statistical quality of diffraction data and their resolution, and in the worst cases results in the failure of structure determination. Even in the event of successful structure determination, site-specific damage can lead to the misinterpretation of structural features. In order to overcome this issue, technological developments in sample handling and delivery, data-collection strategy and data processing have been made. For a few crystals with dimensions of the order of 10 µm, an elegant two-step scanning strategy works well. For smaller samples, the development of a novel method to analyze multiple isomorphous microcrystals was motivated by the success of serial femtosecond crystallography with X-ray free-electron lasers. This method overcame the radiation-dose limit in diffraction data collection by using a sufficient number of crystals. Here, important technologies and the future prospects for microcrystallography are discussed.
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Affiliation(s)
- Masaki Yamamoto
- Advanced Photon Technology Division, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Kunio Hirata
- Advanced Photon Technology Division, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Keitaro Yamashita
- Advanced Photon Technology Division, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Kazuya Hasegawa
- Advanced Photon Technology Division, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Protein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Go Ueno
- Advanced Photon Technology Division, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Hideo Ago
- Advanced Photon Technology Division, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Takashi Kumasaka
- Advanced Photon Technology Division, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Protein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
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24
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Abstract
Radiation damage inflicted on macromolecular crystals during X-ray diffraction experiments remains a limiting factor for structure solution, even when samples are cooled to cryotemperatures (~100 K). Efforts to establish mitigation strategies are ongoing and various approaches, summarized below, have been investigated over the last 15 years, resulting in a deeper understanding of the physical and chemical factors affecting damage rates. The recent advent of X-ray free electron lasers permits "diffraction-before-destruction" by providing highly brilliant and short (a few tens of fs) X-ray pulses. New fourth generation synchrotron sources now coming on line with higher X-ray flux densities than those available from third generation synchrotrons will bring the issue of radiation damage once more to the fore for structural biologists.
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Affiliation(s)
- Elspeth F Garman
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
| | - Martin Weik
- Institut de Biologie Structurale, University of Grenoble Alpes, CEA, CNRS, 71 Avenue des Martyrs, 38044, Grenoble, France.
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25
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Crosas E, Castellvi A, Crespo I, Fulla D, Gil-Ortiz F, Fuertes G, Kamma-Lorger CS, Malfois M, Aranda MAG, Juanhuix J. Uridine as a new scavenger for synchrotron-based structural biology techniques. JOURNAL OF SYNCHROTRON RADIATION 2017; 24:53-62. [PMID: 28009546 DOI: 10.1107/s1600577516018452] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 11/17/2016] [Indexed: 06/06/2023]
Abstract
Macromolecular crystallography (MX) and small-angle X-ray scattering (SAXS) studies on proteins at synchrotron light sources are commonly limited by the structural damage produced by the intense X-ray beam. Several effects, such as aggregation in protein solutions and global and site-specific damage in crystals, reduce the data quality or even introduce artefacts that can result in a biologically misguiding structure. One strategy to reduce these negative effects is the inclusion of an additive in the buffer solution to act as a free radical scavenger. Here the properties of uridine as a scavenger for both SAXS and MX experiments on lysozyme at room temperature are examined. In MX experiments, upon addition of uridine at 1 M, the critical dose D1/2 is increased by a factor of ∼1.7, a value similar to that obtained in the presence of the most commonly used scavengers such as ascorbate and sodium nitrate. Other figures of merit to assess radiation damage show a similar trend. In SAXS experiments, the scavenging effect of 40 mM uridine is similar to that of 5% v/v glycerol, and greater than 2 mM DTT and 1 mM ascorbic acid. In all cases, the protective effect of uridine is proportional to its concentration.
