{"entity": "researcher", "timestamp": "2026-07-20T23:06:08.374Z", "family": "Ihalainen", "given": "Janne A", "initials": "JA", "orcid": "0000-0002-8741-1587", "affiliations": ["Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/4730f17c203e496bb52a8812767bf37b.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/4730f17c203e496bb52a8812767bf37b"}}, "publications": [{"entity": "publication", "iuid": "d2a2d6d880234ac78144a60503cbbe20", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d2a2d6d880234ac78144a60503cbbe20.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d2a2d6d880234ac78144a60503cbbe20"}}, "title": "Ultrafast, remote-controlled protonation reaction enables structural changes in a phytochrome.", "authors": [{"family": "Shankar", "given": "Madan Kumar", "initials": "MK", "orcid": "0000-0002-7944-1081", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd956823ccdf480a8f079fbc11a6815a.json"}}, {"family": "Grunewald", "given": "Lukas", "initials": "L", "orcid": "0009-0006-2976-8680", "researcher": {"href": "https://publications.scilifelab.se/researcher/bfc954183b184d28b1de95594ab07564.json"}}, {"family": "Wahlgren", "given": "Weixiao Yuan", "initials": "WY", "orcid": "0000-0003-0413-165X", "researcher": {"href": "https://publications.scilifelab.se/researcher/18c55c12fa894dffa8f95f325affa529.json"}}, {"family": "Stucki-Buchli", "given": "Brigitte", "initials": "B", "orcid": "0000-0002-6756-0665", "researcher": {"href": "https://publications.scilifelab.se/researcher/7755ea9da8ee490fa808a0ff505406c6.json"}}, {"family": "Nimmrich", "given": "Amke", "initials": "A", "orcid": "0000-0003-0425-2101", "researcher": {"href": "https://publications.scilifelab.se/researcher/72e8a83ab0cb4d7dad20f00784045ba4.json"}}, {"family": "Kurttila", "given": "Moona", "initials": "M"}, {"family": "Fischer", "given": "Anna-Lena", "initials": "AL", "orcid": "0009-0009-3310-5021", "researcher": {"href": "https://publications.scilifelab.se/researcher/979212c2ef024d249845258e2b322f0e.json"}}, {"family": "Salvadori", "given": "Giacomo", "initials": "G", "orcid": "0000-0001-7330-6228", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f6eae0cdb9e45f99874d6bd200b81c6.json"}}, {"family": "Cellini", "given": "Andrea", "initials": "A"}, {"family": "Maj", "given": "Piotr", "initials": "P", "orcid": "0000-0002-9832-2344", "researcher": {"href": "https://publications.scilifelab.se/researcher/70b8070ad9c349aa875c84d6e101c97a.json"}}, {"family": "Anindya", "given": "Atsarina Larasati", "initials": "AL"}, {"family": "Claesson", "given": "Elin", "initials": "E", "orcid": "0000-0001-8232-7725", "researcher": {"href": "https://publications.scilifelab.se/researcher/10fe8a3b1cc3431384cd9dbe7c9e3865.json"}}, {"family": "Luo", "given": "Fangjia", "initials": "F", "orcid": "0000-0003-0631-6236", "researcher": {"href": "https://publications.scilifelab.se/researcher/5c5507f74fe84eee866fdf2ee3a82b44.json"}}, {"family": "Malla", "given": "Tek Narsingh", "initials": "TN", "orcid": "0000-0002-1387-0801", "researcher": {"href": "https://publications.scilifelab.se/researcher/800976e6911240d080bbf9602f26ce7c.json"}}, {"family": "Pandey", "given": "Suraj", "initials": "S", "orcid": "0000-0002-7097-2185", "researcher": {"href": "https://publications.scilifelab.se/researcher/85d34f3408e14d3a9bd538656c3220ab.json"}}, {"family": "Tosha", "given": "Takehiko", "initials": "T", "orcid": "0000-0002-8971-0759", "researcher": {"href": "https://publications.scilifelab.se/researcher/f1075f4e3f1d4966bee737cea1060f75.json"}}, {"family": "Nipawan", "given": "Nuemket", "initials": "N"}, {"family": "Owada", "given": "Shigeki", "initials": "S", "orcid": "0000-0002-1451-7612", "researcher": {"href": "https://publications.scilifelab.se/researcher/78948368f25e4fffba5f79203efb84d9.json"}}, {"family": "Tono", "given": "Kensuke", "initials": "K", "orcid": "0000-0003-1218-3759", "researcher": {"href": "https://publications.scilifelab.se/researcher/3afc0496078b4d719b0653069800e667.json"}}, {"family": "Tanaka", "given": "Rie", "initials": "R", "orcid": "0000-0003-1062-4792", "researcher": {"href": "https://publications.scilifelab.se/researcher/69908679d76c42d6ad9aa42264c60de0.json"}}, {"family": "Stojkovi\u0107", "given": "Emina A", "initials": "EA", "orcid": "0000-0002-4971-5213", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e203482fbc54cbbbcd4a712f6184dd9.json"}}, {"family": "Mozorov", "given": "Dmitry", "initials": "D", "orcid": "0000-0001-9524-948X", "researcher": {"href": "https://publications.scilifelab.se/researcher/fce1c5072a0a445f918e621e23e4687b.json"}}, {"family": "Myllyperki\u00f6", "given": "Pasi", "initials": "P", "orcid": "0000-0003-1651-1676", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e10ceedb7594f5698b53af01f444a21.json"}}, {"family": "Kumpulainen", "given": "Tatu", "initials": "T", "orcid": "0000-0001-9469-9294", "researcher": {"href": "https://publications.scilifelab.se/researcher/e94b734da6774d0fb880f361b50892e9.json"}}, {"family": "Takala", "given": "Heikki", "initials": "H", "orcid": "0000-0003-2518-8583", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf65baa23c3349caa07bc0f44cb52d88.json"}}, {"family": "Schmidt", "given": "Marius", "initials": "M", "orcid": "0000-0002-0962-9468", "researcher": {"href": "https://publications.scilifelab.se/researcher/76e24cc255b246e8a44c52d4002eb46c.json"}}, {"family": "Ihalainen", "given": "Janne