Neorhodopsin (NeoR) is a newly discovered fungal bistable rhodopsin that reversibly photoswitches between UV- and near-IR absorbing states denoted NeoR367 and NeoR690, respectively. NeoR367 represents a deprotonated retinal Schiff base (RSB), while NeoR690 represents a protonated RSB. Cryo-EM studies indicate that NeoR forms homodimers with 29 Å center-to-center distance between the retinal chromophores. UV excitation of NeoR367 takes place to an optically allowed S3 state of 1Bu+ symmetry, which rapidly converts to a low-lying optically forbidden S1 state of 2Ag- symmetry in 39 fs, followed by a multiexponential decay to the ground state on the 1-100 ps time scale. A theoretically predicted nπ* (S2) state does not get populated in any appreciable transient concentration during the excited-state relaxation cascade. We observe an intradimer retinal to retinal excitation energy transfer (EET) process from the NeoR367 S1 state to NeoR690, in competition with photoproduct formation. To quantitatively assess the EET mechanism and rate, we experimentally addressed and modeled the EET process under varying NeoR367-NeoR690 photoequilibrium conditions and determined the EET rate at (200 ps)-1. The NeoR367 S1 state shows a weak stimulated emission band in the near-IR around 700 nm, which may result from mixing with an intramolecular charge-transfer (ICT) state, enhancing the transition dipole moment of the S1-S0 transition and possibly facilitating the EET process. We suggest that EET may bear general relevance to the function of bistable multiwavelength rhodopsin oligomers.

Department of Physics and Astronomy Faculty of Science Vrije Universiteit Amsterdam De Boelelaan 1081 1081 HV Amsterdam The Netherlands

Department of Structural Biology Biophysics 2 University of Regensburg DE 93053 Regensburg Germany

ELI Beamlines Facility The Extreme Light Infrastructure ERIC Za Radnicí 835 25241 Dolní Břežany Czech Republic

Institut für Biologie Experimentelle Biophysik Humboldt Universität zu Berlin Invalidenstr 42 D 10115 Berlin Germany

Zobrazit více v PubMed

Ernst O. P.; Lodowski D. T.; Elstner M.; Hegemann P.; Brown L. S.; Kandori H. Microbial and animal rhodopsins: structures, functions, and molecular mechanisms. Chem. Rev. 2014, 114 (1), 126–163. 10.1021/cr4003769. PubMed DOI PMC

Zhang F.; Vierock J.; Yizhar O.; Fenno L. E.; Tsunoda S.; Kianianmomeni A.; Prigge M.; Berndt A.; Cushman J.; Polle J.; et al. The Microbial Opsin Family of Optogenetic Tools. Cell 2011, 147 (7), 1446–1457. 10.1016/j.cell.2011.12.004. PubMed DOI PMC

Hochbaum D. R.; Zhao Y.; Farhi S. L.; Klapoetke N.; Werley C. A.; Kapoor V.; Zou P.; Kralj J. M.; Maclaurin D.; Smedemark-Margulies N.; et al. All-optical electrophysiology in mammalian neurons using engineered microbial rhodopsins. Nat. Methods 2014, 11 (8), 825–833. 10.1038/nmeth.3000. PubMed DOI PMC

Broser M.; Spreen A.; Konold P. E.; Schiewer E.; Adam S.; Borin V.; Schapiro I.; Seifert R.; Kennis J. T. M.; Bernal Sierra Y. A.; et al. NeoR, a near-infrared absorbing rhodopsin. Nat. Commun. 2020, 11 (1), 5682.10.1038/s41467-020-19375-8. PubMed DOI PMC

Rozenberg A.; Kaczmarczyk I.; Matzov D.; Vierock J.; Nagata T.; Sugiura M.; Katayama K.; Kawasaki Y.; Konno M.; Nagasaka Y.; et al. Rhodopsin-bestrophin fusion proteins from unicellular algae form gigantic pentameric ion channels. Nat. Struct. Mol. Biol. 2022, 29 (6), 592.10.1038/s41594-022-00783-x. PubMed DOI

Kaziannis S.; Broser M.; van Stokkum I. H. M.; Dostal J.; Busse W.; Munhoven A.; Bernardo C.; Kloz M.; Hegemann P.; Kennis J. T. M. Multiple retinal isomerizations during the early phase of the bestrhodopsin photoreaction. Proc. Natl. Acad. Sci. U.S.A. 2024, 121 (12), e231899612110.1073/pnas.2318996121. PubMed DOI PMC

Broser M.; Busse W.; Spreen A.; Reh M.; Bernal Sierra Y. A.; Hwang S.; Utesch T.; Sun H.; Hegemann P. Diversity of rhodopsin cyclases in zoospore-forming fungi. Proc. Natl. Acad. Sci. U.S.A. 2023, 120, e231060012010.1073/pnas.2310600120. PubMed DOI PMC

