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      Development of tools to automate quantitative analysis of radiation damage in SAXS experiments

      a , a , a , a , b , c , d , e , a , *

      Journal of Synchrotron Radiation

      International Union of Crystallography

      Includes papers presented at the 9th International Workshop on X-ray Radiation Damage to Biological Crystalline Samples

      SAXS, radiation damage, RADDOSE-3D, radioprotectants, CorMap visualization

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          Abstract

          Radiation damage analysis with experimental SAXS data allows for the quantitative comparison of the efficacy of various additive radioprotectant compounds. Relevant extensions to RADDOSE-3D and the creation of a new visualization library to enable this study are presented.

          Abstract

          Biological small-angle X-ray scattering (SAXS) is an increasingly popular technique used to obtain nanoscale structural information on macromolecules in solution. However, radiation damage to the samples limits the amount of useful data that can be collected from a single sample. In contrast to the extensive analytical resources available for macromolecular crystallography (MX), there are relatively few tools to quantitate radiation damage for SAXS, some of which require a significant level of manual characterization, with the potential of leading to conflicting results from different studies. Here, computational tools have been developed to automate and standardize radiation damage analysis for SAXS data. RADDOSE-3D, a dose calculation software utility originally written for MX experiments, has been extended to account for the cylindrical geometry of the capillary tube, the liquid composition of the sample and the attenuation of the beam by the capillary material to allow doses to be calculated for many SAXS experiments. Furthermore, a library has been written to visualize and explore the pairwise similarity of frames. The calculated dose for the frame at which three subsequent frames are determined to be dissimilar is defined as the radiation damage onset threshold (RDOT). Analysis of RDOTs has been used to compare the efficacy of radioprotectant compounds to extend the useful lifetime of SAXS samples. Comparison of the RDOTs shows that, for radioprotectant compounds at 5 and 10 m M concentration, glycerol is the most effective compound. However, at 1 and 2 m M concentrations, di­thio­threitol (DTT) appears to be most effective. Our newly developed visualization library contains methods that highlight the unusual radiation damage results given by SAXS data collected using higher concentrations of DTT: these observations should pave the way to the development of more sophisticated frame merging strategies.

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          Author and article information

          Affiliations
          [a ]Department of Biochemistry, University of Oxford , Oxford OX1 3QU, UK
          [b ]Division of Structural Biology, Wellcome Trust Centre for Human Genetics , Roosevelt Drive, Oxford OX3 7BN, UK
          [c ]European Molecular Biology Laboratory, Grenoble Outstation , 71 avenue des Martyrs, CS 90181, 38042 Grenoble, France
          [d ]SPB/SFX European XFEL , Holzkoppel 4, 22869 Schenefeld, Germany
          [e ]Faculty of Natural Sciences, Keele University , Staffordshire ST5 5BG, UK
          Author notes
          Conference
          J Synchrotron Radiat
          J Synchrotron Radiat
          J. Synchrotron Rad.
          Journal of Synchrotron Radiation
          International Union of Crystallography
          0909-0495
          1600-5775
          01 January 2017
          01 January 2017
          01 January 2017
          : 24
          : Pt 1 ( publisher-idID: s170100 )
          : 63-72
          28009547 5182020 xh5050 10.1107/S1600577516015083 JSYRES S1600577516015083
          © Jonathan C. Brooks-Bartlett et al. 2017

          This is an open-access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.

          Includes papers presented at the 9th International Workshop on X-ray Radiation Damage to Biological Crystalline Samples
          Categories
          Radiation Damage

          Radiology & Imaging

          saxs, radiation damage, raddose-3d, radioprotectants, cormap visualization

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