Design of AsLOV2 domain as a carrier of light-induced dissociable FMN photosensitizer

. 2024 Apr ; 33 (4) : e4921.

Jazyk angličtina Země Spojené státy americké Médium print

Typ dokumentu časopisecké články

Perzistentní odkaz   https://www.medvik.cz/link/pmid38501448

Grantová podpora
HORIZON EUROPE Innovative Europe
Agentúra na Podporu Výskumu a Vývoja
Slovak Research and Development Agency
LX22NPO5107 Ministry of Education, Youth and Sports of the Czech Republic
Grant Agency of Charles University
RVO61388971 Czech Academy of Sciences

Flavin mononucleotide (FMN) is a highly efficient photosensitizer (PS) yielding singlet oxygen (1 O2 ). However, its 1 O2 production efficiency significantly decreases upon isoalloxazine ring encapsulation into the protein matrix in genetically encoded photosensitizers (GEPS). Reducing isoalloxazine ring interactions with surrounding amino acids by protein engineering may increase 1 O2 production efficiency GEPS, but at the same time weakened native FMN-protein interactions may cause undesirable FMN dissociation. Here, in contrast, we intentionally induce the FMN release by light-triggered sulfur oxidation of strategically placed cysteines (oxidation-prone amino acids) in the isoalloxazine-binding site due to significantly increased volume of the cysteinyl side residue(s). As a proof of concept, in three variants of the LOV2 domain of Avena sativa (AsLOV2), namely V416C, T418C, and V416C/T418C, the effective 1 O2 production strongly correlated with the efficiency of irradiation-induced FMN dissociation (wild type (WT) < V416C < T418C < V416C/T418C). This alternative approach enables us: (i) to overcome the low 1 O2 production efficiency of flavin-based GEPSs without affecting native isoalloxazine ring-protein interactions and (ii) to utilize AsLOV2, due to its inherent binding propensity to FMN, as a PS vehicle, which is released at a target by light irradiation.

Zobrazit více v PubMed

Akasov R, Khaydukov EV, Yamada M, Zvyagin AV, Leelahavanichkul A, Leanse LG, et al. Nanoparticle enhanced blue light therapy. Adv Drug Deliv Rev. 2022;184:114198. 10.1016/j.addr.2022.114198 PubMed DOI

Andersen HC. RATTLE – a velocity version of the SHAKE algorithms for molecular‐dynamics calculations. J Comput Phys. 1983;52(1):24–34. 10.1016/0021-9991(83)90014-1 DOI

Baier J, Maisch T, Maier M, Engel E, Landthaler M, Baumler W. Singlet oxygen generation by UVA light exposure of endogenous photosensitizers. Biophys J. 2006;91(4):1452–1459. 10.1529/biophysj.106.082388 PubMed DOI PMC

Bulina ME, Chudakov DM, Britanova OV, Yanushevich YG, Staroverov DB, Chepurnykh TV, et al. A genetically encoded photosensitizer. Nat Biotechnol. 2006;24(1):95–99. 10.1038/nbt1175 PubMed DOI

Darden T, York D, Pedersen L. Particle mesh Ewald – an N.Log(N) method for Ewald sums in large systems. J Chem Phys. 1993;98(12):10089–10092. 10.1063/1.464397 DOI

Debele TA, Peng S, Tsai HC. Drug carrier for photodynamic cancer therapy. Int J Mol Sci. 2015;16(9):22094–22136. 10.3390/ijms160922094 PubMed DOI PMC

Dougherty TJ, Gomer CJ, Henderson BW, Jori G, Kessel D, Korbelik M, et al. Photodynamic therapy. J Natl Cancer Inst. 1998;90(12):889–905. 10.1093/jnci/90.12.889 PubMed DOI PMC

Endres S, Wingen M, Torra J, Ruiz‐Gonzalez R, Polen T, Bosio G, et al. An optogenetic toolbox of LOV‐based photosensitizers for light‐driven killing of bacteria. Sci Rep. 2018;8:15021. 10.1038/s41598-018-33291-4 PubMed DOI PMC

Feller SE, Zhang YH, Pastor RW, Brooks BR. Constant‐pressure molecular‐dynamics simulation – the Langevin piston method. J Chem Phys. 1995;103(11):4613–4621. 10.1063/1.470648 DOI

Gorbachev DA, Staroverov DB, Lukyanov KA, Sarkisyan KS. Genetically encoded red photosensitizers with enhanced phototoxicity. Int J Mol Sci. 2020;21(22):8800. 10.3390/ijms21228800 PubMed DOI PMC

