Sub-Millisecond Photoinduced Dynamics of Free and EL222-Bound FMN by Stimulated Raman and Visible Absorption Spectroscopies
Jazyk angličtina Země Švýcarsko Médium electronic
Typ dokumentu časopisecké články, práce podpořená grantem
Grantová podpora
CZ.02.1.01/0.0/0.0/15_003/0000447
European Regional Development Fund (ERDF)
CZ.02.1.01/0.0/0.0/18_046/0015974
European Regional Development Fund (ERDF)
RVO86652036
Czech Academy of Sciences, Institute of Biotechnology
LM2018127
Ministry of Education, Youth and Sports (MEYS) of the Czech Republic
PID2019-106103GBI00
Ministerio de Ciencia e Innovacion
CTQ2017-87372-P
Ministerio de Ciencia e Innovacion
LQ1606
Ministry of Education, Youth and Sports (MEYS) of the Czech Republic
PubMed
36671546
PubMed Central
PMC9855911
DOI
10.3390/biom13010161
PII: biom13010161
Knihovny.cz E-zdroje
- Klíčová slova
- femtosecond-stimulated Raman spectroscopy (FSRS), flavins, kinetic isotope effect (KIE), lifetime distribution analysis (LDA), light-oxygen-voltage (LOV) photosensors, maximum entropy method, photobiology, photochemistry, protein structural dynamics, time-resolved vibrational spectroscopy, transient visible absorption (visTA) spectroscopy,
- MeSH
- Ramanova spektroskopie * metody MeSH
- spektrofotometrie infračervená MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Time-resolved femtosecond-stimulated Raman spectroscopy (FSRS) provides valuable information on the structural dynamics of biomolecules. However, FSRS has been applied mainly up to the nanoseconds regime and above 700 cm-1, which covers only part of the spectrum of biologically relevant time scales and Raman shifts. Here we report on a broadband (~200-2200 cm-1) dual transient visible absorption (visTA)/FSRS set-up that can accommodate time delays from a few femtoseconds to several hundreds of microseconds after illumination with an actinic pump. The extended time scale and wavenumber range allowed us to monitor the complete excited-state dynamics of the biological chromophore flavin mononucleotide (FMN), both free in solution and embedded in two variants of the bacterial light-oxygen-voltage (LOV) photoreceptor EL222. The observed lifetimes and intermediate states (singlet, triplet, and adduct) are in agreement with previous time-resolved infrared spectroscopy experiments. Importantly, we found evidence for additional dynamical events, particularly upon analysis of the low-frequency Raman region below 1000 cm-1. We show that fs-to-sub-ms visTA/FSRS with a broad wavenumber range is a useful tool to characterize short-lived conformationally excited states in flavoproteins and potentially other light-responsive proteins.
ELI Beamlines Facility Extreme Light Infrastructure ERIC 25241 Dolni Brezany Czech Republic
Faculty of Science Charles University 12800 Prague Czech Republic
Institute of Biotechnology of the Czech Academy of Sciences 25250 Vestec Czech Republic
Institute of Molecular Science University of Valencia 46980 Paterna Spain
The Hamburg Centre for Ultrafast Imaging Hamburg University 22761 Hamburg Germany
