Literature DB >> 23815809

Kinetic modeling of the X-ray-induced damage to a metalloprotein.

Katherine M Davis1, Irina Kosheleva, Robert W Henning, Gerald T Seidler, Yulia Pushkar.   

Abstract

It is well-known that biological samples undergo X-ray-induced degradation. One of the fastest occurring X-ray-induced processes involves redox modifications (reduction or oxidation) of redox-active cofactors in proteins. Here we analyze room-temperature data on the photoreduction of Mn ions in the oxygen-evolving complex (OEC) of photosystem II, one of the most radiation damage-sensitive proteins and a key constituent of natural photosynthesis in plants, green algae, and cyanobacteria. Time-resolved X-ray emission spectroscopy with wavelength-dispersive detection was used to collect data on the progression of X-ray-induced damage. A kinetic model was developed to fit experimental results, and the rate constant for the reduction of OEC Mn(III) and Mn(IV) ions by solvated electrons was determined. From this model, the possible kinetics of X-ray-induced damage at a variety of experimental conditions, such as different rates of dose deposition as well as different excitation wavelengths, can be inferred. We observed a trend of increasing dosage threshold prior to the onset of X-ray-induced damage with increasing rates of dose deposition. This trend suggests that experimentation with higher rates of dose deposition is beneficial for measurements of biological samples sensitive to radiation damage, particularly at pink beam and X-ray free electron laser sources.

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Year:  2013        PMID: 23815809      PMCID: PMC3897202          DOI: 10.1021/jp403654n

Source DB:  PubMed          Journal:  J Phys Chem B        ISSN: 1520-5207            Impact factor:   2.991


  32 in total

1.  Potential for biomolecular imaging with femtosecond X-ray pulses.

Authors:  R Neutze; R Wouts; D van der Spoel; E Weckert; J Hajdu
Journal:  Nature       Date:  2000-08-17       Impact factor: 49.962

2.  Crystal structure of oxygen-evolving photosystem II at a resolution of 1.9 Å.

Authors:  Yasufumi Umena; Keisuke Kawakami; Jian-Ren Shen; Nobuo Kamiya
Journal:  Nature       Date:  2011-04-17       Impact factor: 49.962

3.  Effective scavenging at cryotemperatures: further increasing the dose tolerance of protein crystals.

Authors:  Eugenio De la Mora; Ian Carmichael; Elspeth F Garman
Journal:  J Synchrotron Radiat       Date:  2011-04-01       Impact factor: 2.616

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

Authors:  Matthew Warkentin; Ryan Badeau; Jesse Hopkins; Robert E Thorne
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2011-08-09

5.  Radiation damage in protein crystals is reduced with a micron-sized X-ray beam.

Authors:  Ruslan Sanishvili; Derek W Yoder; Sudhir Babu Pothineni; Gerd Rosenbaum; Shenglan Xu; Stefan Vogt; Sergey Stepanov; Oleg A Makarov; Stephen Corcoran; Richard Benn; Venugopalan Nagarajan; Janet L Smith; Robert F Fischetti
Journal:  Proc Natl Acad Sci U S A       Date:  2011-03-28       Impact factor: 11.205

Review 6.  Toward structure determination using membrane-protein nanocrystals and microcrystals.

Authors:  Mark S Hunter; Petra Fromme
Journal:  Methods       Date:  2011-12-22       Impact factor: 3.608

7.  Absence of Mn-centered oxidation in the S(2) --> S(3) transition: implications for the mechanism of photosynthetic water oxidation.

