Literature DB >> 21931220

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

Jan Kmetko1, Matthew Warkentin, Ulrich Englich, Robert E Thorne.   

Abstract

Recent studies have defined a data-collection protocol and a metric that provide a robust measure of global radiation damage to protein crystals. Using this protocol and metric, 19 small-molecule compounds (introduced either by cocrystallization or soaking) were evaluated for their ability to protect lysozyme crystals from radiation damage. The compounds were selected based upon their ability to interact with radiolytic products (e.g. hydrated electrons, hydrogen, hydroxyl and perhydroxyl radicals) and/or their efficacy in protecting biological molecules from radiation damage in dilute aqueous solutions. At room temperature, 12 compounds had no effect and six had a sensitizing effect on global damage. Only one compound, sodium nitrate, appeared to extend crystal lifetimes, but not in all proteins and only by a factor of two or less. No compound provided protection at T=100 K. Scavengers are ineffective in protecting protein crystals from global damage because a large fraction of primary X-ray-induced excitations are generated in and/or directly attack the protein and because the ratio of scavenger molecules to protein molecules is too small to provide appreciable competitive protection. The same reactivity that makes some scavengers effective radioprotectors in protein solutions may explain their sensitizing effect in the protein-dense environment of a crystal. A more productive focus for future efforts may be to identify and eliminate sensitizing compounds from crystallization solutions.

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Year:  2011        PMID: 21931220      PMCID: PMC3176623          DOI: 10.1107/S0907444911032835

Source DB:  PubMed          Journal:  Acta Crystallogr D Biol Crystallogr        ISSN: 0907-4449


  63 in total

Review 1.  Entering a new phase: using solvent halide ions in protein structure determination.

Authors:  Z Dauter; M Dauter
Journal:  Structure       Date:  2001-02-07       Impact factor: 5.006

Review 2.  Cryocooling and radiation damage in macromolecular crystallography.

Authors:  Elspeth F Garman; Robin Leslie Owen
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2005-12-14

3.  Reduction of X-ray-induced radiation damage of macromolecular crystals by data collection at 15 K: a systematic study.

Authors:  A Meents; A Wagner; R Schneider; C Pradervand; E Pohl; C Schulze-Briese
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2007-02-21

4.  Electron paramagnetic resonance study of radiation damage in photosynthetic reaction center crystals.

Authors:  Lisa M Utschig; Sergey D Chemerisov; David M Tiede; Oleg G Poluektov
Journal:  Biochemistry       Date:  2008-08-09       Impact factor: 3.162

Review 5.  Radiation damage in macromolecular cryocrystallography.

Authors:  Raimond B G Ravelli; Elspeth F Garman
Journal:  Curr Opin Struct Biol       Date:  2006-08-30       Impact factor: 6.809

6.  Crystallographic studies on lactate dehydrogenase at-75 degrees C.

Authors:  D J Haas; M G Rossmann
Journal:  Acta Crystallogr B       Date:  1970-07-15       Impact factor: 2.266

7.  Novel approach to phasing proteins: derivatization by short cryo-soaking with halides.

Authors:  Z Dauter; M Dauter; K R Rajashankar
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2000-02

8.  SELENOAMINO ACIDS: DECREASE OF RADIATION DAMAGE TO AMINO ACIDS AND PROTEINS.

Authors:  F SHIMAZU; A L TAPPEL
Journal:  Science       Date:  1964-01-24       Impact factor: 47.728

9.  Room-temperature scavengers for macromolecular crystallography: increased lifetimes and modified dose dependence of the intensity decay.

Authors:  Adam I Barker; Robert J Southworth-Davies; Karthik S Paithankar; Ian Carmichael; Elspeth F Garman
Journal:  J Synchrotron Radiat       Date:  2009-02-25       Impact factor: 2.616

10.  Colouring cryo-cooled crystals: online microspectrophotometry.

Authors:  John McGeehan; Raimond B G Ravelli; James W Murray; Robin Leslie Owen; Florent Cipriani; Sean McSweeney; Martin Weik; Elspeth F Garman
Journal:  J Synchrotron Radiat       Date:  2009-02-25       Impact factor: 2.616

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  18 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.  Temperature-dependent radiation sensitivity and order of 70S ribosome crystals.

Authors:  Matthew Warkentin; Jesse B Hopkins; Jonah B Haber; Gregor Blaha; Robert E Thorne
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2014-10-23

3.  Spatial distribution of radiation damage to crystalline proteins at 25-300 K.

Authors:  Matthew Warkentin; Ryan Badeau; Jesse B Hopkins; Robert E Thorne
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2012-08-18

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.  Breaking the radiation damage limit with Cryo-SAXS.

Authors:  Steve P Meisburger; Matthew Warkentin; Huimin Chen; Jesse B Hopkins; Richard E Gillilan; Lois Pollack; Robert E Thorne
Journal:  Biophys J       Date:  2013-01-08       Impact factor: 4.033

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

Authors:  Jesse B Hopkins; Robert E Thorne
Journal:  J Appl Crystallogr       Date:  2016-05-04       Impact factor: 3.304

7.  Estimate your dose: RADDOSE-3D.

Authors:  Charles S Bury; Jonathan C Brooks-Bartlett; Steven P Walsh; Elspeth F Garman
Journal:  Protein Sci       Date:  2017-11-06       Impact factor: 6.725

8.  Effects of cryoprotectants on the structure and thermostability of the human carbonic anhydrase II-acetazolamide complex.

Authors:  Mayank Aggarwal; Christopher D Boone; Bhargav Kondeti; Chingkuang Tu; David N Silverman; Robert McKenna
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2013-04-19

9.  The kinetic dose limit in room-temperature time-resolved macromolecular crystallography.

Authors:  M Schmidt; V Šrajer; N Purwar; S Tripathi
Journal:  J Synchrotron Radiat       Date:  2012-01-18       Impact factor: 2.616

10.  To scavenge or not to scavenge, that is STILL the question.

Authors:  Elizabeth G Allan; Melissa C Kander; Ian Carmichael; Elspeth F Garman
Journal:  J Synchrotron Radiat       Date:  2012-12-05       Impact factor: 2.616

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