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Kottke T., Xie A., Larsen D.S., Hoff W.D. Photoreceptors Take Charge: Emerging Principles for Light Sensing. Annu. Rev. Biophys. 2018;47:291–313. doi: 10.1146/annurev-biophys-070317-033047. PubMed DOI
Poddar H., Heyes D.J., Schirò G., Weik M., Leys D., Scrutton N.S. A guide to time-resolved structural analysis of light-activated proteins. FEBS J. 2021;289:576–595. doi: 10.1111/febs.15880. PubMed DOI
Herrou J., Crosson S. Function, structure and mechanism of bacterial photosensory LOV proteins. Nat. Rev. Microbiol. 2011;9:713–723. doi: 10.1038/nrmicro2622. PubMed DOI PMC
Losi A., Gärtner W. Solving Blue Light Riddles: New Lessons from Flavin-binding LOV Photoreceptors. Photochem. Photobiol. 2017;93:141–158. doi: 10.1111/php.12674. PubMed DOI
Iwata T., Masuda S. Optogenetics. Springer; Berlin/Heidelberg, Germany: 2021. Photoreaction Mechanisms of Flavoprotein Photoreceptors and Their Applications; pp. 189–206. PubMed DOI
Nash A.I., McNulty R., Shillito M.E., Swartz T.E., Bogomolni R.A., Luecke H., Gardner K.H. Structural basis of photosensitivity in a bacterial light-oxygen-voltage/helix-turn-helix (LOV-HTH) DNA-binding protein. Proc. Natl. Acad. Sci. USA. 2011;108:9449–9454. doi: 10.1073/pnas.1100262108. PubMed DOI PMC
Takakado A., Nakasone Y., Terazima M. Sequential DNA Binding and Dimerization Processes of the Photosensory Protein EL222. Biochemistry. 2018;57:1603–1610. doi: 10.1021/acs.biochem.7b01206. PubMed DOI
Takakado A., Nakasone Y., Terazima M. Photoinduced dimerization of a photosensory DNA-binding protein EL222 and its LOV domain. Phys. Chem. Chem. Phys. 2017;19:24855–24865. doi: 10.1039/C7CP03686H. PubMed DOI
Crosson S., Moffat K. Photoexcited Structure of a Plant Photoreceptor Domain Reveals a Light-Driven Molecular Switch. Plant Cell. 2002;14:1067–1075. doi: 10.1105/tpc.010475. PubMed DOI PMC
Losi A., Gardner K.H., Möglich A. Blue-Light Receptors for Optogenetics. Chem. Rev. 2018;118:10659–10709. doi: 10.1021/acs.chemrev.8b00163. PubMed DOI PMC
Seifert S., Brakmann S. LOV Domains in the Design of Photoresponsive Enzymes. ACS Chem. Biol. 2018;13:1914–1920. doi: 10.1021/acschembio.8b00159. PubMed DOI
Pudasaini A., El-Arab K.K., Zoltowski B.D. LOV-based optogenetic devices: Light-driven modules to impart photoregulated control of cellular signaling. Front. Mol. Biosci. 2015;2:18. doi: 10.3389/fmolb.2015.00018. PubMed DOI PMC
Iuliano J.N., French J.B., Tonge P.J. New Approaches for Flavin Catalysis. Springer; Berlin/Heidelberg, Germany: 2019. Vibrational spectroscopy of flavoproteins; pp. 189–214. PubMed DOI
Zayner J.P., Sosnick T.R. Factors That Control the Chemistry of the LOV Domain Photocycle. PLoS ONE. 2014;9:e87074. doi: 10.1371/journal.pone.0087074. PubMed DOI PMC
Fang C., Tang L. Mapping Structural Dynamics of Proteins with Femtosecond Stimulated Raman Spectroscopy. Annu. Rev. Phys. Chem. 2020;71:239–265. doi: 10.1146/annurev-physchem-071119-040154. PubMed DOI
Dietze D.R., Mathies R.A. Femtosecond Stimulated Raman Spectroscopy. ChemPhysChem. 2016;17:1224–1251. doi: 10.1002/cphc.201600104. PubMed DOI
