Literature DB >> 19240331

Can soaked-in scavengers protect metalloprotein active sites from reduction during data collection?

Sofia Macedo1, Maria Pechlaner, Walther Schmid, Martin Weik, Katsuko Sato, Christopher Dennison, Kristina Djinović-Carugo.   

Abstract

One of the first events taking place when a crystal of a metalloprotein is exposed to X-ray radiation is photoreduction of the metal centres. The oxidation state of a metal cannot always be determined from routine X-ray diffraction experiments alone, but it may have a crucial impact on the metal's environment and on the analysis of the structural data when considering the functional mechanism of a metalloenzyme. Here, UV-Vis microspectrophotometry is used to test the efficacy of selected scavengers in reducing the undesirable photoreduction of the iron and copper centres in myoglobin and azurin, respectively, and X-ray crystallography to assess their capacity of mitigating global and specific radiation damage effects. UV-Vis absorption spectra of native crystals, as well as those soaked in 18 different radioprotectants, show dramatic metal reduction occurring in the first 60 s of irradiation with an X-ray beam from a third-generation synchrotron source. Among the tested radioprotectants only potassium hexacyanoferrate(III) seems to be capable of partially mitigating the rate of metal photoreduction at the concentrations used, but not to a sufficient extent that would allow a complete data set to be recorded from a fully oxidized crystal. On the other hand, analysis of the X-ray crystallographic data confirms ascorbate as an efficient protecting agent against radiation damage, other than metal centre reduction, and suggests further testing of HEPES and 2,3-dichloro-1,4-naphtoquinone as potential scavengers.

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Year:  2009        PMID: 19240331     DOI: 10.1107/S0909049509003331

Source DB:  PubMed          Journal:  J Synchrotron Radiat        ISSN: 0909-0495            Impact factor:   2.616


  25 in total

1.  To scavenge or not to scavenge: that is the question.

Authors:  Elzbieta Nowak; Anna Brzuszkiewicz; Miroslawa Dauter; Zbigniew Dauter; Gerd Rosenbaum
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-08-14

2.  Energy dependence of site-specific radiation damage in protein crystals.

Authors:  Christina Homer; Laura Cooper; Ana Gonzalez
Journal:  J Synchrotron Radiat       Date:  2011-03-15       Impact factor: 2.616

3.  Can radiation damage to protein crystals be reduced using small-molecule compounds?

Authors:  Jan Kmetko; Matthew Warkentin; Ulrich Englich; Robert E Thorne
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2011-09-08

4.  Global radiation damage: temperature dependence, time dependence and how to outrun it.

Authors:  Matthew Warkentin; Jesse B Hopkins; Ryan Badeau; Anne M Mulichak; Lisa J Keefe; Robert E Thorne
Journal:  J Synchrotron Radiat       Date:  2012-11-29       Impact factor: 2.616

5.  Real-space analysis of radiation-induced specific changes with independent component analysis.

Authors:  Dominika Borek; Raquel Bromberg; Johan Hattne; Zbyszek Otwinowski
Journal:  J Synchrotron Radiat       Date:  2018-02-22       Impact factor: 2.616

6.  Thermostable multicopper oxidase from Thermus thermophilus HB27: crystallization and preliminary X-ray diffraction analysis of apo and holo forms.

Authors:  Hugo Serrano-Posada; Brenda Valderrama; Vivian Stojanoff; Enrique Rudiño-Piñera
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2011-11-26

7.  X-ray-induced catalytic active-site reduction of a multicopper oxidase: structural insights into the proton-relay mechanism and O2-reduction states.

Authors:  Hugo Serrano-Posada; Sara Centeno-Leija; Sonia Patricia Rojas-Trejo; Claudia Rodríguez-Almazán; Vivian Stojanoff; Enrique Rudiño-Piñera
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2015-11-26

8.  Characterizing metal-binding sites in proteins with X-ray crystallography.

Authors:  Katarzyna B Handing; Ewa Niedzialkowska; Ivan G Shabalin; Misty L Kuhn; Heping Zheng; Wladek Minor
Journal:  Nat Protoc       Date:  2018-04-19       Impact factor: 13.491

9.  Radiation damage in macromolecular crystallography: what is it and why should we care?

Authors:  Elspeth F Garman
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2010-03-24

10.  Fast Detection Allows Analysis of the Electronic Structure of Metalloprotein by X-ray Emission Spectroscopy at Room Temperature.

Authors:  Katherine M Davis; Brian A Mattern; Joseph I Pacold; Taisiya Zakharova; Dale Brewe; Irina Kosheleva; Robert W Henning; Timothy J Graber; Steve M Heald; Gerald T Seidler; Yulia Pushkar
Journal:  J Phys Chem Lett       Date:  2012-06-26       Impact factor: 6.475

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