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Title: OH cleavage from tyrosine: debunking a myth

Abstract

During macromolecular X-ray crystallography experiments, protein crystals held at 100 K have been widely reported to exhibit reproducible bond scission events at doses on the order of several MGy. With the objective to mitigate the impact of radiation damage events on valid structure determination, it is essential to correctly understand the radiation chemistry mechanisms at play. OH-cleavage from tyrosine residues is regularly cited as amongst the most available damage pathways in protein crystals at 100 K, despite a lack of widespread reports of this phenomenon in protein crystal radiation damage studies. Furthermore, no clear mechanism for phenolic C—O bond cleavage in tyrosine has been reported, with the tyrosyl radical known to be relatively robust and long-lived in both aqueous solutions and the solid state. Here, the initial findings of Tyr –OH group damage in a myrosinase protein crystal have been reviewed. Consistent with that study, at increasing doses, clear electron density loss was detectable local to Tyr –OH groups. A systematic investigation performed on a range of protein crystal damage series deposited in the Protein Data Bank has established that Tyr –OH electron density loss is not generally a dominant damage pathway in protein crystals at 100 K. Full Tyrmore » aromatic ring displacement is here proposed to account for instances of observable Tyr –OH electron density loss, with the original myrosinase data shown to be consistent with such a damage model. Also presented are systematic analysis of the effects of other environmental factors, including solvent accessibility and proximity to disulfide bonds or hydrogen bond interactions. Residues in known active sites showed enhanced sensitivity to radiation-induced disordering, as has previously been reported.« less

Authors:
 [1];  [2];  [1]
  1. Univ. of Oxford (United Kingdom). Lab. of Molecular Biophysics
  2. Univ. of Notre Dame, IN (United States). Radiation Lab.
Publication Date:
Research Org.:
Univ. of Notre Dame, IN (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22); Engineering and Physical Sciences Research Council (EPSRC); Univ. of Oxford (United Kingdom)
OSTI Identifier:
1427170
Grant/Contract Number:  
FC02-04ER15533
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Synchrotron Radiation (Online)
Additional Journal Information:
Journal Name: Journal of Synchrotron Radiation (Online); Journal Volume: 24; Journal Issue: 1; Journal ID: ISSN 1600-5775
Publisher:
International Union of Crystallography
Country of Publication:
United States
Language:
English
Subject:
38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEAR CHEMISTRY; 74 ATOMIC AND MOLECULAR PHYSICS; 59 BASIC BIOLOGICAL SCIENCES; tyrosine; specific damage; radiation chemistry; electron density loss; Fourier difference maps

Citation Formats

Bury, Charles S., Carmichael, Ian, and Garman, Elspeth F. OH cleavage from tyrosine: debunking a myth. United States: N. p., 2017. Web. doi:10.1107/S1600577516016775.
Bury, Charles S., Carmichael, Ian, & Garman, Elspeth F. OH cleavage from tyrosine: debunking a myth. United States. doi:10.1107/S1600577516016775.
Bury, Charles S., Carmichael, Ian, and Garman, Elspeth F. Sun . "OH cleavage from tyrosine: debunking a myth". United States. doi:10.1107/S1600577516016775. https://www.osti.gov/servlets/purl/1427170.
@article{osti_1427170,
title = {OH cleavage from tyrosine: debunking a myth},
author = {Bury, Charles S. and Carmichael, Ian and Garman, Elspeth F.},
abstractNote = {During macromolecular X-ray crystallography experiments, protein crystals held at 100 K have been widely reported to exhibit reproducible bond scission events at doses on the order of several MGy. With the objective to mitigate the impact of radiation damage events on valid structure determination, it is essential to correctly understand the radiation chemistry mechanisms at play. OH-cleavage from tyrosine residues is regularly cited as amongst the most available damage pathways in protein crystals at 100 K, despite a lack of widespread reports of this phenomenon in protein crystal radiation damage studies. Furthermore, no clear mechanism for phenolic C—O bond cleavage in tyrosine has been reported, with the tyrosyl radical known to be relatively robust and long-lived in both aqueous solutions and the solid state. Here, the initial findings of Tyr –OH group damage in a myrosinase protein crystal have been reviewed. Consistent with that study, at increasing doses, clear electron density loss was detectable local to Tyr –OH groups. A systematic investigation performed on a range of protein crystal damage series deposited in the Protein Data Bank has established that Tyr –OH electron density loss is not generally a dominant damage pathway in protein crystals at 100 K. Full Tyr aromatic ring displacement is here proposed to account for instances of observable Tyr –OH electron density loss, with the original myrosinase data shown to be consistent with such a damage model. Also presented are systematic analysis of the effects of other environmental factors, including solvent accessibility and proximity to disulfide bonds or hydrogen bond interactions. Residues in known active sites showed enhanced sensitivity to radiation-induced disordering, as has previously been reported.},
doi = {10.1107/S1600577516016775},
journal = {Journal of Synchrotron Radiation (Online)},
number = 1,
volume = 24,
place = {United States},
year = {2017},
month = {1}
}

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Cited by: 6 works
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    Comprehensive model for X-ray-induced damage in protein crystallography
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    • DOI: 10.1107/s1600577519005083

    Structural knowledge or X-ray damage? A case study on xylose isomerase illustrating both
    journal, June 2019

    • Taberman, Helena; Bury, Charles S.; van der Woerd, Mark J.
    • Journal of Synchrotron Radiation, Vol. 26, Issue 4
    • DOI: 10.1107/s1600577519005599

    The potential benefits of using higher X-ray energies for macromolecular crystallography
    journal, June 2019

    • Dickerson, Joshua L.; Garman, Elspeth F.; Dickerson, Joshua L.
    • Journal of Synchrotron Radiation, Vol. 26, Issue 4
    • DOI: 10.1107/s160057751900612x

    Radiation-damage investigation of a DNA 16-mer
    journal, June 2019

    • Bugris, Valéria; Harmat, Veronika; Ferenc, Györgyi
    • Journal of Synchrotron Radiation, Vol. 26, Issue 4
    • DOI: 10.1107/s160057751900763x