Dark progression reveals slow timescales for radiation damage between T = 180 and 240 K.

Can radiation damage to protein crystals be `outrun' by collecting a structural data set before damage is manifested? Recent experiments using ultra-intense pulses from a free-electron laser show that the answer is yes. Here, evidence is presented that significant reductions in global damage at temperatures above 200 K may be possible using conventional X-ray sources and current or soon-to-be available detectors. Specifically, `dark progression' (an increase in damage with time after the X-rays have been turned off) was observed at temperatures between 180 and 240 K and on timescales from 200 to 1200 s. This allowed estimation of the temperature-dependent timescale for damage. The rate of dark progression is consistent with an Arrhenius law with an activation energy of 14 kJ mol(-1). This is comparable to the activation energy for the solvent-coupled diffusive damage processes responsible for the rapid increase in radiation sensitivity as crystals are warmed above the glass transition near 200 K. Analysis suggests that at T = 300 K data-collection times of the order of 1 s (and longer at lower temperatures) may allow significant reductions in global radiation damage, facilitating structure solution on crystals with liquid solvent. No dark progression was observed below T = 180 K, indicating that no important damage process is slowed through this timescale window in this temperature range.

[1]  Dr. Hermann Dertinger,et al.  Molecular Radiation Biology , 1970, Heidelberg Science Library.

[2]  K. Moffat,et al.  Primary radiation damage of protein crystals by an intense synchrotron X-ray beam. , 2000, Journal of synchrotron radiation.

[3]  Stephen Corcoran,et al.  Radiation damage in protein crystals is reduced with a micron-sized X-ray beam , 2011, Proceedings of the National Academy of Sciences.

[4]  F. Zemlin,et al.  Effect of temperature on radiation damage to aromatic organic molecules , 1992 .

[5]  Naji S Husseini,et al.  Quantifying X-ray radiation damage in protein crystals at cryogenic temperatures. , 2006, Acta crystallographica. Section D, Biological crystallography.

[6]  Holger Dau,et al.  Rapid Loss of Structural Motifs in the Manganese Complex of Oxygenic Photosynthesis by X-ray Irradiation at 10–300 K* , 2006, Journal of Biological Chemistry.

[7]  S. Benkovic,et al.  Enzyme Motions Inside and Out , 2006, Science.

[8]  Z. Otwinowski,et al.  [20] Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.

[9]  N. Go,et al.  Dynamical transition of myoglobin in a crystal: comparative studies of X-ray crystallography and Mössbauer spectroscopy , 2001, European Biophysics Journal.

[10]  P. Lindop Biological Effects of Radiation , 1957, Nature.

[11]  J. Onuchic,et al.  DIFFUSIVE DYNAMICS OF THE REACTION COORDINATE FOR PROTEIN FOLDING FUNNELS , 1996, cond-mat/9601091.

[12]  James Raftery,et al.  The structure of concanavalin A and its bound solvent determined with small-molecule accuracy at 0.94 [Aring ]resolution , 1997 .

[13]  J. Sussman,et al.  Specific protein dynamics near the solvent glass transition assayed by radiation‐induced structural changes , 2001, Protein science : a publication of the Protein Society.

[14]  C. Schulze-Briese,et al.  Reduction of X-ray-induced radiation damage of macromolecular crystals by data collection at 15 K: a systematic study. , 2007, Acta crystallographica. Section D, Biological crystallography.

[15]  R. Banerjee,et al.  Three-dimensional numerical analysis of convection and conduction cooling of spherical biocrystals with localized heating from synchrotron X-ray beams. , 2005, Journal of synchrotron radiation.

[16]  Elspeth F Garman,et al.  Observation of decreased radiation damage at higher dose rates in room temperature protein crystallography. , 2007, Structure.

[17]  E. Weckert,et al.  Investigation of radiation-dose-induced changes in organic light-atom crystals by accurate d-spacing measurements. , 2002, Journal of synchrotron radiation.

[18]  G. Schneider,et al.  Structure of dethiobiotin synthetase at 0.97 A resolution. , 1999, Acta crystallographica. Section D, Biological crystallography.

[19]  S. Benkovic,et al.  Coupled motions in enzyme catalysis. , 2010, Current opinion in chemical biology.

[20]  M. Anbar,et al.  Activation energy of hydrated electron reactions , 1967 .

