Indications of radiation damage in ferredoxin microcrystals using high-intensity X-FEL beams.

Proteins that contain metal cofactors are expected to be highly radiation sensitive since the degree of X-ray absorption correlates with the presence of high-atomic-number elements and X-ray energy. To explore the effects of local damage in serial femtosecond crystallography (SFX), Clostridium ferredoxin was used as a model system. The protein contains two [4Fe-4S] clusters that serve as sensitive probes for radiation-induced electronic and structural changes. High-dose room-temperature SFX datasets were collected at the Linac Coherent Light Source of ferredoxin microcrystals. Difference electron density maps calculated from high-dose SFX and synchrotron data show peaks at the iron positions of the clusters, indicative of decrease of atomic scattering factors due to ionization. The electron density of the two [4Fe-4S] clusters differs in the FEL data, but not in the synchrotron data. Since the clusters differ in their detailed architecture, this observation is suggestive of an influence of the molecular bonding and geometry on the atomic displacement dynamics following initial photoionization. The experiments are complemented by plasma code calculations.

[1]  R. Read.  Improved Fourier Coefficients for Maps Using Phases from Partial Structures with Errors , 1986 .

[2]  Gwyndaf Evans,et al.  Outrunning free radicals in room-temperature macromolecular crystallography , 2012, Acta crystallographica. Section D, Biological crystallography.

[3]  Carl Caleman,et al.  Diffraction before destruction , 2014, Philosophical Transactions of the Royal Society B: Biological Sciences.

[4]  Randy J. Read,et al.  Phaser crystallographic software , 2007, Journal of applied crystallography.

[5]  J Berendzen,et al.  The catalytic pathway of cytochrome p450cam at atomic resolution. , 2000, Science.

[6]  H N Chapman,et al.  Saturated ablation in metal hydrides and acceleration of protons and deuterons to keV energies with a soft-x-ray laser. , 2011, Physical review. E, Statistical, nonlinear, and soft matter physics.

[7]  C. Bostedt,et al.  Ultrafast charge rearrangement and nuclear dynamics upon inner-shell multiple ionization of small polyatomic molecules. , 2013, Physical review letters.

[8]  Kay Diederichs,et al.  Some aspects of quantitative analysis and correction of radiation damage. , 2006, Acta crystallographica. Section D, Biological crystallography.

[9]  Yuri Ralchenko,et al.  Review of the 9th NLTE code comparison workshop. , 2007, High energy density physics.

[10]  Anton Barty,et al.  CASS - CFEL-ASG software suite , 2012, Comput. Phys. Commun..

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

[12]  Sang-Kil Son,et al.  Multiwavelength anomalous diffraction at high x-ray intensity. , 2011, Physical review letters.

[13]  Garth J. Williams,et al.  High-Resolution Protein Structure Determination by Serial Femtosecond Crystallography , 2012, Science.

[14]  P. Krejcik,et al.  Few-femtosecond time-resolved measurements of X-ray free-electron lasers , 2014, Nature Communications.

[15]  Britt Hedman,et al.  Photoreduction of the active site of the metalloprotein putidaredoxin by synchrotron radiation. , 2007, Acta crystallographica. Section D, Biological crystallography.

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

[17]  H. Chapman,et al.  Femtosecond protein nanocrystallography-data analysis methods. , 2010, Optics express.

[18]  J. Sussman,et al.  Electronic Reprint Synchrotron Radiation Evidence for the Formation of Disulfide Radicals in Protein Crystals upon X-ray Irradiation Radiation Damage Workshop Evidence for the Formation of Disul®de Radicals in Protein Crystals upon X-ray Irradiation² , 2022 .

[19]  M. Tate,et al.  Femtosecond Radiation Experiment Detector for X-Ray Free-Electron Laser (XFEL) Coherent X-Ray Imaging , 2010, IEEE Transactions on Nuclear Science.

[20]  Howard A. Scott,et al.  Cretin—a radiative transfer capability for laboratory plasmas , 2001 .

[21]  Anton Barty,et al.  CrystFEL: a software suite for snapshot serial crystallography , 2012 .

[22]  N. Pannu,et al.  REFMAC5 for the refinement of macromolecular crystal structures , 2011, Acta crystallographica. Section D, Biological crystallography.

[23]  Anton Barty,et al.  Ultrafast self-gating Bragg diffraction of exploding nanocrystals in an X-ray laser. , 2015, Optics express.

[24]  Sang-Kil Son,et al.  Impact of hollow-atom formation on coherent x-ray scattering at high intensity , 2011, 1101.4932.

[25]  Elspeth F. Garman,et al.  RADDOSE-3D: time- and space-resolved modelling of dose in macromolecular crystallography , 2013 .

[26]  Sébastien Boutet,et al.  Simultaneous Femtosecond X-ray Spectroscopy and Diffraction of Photosystem II at Room Temperature , 2013, Science.

[27]  W. Burmeister,et al.  Structural changes in a cryo-cooled protein crystal owing to radiation damage. , 2000, Acta crystallographica. Section D, Biological crystallography.

