1
|
Nam KH. Data of radiation damage on selenomethionine-substituted single-domain substrate-binding protein. Data Brief 2024; 53:110114. [PMID: 38348329 PMCID: PMC10859252 DOI: 10.1016/j.dib.2024.110114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 02/15/2024] Open
Abstract
Radiation damage is an inherent issue in X-ray crystallography. It not only damages macromolecular crystals, which lowers the quality of the diffraction intensity, but results in inaccurate structural information. Among the various types of radiation damage, little is known regarding the damage to selenomethionine, an amino acid contained in some proteins. Recently, radiation damage to the selenomethionine-substituted single-domain substrate-binding domain from Rhodothermus marinus (SeMet-RmSBP) was investigated. Global and specific radiation damage from four datasets collected by repeatedly exposing a single RmSBP-SeMet crystal to X-rays were analyzed. The results indicated that the B-factor value of the selenium atom in selenomethionine was significantly increased compared with other atoms. To date, no images of radiation damage have been reported for selenomethionine-substituted proteins. Therefore, these data may be used to study radiation damage in macromolecular crystallography. This study provides insight into radiation damage associated with selenomethionine.
Collapse
Affiliation(s)
- Ki Hyun Nam
- College of General Education, Kookmin University, Seoul 02707, South Korea
| |
Collapse
|
2
|
Nam KH. Guide to serial synchrotron crystallography. Curr Res Struct Biol 2024; 7:100131. [PMID: 38371325 PMCID: PMC10869752 DOI: 10.1016/j.crstbi.2024.100131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 01/24/2024] [Accepted: 02/05/2024] [Indexed: 02/20/2024] Open
Abstract
Serial crystallography (SX) is an emerging technique that can be used to determine the noncryogenic crystal structure of macromolecules while minimizing radiation damage. Applying SX using pump-probe or mix-and-inject techniques enables the observation of time-resolved molecular reactions and dynamics in macromolecules. After the successful demonstration of the SX experimental technique with structure determination in serial femtosecond crystallography using an X-ray free electron laser, this method was adapted to the synchrotron, leading to the development of serial synchrotron crystallography (SSX). SSX offers new opportunities for researchers to leverage SX techniques, contributing to the advancement of structural biology and offering a deeper understanding of the structure and function of macromolecules. This review covers the background and advantages of SSX and its experimental approach. It also discusses important considerations when conducting SSX experiments.
Collapse
Affiliation(s)
- Ki Hyun Nam
- College of General Education, Kookmin University, Seoul, 02707, Republic of Korea
| |
Collapse
|
3
|
Fernando NK, Bostrom HLB, Murray CA, Owen RL, Thompson AL, Dickerson JL, Garman EF, Cairns AB, Regoutz A. Variability in X-ray induced effects in [Rh(COD)Cl] 2 with changing experimental parameters. Phys Chem Chem Phys 2022; 24:28444-28456. [PMID: 36399064 PMCID: PMC7614095 DOI: 10.1039/d2cp03928a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
X-ray characterisation methods have undoubtedly enabled cutting-edge advances in all aspects of materials research. Despite the enormous breadth of information that can be extracted from these techniques, the challenge of radiation-induced sample change and damage remains prevalent. This is largely due to the emergence of modern, high-intensity X-ray source technologies and the growing potential to carry out more complex, longer duration in situ or in operando studies. The tunability of synchrotron beamlines enables the routine application of photon energy-dependent experiments. This work explores the structural stability of [Rh(COD)Cl]2, a widely used catalyst and precursor in the chemical industry, across a range of beamline parameters that target X-ray energies of 8 keV, 15 keV, 18 keV and 25 keV, on a powder X-ray diffraction synchrotron beamline at room temperature. Structural changes are discussed with respect to absorbed X-ray dose at each experimental setting associated with the respective photon energy. In addition, the X-ray radiation hardness of the catalyst is discussed, by utilising the diffraction data collected at the different energies to determine a dose limit, which is often considered in protein crystallography and typically overlooked in small molecule crystallography. This work not only gives fundamental insight into how damage manifests in this organometallic catalyst, but will encourage careful consideration of experimental X-ray parameters before conducting diffraction on similar radiation-sensitive organometallic materials.
Collapse
Affiliation(s)
- Nathalie K. Fernando
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Hanna L. B. Bostrom
- Max Planck Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany
| | - Claire A. Murray
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK
| | - Robin L. Owen
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK
| | - Amber L. Thompson
- Chemical Crystallography, Chemistry Research Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, UK
| | - Joshua L. Dickerson
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Elspeth F. Garman
- Department of Biochemistry, Dorothy Crowfoot Hodgkin Building, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Andrew B. Cairns
- Department of Materials, Imperial College London, Royal School of Mines, Exhibition Road, SW7 2AZ, UK
| | - Anna Regoutz
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| |
Collapse
|
4
|
Naydenova K, Kamegawa A, Peet MJ, Henderson R, Fujiyoshi Y, Russo CJ. On the reduction in the effects of radiation damage to two-dimensional crystals of organic and biological molecules at liquid-helium temperature. Ultramicroscopy 2022; 237:113512. [PMID: 35367901 PMCID: PMC9355890 DOI: 10.1016/j.ultramic.2022.113512] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/24/2022] [Accepted: 03/06/2022] [Indexed: 11/17/2022]
Abstract
We have studied the fading of electron diffraction spots from two-dimensional (2D) crystals of paraffin (C44H90), purple membrane (bacteriorhodopsin) and aquaporin 4 (AQP4) at stage temperatures between 4K and 100K. We observed that the diffraction spots at resolutions between 3 Å and 20 Å fade more slowly at liquid-helium temperatures compared to liquid-nitrogen temperatures, by a factor of between 1.2 and 1.8, depending on the specimens. If the reduction in the effective rate of radiation damage for 2D crystals at liquid-helium temperature (as measured by spot fading) can be shown to extend to macromolecular assemblies embedded in amorphous ice, this would suggest that valuable improvements to electron cryomicroscopy (cryoEM) of biological specimens could be made by reducing the temperature of the specimens under irradiation below what is obtainable using standard liquid-nitrogen cryostats.
Collapse
Affiliation(s)
- Katerina Naydenova
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Akiko Kamegawa
- Cellular and Structural Physiology Laboratory (CeSPL), Tokyo Medical and Dental University, Yushima, Bunkyo-ku, Tokyo, Japan
| | - Mathew J Peet
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Richard Henderson
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Yoshinori Fujiyoshi
- Cellular and Structural Physiology Laboratory (CeSPL), Tokyo Medical and Dental University, Yushima, Bunkyo-ku, Tokyo, Japan
| | - Christopher J Russo
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
| |
Collapse
|
5
|
Fernando NK, Cairns AB, Murray CA, Thompson AL, Dickerson JL, Garman EF, Ahmed N, Ratcliff LE, Regoutz A. Structural and Electronic Effects of X-ray Irradiation on Prototypical [M(COD)Cl] 2 Catalysts. J Phys Chem A 2021; 125:7473-7488. [PMID: 34420303 DOI: 10.1021/acs.jpca.1c05759] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
X-ray characterization techniques are invaluable for probing material characteristics and properties, and have been instrumental in discoveries across materials research. However, there is a current lack of understanding of how X-ray-induced effects manifest in small molecular crystals. This is of particular concern as new X-ray sources with ever-increasing brilliance are developed. In this paper, systematic studies of X-ray-matter interactions are reported on two industrially important catalysts, [Ir(COD)Cl]2 and [Rh(COD)Cl]2, exposed to radiation in X-ray diffraction (XRD) and X-ray photoelectron spectroscopy (XPS) experiments. From these complementary techniques, changes to structure, chemical environments, and electronic structure are observed as a function of X-ray exposure, allowing comparisons of stability to be made between the two catalysts. Radiation dose is estimated using recent developments to the RADDOSE-3D software for small molecules and applied to powder XRD and XPS experiments. Further insights into the electronic structure of the catalysts and changes occurring as a result of the irradiation are drawn from density functional theory (DFT). The techniques combined here offer much needed insight into the X-ray-induced effects in transition-metal catalysts and, consequently, their intrinsic stabilities. There is enormous potential to extend the application of these methods to other small molecular systems of scientific or industrial relevance.