Palombo R.; Barneschi L.; Pedraza-González L.; Padula D.; Schapiro I.; Olivucci M. Retinal chromophore charge delocalization and confinement explain the extreme photophysics of Neorhodopsin. Nat. Commun. 2022, 13 (1), 6652.10.1038/s41467-022-33953-y. PubMed DOI PMC

Broser M.; Andruniów T.; Kraskov A.; Palombo R.; Katz S.; Kloz M.; Dostál J.; Bernardo C.; Kennis J. T. M.; Hegemann P.; et al. Experimental Assessment of the Electronic and Geometrical Structure of a Near-Infrared Absorbing and Highly Fluorescent Microbial Rhodopsin. J. Phys. Chem. Lett. 2023, 14, 9291–9295. 10.1021/acs.jpclett.3c02167. PubMed DOI

Sugiura M.; Ishikawa K.; Katayama K.; Sumii Y.; Abe-Yoshizumi R.; Tsunoda S. P.; Furutani Y.; Shibata N.; Brown L. S.; Kandori H. Unusual Photoisomerization Pathway in a Near-Infrared Light Absorbing Enzymerhodopsin. J. Phys. Chem. Lett. 2022, 13 (40), 9539–9543. 10.1021/acs.jpclett.2c02334. PubMed DOI

Luck M.; Mathes T.; Bruun S.; Fudim R.; Hagedorn R.; Tran Nguyen T. M.; Kateriya S.; Kennis J. T. M.; Hildebrandt P.; Hegemann P. A Photochromic Histidine Kinase Rhodopsin (HKR1) That Is Bimodally Switched by Ultraviolet and Blue Light. J. Biol. Chem. 2012, 287 (47), 40083–40090. 10.1074/jbc.M112.401604. PubMed DOI PMC

Hontani Y.; Broser M.; Luck M.; Weissenborn J.; Kloz M.; Hegemann P.; Kennis J. T. M. Dual Photoisomerization on Distinct Potential Energy Surfaces in a UV-Absorbing Rhodopsin. J. Am. Chem. Soc. 2020, 142 (26), 11464–11473. 10.1021/jacs.0c03229. PubMed DOI PMC

Arikawa S.; Sugimoto T.; Okitsu T.; Wada A.; Katayama K.; Kandori H.; Kawamura I. Solid-state NMR for the characterization of retinal chromophore and Schiff base in TAT rhodopsin embedded in membranes under weakly acidic conditions. Biophys. Physicobiol. 2023, 20, e20101710.2142/biophysico.bppb-v20.s017. PubMed DOI PMC

Kataoka C.; Sugimoto T.; Shigemura S.; Katayama K.; Tsunoda S. P.; Inoue K.; Béjà O.; Kandori H. TAT Rhodopsin Is an Ultraviolet-Dependent Environmental pH Sensor. Biochemistry 2021, 60 (12), 899–907. 10.1021/acs.biochem.0c00951. PubMed DOI

Sugimoto T.; Miyagawa K.; Shoji M.; Katayama K.; Shigeta Y.; Kandori H. Calcium Binding Mechanism in TAT Rhodopsin. J. Phys. Chem. B 2024, 128 (29), 7102–7111. 10.1021/acs.jpcb.4c02363. PubMed DOI

Mannen K.; Nagata T.; Rozenberg A.; Konno M.; del Carmen Marín M.; Bagherzadeh R.; Béjà O.; Uchihashi T.; Inoue K. Multiple Roles of a Conserved Glutamate Residue for Unique Biophysical Properties in a New Group of Microbial Rhodopsins Homologous to TAT Rhodopsin. J. Mol. Biol. 2024, 436 (5), 168331.10.1016/j.jmb.2023.168331. PubMed DOI

Cronin T. W.; Bok M. J. Photoreception and vision in the ultraviolet. J. Exp. Biol. 2016, 219 (18), 2790–2801. 10.1242/jeb.128769. PubMed DOI

Birge R. R. 2-photon spectroscopy of protein-bound chromophores. Acc. Chem. Res. 1986, 19 (5), 138–146. 10.1021/ar00125a003. DOI

Birge R. R.; Zhang C. F. 2-photon double-resonance spectroscopy of bacteriorhodopsin - assignment of the electronic and dipolar properties of the low-lying 1AG-star(−)-like and 1B-U-star+-like pi,pi-star states. J. Chem. Phys. 1990, 92 (12), 7179–7195.

