1
|
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
|
2
|
Bhattacharyya R, Dhar J, Ghosh Dastidar S, Chakrabarti P, Weiss MS. The susceptibility of disulfide bonds towards radiation damage may be explained by S⋯O interactions. IUCRJ 2020; 7:825-834. [PMID: 32939274 PMCID: PMC7467163 DOI: 10.1107/s2052252520008520] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 06/25/2020] [Indexed: 05/30/2023]
Abstract
Radiation-induced damage to protein crystals during X-ray diffraction data collection is a major impediment to obtaining accurate structural information on macromolecules. Some of the specific impairments that are inflicted upon highly brilliant X-ray irradiation are metal-ion reduction, disulfide-bond cleavage and a loss of the integrity of the carboxyl groups of acidic residues. With respect to disulfide-bond reduction, previous results have indicated that not all disulfide bridges are equally susceptible to damage. A careful analysis of the chemical environment of disulfide bonds in the structures of elastase, lysozyme, acetylcholinesterase and other proteins suggests that S-S bonds which engage in a close contact with a carbonyl O atom along the extension of the S-S bond vector are more susceptible to reduction than the others. Such an arrangement predisposes electron transfer to occur from the O atom to the disulfide bond, leading to its reduction. The interaction between a nucleophile and an electrophile, akin to hydrogen bonding, stabilizes protein structures, but it also provides a pathway of electron transfer to the S-S bond, leading to its reduction during exposure of the protein crystal to an intense X-ray beam. An otherwise stabilizing interaction can thus be the cause of destabilization under the condition of radiation exposure.
Collapse
Affiliation(s)
- Rajasri Bhattacharyya
- Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700 054, India
| | - Jesmita Dhar
- Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700 054, India
| | - Shubhra Ghosh Dastidar
- Division of Bioinformatics, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700 054, India
| | - Pinak Chakrabarti
- Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700 054, India
| | - Manfred S. Weiss
- Macromolecular Crystallography (HZB-MX), Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, D-12489 Berlin, Germany
| |
Collapse
|
3
|
Dickerson JL, Garman EF. The potential benefits of using higher X-ray energies for macromolecular crystallography. JOURNAL OF SYNCHROTRON RADIATION 2019; 26:922-930. [PMID: 31274414 DOI: 10.1107/s160057751900612x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 05/01/2019] [Indexed: 05/06/2023]
Abstract
Using X-ray energies higher than those normally used (5-15 keV) for macromolecular X-ray crystallography (MX) at synchrotron sources can theoretically increase the achievable signal as a function of dose and reduce the rate of radiation damage. In practice, a major stumbling block to the use of higher X-ray energy has been the reduced quantum efficiency of silicon detectors as the X-ray energy increases, but hybrid photon-counting CdTe detectors are optimized for higher X-ray energies, and their performance has been steadily improving. Here the potential advantages of using higher incident beam energy together with a CdTe detector for MX are explored, with a particular focus on the advantages that higher beam energies may have for MX experiments with microbeams or microcrystals. Monte Carlo simulations are presented here which for the first time include the efficiency responses of some available X-ray detectors, as well as the possible escape of photoelectrons from the sample and their entry from surrounding material. The results reveal a `sweet spot' at an incident X-ray energy of 26 keV, and show a greater than factor of two improvement in diffraction efficiency at this energy when using microbeams and microcrystals of 5 µm or less.