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Affiliation(s)
- Eva Crosas
- ALBA Synchrotron, Carrer de la llum 2-26, 08290 Cerdanyola del Vallès, Barcelona, Spain
| | - Albert Castellvi
- ALBA Synchrotron, Carrer de la llum 2-26, 08290 Cerdanyola del Vallès, Barcelona, Spain
| | - Isidro Crespo
- ALBA Synchrotron, Carrer de la llum 2-26, 08290 Cerdanyola del Vallès, Barcelona, Spain
| | - Daniel Fulla
- ALBA Synchrotron, Carrer de la llum 2-26, 08290 Cerdanyola del Vallès, Barcelona, Spain
| | - Fernando Gil-Ortiz
- ALBA Synchrotron, Carrer de la llum 2-26, 08290 Cerdanyola del Vallès, Barcelona, Spain
| | | | | | - Marc Malfois
- ALBA Synchrotron, Carrer de la llum 2-26, 08290 Cerdanyola del Vallès, Barcelona, Spain
| | - Miguel A G Aranda
- ALBA Synchrotron, Carrer de la llum 2-26, 08290 Cerdanyola del Vallès, Barcelona, Spain
| | - Jordi Juanhuix
- ALBA Synchrotron, Carrer de la llum 2-26, 08290 Cerdanyola del Vallès, Barcelona, Spain
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26
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Hirata K, Foadi J, Evans G, Hasegawa K, Zeldin OB. Structural Biology with Microfocus Beamlines. ACTA ACUST UNITED AC 2016. [DOI: 10.1007/978-4-431-56030-2_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
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27
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Hopkins JB, Thorne RE. Quantifying radiation damage in biomolecular small-angle X-ray scattering. J Appl Crystallogr 2016; 49:880-890. [PMID: 27275138 PMCID: PMC4886981 DOI: 10.1107/s1600576716005136] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 03/25/2016] [Indexed: 11/10/2022] Open
Abstract
Small-angle X-ray scattering (SAXS) is an increasingly popular technique that provides low-resolution structural information about biological macromolecules in solution. Many of the practical limitations of the technique, such as minimum required sample volume, and of experimental design, such as sample flow cells, are necessary because the biological samples are sensitive to damage from the X-rays. Radiation damage typically manifests as aggregation of the sample, which makes the collected data unreliable. However, there has been little systematic investigation of the most effective methods to reduce damage rates, and results from previous damage studies are not easily compared with results from other beamlines. Here a methodology is provided for quantifying radiation damage in SAXS to provide consistent results between different experiments, experimenters and beamlines. These methods are demonstrated on radiation damage data collected from lysozyme, glucose isomerase and xylanase, and it is found that no single metric is sufficient to describe radiation damage in SAXS for all samples. The radius of gyration, molecular weight and integrated SAXS profile intensity constitute a minimal set of parameters that capture all types of observed behavior. Radiation sensitivities derived from these parameters show a large protein dependence, varying by up to six orders of magnitude between the different proteins tested. This work should enable consistent reporting of radiation damage effects, allowing more systematic studies of the most effective minimization strategies.
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Affiliation(s)
| | - Robert E. Thorne
- Department of Physics, Cornell University, Ithaca, NY 14853, USA
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Shen C, Julius EF, Tyree TJ, Moreau DW, Atakisi H, Thorne RE. Thermal contraction of aqueous glycerol and ethylene glycol solutions for optimized protein-crystal cryoprotection. Acta Crystallogr D Struct Biol 2016; 72:742-52. [PMID: 27303794 PMCID: PMC8493611 DOI: 10.1107/s2059798316005490] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 04/01/2016] [Indexed: 11/10/2022] Open
Abstract
The thermal contraction of aqueous cryoprotectant solutions on cooling to cryogenic temperatures is of practical importance in protein cryocrystallography and in biological cryopreservation. In the former case, differential contraction on cooling of protein molecules and their lattice relative to that of the internal and surrounding solvent may lead to crystal damage and the degradation of crystal diffraction properties. Here, the amorphous phase densities of aqueous solutions of glycerol and ethylene glycol at T = 77 K have been determined. Densities with accuracies of <0.5% to concentrations as low as 30%(w/v) were determined by rapidly cooling drops with volumes as small as 70 pl, assessing their optical clarity and measuring their buoyancy in liquid nitrogen-argon solutions. The use of these densities in contraction matching of internal solvent to the available solvent spaces is complicated by several factors, most notably the exclusion of cryoprotectants from protein hydration shells and the expected deviation of the contraction behavior of hydration water from bulk water. The present methods and results will assist in developing rational approaches to cryoprotection and an understanding of solvent behavior in protein crystals.
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Affiliation(s)
- Chen Shen
- Cornell University, Ithaca, NY 14853, USA
| | | | | | - David W. Moreau
- Physics Department, Cornell University, Ithaca, NY 14853, USA
| | - Hakan Atakisi
- Physics Department, Cornell University, Ithaca, NY 14853, USA
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Roedig P, Duman R, Sanchez-Weatherby J, Vartiainen I, Burkhardt A, Warmer M, David C, Wagner A, Meents A. Room-temperature macromolecular crystallography using a micro-patterned silicon chip with minimal background scattering. J Appl Crystallogr 2016; 49:968-975. [PMID: 27275143 PMCID: PMC4886986 DOI: 10.1107/s1600576716006348] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 04/14/2016] [Indexed: 11/25/2022] Open
Abstract
Recent success at X-ray free-electron lasers has led to serial crystallography experiments staging a comeback at synchrotron sources as well. With crystal lifetimes typically in the millisecond range and the latest-generation detector technologies with high framing rates up to 1 kHz, fast sample exchange has become the bottleneck for such experiments. A micro-patterned chip has been developed from single-crystalline silicon, which acts as a sample holder for up to several thousand microcrystals at a very low background level. The crystals can be easily loaded onto the chip and excess mother liquor can be efficiently removed. Dehydration of the crystals is prevented by keeping them in a stream of humidified air during data collection. Further sealing of the sample holder, for example with Kapton, is not required. Room-temperature data collection from insulin crystals loaded onto the chip proves the applicability of the chip for macromolecular crystallography. Subsequent structure refinements reveal no radiation-damage-induced structural changes for insulin crystals up to a dose of 565.6 kGy, even though the total diffraction power of the crystals has on average decreased to 19.1% of its initial value for the same dose. A decay of the diffracting power by half is observed for a dose of D1/2 = 147.5 ± 19.1 kGy, which is about 1/300 of the dose before crystals show a similar decay at cryogenic temperatures.