Filiba O.; Borin V. A.; Schapiro I. The involvement of triplet states in the isomerization of retinaloids. Phys. Chem. Chem. Phys. 2022, 24 (42), 26223–26231. 10.1039/D2CP03791B. PubMed DOI

Bonvicini A.; Demoulin B.; Altavilla S. F.; Nenov A.; El-Tahawy M. M. T.; Segarra-Marti J.; Giussani A.; Batista V. S.; Garavelli M.; Rivalta I. Ultraviolet vision: photophysical properties of the unprotonated retinyl Schiff base in the Siberian hamster cone pigment. Theor. Chem. Acc. 2016, 135 (4), 110.10.1007/s00214-016-1869-x. DOI

Bachilo S. M.; Bondarev S. L.; Gillbro T. Fluorescence properties of protonated and unprotonated Schiff bases of retinal at room temperature. J. Photochem. Photobiol., B 1996, 34 (1), 39–46. 10.1016/1011-1344(95)07271-3. DOI

Bachilo S. M.; Gillbro T. Fluorescence of retinal Schiff base in alcohols. J. Phys. Chem. A 1999, 103 (15), 2481–2488. 10.1021/jp983646a. DOI

Berera R.; van Grondelle R.; Kennis J. T. M. Ultrafast transient absorption spectroscopy: principles and application to photosynthetic systems. Photosynth. Res. 2009, 101 (2–3), 105–118. 10.1007/s11120-009-9454-y. PubMed DOI PMC

Kukura P.; McCamant D. W.; Mathies R. A. Femtosecond stimulated Raman spectroscopy. Annu. Rev. Phys. Chem. 2007, 58, 461–488. 10.1146/annurev.physchem.58.032806.104456. PubMed DOI

Kloz M.; Weissenborn J.; Polivka T.; Frank H. A.; Kennis J. T. M. Spectral watermarking in femtosecond stimulated Raman spectroscopy: resolving the nature of the carotenoid S-star state. Phys. Chem. Chem. Phys. 2016, 18 (21), 14619–14628. 10.1039/C6CP01464J. PubMed DOI

Hontani Y.; Inoue K.; Kloz M.; Kato Y.; Kandori H.; Kennis J. T. M. The photochemistry of sodium ion pump rhodopsin observed by watermarked femto- to submillisecond stimulated Raman spectroscopy. Phys. Chem. Chem. Phys. 2016, 18 (35), 24729–24736. 10.1039/C6CP05240A. PubMed DOI

Jumper J.; Evans R.; Pritzel A.; Green T.; Figurnov M.; Ronneberger O.; Tunyasuvunakool K.; Bates R.; Zídek A.; Potapenko A.; et al. Highly accurate protein structure prediction with AlphaFold. Nature 2021, 596 (7873), 583.10.1038/s41586-021-03819-2. PubMed DOI PMC

Ikuta T.; Shihoya W.; Sugiura M.; Yoshida K.; Watari M.; Tokano T.; Yamashita K.; Katayama K.; Tsunoda S. P.; Uchihashi T.; et al. Structural insights into the mechanism of rhodopsin phosphodiesterase. Nat. Commun. 2020, 11 (1), 5605.10.1038/s41467-020-19376-7. PubMed DOI PMC

van Stokkum I. H. M.; Weißenborn J.; Weigand S.; Snellenburg J. J. Pyglotaran: a lego-like Python framework for global and target analysis of time resolved spectra. Photochem. Photobiol. Sci. 2023, 22, 2413–2431. 10.1007/s43630-023-00460-y. PubMed DOI

van Stokkum I. H. M.; Larsen D. S.; van Grondelle R. Global and target analysis of time-resolved spectra. Biochim. Biophys. Acta, Bioenerg. 2004, 1657 (2–3), 82–104. 10.1016/j.bbabio.2004.04.011. PubMed DOI

Hirata Y.; Mataga N.; Mukai Y.; Koyama Y. Picosecond Time-Resolved Absorption Study Of All-Trans-Retinal And 9-Cis-Retinal - Configurational Relaxation In The Triplet-State. Chem. Phys. Lett. 1987, 134 (2), 166–170. 10.1016/0009-2614(87)87115-4. DOI

Gozem S.; Luk H. L.; Schapiro I.; Olivucci M. Theory and Simulation of the Ultrafast Double-Bond lsomerization of Biological Chromophores. Chem. Rev. 2017, 117 (22), 13502–13565. 10.1021/acs.chemrev.7b00177. PubMed DOI

Barneschi L.; Marsili E.; Pedraza-González L.; Padula D.; De Vico L.; Kaliakin D.; Blanco-González A.; Ferré N.; Huix-Rotllant M.; Filatov M.; et al. On the fluorescence enhancement of arch neuronal optogenetic reporters. Nat. Commun. 2022, 13 (1), 6432.10.1038/s41467-022-33993-4. PubMed DOI PMC

Marín M. D.; Agathangelou D.; Orozco-Gonzalez Y.; Valentini A.; Kato Y.; Abe-Yoshizumi R.; Kandori H.; Choi A.; Jung K. H.; Haacke S.; et al. Fluorescence Enhancement of a Microbial Rhodopsin via Electronic Reprogramming. J. Am. Chem. Soc. 2019, 141 (1), 262–271. 10.1021/jacs.8b09311. PubMed DOI PMC

Malakar P.; Gholami S.; Aarabi M.; Rivalta I.; Sheves M.; Garavelli M.; Ruhman S. Retinal photoisomerization versus counterion protonation in light and dark-adapted bacteriorhodopsin and its primary photoproduct. Nat. Commun. 2024, 15 (1), 2136.10.1038/s41467-024-46061-w. PubMed DOI PMC

