Literature DB >> 25477465

Time-resolved serial crystallography captures high-resolution intermediates of photoactive yellow protein.

Jason Tenboer1, Shibom Basu2, Nadia Zatsepin3, Kanupriya Pande1, Despina Milathianaki4, Matthias Frank5, Mark Hunter5, Sébastien Boutet4, Garth J Williams4, Jason E Koglin4, Dominik Oberthuer6, Michael Heymann7, Christopher Kupitz2, Chelsie Conrad2, Jesse Coe2, Shatabdi Roy-Chowdhury2, Uwe Weierstall3, Daniel James3, Dingjie Wang3, Thomas Grant8, Anton Barty7, Oleksandr Yefanov7, Jennifer Scales1, Cornelius Gati6,7, Carolin Seuring6, Vukica Srajer9, Robert Henning9, Peter Schwander1, Raimund Fromme2, Abbas Ourmazd1, Keith Moffat9,10, Jasper J Van Thor11, John C H Spence3, Petra Fromme2, Henry N Chapman6,7, Marius Schmidt1,12.   

Abstract

Serial femtosecond crystallography using ultrashort pulses from x-ray free electron lasers (XFELs) enables studies of the light-triggered dynamics of biomolecules. We used microcrystals of photoactive yellow protein (a bacterial blue light photoreceptor) as a model system and obtained high-resolution, time-resolved difference electron density maps of excellent quality with strong features; these allowed the determination of structures of reaction intermediates to a resolution of 1.6 angstroms. Our results open the way to the study of reversible and nonreversible biological reactions on time scales as short as femtoseconds under conditions that maximize the extent of reaction initiation throughout the crystal.
Copyright © 2014, American Association for the Advancement of Science.

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Year:  2014        PMID: 25477465      PMCID: PMC4361027          DOI: 10.1126/science.1259357

Source DB:  PubMed          Journal:  Science        ISSN: 0036-8075            Impact factor:   47.728


  33 in total

1.  The Protein Data Bank.

Authors:  Helen M Berman; Tammy Battistuz; T N Bhat; Wolfgang F Bluhm; Philip E Bourne; Kyle Burkhardt; Zukang Feng; Gary L Gilliland; Lisa Iype; Shri Jain; Phoebe Fagan; Jessica Marvin; David Padilla; Veerasamy Ravichandran; Bohdan Schneider; Narmada Thanki; Helge Weissig; John D Westbrook; Christine Zardecki
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2002-05-29

2.  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

3.  New photocycle intermediates in the photoactive yellow protein from Ectothiorhodospira halophila: picosecond transient absorption spectroscopy.

Authors:  L Ujj; S Devanathan; T E Meyer; M A Cusanovich; G Tollin; G H Atkinson
Journal:  Biophys J       Date:  1998-07       Impact factor: 4.033

4.  Signal to noise considerations for single crystal femtosecond time resolved crystallography of the Photoactive Yellow Protein.

Authors:  Jasper J van Thor; Mark M Warren; Craig N Lincoln; Matthieu Chollet; Henrik Till Lemke; David M Fritz; Marius Schmidt; Jason Tenboer; Zhong Ren; Vukica Srajer; Keith Moffat; Tim Graber
Journal:  Faraday Discuss       Date:  2014-07-30       Impact factor: 4.008

Review 5.  X-ray lasers for structural and dynamic biology.

Authors:  J C H Spence; U Weierstall; H N Chapman
Journal:  Rep Prog Phys       Date:  2012-09-13

6.  Ultrafast infrared spectroscopy reveals a key step for successful entry into the photocycle for photoactive yellow protein.

Authors:  L J G W van Wilderen; M A van der Horst; I H M van Stokkum; K J Hellingwerf; R van Grondelle; M L Groot
Journal:  Proc Natl Acad Sci U S A       Date:  2006-10-02       Impact factor: 11.205

7.  Visualizing a protein quake with time-resolved X-ray scattering at a free-electron laser.

Authors:  David Arnlund; Linda C Johansson; Cecilia Wickstrand; Anton Barty; Garth J Williams; Erik Malmerberg; Jan Davidsson; Despina Milathianaki; Daniel P DePonte; Robert L Shoeman; Dingjie Wang; Daniel James; Gergely Katona; Sebastian Westenhoff; Thomas A White; Andrew Aquila; Sadia Bari; Peter Berntsen; Mike Bogan; Tim Brandt van Driel; R Bruce Doak; Kasper Skov Kjær; Matthias Frank; Raimund Fromme; Ingo Grotjohann; Robert Henning; Mark S Hunter; Richard A Kirian; Irina Kosheleva; Christopher Kupitz; Mengning Liang; Andrew V Martin; Martin Meedom Nielsen; Marc Messerschmidt; M Marvin Seibert; Jennie Sjöhamn; Francesco Stellato; Uwe Weierstall; Nadia A Zatsepin; John C H Spence; Petra Fromme; Ilme Schlichting; Sébastien Boutet; Gerrit Groenhof; Henry N Chapman; Richard Neutze
Journal:  Nat Methods       Date:  2014-08-10       Impact factor: 28.547

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.  Volume-conserving trans-cis isomerization pathways in photoactive yellow protein visualized by picosecond X-ray crystallography.

