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Here we quantify this Pr\u2013Pg separation using quantum-mechanical\/molecular-mechanical geometry optimization and wave function-based excited-state calculations. Calculated spectra reproduce the Pr\u2013Pg trend and show that the shift is dominated by a Pg-specific increase in phycocyanobilin A\u2013B inter-ring torsion, which truncates \u03c0-conjugation and widens the HOMO\u2013LUMO gap. Protein electrostatics red-shifts both states similarly and thus does not set the Pr\u2013Pg gap. Residue\u2013chromophore interaction energies reveal state-dependent rewiring: Trp655 dominates in Pr and regulates the C\u2013D dihedral orientation, whereas in Pg this role shifts to Ile691, and Thr658 becomes a major Pg-specific stabilizer acting at the A\u2013B linkage. These results establish trapped-twist tuning as a geometry-driven mechanism with residue-level handles for engineering CBCR absorption.<\/jats:p>","DOI":"10.1021\/acs.jpcb.6c05208","type":"journal-article","created":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T05:02:36Z","timestamp":1790658156000},"page":"10455-10466","source":"Crossref","is-referenced-by-count":0,"title":["A Residue-Resolved\nMechanism for Trapped-Twist Spectral\nTuning in Cyanobacteriochromes"],"prefix":"10.1021","volume":"130","author":[{"given":"Shun","family":"Kohase","sequence":"first","affiliation":[{"name":"Nagoya University , , Furocho , , ,","place":["Chikusa, Nagoya, Japan, 464-8601"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0286-3646","authenticated-orcid":true,"given":"Kazuhiro J.","family":"Fujimoto","sequence":"additional","affiliation":[{"name":"Nagoya University , , Furocho , , ,","place":["Chikusa, Nagoya, Japan, 464-8601"]},{"name":"Nagoya University , , Furocho , , ,","place":["Chikusa, Nagoya, Japan, 464-8601"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rei","family":"Narikawa","sequence":"additional","affiliation":[{"name":"Tokyo Metropolitan University , , 1-1 Minami-Osawa , , ,","place":["Hachioji, Tokyo, Japan, 192-0397"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3933-8546","authenticated-orcid":true,"given":"Takeshi","family":"Yanai","sequence":"additional","affiliation":[{"name":"Nagoya University , , Furocho , , ,","place":["Chikusa, Nagoya, Japan, 464-8601"]},{"name":"Nagoya University , , Furocho , , ,","place":["Chikusa, Nagoya, Japan, 464-8601"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,9,29]]},"reference":[{"key":"2026100809091270600_cit1","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1021\/ar020219d","article-title":"Photoreceptor Proteins, \u201cStar\nActors of Modern Times\u201d: A Review of the Functional Dynamics\nin the Structure of Representative Members of Six Different Photoreceptor\nFamilies","volume":"37","author":"van der Horst","year":"2004","journal-title":"Acc. Chem. Res."},{"key":"2026100809091270600_cit2","doi-asserted-by":"publisher","first-page":"61","DOI":"10.1146\/annurev-micro-041522-094613","article-title":"Cyanobacteriochromes:\nA Rainbow of Photoreceptors","volume":"78","author":"Rockwell","year":"2024","journal-title":"Annu. Rev. Microbiol."},{"key":"2026100809091270600_cit3","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1016\/j.sbi.2019.01.018","article-title":"Cyanobacteriochromes:\nPhotoreceptors Covering the Entire\nUV-to-Visible Spectrum","volume":"57","author":"Fushimi","year":"2019","journal-title":"Curr. Opin. Struct.\nBiol."