Collapse
Affiliation(s)
- Nathalie K Fernando
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, U.K
| | - Andrew B Cairns
- Department of Materials, Royal School of Mines, Imperial College London, Exhibition Road, London SW7 2AZ, U.K
| | - Claire A Murray
- Diamond Light Source Ltd., Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, U.K
| | - Amber L Thompson
- Chemical Crystallography, Chemistry Research Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, U.K
| | - Joshua L Dickerson
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, U.K
| | - Elspeth F Garman
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K
| | - Nayera Ahmed
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, U.K
| | - Laura E Ratcliff
- Department of Materials, Royal School of Mines, Imperial College London, Exhibition Road, London SW7 2AZ, U.K
| | - Anna Regoutz
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, U.K
| |
Collapse
|
6
|
Stachowski TR, Snell ME, Snell EH. A SAXS-based approach to rationally evaluate radical scavengers - toward eliminating radiation damage in solution and crystallographic studies. JOURNAL OF SYNCHROTRON RADIATION 2021; 28:1309-1320. [PMID: 34475280 PMCID: PMC8415334 DOI: 10.1107/s1600577521004045] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 04/15/2021] [Indexed: 05/30/2023]
Abstract
X-ray-based techniques are a powerful tool in structural biology but the radiation-induced chemistry that results can be detrimental and may mask an accurate structural understanding. In the crystallographic case, cryocooling has been employed as a successful mitigation strategy but also has its limitations including the trapping of non-biological structural states. Crystallographic and solution studies performed at physiological temperatures can reveal otherwise hidden but relevant conformations, but are limited by their increased susceptibility to radiation damage. In this case, chemical additives that scavenge the species generated by radiation can mitigate damage but are not always successful and the mechanisms are often unclear. Using a protein designed to undergo a large-scale structural change from breakage of a disulfide bond, radiation damage can be monitored with small-angle X-ray scattering. Using this, we have quantitatively evaluated how three scavengers commonly used in crystallographic experiments - sodium nitrate, cysteine, and ascorbic acid - perform in solution at 10°C. Sodium nitrate was the most effective scavenger and completely inhibited fragmentation of the disulfide bond at a lower concentration (500 µM) compared with cysteine (∼5 mM) while ascorbic acid performed best at 5 mM but could only reduce fragmentation by ∼75% after a total accumulated dose of 792 Gy. The relative effectiveness of each scavenger matches their reported affinities for solvated electrons. Saturating concentrations of each scavenger shifted fragmentation from first order to a zeroth-order process, perhaps indicating the direct contribution of photoabsorption. The SAXS-based method can detect damage at X-ray doses far lower than those accessible crystallographically, thereby providing a detailed picture of scavenger processes. The solution results are also in close agreement with what is known about scavenger performance and mechanism in a crystallographic setting and suggest that a link can be made between the damage phenomenon in the two scenarios. Therefore, our engineered approach might provide a platform for more systematic and comprehensive screening of radioprotectants that can directly inform mitigation strategies for both solution and crystallographic experiments, while also clarifying fundamental radiation damage mechanisms.
Collapse
Affiliation(s)
- Timothy R. Stachowski
- Hauptman-Woodward Medical Research Institute, 700 Ellicott St, Buffalo, NY 14203, USA
- Cell Stress Biology, Roswell Park Comprehensive Cancer Center, 665 Elm Street, Buffalo, NY 14203, USA
| | - Mary E. Snell
- Hauptman-Woodward Medical Research Institute, 700 Ellicott St, Buffalo, NY 14203, USA
| | - Edward H. Snell
- Hauptman-Woodward Medical Research Institute, 700 Ellicott St, Buffalo, NY 14203, USA
- Materials Design and Innovation, State University at New York at Buffalo, 700 Ellicott St, Buffalo, NY 14203, USA
| |
Collapse
|
7
|
Coates CS, Murray CA, Boström HLB, Reynolds EM, Goodwin AL. Negative X-ray expansion in cadmium cyanide. MATERIALS HORIZONS 2021; 8:1446-1453. [PMID: 34846452 PMCID: PMC8111741 DOI: 10.1039/d0mh01989e] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 02/12/2021] [Indexed: 06/12/2023]
Abstract
Cadmium cyanide, Cd(CN)2, is a flexible coordination polymer best studied for its strong and isotropic negative thermal expansion (NTE) effect. Here we show that this NTE is actually X-ray-exposure dependent: Cd(CN)2 contracts not only on heating but also on irradiation by X-rays. This behaviour contrasts that observed in other beam-sensitive materials, for which X-ray exposure drives lattice expansion. We call this effect 'negative X-ray expansion' (NXE) and suggest its origin involves an interaction between X-rays and cyanide 'flips'; in particular, we rule out local heating as a possible mechanism. Irradiation also affects the nature of a low-temperature phase transition. Our analysis resolves discrepancies in NTE coefficients reported previously on the basis of X-ray diffraction measurements, and we establish the 'true' NTE behaviour of Cd(CN)2 across the temperature range 150-750 K. The interplay between irradiation and mechanical response in Cd(CN)2 highlights the potential for exploiting X-ray exposure in the design of functional materials.
Collapse
Affiliation(s)
- Chloe S. Coates
- Inorganic Chemistry Laboratory, South Parks RoadOxfordOX1 3QRUK+44 1865 272137
- Department of Chemistry, Lensfield RoadCambridgeUK
| | - Claire A. Murray
- Diamond Light Source, Harwell CampusDidcotOxfordshire OX11 0DEUK
| | - Hanna L. B. Boström
- Inorganic Chemistry Laboratory, South Parks RoadOxfordOX1 3QRUK+44 1865 272137
- Nanochemistry Department, Max Planck Institute for Solid State Research, Heisenbergstr. 1Stuttgart70569Germany
| | - Emily M. Reynolds
- Inorganic Chemistry Laboratory, South Parks RoadOxfordOX1 3QRUK+44 1865 272137
- ISIS Facility, STFC Rutherford Appleton LaboratoryDidcotOxfordshire OX11 0QXUK
| | - Andrew L. Goodwin
- Inorganic Chemistry Laboratory, South Parks RoadOxfordOX1 3QRUK+44 1865 272137
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
Christensen J, Horton PN, Bury CS, Dickerson JL, Taberman H, Garman EF, Coles SJ. Radiation damage in small-molecule crystallography: fact not fiction. IUCRJ 2019; 6:703-713. [PMID: 31316814 PMCID: PMC6608633 DOI: 10.1107/s2052252519006948] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 05/14/2019] [Indexed: 05/29/2023]
Abstract
Traditionally small-molecule crystallographers have not usually observed or recognized significant radiation damage to their samples during diffraction experiments. However, the increased flux densities provided by third-generation synchrotrons have resulted in increasing numbers of observations of this phenomenon. The diversity of types of small-molecule systems means it is not yet possible to propose a general mechanism for their radiation-induced sample decay, however characterization of the effects will permit attempts to understand and mitigate it. Here, systematic experiments are reported on the effects that sample temperature and beam attenuation have on radiation damage progression, allowing qualitative and quantitative assessment of their impact on crystals of a small-molecule test sample. To allow inter-comparison of different measurements, radiation-damage metrics (diffraction-intensity decline, resolution fall-off, scaling B-factor increase) are plotted against the absorbed dose. For ease-of-dose calculations, the software developed for protein crystallography, RADDOSE-3D, has been modified for use in small-molecule crystallography. It is intended that these initial experiments will assist in establishing protocols for small-molecule crystallographers to optimize the diffraction signal from their samples prior to the onset of the deleterious effects of radiation damage.
Collapse
Affiliation(s)
- Jeppe Christensen
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
- National Crystallography Service, School of Chemistry, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Peter N. Horton
- National Crystallography Service, School of Chemistry, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Charles S. Bury
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Joshua L. Dickerson
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Helena Taberman
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Elspeth F. Garman
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Simon J. Coles
- National Crystallography Service, School of Chemistry, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton SO17 1BJ, UK
| |
Collapse
|
10
|
Taube M, Pietralik Z, Szymanska A, Szutkowski K, Clemens D, Grubb A, Kozak M. The domain swapping of human cystatin C induced by synchrotron radiation. Sci Rep 2019; 9:8548. [PMID: 31189973 PMCID: PMC6561922 DOI: 10.1038/s41598-019-44811-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 05/13/2019] [Indexed: 02/04/2023] Open
Abstract
Domain swapping is observed for many proteins with flexible conformations. This phenomenon is often associated with the development of conformational diseases. Importantly, domain swapping has been observed for human cystatin C (HCC), a protein capable of forming amyloid deposits in brain arteries. In this study, the ability of short exposure to high-intensity X-ray radiation to induce domain swapping in solutions of several HCC variants (wild-type HCC and V57G, V57D, V57N, V57P, and L68V mutants) was determined. The study was conducted using time-resolved small-angle X-ray scattering (TR-SAXS) synchrotron radiation. The protein samples were also analysed using small-angle neutron scattering and NMR diffusometry. Exposing HCC to synchrotron radiation (over 50 ms) led to a gradual increase in the dimeric fraction, and for exposures longer than 150 ms, the oligomer fraction was dominant. In contrast, the non-irradiated protein solutions, apart from the V57P variant, were predominantly monomeric (e.g., V57G) or in monomer/dimer equilibrium. This work might represent the first observation of domain swapping induced by high-intensity X-rays.
