Structural and spectroscopic characterization of photoactive yellow protein and photoswitchable fluorescent protein constructs containing heavy atoms
Abstract
Photo-induced structural rearrangements of chromophore-containing proteins are essential for various light-dependent signaling pathways and optogenetic applications. Ultrafast structural and spectroscopic methods have offered insights into these structural rearrangements across many timescales. However, questions still remain about exact mechanistic details, especially regarding photoisomerization of the chromophore within these proteins femtoseconds to picoseconds after photoexcitation. Instrumentation advancements for time-resolved crystallography and ultrafast electron diffraction provide a promising opportunity to study these reactions, but achieving enough signal-to-noise is a constant challenge. In this work, we present four new photoactive yellow protein constructs and one new fluorescent protein construct that contain heavy atoms either within or around the chromophore and can be expressed with high yields. Structural characterization of these constructs, most at atomic resolution, show minimal perturbation caused by the heavy atoms compared to wild-type structures. Spectroscopic studies report the effects of the heavy atom identity and location on the chromophore’s photophysical properties. None of the substitutions prevent photoisomerization, although certain rates within the photocycle may be affected. Overall, these new proteins containing heavy atoms are ideal samples for state-of-the-art time-resolved crystallography and electron diffraction experiments to elucidate crucial mechanistic information of photoisomerization.
- Authors:
-
- Stanford Univ., CA (United States)
- Publication Date:
- Research Org.:
- SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Basic Energy Sciences (BES); National Science Foundation (NSF); National Institutes of Health (NIH)
- OSTI Identifier:
- 1770137
- Grant/Contract Number:
- AC02-76SF00515; CHE-1740645; P41GM103393
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Journal of Photochemistry and Photobiology. A, Chemistry
- Additional Journal Information:
- Journal Volume: 401; Journal ID: ISSN 1010-6030
- Publisher:
- Elsevier
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; Photoisomerization; photophysics; optogenetics; x-ray crystallography; noncanonical amino acid incorporation
Citation Formats
Romei, Matthew G., Lin, Chi-Yun, and Boxer, Steven G. Structural and spectroscopic characterization of photoactive yellow protein and photoswitchable fluorescent protein constructs containing heavy atoms. United States: N. p., 2020.
Web. doi:10.1016/j.jphotochem.2020.112738.
Romei, Matthew G., Lin, Chi-Yun, & Boxer, Steven G. Structural and spectroscopic characterization of photoactive yellow protein and photoswitchable fluorescent protein constructs containing heavy atoms. United States. https://doi.org/10.1016/j.jphotochem.2020.112738
Romei, Matthew G., Lin, Chi-Yun, and Boxer, Steven G. Tue .
"Structural and spectroscopic characterization of photoactive yellow protein and photoswitchable fluorescent protein constructs containing heavy atoms". United States. https://doi.org/10.1016/j.jphotochem.2020.112738. https://www.osti.gov/servlets/purl/1770137.
@article{osti_1770137,
title = {Structural and spectroscopic characterization of photoactive yellow protein and photoswitchable fluorescent protein constructs containing heavy atoms},
author = {Romei, Matthew G. and Lin, Chi-Yun and Boxer, Steven G.},
abstractNote = {Photo-induced structural rearrangements of chromophore-containing proteins are essential for various light-dependent signaling pathways and optogenetic applications. Ultrafast structural and spectroscopic methods have offered insights into these structural rearrangements across many timescales. However, questions still remain about exact mechanistic details, especially regarding photoisomerization of the chromophore within these proteins femtoseconds to picoseconds after photoexcitation. Instrumentation advancements for time-resolved crystallography and ultrafast electron diffraction provide a promising opportunity to study these reactions, but achieving enough signal-to-noise is a constant challenge. In this work, we present four new photoactive yellow protein constructs and one new fluorescent protein construct that contain heavy atoms either within or around the chromophore and can be expressed with high yields. Structural characterization of these constructs, most at atomic resolution, show minimal perturbation caused by the heavy atoms compared to wild-type structures. Spectroscopic studies report the effects of the heavy atom identity and location on the chromophore’s photophysical properties. None of the substitutions prevent photoisomerization, although certain rates within the photocycle may be affected. Overall, these new proteins containing heavy atoms are ideal samples for state-of-the-art time-resolved crystallography and electron diffraction experiments to elucidate crucial mechanistic information of photoisomerization.},
doi = {10.1016/j.jphotochem.2020.112738},
journal = {Journal of Photochemistry and Photobiology. A, Chemistry},
number = ,
volume = 401,
place = {United States},
year = {Tue Jun 30 00:00:00 EDT 2020},
month = {Tue Jun 30 00:00:00 EDT 2020}
}
Free Publicly Available Full Text
Publisher's Version of Record
Other availability
Search WorldCat to find libraries that may hold this journal
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
Heteroatom Substitution Induced Changes in Excited-State Photophysics and Singlet Oxygen Generation in Chalcogenoxanthylium Dyes: Effect of Sulfur and Selenium Substitutions †
journal, June 2004
- Ohulchanskyy, Tymish Y.; Donnelly, David J.; Detty, Michael R.
