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Title: Femtosecond structural dynamics drives the trans/cis isomerization in photoactive yellow protein

Journal Article · · Science

A variety of organisms have evolved mechanisms to detect and respond to light, in which the response is mediated by protein structural changes following photon absorption. The initial step is often the photo-isomerization of a conjugated chromophore. Furthermore, isomerization occurs on ultrafast timescales and is substantially influenced by the chromophore environment. Here we identify structural changes associated with the earliest steps in the trans to cis isomerization of the chromophore in photoactive yellow protein. Femtosecond, hard X-ray pulses emitted by the Linac Coherent Light Source were used to conduct time-resolved serial femtosecond crystallography on PYP microcrystals over the time range from 100 femtoseconds to 3 picoseconds to determine the structural dynamics of the photoisomerization reaction.

Research Organization:
Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)
Sponsoring Organization:
USDOE National Nuclear Security Administration (NNSA); USDOE Office of Science (SC), Basic Energy Sciences (BES); USDOE Laboratory Directed Research and Development (LDRD) Program; National Science Foundation (NSF); National Institutes of Health (NIH); Federal Ministry of Education and Research (BMBF)
Grant/Contract Number:
AC52-07NA27344; AC02-76SF00515; 012-ERD-031; NSF-1231306; NSF-0952643; NSF-1158138; R01GM095583; R01EY024363; R24GM111072; P41GM103393; 05K14CHA
OSTI ID:
1355852
Alternate ID(s):
OSTI ID: 2229607
Report Number(s):
LLNL-JRNL-857679; 352/6286/725
Journal Information:
Science, Journal Name: Science Vol. 352 Journal Issue: 6286; ISSN 0036-8075
Publisher:
American Association for the Advancement of Science (AAAS)Copyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 289 works
Citation information provided by
Web of Science

References (78)