Collapse
Affiliation(s)
- Michal Taube
- Department of Macromolecular Physics, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 2, 61-614, Poznań, Poland
- Joint Laboratory for SAXS Studies, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 2, 61-614, Poznań, Poland
| | - Zuzanna Pietralik
- Department of Macromolecular Physics, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 2, 61-614, Poznań, Poland
| | - Aneta Szymanska
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Kosma Szutkowski
- Department of Macromolecular Physics, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 2, 61-614, Poznań, Poland
- NanoBioMedical Centre at Adam Mickiewicz University in Poznań, Wszechnicy Piastowskiej 3, 61-614, Poznań, Poland
| | - Daniel Clemens
- Helmholtz-Zentrum Berlin für Materialien und Energie Lise-Meitner-Campus Hahn-Meitner-Platz 1, 14109, Berlin, Germany
| | - Anders Grubb
- Department of Clinical Chemistry, Lund University Hospital, S-22185, Lund, Sweden
| | - Maciej Kozak
- Department of Macromolecular Physics, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 2, 61-614, Poznań, Poland.
- Joint Laboratory for SAXS Studies, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 2, 61-614, Poznań, Poland.
| |
Collapse
|
11
|
Basu S, Olieric V, Leonarski F, Matsugaki N, Kawano Y, Takashi T, Huang CY, Yamada Y, Vera L, Olieric N, Basquin J, Wojdyla JA, Bunk O, Diederichs K, Yamamoto M, Wang M. Long-wavelength native-SAD phasing: opportunities and challenges. IUCRJ 2019; 6:373-386. [PMID: 31098019 PMCID: PMC6503925 DOI: 10.1107/s2052252519002756] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 02/22/2019] [Indexed: 05/04/2023]
Abstract
Native single-wavelength anomalous dispersion (SAD) is an attractive experimental phasing technique as it exploits weak anomalous signals from intrinsic light scatterers (Z < 20). The anomalous signal of sulfur in particular, is enhanced at long wavelengths, however the absorption of diffracted X-rays owing to the crystal, the sample support and air affects the recorded intensities. Thereby, the optimal measurable anomalous signals primarily depend on the counterplay of the absorption and the anomalous scattering factor at a given X-ray wavelength. Here, the benefit of using a wavelength of 2.7 over 1.9 Å is demonstrated for native-SAD phasing on a 266 kDa multiprotein-ligand tubulin complex (T2R-TTL) and is applied in the structure determination of an 86 kDa helicase Sen1 protein at beamline BL-1A of the KEK Photon Factory, Japan. Furthermore, X-ray absorption at long wavelengths was controlled by shaping a lysozyme crystal into spheres of defined thicknesses using a deep-UV laser, and a systematic comparison between wavelengths of 2.7 and 3.3 Å is reported for native SAD. The potential of laser-shaping technology and other challenges for an optimized native-SAD experiment at wavelengths >3 Å are discussed.
Collapse
Affiliation(s)
- Shibom Basu
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
| | - Vincent Olieric
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
| | - Filip Leonarski
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
| | - Naohiro Matsugaki
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, Tsukuba, 305-0801, Japan
| | - Yoshiaki Kawano
- Advanced Photon Technology Division, RIKEN SPring-8 Center, Hyogo 679-5148, Japan
| | - Tomizaki Takashi
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
| | - Chia-Ying Huang
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
| | - Yusuke Yamada
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, Tsukuba, 305-0801, Japan
| | - Laura Vera
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
| | - Natacha Olieric
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institut, Villigen, PSI 5232, Switzerland
| | - Jerome Basquin
- Department of Biochemistry, Max Planck Institute of Biochemistry, Munich, Germany
| | - Justyna A. Wojdyla
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
| | - Oliver Bunk
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
| | - Kay Diederichs
- Department of Biology, University of Konstanz, Konstanz, 78457, Germany
| | - Masaki Yamamoto
- Advanced Photon Technology Division, RIKEN SPring-8 Center, Hyogo 679-5148, Japan
| | - Meitian Wang
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
| |
Collapse
|
12
|
Ebrahim A, Appleby MV, Axford D, Beale J, Moreno-Chicano T, Sherrell DA, Strange RW, Hough MA, Owen RL. Resolving polymorphs and radiation-driven effects in microcrystals using fixed-target serial synchrotron crystallography. Acta Crystallogr D Struct Biol 2019; 75:151-159. [PMID: 30821704 PMCID: PMC6400251 DOI: 10.1107/s2059798318010240] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 07/16/2018] [Indexed: 11/11/2022] Open
Abstract
The ability to determine high-quality, artefact-free structures is a challenge in micro-crystallography, and the rapid onset of radiation damage and requirement for a high-brilliance X-ray beam mean that a multi-crystal approach is essential. However, the combination of crystal-to-crystal variation and X-ray-induced changes can make the formation of a final complete data set challenging; this is particularly true in the case of metalloproteins, where X-ray-induced changes occur rapidly and at the active site. An approach is described that allows the resolution, separation and structure determination of crystal polymorphs, and the tracking of radiation damage in microcrystals. Within the microcrystal population of copper nitrite reductase, two polymorphs with different unit-cell sizes were successfully separated to determine two independent structures, and an X-ray-driven change between these polymorphs was followed. This was achieved through the determination of multiple serial structures from microcrystals using a high-throughput high-speed fixed-target approach coupled with robust data processing.
Collapse
Affiliation(s)
- Ali Ebrahim
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Martin V. Appleby
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Danny Axford
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - John Beale
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Tadeo Moreno-Chicano
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
| | - Darren A. Sherrell
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Richard W. Strange
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
| | - Michael A. Hough
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
| | - Robin L. Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| |
Collapse
|
13
|
Bedolla DE, Mantuano A, Pickler A, Mota CL, Braz D, Salata C, Almeida CE, Birarda G, Vaccari L, Barroso RC, Gianoncelli A. Effects of soft X-ray radiation damage on paraffin-embedded rat tissues supported on ultralene: a chemical perspective. JOURNAL OF SYNCHROTRON RADIATION 2018; 25:848-856. [PMID: 29714196 DOI: 10.1107/s1600577518003235] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 02/24/2018] [Indexed: 06/08/2023]
Abstract
Radiation damage is an important aspect to be considered when analysing biological samples with X-ray techniques as it can induce chemical and structural changes in the specimens. This work aims to provide new insights into the soft X-ray induced radiation damage of the complete sample, including not only the biological tissue itself but also the substrate and embedding medium, and the tissue fixation procedure. Sample preparation and handling involves an unavoidable interaction with the sample matrix and could play an important role in the radiation-damage mechanism. To understand the influence of sample preparation and handling on radiation damage, the effects of soft X-ray exposure at different doses on ultralene, paraffin and on paraffin-embedded rat tissues were studied using Fourier-transform infrared (FTIR) microspectroscopy and X-ray microscopy. Tissues were preserved with three different commonly used fixatives: formalin, glutaraldehyde and Karnovsky. FTIR results showed that ultralene and paraffin undergo a dose-dependent degradation of their vibrational profiles, consistent with radiation-induced oxidative damage. In addition, formalin fixative has been shown to improve the preservation of the secondary structure of proteins in tissues compared with both glutaraldehyde and Karnovsky fixation. However, conclusive considerations cannot be drawn on the optimal fixation protocol because of the interference introduced by both substrate and embedding medium in the spectral regions specific to tissue lipids, nucleic acids and carbohydrates. Notably, despite the detected alterations affecting the chemical architecture of the sample as a whole, composed of tissue, substrate and embedding medium, the structural morphology of the tissues at the micrometre scale is essentially preserved even at the highest exposure dose.