- The Journal of Physical Chemistry B, Vol. 108, Issue 25
Short Hydrogen Bonds and Proton Delocalization in Green Fluorescent Protein (GFP)
journal, June 2015
- Oltrogge, Luke M.; Boxer, Steven G.
- ACS Central Science, Vol. 1, Issue 3
19 F NMR Studies of the Native and Denatured States of Green Fluorescent Protein
journal, August 2006
- Khan, Farid; Kuprov, Ilya; Craggs, Timothy D.
- Journal of the American Chemical Society, Vol. 128, Issue 33
The Formation of Diselenide Bridges in Proteins by Incorporation of Selenocysteine Residues: Biosynthesis and Characterization of (Se)2-Thioredoxin
journal, March 1994
- Mueller, Sabine; Senn, Hans; Gsell, Bernard
- Biochemistry, Vol. 33, Issue 11
Tables of bond lengths determined by X-ray and neutron diffraction. Part 1. Bond lengths in organic compounds
journal, January 1987
- Allen, Frank H.; Kennard, Olga; Watson, David G.
- Journal of the Chemical Society, Perkin Transactions 2, Issue 12
Spectral Tuning, Fluorescence, and Photoactivity in Hybrids of Photoactive Yellow Protein, Reconstituted with Native or Modified Chromophores
journal, December 1996
- Kroon, Arthur R.; Hoff, Wouter D.; Fennema, HermanP. M.
- Journal of Biological Chemistry, Vol. 271, Issue 50
Fluorescence imaging using synthetic GFP chromophores
journal, August 2015
- Walker, Christopher L.; Lukyanov, Konstantin A.; Yampolsky, Ilia V.
- Current Opinion in Chemical Biology, Vol. 27
rsEGFP2 enables fast RESOLFT nanoscopy of living cells
journal, December 2012
- Grotjohann, Tim; Testa, Ilaria; Reuss, Matthias
- eLife, Vol. 1
Relative and absolute determination of fluorescence quantum yields of transparent samples
journal, July 2013
- Würth, Christian; Grabolle, Markus; Pauli, Jutta
- Nature Protocols, Vol. 8, Issue 8
Optogenetics: A Primer for Chemists
journal, May 2018
- O'Banion, Colin P.; Lawrence, David S.
- ChemBioChem, Vol. 19, Issue 12
Highlighted Generation of Fluorescence Signals Using Simultaneous Two-Color Irradiation on Dronpa Mutants
journal, June 2007
- Ando, Ryoko; Flors, Cristina; Mizuno, Hideaki
- Biophysical Journal, Vol. 92, Issue 12
Application of photoactive yellow protein as a photoresponsive module for controlling hemolytic activity of staphylococcal α-hemolysin
journal, January 2012
- Ui, Mihoko; Tanaka, Yoshikazu; Araki, Yasuyuki
- Chemical Communications, Vol. 48, Issue 39
Chromophore twisting in the excited state of a photoswitchable fluorescent protein captured by time-resolved serial femtosecond crystallography
journal, September 2017
- Coquelle, Nicolas; Sliwa, Michel; Woodhouse, Joyce
- Nature Chemistry, Vol. 10, Issue 1
Structure of the photoactive yellow protein reconstituted with caffeic acid at 1.16 Å resolution
journal, March 2002
- van Aalten, Daan M. F.; Crielaard, Wim; Hellingwerf, Klaas J.
- Acta Crystallographica Section D Biological Crystallography, Vol. 58, Issue 4
Volume-conserving trans–cis isomerization pathways in photoactive yellow protein visualized by picosecond X-ray crystallography
journal, February 2013
- Jung, Yang Ouk; Lee, Jae Hyuk; Kim, Joonghan
- Nature Chemistry, Vol. 5, Issue 3
Integration, scaling, space-group assignment and post-refinement
journal, January 2010
- Kabsch, Wolfgang
- Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 133-144
Preparation and Properties of a 3,4-Dihydroxycinnamic Acid Chromophore Variant of the Photoactive Yellow Protein
journal, April 1997
- Devanathan, S.; Genick, U. K.; Getzoff, E. D.
- Archives of Biochemistry and Biophysics, Vol. 340, Issue 1
XDS
journal, January 2010
- Kabsch, Wolfgang
- Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2
Structural Evidence of Photoisomerization Pathways in Fluorescent Proteins
journal, September 2019
- Chang, Jeffrey; Romei, Matthew G.; Boxer, Steven G.