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Affiliation(s)
- Philip Roedig
- Deutsches Elektronen-Synchrotron DESY, Photon Science, Notkestrasse 85, Hamburg 22607, Germany
| | - Ramona Duman
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Juan Sanchez-Weatherby
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | | | - Anja Burkhardt
- Deutsches Elektronen-Synchrotron DESY, Photon Science, Notkestrasse 85, Hamburg 22607, Germany
| | - Martin Warmer
- Deutsches Elektronen-Synchrotron DESY, Photon Science, Notkestrasse 85, Hamburg 22607, Germany
| | | | - Armin Wagner
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Alke Meents
- Deutsches Elektronen-Synchrotron DESY, Photon Science, Notkestrasse 85, Hamburg 22607, Germany
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30
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Alkire RW, Rotella FJ, Duke NEC, Otwinowski Z, Borek D. Taking a look at the calibration of a CCD detector with a fiber-optic taper. J Appl Crystallogr 2016; 49:415-425. [PMID: 27047303 DOI: 10.1107/s1600576716000431] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 01/08/2016] [Indexed: 11/11/2022] Open
Abstract
At the Structural Biology Center beamline 19BM, located at the Advanced Photon Source, the operational characteristics of the equipment are routinely checked to ensure they are in proper working order. After performing a partial flat-field calibration for the ADSC Quantum 210r CCD detector, it was confirmed that the detector operates within specifications. However, as a secondary check it was decided to scan a single reflection across one-half of a detector module to validate the accuracy of the calibration. The intensities from this single reflection varied by more than 30% from the module center to the corner of the module. Redistribution of light within bent fibers of the fiber-optic taper was identified to be a source of this variation. The degree to which the diffraction intensities are corrected to account for characteristics of the fiber-optic tapers depends primarily upon the experimental strategy of data collection, approximations made by the data processing software during scaling, and crystal symmetry.
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Affiliation(s)
- R W Alkire
- Biosciences Division, Argonne National Laboratory , 9700 S. Cass Avenue, Argonne, Illinois 60439, USA
| | - F J Rotella
- Biosciences Division, Argonne National Laboratory , 9700 S. Cass Avenue, Argonne, Illinois 60439, USA
| | - N E C Duke
- Biosciences Division, Argonne National Laboratory , 9700 S. Cass Avenue, Argonne, Illinois 60439, USA
| | - Zbyszek Otwinowski
- Department of Biophysics, University of Texas Southwestern Medical Center , 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Dominika Borek
- Department of Biophysics, University of Texas Southwestern Medical Center , 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
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Trofimov AA, Polyakov KM, Lazarenko VA, Popov AN, Tikhonova TV, Tikhonov AV, Popov VO. Structural study of the X-ray-induced enzymatic reaction of octahaem cytochromecnitrite reductase. ACTA ACUST UNITED AC 2015; 71:1087-94. [DOI: 10.1107/s1399004715003053] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 02/12/2015] [Indexed: 11/10/2022]
Abstract
Octahaem cytochromecnitrite reductase from the bacteriumThioalkalivibrio nitratireducenscatalyzes the reduction of nitrite to ammonium and of sulfite to sulfide. The reducing properties of X-ray radiation and the high quality of the enzyme crystals allow study of the catalytic reaction of cytochromecnitrite reductase directly in a crystal of the enzyme, with the reaction being induced by X-rays. Series of diffraction data sets with increasing absorbed dose were collected from crystals of the free form of the enzyme and its complexes with nitrite and sulfite. The corresponding structures revealed gradual changes associated with the reduction of the catalytic haems by X-rays. In the case of the nitrite complex the conversion of the nitrite ions bound in the active sites to NO species was observed, which is the beginning of the catalytic reaction. For the free form, an increase in the distance between the oxygen ligand bound to the catalytic haem and the iron ion of the haem took place. In the case of the sulfite complex no enzymatic reaction was detected, but there were changes in the arrangement of the active-site water molecules that were presumably associated with a change in the protonation state of the sulfite ions.
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32
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Liebschner D, Rosenbaum G, Dauter M, Dauter Z. Radiation decay of thaumatin crystals at three X-ray energies. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:772-8. [PMID: 25849388 PMCID: PMC4388262 DOI: 10.1107/s1399004715001030] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 01/17/2015] [Indexed: 11/10/2022]
Abstract
Radiation damage is an unavoidable obstacle in X-ray crystallographic data collection for macromolecular structure determination, so it is important to know how much radiation a sample can endure before being degraded beyond an acceptable limit. In the literature, the threshold at which the average intensity of all recorded reflections decreases to a certain fraction of the initial value is called the `dose limit'. The first estimated D50 dose-limit value, at which the average diffracted intensity was reduced to 50%, was 20 MGy and was derived from observing sample decay in electron-diffraction experiments. A later X-ray study carried out at 100 K on ferritin protein crystals arrived at a D50 of 43 MGy, and recommended an intensity reduction of protein reflections to 70%, D70, corresponding to an absorbed dose of 30 MGy, as a more appropriate limit for macromolecular crystallography. In the macromolecular crystallography community, the rate of intensity decay with dose was then assumed to be similar for all protein crystals. A series of diffraction images of cryocooled (100 K) thaumatin crystals at identical small, 2° rotation intervals were recorded at X-ray energies of 6.33 , 12.66 and 19.00 keV. Five crystals were used for each wavelength. The decay in the average diffraction intensity to 70% of the initial value, for data extending to 2.45 Å resolution, was determined to be about 7.5 MGy at 6.33 keV and about 11 MGy at the two higher energies.