Kukura P., McCamant D.W., Mathies R.A. Femtosecond Stimulated Raman Spectroscopy. Annu. Rev. Phys. Chem. 2007;58:461–488. doi: 10.1146/annurev.physchem.58.032806.104456. PubMed DOI
Kottke T., Lórenz-Fonfría V.A., Heberle J. The Grateful Infrared: Sequential Protein Structural Changes Resolved by Infrared Difference Spectroscopy. J. Phys. Chem. B. 2016;121:335–350. doi: 10.1021/acs.jpcb.6b09222. PubMed DOI
Schubert L., Langner P., Ehrenberg D., Lorenz-Fonfria V.A., Heberle J. Protein conformational changes and protonation dynamics probed by a single shot using quantum-cascade-laser-based IR spectroscopy. J. Chem. Phys. 2022;156:204201. doi: 10.1063/5.0088526. PubMed DOI
Greetham G.M., Sole D., Clark I.P., Parker A.W., Pollard M.R., Towrie M. Time-resolved multiple probe spectroscopy. Rev. Sci. Instrum. 2012;83:103107. doi: 10.1063/1.4758999. PubMed DOI
Weigel A., Dobryakov A., Klaumünzer B., Sajadi M., Saalfrank P., Ernsting N.P. Femtosecond Stimulated Raman Spectroscopy of Flavin after Optical Excitation. J. Phys. Chem. B. 2011;115:3656–3680. doi: 10.1021/jp1117129. PubMed DOI
Andrikopoulos P.C., Liu Y., Picchiotti A., Lenngren N., Kloz M., Chaudhari A.S., Precek M., Rebarz M., Andreasson J., Hajdu J., et al. Femtosecond-to-nanosecond dynamics of flavin mononucleotide monitored by stimulated Raman spectroscopy and simulations. Phys. Chem. Chem. Phys. 2020;22:6538–6552. doi: 10.1039/C9CP04918E. PubMed DOI
Iuliano J.N., Hall C.R., Green D., Jones G.A., Lukacs A., Illarionov B., Bacher A., Fischer M., French J.B., Tonge P.J., et al. Excited State Vibrations of Isotopically Labeled FMN Free and Bound to a Light–Oxygen–Voltage (LOV) Protein. J. Phys. Chem. B. 2020;124:7152–7165. doi: 10.1021/acs.jpcb.0c04943. PubMed DOI PMC
Iuliano J.N., Gil A.A., Laptenok S.P., Hall C.R., Tolentino Collado J., Lukacs A., Hag Ahmed S.A., Abyad J., Daryaee T., Greetham G.M., et al. Variation in LOV Photoreceptor Activation Dynamics Probed by Time-Resolved Infrared Spectroscopy. Biochemistry. 2018;57:620–630. doi: 10.1021/acs.biochem.7b01040. PubMed DOI PMC
Ferrante C., Batignani G., Pontecorvo E., Montemiglio L.C., Vos M.H., Scopigno T. Ultrafast Dynamics and Vibrational Relaxation in Six-Coordinate Heme Proteins Revealed by Femtosecond Stimulated Raman Spectroscopy. J. Am. Chem. Soc. 2020;142:2285–2292. doi: 10.1021/jacs.9b10560. PubMed DOI PMC
Fang C., Frontiera R.R., Tran R., Mathies R.A. Mapping GFP structure evolution during proton transfer with femtosecond Raman spectroscopy. Nature. 2009;462:200–204. doi: 10.1038/nature08527. PubMed DOI
Kukura P., McCamant D.W., Yoon S., Wandschneider D.B., Mathies R.A. Structural Observation of the Primary Isomerization in Vision with Femtosecond-Stimulated Raman. Science. 2005;310:1006–1009. doi: 10.1126/science.1118379. PubMed DOI
Konold P.E., Mathes T., Weiβenborn J., Groot M.L., Hegemann P., Kennis J.T.M. Unfolding of the C-Terminal Jα Helix in the LOV2 Photoreceptor Domain Observed by Time-Resolved Vibrational Spectroscopy. J. Phys. Chem. Lett. 2016;7:3472–3476. doi: 10.1021/acs.jpclett.6b01484. PubMed DOI