Demoulin B.; Maiuri M.; Berbasova T.; Geiger J. H.; Borhan B.; Garavelli M.; Cerullo G.; Rivalta I. Control of Protonated Schiff Base Excited State Decay within Visual Protein Mimics: A Unified Model for Retinal Chromophores. Chem.—Eur. J. 2021, 27 (66), 16389–16400. 10.1002/chem.202102383. PubMed DOI PMC

Tavan P.; Schulten K. 21ag-11bu Energy-Gap In The Polyenes - Extended Configuration Interaction Study. J. Chem. Phys. 1979, 70 (12), 5407–5413. 10.1063/1.437475. DOI

Cantor C. R.; Schimmel P. R.. Biophysical Chemistry; W.H. Freeman and Company, 1980.

Lenz M. O.; Huber R.; Schmidt B.; Gilch P.; Kalmbach R.; Engelhard M.; Wachtveitl J. First steps of retinal photoisomerization in proteorhodopsin. Biophys. J. 2006, 91 (1), 255–262. 10.1529/biophysj.105.074690. PubMed DOI PMC

Merchan M.; GonzalezLuque R. Ab initio study on the low-lying excited states of retinal. J. Chem. Phys. 1997, 106 (3), 1112–1122. 10.1063/1.473207. DOI

Yamaguchi S.; Hamaguchi H. Femtosecond ultraviolet-visible absorption study of all-trans→13-cis•9-cis photoisomerization of retinal. J. Chem. Phys. 1998, 109 (4), 1397–1408. 10.1063/1.476692. DOI

Takeuchi S.; Tahara T. Ultrafast fluorescence study on the excited singlet-state dynamics of all-trans-retinal. J. Phys. Chem. A 1997, 101 (17), 3052–3060. 10.1021/jp962765s. DOI

Ishii K.; Takeuchi S.; Tahara T. A 35-fs time-resolved absorption study of all-trans retinal in a nonpolar solvent:: Ultrafast photophysics revisited. Chem. Phys. Lett. 2006, 418 (4–6), 307–310. 10.1016/j.cplett.2005.11.002. DOI

Shimojima A.; Tahara T. Picosecond time-resolved resonance Raman study of the photoisomerization of retinal. J. Phys. Chem. B 2000, 104 (39), 9288–9300. 10.1021/jp000873f. DOI

Polívka T.; Kaligotla S.; Chábera P.; Frank H. A. An intramolecular charge transfer state of carbonyl carotenoids: implications for excited state dynamics of apo-carotenals and retinal. Phys. Chem. Chem. Phys. 2011, 13 (22), 10787–10796. 10.1039/c1cp20269c. PubMed DOI

Christensen R. L.; Kohler B. E. Vibronic Coupling In Polyenes - High-Resolution Optical Spectroscopy Of 2,10-Dimethylundecapentaene. J. Chem. Phys. 1975, 63 (5), 1837–1846. 10.1063/1.431560. DOI

Simpson J. H.; McLaughlin L.; Smith D. S.; Christensen R. L. Vibronic Coupling In Polyenes–High-Resolution Optical Spectroscopy Of All-Trans-2,4,6,8,10,12,14-Hexadecaheptaene. J. Chem. Phys. 1987, 87 (6), 3360–3365. 10.1063/1.452978. DOI

Noguchi T.; Kolaczkowski S.; Arbour C.; Aramaki S.; Atkinson G. H.; Hayashi H.; Tasumi M. Resonance Raman-Spectrum Of The Excited (2ag)-Ag-1 State Of Beta-Carotene. Photochem. Photobiol. 1989, 50 (5), 603–609. 10.1111/j.1751-1097.1989.tb04315.x. DOI

Hashimoto H.; Koyama Y. The C = C Stretching Raman Lines Of Beta-Carotene Isomers In The S1 State As Detected By Pump-Probe Resonance Raman-Spectroscopy. Chem. Phys. Lett. 1989, 154 (4), 321–325. 10.1016/0009-2614(89)85363-1. DOI

Artes Vivancos J. M.; Van Stokkum I. H. M.; Saccon F.; Hontani Y.; Kloz M.; Ruban A.; van Grondelle R.; Kennis J. T. M. Unraveling the Excited-State Dynamics and Light-Harvesting Functions of Xanthophylls in Light-Harvesting Complex II Using Femtosecond Stimulated Raman Spectroscopy. J. Am. Chem. Soc. 2020, 142 (41), 17346–17355. 10.1021/jacs.0c04619. PubMed DOI PMC

Hontani Y.; Kloz M.; Polivka T.; Shukla M. K.; Sobotka R.; Kennis J. T. M. Molecular Origin of Photoprotection in Cyanobacteria Probed by Watermarked Femtosecond Stimulated Raman Spectroscopy. J. Phys. Chem. Lett. 2018, 9 (7), 1788–1792. 10.1021/acs.jpclett.8b00663. PubMed DOI PMC