Authors:  J Messinger; J H Robblee; U Bergmann; C Fernandez; P Glatzel; H Visser; R M Cinco; K L McFarlane; E Bellacchio; S A Pizarro; S P Cramer; K Sauer; M P Klein; V K Yachandra
Journal:  J Am Chem Soc       Date:  2001-08-15       Impact factor: 15.419

8.  Radiation damage in protein serial femtosecond crystallography using an x-ray free-electron laser.

Authors:  Lukas Lomb; Thomas R M Barends; Stephan Kassemeyer; Andrew Aquila; Sascha W Epp; Benjamin Erk; Lutz Foucar; Robert Hartmann; Benedikt Rudek; Daniel Rolles; Artem Rudenko; Robert L Shoeman; Jakob Andreasson; Sasa Bajt; Miriam Barthelmess; Anton Barty; Michael J Bogan; Christoph Bostedt; John D Bozek; Carl Caleman; Ryan Coffee; Nicola Coppola; Daniel P Deponte; R Bruce Doak; Tomas Ekeberg; Holger Fleckenstein; Petra Fromme; Maike Gebhardt; Heinz Graafsma; Lars Gumprecht; Christina Y Hampton; Andreas Hartmann; Günter Hauser; Helmut Hirsemann; Peter Holl; James M Holton; Mark S Hunter; Wolfgang Kabsch; Nils Kimmel; Richard A Kirian; Mengning Liang; Filipe R N C Maia; Anton Meinhart; Stefano Marchesini; Andrew V Martin; Karol Nass; Christian Reich; Joachim Schulz; M Marvin Seibert; Raymond Sierra; Heike Soltau; John C H Spence; Jan Steinbrener; Francesco Stellato; Stephan Stern; Nicusor Timneanu; Xiaoyu Wang; Georg Weidenspointner; Uwe Weierstall; Thomas A White; Cornelia Wunderer; Henry N Chapman; Joachim Ullrich; Lothar Strüder; Ilme Schlichting
Journal:  Phys Rev B Condens Matter Mater Phys       Date:  2011-12-01

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.  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

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  10 in total

1.  DIY XES - development of an inexpensive, versatile, and easy to fabricate XES analyzer and sample delivery system.

Authors:  Scott C Jensen; Brendan Sullivan; Daniel A Hartzler; Yulia Pushkar
Journal:  Xray Spectrom       Date:  2019-02-13       Impact factor: 1.488

2.  Goniometer-based femtosecond crystallography with X-ray free electron lasers.

Authors:  Aina E Cohen; S Michael Soltis; Ana González; Laura Aguila; Roberto Alonso-Mori; Christopher O Barnes; Elizabeth L Baxter; Winnie Brehmer; Aaron S Brewster; Axel T Brunger; Guillermo Calero; Joseph F Chang; Matthieu Chollet; Paul Ehrensberger; Thomas L Eriksson; Yiping Feng; Johan Hattne; Britt Hedman; Michael Hollenbeck; James M Holton; Stephen Keable; Brian K Kobilka; Elena G Kovaleva; Andrew C Kruse; Henrik T Lemke; Guowu Lin; Artem Y Lyubimov; Aashish Manglik; Irimpan I Mathews; Scott E McPhillips; Silke Nelson; John W Peters; Nicholas K Sauter; Clyde A Smith; Jinhu Song; Hilary P Stevenson; Yingssu Tsai; Monarin Uervirojnangkoorn; Vladimir Vinetsky; Soichi Wakatsuki; William I Weis; Oleg A Zadvornyy; Oliver B Zeldin; Diling Zhu; Keith O Hodgson
Journal:  Proc Natl Acad Sci U S A       Date:  2014-10-31       Impact factor: 11.205

3.  Serial time-resolved crystallography of photosystem II using a femtosecond X-ray laser.

Authors:  Christopher Kupitz; Shibom Basu; Ingo Grotjohann; Raimund Fromme; Nadia A Zatsepin; Kimberly N Rendek; Mark S Hunter; Robert L Shoeman; Thomas A White; Dingjie Wang; Daniel James; Jay-How Yang; Danielle E Cobb; Brenda Reeder; Raymond G Sierra; Haiguang Liu; Anton Barty; Andrew L Aquila; Daniel Deponte; Richard A Kirian; Sadia Bari; Jesse J Bergkamp; Kenneth R Beyerlein; Michael J Bogan; Carl Caleman; Tzu-Chiao Chao; Chelsie E Conrad; Katherine M Davis; Holger Fleckenstein; Lorenzo Galli; Stefan P Hau-Riege; Stephan Kassemeyer; Hartawan Laksmono; Mengning Liang; Lukas Lomb; Stefano Marchesini; Andrew V Martin; Marc Messerschmidt; Despina Milathianaki; Karol Nass; Alexandra Ros; Shatabdi Roy-Chowdhury; Kevin Schmidt; Marvin Seibert; Jan Steinbrener; Francesco Stellato; Lifen Yan; Chunhong Yoon; Thomas A Moore; Ana L Moore; Yulia Pushkar; Garth J Williams; Sébastien Boutet; R Bruce Doak; Uwe Weierstall; Matthias Frank; Henry N Chapman; John C H Spence; Petra Fromme
Journal:  Nature       Date:  2014-07-09       Impact factor: 49.962