Nakasone Y., Eitoku T., Matsuoka D., Tokutomi S., Terazima M. Dynamics of Conformational Changes of Arabidopsis Phototropin 1 LOV2 with the Linker Domain. J. Mol. Biol. 2007;367:432–442. doi: 10.1016/j.jmb.2006.12.074. PubMed DOI
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;142:11464–11473. doi: 10.1021/jacs.0c03229. PubMed DOI PMC
Takaya T., Anan M., Iwata K. Vibrational relaxation dynamics of β-carotene and its derivatives with substituents on terminal rings in electronically excited states as studied by femtosecond time-resolved stimulated Raman spectroscopy in the near-IR region. Phys. Chem. Chem. Phys. 2018;20:3320–3327. doi: 10.1039/C7CP06343A. PubMed DOI
Challa J.R., Du Y., McCamant D.W. Femtosecond Stimulated Raman Spectroscopy Using a Scanning Multichannel Technique. Appl. Spectrosc. 2012;66:227–232. doi: 10.1366/11-06457. PubMed DOI
Lipkin M., Nixdorf J., Gilch P. Optimized amplitude modulation in femtosecond stimulated Raman microscopy. Opt. Lett. 2020;45:4204–4207. doi: 10.1364/OL.397589. PubMed DOI
Wang Z., Zhang Y., Chen C., Zhu R., Jiang J., Weng T.-C., Ji Q., Huang Y., Fang C., Liu W. Mapping the Complete Photocycle that Powers a Large Stokes Shift Red Fluorescent Protein. Angew. Chem. Int. Ed. 2022:e202212209. doi: 10.1002/anie.202212209. PubMed DOI
Andrikopoulos P.C., Chaudhari A.S., Liu Y., Konold P.E., Kennis J.T.M., Schneider B., Fuertes G. QM calculations predict the energetics and infrared spectra of transient glutamine isomers in LOV photoreceptors. Phys. Chem. Chem. Phys. 2021;23:13934–13950. doi: 10.1039/D1CP00447F. PubMed DOI PMC
Green D., Roy P., Hall C.R., Iuliano J.N., Jones G.A., Lukacs A., Tonge P.J., Meech S.R. Excited State Resonance Raman of Flavin Mononucleotide: Comparison of Theory and Experiment. J. Phys. Chem. A. 2021;125:6171–6179. doi: 10.1021/acs.jpca.1c04063. PubMed DOI PMC
Hall C.R., Heisler I.A., Jones G.A., Frost J.E., Gil A.A., Tonge P.J., Meech S.R. Femtosecond stimulated Raman study of the photoactive flavoprotein AppABLUF. Chem. Phys. Lett. 2017;683:365–369. doi: 10.1016/j.cplett.2017.03.030. DOI
Chaudhari A.S., Chatterjee A., Domingos C.A.O., Andrikopoulos P.C., Liu Y., Andersson I., Schneider B., Lórenz-Fonfría V.A., Fuertes G. Genetically encoded non-canonical amino acids reveal asynchronous dark reversion of chromophore, backbone and side-chains in EL222. bioRxiv. 2022 doi: 10.1101/2022.09.16.506679. PubMed DOI PMC
Kloz M., Weißenborn J., Polívka T., Frank H.A., Kennis J.T.M. Spectral watermarking in femtosecond stimulated Raman spectroscopy: Resolving the nature of the carotenoid S* state. Phys. Chem. Chem. Phys. 2016;18:14619–14628. doi: 10.1039/C6CP01464J. PubMed DOI
Pimenta F.M., Jensen R.L., Breitenbach T., Etzerodt M., Ogilby P.R. Oxygen-Dependent Photochemistry and Photophysics of “MiniSOG”, a Protein-Encased Flavin. Photochem. Photobiol. 2013;89:1116–1126. doi: 10.1111/php.12111. PubMed DOI
McIntosh J.R., Shu X., Lev-Ram V., Deerinck T.J., Qi Y., Ramko E.B., Davidson M.W., Jin Y., Ellisman M.H., Tsien R.Y. A Genetically Encoded Tag for Correlated Light and Electron Microscopy of Intact Cells, Tissues, and Organisms. PLoS Biol. 2011;9:e1001041. doi: 10.1371/journal.pbio.1001041. PubMed DOI PMC