Authors:  Yang Ouk Jung; Jae Hyuk Lee; Joonghan Kim; Marius Schmidt; Keith Moffat; Vukica Srajer; Hyotcherl Ihee
Journal:  Nat Chem       Date:  2013-02-03       Impact factor: 24.427

10.  Spectroscopic studies of model photo-receptors: validation of a nanosecond time-resolved micro-spectrophotometer design using photoactive yellow protein and α-phycoerythrocyanin.

Authors:  Namrta Purwar; Jason Tenboer; Shailesh Tripathi; Marius Schmidt
Journal:  Int J Mol Sci       Date:  2013-09-13       Impact factor: 5.923

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  171 in total

1.  Monitoring one-electron photo-oxidation of guanine in DNA crystals using ultrafast infrared spectroscopy.

Authors:  James P Hall; Fergus E Poynton; Páraic M Keane; Sarah P Gurung; John A Brazier; David J Cardin; Graeme Winter; Thorfinnur Gunnlaugsson; Igor V Sazanovich; Michael Towrie; Christine J Cardin; John M Kelly; Susan J Quinn
Journal:  Nat Chem       Date:  2015-10-19       Impact factor: 24.427

Review 2.  Protein Allostery and Conformational Dynamics.

Authors:  Jingjing Guo; Huan-Xiang Zhou
Journal:  Chem Rev       Date:  2016-02-15       Impact factor: 60.622

3.  The New Macromolecular Femtosecond Crystallography (MFX) Instrument at LCLS.

Authors:  Sébastien Boutet; Aina Cohen; Soichi Wakatsuki
Journal:  Synchrotron Radiat News       Date:  2016-02-01

Review 4.  A Bright Future for Serial Femtosecond Crystallography with XFELs.

Authors:  Linda C Johansson; Benjamin Stauch; Andrii Ishchenko; Vadim Cherezov
Journal:  Trends Biochem Sci       Date:  2017-07-18       Impact factor: 13.807

5.  Towards time-resolved serial crystallography in a microfluidic device.

Authors:  Ashtamurthy S Pawate; Vukica Šrajer; Jeremy Schieferstein; Sudipto Guha; Robert Henning; Irina Kosheleva; Marius Schmidt; Zhong Ren; Paul J A Kenis; Sarah L Perry
Journal:  Acta Crystallogr F Struct Biol Commun       Date:  2015-06-27       Impact factor: 1.056

Review 6.  Structural biology of G protein-coupled receptors: new opportunities from XFELs and cryoEM.

Authors:  Andrii Ishchenko; Cornelius Gati; Vadim Cherezov
Journal:  Curr Opin Struct Biol       Date:  2018-03-16       Impact factor: 6.809

Review 7.  Serial Femtosecond Crystallography of G Protein-Coupled Receptors.

Authors:  Benjamin Stauch; Vadim Cherezov
Journal:  Annu Rev Biophys       Date:  2018-03-15       Impact factor: 12.981

8.  X-ray Emission Spectroscopy as an in Situ Diagnostic Tool for X-ray Crystallography of Metalloproteins Using an X-ray Free-Electron Laser.

Authors:  Thomas Fransson; Ruchira Chatterjee; Franklin D Fuller; Sheraz Gul; Clemens Weninger; Dimosthenis Sokaras; Thomas Kroll; Roberto Alonso-Mori; Uwe Bergmann; Jan Kern; Vittal K Yachandra; Junko Yano
Journal:  Biochemistry       Date:  2018-06-28       Impact factor: 3.162

9.  qFit-ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps.

Authors:  Gydo C P van Zundert; Brandi M Hudson; Saulo H P de Oliveira; Daniel A Keedy; Rasmus Fonseca; Amelie Heliou; Pooja Suresh; Kenneth Borrelli; Tyler Day; James S Fraser; Henry van den Bedem
Journal:  J Med Chem       Date:  2018-12-06       Impact factor: 7.446

10.  XFELs open a new era in structural chemical biology.

Authors:  Petra Fromme
Journal:  Nat Chem Biol       Date:  2015-12       Impact factor: 15.040

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