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Affiliation(s)
- Dorothee Liebschner
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, Tsukuba, Japan
| | - Gerold Rosenbaum
- Department of Biochemistry, University of Georgia and Structural Biology Center, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Miroslawa Dauter
- Leidos Biomedical Research Inc., Basic Science Program, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Zbigniew Dauter
- Synchrotron Radiation Research Section, MCL, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA
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Gerstel M, Deane CM, Garman EF. Identifying and quantifying radiation damage at the atomic level. JOURNAL OF SYNCHROTRON RADIATION 2015; 22:201-12. [PMID: 25723922 PMCID: PMC4344357 DOI: 10.1107/s1600577515002131] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 02/01/2015] [Indexed: 05/23/2023]
Abstract
Radiation damage impedes macromolecular diffraction experiments. Alongside the well known effects of global radiation damage, site-specific radiation damage affects data quality and the veracity of biological conclusions on protein mechanism and function. Site-specific radiation damage follows a relatively predetermined pattern, in that different structural motifs are affected at different dose regimes: in metal-free proteins, disulfide bonds tend to break first followed by the decarboxylation of aspartic and glutamic acids. Even within these damage motifs the decay does not progress uniformly at equal rates. Within the same protein, radiation-induced electron density decay of a particular chemical group is faster than for the same group elsewhere in the protein: an effect known as preferential specific damage. Here, BDamage, a new atomic metric, is defined and validated to recognize protein regions susceptible to specific damage and to quantify the damage at these sites. By applying BDamage to a large set of known protein structures in a statistical survey, correlations between the rates of damage and various physicochemical parameters were identified. Results indicate that specific radiation damage is independent of secondary protein structure. Different disulfide bond groups (spiral, hook, and staple) show dissimilar radiation damage susceptibility. There is a consistent positive correlation between specific damage and solvent accessibility.
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Affiliation(s)
- Markus Gerstel
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Charlotte M. Deane
- Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
| | - Elspeth F. Garman
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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Warkentin M, Hopkins JB, Haber JB, Blaha G, Thorne RE. Temperature-dependent radiation sensitivity and order of 70S ribosome crystals. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:2890-6. [PMID: 25372680 PMCID: PMC4220972 DOI: 10.1107/s1399004714017672] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 08/01/2014] [Indexed: 11/10/2022]
Abstract
All evidence to date indicates that at T = 100 K all protein crystals exhibit comparable sensitivity to X-ray damage when quantified using global metrics such as change in scaling B factor or integrated intensity versus dose. This is consistent with observations in cryo-electron microscopy, and results because nearly all diffusive motions of protein and solvent, including motions induced by radiation damage, are frozen out. But how do the sensitivities of different proteins compare at room temperature, where radiation-induced radicals are free to diffuse and protein and lattice structures are free to relax in response to local damage? It might be expected that a large complex with extensive conformational degrees of freedom would be more radiation sensitive than a small, compact globular protein. As a test case, the radiation sensitivity of 70S ribosome crystals has been examined. At T = 100 and 300 K, the half doses are 64 MGy (at 3 Å resolution) and 150 kGy (at 5 Å resolution), respectively. The maximum tolerable dose in a crystallography experiment depends upon the initial or desired resolution. When differences in initial data-set resolution are accounted for, the former half dose is roughly consistent with that for model proteins, and the 100/300 K half-dose ratio is roughly a factor of ten larger. 70S ribosome crystals exhibit substantially increased resolution at 100 K relative to 300 K owing to cooling-induced ordering and not to reduced radiation sensitivity and slower radiation damage.
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Affiliation(s)
| | | | - Jonah B. Haber
- Physics Department, Cornell University, Ithaca, NY 14853, USA
| | - Gregor Blaha
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
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35
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Farley C, Juers DH. Efficient cryoprotection of macromolecular crystals using vapor diffusion of volatile alcohols. J Struct Biol 2014; 188:102-6. [PMID: 25286441 DOI: 10.1016/j.jsb.2014.09.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 09/14/2014] [Accepted: 09/25/2014] [Indexed: 10/24/2022]
Abstract
Macromolecular X-ray crystallography, usually done at cryogenic temperature to limit radiation damage, often requires liquid cryoprotective soaking that can be labor intensive and damaging to crystals. Here we describe a method for cryoprotection that uses vapor diffusion of volatile cryoprotective agents into loop-mounted crystals. The crystal is mounted into a vial containing a small volume of an alcohol-based cryosolution. After a short incubation with the looped crystal sitting in the cryosolution vapor, the crystal is transferred directly from the vial into the cooling medium. Effective for several different protein crystals, the approach obviates the need for liquid soaking and opens up a heretofore underutilized class of cryoprotective agents for macromolecular crystallography.
