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

Journal Article · · Science
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  1. Univ. of Wisconsin, Milwaukee, WI (United States). Physics Dept.
  2. Arizona State Univ., Tempe, AZ (United States). Dept. of Chemistry and Biochemistry
  3. Arizona State Univ., Tempe, AZ (United States). Dept. of Physics
  4. SLAC National Accelerator Lab., Menlo Park, CA (United States). Linac Coherent Light Source (LCLS)
  5. Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
  6. Univ. of Hamburg (Germany). Centre for Ultrafast Imaging
  7. Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany). Center for Free-Electron Laser Science
  8. State Univ. of New York at Buffalo (SUNY), Buffalo, NY (United States). Hauptman-Woodward Inst.
  9. Univ. of Hamburg (Germany). Centre for Ultrafast Imaging; Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany). Center for Free-Electron Laser Science
  10. Univ. of Chicago, IL (United States). Center for Advanced Radiation Sources
  11. Univ. of Chicago, IL (United States). Center for Advanced Radiation Sources; Univ. of Chicago, IL (United States). Dept. of Biochemistry and Molecular Biology and Inst. for Biophysical Dynamics
  12. Univ. of Chicago, IL (United States). Dept. of Biochemistry and Molecular Biology and Inst. for Biophysical Dynamics

We report that serial femtosecond crystallography using ultrashort pulses from X-ray Free Electron Lasers (XFELs) offers the possibility to study light-triggered dynamics of biomolecules. Using microcrystals of the blue light photoreceptor, photoactive yellow protein, as a model system, we present high resolution, time-resolved difference electron density maps of excellent quality with strong features, which allow the determination of structures of reaction intermediates to 1.6 Å resolution. These results open the way to the study of reversible and non-reversible biological reactions on time scales as short as femtoseconds under conditions which maximize the extent of reaction initiation throughout the crystal.

Research Organization:
Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Organization:
USDOE; National Institutes of Health (NIH); National Science Foundation (NSF)
Grant/Contract Number:
NSF-1231306; R01GM095583; AC52-07NA27344; 012-ERD-031; R24GM111072
OSTI ID:
1165312
Journal Information:
Science, Vol. 346, Issue 6214; ISSN 0036-8075
Publisher:
AAASCopyright Statement
Country of Publication:
United States
Language:
ENGLISH
Citation Metrics:
Cited by: 345 works
Citation information provided by
Web of Science

References (55)