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
Time-resolved Laue diffraction of excited species at atomic resolution: 100 ps single-pulse diffraction of the excited state of the organometallic complex Rh2(μ-PNP)2(PNP)2·BPh4 journal January 2011
Overview of the CCP 4 suite and current developments journal March 2011
Photoisomerization and Photoionization of the Photoactive Yellow Protein Chromophore in Solution journal April 2004
Time-resolved pump-probe experiments at the LCLS journal January 2010
The hydration shell of myoglobin journal November 1992
GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation journal February 2008
Mapping molecular motions leading to charge delocalization with ultrabright electrons journal April 2013
Approximate switching algorithms for trajectory surface hopping journal July 2008
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
GROMACS: Fast, flexible, and free journal January 2005
Coherent oscillations in ultrafast fluorescence of photoactive yellow protein journal December 2007
Contrasting the Excited-State Dynamics of the Photoactive Yellow Protein Chromophore: Protein versus Solvent Environments journal September 2004
Comparison of simple potential functions for simulating liquid water journal July 1983
Injector for scattering measurements on fully solvated biospecies journal March 2012
Sub-femtosecond precision measurement of relative X-ray arrival time for free-electron lasers journal July 2014
A new mixing of Hartree–Fock and local density‐functional theories journal January 1993
Bicycle-pedal model for the first step in the vision process journal April 1976
Frequency-resolved optical gating and single-shot spectral measurements reveal fine structure in microstructure-fiber continuum journal January 2002
Molecular Basis of Visual Excitation journal October 1968
Ultrafast photoinduced reaction dynamics of photoactive yellow protein (PYP): observation of coherent oscillations in the femtosecond fluorescence decay dynamics journal January 2002
Femtosecond Spectroscopic Observations of Initial Intermediates in the Photocycle of the Photoactive Yellow Protein from Ectothiorhodospira halophila journal August 1999
Time-resolved serial crystallography captures high-resolution intermediates of photoactive yellow protein journal December 2014
Visualizing Photochemical Dynamics in Solution through Picosecond X-Ray Scattering journal October 2001
Volume-conserving trans–cis isomerization pathways in photoactive yellow protein visualized by picosecond X-ray crystallography journal February 2013
Excited-state structure by time-resolved X-ray diffraction journal February 2002
UCSF Chimera?A visualization system for exploratory research and analysis journal January 2004
Quantum Mechanical Continuum Solvation Models journal August 2005
Selective Excitation of Vibrational Wave Packet Motion Using Chirped Pulses journal November 1995
Ultrafast X-ray Diffraction of Transient Molecular Structures in Solution journal August 2005
Post-refinement method for snapshot serial crystallography journal July 2014
Femtochemistry: Atomic-Scale Dynamics of the Chemical Bond Using Ultrafast Lasers (Nobel Lecture) journal August 2000
From The Cover: Visualizing reaction pathways in photoactive yellow protein from nanoseconds to seconds journal May 2005
Extended multi-configuration quasi-degenerate perturbation theory: The new approach to multi-state multi-reference perturbation theory journal June 2011
Photoisomerisation quantum yield and non-linear cross-sections with femtosecond excitation of the photoactive yellow protein journal January 2012
A complete active space SCF method (CASSCF) using a density matrix formulated super-CI approach journal May 1980
Photoactivation of the Photoactive Yellow Protein:  Why Photon Absorption Triggers a Trans-to-Cis Isomerization of the Chromophore in the Protein journal April 2004
Application of Singular Value Decomposition to the Analysis of Time-Resolved Macromolecular X-Ray Data journal March 2003
Canonical sampling through velocity rescaling journal January 2007
Watching a signaling protein function in real time via 100-ps time-resolved Laue crystallography journal November 2012
Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density journal January 1988
LINCS: A linear constraint solver for molecular simulations journal September 1997
Low-barrier hydrogen bond in photoactive yellow protein journal January 2009
Visualizing a protein quake with time-resolved X-ray scattering at a free-electron laser journal August 2014
Control of selectivity of chemical reaction via control of wave packet evolution journal November 1985
REFMAC 5 for the refinement of macromolecular crystal structures journal March 2011
Quantum model simulation of complete S0→S1 population transfer by means of intense laser pulses with opposite chirp journal November 2000
Ultrafast myoglobin structural dynamics observed with an X-ray free-electron laser journal April 2015
Force Spectroscopy of Single Biomolecules journal March 2002
Use of Non-crystallographic Symmetry in Protein Structure Refinement journal July 1996
Direct Observation of Cooling of Heme Upon Photodissociation of Carbonmonoxy Myoglobin journal October 1997
Short hydrogen bonds in photoactive yellow protein journal May 2004
The CSPAD megapixel x-ray camera at LCLS conference October 2012
Investigations of ultrafast nuclear response induced by resonant and nonresonant laser pulses journal April 2001
Application of chirped ultrashort pulses for generating large-amplitude ground-state vibrational coherence: a computer simulation journal January 1990
Myoglobin Dynamics Measured With Vibrational Echo Experiments journal January 1999
The interpretation of protein structures: Estimation of static accessibility journal February 1971
Solvent cage effects and chemical dynamics in liquids journal April 1991
Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models journal October 1992
Initial Steps of Signal Generation in Photoactive Yellow Protein Revealed with Femtosecond Mid-Infrared Spectroscopy journal September 2003
Picosecond X-Ray Diffraction Probed Transient Structural Changes in Organic Solids journal March 2001
Tools for macromolecular model building and refinement into electron cryo-microscopy reconstructions journal January 2015
Direct observation of global protein motion in hemoglobin and myoglobin on picosecond time scales journal March 1991
Structural Evolution of the Chromophore in the Primary Stages of Trans/Cis Isomerization in Photoactive Yellow Protein journal December 2005
Spectral encoding of x-ray/optical relative delay journal January 2011
Photochemical reactions in biological systems: probing the effect of the environment by means of hybrid quantum chemistry/molecular mechanics simulations journal January 2012
Protein energy landscapes determined by five-dimensional crystallography journal November 2013
3V: cavity, channel and cleft volume calculator and extractor journal May 2010
A smooth particle mesh Ewald method journal November 1995
CHEMISTRY: Following the Flow of Energy in Biomolecules journal November 2005
A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations journal October 2003
The Protein Data Bank journal May 2002
Measuring ultrashort laser pulses in the time-frequency domain using frequency-resolved optical gating journal September 1997
Incoherent Manipulation of the Photoactive Yellow Protein Photocycle with Dispersed Pump-Dump-Probe Spectroscopy journal September 2004
Chromophore Dynamics in the PYP Photocycle from Femtosecond Stimulated Raman Spectroscopy journal January 2014
Ultrafast infrared spectroscopy reveals a key step for successful entry into the photocycle for photoactive yellow protein journal October 2006
Direct observation of ultrafast collective motions in CO myoglobin upon ligand dissociation journal September 2015