Review 4.  Assembly of nonheme Mn/Fe active sites in heterodinuclear metalloproteins.

Authors:  Julia J Griese; Vivek Srinivas; Martin Högbom
Journal:  J Biol Inorg Chem       Date:  2014-04-26       Impact factor: 3.358

Review 5.  From protein structure to function via single crystal optical spectroscopy.

Authors:  Luca Ronda; Stefano Bruno; Stefano Bettati; Paola Storici; Andrea Mozzarelli
Journal:  Front Mol Biosci       Date:  2015-04-28

6.  Lipidic cubic phase serial millisecond crystallography using synchrotron radiation.

Authors:  Przemyslaw Nogly; Daniel James; Dingjie Wang; Thomas A White; Nadia Zatsepin; Anastasya Shilova; Garrett Nelson; Haiguang Liu; Linda Johansson; Michael Heymann; Kathrin Jaeger; Markus Metz; Cecilia Wickstrand; Wenting Wu; Petra Båth; Peter Berntsen; Dominik Oberthuer; Valerie Panneels; Vadim Cherezov; Henry Chapman; Gebhard Schertler; Richard Neutze; John Spence; Isabel Moraes; Manfred Burghammer; Joerg Standfuss; Uwe Weierstall
Journal:  IUCrJ       Date:  2015-01-27       Impact factor: 4.769

7.  High-density grids for efficient data collection from multiple crystals.

Authors:  Elizabeth L Baxter; Laura Aguila; Roberto Alonso-Mori; Christopher O Barnes; Christopher A Bonagura; Winnie Brehmer; Axel T Brunger; Guillermo Calero; Tom T Caradoc-Davies; Ruchira Chatterjee; William F Degrado; James S Fraser; Mohamed Ibrahim; Jan Kern; Brian K Kobilka; Andrew C Kruse; Karl M Larsson; Heinrik T Lemke; Artem Y Lyubimov; Aashish Manglik; Scott E McPhillips; Erik Norgren; Siew S Pang; S M Soltis; Jinhu Song; Jessica Thomaston; Yingssu Tsai; William I Weis; Rahel A Woldeyes; Vittal Yachandra; Junko Yano; Athina Zouni; Aina E Cohen
Journal:  Acta Crystallogr D Struct Biol       Date:  2016-01-01       Impact factor: 7.652

8.  Pink-beam serial crystallography.

Authors:  A Meents; M O Wiedorn; V Srajer; R Henning; I Sarrou; J Bergtholdt; M Barthelmess; P Y A Reinke; D Dierksmeyer; A Tolstikova; S Schaible; M Messerschmidt; C M Ogata; D J Kissick; M H Taft; D J Manstein; J Lieske; D Oberthuer; R F Fischetti; H N Chapman
Journal:  Nat Commun       Date:  2017-11-03       Impact factor: 14.919

9.  X-ray-induced sample damage at the Mn L-edge: a case study for soft X-ray spectroscopy of transition metal complexes in solution.

Authors:  Markus Kubin; Jan Kern; Meiyuan Guo; Erik Källman; Rolf Mitzner; Vittal K Yachandra; Marcus Lundberg; Junko Yano; Philippe Wernet
Journal:  Phys Chem Chem Phys       Date:  2018-06-20       Impact factor: 3.676

10.  Diffraction before destruction.

Authors:  Henry N Chapman; Carl Caleman; Nicusor Timneanu
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2014-07-17       Impact factor: 6.237

  10 in total

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