Site-by-site tracking of signal transduction in an azidophenylalanine-labeled bacteriophytochrome with step-scan FTIR spectroscopy

Moona Kurttila, Brigitte Stucki-Buchli, Jessica Rumfeldt, Lea Schroeder, Heikki Häkkänen, Alli Liukkonen, Heikki Takala, Tilman Kottke and Janne A. Ihalainen

Phys. Chem. Chem. Phys., 2021, 23, 5615
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The structural changes in the signaling mechanism of bacteriophytochromes in solution revealed by a multiscale computational investigation

Veronica Macaluso, Giacomo Salvadori, Lorenzo Cupellini and Benedetta Mennucci

Chem. Sci., 2021, 12, 5555
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Conserved histidine and tyrosine determine spectral responses through the water network in Deinococcus radiodurans phytochrome

Heli Lehtivuori, Jessica Rumfeldt, Satu Mustalahti, Sami Kurkinen and Heikki Takala

Photochem Photobiol Sci, 2022, 21, 1975
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A sensitive red/far-red photoswitch for controllable gene therapy in mouse models of metabolic diseases

Longliang Qiao, Lingxue Niu, Meiyan Wang, Zhihao Wang, Deqiang Kong, Guiling Yu and Haifeng Ye

Nat Commun, 2024, 15
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Structural basis for the Pr-Pfr long-range signaling mechanism of a full-length bacterial phytochrome at the atomic level

Lisandro H. Otero, Sabrina Foscaldi, Giuliano T. Antelo, Germán L. Rosano, Serena Sirigu, Sebastián Klinke, Lucas A. Defelipe, Maximiliano Sánchez-Lamas, Giovanni Battocchio, Valeria Conforte, Adrián A. Vojnov, Leonard M. G. Chavas, Fernando A. Goldbaum, Maria-Andrea Mroginski, Jimena Rinaldi and Hernán R. Bonomi

Sci. Adv., 2021, 7
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The interconnecting hairpin extension "arm": An essential allosteric element of phytochrome activity

Moona Kurttila, Jessica Rumfeldt, Heikki Takala and Janne A. Ihalainen

Structure, 2023, 31, 1100
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Darkness inhibits autokinase activity of bacterial bathy phytochromes

Christina Huber, Merle Strack, Isabel Schultheiß, Julia Pielage, Xenia Mechler, Justin Hornbogen, Rolf Diller and Nicole Frankenberg-Dinkel

Journal of Biological Chemistry, 2024, 300, 107148
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Optogenetic Control of Bacterial Expression by Red Light

Elina Multamäki, Andrés García de Fuentes, Oleksii Sieryi, Alexander Bykov, Uwe Gerken, Américo Tavares Ranzani, Jürgen Köhler, Igor Meglinski, Andreas Möglich and Heikki Takala

ACS Synth. Biol., 2022, 11, 3354
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Optogenetic Control of Bacterial Expression by Red Light

Elina Multamäki, Andrés García de Fuentes, Oleksii Sieryi, Alexander Bykov, Uwe Gerken, Américo Tavares Ranzani, Jürgen Köhler, Igor Meglinski, Andreas Möglich and Heikki Takala

SSRN Journal, 2022
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Photocobilins integrate B12 and bilin photochemistry for enzyme control

Shaowei Zhang, Laura N. Jeffreys, Harshwardhan Poddar, Yuqi Yu, Chuanyang Liu, Kaylee Patel, Linus O. Johannissen, Lingyun Zhu, Matthew J. Cliff, Cunyu Yan, Giorgio Schirò, Martin Weik, Michiyo Sakuma, Colin W. Levy, David Leys, Derren J. Heyes and Nigel S. Scrutton

Nat Commun, 2024, 15
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Engineered bacteriophytochrome heterodimers for research and applications

Iida Tuure, Cornelia Böhm, Jessica Rumfeldt, Elina Multamäki and Heikki Takala

Journal of Biological Chemistry, 2025, 301, 110452
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Traits of Bathy Phytochromes and Application to Bacterial Optogenetics

Cornelia Böhm, Kimmo Lehtinen, Elina Multamäki, Roosa Vanhatalo, Oscar Brander, Stefanie S. M. Meier, Jessica Rumfeldt, Andreas Möglich and Heikki Takala

ACS Synth. Biol., 2025, 14, 3207
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Pr‐favoured variants of the bacteriophytochrome from the plant pathogen Xanthomonas campestris hint on light regulation of virulence‐associated mechanisms

Valeria Conforte, Lisandro Horacio Otero, Laila Toum, Serena Sirigu, Giuliano Tomás Antelo, Jimena Rinaldi, Sabrina Foscaldi, Sebastián Klinke, Leonard Michel Gabriel Chavas, Adrián Alberto Vojnov, Fernando Alberto Goldbaum, Florencia Malamud and Hernán Ruy Bonomi