McCamant D. W.; Kukura P.; Mathies R. A. Femtosecond time-resolved stimulated Raman spectroscopy:: Application to the ultrafast internal conversion in β-carotene. J. Phys. Chem. A 2003, 107 (40), 8208–8214. 10.1021/jp030147n. PubMed DOI PMC

Nagae H.; Kuki M.; Zhang J. P.; Sashima T.; Mukai Y.; Koyama Y. Vibronic coupling through the in-phase, C = C stretching mode plays a major role in the 2Ag– to 1Ag– internal conversion of all-trans-β-carotene. J. Phys. Chem. A 2000, 104 (18), 4155–4166. 10.1021/jp9924833. DOI

Mukai Y.; Hashimoto H.; Koyama Y.; Kuroda S.; Hirata Y.; Mataga N. S1-State And T1-State Properties Of Normal-Butylamine Schiff-Bases Of Isomeric Retinylideneacetaldehyde As Revealed By Transient Absorption And Transient Raman Spectroscopies And By Hplc Analysis Of Triplet-Sensitized Isomerization. J. Phys. Chem. 1991, 95 (26), 10586–10592. 10.1021/j100179a019. DOI

Polívka T.; Sundström V. Ultrafast dynamics of carotenoid excited states -: From solution to natural and artificial systems. Chem. Rev. 2004, 104 (4), 2021–2071. 10.1021/cr020674n. PubMed DOI

Di Donato M.; Ragnoni E.; Lapini A.; Foggi P.; Hiller R. G.; Righini R. Femtosecond transient infrared and stimulated Raman spectroscopy shed light on the relaxation mechanisms of photo-excited peridinin. J. Chem. Phys. 2015, 142 (21), 212409.10.1063/1.4915072. PubMed DOI

Zigmantas D.; Hiller R. G.; Sharples F. P.; Frank H. A.; Sundström V.; Polivka T. Effect of a conjugated carbonyl group on the photophysical properties of carotenoids. Phys. Chem. Chem. Phys. 2004, 6 (11), 3009–3016. 10.1039/B315786E. DOI

Frank H. A.; Bautista J. A.; Josue J.; Pendon Z.; Hiller R. G.; Sharples F. P.; Gosztola D.; Wasielewski M. R. Effect of the solvent environment on the spectroscopic properties and dynamics of the lowest excited states of carotenoids. J. Phys. Chem. B 2000, 104 (18), 4569–4577. 10.1021/jp000079u. DOI

Bautista J. A.; Connors R. E.; Raju B. B.; Hiller R. G.; Sharples F. P.; Gosztola D.; Wasielewski M. R.; Frank H. A. Excited state properties of peridinin: Observation of a solvent dependence of the lowest excited singlet state lifetime and spectral behavior unique among carotenoids. J. Phys. Chem. B 1999, 103 (41), 8751–8758. 10.1021/jp9916135. DOI

Vaswani H. M.; Hsu C. P.; Head-Gordon M.; Fleming G. R. Quantum chemical evidence for an intramolecular charge-transfer state in the carotenoid peridinin of peridinin-chlorophyll-protein. J. Phys. Chem. B 2003, 107 (31), 7940–7946. 10.1021/jp030086t. DOI

Zigmantas D.; Hiller R. G.; Sundström V.; Polívka T. Carotenoid to chlorophyll energy transfer in the peridinin-chlorophyll-a-protein complex involves an intramolecular charge transfer state. Proc. Natl. Acad. Sci. U.S.A. 2002, 99 (26), 16760–16765. 10.1073/pnas.262537599. PubMed DOI PMC

Bonetti C.; Alexandre M. T. A.; van Stokkum I. H. M.; Hiller R. G.; Groot M. L.; van Grondelle R.; Kennis J. T. M. Identification of excited-state energy transfer and relaxation pathways in the peridinin-chlorophyll complex: an ultrafast mid-infrared study. Phys. Chem. Chem. Phys. 2010, 12 (32), 9256–9266. 10.1039/b923695c. PubMed DOI

Redeckas K.; Voiciuk V.; Zigmantas D.; Hiller R. G.; Vengris M. Unveiling the excited state energy transfer pathways in peridinin-chlorophyll a-protein by ultrafast multi-pulse transient absorption spectroscopy. Biochim. Biophys. Acta, Bioenerg. 2017, 1858 (4), 297–307. 10.1016/j.bbabio.2017.01.014. PubMed DOI

Polívka T.; Kerfeld C. A.; Pascher T.; Sundström V. Spectroscopic properties of the carotenoid 3′-hydroxyechinenone in the orange carotenoid protein from the cyanobacterium Arthrospira maxima. Biochemistry 2005, 44 (10), 3994–4003. 10.1021/bi047473t. PubMed DOI