Collapse
Affiliation(s)
- Joshua L Dickerson
- 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
| |
Collapse
|
4
|
Garman EF, Weik M. X-ray radiation damage to biological samples: recent progress. JOURNAL OF SYNCHROTRON RADIATION 2019; 26:907-911. [PMID: 31274412 DOI: 10.1107/s1600577519009408] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 06/30/2019] [Indexed: 05/20/2023]
Abstract
With the continuing development of beamlines for macromolecular crystallography (MX) over the last few years providing ever higher X-ray flux densities, it has become even more important to be aware of the effects of radiation damage on the resulting structures. Nine papers in this issue cover a range of aspects related to the physics and chemistry of the manifestations of this damage, as observed in both MX and small-angle X-ray scattering (SAXS) on crystals, solutions and tissue samples. The reports include measurements of the heating caused by X-ray irradiation in ruby microcrystals, low-dose experiments examining damage rates as a function of incident X-ray energy up to 30 keV on a metallo-enzyme using a CdTe detector of high quantum efficiency as well as a theoretical analysis of the gains predicted in diffraction efficiency using these detectors, a SAXS examination of low-dose radiation exposure effects on the dissociation of a protein complex related to human health, theoretical calculations describing radiation chemistry pathways which aim to explain the specific structural damage widely observed in proteins, investigation of radiation-induced damage effects in a DNA crystal, a case study on a metallo-enzyme where structural movements thought to be mechanism related might actually be radiation-damage-induced changes, and finally a review describing what X-ray radiation-induced cysteine modifications can teach us about protein dynamics and catalysis. These papers, along with some other relevant literature published since the last Journal of Synchrotron Radiation Radiation Damage special issue in 2017, are briefly summarized below.
Collapse
Affiliation(s)
- Elspeth F Garman
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Martin Weik
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044 Grenoble, France
| |
Collapse
|
5
|
Ueno G, Shimada A, Yamashita E, Hasegawa K, Kumasaka T, Shinzawa-Itoh K, Yoshikawa S, Tsukihara T, Yamamoto M. Low-dose X-ray structure analysis of cytochrome c oxidase utilizing high-energy X-rays. JOURNAL OF SYNCHROTRON RADIATION 2019; 26:912-921. [PMID: 31274413 PMCID: PMC6613116 DOI: 10.1107/s1600577519006805] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 05/12/2019] [Indexed: 05/29/2023]
Abstract
To investigate the effect of high-energy X-rays on site-specific radiation-damage, low-dose diffraction data were collected from radiation-sensitive crystals of the metal enzyme cytochrome c oxidase. Data were collected at the Structural Biology I beamline (BL41XU) at SPring-8, using 30 keV X-rays and a highly sensitive pixel array detector equipped with a cadmium telluride sensor. The experimental setup of continuous sample translation using multiple crystals allowed the average diffraction weighted dose per data set to be reduced to 58 kGy, and the resulting data revealed a ligand structure featuring an identical bond length to that in the damage-free structure determined using an X-ray free-electron laser. However, precise analysis of the residual density around the ligand structure refined with the synchrotron data showed the possibility of a small level of specific damage, which might have resulted from the accumulated dose of 58 kGy per data set. Further investigation of the photon-energy dependence of specific damage, as assessed by variations in UV-vis absorption spectra, was conducted using an on-line spectrometer at various energies ranging from 10 to 30 keV. No evidence was found for specific radiation damage being energy dependent.
Collapse
Affiliation(s)
- Go Ueno
- SR Life Science Instrumentation Team, Life Science Research Infrastructure Group, Advanced Photon Technology Division, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Atsuhiro Shimada
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Akoh, Hyogo 678-1297, Japan
| | - Eiki Yamashita
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kazuya Hasegawa
- Protein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute (JASRI), 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Takashi Kumasaka
- Protein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute (JASRI), 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Kyoko Shinzawa-Itoh
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Akoh, Hyogo 678-1297, Japan
| | - Shinya Yoshikawa
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Akoh, Hyogo 678-1297, Japan
| | - Tomitake Tsukihara
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Akoh, Hyogo 678-1297, Japan
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Masaki Yamamoto
- SR Life Science Instrumentation Team, Life Science Research Infrastructure Group, Advanced Photon Technology Division, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| |
Collapse
|
6
|
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
|
7
|
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
|
8
|
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
|
9
|
Liebschner D, Rosenbaum G, Dauter M, Dauter Z. Radiation decay of thaumatin crystals at three X-ray energies. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:772-8. [PMID: 25849388 PMCID: PMC4388262 DOI: 10.1107/s1399004715001030] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 01/17/2015] [Indexed: 11/10/2022]
Abstract
Radiation damage is an unavoidable obstacle in X-ray crystallographic data collection for macromolecular structure determination, so it is important to know how much radiation a sample can endure before being degraded beyond an acceptable limit. In the literature, the threshold at which the average intensity of all recorded reflections decreases to a certain fraction of the initial value is called the `dose limit'. The first estimated D50 dose-limit value, at which the average diffracted intensity was reduced to 50%, was 20 MGy and was derived from observing sample decay in electron-diffraction experiments. A later X-ray study carried out at 100 K on ferritin protein crystals arrived at a D50 of 43 MGy, and recommended an intensity reduction of protein reflections to 70%, D70, corresponding to an absorbed dose of 30 MGy, as a more appropriate limit for macromolecular crystallography. In the macromolecular crystallography community, the rate of intensity decay with dose was then assumed to be similar for all protein crystals. A series of diffraction images of cryocooled (100 K) thaumatin crystals at identical small, 2° rotation intervals were recorded at X-ray energies of 6.33 , 12.66 and 19.00 keV. Five crystals were used for each wavelength. The decay in the average diffraction intensity to 70% of the initial value, for data extending to 2.45 Å resolution, was determined to be about 7.5 MGy at 6.33 keV and about 11 MGy at the two higher energies.
