Year: 2016
Type: article
Abstract: Radiation damage has been a curse of macromolecular crystallography from its early days.This problem was very acute when diffraction data used to be measured from crystals kept at ambient temperatures.The introduction of cryo-cooling techniques to some extent alleviated the severity of damaging effects incurred by protein and nucleic acid crystals because of irradiation by X-rays, but very intense currently available synchrotron sources may destroy diffracting crystals after minutes or seconds of exposure.Not only does the quality of diffraction data and structure solution processes suffer, but, more importantly, radiation damage may lead to misinterpretation of chemical and biological results and to false mechanistic conclusions.Investigations into the effect of radiation damage, and of the ways of dealing with this effect, is a hot topic of contemporary macromolecular methodology.Dedicated international workshops are regularly organized every two years as a forum for discussion of novel results, with the proceedings published in the Journal of Synchrotron Radiation (see http://journals.iucr.org/s/services/specialissues.html for a list of radiation damage special issues).The effects of radiation damage are manifested globally after absorbing doses of several tens of MGy by a decrease in the total crystal diffraction power, a change of unitcell dimensions, an increase of crystal mosaicity or eventually its cracking and disintegration.However, even after absorbing much smaller energy doses of 1-2 MGy, many specific local effects of damage can be identified within the structures of macromolecules.Those most often observed are breakage of disulfide bonds, decarboxylation of acids, reduction of metal ions and conformational changes of side chains (Ravelli & McSweeney, 2000).Certain effects severely affect SAD and MAD phasing procedures which are based on very accurate measurement of the anomalous signal from crystals preserving a high degree of isomorphism throughout the whole data measurement session.The accuracy of the anomalous signal can deteriorate significantly as a result of the cleavage of Se-C bonds in selenomethionines (Holton, 2007), Hg-S bonds in mercury derivatives (Ramagopal et al., 2005), Br-C bonds in brominated nucleic acid bases or I-C bonds iodinated tyrosine residues (Zwart et al., 2004).A significant amount of effort has been directed in the last decade to investigating the effects of radiation damage, relating these effects quantitatively to the amount of the absorbed dose or to the X-ray energy (Shimizu et al., 2007;Liebschner et al., 2015), or to finding ways to ameliorate them by the use of scavengers (Allan et al., 2013) or extrapolation of reflection intensities to zero dose (Diederichs et al., 2003).Particularly active in this field is the group at the University of Oxford headed by Elspeth Garman.In this issue of Acta Cryst.D this group and their collaborators describe an ingenious method to systematically quantify the effect of increasing absorbed dose on individual atoms of the structure and then apply it to a crystal structure containing simultaneously an uncomplexed protein and its complex with nucleic acid (Bury et al., 2016).The way they trace the effects of specific radiation damage at the individual atomic sites is simple and objective.They collected a series of ten data sets from the same crystal, each affected by increasing X-ray dose from 1.3 to 25 MGy, and calculated nine sets of difference Fourier maps, (F n À F 1 , ' 1 ) based on differences of reflection amplitudes between the first and each successive data set with phases obtained from model refinement against the first set.A per-atom density loss metric D loss was computed from changes in electron density around each individual site at each dose.All calculations were performed automatically by a pipeline using popular programs, producing objective information about the damage effect at each atom of the structure.
Author: Zbigniew Dauter
Institutions: Argonne National Laboratory, National Cancer Institute
Language: English
Subfield: Materials Chemistry
Field: Materials Science
Domain: Physical Sciences
Open Access status: bronze
OpenAlex ID: W2472077646