Konold P. E.; van Stokkum I. H. M.; Muzzopappa F.; Wilson A.; Groot M. L.; Kirilovsky D.; Kennis J. T. M. Photoactivation Mechanism, Timing of Protein Secondary Structure Dynamics and Carotenoid Translocation in the Orange Carotenoid Protein. J. Am. Chem. Soc. 2019, 141 (1), 520–530. 10.1021/jacs.8b11373. PubMed DOI PMC

Sauer P. V.; Cupellini L.; Sutter M.; Bondanza M.; Domínguez Martin M. A.; Kirst H.; Bína D.; Koh A. F.; Kotecha A.; Greber B. J.; et al. Structural and quantum chemical basis for OCP-mediated quenching of phycobilisomes. Sci. Adv. 2024, 10 (14), eadk753510.1126/sciadv.adk7535. PubMed DOI PMC

Krueger B. P.; Scholes G. D.; Fleming G. R. Calculation of couplings and energy-transfer pathways between the pigments of LH2 by the ab initio transition density cube method. J. Phys. Chem. B 1998, 102 (27), 5378–5386. 10.1021/jp9811171. DOI

Gray C.; Wei T. J.; Polívka T.; Daskalakis V.; Duffy C. D. P. Trivial Excitation Energy Transfer to Carotenoids Is an Unlikely Mechanism for Non-photochemical Quenching in LHCII. Front. Plant Sci. 2022, 12, 797373.10.3389/fpls.2021.797373. PubMed DOI PMC

Chmeliov J.; Bricker W. P.; Lo C.; Jouin E.; Valkunas L.; Ruban A. V.; Duffy C. D. P. An ’all pigment’ model of excitation quenching in LHCII. Phys. Chem. Chem. Phys. 2015, 17 (24), 15857–15867. 10.1039/C5CP01905B. PubMed DOI

Gradinaru C. C.; van Stokkum I. H. M.; Pascal A. A.; van Grondelle R.; van Amerongen H. Identifying the pathways of energy transfer between carotenoids and chlorophylls in LHCII and CP29. A multicolor, femtosecond pump-probe study. J. Phys. Chem. B 2000, 104 (39), 9330–9342. 10.1021/jp001752i. DOI

de Weerd F. L.; Kennis J. T. M.; Dekker J. P.; van Grondelle R. β-carotene to chlorophyll singlet energy transfer in the photosystem I core of Synechococcus elongatus proceeds via the β-carotene S2 and S1 states. J. Phys. Chem. B 2003, 107 (24), 5995–6002. 10.1021/jp027758k. DOI

Kodis G.; Herrero C.; Palacios R.; Mariño-Ochoa E.; Gould S.; de la Garza L.; van Grondelle R.; Gust D.; Moore T. A.; Moore A. L.; et al. Light harvesting and photoprotective functions of carotenoids in compact artificial photosynthetic antenna designs. J. Phys. Chem. B 2004, 108 (1), 414–425. 10.1021/jp036139o. DOI

Kloz M.; Pillai S.; Kodis G.; Gust D.; Moore T. A.; Moore A. L.; Grondelle R. v.; Kennis J. T. M. New light-harvesting roles of hot and forbidden carotenoid states in artificial photosynthetic constructs. Chem. Sci. 2012, 3 (6), 2052–2061. 10.1039/c2sc01023b. DOI

Ruban A. V.; Berera R.; Ilioaia C.; van Stokkum I. H. M.; Kennis J. T. M.; Pascal A. A.; van Amerongen H.; Robert B.; Horton P.; van Grondelle R. Identification of a mechanism of photoprotective energy dissipation in higher plants. Nature 2007, 450 (7169), 575–578. 10.1038/nature06262. PubMed DOI

Staleva H.; Komenda J.; Shukla M. K.; Slouf V.; Kana R.; Polívka T.; Sobotka R. Mechanism of photoprotection in the cyanobacterial ancestor of plant antenna proteins. Nat. Chem. Biol. 2015, 11 (4), 287–U296. 10.1038/nchembio.1755. PubMed DOI

Berera R.; Herrero C.; van Stokkum I. H. M.; Vengris M.; Kodis G.; Palacios R. E.; van Amerongen H.; van Grondelle R.; Gust D.; Moore T. A.; et al. A simple artificial light-harvesting dyad as a model for excess energy dissipation in oxygenic photosynthesis. Proc. Natl. Acad. Sci. U.S.A. 2006, 103 (14), 5343–5348. 10.1073/pnas.0508530103. PubMed DOI PMC

Cignoni E.; Lapillo M.; Cupellini L.; Acosta-Gutiérrez S.; Gervasio F. L.; Mennucci B. A different perspective for nonphotochemical quenching in plant antenna complexes. Nat. Commun. 2021, 12 (1), 7152.10.1038/s41467-021-27526-8. PubMed DOI PMC

Hsu C. P.; Walla P. J.; Head-Gordon M.; Fleming G. R. The role of the S1 state of carotenoids in photosynthetic energy transfer: The light-harvesting complex II of purple bacteria. J. Phys. Chem. B 2001, 105 (44), 11016–11025. 10.1021/jp0119835. DOI