[21]  S. Kriminski,et al.  Dynamic response of tetragonal lysozyme crystals to changes in relative humidity: implications for post-growth crystal treatments. , 2001, Acta crystallographica. Section D, Biological crystallography.

[22]  D. Juers,et al.  Similarities and differences in radiation damage at 100 K versus 160 K in a crystal of thermolysin. , 2011, Journal of synchrotron radiation.

[23]  D. Kern,et al.  Dynamic personalities of proteins , 2007, Nature.

[24]  G. Kimmel,et al.  Electron-stimulated production of molecular hydrogen at the interfaces of amorphous solid water films on Pt(111). , 2004, The Journal of chemical physics.

[25]  R. Ravelli,et al.  Is radiation damage dependent on the dose rate used during macromolecular crystallography data collection? , 2006, Acta crystallographica. Section D, Biological crystallography.

[26]  Hans Frauenfelder,et al.  Temperature-dependent X-ray diffraction as a probe of protein structural dynamics , 1979, Nature.

[27]  D. Stuart,et al.  Hybrid vigor: hybrid methods in viral structure determination. , 2003, Advances in protein chemistry.

[28]  Elspeth F Garman,et al.  Experimental determination of the radiation dose limit for cryocooled protein crystals. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[29]  Antoine Royant,et al.  Advances in kinetic protein crystallography. , 2005, Current opinion in structural biology.

[30]  Meitian Wang,et al.  Radiation damage in room-temperature data acquisition with the PILATUS 6M pixel detector , 2011, Journal of synchrotron radiation.

[31]  Temperature Dependence of the Formation of Hydrogen, Oxygen, and Hydrogen Peroxide in Electron-Irradiated Crystalline Water Ice , 2006 .

[32]  Clemens Schulze-Briese,et al.  Origin and temperature dependence of radiation damage in biological samples at cryogenic temperatures , 2009, Proceedings of the National Academy of Sciences.

[33]  H. Hope Cryocrystallography of biological macromolecules: a generally applicable method. , 1988, Acta crystallographica. Section B, Structural science.

[34]  J. Pletcher,et al.  STUDIES OF INSULIN CRYSTALS AT LOW TEMPERATURES: EFFECTS ON MOSAIC CHARACTER AND RADIATION SENSITIVITY* , 1966, Proceedings of the National Academy of Sciences of the United States of America.

[35]  G. Petsko,et al.  How Enzymes Work , 2008, Science.

[36]  G. G. Stokes "J." , 1890, The New Yale Book of Quotations.

[37]  S. Benkovic,et al.  Relating protein motion to catalysis. , 2006, Annual review of biochemistry.

[38]  H. Hope Crystallography of biological macromolecules at ultra-low temperature. , 1990, Annual review of biophysics and biophysical chemistry.

[39]  S Kriminski,et al.  Heat transfer from protein crystals: implications for flash-cooling and X-ray beam heating. , 2003, Acta crystallographica. Section D, Biological crystallography.

[40]  E. Garman,et al.  Room-temperature scavengers for macromolecular crystallography: increased lifetimes and modified dose dependence of the intensity decay. , 2009, Journal of synchrotron radiation.

[41]  E. Knapp,et al.  Protein dynamics. Mössbauer spectroscopy on deoxymyoglobin crystals. , 1982, Journal of molecular biology.

[42]  R. Ravelli,et al.  Supercooled liquid-like solvent in trypsin crystals: implications for crystal annealing and temperature-controlled X-ray radiation damage studies. , 2005, Journal of synchrotron radiation.

[43]  J. Sussman,et al.  Solvent behaviour in flash-cooled protein crystals at cryogenic temperatures. , 2001, Acta crystallographica. Section D, Biological crystallography.

[44]  J. Hajdu,et al.  Potential for biomolecular imaging with femtosecond X-ray pulses , 2000, Nature.

[45]  R. Goody,et al.  The pre-hydrolysis state of p21(ras) in complex with GTP: new insights into the role of water molecules in the GTP hydrolysis reaction of ras-like proteins. , 1999, Structure.

[46]  K. Moffat,et al.  Radiation damage of protein crystals at cryogenic temperatures between 40 K and 150 K. , 2002, Journal of synchrotron radiation.

[47]  D. Bourgeois,et al.  Temperature derivative fluorescence spectroscopy as a tool to study dynamical changes in protein crystals. , 2004, Biophysical journal.