- Journal of the American Chemical Society, Vol. 141, Issue 39
An Evolved Aminoacyl-tRNA Synthetase with Atypical Polysubstrate Specificity,
journal, March 2011
- Young, Douglas D.; Young, Travis S.; Jahnz, Michael
- Biochemistry, Vol. 50, Issue 11
Electrostatic control of photoisomerization pathways in proteins
journal, January 2020
- Romei, Matthew G.; Lin, Chi-Yun; Mathews, Irimpan I.
- Science, Vol. 367, Issue 6473
Photoactive Yellow Protein: A Prototypic PAS Domain Sensory Protein and Development of a Common Signaling Mechanism †
journal, May 2003
- Cusanovich, Michael A.; Meyer, Terry E.
- Biochemistry, Vol. 42, Issue 17
Perturbation of Short Hydrogen Bonds in Photoactive Yellow Protein via Noncanonical Amino Acid Incorporation
journal, May 2019
- Thomson, Benjamin; Both, Johan; Wu, Yufan
- The Journal of Physical Chemistry B, Vol. 123, Issue 23
Photo-control of DNA binding by an engrailed homeodomain–photoactive yellow protein hybrid
journal, January 2015
- Kumar, A.; Ali, A. M.; Woolley, G. A.
- Photochemical & Photobiological Sciences, Vol. 14, Issue 9
Influence of a chromophore analogue in the protein cage of a photoactive yellow protein
journal, January 2015
- Hamada, Norio; Tan, Zhe; Kanematsu, Yasuo
- Photochemical & Photobiological Sciences, Vol. 14, Issue 9
Telluropyrylium dyes. 1. 2,6-Diphenyltelluropyrylium dyes
journal, December 1982
- Detty, Michael R.; Murray, Bruce J.
- The Journal of Organic Chemistry, Vol. 47, Issue 27
Photoinduced Chemistry in Fluorescent Proteins: Curse or Blessing?
journal, March 2016
- Acharya, Atanu; Bogdanov, Alexey M.; Grigorenko, Bella L.
- Chemical Reviews, Vol. 117, Issue 2
Imaging CF 3 I conical intersection and photodissociation dynamics with ultrafast electron diffraction
journal, July 2018
- Yang, Jie; Zhu, Xiaolei; Wolf, Thomas J. A.
- Science, Vol. 361, Issue 6397
Fluorescence nanoscopy in cell biology
journal, September 2017
- Sahl, Steffen J.; Hell, Stefan W.; Jakobs, Stefan
- Nature Reviews Molecular Cell Biology, Vol. 18, Issue 11
Ultrafast non-radiative dynamics of atomically thin MoSe2
journal, November 2017
- Lin, Ming-Fu; Kochat, Vidya; Krishnamoorthy, Aravind
- Nature Communications, Vol. 8, Issue 1
Ultrafast Dynamics of Isolated Model Photoactive Yellow Protein Chromophores: “Chemical Perturbation Theory” in the Laboratory
journal, March 2005
- Vengris, Mikas; Larsen, Delmar S.; van der Horst, Michael A.
- The Journal of Physical Chemistry B, Vol. 109, Issue 9
Unified Model for Photophysical and Electro-Optical Properties of Green Fluorescent Proteins
journal, August 2019
- Lin, Chi-Yun; Romei, Matthew G.; Oltrogge, Luke M.
- Journal of the American Chemical Society, Vol. 141, Issue 38
The photochemical ring-opening of 1,3-cyclohexadiene imaged by ultrafast electron diffraction
journal, April 2019
- Wolf, T. J. A.; Sanchez, D. M.; Yang, J.
- Nature Chemistry, Vol. 11, Issue 6
Coot model-building tools for molecular graphics
journal, November 2004
- Emsley, Paul; Cowtan, Kevin
- Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132
Significant Expansion of Fluorescent Protein Sensing Ability through the Genetic Incorporation of Superior Photo-Induced Electron-Transfer Quenchers
journal, September 2014
- Liu, Xiaohong; Jiang, Li; Li, Jiasong
- Journal of the American Chemical Society, Vol. 136, Issue 38
Anticipatory active-site motions and chromophore distortion prime photoreceptor PYP for light activation
journal, July 2003
- Getzoff, Elizabeth D.; Gutwin, Karl N.; Genick, Ulrich K.
- Nature Structural & Molecular Biology, Vol. 10, Issue 8
Binding, tuning and mechanical function of the 4-hydroxy-cinnamic acid chromophore in photoactive yellow protein
journal, January 2007
- van der Horst, Michael A.; Arents, Jos C.; Kort, Remco
- Photochemical & Photobiological Sciences, Vol. 6, Issue 5
PHENIX: a comprehensive Python-based system for macromolecular structure solution
journal, January 2010
- Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
- Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221
Chalcogenapyrylium dyes as potential photochemotherapeutic agents. Solution studies of heavy atom effects on triplet yields, quantum efficiencies of singlet oxygen generation, rates of reaction with singlet oxygen, and emission quantum yields
journal, May 1990
- Detty, Michael R.; Merkel, Paul B.