A", "initials": "JA", "orcid": "0000-0002-8741-1587", "researcher": {"href": "https://publications.scilifelab.se/researcher/4730f17c203e496bb52a8812767bf37b.json"}}, {"family": "Westenhoff", "given": "Sebastian", "initials": "S", "orcid": "0000-0002-6961-8015", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f1519bb234b43c6a13833b04e6720b8.json"}}], "type": "journal article", "published": "2025-10-17", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "11", "issue": "42", "pages": "eady0499", "issn-l": "2375-2548"}, "abstract": "In photoactive proteins, coupling between the chromophore and protein matrix is exquisitely tuned. Proton transfer reactions can mediate this coupling, as in proton-coupled electron transfer and excited-state proton transfer. Additional mechanisms involving proton dislocations may exist but remain undiscovered. Here, we present a femtosecond crystallographic movie of the phytochrome from Deinococcus radiodurans. The structures reveal a space-conserving mechanism for rotation of the D-ring in the excited state. We observe rearrangement of a conserved hydrogen bond network within 300 fs, which precedes the isomerization reaction of the chromophore. Aided by molecular modeling and independently confirmed by femtosecond infrared spectroscopy, we attribute these changes to a protonation shift of the strictly conserved histidine-260. Although this histidine lies close to the photoexcited \u03c0-orbitals of the chromophore, it is not directly part of them. We propose that this \"remote-controlled\" proton transfer relays photoexcitation near-instantaneously to the protein matrix. This mechanism may be widely used to transduce cofactor signals to their hosting enzymes.", "doi": "10.1126/sciadv.ady0499", "pmid": "41105772", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12533598"}], "notes": [], "created": "2025-11-28T10:51:47.654Z", "modified": "2025-11-28T10:51:48.542Z"}, {"entity": "publication", "iuid": "376ba41322394bb49764039bc6081e06", "links": {"self": {"href": "https://publications.scilifelab.se/publication/376ba41322394bb49764039bc6081e06.json"}, "display": {"href": "https://publications.scilifelab.se/publication/376ba41322394bb49764039bc6081e06"}}, "title": "Structural mechanism of signal transduction in a phytochrome histidine kinase.", "authors": [{"family": "Wahlgren", "given": "Weixiao Yuan", "initials": "WY"}, {"family": "Claesson", "given": "Elin", "initials": "E"}, {"family": "Tuure", "given": "Iida", "initials": "I", "orcid": "0000-0002-9754-6848", "researcher": {"href": "https://publications.scilifelab.se/researcher/70e380355782434ca0c2bd050a108786.json"}}, {"family": "Trillo-Muyo", "given": "Sergio", "initials": "S", "orcid": "0000-0002-3135-9134", "researcher": {"href": "https://publications.scilifelab.se/researcher/2e6b6b830e9145a2ae3e6c10895acbee.json"}}, {"family": "B\u00f3dizs", "given": "Szabolcs", "initials": "S", "orcid": "0000-0002-3303-5897", "researcher": {"href": "https://publications.scilifelab.se/researcher/f9848a63af6e4d019bbce45745b2bd8c.json"}}, {"family": "Ihalainen", "given": "Janne A", "initials": "JA", "orcid": "0000-0002-8741-1587", "researcher": {"href": "https://publications.scilifelab.se/researcher/4730f17c203e496bb52a8812767bf37b.json"}}, {"family": "Takala", "given": "Heikki", "initials": "H", "orcid": "0000-0003-2518-8583", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf65baa23c3349caa07bc0f44cb52d88.json"}}, {"family": "Westenhoff", "given": "Sebastian", "initials": "S", "orcid": "0000-0002-6961-8015", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f1519bb234b43c6a13833b04e6720b8.json"}}], "type": "journal article", "published": "2022-12-12", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "13", "issue": "1", "pages": "7673", "issn-l": "2041-1723"}, "abstract": "Phytochrome proteins detect red/far-red light to guide the growth, motion, development and reproduction in plants, fungi, and bacteria. Bacterial phytochromes commonly function as an entrance signal in two-component sensory systems. Despite the availability of three-dimensional structures of phytochromes and other two-component proteins, the conformational changes, which lead to activation of the protein, are not understood. We reveal cryo electron microscopy structures of the complete phytochrome from Deinoccocus radiodurans in its resting and photoactivated states at 3.6 \u00c5 and 3.5 \u00c5 resolution, respectively. Upon photoactivation, the photosensory core module hardly changes its tertiary domain arrangement, but the connector helices between the photosensory and the histidine kinase modules open up like a zipper, causing asymmetry and disorder in the effector domains. The structures provide a framework for atom-scale understanding of signaling in phytochromes, visualize allosteric communication over several nanometers, and suggest that disorder in the dimeric arrangement of the effector domains is important for phosphatase activity in a two-component system. The results have implications for the development of optogenetic applications.", "doi": "10.1038/s41467-022-34893-3", "pmid": "36509762", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9744887"}, {"db": "pii", "key": "10.1038/s41467-022-34893-3"}], "notes": [], "created": "2023-11-26T14:06:55.998Z", "modified": "2023-11-26T14:06:56.176Z"}]}