scholarly journals Radiation damage to nucleoprotein complexes in macromolecular crystallography

2015 ◽  
Vol 22 (2) ◽  
pp. 213-224 ◽  
Author(s):  
Charles Bury ◽  
Elspeth F. Garman ◽  
Helen Mary Ginn ◽  
Raimond B. G. Ravelli ◽  
Ian Carmichael ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Radiation Damage ◽  
Diffraction Data ◽  
Dose Range ◽  
Computational Method ◽  
Large Field ◽  
Macromolecular Crystallography ◽  
Damage Mechanisms ◽  
X Ray ◽  
Nucleoprotein Complexes

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.

scholarly journals Sub-atomic resolution X-ray crystallography and neutron crystallography: promise, challenges and potential

IUCrJ ◽  
2015 ◽  
Vol 2 (4) ◽  
pp. 464-474 ◽  
Author(s):  
Matthew P. Blakeley ◽  
Samar S. Hasnain ◽  
Svetlana V. Antonyuk
Keyword(s):  
Radiation Damage ◽  
Diffraction Data ◽  
Atomic Resolution ◽  
Current Status ◽  
X Rays ◽  
Macromolecular Crystallography ◽  
X Ray ◽  
X Ray Crystallography ◽  
Small Proteins ◽  
Neutron Crystallography

The International Year of Crystallography saw the number of macromolecular structures deposited in the Protein Data Bank cross the 100000 mark, with more than 90000 of these provided by X-ray crystallography. The number of X-ray structures determined to sub-atomic resolution (i.e.≤1 Å) has passed 600 and this is likely to continue to grow rapidly with diffraction-limited synchrotron radiation sources such as MAX-IV (Sweden) and Sirius (Brazil) under construction. A dozen X-ray structures have been deposited to ultra-high resolution (i.e.≤0.7 Å), for which precise electron density can be exploited to obtain charge density and provide information on the bonding character of catalytic or electron transfer sites. Although the development of neutron macromolecular crystallography over the years has been far less pronounced, and its application much less widespread, the availability of new and improved instrumentation, combined with dedicated deuteration facilities, are beginning to transform the field. Of the 83 macromolecular structures deposited with neutron diffraction data, more than half (49/83, 59%) were released since 2010. Sub-mm3crystals are now regularly being used for data collection, structures have been determined to atomic resolution for a few small proteins, and much larger unit-cell systems (cell edges >100 Å) are being successfully studied. While some details relating to H-atom positions are tractable with X-ray crystallography at sub-atomic resolution, the mobility of certain H atoms precludes them from being located. In addition, highly polarized H atoms and protons (H+) remain invisible with X-rays. Moreover, the majority of X-ray structures are determined from cryo-cooled crystals at 100 K, and, although radiation damage can be strongly controlled, especially since the advent of shutterless fast detectors, and by using limited doses and crystal translation at micro-focus beams, radiation damage can still take place. Neutron crystallography therefore remains the only approach where diffraction data can be collected at room temperature without radiation damage issues and the only approach to locate mobile or highly polarized H atoms and protons. Here a review of the current status of sub-atomic X-ray and neutron macromolecular crystallography is given and future prospects for combined approaches are outlined. New results from two metalloproteins, copper nitrite reductase and cytochromec′, are also included, which illustrate the type of information that can be obtained from sub-atomic-resolution (∼0.8 Å) X-ray structures, while also highlighting the need for complementary neutron studies that can provide details of H atoms not provided by X-ray crystallography.

Studies of metaphase chromosomes in the scanning transmission x-ray microscope: Image fidelity, radiation damage and specimen preparation

1992 ◽  
Vol 50 (2) ◽  
pp. 1038-1039
Author(s):  
Shawn Williams ◽  
Xiaodong Zhang ◽  
Susan Lamm ◽  
Jack Van’t Hof
Keyword(s):  
Visible Light ◽  
Radiation Damage ◽  
Cross Section ◽  
Imaging Techniques ◽  
Dose Range ◽  
Specimen Preparation ◽  
X Rays ◽  
Metaphase Chromosomes ◽  
X Ray ◽  
Scanning Transmission