Collapse
Affiliation(s)
- Diana E Bedolla
- Elettra-Sincrotrone Trieste SCpA, SS 14, km 163,5, Basovizza, Trieste, TS 34149, Italy
| | - Andrea Mantuano
- Physics Institute, State University of Rio de Janeiro (UERJ), Rua São Francisco Xavier 524 PJLF sala 3007F, Rio de Janeiro, RJ 20550-900, Brazil
| | - Arissa Pickler
- COPPE, Federal University of Rio de Janeiro, Av. Horácio Macedo 2030, Bloco G - Sala 206 - CT, Rio de Janeiro, RJ 21941-594, Brazil
| | - Carla Lemos Mota
- Radiological Sciences Laboratory, State University of Rio de Janeiro (UERJ), Rua São Francisco Xavier 524 PHLC Sala 136, Rio de Janeiro, RJ 20550-900, Brazil
| | - Delson Braz
- COPPE, Federal University of Rio de Janeiro, Av. Horácio Macedo 2030, Bloco G - Sala 206 - CT, Rio de Janeiro, RJ 21941-594, Brazil
| | - Camila Salata
- Medical Physics Department, Comissão Nacional de Energia Nuclear, Rua General Severiano 90, Rio de Janeiro, RJ 22290-901, Brazil
| | - Carlos Eduardo Almeida
- Radiological Sciences Laboratory, State University of Rio de Janeiro (UERJ), Rua São Francisco Xavier 524 PHLC Sala 136, Rio de Janeiro, RJ 20550-900, Brazil
| | - Giovanni Birarda
- Elettra-Sincrotrone Trieste SCpA, SS 14, km 163,5, Basovizza, Trieste, TS 34149, Italy
| | - Lisa Vaccari
- Elettra-Sincrotrone Trieste SCpA, SS 14, km 163,5, Basovizza, Trieste, TS 34149, Italy
| | - Regina Cély Barroso
- Physics Institute, State University of Rio de Janeiro (UERJ), Rua São Francisco Xavier 524 PJLF sala 3007F, Rio de Janeiro, RJ 20550-900, Brazil
| | | |
Collapse
|
14
|
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: 113] [Impact Index Per Article: 18.8] [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.
Collapse
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.
| |
Collapse
|
15
|
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.
Collapse
|
16
|
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: 84] [Impact Index Per Article: 12.0] [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.
Collapse
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
| |
Collapse
|
17
|
Mehta P, Bhayani D. Impact of space environment on stability of medicines: Challenges and prospects. J Pharm Biomed Anal 2017; 136:111-119. [PMID: 28068518 DOI: 10.1016/j.jpba.2016.12.040] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 12/29/2016] [Accepted: 12/31/2016] [Indexed: 11/18/2022]
Abstract
To upkeep health of astronauts in a unique, isolated, and extreme environment of space is the primary goal for a successful space mission, hence, safe and efficacious medications are essential for the wellness of astronauts. Space medication has been challenged with problems related to efficacy. Along with altered physiology, one of the possible reasons could be instability of space medications in the presence of harsh spaceflight environmental conditions. Altered physical and chemical stability can result in reduced potency which can result in reduced efficacy. Right now, medicines from the International Space Station are replaced before their expiration. But, for longer duration missions to Mars or any other asteroid, there will not be any chance of replacement of medicines. Hence, it is desired that medicines maintain the shelf-life throughout the space mission. Stability of medicines used for short term or long term space missions cannot be judged by drug stability guidelines based on terrestrial environmental factors. Unique environmental conditions related to spaceflight include microgravity, excessive vibration, hard vacuum, humidity variation, temperature differences and excessive radiation, which may cause instability of medicines. This write-up provides a review of the problem and countermeasure approaches for pharmaceuticals exposed to the space environment. The first part of the article discusses thought processes behind outlining of International Conference on Harmonization drug stability guidelines, Q1A (R2) and Q1B, and its acceptance limits for accelerated stability study. The second part of the article describes the difference in the radiation environment of deep space compared to radiation environment inside the space shuttle based on penetration power of different types of radiation. In the third part of the article, various promising approaches are listed which can be used for assurance of space medicine stability. One of the approaches is the use of ground-based space simulation analogues and statistical treatment to data to calculate failure rate of drugs and probabilistic risk assessment. Another approach is to innovate storage and packaging technology using radiation harden polymer or using cryogenic temperatures.
Collapse
Affiliation(s)
- Priti Mehta
- Department of Pharmaceutical Analysis, Institute of Pharmacy, Nirma University, Ahmedabad, Gujarat, 382481, India.
| | - Dhara Bhayani
- Department of Pharmaceutical Analysis, Institute of Pharmacy, Nirma University, Ahmedabad, Gujarat, 382481, India
| |
Collapse
|
18
|
Coughlan HD, Darmanin C, Kirkwood HJ, Phillips NW, Hoxley D, Clark JN, Vine DJ, Hofmann F, Harder RJ, Maxey E, Abbey B. Bragg coherent diffraction imaging and metrics for radiation damage in protein micro-crystallography. JOURNAL OF SYNCHROTRON RADIATION 2017; 24:83-94. [PMID: 28009549 PMCID: PMC5182022 DOI: 10.1107/s1600577516017525] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 11/01/2016] [Indexed: 05/09/2023]
Abstract
The proliferation of extremely intense synchrotron sources has enabled ever higher-resolution structures to be obtained using data collected from smaller and often more imperfect biological crystals (Helliwell, 1984). Synchrotron beamlines now exist that are capable of measuring data from single crystals that are just a few micrometres in size. This provides renewed motivation to study and understand the radiation damage behaviour of small protein crystals. Reciprocal-space mapping and Bragg coherent diffractive imaging experiments have been performed on cryo-cooled microcrystals of hen egg-white lysozyme as they undergo radiation damage. Several well established metrics, such as intensity-loss and lattice expansion, are applied to the diffraction data and the results are compared with several new metrics that can be extracted from the coherent imaging experiments. Individually some of these metrics are inconclusive. However, combining metrics, the results suggest that radiation damage behaviour in protein micro-crystals differs from that of larger protein crystals and may allow them to continue to diffract for longer. A possible mechanism to account for these observations is proposed.
Collapse
Affiliation(s)
- H. D. Coughlan
- ARC Centre of Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Victoria 3086, Australia
- CSIRO Manufacturing Flagship, Parkville 3052, Australia
| | - C. Darmanin
- ARC Centre of Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Victoria 3086, Australia
| | - H. J. Kirkwood
- ARC Centre of Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Victoria 3086, Australia
| | - N. W. Phillips
- ARC Centre of Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Victoria 3086, Australia
- CSIRO Manufacturing Flagship, Parkville 3052, Australia
| | - D. Hoxley
- ARC Centre of Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Victoria 3086, Australia
| | - J. N. Clark
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronensynchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - D. J. Vine
- Advanced Light Source, Berkeley Lab, Berkeley, CA 94720, USA
| | - F. Hofmann
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, UK
| | - R. J. Harder
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - E. Maxey
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - B. Abbey
- ARC Centre of Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Victoria 3086, Australia
| |
Collapse
|
19
|
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.
Collapse
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.
| |
Collapse
|
20
|
Polsinelli I, Savko M, Rouanet-Mehouas C, Ciccone L, Nencetti S, Orlandini E, Stura EA, Shepard W. Comparison of helical scan and standard rotation methods in single-crystal X-ray data collection strategies. JOURNAL OF SYNCHROTRON RADIATION 2017; 24:42-52. [PMID: 28009545 DOI: 10.1107/s1600577516018488] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 11/18/2016] [Indexed: 06/06/2023]
Abstract
X-ray radiation in macromolecular crystallography can chemically alter the biological material and deteriorate the integrity of the crystal lattice with concomitant loss of resolution. Typical alterations include decarboxylation of glutamic and aspartic residues, breaking of disulfide bonds and the reduction of metal centres. Helical scans add a small translation to the crystal in the rotation method, so that for every image the crystal is shifted to expose a fresh part. On beamline PROXIMA 2A at Synchrotron SOLEIL, this procedure has been tested with various parameters in an attempt to understand how to mitigate the effects of radiation damage. Here, the strategies used and the crystallographic metrics for various scenarios are reported. Among these, the loss of bromine from bromophenyl moieties appears to be a useful monitor of radiation damage as the carbon-bromine bond is very sensitive to X-ray irradiation. Two cases are focused on where helical scans are shown to be superior in obtaining meaningful data compared with conventional methods. In one case the initial resolution of the crystal is extended over time, and in the second case the anomalous signal is preserved to provide greater effective multiplicity and easier phasing.