Gunaydin G, Gedik ME, Ayan S. Photodynamic therapy for the treatment and diagnosis of cancer – a review of the current clinical status. Front Chem. 2021;9(26):686303. 10.3389/fchem.2021.686303 PubMed DOI PMC

Halavaty AS, 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(49):14001–14009. 10.1021/bi701543e PubMed DOI

Hilgers F, Bitzenhofer NL, Ackermann Y, Burmeister A, Grunberger A, Jaeger KE, et al. Genetically encoded photosensitizers as light‐triggered antimicrobial agents. Int J Mol Sci. 2019;20(18):4608. 10.3390/ijms20184608 PubMed DOI PMC

Hovan A, Pevna V, Huntosova V, Miskovsky P, Bano G. Singlet oxygen lifetime changes in dying glioblastoma cells. Photochem Photobiol. 2023;100:1–13. 10.1111/php.13828 PubMed DOI

Huang J, Rauscher S, Nawrocki G, Ran T, Feig M, de Groot BL, et al. CHARMM36m: an improved force field for folded and intrinsically disordered proteins. Nat Methods. 2017;14(1):71–73. 10.1038/nmeth.4067 PubMed DOI PMC

Humphrey W, Dalke A, Schulten K. VMD: visual molecular dynamics. J Mol Graph. 1996;14(1):33–38. 10.1016/0263-7855(96)00018-5 PubMed DOI

Jarzynski C. Nonequilibrium equality for free energy differences. Phys Rev Lett. 1997;78(14):2690–2693. 10.1103/PhysRevLett.78.2690 DOI

Jimenez‐Banzo A, Ragas X, Kapusta P, Nonell S. Time‐resolved methods in biophysics. 7. Photon counting vs. analog time‐resolved singlet oxygen phosphorescence detection. Photochem Photobiol Sci. 2008;7(9):1003–1010. 10.1039/b804333g PubMed DOI

Kelly SM, Jess TJ, Price NC. How to study proteins by circular dichroism. Biochim Biophys Acta Proteins Proteom. 2005;1751(2):119–139. 10.1016/j.bbapap.2005.06.005 PubMed DOI

Kong AT, Leprevost FV, Avtonomov DM, Mellacheruvu D, Nesvizhskii AI. MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry‐based proteomics. Nat Methods. 2017;14(5):513–520. 10.1038/nmeth.4256 PubMed DOI PMC

Lee CN, Hsu R, Chen H, Wong TW. Daylight photodynamic therapy: an update. Molecules. 2020;25(21):5195. 10.3390/molecules25215195 PubMed DOI PMC

Loginov DS, Fiala J, Brechlin P, Kruppa G, Novak P. Hydroxyl radical footprinting analysis of a human haptoglobin‐hemoglobin complex. Biochim Biophys Acta Proteins Proteom. 2022;1870(2):140735. 10.1016/j.bbapap.2021.140735 PubMed DOI

MacLean B, Tomazela DM, Shulman N, Chambers M, Finney GL, Frewen B, et al. Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics. 2010;26(7):966–968. 10.1093/bioinformatics/btq054 PubMed DOI PMC

Maestro . 2022‐2. Schrödinger, LLC. 2022. https://www.schrodinger.com/sites/default/files/s3/public/python_api/2022‐2/api/schrodinger.maestro.html.

Mansoori B, Mohammadi A, Doustvandi MA, Mohammadnejad F, Kamari F, Gjerstorff MF, et al. Photodynamic therapy for cancer: role of natural products. Photodiagnosis Photodyn Ther. 2019;26:395–404. 10.1016/j.pdpdt.2019.04.033 PubMed DOI PMC

Martyna GJ, Tobias DJ, Klein ML. Constant‐pressure molecular‐dynamics algorithms. J Chem Phys. 1994;101(5):4177–4189. 10.1063/1.467468 DOI

Meissner B, Schleicher E, Weber S, Essen LO. The dodecin from Thermus thermophilus, a bifunctional cofactor storage protein. J Biol Chem. 2007;282(45):33142–33154. 10.1074/jbc.M704951200 PubMed DOI

Micheletto MC, Guidelli EJ, Costa AJ. Interaction of genetically encoded photosensitizers with scintillating nanoparticles for X‐ray activated photodynamic therapy. ACS Appl Mater Interfaces. 2021;13(2):2289–2302. 10.1021/acsami.0c19041 PubMed DOI