Collapse
Affiliation(s)
- Dorothee Liebschner
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, Tsukuba, Japan
| | - Gerold Rosenbaum
- Department of Biochemistry, University of Georgia and Structural Biology Center, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Miroslawa Dauter
- Leidos Biomedical Research Inc., Basic Science Program, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Zbigniew Dauter
- Synchrotron Radiation Research Section, MCL, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA
| |
Collapse
|
10
|
Liu Q, Guo Y, Chang Y, Cai Z, Assur Z, Mancia F, Greene MI, Hendrickson WA. Multi-crystal native SAD analysis at 6 keV. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:2544-57. [PMID: 25286840 PMCID: PMC4188002 DOI: 10.1107/s1399004714013376] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 06/08/2014] [Indexed: 11/10/2022]
Abstract
Anomalous diffraction signals from typical native macromolecules are very weak, frustrating their use in de novo structure determination. Here, native SAD procedures are described to enhance signal to noise in anomalous diffraction by using multiple crystals in combination with synchrotron X-rays at 6 keV. Increased anomalous signals were obtained at 6 keV compared with 7 keV X-ray energy, which was used for previous native SAD analyses. A feasibility test of multi-crystal-based native SAD phasing was performed at 3.2 Å resolution for a known tyrosine protein kinase domain, and real-life applications were made to two novel membrane proteins at about 3.0 Å resolution. The three applications collectively serve to validate the robust feasibility of native SAD phasing at lower energy.
Collapse
Affiliation(s)
- Qun Liu
- NYCOMPS, New York Structural Biology Center, New York, NY 10032, USA
- New York Structural Biology Center, NSLS X4, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Youzhong Guo
- NYCOMPS, New York Structural Biology Center, New York, NY 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Yanqi Chang
- NYCOMPS, New York Structural Biology Center, New York, NY 10032, USA
| | - Zheng Cai
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Zahra Assur
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | - Mark I. Greene
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wayne A. Hendrickson
- NYCOMPS, New York Structural Biology Center, New York, NY 10032, USA
- New York Structural Biology Center, NSLS X4, Brookhaven National Laboratory, Upton, NY 11973, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| |
Collapse
|
11
|
Sutton KA, Black PJ, Mercer KR, Garman EF, Owen RL, Snell EH, Bernhard WA. Insights into the mechanism of X-ray-induced disulfide-bond cleavage in lysozyme crystals based on EPR, optical absorption and X-ray diffraction studies. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:2381-94. [PMID: 24311579 PMCID: PMC3852651 DOI: 10.1107/s0907444913022117] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 08/07/2013] [Indexed: 11/24/2022]
Abstract
Electron paramagnetic resonance (EPR) and online UV-visible absorption microspectrophotometry with X-ray crystallography have been used in a complementary manner to follow X-ray-induced disulfide-bond cleavage. Online UV-visible spectroscopy showed that upon X-irradiation, disulfide radicalization appeared to saturate at an absorbed dose of approximately 0.5-0.8 MGy, in contrast to the saturating dose of ∼0.2 MGy observed using EPR at much lower dose rates. The observations suggest that a multi-track model involving product formation owing to the interaction of two separate tracks is a valid model for radiation damage in protein crystals. The saturation levels are remarkably consistent given the widely different experimental parameters and the range of total absorbed doses studied. The results indicate that even at the lowest doses used for structural investigations disulfide bonds are already radicalized. Multi-track considerations offer the first step in a comprehensive model of radiation damage that could potentially lead to a combined computational and experimental approach to identifying when damage is likely to be present, to quantitate it and to provide the ability to recover the native unperturbed structure.