},{"key":"2026100809091270600_cit4","doi-asserted-by":"publisher","first-page":"88","DOI":"10.1016\/j.str.2012.11.001","article-title":"A Photo-Labile Thioether\nLinkage to Phycoviolobilin Provides the Foundation for the Blue\/Green\nPhotocycles in DXCF-Cyanobacteriochromes","volume":"21","author":"Burgie","year":"2013","journal-title":"Structure"},{"key":"2026100809091270600_cit5","doi-asserted-by":"publisher","first-page":"918","DOI":"10.1073\/pnas.1212098110","article-title":"Structures of Cyanobacteriochromes\nfrom Phototaxis\nRegulators AnPixJ and TePixJ Reveal General and Specific Photoconversion\nMechanism","volume":"110","author":"Narikawa","year":"2013","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2026100809091270600_cit6","doi-asserted-by":"publisher","first-page":"4387","DOI":"10.1073\/pnas.1720682115","article-title":"Correlating\nStructural and Photochemical Heterogeneity in Cyanobacteriochrome\nNpR6012g4","volume":"115","author":"Lim","year":"2018","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2026100809091270600_cit7","doi-asserted-by":"publisher","first-page":"2432","DOI":"10.1073\/pnas.1910208117","article-title":"Structural\nElements Regulating the Photochromicity\nin a Cyanobacteriochrome","volume":"117","author":"Xu","year":"2020","journal-title":"Proc. Natl. Acad.\nSci. U.S.A."},{"key":"2026100809091270600_cit8","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.adn8386","article-title":"Green\/Red Light-Sensing Mechanism in the Chromatic\nAcclimation Photosensor","volume":"10","author":"Nagae","year":"2024","journal-title":"Sci. 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Reverse Dynamics","volume":"51","author":"Kim","year":"2012","journal-title":"Biochemistry"},{"key":"2026100809091270600_cit17","doi-asserted-by":"publisher","first-page":"844","DOI":"10.1016\/j.jmb.2008.05.035","article-title":"A Novel Photoactive\nGAF Domain of Cyanobacteriochrome AnPixJ That Shows Reversible Green\/Red\nPhotoconversion","volume":"380","author":"Narikawa","year":"2008","journal-title":"J. Mol. Biol."},{"key":"2026100809091270600_cit18","doi-asserted-by":"publisher","first-page":"9667","DOI":"10.1021\/bi3013565","article-title":"Red\/Green\nCyanobacteriochromes: Sensors\nof Color and Power","volume":"51","author":"Rockwell","year":"2012","journal-title":"Biochemistry"},{"key":"2026100809091270600_cit19","doi-asserted-by":"publisher","first-page":"40","DOI":"10.1111\/j.1742-4658.2011.08397.x","article-title":"Photophysical\nDiversity of Two Novel Cyanobacteriochromes with Phycocyanobilin Chromophores:\nPhotochemistry and Dark Reversion Kinetics","volume":"279","author":"Chen","year":"2012","journal-title":"FEBS J."},{"key":"2026100809091270600_cit20","doi-asserted-by":"publisher","first-page":"2539","DOI":"10.1039\/c9pp00295b","article-title":"Conservation and Diversity in the\nSecondary Forward Photodynamics of Red\/Green Cyanobacteriochromes","volume":"18","author":"Jenkins","year":"2019","journal-title":"Photochem. Photobiol. Sci."},{"key":"2026100809091270600_cit21","doi-asserted-by":"publisher","first-page":"471","DOI":"10.1007\/s43630-022-00213-3","article-title":"Protein\u2013Chromophore\nInteractions Controlling Photoisomerization in Red\/Green Cyanobacteriochromes","volume":"21","author":"Rockwell","year":"2022","journal-title":"Photochem. Photobiol. Sci."},{"key":"2026100809091270600_cit22","doi-asserted-by":"publisher","first-page":"681","DOI":"10.1111\/php.12732","article-title":"Distinctive Properties\nof Dark Reversion Kinetics between Two Red\/Green-Type Cyanobacteriochromes\nand Their Application in the Photoregulation of cAMP Synthesis","volume":"93","author":"Fushimi","year":"2017","journal-title":"Photochem. Photobiol."