Identifying and quantifying radiation damage at the atomic level

Journal of Synchrotron Radiation
Markus GerstelElspeth F Garman

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...Continue Reading

References

Jul 1, 1980·International Journal of Peptide and Protein Research·K Nishikawa, T Ooi
Dec 1, 1995·Proteins·D Frishman, P Argos
Sep 9, 1998·Bioinformatics·K MizuguchiJ P Overington
Mar 25, 1999·Acta Crystallographica. Section D, Biological Crystallography·O Carugo, P Argos
Jan 19, 2000·Proceedings of the National Academy of Sciences of the United States of America·M WeikJ L Sussman
Mar 14, 2000·Acta Crystallographica. Section D, Biological Crystallography·W P Burmeister
Apr 4, 2000·Structure·R B Ravelli, S M McSweeney
Jan 31, 2002·Proceedings of the National Academy of Sciences of the United States of America·Bertil Halle
Jul 16, 2002·Bioinformatics·Alessandro PintarSándor Pongor
Jul 24, 2002·Acta Crystallographica. Section D, Biological Crystallography·E EnnifarP Dumas
Nov 1, 2002·Journal of Synchrotron Radiation·Martin WeikRaimond B G Ravelli
Nov 1, 2002·Journal of Synchrotron Radiation·Raimond B G RavelliMartin Caffrey
Feb 11, 2003·Structure·Raimond B G RavelliSean McSweeney
Aug 13, 2003·Bioinformatics·Guoli Wang, Roland L Dunbrack
Nov 25, 2003·Nature Structural Biology·Helen BermanHaruki Nakamura
Mar 18, 2004·The Journal of Biological Chemistry·Remco KortRaimond B G Ravelli
Aug 17, 2005·Proceedings of the National Academy of Sciences of the United States of America·Junko YanoVittal K Yachandra
Sep 1, 2005·Acta Crystallographica. Section D, Biological Crystallography·Max H NanaoRaimond B G Ravelli
Sep 1, 2005·Acta Crystallographica. Section D, Biological Crystallography·Udupi A RamagopalSteven C Almo
Mar 22, 2006·Proceedings of the National Academy of Sciences of the United States of America·Robin Leslie OwenElspeth F Garman
Mar 23, 2006·Acta Crystallographica. Section D, Biological Crystallography·Jay Painter, Ethan A Merritt
Jun 14, 2006·Biochemistry·Bryan SchmidtPhilip J Hogg
Aug 25, 2006·Acta Crystallographica. Section D, Biological Crystallography·Jan KmetkoRobert E Thorne
Jan 11, 2007·Journal of Synchrotron Radiation·Nobutaka ShimizuMasaki Yamamoto
Jan 11, 2007·Journal of Synchrotron Radiation·Emanuela FioravantiMartin Weik
Dec 18, 2007·Acta Crystallographica. Section D, Biological Crystallography·Manfred S Weiss
Jan 9, 2009·Bioinformatics·Benjamin M Bulheller, Jonathan D Hirst
Jan 19, 2010·Proceedings of the National Academy of Sciences of the United States of America·Alke MeentsClemens Schulze-Briese
Apr 13, 2010·Acta Crystallographica. Section D, Biological Crystallography·Elspeth F Garman
Apr 13, 2010·Acta Crystallographica. Section D, Biological Crystallography·Gleb P Bourenkov, Alexander N Popov
Apr 13, 2010·Acta Crystallographica. Section D, Biological Crystallography·George M Sheldrick
Apr 13, 2010·Acta Crystallographica. Section D, Biological Crystallography·P EmsleyK Cowtan
Oct 15, 2010·Acta Crystallographica. Section D, Biological Crystallography·Tatiana PetrovaAndrzej Joachimiak
Apr 5, 2011·Acta Crystallographica. Section D, Biological Crystallography·Martyn D WinnKeith S Wilson
Apr 29, 2011·Journal of Synchrotron Radiation·Douglas H Juers, Martin Weik
Apr 29, 2011·Journal of Synchrotron Radiation·Christina HomerAna Gonzalez
Apr 6, 2012·Journal of Applied Crystallography·Andrea Thorn, George M Sheldrick
Sep 6, 2012·Acta Crystallographica. Section D, Biological Crystallography·Matthew WarkentinRobert E Thorne
Feb 7, 2013·Acta Crystallographica. Section D, Biological Crystallography·Edwin PozharskiBernhard Rupp
May 11, 2013·Nature Reviews. Cancer·Philip J Hogg
Dec 7, 2013·Acta Crystallographica. Section D, Biological Crystallography·Kristin A SuttonWilliam A Bernhard

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Citations

Feb 28, 2015·Journal of Synchrotron Radiation·Elspeth F Garman, Martin Weik
May 4, 2016·Acta Crystallographica. Section D, Structural Biology·Charles S BuryElspeth F Garman
May 10, 2016·Biochimica Et Biophysica Acta. General Subjects·Zehra SayersInes Karmous
Dec 24, 2016·Journal of Synchrotron Radiation·Charles S BuryElspeth F Garman
Dec 24, 2016·Journal of Synchrotron Radiation·Eva CrosasJordi Juanhuix
Dec 24, 2016·Journal of Synchrotron Radiation·Ivan PolsinelliWilliam Shepard
Jun 4, 2019·Journal of Computer-aided Molecular Design·Pedro A Sánchez-MurciaFederico Gago
Jul 6, 2019·Journal of Synchrotron Radiation·Helena TabermanElspeth F Garman
Oct 3, 2020·Acta Crystallographica. Section F, Structural Biology Communications·Gareth D FennBenjamin D Bax
Apr 17, 2018·Journal of Applied Crystallography·Kathryn L ShelleyElspeth F Garman
Sep 3, 2020·Acta Crystallographica. Section D, Structural Biology·Marina Plaza-GarridoAna Camara-Artigas
Apr 26, 2019·Proceedings of the National Academy of Sciences of the United States of America·Christopher O BarnesGuillermo Calero
Mar 1, 2018·Journal of Synchrotron Radiation·Dominika BorekZbyszek Otwinowski
Dec 3, 2020·Acta Crystallographica. Section D, Structural Biology·Alexander MehrTrevor Huyton
Jan 9, 2021·Quarterly Reviews of Biophysics·Marcus Fischer
Apr 29, 2019·Methods : a Companion to Methods in Enzymology·Guowu LinGuillermo Calero
May 29, 2021·Journal of Photochemistry and Photobiology. B, Biology·Chao YangShengjie Xia
Jan 30, 2019·Journal of Chemical Information and Modeling·Theodore L FobeDemian Riccardi
Aug 22, 2021·Proceedings of the National Academy of Sciences of the United States of America·Baldeep KhareRichard J Kuhn
Jan 5, 2022·Acta Crystallographica. Section D, Structural Biology·Oliviero Carugo

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Methods Mentioned

BETA
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Software Mentioned

PISCES
PDBCUR
PSA
PyMOL
PERL
ParsePDB
STRIDE
R
WinCoot
ANODE

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