Damjanovic A.; Ritz T.; Schulten K. Energy transfer between carotenoids and bacteriochlorophylls in light-harvesting complex II of purple bacteria. Phys. Rev. E:Stat. Phys., Plasmas, Fluids, Relat. Interdiscip. Top. 1999, 59 (3), 3293–3311. 10.1103/PhysRevE.59.3293. DOI

Staleva-Musto H.; West R.; Trathnigg M.; Bína D.; Litvín R.; Polívka T. Carotenoid-chlorophyll energy transfer in the fucoxanthin-chlorophyll complex binding a fucoxanthin acyloxy derivative. Faraday Discuss. 2019, 216, 460–475. 10.1039/C8FD00193F. PubMed DOI

Domínguez-Martín M. A.; Sauer P.; Kirst H.; Sutter M.; Bína D.; Greber B. J.; Nogales E.; Polívka T.; Kerfeld C. A. Structures of a phycobilisome in light-harvesting and photoprotected states. Nature 2022, 609 (7928), 835.10.1038/s41586-022-05156-4. PubMed DOI

Liguori N.; van Stokkum I. H. M.; Muzzopappa F.; Kennis J. T. M.; Kirilovsky D.; Croce R. The Orange Carotenoid Protein Triggers Cyanobacterial Photoprotection by Quenching Bilins via a Structural Switch of Its Carotenoid. J. Am. Chem. Soc. 2024, 146 (31), 21913–21921. 10.1021/jacs.4c06695. PubMed DOI PMC

Balashov S. P.; Imasheva E. S.; Boichenko V. A.; Antón J.; Wang J. M.; Lanyi J. K. Xanthorhodopsin A proton pump with a light-harvesting carotenoid antenna. Science 2005, 309 (5743), 2061–2064. 10.1126/science.1118046. PubMed DOI PMC

Chazan A.; Das I.; Fujiwara T.; Murakoshi S.; Rozenberg A.; Molina-Márquez A.; Sano F. K.; Tanaka T.; Gómez-Villegas P.; Larom S.; et al. Phototrophy by antenna-containing rhodopsin pumps in aquatic environments. Nature 2023, 615 (7952), 535–540. 10.1038/s41586-023-05774-6. PubMed DOI

Polívka T.; Balashov S. P.; Chábera P.; Imasheva E. S.; Yartsev A.; Sundström V.; Lanyi J. K. Femtosecond Carotenoid to Retinal Energy Transfer in Xanthorhodopsin. Biophys. J. 2009, 96 (6), 2268–2277. 10.1016/j.bpj.2009.01.004. PubMed DOI PMC

Gdor I.; Zhu J. Y.; Loevsky B.; Smolensky E.; Friedman N.; Sheves M.; Ruhman S. Investigating excited state dynamics of salinixanthin and xanthorhodopsin in the near-infrared. Phys. Chem. Chem. Phys. 2011, 13 (9), 3782–3787. 10.1039/C0CP01734E. PubMed DOI

Segatta F.; Gdor I.; Réhault J.; Taioli S.; Friedman N.; Sheves M.; Rivalta I.; Ruhman S.; Cerullo G.; Garavelli M. Ultrafast Carotenoid to Retinal Energy Transfer in Xanthorhodopsin Revealed by the Combination of Transient Absorption and Two-Dimensional Electronic Spectroscopy. Chem.–Eur. J. 2018, 24 (46), 12084–12092. 10.1002/chem.201803525. PubMed DOI

Zhu J. Y.; Gdor I.; Smolensky E.; Friedman N.; Sheves M.; Ruhman S. Photoselective Ultrafast Investigation of Xanthorhodopsin and Its Carotenoid Antenna Salinixanthin. J. Phys. Chem. B 2010, 114 (8), 3038–3045. 10.1021/jp910845h. PubMed DOI

Luecke H.; Schobert B.; Stagno J.; Imasheva E. S.; Wang J. M.; Balashov S. P.; Lanyi J. K. Crystallographic structure of xanthorhodopsin, the light-driven proton pump with a dual chromophore. Proc. Natl. Acad. Sci. U.S.A. 2008, 105 (43), 16561–16565. 10.1073/pnas.0807162105. PubMed DOI PMC

Oda K.; Vierock J.; Oishi S.; Rodriguez-Rozada S.; Taniguchi R.; Yamashita K.; Wiegert J. S.; Nishizawa T.; Hegemann P.; Nureki O. Crystal structure of the red light-activated channelrhodopsin Chrimson. Nat. Commun. 2018, 9, 3949.10.1038/s41467-018-06421-9. PubMed DOI PMC

Pushkarev A.; Inoue K.; Larom S.; Flores-Uribe J.; Singh M.; Konno M.; Tomida S.; Ito S.; Nakamura R.; Tsunoda S. P.; et al. A distinct abundant group of microbial rhodopsins discovered using functional metagenomics. Nature 2018, 558 (7711), 595.10.1038/s41586-018-0225-9. PubMed DOI PMC