Collapse
Affiliation(s)
- Ivan Polsinelli
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, BP 48, 91192 Gif-sur-Yvette, France
| | - Martin Savko
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, BP 48, 91192 Gif-sur-Yvette, France
| | - Cecile Rouanet-Mehouas
- CEA, iBiTec-S, Service d'Ingénierie Moléculaire des Protéines (SIMOPRO), F-91191 Gif-sur-Yvette, France
| | - Lidia Ciccone
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, BP 48, 91192 Gif-sur-Yvette, France
| | - Susanna Nencetti
- Dipartimento di Farmacia, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | | | - Enrico A Stura
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, BP 48, 91192 Gif-sur-Yvette, France
| | - William Shepard
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, BP 48, 91192 Gif-sur-Yvette, France
| |
Collapse
|
21
|
Bury CS, Carmichael I, Garman EF. OH cleavage from tyrosine: debunking a myth. JOURNAL OF SYNCHROTRON RADIATION 2017; 24:7-18. [PMID: 28009542 PMCID: PMC5182017 DOI: 10.1107/s1600577516016775] [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: 07/15/2016] [Accepted: 10/19/2016] [Indexed: 05/09/2023]
Abstract
During macromolecular X-ray crystallography experiments, protein crystals held at 100 K have been widely reported to exhibit reproducible bond scission events at doses on the order of several MGy. With the objective to mitigate the impact of radiation damage events on valid structure determination, it is essential to correctly understand the radiation chemistry mechanisms at play. OH-cleavage from tyrosine residues is regularly cited as amongst the most available damage pathways in protein crystals at 100 K, despite a lack of widespread reports of this phenomenon in protein crystal radiation damage studies. Furthermore, no clear mechanism for phenolic C-O bond cleavage in tyrosine has been reported, with the tyrosyl radical known to be relatively robust and long-lived in both aqueous solutions and the solid state. Here, the initial findings of Tyr -OH group damage in a myrosinase protein crystal have been reviewed. Consistent with that study, at increasing doses, clear electron density loss was detectable local to Tyr -OH groups. A systematic investigation performed on a range of protein crystal damage series deposited in the Protein Data Bank has established that Tyr -OH electron density loss is not generally a dominant damage pathway in protein crystals at 100 K. Full Tyr aromatic ring displacement is here proposed to account for instances of observable Tyr -OH electron density loss, with the original myrosinase data shown to be consistent with such a damage model. Systematic analysis of the effects of other environmental factors, including solvent accessibility and proximity to disulfide bonds or hydrogen bond interactions, is also presented. Residues in known active sites showed enhanced sensitivity to radiation-induced disordering, as has previously been reported.
Collapse
Affiliation(s)
- Charles S. Bury
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Ian Carmichael
- Notre Dame Radiation Laboratory, University of Notre Dame, 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
| |
Collapse
|
22
|
Radiation damage within nucleoprotein complexes studied by macromolecular X-ray crystallography. Radiat Phys Chem Oxf Engl 1993 2016. [DOI: 10.1016/j.radphyschem.2016.05.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
23
|
Bury CS, McGeehan JE, Antson AA, Carmichael I, Gerstel M, Shevtsov MB, Garman EF. RNA protects a nucleoprotein complex against radiation damage. Acta Crystallogr D Struct Biol 2016; 72:648-57. [PMID: 27139628 PMCID: PMC4854314 DOI: 10.1107/s2059798316003351] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 02/26/2016] [Indexed: 11/10/2022] Open
Abstract
Radiation damage during macromolecular X-ray crystallographic data collection is still the main impediment for many macromolecular structure determinations. Even when an eventual model results from the crystallographic pipeline, the manifestations of radiation-induced structural and conformation changes, the so-called specific damage, within crystalline macromolecules can lead to false interpretations of biological mechanisms. Although this has been well characterized within protein crystals, far less is known about specific damage effects within the larger class of nucleoprotein complexes. Here, a methodology has been developed whereby per-atom density changes could be quantified with increasing dose over a wide (1.3-25.0 MGy) range and at higher resolution (1.98 Å) than the previous systematic specific damage study on a protein-DNA complex. Specific damage manifestations were determined within the large trp RNA-binding attenuation protein (TRAP) bound to a single-stranded RNA that forms a belt around the protein. Over a large dose range, the RNA was found to be far less susceptible to radiation-induced chemical changes than the protein. The availability of two TRAP molecules in the asymmetric unit, of which only one contained bound RNA, allowed a controlled investigation into the exact role of RNA binding in protein specific damage susceptibility. The 11-fold symmetry within each TRAP ring permitted statistically significant analysis of the Glu and Asp damage patterns, with RNA binding unexpectedly being observed to protect these otherwise highly sensitive residues within the 11 RNA-binding pockets distributed around the outside of the protein molecule. Additionally, the method enabled a quantification of the reduction in radiation-induced Lys and Phe disordering upon RNA binding directly from the electron density.
Collapse
Affiliation(s)
- Charles S. Bury
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England
| | - John E. McGeehan
- Molecular Biophysics, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, King Henry I Street, Portsmouth PO1 2DY, England
| | - Alfred A. Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York Y010 5DD, England
| | - Ian Carmichael
- Notre Dame Radiation Laboratory, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Markus Gerstel
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England
| | - Mikhail B. Shevtsov
- Laboratory of Structural Biology of GPCRs, Moscow Institute of Physics and Technology, Dolgoprudniy 141700, Russian Federation
| | - Elspeth F. Garman
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England
| |
Collapse
|
24
|
Owen RL, Sherrell DA. Radiation damage and derivatization in macromolecular crystallography: a structure factor's perspective. Acta Crystallogr D Struct Biol 2016; 72:388-94. [PMID: 26960125 PMCID: PMC4784669 DOI: 10.1107/s2059798315021555] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 11/13/2015] [Indexed: 11/11/2022] Open
Abstract
During, or even after, data collection the presence and effects of radiation damage in macromolecular crystallography may not always be immediately obvious. Despite this, radiation damage is almost always present, with site-specific damage occurring on very short time (dose) scales well before global damage becomes apparent. A result of both site-specific radiation damage and derivatization is a change in the relative intensity of reflections. The size and approximate rate of onset of X-ray-induced transformations is compared with the changes expected from derivatization, and strategies for minimizing radiation damage are discussed.
Collapse
Affiliation(s)
- Robin L. Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, England
| | - Darren A. Sherrell
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, England
| |
Collapse
|
25
|
Abstract
Although crystallographers typically seek to mitigate radiation damage in macromolecular crystals, in some cases, radiation damage to specific atoms can be used to determine phases de novo. This process is called radiation damage-induced phasing or "RIP." Here, we provide a general overview of the method and a practical set of data collection and processing strategies for phasing macromolecular structures using RIP.
Collapse
Affiliation(s)
- Chloe Zubieta
- Structural Biology Group, European Synchrotron Radiation Facility, Grenoble, France
| | | |
Collapse
|
26
|
Dauter Z, Wlodawer A. On the accuracy of unit-cell parameters in protein crystallography. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:2217-26. [PMID: 26527139 PMCID: PMC4631477 DOI: 10.1107/s1399004715015503] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2015] [Accepted: 08/19/2015] [Indexed: 11/10/2022]
Abstract
The availability in the Protein Data Bank (PDB) of a number of structures that are presented in space group P1 but in reality possess higher symmetry allowed the accuracy and precision of the unit-cell parameters of the crystals of macromolecules to be evaluated. In addition, diffraction images from crystals of several proteins, previously collected as part of in-house projects, were processed independently with three popular software packages. An analysis of the results, augmented by published serial crystallography data, suggests that the apparent precision of the presentation of unit-cell parameters in the PDB to three decimal points is not justified, since these parameters are subject to errors of not less than 0.2%. It was also noticed that processing data including full crystallographic symmetry does not lead to deterioration of the refinement parameters; thus, it is not beneficial to treat the crystals as belonging to space group P1 when higher symmetry can be seen.
Collapse
Affiliation(s)
- Zbigniew Dauter
- Synchrotron Radiation Research Section, MCL, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Alexander Wlodawer
- Protein Structure Section, MCL, National Cancer Institute, Frederick, MD 21702, USA
| |
Collapse
|
27
|
Coughlan HD, Darmanin C, Phillips NW, Hofmann F, Clark JN, Harder RJ, Vine DJ, Abbey B. Radiation damage in a micron-sized protein crystal studied via reciprocal space mapping and Bragg coherent diffractive imaging. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2015; 2:041704. [PMID: 26798804 PMCID: PMC4711611 DOI: 10.1063/1.4919641] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Accepted: 04/22/2015] [Indexed: 05/11/2023]
Abstract
For laboratory and synchrotron based X-ray sources, radiation damage has posed a significant barrier to obtaining high-resolution structural data from biological macromolecules. The problem is particularly acute for micron-sized crystals where the weaker signal often necessitates the use of higher intensity beams to obtain the relevant data. Here, we employ a combination of techniques, including Bragg coherent diffractive imaging to characterise the radiation induced damage in a micron-sized protein crystal over time. The approach we adopt here could help screen for potential protein crystal candidates for measurement at X-ray free election laser sources.