Lórenz-Fonfría V.A., Kandori H. Bayesian Maximum Entropy (Two-Dimensional) Lifetime Distribution Reconstruction from Time-Resolved Spectroscopic Data. Appl. Spectrosc. 2016;61:428–443. doi: 10.1366/000370207780466172. PubMed DOI
Lórenz-Fonfría V.A., Kandori H. Practical Aspects of the Maximum Entropy Inversion of the Laplace Transform for the Quantitative Analysis of Multi-Exponential Data. Appl. Spectrosc. 2016;61:74–84. doi: 10.1366/000370207779701460. PubMed DOI
Lórenz-Fonfría V.A., Kandori H. Transformation of Time-Resolved Spectra to Lifetime-Resolved Spectra by Maximum Entropy Inversion of the Laplace Transform. Appl. Spectrosc. 2016;60:407–417. doi: 10.1366/000370206776593654. PubMed DOI
Bozovic O., Zanobini C., Gulzar A., Jankovic B., Buhrke D., Post M., Wolf S., Stock G., Hamm P. Real-time observation of ligand-induced allosteric transitions in a PDZ domain. Proc. Natl. Acad. Sci. USA. 2020;117:26031–26039. doi: 10.1073/pnas.2012999117. PubMed DOI PMC
Stock G., Hamm P. A non-equilibrium approach to allosteric communication. Philos. Trans. R. Soc. B Biol. Sci. 2018;373:20170187. doi: 10.1098/rstb.2017.0187. PubMed DOI PMC
Van Stokkum I.H.M., Larsen D.S., van Grondelle R. Global and target analysis of time-resolved spectra. Biochim. Biophys. Acta (BBA) Bioenerg. 2004;1657:82–104. doi: 10.1016/j.bbabio.2004.04.011. PubMed DOI
Snellenburg J.J., Laptenok S.P., Seger R., Mullen K.M., Stokkum I.H.M.v. Glotaran: AJava-Based Graphical User Interface for theRPackageTIMP. J. Stat. Softw. 2012;49:1–22. doi: 10.18637/jss.v049.i03. DOI
Beckwith J.S., Rumble C.A., Vauthey E. Data analysis in transient electronic spectroscopy—An experimentalist’s view. Int. Rev. Phys. Chem. 2020;39:135–216. doi: 10.1080/0144235X.2020.1757942. DOI
Slavov C., Hartmann H., Wachtveitl J. Implementation and Evaluation of Data Analysis Strategies for Time-Resolved Optical Spectroscopy. Anal. Chem. 2015;87:2328–2336. doi: 10.1021/ac504348h. PubMed DOI
Sun M., Moore T.A., Song P.-S. Molecular luminescence studies of flavines. I. Excited states of flavines. J. Am. Chem. Soc. 2002;94:1730–1740. doi: 10.1021/ja00760a052. PubMed DOI
Van Stokkum I.H.M., Gauden M., Crosson S., van Grondelle R., Moffat K., Kennis J.T.M. The Primary Photophysics of the Avena sativa Phototropin 1 LOV2 Domain Observed with Time-resolved Emission Spectroscopy†. Photochem. Photobiol. 2011;87:534–541. doi: 10.1111/j.1751-1097.2011.00903.x. PubMed DOI PMC
Kutta R.J., Magerl K., Kensy U., Dick B. A search for radical intermediates in the photocycle of LOV domains. Photochem. Photobiol. Sci. 2015;14:288–299. doi: 10.1039/c4pp00155a. PubMed DOI
Yee E.F., Diensthuber R.P., Vaidya A.T., Borbat P.P., Engelhard C., Freed J.H., Bittl R., Möglich A., Crane B.R. Signal transduction in light–oxygen–voltage receptors lacking the adduct-forming cysteine residue. Nat. Commun. 2015;6 doi: 10.1038/ncomms10079. PubMed DOI PMC
Dietler J., Gelfert R., Kaiser J., Borin V., Renzl C., Pilsl S., Ranzani A.T., García de Fuentes A., Gleichmann T., Diensthuber R.P., et al. Signal transduction in light-oxygen-voltage receptors lacking the active-site glutamine. Nat. Commun. 2022;13:10079. doi: 10.1038/s41467-022-30252-4. PubMed DOI PMC