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Affiliation(s)
- Christopher Farley
- Department of Physics, Whitman College, Walla Walla, WA 99362, United States
| | - Douglas H Juers
- Department of Physics, Whitman College, Walla Walla, WA 99362, United States; Program in Biochemistry, Biophysics and Molecular Biology, Whitman College, Walla Walla, WA 99362, United States.
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36
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Nannenga BL, Gonen T. Protein structure determination by MicroED. Curr Opin Struct Biol 2014; 27:24-31. [PMID: 24709395 PMCID: PMC5656570 DOI: 10.1016/j.sbi.2014.03.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 02/21/2014] [Accepted: 03/07/2014] [Indexed: 11/17/2022]
Abstract
In this review we discuss the current advances relating to structure determination from protein microcrystals with special emphasis on the newly developed method called MicroED. This method uses a transmission electron cryo-microscope to collect electron diffraction data from extremely small 3-dimensional (3D) crystals. MicroED has been used to solve the 3D structure of the model protein lysozyme to 2.9Å resolution. As the method further matures, MicroED promises to offer a unique and widely applicable approach to protein crystallography using nanocrystals.
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Affiliation(s)
- Brent L Nannenga
- Janelia Farm Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Tamir Gonen
- Janelia Farm Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA.
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37
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Abstract
Radiation damage is a major cause of failure in macromolecular crystallography experiments. Although it is always best to evenly illuminate the entire volume of a homogeneously diffracting crystal, limitations of the available equipment and imperfections in the sample often require a more sophisticated targeting strategy, involving microbeams smaller than the crystal, and translations of the crystal during data collection. This leads to a highly inhomogeneous distribution of absorbed X-rays (i.e., dose). Under these common experimental conditions, the relationship between dose and time is nonlinear, making it difficult to design an experimental strategy that optimizes the radiation damage lifetime of the crystal, or to assign appropriate dose values to an experiment. We present, and experimentally validate, a predictive metric diffraction-weighted dose for modeling the rate of decay of total diffracted intensity from protein crystals in macromolecular crystallography, and hence we can now assign appropriate "dose" values to modern experimental setups. Further, by taking the ratio of total elastic scattering to diffraction-weighted dose, we show that it is possible to directly compare potential data-collection strategies to optimize the diffraction for a given level of damage under specific experimental conditions. As an example of the applicability of this method, we demonstrate that by offsetting the rotation axis from the beam axis by 1.25 times the full-width half maximum of the beam, it is possible to significantly extend the dose lifetime of the crystal, leading to a higher number of diffracted photons, better statistics, and lower overall radiation damage.
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Finfrock YZ, Stern EA, Alkire RW, Kas JJ, Evans-Lutterodt K, Stein A, Duke N, Lazarski K, Joachimiak A. Mitigation of X-ray damage in macromolecular crystallography by submicrometre line focusing. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1463-9. [PMID: 23897469 DOI: 10.1107/s0907444913009335] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 04/06/2013] [Indexed: 11/10/2022]
Abstract
Reported here are measurements of the penetration depth and spatial distribution of photoelectron (PE) damage excited by 18.6 keV X-ray photons in a lysozyme crystal with a vertical submicrometre line-focus beam of 0.7 µm full-width half-maximum (FWHM). The experimental results determined that the penetration depth of PEs is 5 ± 0.5 µm with a monotonically decreasing spatial distribution shape, resulting in mitigation of diffraction signal damage. This does not agree with previous theoretical predication that the mitigation of damage requires a peak of damage outside the focus. A new improved calculation provides some qualitative agreement with the experimental results, but significant errors still remain. The mitigation of radiation damage by line focusing was measured experimentally by comparing the damage in the X-ray-irradiated regions of the submicrometre focus with the large-beam case under conditions of equal exposure and equal volumes of the protein crystal, and a mitigation factor of 4.4 ± 0.4 was determined. The mitigation of radiation damage is caused by spatial separation of the dominant PE radiation-damage component from the crystal region of the line-focus beam that contributes the diffraction signal. The diffraction signal is generated by coherent scattering of incident X-rays (which introduces no damage), while the overwhelming proportion of damage is caused by PE emission as X-ray photons are absorbed.
