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M. E. Auldridge and K. T. Forest, “ Bacterial phytochromes: More than meets the light,” Crit. Rev. Biochem. Mol. Biol. 46, 6788 (2011).
G. Bae and G. Choi, “ Decoding of light signals by plant phytochromes and their interacting proteins,” Annu. Rev. Plant. Biol. 59, 281311 (2008).
J. Hughes, “ Phytochrome cytoplasmic signaling,” Annu. Rev. Plant. Biol. 64, 377402 (2013).
F. Andel III, J. C. Lagarias, and R. A. Mathies, “ Resonance Raman analysis of chromophore structure in the lumi-R photoproduct of phytochrome,” Biochemistry 35, 1599716008 (1996).
M. A. Mroginski, D. H. Murgida, and P. Hildebrandt, “ The chromophore structural changes during the photocycle of phytochrome: A combined resonance Raman and quantum chemical approach,” Acc. Chem. Res. 40, 258266 (2007).
K. C. Toh, E. A. Stojkovic, I. H. van Stokkum, K. Moffat, and J. T. Kennis, “ Proton-transfer and hydrogen-bond interactions determine fluorescence quantum yield and photochemical efficiency of bacteriophytochrome,” Proc. Natl. Acad. Sci. U.S.A. 107, 91709175 (2010).
X. Yang, Z. Ren, J. Kuk, and K. Moffat, “ Temperature-scan cryocrystallography reveals reaction intermediates in bacteriophytochrome,” Nature 479, 428432 (2011).
K. Anders, G. Daminelli-Widany, M. A. Mroginski, D. von Stetten, and L. O. Essen, “ Structure of the cyanobacterial phytochrome 2 photosensor implies a tryptophan switch for phytochrome signaling,” J. Biol. Chem. 288, 3571435725 (2013).
E. A. Stojkovic, K. C. Toh, M. T. Alexandre, M. Baclayon, K. Moffat, and J. T. Kennis, “ FTIR spectroscopy revealing light-dependent refolding of the conserved tongue region of bacteriophytochrome,” J. Phys. Chem. Lett. 5, 25122515 (2014).
H. Takala, A. Björling, O. Berntsson, H. Lehtivuori, S. Niebling, M. Hoernke, I. Kosheleva, R. Henning, A. Menzel, J. A. Ihalainen, and S. Westenhoff, “ Signal amplification and transduction in phytochrome photosensors,” Nature 509, 245248 (2014).
L. O. Essen, J. Mailliet, and J. Hughes, “ The structure of a complete phytochrome sensory module in the Pr ground state,” Proc. Natl. Acad. Sci. U.S.A. 105, 1470914714 (2008).
X. Yang, J. Kuk, and K. Moffat, “ Crystal structure of Pseudomonas aeruginosa bacteriophytochrome: Photoconversion and signal transduction,” Proc. Natl. Acad. Sci. U.S.A. 105, 1471514720 (2008).
M. P. Bhate, K. S. Molnar, M. Goulian, and W. F. DeGrado, “ Signal transduction in histidine kinases: Insights from new structures,” Structure 23, 981994 (2015).
E. S. Burgie, J. Zhang, and R. D. Vierstra, “ Crystal structure of deinococcus phytochrome in the photoactivated state reveals a cascade of structural rearrangements during photoconversion,” Structure 24, 448 (2016).
M. E. Auldridge, K. A. Satyshur, D. M. Anstrom, and K. T. Forest, “ Structure-guided engineering enhances a phytochrome-based infrared fluorescent protein,” J. Biol. Chem. 287, 70007009 (2012).
H. Takala, A. Bjorling, M. Linna, S. Westenhoff, and J. A. Ihalainen, “ Light-induced changes in the dimerization interface of bacteriophytochromes,” J. Biol. Chem. 290, 1638316392 (2015).
H. Lehtivuori, I. Rissanen, H. Takala, J. Bamford, N. V. Tkachenko, and J. A. Ihalainen, “ Fluorescence properties of the chromophore-binding domain of bacteriophytochrome from Deinococcus radiodurans,” J. Phys. Chem. B 117, 1104911057 (2013).