- Journal of the American Chemical Society, Vol. 112, Issue 10
Electric Field Keeps Chromophore Planar and Produces High Yield Fluorescence in Green Fluorescent Protein
journal, October 2016
- Park, Jae Woo; Rhee, Young Min
- Journal of the American Chemical Society, Vol. 138, Issue 41
Femtosecond structural dynamics drives the trans/cis isomerization in photoactive yellow protein
journal, May 2016
- Pande, K.; Hutchison, C. D. M.; Groenhof, G.
- Science, Vol. 352, Issue 6286
Rational design of ultrastable and reversibly photoswitchable fluorescent proteins for super-resolution imaging of the bacterial periplasm
journal, January 2016
- El Khatib, Mariam; Martins, Alexandre; Bourgeois, Dominique
- Scientific Reports, Vol. 6, Issue 1
The Role of the Protein Matrix in Green Fluorescent Protein Fluorescence
journal, January 2006
- Maddalo, Scott L.; Zimmer, Marc
- Photochemistry and Photobiology, Vol. 82, Issue 2
Theory and Simulation of the Ultrafast Double-Bond Isomerization of Biological Chromophores
journal, October 2017
- Gozem, Samer; Luk, Hoi Ling; Schapiro, Igor
- Chemical Reviews, Vol. 117, Issue 22
Photoswitching mechanism of a fluorescent protein revealed by time-resolved crystallography and transient absorption spectroscopy
journal, February 2020
- Woodhouse, Joyce; Nass Kovacs, Gabriela; Coquelle, Nicolas
- Nature Communications, Vol. 11, Issue 1
Evolving tRNASec for Efficient Canonical Incorporation of Selenocysteine
journal, December 2014
- Thyer, Ross; Robotham, Scott A.; Brodbelt, Jennifer S.
- Journal of the American Chemical Society, Vol. 137, Issue 1, p. 46-49
A split fluorescent reporter with rapid and reversible complementation
journal, June 2019
- Tebo, Alison G.; Gautier, Arnaud
- Nature Communications, Vol. 10, Issue 1
Generation and characterization of ultrathin free-flowing liquid sheets
journal, April 2018
- Koralek, Jake D.; Kim, Jongjin B.; Brůža, Petr
- Nature Communications, Vol. 9, Issue 1
Synthesis and photophysical characterization of chalcogen substituted BODIPY dyes
journal, January 2009
- Fron, Eduard; Coutiño-Gonzalez, Eduardo; Pandey, Lesley
- New Journal of Chemistry, Vol. 33, Issue 7
A Versatile Platform for Single- and Multiple-Unnatural Amino Acid Mutagenesis in Escherichia coli
journal, February 2013
- Chatterjee, Abhishek; Sun, Sophie B.; Furman, Jennifer L.
- Biochemistry, Vol. 52, Issue 10
Structural Effects on the Ultrafast Photoisomerization of Photoactive Yellow Protein. Transient Absorption Spectroscopy of Two Point Mutants
journal, April 2009
- Changenet-Barret, Pascale; Plaza, Pascal; Martin, Monique M.
- The Journal of Physical Chemistry C, Vol. 113, Issue 27
Ultrafast Electron Diffraction (UED): A New Development for the 4D Determination of Transient Molecular Structures
journal, June 2003
- Srinivasan, Ramesh; Lobastov, Vladimir A.; Ruan, Chong-Yu
- Helvetica Chimica Acta, Vol. 86, Issue 6
Selenomethionine and Selenocysteine Double Labeling Strategy for Crystallographic Phasing
journal, November 2003
- Strub, Marie-Paule; Hoh, François; Sanchez, Jean-Frédéric
- Structure, Vol. 11, Issue 11
Optogenetic Inhibitor of the Transcription Factor CREB
journal, November 2015
- Ali, Ahmed M.; Reis, Jakeb M.; Xia, Yan
- Chemistry & Biology, Vol. 22, Issue 11
Ultrafast X-Ray Crystallography and Liquidography
journal, May 2017
- Ki, Hosung; Oang, Key Young; Kim, Jeongho
- Annual Review of Physical Chemistry, Vol. 68, Issue 1
Chromophore twisting in the excited state of a photoswitchable fluorescent protein captured by time-resolved serial femtosecond crystallography
dataset, January 2017
- Coquelle, Coquelle
- Coherent X-ray Imaging Data Bank (Lawrence Berkeley National Laboratory); Institut Laue Langevin