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Affiliation(s)
- Y Zou Finfrock
- Physics Department, University of Washington, Seattle, WA 98195, USA
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39
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Krojer T, Pike ACW, von Delft F. Squeezing the most from every crystal: the fine details of data collection. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1303-13. [PMID: 23793157 PMCID: PMC3689534 DOI: 10.1107/s0907444913013280] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2013] [Accepted: 05/14/2013] [Indexed: 11/11/2022]
Abstract
Modern synchrotron beamlines offer instrumentation of unprecedented quality, which in turn encourages increasingly marginal experiments, and for these, as much as ever, the ultimate success of data collection depends on the experience, but especially the care, of the experimenter. A representative set of difficult cases has been encountered at the Structural Genomics Consortium, a worldwide structural genomics initiative of which the Oxford site currently deposits three novel human structures per month. Achieving this target relies heavily on frequent visits to the Diamond Light Source, and the variety of crystal systems still demand customized data collection, diligent checks and careful planning of each experiment. Here, an overview is presented of the techniques and procedures that have been refined over the years and that are considered synchrotron best practice.
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Affiliation(s)
- Tobias Krojer
- Structural Genomics Consortium, Oxford University, Roosevelt Drive, Oxford OX3 7DQ, England
| | - Ashley C. W. Pike
- Structural Genomics Consortium, Oxford University, Roosevelt Drive, Oxford OX3 7DQ, England
| | - Frank von Delft
- Structural Genomics Consortium, Oxford University, Roosevelt Drive, Oxford OX3 7DQ, England
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
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40
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Zeldin OB, Gerstel M, Garman EF. RADDOSE-3D: time- and space-resolved modelling of dose in macromolecular crystallography. J Appl Crystallogr 2013. [DOI: 10.1107/s0021889813011461] [Citation(s) in RCA: 166] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
RADDOSE-3D allows the macroscopic modelling of an X-ray diffraction experiment for the purpose of better predicting radiation-damage progression. The distribution of dose within the crystal volume is calculated for a number of iterations in small angular steps across one or more data collection wedges, providing a time-resolved picture of the dose state of the crystal. The code is highly modular so that future contributions from the community can be easily integrated into it, in particular to incorporate online methods for determining the shape of macromolecular crystals and better protocols for imaging real experimental X-ray beam profiles.
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41
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42
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Meisburger SP, Warkentin M, Chen H, Hopkins JB, Gillilan RE, Pollack L, Thorne RE. Breaking the radiation damage limit with Cryo-SAXS. Biophys J 2013; 104:227-36. [PMID: 23332075 DOI: 10.1016/j.bpj.2012.11.3817] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Revised: 11/27/2012] [Accepted: 11/29/2012] [Indexed: 11/27/2022] Open
Abstract
Small angle x-ray scattering (SAXS) is a versatile and widely used technique for obtaining low-resolution structures of macromolecules and complexes. SAXS experiments measure molecules in solution, without the need for labeling or crystallization. However, radiation damage currently limits the application of SAXS to molecules that can be produced in microgram quantities; for typical proteins, 10-20 μL of solution at 1 mg/mL is required to accumulate adequate signal before irreversible x-ray damage is observed. Here, we show that cryocooled proteins and nucleic acids can withstand doses at least two orders of magnitude larger than room temperature samples. We demonstrate accurate T = 100 K particle envelope reconstructions from sample volumes as small as 15 nL, a factor of 1000 smaller than in current practice. Cryo-SAXS will thus enable structure determination of difficult-to-express proteins and biologically important, highly radiation-sensitive proteins including light-activated switches and metalloenzymes.
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Affiliation(s)
- Steve P Meisburger
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York, USA
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43
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Zeldin OB, Gerstel M, Garman EF. Optimizing the spatial distribution of dose in X-ray macromolecular crystallography. JOURNAL OF SYNCHROTRON RADIATION 2013; 20:49-57. [PMID: 23254655 DOI: 10.1107/s0909049512044706] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 10/29/2012] [Indexed: 06/01/2023]
Abstract
X-ray data collection for macromolecular crystallography can lead to highly inhomogeneous distributions of dose within the crystal volume for cases when the crystal is larger than the beam or when the beam is non-uniform (gaussian-like), particularly when crystal rotation is fully taken into account. Here the spatial distribution of dose is quantitatively modelled in order to compare the effectiveness of two dose-spreading data-collection protocols: helical scanning and translational collection. Their effectiveness in reducing the peak dose per unit diffraction is investigated via simulations for four common crystal shapes (cube, plate, long and short needles) and beams with a wide range of full width half maximum values. By inspection of the chosen metric, it is concluded that the optimum strategy is always to use as flat (top-hat) a beam as possible and to either match the beam size in both dimensions to the crystal, or to perform a helical scan with a beam which is narrow along the rotation axis and matched to the crystal size along the perpendicular axis. For crystal shapes where this is not possible, the reduction in peak dose per unit diffraction achieved through dose spreading is quantified and tabulated as a reference for experimenters.