Collapse
Affiliation(s)
- Kristin A. Sutton
- Hauptman–Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14086, USA
| | - Paul J. Black
- University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Kermit R. Mercer
- University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Elspeth F. Garman
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, Oxfordshire OX1 3QU, England
| | - Robin L. Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, England
| | - Edward H. Snell
- Hauptman–Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14086, USA
- Department of Structural Biology, SUNY Buffalo Medical School, 700 Ellicott Street, Buffalo, NY 14203, USA
| | | |
Collapse
|
12
|
Vijayakumar B, Velmurugan D. Use of europium ions for SAD phasing of lysozyme at the Cu Kα wavelength. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:20-4. [PMID: 23295480 PMCID: PMC3539697 DOI: 10.1107/s1744309112047562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 11/19/2012] [Indexed: 11/10/2022]
Abstract
Europium is shown to be a good anomalous scatterer in SAD phasing for solving the structure of biological macromolecules. The large value of the anomalous contribution of europium, f'' = 11.17 e(-), at the Cu Kα wavelength is an advantage in de novo phasing and automated model building. Tetragonal crystals of hen egg-white lysozyme (HEWL) incorporating europium(III) chloride (50 mM) were obtained which diffracted to a resolution of 2.3 Å at a wavelength of 1.54 Å (Cu Kα). The master data set (360° frames) was split and analyzed for anomalous signal-to-noise ratio, multiplicity, completeness, SAD phasing and automated building. The structure solution and model building of the split data sets were carried out using phenix.autosol and phenix.autobuild. The contributions of the Eu ions to SAD phasing using in-house data collection are discussed. This study revealed successful lysozyme phasing by SAD using laboratory-source data involving Eu ions, which are mainly coordinated by the side chains of Asn46, Asp52 and Asp101 together with some water molecules.
Collapse
Affiliation(s)
- Balakrishnan Vijayakumar
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Maraimalai (Guindy) Campus, Chennai 600 025, India
| | - Devadasan Velmurugan
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Maraimalai (Guindy) Campus, Chennai 600 025, India
| |
Collapse
|
13
|
Zhu JY, Fu ZQ, Chen L, Xu H, Chrzas J, Rose J, Wang BC. Structure of the Archaeoglobus fulgidus orphan ORF AF1382 determined by sulfur SAD from a moderately diffracting crystal. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:1242-52. [PMID: 22948926 PMCID: PMC3489105 DOI: 10.1107/s0907444912026212] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Accepted: 06/09/2012] [Indexed: 12/22/2022]
Abstract
The crystal structure of the 11.14 kDa orphan ORF 1382 from Archaeoglobus fulgidus (AF1382) has been determined by sulfur SAD phasing using a moderately diffracting crystal and 1.9 Å wavelength synchrotron X-rays. AF1382 was selected as a structural genomics target by the Southeast Collaboratory for Structural Genomics (SECSG) since sequence analyses showed that it did not belong to the Pfam-A database and thus could represent a novel fold. The structure was determined by exploiting longer wavelength X-rays and data redundancy to increase the anomalous signal in the data. AF1382 is a 95-residue protein containing five S atoms associated with four methionine residues and a single cysteine residue that yields a calculated Bijvoet ratio (ΔF(anom)/F) of 1.39% for 1.9 Å wavelength X-rays. Coupled with an average Bijvoet redundancy of 25 (two 360° data sets), this produced an excellent electron-density map that allowed 69 of the 95 residues to be automatically fitted. The S-SAD model was then manually completed and refined (R = 23.2%, R(free) = 26.8%) to 2.3 Å resolution (PDB entry 3o3k). High-resolution data were subsequently collected from a better diffracting crystal using 0.97 Å wavelength synchrotron X-rays and the S-SAD model was refined (R = 17.9%, R(free) = 21.4%) to 1.85 Å resolution (PDB entry 3ov8). AF1382 has a winged-helix-turn-helix structure common to many DNA-binding proteins and most closely resembles the N-terminal domain (residues 1-82) of the Rio2 kinase from A. fulgidus, which has been shown to bind DNA, and a number of MarR-family transcriptional regulators, suggesting a similar DNA-binding function for AF1382. The analysis also points out the advantage gained from carrying out data reduction and structure determination on-site while the crystal is still available for further data collection.
