Literature DB >> 27275138

Quantifying radiation damage in biomolecular small-angle X-ray scattering.

Jesse B Hopkins1, Robert E Thorne2.   

Abstract

Small-angle X-ray scattering (SAXS) is an increasingly popular technique that provides low-resolution structural information about biological macromolecules in solution. Many of the practical limitations of the technique, such as minimum required sample volume, and of experimental design, such as sample flow cells, are necessary because the biological samples are sensitive to damage from the X-rays. Radiation damage typically manifests as aggregation of the sample, which makes the collected data unreliable. However, there has been little systematic investigation of the most effective methods to reduce damage rates, and results from previous damage studies are not easily compared with results from other beamlines. Here a methodology is provided for quantifying radiation damage in SAXS to provide consistent results between different experiments, experimenters and beamlines. These methods are demonstrated on radiation damage data collected from lysozyme, glucose isomerase and xylanase, and it is found that no single metric is sufficient to describe radiation damage in SAXS for all samples. The radius of gyration, molecular weight and integrated SAXS profile intensity constitute a minimal set of parameters that capture all types of observed behavior. Radiation sensitivities derived from these parameters show a large protein dependence, varying by up to six orders of magnitude between the different proteins tested. This work should enable consistent reporting of radiation damage effects, allowing more systematic studies of the most effective minimization strategies.

Entities:  

Keywords:  SAXS; radiation damage; small-angle X-ray scattering

Year:  2016        PMID: 27275138      PMCID: PMC4886981          DOI: 10.1107/S1600576716005136

Source DB:  PubMed          Journal:  J Appl Crystallogr        ISSN: 0021-8898            Impact factor:   3.304


  45 in total

1.  Global radiation damage at 300 and 260 K with dose rates approaching 1 MGy s⁻¹.

Authors:  Matthew Warkentin; Ryan Badeau; Jesse B Hopkins; Anne M Mulichak; Lisa J Keefe; Robert E Thorne
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2012-01-17

2.  Dose dependence of radiation damage for protein crystals studied at various X-ray energies.

Authors:  Nobutaka Shimizu; Kunio Hirata; Kazuya Hasegawa; Go Ueno; Masaki Yamamoto
Journal:  J Synchrotron Radiat       Date:  2006-12-15       Impact factor: 2.616

3.  High-resolution wide-angle X-ray scattering of protein solutions: effect of beam dose on protein integrity.

Authors:  Robert F Fischetti; Diane J Rodi; Ahmed Mirza; Thomas C Irving; Elena Kondrashkina; Lee Makowski
Journal:  J Synchrotron Radiat       Date:  2003-08-28       Impact factor: 2.616

4.  Upgrade of MacCHESS facility for X-ray scattering of biological macromolecules in solution.

Authors:  Alvin Samuel Acerbo; Michael J Cook; Richard Edward Gillilan
Journal:  J Synchrotron Radiat       Date:  2015-01-01       Impact factor: 2.616

5.  Protein damage and degradation by oxygen radicals. III. Modification of secondary and tertiary structure.

Authors:  K J Davies; M E Delsignore
Journal:  J Biol Chem       Date:  1987-07-15       Impact factor: 5.157

6.  Know your dose: RADDOSE.

Authors:  Karthik S Paithankar; Elspeth F Garman
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2010-03-24

7.  Versatile sample environments and automation for biological solution X-ray scattering experiments at the P12 beamline (PETRA III, DESY).

Authors:  Clement E Blanchet; Alessandro Spilotros; Frank Schwemmer; Melissa A Graewert; Alexey Kikhney; Cy M Jeffries; Daniel Franke; Daniel Mark; Roland Zengerle; Florent Cipriani; Stefan Fiedler; Manfred Roessle; Dmitri I Svergun
Journal:  J Appl Crystallogr       Date:  2015-03-12       Impact factor: 3.304

8.  Sub-millisecond time-resolved SAXS using a continuous-flow mixer and X-ray microbeam.

Authors:  Rita Graceffa; R Paul Nobrega; Raul A Barrea; Sagar V Kathuria; Srinivas Chakravarthy; Osman Bilsel; Thomas C Irving
Journal:  J Synchrotron Radiat       Date:  2013-10-01       Impact factor: 2.616