},{"key":"2026100809091270600_cit23","doi-asserted-by":"publisher","first-page":"432","DOI":"10.1038\/s41592-023-01764-8","article-title":"Engineering of Bidirectional,\nCyanobacteriochrome-Based Light-Inducible Dimers (BICYCL)s","volume":"20","author":"Jang","year":"2023","journal-title":"Nat. Methods"},{"key":"2026100809091270600_cit24","doi-asserted-by":"publisher","first-page":"106","DOI":"10.1002\/prot.26586","article-title":"Computational\nIdentification of Key Residues Regulating Fluorescence Emission in\na Red\/Green Cyanobacteriochrome","volume":"92","author":"Kannan","year":"2024","journal-title":"Proteins"},{"key":"2026100809091270600_cit25","doi-asserted-by":"publisher","first-page":"8082","DOI":"10.1073\/pnas.1504228112","article-title":"Three Cyanobacteriochromes\nWork Together to Form a\nLight Color-Sensitive Input System for c-Di-GMP Signaling of Cell\nAggregation","volume":"112","author":"Enomoto","year":"2015","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2026100809091270600_cit26","doi-asserted-by":"publisher","first-page":"4974","DOI":"10.1073\/pnas.1302909110","article-title":"Green\/Red Cyanobacteriochromes\nRegulate Complementary Chromatic Acclimation via a Protochromic Photocycle","volume":"110","author":"Hirose","year":"2013","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2026100809091270600_cit27","doi-asserted-by":"publisher","first-page":"7304","DOI":"10.1021\/bi800088t","article-title":"A Second Conserved\nGAF Domain Cysteine Is Required for the Blue\/Green Photoreversibility\nof Cyanobacteriochrome Tlr0924 from Thermosynechococcuselongatus","volume":"47","author":"Rockwell","year":"2008","journal-title":"Biochemistry"},{"key":"2026100809091270600_cit28","doi-asserted-by":"publisher","first-page":"2581","DOI":"10.1021\/bi501548t","article-title":"Characterization\nof Red\/Green Cyanobacteriochrome NpR6012g4 by Solution Nuclear Magnetic\nResonance Spectroscopy: A Protonated Bilin Ring System in Both Photostates","volume":"54","author":"Rockwell","year":"2015","journal-title":"Biochemistry"},{"key":"2026100809091270600_cit29","doi-asserted-by":"publisher","first-page":"3118","DOI":"10.1021\/bi500037a","article-title":"Conserved Phenylalanine\nResidues Are Required for Blue-Shifting of Cyanobacteriochrome Photoproducts","volume":"53","author":"Rockwell","year":"2014","journal-title":"Biochemistry"},{"key":"2026100809091270600_cit30","doi-asserted-by":"publisher","first-page":"1934","DOI":"10.1002\/anie.201810266","article-title":"The Effective Conjugation\nLength Is Responsible for the Red\/Green Spectral Tuning in the Cyanobacteriochrome\nSlr1393g3","volume":"58","author":"Wiebeler","year":"2019","journal-title":"Angew. Chem., Int. Ed."},{"key":"2026100809091270600_cit31","doi-asserted-by":"publisher","first-page":"509","DOI":"10.1021\/acs.biochem.9b00931","article-title":"Red, Orange,\nGreen: Light- and Temperature-Dependent\nColor Tuning in a Cyanobacteriochrome","volume":"59","author":"Buhrke","year":"2020","journal-title":"Biochemistry"},{"key":"2026100809091270600_cit32","doi-asserted-by":"publisher","first-page":"171","DOI":"10.1007\/s11120-023-01066-2","article-title":"Crystallographic\nand Biochemical Analyses of a Far-Red\nAllophycocyanin to Address the Mechanism of the Super-Red-Shift","volume":"162","author":"Zhou","year":"2024","journal-title":"Photosynth. Res."