Collapse
Affiliation(s)
- Jin-Yi Zhu
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Zheng-Qing Fu
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
- Southeast Regional Collaborative Access Team (SER-CAT), Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois, USA
| | - Lirong Chen
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Hao Xu
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - John Chrzas
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
- Southeast Regional Collaborative Access Team (SER-CAT), Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois, USA
| | - John Rose
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
- Southeast Regional Collaborative Access Team (SER-CAT), Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois, USA
| | - Bi-Cheng Wang
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
- Southeast Regional Collaborative Access Team (SER-CAT), Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois, USA
| |
Collapse
|
14
|
Liu Q, Dahmane T, Zhang Z, Assur Z, Brasch J, Shapiro L, Mancia F, Hendrickson WA. Structures from anomalous diffraction of native biological macromolecules. Science 2012; 336:1033-7. [PMID: 22628655 DOI: 10.1126/science.1218753] [Citation(s) in RCA: 138] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Crystal structure analyses for biological macromolecules without known structural relatives entail solving the crystallographic phase problem. Typical de novo phase evaluations depend on incorporating heavier atoms than those found natively; most commonly, multi- or single-wavelength anomalous diffraction (MAD or SAD) experiments exploit selenomethionyl proteins. Here, we realize routine structure determination using intrinsic anomalous scattering from native macromolecules. We devised robust procedures for enhancing the signal-to-noise ratio in the slight anomalous scattering from generic native structures by combining data measured from multiple crystals at lower-than-usual x-ray energy. Using this multicrystal SAD method (5 to 13 equivalent crystals), we determined structures at modest resolution (2.8 to 2.3 angstroms) for native proteins varying in size (127 to 1148 unique residues) and number of sulfur sites (3 to 28). With no requirement for heavy-atom incorporation, such experiments provide an attractive alternative to selenomethionyl SAD experiments.
Collapse
Affiliation(s)
- Qun Liu
- New York Structural Biology Center, National Synchrotron Light Source (NSLS) X4, Brookhaven National Laboratory, Upton, NY 11973, USA
| | | | | | | | | | | | | | | |
Collapse
|
15
|
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
|
16
|
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
|
17
|
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
|
18
|
Paithankar KS, Garman EF. Know your dose: RADDOSE. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2010; 66:381-8. [PMID: 20382991 PMCID: PMC2852302 DOI: 10.1107/s0907444910006724] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2009] [Accepted: 02/22/2010] [Indexed: 11/10/2022]
Abstract
The program RADDOSE is widely used to compute the dose absorbed by a macromolecular crystal during an X-ray diffraction experiment. A number of factors affect the absorbed dose, including the incident X-ray flux density, the photon energy and the composition of the macromolecule and of the buffer in the crystal. An experimental dose limit for macromolecular crystallography (MX) of 30 MGy at 100 K has been reported, beyond which the biological information obtained may be compromised. Thus, for the planning of an optimized diffraction experiment the estimation of dose has become an additional tool. A number of approximations were made in the original version of RADDOSE. Recently, the code has been modified in order to take into account fluorescent X-ray escape from the crystal (version 2) and the inclusion of incoherent (Compton) scattering into the dose calculation is now reported (version 3). The Compton cross-section, although negligible at the energies currently commonly used in MX, should be considered in dose calculations for incident energies above 20 keV. Calculations using version 3 of RADDOSE reinforce previous studies that predict a reduction in the absorbed dose when data are collected at higher energies compared with data collected at 12.4 keV. Hence, a longer irradiation lifetime for the sample can be achieved at these higher energies but this is at the cost of lower diffraction intensities. The parameter 'diffraction-dose efficiency', which is the diffracted intensity per absorbed dose, is revisited in an attempt to investigate the benefits and pitfalls of data collection using higher and lower energy radiation, particularly for thin crystals.