9.  ISPyB for BioSAXS, the gateway to user autonomy in solution scattering experiments.

Authors:  Alejandro De Maria Antolinos; Petra Pernot; Martha E Brennich; Jérôme Kieffer; Matthew W Bowler; Solange Delageniere; Staffan Ohlsson; Stephanie Malbet Monaco; Alun Ashton; Daniel Franke; Dmitri Svergun; Sean McSweeney; Elspeth Gordon; Adam Round
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2015-01-01

10.  The accurate assessment of small-angle X-ray scattering data.

Authors:  Thomas D Grant; Joseph R Luft; Lester G Carter; Tsutomu Matsui; Thomas M Weiss; Anne Martel; Edward H Snell
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2015-01-01
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  14 in total

Review 1.  Predicting data quality in biological X-ray solution scattering.

Authors:  Chenzheng Wang; Yuexia Lin; Devin Bougie; Richard E Gillilan
Journal:  Acta Crystallogr D Struct Biol       Date:  2018-07-24       Impact factor: 7.652

2.  Structural consequences of transforming growth factor beta-1 activation from near-therapeutic X-ray doses.

Authors:  Timothy Stachowski; Thomas D Grant; Edward H Snell
Journal:  J Synchrotron Radiat       Date:  2019-06-13       Impact factor: 2.616

3.  Resonant Soft X-Ray Scattering Provides Protein Structure with Chemical Specificity.

Authors:  Dan Ye; Thinh P Le; Brooke Kuei; Chenhui Zhu; Peter H Zwart; Cheng Wang; Enrique D Gomez; Esther W Gomez
Journal:  Structure       Date:  2018-09-13       Impact factor: 5.006

4.  High-pressure small-angle X-ray scattering cell for biological solutions and soft materials.

Authors:  Durgesh K Rai; Richard E Gillilan; Qingqiu Huang; Robert Miller; Edmund Ting; Alexander Lazarev; Mark W Tate; Sol M Gruner
Journal:  J Appl Crystallogr       Date:  2021-02-01       Impact factor: 3.304

5.  Small-angle X-ray scattering experiments of monodisperse intrinsically disordered protein samples close to the solubility limit.

Authors:  Erik W Martin; Jesse B Hopkins; Tanja Mittag
Journal:  Methods Enzymol       Date:  2020-08-04       Impact factor: 1.600

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

Authors:  Jonathan C Brooks-Bartlett; Rebecca A Batters; Charles S Bury; Edward D Lowe; Helen Mary Ginn; Adam Round; Elspeth F Garman
Journal:  J Synchrotron Radiat       Date:  2017-01-01       Impact factor: 2.616

7.  Improved radiation dose efficiency in solution SAXS using a sheath flow sample environment.

Authors:  Nigel Kirby; Nathan Cowieson; Adrian M Hawley; Stephen T Mudie; Duncan J McGillivray; Michael Kusel; Vesna Samardzic-Boban; Timothy M Ryan
Journal:  Acta Crystallogr D Struct Biol       Date:  2016-11-29       Impact factor: 7.652

8.  Quantitative evaluation of statistical errors in small-angle X-ray scattering measurements.

Authors:  Steffen M Sedlak; Linda K Bruetzel; Jan Lipfert
Journal:  J Appl Crystallogr       Date:  2017-03-29       Impact factor: 3.304

9.  Smaller capillaries improve the small-angle X-ray scattering signal and sample consumption for biomacromolecular solutions.

Authors:  Martin A Schroer; Clement E Blanchet; Andrey Yu Gruzinov; Melissa A Gräwert; Martha E Brennich; Nelly R Hajizadeh; Cy M Jeffries; Dmitri I Svergun
Journal:  J Synchrotron Radiat       Date:  2018-06-26       Impact factor: 2.616

10.  Solution scattering at the Life Science X-ray Scattering (LiX) beamline.

Authors:  Lin Yang; Stephen Antonelli; Shirish Chodankar; James Byrnes; Edwin Lazo; Kun Qian
Journal:  J Synchrotron Radiat       Date:  2020-03-31       Impact factor: 2.616

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