Mogensen DJ, Westberg M, Breitenbach T, Etzerodt M, Ogilby PR. Stable transfection of the singlet oxygen photosensitizing protein SOPP3: examining aspects of intracellular behavior. Photochem Photobiol. 2021;97(6):1417–1430. 10.1111/php.13440 PubMed DOI

O'Connor AE, Gallagher WM, Byrne AT. Porphyrin and nonporphyrin photosensitizers in oncology: preclinical and clinical advances in photodynamic therapy. Photochem Photobiol. 2009;85(5):1053–1074. 10.1111/j.1751-1097.2009.00585.x PubMed DOI

Park S, Schulten K. Calculating potentials of mean force from steered molecular dynamics simulations. J Chem Phys. 2004;120(13):5946–5961. 10.1063/1.1651473 PubMed DOI

Petrencakova M, Filandr F, Hovan A, Yassaghi G, Man P, Kozar T, et al. Photoinduced damage of AsLOV2 domain is accompanied by increased singlet oxygen production due to flavin dissociation. Sci Rep. 2020;10(1):4119. 10.1038/s41598-020-60861-2 PubMed DOI PMC

Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, et al. Scalable molecular dynamics with NAMD. J Comput Chem. 2005;26(16):1781–1802. 10.1002/jcc.20289 PubMed DOI PMC

Pimenta FM, Jensen RL, Breitenbach T, Etzerodt M, Ogilby PR. Oxygen‐dependent photochemistry and Photophysics of “MiniSOG,” a protein‐encased flavin. Photochem Photobiol. 2013;89(5):1116–1126. 10.1111/php.12111 PubMed DOI

Polak M, Yassaghi G, Kavan D, Filandr F, Fiala J, Kukacka Z, et al. Utilization of fast photochemical oxidation of proteins and both bottom‐up and top‐down mass spectrometry for structural characterization of a transcription factor‐dsDNA complex. Anal Chem. 2022;94(7):3203–3210. 10.1021/acs.analchem.1c04746 PubMed DOI

Price DJ, Brooks CL. A modified TIP3P water potential for simulation with Ewald summation. J Chem Phys. 2004;121(20):10096–10103. 10.1063/1.1808117 PubMed DOI

Proshkina GM, Shilova ON, Ryabova AV, Stremovskiy OA, Deyev SM. A new anticancer toxin based on HER2/neu‐specific DARPin and photoactive flavoprotein miniSOG. Biochimie. 2015;118:116–122. 10.1016/j.biochi.2015.08.013 PubMed DOI

Ragas X, Cooper LP, White JH, Nonell S, Flors C. Quantification of photosensitized singlet oxygen production by a fluorescent protein. ChemPhysChem. 2011;12(1):161–165. 10.1002/cphc.201000919 PubMed DOI

Ragas X, He X, Agut M, Roxo‐Rosa M, Gonsalves AR, Serra AC, et al. Singlet oxygen in antimicrobial photodynamic therapy: photosensitizer‐dependent production and decay in E. coli . Molecules. 2013;18(3):2712–2725. 10.3390/molecules18032712 PubMed DOI PMC

Rodríguez‐Pulido A, Cortajarena AL, Torra J, Ruiz‐González R, Nonell S, Flors C. Assessing the potential of photosensitizing flavoproteins as tags for correlative microscopy. Chem Commun. 2016;52:8405–8408. 10.1039/C6CC03119F PubMed DOI

Ruiz‐Gonzalez R, Cortajarena AL, Mejias SH, Agut M, Nonell S, Flors C. Singlet oxygen generation by the genetically encoded tag miniSOG. J Am Chem Soc. 2013;135(26):9564–9567. 10.1021/ja4020524 PubMed DOI

Sarkisyan KS, Zlobovskaya OA, Gorbachev DA, Bozhanova NG, Sharonov GV, Staroverov DB, et al. KillerOrange, a genetically encoded photosensitizer activated by blue and green light. PloS One. 2015;10(12):e0145287. 10.1371/journal.pone.0145287 PubMed DOI PMC

Schrödinger L. Schrödinger. Version release 2022‐2. 2022. https://www.schrodinger.com/releases/release-2022-2

Serebrovskaya EO, Edelweiss EF, Stremovskiy OA, Lukyanov KA, Chudakov DM, Deyev SM. Targeting cancer cells by using an antireceptor antibody‐photosensitizer fusion protein. Proc Natl Acad Sci U S A. 2009;106(23):9221–9225. 10.1073/pnas.0904140106 PubMed DOI PMC

Shaw DE. Desmond molecular dynamics system. D E Shaw Research. 2020. https://www.deshawresearch.com/resources.html