The Scanning Transmission X-ray Microscope (STXM) is well suited for investigating metaphase chromosome structure. The absorption cross-section of soft x-rays having energies between the carbon and oxygen K edges (284 - 531 eV) is 6 - 9.5 times greater for organic specimens than for water, which permits one to examine unstained, wet biological specimens with resolution superior to that attainable using visible light. The attenuation length of the x-rays is suitable for imaging micron thick specimens without sectioning. This large difference in cross-section yields good specimen contrast, so that fewer soft x-rays than electrons are required to image wet biological specimens at a given resolution. But most imaging techniques delivering better resolution than visible light produce radiation damage. Soft x-rays are known to be very effective in damaging biological specimens. The STXM is constructed to minimize specimen dose, but it is important to measure the actual damage induced as a function of dose in order to determine the dose range within which radiation damage does not compromise image quality.

scholarly journals Die Kristallstruktur von Methylquecksilberazid / The Crystal Structure of Methyl Mercury Azide

1973 ◽  
Vol 28 (7-8) ◽  
pp. 426-428 ◽  
Author(s):  
Ulrich Müller
Keyword(s):  
Crystal Structure ◽  
Radiation Damage ◽  
Diffraction Data ◽  
Methyl Mercury ◽  
Unit Cell ◽  
Outer Side ◽  
Methyl Groups ◽  
X Ray Diffraction ◽  
Space Group ◽  
X Ray

CH3HgN3 crystallizes in the space group P21/c with four molecules per unit cell. The structure was solved by common crystallographic methods using X-ray diffraction data that were collected at a temperature of 100°K. The cooling was necessary to limit the radiation damage of the crystals. The molecules possess an essentially linear C-Hg-N group; in the crystals they are associated to layers bearing the methyl groups on their outer side.

RADDOSE-3D: time- and space-resolved modelling of dose in macromolecular crystallography

2013 ◽  
Vol 46 (4) ◽  
pp. 1225-1230 ◽  
Author(s):  
Oliver B. Zeldin ◽  
Markus Gerstel ◽  
Elspeth F. Garman
Keyword(s):  
Data Collection ◽  
Radiation Damage ◽  
Diffraction Experiment ◽  
Macromolecular Crystallography ◽  
X Ray Diffraction ◽  
Time Resolved ◽  
X Ray ◽  
Online Methods ◽  
Crystal Volume ◽  
Number Of Iterations

RADDOSE-3D allows the macroscopic modelling of an X-ray diffraction experiment for the purpose of better predicting radiation-damage progression. The distribution of dose within the crystal volume is calculated for a number of iterations in small angular steps across one or more data collection wedges, providing a time-resolved picture of the dose state of the crystal. The code is highly modular so that future contributions from the community can be easily integrated into it, in particular to incorporate online methods for determining the shape of macromolecular crystals and better protocols for imaging real experimental X-ray beam profiles.

scholarly journals XAS at the Canadian Macromolecular Crystallography Facility

2014 ◽  
Vol 70 (a1) ◽  
pp. C1525-C1525
Author(s):  
Julien Cotelesage ◽  
Pawel Grochulski ◽  
Michel Fodje ◽  
James Gorin ◽  
Kathryn Janzen ◽  
...  
Keyword(s):  
Data Collection ◽  
Diffraction Data ◽  
Three Dimensional ◽  
Minimal Risk ◽  
Macromolecular Crystallography ◽  
X Ray ◽  
Biologically Relevant ◽  
Wide Range ◽  
X Ray Absorption ◽  
Do So

Recent additions to the Canadian Macromolecular Crystallography Facility have expanded the capabilities of its bending magnet beamline. It is now possible to perform x-ray absorption spectroscopy (XAS) on crystals. A wide range of biologically relevant metals can be further studied, supplementing diffraction data. XAS can be used to determine if metalloproteins are photoreducing during diffraction data collection. The geometries of metal complexes can also be inferred with near-edge and EXAFS data, often more accurately than crystallography. CMCF-BM can be employed to do the abovementioned techniques on powder and solution samples that contain a metal of interest. One XAS-based technique that shows promise is single crystal plane polarized EXAFS. This technique combines crystallographic data with the findings from XAS to yield a high resolution three dimensional atomic model. More recently a number of the procedural steps required for the acquisition of XAS-based data have been automated in the MxDC software suite. These changes to data collection make it easier for users new to these disciplines to run the XAS-based experiments. By having the necessary equipment to do XAS at a protein crystallography facility, researchers who may not have had the opportunity delve into the field of XAS now can do so with minimal risk in terms of materials, funds and time.