Time-Resolved Macromolecular Crystallography journal June 1989
Structure Based Kinetics by Time-Resolved X-ray Crystallography book January 2008
Protein energy landscapes determined by five-dimensional crystallography journal November 2013
Volume-conserving trans–cis isomerization pathways in photoactive yellow protein visualized by picosecond X-ray crystallography journal February 2013
Watching a signaling protein function in real time via 100-ps time-resolved Laue crystallography journal November 2012
Watching a Protein as it Functions with 150-ps Time-Resolved X-ray Crystallography journal June 2003
Extended subnanosecond structural dynamics of myoglobin revealed by Laue crystallography journal March 2006
Femtosecond X-ray protein nanocrystallography journal February 2011
X-ray lasers for structural and dynamic biology journal September 2012
Time-resolved structural studies at synchrotrons and X-ray free electron lasers: opportunities and challenges journal October 2012
Injector for scattering measurements on fully solvated biospecies journal March 2012
Radiation damage in protein serial femtosecond crystallography using an x-ray free-electron laser journal December 2011
Self-terminating diffraction gates femtosecond X-ray nanocrystallography measurements journal December 2011
Potential for biomolecular imaging with femtosecond X-ray pulses journal August 2000
High-Resolution Protein Structure Determination by Serial Femtosecond Crystallography journal May 2012
Natively Inhibited Trypanosoma brucei Cathepsin B Structure Determined by Using an X-ray Laser journal November 2012
Visualizing a protein quake with time-resolved X-ray scattering at a free-electron laser journal August 2014
Structure-factor analysis of femtosecond microdiffraction patterns from protein nanocrystals journal February 2011
De novo protein crystal structure determination from X-ray free-electron laser data journal November 2013
Time-resolved protein nanocrystallography using an X-ray free-electron laser journal January 2012
Simultaneous Femtosecond X-ray Spectroscopy and Diffraction of Photosystem II at Room Temperature journal February 2013
Serial time-resolved crystallography of photosystem II using a femtosecond X-ray laser journal July 2014
Ultrafast infrared spectroscopy reveals a key step for successful entry into the photocycle for photoactive yellow protein journal October 2006
Photoisomerisation quantum yield and non-linear cross-sections with femtosecond excitation of the photoactive yellow protein journal January 2012
New Photocycle Intermediates in the Photoactive Yellow Protein from Ectothiorhodospira halophila: Picosecond Transient Absorption Spectroscopy journal July 1998
From The Cover: Visualizing reaction pathways in photoactive yellow protein from nanoseconds to seconds journal May 2005
The Protein Data Bank journal May 2002
Phasing of coherent femtosecond X-ray diffraction from size-varying nanocrystals journal January 2011
Application of Singular Value Decomposition to the Analysis of Time-Resolved Macromolecular X-Ray Data journal March 2003
Spectroscopic Studies of Model Photo-Receptors: Validation of a Nanosecond Time-Resolved Micro-Spectrophotometer Design Using Photoactive Yellow Protein and α-Phycoerythrocyanin journal September 2013
Photoactivation of the Photoactive Yellow Protein:  Why Photon Absorption Triggers a Trans-to-Cis Isomerization of the Chromophore in the Protein journal April 2004
Protein Structural Dynamics of Photoactive Yellow Protein in Solution Revealed by Pump–Probe X-ray Solution Scattering journal February 2012
The Coherent X-ray Imaging (CXI) instrument at the Linac Coherent Light Source (LCLS) journal March 2010
CSPAD-140k: A versatile detector for LCLS experiments
  • Herrmann, Sven; Boutet, Sébastien; Duda, Brian
  • Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, Vol. 718 https://doi.org/10.1016/j.nima.2013.01.057
journal August 2013
Cheetah : software for high-throughput reduction and analysis of serial femtosecond X-ray diffraction data journal May 2014
CrystFEL : a software suite for snapshot serial crystallography journal March 2012
1.4 .ANG. Structure of Photoactive Yellow Protein, a Cytosolic Photoreceptor: Unusual Fold, Active Site, and Chromophore journal May 1995
Ultra-precise characterization of LCLS hard X-ray focusing mirrors by high resolution slope measuring deflectometry journal January 2012
Breaking the indexing ambiguity in serial crystallography journal December 2013
Macromolecular TLS Refinement in REFMAC at Moderate Resolutions book January 2003
Overview of the CCP 4 suite and current developments journal March 2011
A Molecular Movie at 1.8 Å Resolution Displays the Photocycle of Photoactive Yellow Protein, a Eubacterial Blue-Light Receptor, from Nanoseconds to Seconds journal November 2001
XtalView, protein structure solution and protein graphics, a short history journal September 2008
Features and development of Coot journal March 2010
Protein kinetics: Structures of intermediates and reaction mechanism from time-resolved x-ray data journal March 2004
Structure of a Protein Photocycle Intermediate by Millisecond Time-Resolved Crystallography journal March 1997
pH Dependence of the Photoactive Yellow Protein Photocycle Investigated by Time-Resolved Crystallography journal January 2012
Optical Studies of a Bacterial Photoreceptor Protein, Photoactive Yellow Protein, in Single Crystals journal January 1995
Pump–Dump–Probe and Pump–Repump–Probe Ultrafast Spectroscopy Resolves Cross Section of an Early Ground State Intermediate and Stimulated Emission in the Photoreactions of the Pr Ground State of the Cyanobacterial Phytochrome Cph1 journal January 2012
Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers journal March 2014
Structural biology at the European X-ray free-electron laser facility journal July 2014
Time-Resolved Macromolecular Crystallography journal January 1989
PARP1 exhibits enhanced association and catalytic efficiency with γH2A.X-nucleosome journal December 2019
Time-resolved macromolecular crystallography journal August 1996
Overview of the CCP4 suite and current developments. text January 2011

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