H. Takala, H. Lehtivuori, H. Hammarén, V. P. Hytönen, and J. A. Ihalainen, “ Connection between absorption properties and conformational changes in Deinococcus radiodurans phytochrome,” Biochemistry 53, 70767085 (2014).
A. Bjorling, O. Berntsson, H. Takala, K. D. Gallagher, H. Patel, E. Gustavsson, R. St Peter, P. Duong, A. Nugent, F. Zhang, P. Berntsen, R. Appio, I. Rajkovic, H. Lehtivuori, M. R. Panman, M. Hoernke, S. Niebling, R. Harimoorthy, T. Lamparter, E. A. Stojkovic, J. A. Ihalainen, and S. Westenhoff, “ Ubiquitous structural signaling in bacterial phytochromes,” J. Phys. Chem. Lett. 6, 33793383 (2015).
S. Westenhoff, E. Malmerberg, D. Arnlund, L. Johansson, E. Nazarenko, M. Cammarata, J. Davidsson, V. Chaptal, J. Abramson, G. Katona, A. Menzel, and R. Neutze, “ Rapid readout detector captures protein time-resolved WAXS,” Nat. Methods 7, 775776 (2010).
A. Björling, O. Berntsson, H. Lehtivuori, H. Takala, A. J. Hughes, M. Panman, M. Hoernke, S. Niebling, L. Henry, R. Henning, I. Kosheleva, V. Chukharev, N. V. Tkachenko, A. Menzel, G. Newby, D. Khakhulin, M. Wulff, J. A. Ihalainen, and S. Westenhoff, “ Structural photoactivation of a full-length bacterial phytochrome,” Sci. Adv. 2, e1600920 (2016).
B. Hess, C. Kutzner, D. van der Spoel, and E. Lindahl, “ GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation,” J. Chem. Theory Comput. 4, 435447 (2008).
S. Pronk, S. Pall, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R. Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl, “ GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit,” Bioinformatics 29, 845854 (2013).
P. Bjelkmar, P. Larsson, M. A. Cuendet, B. Hess, and E. Lindahl, “ Implementation of the CHARMM force field in GROMACS: Analysis of protein stability effects from correction maps, virtual interaction sites, and water models,” J. Chem. Theory Comput. 6, 459466 (2010).
S. Kaminski, G. Daminelli, and M. A. Mroginski, “ Molecular dynamics simulations of the chromophore binding site of Deinococcus radiodurans bacteriophytochrome using new force field parameters for the phytochromobilin chromophore,” J. Phys. Chem. B 113, 945958 (2009).
G. Bussi, D. Donadio, and M. Parrinello, “ Canonical sampling through velocity rescaling,” J. Chem. Phys. 126, 014101 (2007).
M. Parrinello and A. Rahman, “ Polymorphic transitions in single crystals: A new molecular dynamics method,” J. Appl. Phys. 52, 71827190 (1981).
S. Nosé and M. L. Klein, “ Constant pressure molecular dynamics for molecular systems,” Mol. Phys. 50, 10551076 (1983).
B. Hess, H. Bekker, H. J. C. Berendsen, and J. G. E. M. Fraaije, “ LINCS: A linear constraint solver for molecular simulations,” J. Comput. Chem. 18, 14631472 (1997).<1463::AID-JCC4>3.0.CO;2-H
T. Darden, D. York, and L. Pedersen, “ Particle mesh Ewald: An N log(N) method for Ewald sums in large systems,” J. Chem. Phys. 98, 1008910092 (1993).
U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee, and L. G. Pedersen, “ A smooth particle mesh Ewald method,” J. Chem. Phys. 103, 85778593 (1995).
H. Liu, A. Hexemer, and P. H. Zwart, “ The small angle scattering toolbox (SASTBX): An open-source software for biomolecular small-angle scattering,” J. Appl. Crystallogr. 45, 587593 (2012).
M. Cammarata, M. Levantino, F. Schotte, P. A. Anfinrud, F. Ewald, J. Choi, A. Cupane, M. Wulff, and H. Ihee, “ Tracking the structural dynamics of proteins in solution using time-resolved wide-angle X-ray scattering,” Nat. Methods 5, 881886 (2008).