The FEBS Journal, 2021, 288, 5986
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The PHY Domain Dimer Interface of Bacteriophytochromes Mediates Cross-talk between Photosensory Modules and Output Domains

Cornelia Böhm, Nikolina Todorović, Marco Balasso, Geoffrey Gourinchas and Andreas Winkler

Journal of Molecular Biology, 2021, 433, 167092
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Design of a light and Ca 2+ switchable organic–peptide hybrid

Zinah Hilal Khaleel, Young Hyun No, Nam Hyeong Kim, Do Hyun Bae, Yibing Wu, Suhyeon Kim, Hojae Choi, Da Eun Lee, Se Yun Jeong, Yoon-Joo Ko, Seong-Gi Kim, Minah Suh, Jin-Chul Kim, William F. DeGrado, Ki Hyun Kim and Yong Ho Kim

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Insight into the structural dynamics of light sensitive proteins from time-resolved crystallography and quantum chemical calculations

Martin Weik and Tatiana Domratcheva

Current Opinion in Structural Biology, 2022, 77, 102496
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The structural effect between the output module and chromophore-binding domain is a two-way street via the hairpin extension

Moona Kurttila, Stefan Etzl, Jessica Rumfeldt, Heikki Takala, Nadine Galler, Andreas Winkler and Janne A. Ihalainen

Photochem Photobiol Sci, 2022, 21, 1881
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It's a two‐way street: Photoswitching and reversible changes of the protein matrix in photoswitchable fluorescent proteins and bacteriophytochromes

Elsa C. Rodrigues and Andre C. Stiel

FEBS Letters, 2023, 597, 1319
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Signaling by a bacterial phytochrome histidine kinase involves a conformational cascade reorganizing the dimeric photoreceptor

E. Sethe Burgie, Katherine Basore, Michael J. Rau, Brock Summers, Alayna J. Mickles, Vadim Grigura, James A. J. Fitzpatrick and Richard D. Vierstra

Nat Commun, 2024, 15
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Characterisation of sequence–structure–function space in sensor–effector integrators of phytochrome-regulated diguanylate cyclases

Cornelia Böhm, Geoffrey Gourinchas, Sophie Zweytick, Elvira Hujdur, Martina Reiter, Sara Trstenjak, Christoph Wilhelm Sensen and Andreas Winkler

Photochem Photobiol Sci, 2022, 21, 1761
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Engineering Bacteriophytochrome-coupled Photoactivated Adenylyl Cyclases for Enhanced Optogenetic cAMP Modulation

Qianzhao Xu, Arend Vogt, Fabian Frechen, Chengwei Yi, Melike Küçükerden, Neville Ngum, Laia Sitjà-Roqueta, Andreas Greiner, Rhein Parri, Mercè Masana, Nikolaus Wenger, Dagmar Wachten and Andreas Möglich

Journal of Molecular Biology, 2024, 436, 168257
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Current Trends of Bacterial and Fungal Optoproteins for Novel Optical Applications

Carolina Ramírez Martínez, Leonardo S. Gómez-Pérez, Alberto Ordaz, Ana Laura Torres-Huerta and Aurora Antonio-Perez

IJMS, 2023, 24, 14741
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Conserved tyrosine in phytochromes controls the photodynamics through steric demand and hydrogen bonding capabilities

Tobias Fischer, Lisa Köhler, Philipp D. Engel, Chen Song, Wolfgang Gärtner, Josef Wachtveitl and Chavdar Slavov

Biochimica et Biophysica Acta (BBA) - Bioenergetics, 2023, 1864, 148996
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Red Light Optogenetics in Neuroscience

Kimmo Lehtinen, Miriam S. Nokia and Heikki Takala

Front. Cell. Neurosci., 2022, 15
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Cryo-Electron Microscopy of Arabidopsis thaliana Phytochrome A in Its Pr State Reveals Head-to-Head Homodimeric Architecture

Weixiao Yuan Wahlgren, David Golonka, Sebastian Westenhoff and Andreas Möglich

Front. Plant Sci., 2021, 12
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Analogies and Differences in the Photoactivation Mechanism of Bathy and Canonical Bacteriophytochromes Revealed by Multiscale Modeling

Giacomo Salvadori and Benedetta Mennucci

J. Phys. Chem. Lett., 2024, 15, 8078
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Serial-femtosecond crystallography reveals how a phytochrome variant couples chromophore and protein structural changes