Collapse
Affiliation(s)
- Karthik S Paithankar
- Department of Biochemistry, Laboratory of Molecular Biophysics, University of Oxford, South Parks Road, Oxford OX1 3QU, England
| | | |
Collapse
|
19
|
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: 237] [Impact Index Per Article: 16.9] [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
|
20
|
Takeda K, Kusumoto K, Hirano Y, Miki K. Detailed assessment of X-ray induced structural perturbation in a crystalline state protein. J Struct Biol 2010; 169:135-44. [DOI: 10.1016/j.jsb.2009.09.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2009] [Revised: 09/14/2009] [Accepted: 09/21/2009] [Indexed: 10/20/2022]
|
21
|
The Q-cycle reviewed: How well does a monomeric mechanism of the bc(1) complex account for the function of a dimeric complex? BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2008; 1777:1001-19. [PMID: 18501698 DOI: 10.1016/j.bbabio.2008.04.037] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2008] [Revised: 03/26/2008] [Accepted: 04/23/2008] [Indexed: 11/20/2022]
Abstract
Recent progress in understanding the Q-cycle mechanism of the bc(1) complex is reviewed. The data strongly support a mechanism in which the Q(o)-site operates through a reaction in which the first electron transfer from ubiquinol to the oxidized iron-sulfur protein is the rate-determining step for the overall process. The reaction involves a proton-coupled electron transfer down a hydrogen bond between the ubiquinol and a histidine ligand of the [2Fe-2S] cluster, in which the unfavorable protonic configuration contributes a substantial part of the activation barrier. The reaction is endergonic, and the products are an unstable ubisemiquinone at the Q(o)-site, and the reduced iron-sulfur protein, the extrinsic mobile domain of which is now free to dissociate and move away from the site to deliver an electron to cyt c(1) and liberate the H(+). When oxidation of the semiquinone is prevented, it participates in bypass reactions, including superoxide generation if O(2) is available. When the b-heme chain is available as an acceptor, the semiquinone is oxidized in a process in which the proton is passed to the glutamate of the conserved -PEWY- sequence, and the semiquinone anion passes its electron to heme b(L) to form the product ubiquinone. The rate is rapid compared to the limiting reaction, and would require movement of the semiquinone closer to heme b(L) to enhance the rate constant. The acceptor reactions at the Q(i)-site are still controversial, but likely involve a "two-electron gate" in which a stable semiquinone stores an electron. Possible mechanisms to explain the cyt b(150) phenomenon are discussed, and the information from pulsed-EPR studies about the structure of the intermediate state is reviewed. The mechanism discussed is applicable to a monomeric bc(1) complex. We discuss evidence in the literature that has been interpreted as shown that the dimeric structure participates in a more complicated mechanism involving electron transfer across the dimer interface. We show from myxothiazol titrations and mutational analysis of Tyr-199, which is at the interface between monomers, that no such inter-monomer electron transfer is detected at the level of the b(L) hemes. We show from analysis of strains with mutations at Asn-221 that there are coulombic interactions between the b-hemes in a monomer. The data can also be interpreted as showing similar coulombic interaction across the dimer interface, and we discuss mechanistic implications.
Collapse
|
22
|
Kauffmann B, Weiss MS, Lamzin VS, Schmidt A. How to avoid premature decay of your macromolecular crystal: a quick soak for long life. Structure 2006; 14:1099-105. [PMID: 16843891 DOI: 10.1016/j.str.2006.05.015] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2005] [Revised: 05/03/2006] [Accepted: 05/03/2006] [Indexed: 11/22/2022]
Abstract
Radiation damage to biological samples is currently one of the major limiting factors in macromolecular X-ray crystallography, since it severely and irreversibly affects the quality of the data that can be obtained from a diffraction experiment. However, radiation damage can effectively be reduced by utilizing the electron and radical scavenging potential of certain small-molecule compounds. We propose an approach to protect macromolecular crystals prior to data collection by quick soaking with scavengers. This, in favorable cases, can more than double crystal lifetime in the X-ray beam. The approach has the potential to yield diffraction data of superior quality and hence to increase the amount of high-quality diffraction data and of structural information attainable from a single crystal.
Collapse
Affiliation(s)
- Brice Kauffmann
- EMBL Hamburg Outstation, c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany
| | | | | | | |
Collapse
|