Collapse
Affiliation(s)
| | - C Darmanin
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe University , Melbourne 3086, Australia
| | | | - F Hofmann
- Department of Engineering Science, University of Oxford , Oxford OX1 3PJ, United Kingdom
| | | | - R J Harder
- Advanced Photon Source, Argonne National Laboratory , Argonne, Illinois 60439, USA
| | - D J Vine
- Advanced Photon Source, Argonne National Laboratory , Argonne, Illinois 60439, USA
| | | |
Collapse
|
28
|
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.
Collapse
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
| |
Collapse
|
29
|
Bury C, Garman EF, Ginn HM, Ravelli RBG, Carmichael I, Kneale G, McGeehan JE. Radiation damage to nucleoprotein complexes in macromolecular crystallography. JOURNAL OF SYNCHROTRON RADIATION 2015; 22:213-24. [PMID: 25723923 PMCID: PMC4344358 DOI: 10.1107/s1600577514026289] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 11/30/2014] [Indexed: 05/23/2023]
Abstract
Significant progress has been made in macromolecular crystallography over recent years in both the understanding and mitigation of X-ray induced radiation damage when collecting diffraction data from crystalline proteins. In contrast, despite the large field that is productively engaged in the study of radiation chemistry of nucleic acids, particularly of DNA, there are currently very few X-ray crystallographic studies on radiation damage mechanisms in nucleic acids. Quantitative comparison of damage to protein and DNA crystals separately is challenging, but many of the issues are circumvented by studying pre-formed biological nucleoprotein complexes where direct comparison of each component can be made under the same controlled conditions. Here a model protein-DNA complex C.Esp1396I is employed to investigate specific damage mechanisms for protein and DNA in a biologically relevant complex over a large dose range (2.07-44.63 MGy). In order to allow a quantitative analysis of radiation damage sites from a complex series of macromolecular diffraction data, a computational method has been developed that is generally applicable to the field. Typical specific damage was observed for both the protein on particular amino acids and for the DNA on, for example, the cleavage of base-sugar N1-C and sugar-phosphate C-O bonds. Strikingly the DNA component was determined to be far more resistant to specific damage than the protein for the investigated dose range. At low doses the protein was observed to be susceptible to radiation damage while the DNA was far more resistant, damage only being observed at significantly higher doses.
Collapse
Affiliation(s)
- Charles Bury
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Elspeth F. Garman
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Helen Mary Ginn
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Raimond B. G. Ravelli
- Institute of Nanoscopy, Maastricht University, PO Box 616, Maastricht 6200 MD, The Netherlands
| | - Ian Carmichael
- Notre Dame Radiation Laboratory, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Geoff Kneale
- Molecular Biophysics, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, King Henry 1st Street, Portsmouth PO1 2DY, UK
| | - John E. McGeehan
- Molecular Biophysics, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, King Henry 1st Street, Portsmouth PO1 2DY, UK
| |
Collapse
|
30
|
von Stetten D, Giraud T, Carpentier P, Sever F, Terrien M, Dobias F, Juers DH, Flot D, Mueller-Dieckmann C, Leonard GA, de Sanctis D, Royant A. In crystallo optical spectroscopy (icOS) as a complementary tool on the macromolecular crystallography beamlines of the ESRF. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:15-26. [PMID: 25615856 PMCID: PMC4304682 DOI: 10.1107/s139900471401517x] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 06/27/2014] [Indexed: 01/04/2023]
Abstract
The analysis of structural data obtained by X-ray crystallography benefits from information obtained from complementary techniques, especially as applied to the crystals themselves. As a consequence, optical spectroscopies in structural biology have become instrumental in assessing the relevance and context of many crystallographic results. Since the year 2000, it has been possible to record such data adjacent to, or directly on, the Structural Biology Group beamlines of the ESRF. A core laboratory featuring various spectrometers, named the Cryobench, is now in its third version and houses portable devices that can be directly mounted on beamlines. This paper reports the current status of the Cryobench, which is now located on the MAD beamline ID29 and is thus called the ID29S-Cryobench (where S stands for `spectroscopy'). It also reviews the diverse experiments that can be performed at the Cryobench, highlighting the various scientific questions that can be addressed.
Collapse
Affiliation(s)
| | - Thierry Giraud
- European Synchrotron Radiation Facility, F-38043 Grenoble, France
| | | | - Franc Sever
- European Synchrotron Radiation Facility, F-38043 Grenoble, France
| | - Maxime Terrien
- Université Grenoble Alpes, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
| | - Fabien Dobias
- European Synchrotron Radiation Facility, F-38043 Grenoble, France
| | - Douglas H. Juers
- Department of Physics, Whitman College, Walla Walla, WA 99362, USA
| | - David Flot
- European Synchrotron Radiation Facility, F-38043 Grenoble, France
| | | | | | | | - Antoine Royant
- European Synchrotron Radiation Facility, F-38043 Grenoble, France
- Université Grenoble Alpes, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
| |
Collapse
|
31
|
|
32
|
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.
Collapse
Affiliation(s)
- Oliver B Zeldin
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | | | | |
Collapse
|
33
|
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.
Collapse
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
| |
Collapse
|
34
|
Schmidt M, Šrajer V, Purwar N, Tripathi S. The kinetic dose limit in room-temperature time-resolved macromolecular crystallography. JOURNAL OF SYNCHROTRON RADIATION 2012; 19:264-73. [PMID: 22338689 PMCID: PMC3284346 DOI: 10.1107/s090904951105549x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Accepted: 12/23/2011] [Indexed: 05/16/2023]
Abstract
Protein X-ray structures are determined with ionizing radiation that damages the protein at high X-ray doses. As a result, diffraction patterns deteriorate with the increased absorbed dose. Several strategies such as sample freezing or scavenging of X-ray-generated free radicals are currently employed to minimize this damage. However, little is known about how the absorbed X-ray dose affects time-resolved Laue data collected at physiological temperatures where the protein is fully functional in the crystal, and how the kinetic analysis of such data depends on the absorbed dose. Here, direct evidence for the impact of radiation damage on the function of a protein is presented using time-resolved macromolecular crystallography. The effect of radiation damage on the kinetic analysis of time-resolved X-ray data is also explored.
Collapse
Affiliation(s)
- M Schmidt
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA.
| | | | | | | |
Collapse
|
35
|
Warkentin M, Badeau R, Hopkins JB, Mulichak AM, Keefe LJ, Thorne RE. Global radiation damage at 300 and 260 K with dose rates approaching 1 MGy s⁻¹. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:124-33. [PMID: 22281741 DOI: 10.1107/s0907444911052085] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Accepted: 12/02/2011] [Indexed: 11/10/2022]
Abstract
Global radiation damage to 19 thaumatin crystals has been measured using dose rates from 3 to 680 kGy s⁻¹. At room temperature damage per unit dose appears to be roughly independent of dose rate, suggesting that the timescales for important damage processes are less than ∼1 s. However, at T = 260 K approximately half of the global damage manifested at dose rates of ∼10 kGy s⁻¹ can be outrun by collecting data at 680 kGy s⁻¹. Appreciable sample-to-sample variability in global radiation sensitivity at fixed dose rate is observed. This variability cannot be accounted for by errors in dose calculation, crystal slippage or the size of the data sets in the assay.
Collapse
|
36
|
Kmetko J, Warkentin M, Englich U, Thorne RE. Can radiation damage to protein crystals be reduced using small-molecule compounds? ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2011; 67:881-93. [PMID: 21931220 PMCID: PMC3176623 DOI: 10.1107/s0907444911032835] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Accepted: 08/12/2011] [Indexed: 11/10/2022]
Abstract
Recent studies have defined a data-collection protocol and a metric that provide a robust measure of global radiation damage to protein crystals. Using this protocol and metric, 19 small-molecule compounds (introduced either by cocrystallization or soaking) were evaluated for their ability to protect lysozyme crystals from radiation damage. The compounds were selected based upon their ability to interact with radiolytic products (e.g. hydrated electrons, hydrogen, hydroxyl and perhydroxyl radicals) and/or their efficacy in protecting biological molecules from radiation damage in dilute aqueous solutions. At room temperature, 12 compounds had no effect and six had a sensitizing effect on global damage. Only one compound, sodium nitrate, appeared to extend crystal lifetimes, but not in all proteins and only by a factor of two or less. No compound provided protection at T=100 K. Scavengers are ineffective in protecting protein crystals from global damage because a large fraction of primary X-ray-induced excitations are generated in and/or directly attack the protein and because the ratio of scavenger molecules to protein molecules is too small to provide appreciable competitive protection. The same reactivity that makes some scavengers effective radioprotectors in protein solutions may explain their sensitizing effect in the protein-dense environment of a crystal. A more productive focus for future efforts may be to identify and eliminate sensitizing compounds from crystallization solutions.