scholarly journals Macromolecular crystallography using neutrons

2014 ◽  
Vol 36 (3) ◽  
pp. 40-42
Author(s):  
Matthew Blakeley
Keyword(s):  
Nucleic Acids ◽  
Biological Systems ◽  
Biological Macromolecules ◽  
X Rays ◽  
Macromolecular Crystallography ◽  
X Ray Diffraction ◽  
Vast Array ◽  
X Ray ◽  
Macromolecular Assemblies

When you think about macromolecular crystallography, the technique that most often comes to mind is X-ray diffraction and it's no wonder. Over 88000 structures of biological macromolecules – from proteins and nucleic acids to viruses and macromolecular assemblies – have been determined using X-rays, and these have contributed significantly to our understanding of a vast array of biological systems and processes.

scholarly journals A history of experimental phasing in macromolecular crystallography

2016 ◽  
Vol 72 (3) ◽  
pp. 293-295 ◽  
Author(s):  
Neil Isaacs
Keyword(s):  
Crystal Structures ◽  
Electron Density ◽  
Diffraction Data ◽  
Fourier Transforms ◽  
Macromolecular Crystallography ◽  
X Ray Diffraction ◽  
Crystal Lattices ◽  
X Ray ◽  
Experimental Phasing ◽  
History Of

It was just over a century ago that W. L. Bragg published a paper describing the first crystal structures to be determined using X-ray diffraction data. These structures were obtained from considerations of X-ray diffraction (Bragg equation), crystallography (crystal lattices and symmetry) and the scattering power of different atoms. Although W. H. Bragg proposed soon afterwards, in 1915, that the periodic electron density in crystals could be analysed using Fourier transforms, it took some decades before experimental phasing methods were developed. Many scientists contributed to this development and this paper presents the author's own perspective on this history. There will be other perspectives, so what follows isahistory, rather thanthehistory, of experimental phasing.

scholarly journals Visualization of protein crystals by high-energy phase-contrast X-ray imaging

2019 ◽  
Vol 75 (11) ◽  
pp. 947-958 ◽  
Author(s):  
Maxim Polikarpov ◽  
Gleb Bourenkov ◽  
Irina Snigireva ◽  
Anatoly Snigirev ◽  
Sophie Zimmermann ◽  
...  
Keyword(s):  
Synchrotron Radiation ◽  
Data Collection ◽  
Diffraction Data ◽  
Phase Contrast ◽  
High Energy ◽  
Protein Crystals ◽  
Cubic Phase ◽  
Macromolecular Crystallography ◽  
X Ray ◽  
X Ray Imaging

For the extraction of the best possible X-ray diffraction data from macromolecular crystals, accurate positioning of the crystals with respect to the X-ray beam is crucial. In addition, information about the shape and internal defects of crystals allows the optimization of data-collection strategies. Here, it is demonstrated that the X-ray beam available on the macromolecular crystallography beamline P14 at the high-brilliance synchrotron-radiation source PETRA III at DESY, Hamburg, Germany can be used for high-energy phase-contrast microtomography of protein crystals mounted in an optically opaque lipidic cubic phase matrix. Three-dimensional tomograms have been obtained at X-ray doses that are substantially smaller and on time scales that are substantially shorter than those used for diffraction-scanning approaches that display protein crystals at micrometre resolution. Adding a compound refractive lens as an objective to the imaging setup, two-dimensional imaging at sub-micrometre resolution has been achieved. All experiments were performed on a standard macromolecular crystallography beamline and are compatible with standard diffraction data-collection workflows and apparatus. Phase-contrast X-ray imaging of macromolecular crystals could find wide application at existing and upcoming low-emittance synchrotron-radiation sources.

Sign in / Sign up

Export Citation Format

Share Document