[28]  U Weierstall,et al.  Injector for scattering measurements on fully solvated biospecies. , 2012, The Review of scientific instruments.

[29]  Kunio Hirata,et al.  Native structure of photosystem II at 1.95 Å resolution viewed by femtosecond X-ray pulses , 2014, Nature.

[30]  I. Schlichting,et al.  Structure and quantum chemical characterization of chloroperoxidase compound 0, a common reaction intermediate of diverse heme enzymes , 2007, Proceedings of the National Academy of Sciences.

[31]  Georg Weidenspointner,et al.  Radiation damage in protein serial femtosecond crystallography using an x-ray free-electron laser. , 2011, Physical review. B, Condensed matter and materials physics.

[32]  Anton Barty,et al.  Structure of a photosynthetic reaction centre determined by serial femtosecond crystallography , 2013, Nature Communications.

[33]  Stefan P. Hau-Riege,et al.  X-ray atomic scattering factors of low- Z ions with a core hole , 2007 .

[34]  Kunio Hirata,et al.  Determination of damage-free crystal structure of an X-ray–sensitive protein using an XFEL , 2014, Nature Methods.

[35]  K S Wilson,et al.  Atomic resolution (0.94 A) structure of Clostridium acidurici ferredoxin. Detailed geometry of [4Fe-4S] clusters in a protein. , 1997, Biochemistry.

[36]  Michael Krumrey,et al.  High-accuracy detector calibration at the PTB four-crystal monochromator beamline , 2001 .

[37]  Anton Barty,et al.  Structure-factor analysis of femtosecond microdiffraction patterns from protein nanocrystals. , 2011, Acta crystallographica. Section A, Foundations of crystallography.

[38]  Ezequiel Panepucci,et al.  Room-temperature serial crystallography at synchrotron X-ray sources using slowly flowing free-standing high-viscosity microstreams. , 2015, Acta crystallographica. Section D, Biological crystallography.

[39]  Randy J. Read,et al.  Acta Crystallographica Section D Biological , 2003 .

[40]  Sébastien Boutet,et al.  The Coherent X-ray Imaging (CXI) instrument at the Linac Coherent Light Source (LCLS) , 2010 .

[41]  Libor Juha,et al.  Subnanometer-scale measurements of the interaction of ultrafast soft x-ray free-electron-laser pulses with matter. , 2006, Physical review letters.

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

[43]  E. Fanchon,et al.  Refined crystal structure of the 2[4Fe-4S] ferredoxin from Clostridium acidurici at 1.84 A resolution. , 1994, Journal of molecular biology.

[44]  Georg Weidenspointner,et al.  Self-terminating diffraction gates femtosecond X-ray nanocrystallography measurements , 2011, Nature Photonics.

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

[46]  N. Tîmneanu,et al.  Simulations of radiation damage as a function of the temporal pulse profile in femtosecond X-ray protein crystallography. , 2015, Journal of synchrotron radiation.

[47]  Sean McSweeney,et al.  Specific radiation damage can be used to solve macromolecular crystal structures. , 2003, Structure.

[48]  J. Rabinowitz,et al.  Molar extinction coefficient and iron and sulfide content of clostridial ferredoxin. , 1970, The Journal of biological chemistry.

[49]  H. Chapman,et al.  On the feasibility of nanocrystal imaging using intense and ultrashort X-ray pulses. , 2011, ACS nano.

[50]  Collaborative Computational,et al.  The CCP4 suite: programs for protein crystallography. , 1994, Acta crystallographica. Section D, Biological crystallography.

[51]  Uwe Bergmann,et al.  X-ray damage to the Mn4Ca complex in single crystals of photosystem II: a case study for metalloprotein crystallography. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[52]  K. Schmidt,et al.  Gas dynamic virtual nozzle for generation of microscopic droplet streams , 2008, 0803.4181.

[53]  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.

[54]  W. Delano.  The PyMOL Molecular Graphics System , 2002 .

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

[56]  Heike Soltau,et al.  Anomalous signal from S atoms in protein crystallographic data from an X-ray free-electron laser. , 2013, Acta crystallographica. Section D, Biological crystallography.

[57]  D. Stuart,et al.  Exploiting fast detectors to enter a new dimension in room-temperature crystallography , 2014, Acta crystallographica. Section D, Biological crystallography.

[58]  Wolfgang Kabsch,et al.  Evaluation of Single-Crystal X-ray Diffraction Data from a Position-Sensitive Detector , 1988 .

[59]  Garth J. Williams,et al.  Serial Femtosecond Crystallography of G Protein–Coupled Receptors , 2013, Science.

[60]  J. Rawson,et al.  Ferroelastic phase transitions and anelastic dissipation in the LaAlO 3 -PrAlO 3 solid solution series , 2010 .

[61]  S. Hau-Riege,et al.  Interaction of ultrashort x-ray pulses with B4C , SiC, and Si. , 2007, Physical review. E, Statistical, nonlinear, and soft matter physics.

[62]  J. Campbell,et al.  WIDTHS OF THE ATOMIC K–N7 LEVELS , 2001 .