Collapse
Affiliation(s)
- Jan Kmetko
- Physics Department, Kenyon College, Gambier, OH 43022, USA
| | | | - Ulrich Englich
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY 14853, USA
| | | |
Collapse
|
37
|
De la Mora E, Carmichael I, Garman EF. Effective scavenging at cryotemperatures: further increasing the dose tolerance of protein crystals. JOURNAL OF SYNCHROTRON RADIATION 2011; 18:346-57. [PMID: 21525642 DOI: 10.1107/s0909049511007163] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Accepted: 02/24/2011] [Indexed: 05/21/2023]
Abstract
The rate of radiation damage to macromolecular crystals at both room temperature and 100 K has previously been shown to be reduced by the use of certain radical scavengers. Here the effects of sodium nitrate, an electron scavenger, are investigated at 100 K. For sodium nitrate at a concentration of 0.5 M in chicken egg-white lysozyme crystals, the dose tolerance is increased by a factor of two as judged from the global damage parameters, and no specific structural damage to the disulfide bonds is seen until the dose is greatly in excess (more than a factor of five) of the value at which damage appears in electron density maps derived from a scavenger-free crystal. In the electron density maps, ordered nitrate ions adjacent to the disulfide bonds are seen to lose an O atom, and appear to protect the disulfide bonds. In addition, results reinforcing previous reports on the effectiveness of ascorbate are presented. The mechanisms of action of both scavengers in the crystalline environment are elucidated.
Collapse
Affiliation(s)
- Eugenio De la Mora
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | | | | |
Collapse
|
38
|
Garman EF, Weik M. Macromolecular crystallography radiation damage research: what's new? JOURNAL OF SYNCHROTRON RADIATION 2011; 18:313-7. [PMID: 21525638 PMCID: PMC3083910 DOI: 10.1107/s0909049511013859] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Accepted: 04/12/2011] [Indexed: 05/05/2023]
Abstract
Radiation damage in macromolecular crystallography has become a mainstream concern over the last ten years. The current status of research into this area is briefly assessed, and the ten new papers published in this issue are set into the context of previous work in the field. Some novel and exciting developments emerging over the last two years are also summarized.
Collapse
Affiliation(s)
- Elspeth F. Garman
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Martin Weik
- Comissariat à l’Energie Atomique, Institut de Biologie Structurale, F-38054 Grenoble, France
- CNRS, UMR5075, F-38027 Grenoble, France
- Université Joseph Fourier, F-38000 Grenoble, France
- ESRF, 6 rue Jules Horowitz, BP 220, 38043 Grenoble Cedex, France
| |
Collapse
|
39
|
Homer C, Cooper L, Gonzalez A. Energy dependence of site-specific radiation damage in protein crystals. JOURNAL OF SYNCHROTRON RADIATION 2011; 18:338-45. [PMID: 21525641 PMCID: PMC3083911 DOI: 10.1107/s0909049511005504] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2010] [Accepted: 02/14/2011] [Indexed: 05/21/2023]
Abstract
It is important to consider radiation damage to crystals caused by data collection when solving structures and critical when determining protein function, which can often depend on very subtle structural characteristics. In this study the rate of damage to specific sites in protein crystals cooled at 100 K is found to depend on the energy of the incident X-ray beam. Several lysozyme crystals were each subjected to 3-26 MGy of cumulative X-ray exposure by collecting multiple data sets from each crystal at either 9 keV or 14 keV. The integrated electron density surrounding each S atom in the structure was calculated for each data set and the change in electron density was evaluated as a function of dose at the two energies. The rate of electron density decrease per cubic Å per MGy was determined to be greater at 14 keV than at 9 keV for cysteine sulfurs involved in disulphide bridges; no statistically significant differences in the decay rates were found for methionine sulfurs. These preliminary results imply that it might be possible to minimize certain types of specific radiation damage by an appropriate choice of energy. Further experiments studying a variety of photolabile sites over a wider range of energies are needed to confirm this conclusion.
Collapse
Affiliation(s)
| | - Laura Cooper
- SSRL, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Ana Gonzalez
- SSRL, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| |
Collapse
|
40
|
Radiation damage in protein crystals is reduced with a micron-sized X-ray beam. Proc Natl Acad Sci U S A 2011; 108:6127-32. [PMID: 21444772 DOI: 10.1073/pnas.1017701108] [Citation(s) in RCA: 110] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Radiation damage is a major limitation in crystallography of biological macromolecules, even for cryocooled samples, and is particularly acute in microdiffraction. For the X-ray energies most commonly used for protein crystallography at synchrotron sources, photoelectrons are the predominant source of radiation damage. If the beam size is small relative to the photoelectron path length, then the photoelectron may escape the beam footprint, resulting in less damage in the illuminated volume. Thus, it may be possible to exploit this phenomenon to reduce radiation-induced damage during data measurement for techniques such as diffraction, spectroscopy, and imaging that use X-rays to probe both crystalline and noncrystalline biological samples. In a systematic and direct experimental demonstration of reduced radiation damage in protein crystals with small beams, damage was measured as a function of micron-sized X-ray beams of decreasing dimensions. The damage rate normalized for dose was reduced by a factor of three from the largest (15.6 μm) to the smallest (0.84 μm) X-ray beam used. Radiation-induced damage to protein crystals was also mapped parallel and perpendicular to the polarization direction of an incident 1-μm X-ray beam. Damage was greatest at the beam center and decreased monotonically to zero at a distance of about 4 μm, establishing the range of photoelectrons. The observed damage is less anisotropic than photoelectron emission probability, consistent with photoelectron trajectory simulations. These experimental results provide the basis for data collection protocols to mitigate with micron-sized X-ray beams the effects of radiation damage.
Collapse
|
41
|
New and unconventional approaches for advancing resolution in biological transmission electron microscopy by improving macromolecular specimen preparation and preservation. Micron 2011; 42:141-51. [DOI: 10.1016/j.micron.2010.05.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2010] [Revised: 05/16/2010] [Accepted: 05/17/2010] [Indexed: 11/21/2022]
|
42
|
Bąkowicz J, Skarżewski J, Turowska-Tyrk I. Photo-induced structural changes in two crystal forms with different numbers of independent molecules. CrystEngComm 2011. [DOI: 10.1039/c0ce00795a] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
43
|
Carpentier P, Royant A, Weik M, Bourgeois D. Raman-Assisted Crystallography Suggests a Mechanism of X-Ray-Induced Disulfide Radical Formation and Reparation. Structure 2010; 18:1410-9. [DOI: 10.1016/j.str.2010.09.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2010] [Revised: 08/27/2010] [Accepted: 09/23/2010] [Indexed: 11/24/2022]
|
44
|
Garman EF. Radiation damage in macromolecular crystallography: what is it and why should we care? ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2010; 66:339-51. [PMID: 20382986 PMCID: PMC2852297 DOI: 10.1107/s0907444910008656] [Citation(s) in RCA: 240] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2010] [Accepted: 03/06/2010] [Indexed: 11/10/2022]
Abstract
Radiation damage inflicted during diffraction data collection in macromolecular crystallography has re-emerged in the last decade as a major experimental and computational challenge, as even for crystals held at 100 K it can result in severe data-quality degradation and the appearance in solved structures of artefacts which affect biological interpretations. Here, the observable symptoms and basic physical processes involved in radiation damage are described and the concept of absorbed dose as the basic metric against which to monitor the experimentally observed changes is outlined. Investigations into radiation damage in macromolecular crystallography are ongoing and the number of studies is rapidly increasing. The current literature on the subject is compiled as a resource for the interested researcher.