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Affiliation(s)
- Oliver B Zeldin
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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Allan EG, Kander MC, Carmichael I, Garman EF. To scavenge or not to scavenge, that is STILL the question. JOURNAL OF SYNCHROTRON RADIATION 2013; 20:23-36. [PMID: 23254653 PMCID: PMC3526919 DOI: 10.1107/s0909049512046237] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2012] [Accepted: 11/08/2012] [Indexed: 05/23/2023]
Abstract
An extensive radiation chemistry literature would suggest that the addition of certain radical scavengers might mitigate the effects of radiation damage during protein crystallography diffraction data collection. However, attempts to demonstrate and quantify such an amelioration and its dose dependence have not yielded consistent results, either at room temperature (RT) or 100 K. Here the information thus far available is summarized and reasons for this lack of quantitative success are identified. Firstly, several different metrics have been used to monitor and quantify the rate of damage, and, as shown here, these can give results which are in conflict regarding scavenger efficacy. In addition, significant variation in results from data collected from crystals treated in nominally the same way has been observed. Secondly, typical crystallization conditions contain substantial concentrations of chemical species which already interact strongly with some of the X-ray-induced radicals that the added scavengers are intended to intercept. These interactions are probed here by the complementary technique of on-line microspectrophotometry carried out on solutions and crystals held both at 100 K and RT, the latter enabled by the use of a beamline-mounted humidifying device. With the help of computational chemistry, attempts are made to assign some of the characteristic spectral features observed experimentally. A further source of uncertainty undoubtedly lies in the challenge of reliably measuring the parameters necessary for the accurate calculation of the absorbed dose (e.g. crystal size and shape, beam profile) and its distribution within the volume of the crystal (an issue addressed in detail in another article in this issue). While microspectrophotometry reveals that the production of various species can be quenched by the addition of scavengers, it is less clear that this observation can be translated into a significant gain in crystal dose tolerance for macromolecular crystallographers.
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Affiliation(s)
- Elizabeth G. Allan
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Melissa C. Kander
- Notre Dame Radiation Laboratory, and Department of Chemistry and Biochemistry, University of Notre Dame, IN 46556, USA
| | - Ian Carmichael
- Notre Dame Radiation Laboratory, and Department of Chemistry and Biochemistry, University of Notre Dame, IN 46556, USA
| | - Elspeth F. Garman
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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Borek D, Dauter Z, Otwinowski Z. Identification of patterns in diffraction intensities affected by radiation exposure. JOURNAL OF SYNCHROTRON RADIATION 2013; 20:37-48. [PMID: 23254654 PMCID: PMC3526920 DOI: 10.1107/s0909049512048807] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Accepted: 11/27/2012] [Indexed: 05/23/2023]
Abstract
In an X-ray diffraction experiment, the structure of molecules and the crystal lattice changes owing to chemical reactions and physical processes induced by the absorption of X-ray photons. These structural changes alter structure factors, affecting the scaling and merging of data collected at different absorbed doses. Many crystallographic procedures rely on the analysis of consistency between symmetry-equivalent reflections, so failure to account for the drift of their intensities hinders the structure solution and the interpretation of structural results. The building of a conceptual model of radiation-induced changes in macromolecular crystals is the first step in the process of correcting for radiation-induced inconsistencies in diffraction data. Here the complexity of radiation-induced changes in real and reciprocal space is analysed using matrix singular value decomposition applied to multiple complete datasets obtained from single crystals. The model consists of a resolution-dependent decay correction and a uniform-per-unique-reflection term modelling specific radiation-induced changes. This model is typically sufficient to explain radiation-induced effects observed in diffraction intensities. This analysis will guide the parameterization of the model, enabling its use in subsequent crystallographic calculations.
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Affiliation(s)
- Dominika Borek
- Department of Biophysics, UT Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
- Department of Biochemistry, UT Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Zbigniew Dauter
- Macromolecular Crystallography Laboratory, Synchrotron Radiation Research Section, National Cancer Institute, Argonne National Laboratory, Bioscience Division, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - Zbyszek Otwinowski
- Department of Biophysics, UT Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
- Department of Biochemistry, UT Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
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Leal RMF, Bourenkov G, Russi S, Popov AN. A survey of global radiation damage to 15 different protein crystal types at room temperature: a new decay model. JOURNAL OF SYNCHROTRON RADIATION 2013; 20:14-22. [PMID: 23254652 PMCID: PMC3943537 DOI: 10.1107/s0909049512049114] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 11/29/2012] [Indexed: 05/11/2023]
Abstract
The radiation damage rates to crystals of 15 model macromolecular structures were studied using an automated radiation sensitivity characterization procedure. The diffracted intensity variation with dose is described by a two-parameter model. This model includes a strong resolution-independent decay specific to room-temperature measurements along with a linear increase in overall Debye-Waller factors. An equivalent representation of sensitivity via a single parameter, normalized half-dose, is introduced. This parameter varies by an order of magnitude between the different structures studied. The data show a correlation of crystal radiation sensitivity with crystal solvent content but no dose-rate dependency was detected in the range 0.05-300 kGy s(-1). The results of the crystal characterization are suitable for either optimal planning of room-temperature data collection or in situ crystallization plate screening experiments.