Shu X, Lev‐Ram V, Deerinck TJ, Qi Y, Ramko EB, Davidson MW, et al. A genetically encoded tag for correlated light and electron microscopy of intact cells, tissues, and organisms. PLoS Biol. 2011;9(4):e1001041. 10.1371/journal.pbio.1001041 PubMed DOI PMC

Souslova EA, Mironova KE, Deyev SM. Applications of genetically encoded photosensitizer miniSOG: from correlative light electron microscopy to immunophotosensitizing. J Biophotonics. 2017;10(3):338–352. 10.1002/jbio.201600120 PubMed DOI

Stockwell GR, Thornton JM. Conformational diversity of ligands bound to proteins. J Mol Biol. 2006;356(4):928–944. 10.1016/j.jmb.2005.12.012 PubMed DOI

Takemoto K, Matsuda T, Sakai N, Fu D, Noda M, Uchiyama S, et al. SuperNova, a monomeric photosensitizing fluorescent protein for chromophore‐assisted light inactivation. Sci Rep. 2013;3(7):2629. 10.1038/srep02629 PubMed DOI PMC

Taylor BL, Zhulin IB. PAS domains: internal sensors of oxygen, redox potential, and light [review]. Microbiol Mol Biol Rev. 1999;63(2):479–506. 10.1128/mmbr.63.2.479-506.1999 PubMed DOI PMC

Torra J, Lafaye C, Signor L, Aumonier S, Flors C, Shu XK, et al. Tailing miniSOG: structural bases of the complex photophysics of a flavin‐binding singlet oxygen photosensitizing protein. Sci Rep. 2019;9:2428. 10.1038/s41598-019-38955-3 PubMed DOI PMC

van den Berg PAW, Feenstra KA, Mark AE, Berendsen HJC, Visser A. Dynamic conformations of flavin adenine dinucleotide: simulated molecular dynamics of the flavin cofactor related to the time‐resolved fluorescence characteristics. J Phys Chem B. 2002;106(34):8858–8869. 10.1021/jp020356s DOI

Westberg M, Bregnhoj M, Etzerodt M, Ogilby PR. No photon wasted: an efficient and selective singlet oxygen photosensitizing protein. J Phys Chem B. 2017a;121(40):9366–9371. 10.1021/acs.jpcb.7b07831 PubMed DOI

Westberg M, Bregnhoj M, Etzerodt M, Ogilby PR. Temperature sensitive singlet oxygen photosensitization by LOV‐derived fluorescent flavoproteins. J Phys Chem B. 2017b;121(12):2561–2574. 10.1021/acs.jpcb.7b00561 PubMed DOI

Westberg M, Etzerodt M, Ogilby PR. Rational design of genetically encoded singlet oxygen photosensitizing proteins. Curr Opin Struct Biol. 2019;57:56–62. 10.1016/j.sbi.2019.01.025 PubMed DOI

Westberg M, Holmegaard L, Pimenta FM, Etzerodt M, Ogilby PR. Rational design of an efficient, genetically encodable, protein‐encased singlet oxygen photosensitizer. J Am Chem Soc. 2015;137(4):1632–1642. 10.1021/ja511940j PubMed DOI

Yassaghi G, Kukacka Z, Fiala J, Kavan D, Halada P, Volny M, et al. Top‐down detection of oxidative protein footprinting by collision‐induced dissociation, electron‐transfer dissociation, and electron‐capture dissociation. Anal Chem. 2022;94(28):9993–10002. 10.1021/acs.analchem.1c05476 PubMed DOI PMC

Yu F, Haynes SE, Teo GC, Avtonomov DM, Polasky DA, Nesvizhskii AI. Fast quantitative analysis of timsTOF PASEF data with MSFragger and IonQuant. Mol Cell Proteomics. 2020;19(9):1575–1585. 10.1074/mcp.TIR120.002048 PubMed DOI PMC

Zayner JP, Antoniou C, Sosnick TR. The amino‐terminal helix modulates light‐activated conformational changes in AsLOV2. J Mol Biol. 2012;419(1–2):61–74. 10.1016/j.jmb.2012.02.037 PubMed DOI PMC

Zhang J, Jiang CS, Longo JPF, Azevedo RB, Zhang H, Muehlmann LA. An updated overview on the development of new photosensitizers for anticancer photodynamic therapy. Acta Pharm Sin B. 2018;8(2):137–146. 10.1016/j.apsb.2017.09.003 PubMed DOI PMC

Najít záznam

Citační ukazatele

Nahrávání dat ...

    Možnosti archivace