Collapse
Affiliation(s)
- Elspeth F Garman
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England.
| |
Collapse
|
45
|
Borek D, Cymborowski M, Machius M, Minor W, Otwinowski Z. Diffraction data analysis in the presence of radiation damage. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2010; 66:426-36. [PMID: 20382996 PMCID: PMC2852307 DOI: 10.1107/s0907444909040177] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2009] [Accepted: 10/02/2009] [Indexed: 11/10/2022]
Abstract
Radiation-induced decay of crystal diffraction and additional specific chemical changes of macromolecules forming the crystal lattice are currently two of the main limiting factors in the acquisition of macromolecular diffraction data and macromolecular structure determination. Data-processing and phasing protocols are discussed in the context of radiation-induced changes. In macromolecular crystallography, the acquisition of a complete set of diffraction intensities typically involves a high cumulative dose of X-ray radiation. In the process of data acquisition, the irradiated crystal lattice undergoes a broad range of chemical and physical changes. These result in the gradual decay of diffraction intensities, accompanied by changes in the macroscopic organization of crystal lattice order and by localized changes in electron density that, owing to complex radiation chemistry, are specific for a particular macromolecule. The decay of diffraction intensities is a well defined physical process that is fully correctable during scaling and merging analysis and therefore, while limiting the amount of diffraction, it has no other impact on phasing procedures. Specific chemical changes, which are variable even between different crystal forms of the same macromolecule, are more difficult to predict, describe and correct in data. Appearing during the process of data collection, they result in gradual changes in structure factors and therefore have profound consequences in phasing procedures. Examples of various combinations of radiation-induced changes are presented and various considerations pertinent to the determination of the best strategies for handling diffraction data analysis in representative situations are discussed.
Collapse
Affiliation(s)
- Dominika Borek
- University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | | | | | | | | |
Collapse
|
46
|
Cornaby S, Szebenyi DME, Smilgies DM, Schuller DJ, Gillilan R, Hao Q, Bilderback DH. Feasibility of one-shot-per-crystal structure determination using Laue diffraction. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2010; 66:2-11. [PMID: 20057043 PMCID: PMC2803125 DOI: 10.1107/s0907444909037731] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2009] [Accepted: 09/17/2009] [Indexed: 11/10/2022]
Abstract
Crystal size is an important factor in determining the number of diffraction patterns which may be obtained from a protein crystal before severe radiation damage sets in. As crystal dimensions decrease this number is reduced, eventually falling to one, at which point a complete data set must be assembled using data from multiple crystals. When only a single exposure is to be collected from each crystal, the polychromatic Laue technique may be preferable to monochromatic methods owing to its simultaneous recording of a large number of fully recorded reflections per image. To assess the feasibility of solving structures using single Laue images from multiple crystals, data were collected using a 'pink' beam at the CHESS D1 station from groups of lysozyme crystals with dimensions of the order of 20-30 microm mounted on MicroMesh grids. Single-shot Laue data were used for structure determination by molecular replacement and correct solutions were obtained even when as few as five crystals were used.
Collapse
Affiliation(s)
- Sterling Cornaby
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York, USA
- CHESS (Cornell High Energy Synchrotron Source), Cornell University, Ithaca, New York, USA
| | - Doletha M. E. Szebenyi
- MacCHESS (Macromolecular Diffraction Facilities at CHESS), Cornell University, Ithaca, New York, USA
| | - Detlef-M. Smilgies
- CHESS (Cornell High Energy Synchrotron Source), Cornell University, Ithaca, New York, USA
| | - David J. Schuller
- MacCHESS (Macromolecular Diffraction Facilities at CHESS), Cornell University, Ithaca, New York, USA
| | - Richard Gillilan
- MacCHESS (Macromolecular Diffraction Facilities at CHESS), Cornell University, Ithaca, New York, USA
| | - Quan Hao
- MacCHESS (Macromolecular Diffraction Facilities at CHESS), Cornell University, Ithaca, New York, USA
| | - Donald H. Bilderback
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York, USA
- CHESS (Cornell High Energy Synchrotron Source), Cornell University, Ithaca, New York, USA
| |
Collapse
|
47
|
Origin and temperature dependence of radiation damage in biological samples at cryogenic temperatures. Proc Natl Acad Sci U S A 2009; 107:1094-9. [PMID: 20080548 DOI: 10.1073/pnas.0905481107] [Citation(s) in RCA: 134] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Radiation damage is the major impediment for obtaining structural information from biological samples by using ionizing radiation such as x-rays or electrons. The knowledge of underlying processes especially at cryogenic temperatures is still fragmentary, and a consistent mechanism has not been found yet. By using a combination of single-crystal x-ray diffraction, small-angle scattering, and qualitative and quantitative radiolysis experiments, we show that hydrogen gas, formed inside the sample during irradiation, rather than intramolecular bond cleavage between non-hydrogen atoms, is mainly responsible for the loss of high-resolution information and contrast in diffraction experiments and microscopy. The experiments that are presented in this paper cover a temperature range between 5 and 160 K and reveal that the commonly used temperature in x-ray crystallography of 100 K is not optimal in terms of minimizing radiation damage and thereby increasing the structural information obtainable in a single experiment. At 50 K, specific radiation damage to disulfide bridges is reduced by a factor of 4 compared to 100 K, and samples can tolerate a factor of 2.6 and 3.9 higher dose, as judged by the increase of R(free) values of elastase and cubic insulin crystals, respectively.
Collapse
|
48
|
Radiation stability of proteinase K crystals grown by LB nanotemplate method. J Struct Biol 2009; 168:409-18. [PMID: 19686853 DOI: 10.1016/j.jsb.2009.08.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2009] [Revised: 07/29/2009] [Accepted: 08/12/2009] [Indexed: 11/23/2022]
Abstract
A detailed analysis of structural and intensity changes induced by X-ray radiation is presented for two types of proteinase K crystals: crystal grown by classical hanging drop method and those grown by Langmuir-Blodgett (LB) nanotemplate. The comparison of various parameters (e.g. intensity per sigma ratio, unit-cell volume, number of unique reflections, B-factors) and electron density maps as a function of radiation dose, demonstrates that crystals, grown by the LB nanotemplate method, appear to be more resistant against radiation damage than crystals grown by the classical hanging drop method.
Collapse
|
49
|
Nowak E, Brzuszkiewicz A, Dauter M, Dauter Z, Rosenbaum G. To scavenge or not to scavenge: that is the question. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2009; 65:1004-6. [PMID: 19690379 DOI: 10.1107/s0907444909026821] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2009] [Accepted: 07/08/2009] [Indexed: 11/10/2022]
Abstract
Analysis of a series of diffraction data sets measured from four native as well as four nicotinic acid-soaked crystals of trypsin at 100 K shows a high variability in radiation-sensitivity among individual crystals for both nicotinic acid-soaked and native crystals. The level of radiation-sensitivity and the extent of its variability is statistically indistinguishable between the two conditions. This suggests that this potential scavenger does not have any statistically significant effect on the amount of radiation damage incurred in the crystals on X-ray irradiation. This is in contrast to previous results [Kauffmann et al. (2006), Structure, 14, 1099-1105] where only one crystal specimen was used for each condition (native and nicotinic acid-soaked).
Collapse
Affiliation(s)
- Elzbieta Nowak
- Synchrotron Radiation Research Section, MCL, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA
| | | | | | | | | |
Collapse
|
50
|
Petrova T, Lunin VY, Ginell S, Hazemann I, Lazarski K, Mitschler A, Podjarny A, Joachimiak A. X-ray-radiation-induced cooperative atomic movements in protein. J Mol Biol 2009; 387:1092-105. [PMID: 19233199 DOI: 10.1016/j.jmb.2009.02.030] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2008] [Revised: 02/06/2009] [Accepted: 02/10/2009] [Indexed: 11/25/2022]
Abstract
X-rays interact with biological matter and cause damage. Proteins and other macromolecules are damaged primarily by ionizing X-ray photons and secondarily by reactive radiolytic chemical species. In particular, protein molecules are damaged during X-ray diffraction experiments with protein crystals, which is, in many cases, a serious hindrance to structure solution. The local X-ray-induced structural changes of the protein molecule have been studied using a number of model systems. However, it is still not well understood whether these local chemical changes lead to global structural changes in protein and what the mechanism is. We present experimental evidence at atomic resolution indicating the movement of large parts of the protein globule together with bound water molecules in the early stages of radiation damage to the protein crystal. The data were obtained from a crystal cryocooled to approximately 100 K and diffracting to 1 A. The movement of the protein structural elements occurs simultaneously with the decarboxylation of several glutamate and aspartate residues that mediate contacts between moving protein structural elements and with the rearrangement of the water network. The analysis of the anisotropy of atomic displacement parameters reveals that the observed atomic movements occur at different rates in different unit cells of the crystal. Thus, the examination of the cooperative atomic movement enables us to better understand how radiation-induced local chemical and structural changes of the protein molecule eventually lead to disorder in protein crystals.
Collapse
Affiliation(s)
- Tatiana Petrova
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | | | | | | | | | | | | | | |
Collapse
|