Kopka B., Magerl K., Savitsky A., Davari M.D., Röllen K., Bocola M., Dick B., Schwaneberg U., Jaeger K.-E., Krauss U. Electron transfer pathways in a light, oxygen, voltage (LOV) protein devoid of the photoactive cysteine. Sci. Rep. 2017;7:13346. doi: 10.1038/s41598-017-13420-1. PubMed DOI PMC
Atzrodt J., Derdau V., Kerr W.J., Reid M. Deuterium- and Tritium-Labelled Compounds: Applications in the Life Sciences. Angew. Chem. Int. Ed. 2018;57:1758–1784. doi: 10.1002/anie.201704146. PubMed DOI
Alexandre M.T.A., Domratcheva T., Bonetti C., van Wilderen L.J.G.W., van Grondelle R., Groot M.-L., Hellingwerf K.J., Kennis J.T.M. Primary Reactions of the LOV2 Domain of Phototropin Studied with Ultrafast Mid-Infrared Spectroscopy and Quantum Chemistry. Biophys. J. 2009;97:227–237. doi: 10.1016/j.bpj.2009.01.066. PubMed DOI PMC
Alexandre M.T.A., Purcell E.B., van Grondelle R., Robert B., Kennis J.T.M., Crosson S. Electronic and Protein Structural Dynamics of a Photosensory Histidine Kinase. Biochemistry. 2010;49:4752–4759. doi: 10.1021/bi100527a. PubMed DOI PMC
Corchnoy S.B., Swartz T.E., Lewis J.W., Szundi I., Briggs W.R., Bogomolni R.A. Intramolecular Proton Transfers and Structural Changes during the Photocycle of the LOV2 Domain of Phototropin 1. J. Biol. Chem. 2003;278:724–731. doi: 10.1074/jbc.M209119200. PubMed DOI
Sakai M., Takahashi H. One-electron photoreduction of flavin mononucleotide: Time-resolved resonance Raman and absorption study. J. Mol. Struct. 1996;379:9–18. doi: 10.1016/0022-2860(95)09176-9. DOI
Li G., Glusac K.D. Light-Triggered Proton and Electron Transfer in Flavin Cofactors. J. Phys. Chem. A. 2008;112:4573–4583. doi: 10.1021/jp7117218. PubMed DOI
Pan J., Byrdin M., Aubert C., Eker A.P.M., Brettel K., Vos M.H. Excited-State Properties of Flavin Radicals in Flavoproteins: Femtosecond Spectroscopy of DNA Photolyase, Glucose Oxidase, and Flavodoxin. J. Phys. Chem. B. 2004;108:10160–10167. doi: 10.1021/jp037837b. DOI
Glantz S.T., Carpenter E.J., Melkonian M., Gardner K.H., Boyden E.S., Wong G.K.-S., Chow B.Y. Functional and topological diversity of LOV domain photoreceptors. Proc. Natl. Acad. Sci. USA. 2016;113 doi: 10.1073/pnas.1509428113. PubMed DOI PMC
Balakrishnan G., Weeks C.L., Ibrahim M., Soldatova A.V., Spiro T.G. Protein dynamics from time resolved UV Raman spectroscopy. Curr. Opin. Struct. Biol. 2008;18:623–629. doi: 10.1016/j.sbi.2008.06.001. PubMed DOI PMC
Humphrey W., Dalke A., Schulten K. VMD: Visual molecular dynamics. J. Mol. Graph. 1996;14:33–38. doi: 10.1016/0263-7855(96)00018-5. PubMed DOI
Halavaty A.S., Moffat K. N- and C-Terminal Flanking Regions Modulate Light-Induced Signal Transduction in the LOV2 Domain of the Blue Light Sensor Phototropin 1 from Avena sativa. Biochemistry. 2007;46:14001–14009. doi: 10.1021/bi701543e. PubMed DOI
Wallace A.C., Laskowski R.A., Thornton J.M. LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions. Protein Eng. Des. Sel. 1995;8:127–134. doi: 10.1093/protein/8.2.127. PubMed DOI