Luisa Sauthof, Michal Szczepek, Andrea Schmidt, Asmit Bhowmick, Medhanjali Dasgupta, Megan J. Mackintosh, Sheraz Gul, Franklin D. Fuller, Ruchira Chatterjee, Iris D. Young, Norbert Michael, Nicolas Andreas Heyder, Brian Bauer, Anja Koch, Isabel Bogacz, In-Sik Kim, Philipp S. Simon, Agata Butryn, Pierre Aller, Volha U. Chukhutsina, James M. Baxter, Christopher D. M. Hutchison, Dorothee Liebschner, Billy Poon, Nicholas K. Sauter, Mitchell D. Miller, George N. Phillips Jr., Roberto Alonso-Mori, Mark S. Hunter, Alexander Batyuk, Shigeki Owada, Kensuke Tono, Rie Tanaka, Jasper J. van Thor, Norbert Krauß, Tilman Lamparter, Aaron S. Brewster, Igor Schapiro, Allen M. Orville, Vittal K. Yachandra, Junko Yano, Peter Hildebrandt, Jan F. Kern and Patrick Scheerer

Sci. Adv., 2025, 11
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Protein control of photochemistry and transient intermediates in phytochromes

Giacomo Salvadori, Veronica Macaluso, Giulia Pellicci, Lorenzo Cupellini, Giovanni Granucci and Benedetta Mennucci

Nat Commun, 2022, 13
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Deciphering Photoreceptors Through Atomistic Modeling from Light Absorption to Conformational Response

Giacomo Salvadori, Patrizia Mazzeo, Davide Accomasso, Lorenzo Cupellini and Benedetta Mennucci

Journal of Molecular Biology, 2024, 436, 168358
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Structure and effective brightness of near‐infrared fluorescent protein iRFP713/C15S/V254C complexed with phycocyanobilin

Alina A. Remeeva, Olesya V. Stepanenko, Sergey A. Silonov, Alexander S. Kuzmin, Kirill V. Kovalev, Olga V. Stepanenko, Anastasia A. Gavrilova, Eugene Y. Smirnov, Irina M. Kuznetsova, Konstantin K. Turoverov, Ivan Y. Gushchin and Alexander V. Fonin

The FEBS Journal, 2025
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Phytochromes in Agrobacterium fabrum

Tilman Lamparter, Peng Xue, Afaf Elkurdi, Gero Kaeser, Luisa Sauthof, Patrick Scheerer and Norbert Krauß

Front. Plant Sci., 2021, 12
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Cryo-EM structures of a bathy phytochrome histidine kinase reveal a unique light-dependent activation mechanism

Szabolcs Bódizs, Petra Mészáros, Lukas Grunewald, Heikki Takala and Sebastian Westenhoff

Structure, 2024, 32, 1952
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Integrating protein sequence design and evolutionary sequence conservation to uncover spectral tuning sites in red-light photoreceptors

Oliver Maximilian Eder, Massimo Gregorio Totaro, Stefan Minnich, Gustav Oberdorfer and Andreas Winkler

Structure, 2025
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Leveraging the histidine kinase-phosphatase duality to sculpt two-component signaling

Stefanie S. M. Meier, Elina Multamäki, Américo T. Ranzani, Heikki Takala and Andreas Möglich

Nat Commun, 2024, 15
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Dynamics-driven allosteric stimulation of diguanylate cyclase activity in a red light-regulated phytochrome

Quang Hieu Tran, Oliver Maximilian Eder and Andreas Winkler

Journal of Biological Chemistry, 2024, 300, 107217
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Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome

Jakub Rydzewski, Katarzyna Walczewska-Szewc, Sylwia Czach, Wieslaw Nowak and Krzysztof Kuczera

J. Phys. Chem. B, 2022, 126, 2647
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New Insight Into Phytochromes: Connecting Structure to Function

Jon Hughes and Andreas Winkler

Annual Review of Plant Biology, 2024, 75, 153
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High-resolution crystal structures of transient intermediates in the phytochrome photocycle

Melissa Carrillo, Suraj Pandey, Juan Sanchez, Moraima Noda, Ishwor Poudyal, Luis Aldama, Tek Narsingh Malla, Elin Claesson, Weixiao Yuan Wahlgren, Denisse Feliz, Vukica Šrajer, Michał Maj, Leticia Castillon, So Iwata, Eriko Nango, Rie Tanaka, Tomoyuki Tanaka, Luo Fangjia, Kensuke Tono, Shigeki Owada, Sebastian Westenhoff, Emina A. Stojković and Marius Schmidt

Structure, 2021, 29, 743
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Comparative analysis of two paradigm bacteriophytochromes reveals opposite functionalities in two-component signaling

Elina Multamäki, Rahul Nanekar, Dmitry Morozov, Topias Lievonen, David Golonka, Weixiao Yuan Wahlgren, Brigitte Stucki-Buchli, Jari Rossi, Vesa P. Hytönen, Sebastian Westenhoff, Janne A. Ihalainen, Andreas Möglich and Heikki Takala

Nat Commun, 2021, 12
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