M. Andersson, E. Malmerberg, S. Westenhoff, G. Katona, M. Cammarata, A. B. Wohri, L. C. Johansson, F. Ewald, M. Eklund, M. Wulff, J. Davidsson, and R. Neutze, “ Structural dynamics of light-driven proton pumps,” Structure 17, 12651275 (2009).
F. Velazquez Escobar, P. Piwowarski, J. Salewski, N. Michael, M. Fernandez Lopez, A. Rupp, B. M. Qureshi, P. Scheerer, F. Bartl, N. Frankenberg-Dinkel, F. Siebert, M. Andrea Mroginski, and P. Hildebrandt, “ A protonation-coupled feedback mechanism controls the signalling process in bathy phytochromes,” Nat. Chem. 7, 423430 (2015).
H. Foerstendorf, C. Benda, W. Gartner, M. Storf, H. Scheer, and F. Siebert, “ FTIR studies of phytochrome photoreactions reveal the C=O bands of the chromophore: Consequences for its protonation states, conformation, and protein interaction,” Biochemistry 40, 1495214959 (2001).
H. Li, J. Zhang, R. D. Vierstra, and H. Li, “ Quaternary organization of a phytochrome dimer as revealed by cryoelectron microscopy,” Proc. Natl. Acad. Sci. U.S.A. 107, 1087210877 (2010).
E. S. Burgie, T. Wang, A. N. Bussell, J. M. Walker, H. Li, and R. D. Vierstra, “ Crystallographic and electron microscopic analyses of a bacterial phytochrome reveal local and global rearrangements during photoconversion,” J. Biol. Chem. 289, 2457324587 (2014).
P. Piwowarski, E. Ritter, K. P. Hofmann, P. Hildebrandt, D. von Stetten, P. Scheerer, N. Michael, T. Lamparter, and F. Bartl, “ Light-induced activation of bacterial phytochrome Agp1 monitored by static and time-resolved FTIR spectroscopy,” Chemphyschem 11, 12071214 (2010).
J. J. van Thor, N. Fisher, and P. R. Rich, “ Assignments of the Pfr-Pr FTIR difference spectrum of cyanobacterial phytochrome Cph1 using 15N and 13C isotopically labeled phycocyanobilin chromophore,” J. Phys. Chem. B 109, 2059720604 (2005).
E. S. Burgie, A. N. Bussell, J. M. Walker, K. Dubiel, and R. D. Vierstra, “ Crystal structure of the photosensing module from a red/far-red light-absorbing plant phytochrome,” Proc. Natl. Acad. Sci. U.S.A. 111, 1017910184 (2014).
X. Yang, E. A. Stojkovic, W. B. Ozarowski, J. Kuk, E. Davydova, and K. Moffat, “ Light signaling mechanism of two tandem bacteriophytochromes,” Structure 23, 11791189 (2015).
D. Bellini and M. Z. Papiz, “ Structure of a bacteriophytochrome and light-stimulated protomer swapping with a gene repressor,” Structure 20, 14361446 (2012).
K. Evans, J. G. Grossmann, A. P. Fordham-Skelton, and M. Z. Papiz, “ Small-angle X-ray scattering reveals the solution structure of a bacteriophytochrome in the catalytically active Pr state,” J. Mol. Biol. 364, 655666 (2006).
A. M. Jones and H. P. Erickson, “ Domain structure of phytochrome from Avena sativa visualized by electron microscopy,” Photochem. Photobiol. 49, 479483 (1989).

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Phytochromes sense red light in plants and various microorganism. Light absorption causes structural changes within the protein, which alter its biochemical activity. Bacterial phytochromes are dimeric proteins, but the functional relevance of this arrangement remains unclear. Here, we use time-resolved X-ray scattering to reveal the solution structural change of a monomeric variant of the photosensory core module of the phytochrome from The data reveal two motions, a bend and a twist of the PHY domain with respect to the chromophore-binding domains. Infrared spectroscopy shows the refolding of the PHY tongue. We conclude that a monomer of the phytochrome photosensory core is sufficient to perform the light-induced structural changes. This implies that allosteric cooperation with the other monomer is not needed for structural activation. The dimeric arrangement may instead be intrinsic to the biochemical output domains of bacterial phytochromes.


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