Shihoya W.; Inoue K.; Singh M.; Konno M.; Hososhima S.; Yamashita K.; Ikeda K.; Higuchi A.; Izume T.; Okazaki S.; et al. Crystal structure of heliorhodopsin. Nature 2019, 574 (7776), 132.10.1038/s41586-019-1604-6. PubMed DOI

Kovalev K.; Volkov D.; Astashkin R.; Alekseev A.; Gushchin I.; Haro-Moreno J. M.; Chizhov I.; Siletsky S.; Mamedov M.; Rogachev A.; et al. High-resolution structural insights into the heliorhodopsin family. Proc. Natl. Acad. Sci. U.S.A. 2020, 117 (8), 4131–4141. 10.1073/pnas.1915888117. PubMed DOI PMC

Hontani Y.; Broser M.; Silapetere A.; Krause B. S.; Hegemann P.; Kennis J. T. M. The femtosecond-to-second photochemistry of red-shifted fast-closing anion channelrhodopsin PsACR1. Phys. Chem. Chem. Phys. 2017, 19 (45), 30402–30409. 10.1039/C7CP06414D. PubMed DOI

Rozenberg A.; Inoue K.; Kandori H.; Béjà O. Microbial Rhodopsins: The Last Two Decades. Annu. Rev. Microbiol. 2021, 75, 427–447. 10.1146/annurev-micro-031721-020452. PubMed DOI

van Stokkum I. H. M.; Snellenburg J. J.; Chrupková P.; Dostal J.; Weigand S.; Weissenborn J.; Kennis J. T. M.; Kloz M. Target Analysis Resolves the Ground and Excited State Properties from Femtosecond Stimulated Raman Spectra. J. Phys. Chem. Lett. 2024, 15 (37), 9397–9404. 10.1021/acs.jpclett.4c01555. PubMed DOI PMC

Feng Y.; Vinogradov I.; Ge N. H. General noise suppression scheme with reference detection in heterodyne nonlinear spectroscopy. Opt. Express 2017, 25 (21), 26262–26279. 10.1364/OE.25.026262. PubMed DOI

Liu Y. L.; Chaudhari A. S.; Chatterjee A.; Andrikopoulos P. C.; Picchiotti A.; Rebarz M.; Kloz M.; Lorenz-Fonfria V. A.; Schneider B.; Fuertes G. Sub-Millisecond Photoinduced Dynamics of Free and EL222-Bound FMN by Stimulated Raman and Visible Absorption Spectroscopies. Biomolecules 2023, 13 (1), 161.10.3390/biom13010161. PubMed DOI PMC

van Stokkum I. H. M.; Kloz M.; Polli D.; Viola D.; Weißenborn J.; Peerbooms E.; Cerullo G.; Kennis J. T. M. Vibronic dynamics resolved by global and target analysis of ultrafast transient absorption spectra. J. Chem. Phys. 2021, 155 (11), 114113.10.1063/5.0060672. PubMed DOI

van Stokkum I. H. M.; Weissenborn J.; Weigand S.; Snellenburg J. J. Pyglotaran: a lego-like Python framework for global and target analysis of time-resolved spectra. Photochem. Photobiol. Sci. 2023, 22 (10), 2413–2431. 10.1007/s43630-023-00460-y. PubMed DOI

Punjani A.; Rubinstein J. L.; Fleet D. J.; Brubaker M. A. cryoSPARC algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 2017, 14 (3), 290–296. 10.1038/nmeth.4169. PubMed DOI

Zheng S. Q.; Palovcak E.; Armache J. P.; Verba K. A.; Cheng Y. F.; Agard D. A. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 2017, 14 (4), 331–332. 10.1038/nmeth.4193. PubMed DOI PMC

Rohou A.; Grigorieff N. CTFFIND4: Fast and accurate defocus estimation from electron micrographs. J. Struct. Biol. 2015, 192 (2), 216–221. 10.1016/j.jsb.2015.08.008. PubMed DOI PMC

Scheres S. H. W. RELION: Implementation of a Bayesian approach to cryo-EM structure determination. J. Struct. Biol. 2012, 180 (3), 519–530. 10.1016/j.jsb.2012.09.006. PubMed DOI PMC

Sanchez-Garcia R.; Gomez-Blanco J.; Cuervo A.; Carazo J. M.; Sorzano C. O. S.; Vargas J. DeepEMhancer: a deep learning solution for cryo-EM volume post-processing. Commun. Biol. 2021, 4 (1), 874.10.1038/s42003-021-02399-1. PubMed DOI PMC

Meng E. C.; Goddard T. D.; Pettersen E. F.; Couch G. S.; Pearson Z. J.; Morris J. H.; Ferrin T. E. UCSF ChimeraX: Tools for structure building and analysis. Protein Sci. 2023, 32 (11), e479210.1002/pro.4792. PubMed DOI PMC