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Affiliation(s)
| | - Gleb Bourenkov
- EMBL Hamburg Outstation, c/o DESY, Notkestrasse 85b, Hamburg 22607, Germany
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Garman EF, Weik M. Radiation damage to biological macromolecules: some answers and more questions. JOURNAL OF SYNCHROTRON RADIATION 2013; 20:1-6. [PMID: 23254650 DOI: 10.1107/s0909049512050418] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Accepted: 12/11/2012] [Indexed: 06/01/2023]
Abstract
Research into radiation damage in macromolecular crystallography has matured over the last few years, resulting in a better understanding of both the processes and timescales involved. In turn this is now allowing practical recommendations for the optimization of crystal dose lifetime to be suggested. Some long-standing questions have been answered by recent investigations, and from these answers new challenges arise and areas of investigation can be proposed. Six papers published in this volume give an indication of some of the current directions of this field and also that of single-particle cryo-microscopy, and the brief summary below places them into the overall framework of ongoing research into macromolecular crystallography radiation damage.
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Affiliation(s)
- Elspeth F Garman
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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Warkentin M, Hopkins JB, Badeau R, Mulichak AM, Keefe LJ, Thorne RE. Global radiation damage: temperature dependence, time dependence and how to outrun it. JOURNAL OF SYNCHROTRON RADIATION 2013; 20:7-13. [PMID: 23254651 PMCID: PMC3526918 DOI: 10.1107/s0909049512048303] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Accepted: 11/25/2012] [Indexed: 05/22/2023]
Abstract
A series of studies that provide a consistent and illuminating picture of global radiation damage to protein crystals, especially at temperatures above ∼200 K, are described. The radiation sensitivity shows a transition near 200 K, above which it appears to be limited by solvent-coupled diffusive processes. Consistent with this interpretation, a component of global damage proceeds on timescales of several minutes at 180 K, decreasing to seconds near room temperature. As a result, data collection times of order 1 s allow up to half of global damage to be outrun at 260 K. Much larger damage reductions near room temperature should be feasible using larger dose rates delivered using microfocused beams, enabling a significant expansion of structural studies of proteins under more nearly native conditions.
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Affiliation(s)
| | | | - Ryan Badeau
- Physics Department, Cornell University, Ithaca, NY 14853, USA
| | | | - Lisa J. Keefe
- IMCA-CAT, Argonne National Laboratory, Argonne, IL 60439, USA
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Warkentin M, Badeau R, Hopkins JB, Thorne RE. Spatial distribution of radiation damage to crystalline proteins at 25-300 K. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:1108-17. [PMID: 22948911 PMCID: PMC3489100 DOI: 10.1107/s0907444912021361] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Accepted: 05/10/2012] [Indexed: 11/11/2022]
Abstract
The spatial distribution of radiation damage (assayed by increases in atomic B factors) to thaumatin and urease crystals at temperatures ranging from 25 to 300 K is reported. The nature of the damage changes dramatically at approximately 180 K. Above this temperature the role of solvent diffusion is apparent in thaumatin crystals, as solvent-exposed turns and loops are especially sensitive. In urease, a flap covering the active site is the most sensitive part of the molecule and nearby loops show enhanced sensitivity. Below 180 K sensitivity is correlated with poor local packing, especially in thaumatin. At all temperatures, the component of the damage that is spatially uniform within the unit cell accounts for more than half of the total increase in the atomic B factors and correlates with changes in mosaicity. This component may arise from lattice-level, rather than local, disorder. The effects of primary structure on radiation sensitivity are small compared with those of tertiary structure, local packing, solvent accessibility and crystal contacts.
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Affiliation(s)
| | - Ryan Badeau
- Physics Department, Cornell University, Ithaca, NY 14853, USA
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Brockhauser S, Svensson O, Bowler MW, Nanao M, Gordon E, Leal RMF, Popov A, Gerring M, McCarthy AA, Gotz A. The use of workflows in the design and implementation of complex experiments in macromolecular crystallography. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:975-84. [PMID: 22868763 PMCID: PMC3413211 DOI: 10.1107/s090744491201863x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Accepted: 04/25/2012] [Indexed: 11/10/2022]
Abstract
The automation of beam delivery, sample handling and data analysis, together with increasing photon flux, diminishing focal spot size and the appearance of fast-readout detectors on synchrotron beamlines, have changed the way that many macromolecular crystallography experiments are planned and executed. Screening for the best diffracting crystal, or even the best diffracting part of a selected crystal, has been enabled by the development of microfocus beams, precise goniometers and fast-readout detectors that all require rapid feedback from the initial processing of images in order to be effective. All of these advances require the coupling of data feedback to the experimental control system and depend on immediate online data-analysis results during the experiment. To facilitate this, a Data Analysis WorkBench (DAWB) for the flexible creation of complex automated protocols has been developed. Here, example workflows designed and implemented using DAWB are presented for enhanced multi-step crystal characterizations, experiments involving crystal reorientation with kappa goniometers, crystal-burning experiments for empirically determining the radiation sensitivity of a crystal system and the application of mesh scans to find the best location of a crystal to obtain the highest diffraction quality. Beamline users interact with the prepared workflows through a specific brick within the beamline-control GUI MXCuBE.
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Affiliation(s)
- Sandor Brockhauser
- European Molecular Biology Laboratory, 6 Rue Jules Horowitz, BP 181, 38042 Grenoble, France.
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