},{"key":"2026100809091270600_cit33","doi-asserted-by":"publisher","first-page":"3772","DOI":"10.1021\/acs.biochem.5b00438","article-title":"Characterization\nof Red\/Green Cyanobacteriochrome NpR6012g4 by Solution Nuclear Magnetic\nResonance Spectroscopy: A Hydrophobic Pocket for the C15-E,Anti Chromophore\nin the Photoproduct","volume":"54","author":"Rockwell","year":"2015","journal-title":"Biochemistry"},{"key":"2026100809091270600_cit34","doi-asserted-by":"publisher","first-page":"447","DOI":"10.1007\/s43630-022-00204-4","article-title":"Light- and pH-Dependent\nStructural Changes in Cyanobacteriochrome AnPixJg2","volume":"21","author":"Altmayer","year":"2022","journal-title":"Photochem. Photobiol. Sci."},{"key":"2026100809091270600_cit35","doi-asserted-by":"publisher","first-page":"7359","DOI":"10.1039\/D0CP05314G","article-title":"Histidine\nProtonation Controls Structural Heterogeneity in the Cyanobacteriochrome\nAnPixJg2","volume":"23","author":"Rao","year":"2021","journal-title":"Phys. Chem. Chem. Phys."},{"key":"2026100809091270600_cit36","doi-asserted-by":"publisher","first-page":"1720","DOI":"10.3390\/molecules24091720","article-title":"QM\/MM Benchmarking\nof Cyanobacteriochrome Slr1393g3\nAbsorption Spectra","volume":"24","author":"Wiebeler","year":"2019","journal-title":"Molecules"},{"key":"2026100809091270600_cit37","doi-asserted-by":"publisher","first-page":"1784","DOI":"10.1021\/acs.jpclett.2c03619","article-title":"Molecular Mechanism\nof Spectral Tuning by Chloride Binding in Monkey Green Sensitive Visual\nPigment","volume":"14","author":"Fujimoto","year":"2023","journal-title":"J. Phys. Chem. Lett."},{"key":"2026100809091270600_cit38","doi-asserted-by":"publisher","first-page":"11884","DOI":"10.1021\/acs.jpclett.5c02898","article-title":"Protonation-Enhanced\nEnergy Transfer\nin Xanthorhodopsin Kin4B8","volume":"16","author":"Fujimoto","year":"2025","journal-title":"J. Phys. Chem. Lett."},{"key":"2026100809091270600_cit39","doi-asserted-by":"publisher","first-page":"499","DOI":"10.1021\/acsphyschemau.4c00022","article-title":"Prominent Role of Charge\nTransfer in the Spectral Tuning of Photosynthetic Light-Harvesting\nI Complex","volume":"4","author":"Fujimoto","year":"2024","journal-title":"ACS Phys. Chem. Au"},{"key":"2026100809091270600_cit40","doi-asserted-by":"publisher","first-page":"6153","DOI":"10.1021\/acs.jpcb.5c02145","article-title":"Significant Effects of Excitonic\nCoupling and Charge Transfer on\nthe Circular Dichroism Spectrum of Photosynthetic Light-Harvesting\nI Complex","volume":"129","author":"Tsuji","year":"2025","journal-title":"J. Phys. Chem. B"},{"key":"2026100809091270600_cit41","doi-asserted-by":"publisher","first-page":"10459","DOI":"10.1021\/acs.jpcb.1c04457","article-title":"Spectral Tuning\nMechanism of Photosynthetic\nLight-Harvesting Complex II Revealed by Ab InitioDimer Exciton Model","volume":"125","author":"Fujimoto","year":"2021","journal-title":"J. Phys. Chem. B"},{"key":"2026100809091270600_cit42","doi-asserted-by":"publisher","first-page":"3984","DOI":"10.1021\/jacs.3c12045","article-title":"Spectral Tuning and\nExcitation-Energy Transfer by Unique Carotenoids in Diatom Light-Harvesting\nAntenna","volume":"146","author":"Fujimoto","year":"2024","journal-title":"J. Am. Chem. Soc."},{"key":"2026100809091270600_cit43","doi-asserted-by":"publisher","first-page":"997","DOI":"10.1103\/PhysRevLett.52.997","article-title":"Density-Functional\nTheory for Time-Dependent Systems","volume":"52","author":"Runge","year":"1984","journal-title":"Phys. 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