[48]  R. Ravelli,et al.  The 'fingerprint' that X-rays can leave on structures. , 2000, Structure.

[49]  B. Matthews,et al.  Reversible lattice repacking illustrates the temperature dependence of macromolecular interactions. , 2001, Journal of molecular biology.

[50]  Richard Henderson,et al.  Cryo-protection of protein crystals against radiation damage in electron and X-ray diffraction , 1990, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[51]  M. J. van der Woerd,et al.  Non-invasive measurement of X-ray beam heating on a surrogate crystal sample. , 2007, Journal of synchrotron radiation.

[52]  B. Matthews,et al.  Cryo-cooling in macromolecular crystallography: advantages, disadvantages and optimization , 2004, Quarterly Reviews of Biophysics.

[53]  R. Thorne,et al.  Slow cooling of protein crystals. , 2009, Journal of applied crystallography.

[54]  Zbyszek Otwinowski,et al.  The many faces of radiation-induced changes. , 2007, Journal of synchrotron radiation.

[55]  Wolfgang Doster,et al.  Dynamical transition of myoglobin revealed by inelastic neutron scattering , 1989, Nature.

[56]  Georg Weidenspointner,et al.  Femtosecond X-ray protein nanocrystallography , 2011, Nature.

[57]  L. Johnson,et al.  Macromolecular crystallography at synchrotron radiation sources: current status and future developments , 2010, Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences.

[58]  J. Onuchic,et al.  Fast-folding experiments and the topography of protein folding energy landscapes. , 1996, Chemistry & biology.

[59]  D. Tobias,et al.  Coincidence of dynamical transitions in a soluble protein and its hydration water: direct measurements by neutron scattering and MD simulations. , 2008, Journal of the American Chemical Society.

[60]  M. Rossmann Synchrotron radiation as a tool for investigating virus structures , 1999 .

[61]  G A Petsko,et al.  Protein crystallography at sub-zero temperatures: cryo-protective mother liquors for protein crystals. , 1975, Journal of molecular biology.

[62]  R. H. Wade The temperature dependence of radiation damage in organic and biological materials , 1984 .

[63]  R. Thorne,et al.  Glass transition in thaumatin crystals revealed through temperature-dependent radiation-sensitivity measurements. , 2010, Acta crystallographica. Section D, Biological crystallography.

[64]  E. Stern,et al.  Spatial dependence and mitigation of radiation damage by a line-focus mini-beam. , 2010, Acta Crystallographica Section D: Biological Crystallography.

[65]  G. Petsko,et al.  Effects of temperature on protein structure and dynamics: X-ray crystallographic studies of the protein ribonuclease-A at nine different temperatures from 98 to 320 K. , 1993, Biochemistry.

[66]  J. Sussman,et al.  Shoot-and-Trap: Use of specific x-ray damage to study structural protein dynamics by temperature-controlled cryo-crystallography , 2008, Proceedings of the National Academy of Sciences.

[67]  S. Kriminski,et al.  Flash-cooling and annealing of protein crystals. , 2002, Acta crystallographica. Section D, Biological crystallography.

[68]  Elspeth Garman,et al.  'Cool' crystals: macromolecular cryocrystallography and radiation damage. , 2003, Current opinion in structural biology.

[69]  G. Buxton,et al.  Critical Review of rate constants for reactions of hydrated electrons, hydrogen atoms and hydroxyl radicals (⋅OH/⋅O− in Aqueous Solution , 1988 .

[70]  S. Harrison,et al.  How does radiation damage in protein crystals depend on X-ray dose? , 2003, Structure.

[71]  Elspeth F Garman,et al.  Towards an understanding of radiation damage in cryocooled macromolecular crystals. , 2005, Journal of synchrotron radiation.

[72]  Kenneth A. Frankel,et al.  The minimum crystal size needed for a complete diffraction data set , 2010, Acta crystallographica. Section D, Biological crystallography.

[73]  J. Colletier,et al.  Temperature-dependent macromolecular X-ray crystallography , 2010, Acta crystallographica. Section D, Biological crystallography.

[74]  K. Hasegawa,et al.  Dose dependence of radiation damage for protein crystals studied at various X-ray energies. , 2007, Journal of synchrotron radiation.

[75]  R. Ravelli,et al.  Colouring cryo-cooled crystals: online microspectrophotometry , 2009, Journal of synchrotron radiation.