Structural basis of proton release from the water-oxidizing complex in cyanobacterial photosystem II

Principal Investigators: Prof. Dr. Athina Zouni (HU), Prof. Dr. Holger Dobbek (HU)

The central aim of this project is to resolve the individual mechanistic steps of water oxidation at the Mn₄CaO₅ cluster analyzed by diffraction from femtosecond X-ray laser pulses at room temperature. By synchronizing the light-dependent advance of the reaction with diffraction experiments, unprecedented insights into the individual roles of the metal ions and water ligands could be gained. In the next funding period we want to increase the resolution and resolve the later steps of the Kok cycle, during which dioxygen is formed. This will be supported by using alternative substrates, enzyme variants and complementary methods, such as neutron diffraction.

Publications

2021-2024

Bhowmick, A., Hussein, R., Bogacz, I., Simon, P.S., Ibrahim, M., Chatterjee, R., Doyle, M.D., Cheah, M.H., Fransson, T., Chernev, P., Kim, I.-S., Makita, H., Dasgupta, M., Kaminsky, C.J., Zhang, M., Gätcke, J., Haupt, S., Nangca, I.I., Keable, S.M., Aydin, A.O., Tono, K., Owada, S., Gee, L.B., Fuller, F.D., Batyuk, A., Alonso-Mori, R., Holton, J.M., Paley, D.W., Moriarty, N.W., Mamedov, F., Adams, P.D., Brewster, A.S., Dobbek, H., Sauter, N.K., Bergmann, U., Zouni, A., Messinger, J., Kern, J., Yano, J. and Yachandra, V.K. (2023). Structural evidence for intermediates during O₂ formation in photosystem II. Nature. doi: 10.1038/s41586-023-06038-z.

Bhowmick, A., Simon, P. S., Bogacz, I., Hussein, R., Zhang, M., Makita, H., Ibrahim, M., Chatterjee, R., Doyle, M. D., Cheah, M. H., Chernev, P., Fuller, F. D., Fransson, T., Alonso-Mori, R., Brewster, A. S., Sauter, N. K., Bergmann, U., Dobbek, H., Zouni, A., Messinger, J., Kern, J., Yachandra, V. K. and Yano, J. (2023). Going around the Kok cycle of the water oxidation reaction with femtosecond X-ray crystallography. IUCrJ, 10: 642-655. doi: 10.1107/S205225252300892.

Fransson, T., Alonso-Mori, R., Chatterjee, R., Cheah, M.H., Ibrahim, M., Hussein, R., Zhang, M., Fuller, F., Gul, S., Kim, I.S., Simon, P.S., Bogacz, I., Makita, H., de Lichtenberg, C., Song, S., Batyuk, A., Sokaras, D., Massad, R., Doyle, M., Britz, A., Weninger, C., Zouni, A., Messinger, J., Yachandra, V.K., Yano, J., Kern, J., and Bergmann, U. (2021). Effects of x-ray free-electron laser pulse intensity on the Mn K β _{1, 3} x-ray emission spectrum in photosystem II—A case study for metalloprotein crystals and solutions." Struct Dyn, 8,6, 064302. doi: 10.1063/4.0000130.

Golub, M., Gatcke, J., Subramanian, S., Kolsch, A., Darwish, T., Howard, J.K., Feoktystov, A., Matsarskaia, O., Martel, A., Porcar, L., Zouni, A. and Pieper, J. (2022). "Invisible" Detergents Enable a Reliable Determination of Solution Structures of Native Photosystems by Small-Angle Neutron Scattering. J Phys Chem B, 126, 15: 2824-2833. doi: 10.1021/acs.jpcb.2c01591.

Golub, M., Kölsch, A., Feoktystov, A., Zouni, A., and Pieper, J. (2021). Insights into Solution Structures of Photosynthetic Protein Complexes from Small-Angle Scattering Methods. Crystals, 11, 203. doi: 10.3390/cryst11020203.

Hussein, R., Graca, A., Forsman, J., Aydin, A.O., Hall, M., Gaetcke, J., Chernev, P., Wendler, P., Dobbek, H., Messinger, J., Zouni, A. and Schröder, W.P. (2024). Cryo-electron microscopy reveals hydrogen positions and water networks in photosystem II. Science, 384, 6702: 1349-1355. doi: 10.1126/science.adn6541.

Hussein, R., Ibrahim, M., Bhowmick, A., Simon, P.S., Bogacz, I., Doyle, M.D., Dobbek, H., Zouni, A., Messinger, J., Yachandra, V.K., Kern, J.F. and Yano, J. (2023). Evolutionary diversity of proton and water channels on the oxidizing side of photosystem II and their relevance to function. Photosynth Res. doi: 10.1007/s11120-023-01018-w.

Hussein, R., Ibrahim, M., Bhowmick, A., Simon, P.S., Chatterjee, R., Lassalle, L., Doyle, M., Bogacz, I., Kim, I.-S., Cheah, M.H., Gul, S., de Lichtenberg, C., Chernev, P., Pham, C.C., Young, I.D., Carbajo, S., Fuller, F.D., Alonso-Mori, R., Batyuk, A., Sutherlin, K.D., Brewster, A.S., Bolotovsky, R., Mendez, D., Holton, J.M., Moriarty, N.W., Adams, P.D., Bergmann, U., Sauter, N.S., Dobbek, H., Messinger, J., Zouni, A., Kern, J., Yachandra, V.K., and Yano, J. (2021). Structural dynamics in the water and proton channels of photosystem II during the S₂ to S₃ transition. Nat Commun, 12, 6531. doi: 10.1038/s41467-021-26781-z.

Ibrahim, M., Moriarty, N.W., Kern, J., Holton, J.M., Brewster, A.S., Bhowmick, A., Bergmann, U., Zouni, A., Messinger, J., Yachandra, V.K., Yano, J., Dobbek, H., Sauter, N.K., and Adams, P.D. (2021). Reply to Wang et al.: Clear evidence of binding of Ox to the oxygen-evolving complex of photosystem II is best observed in the omit map. PNAS, 118, e2102342118. doi: 10.1073/pnas.2102342118.

Keable, S.M., Kölsch, A., Simon, P.S., Dasgupta, M., Chatterjee, R., Subramanian, S.K., Hussein, R., Ibrahim, M., Kim, I.S., Bogacz, I., Makita, H., Pham, C.C., Fuller, F.D., Gul, S., Paley, D., Lassalle, L., Sutherlin, K.D., Bhowmick, A., Moriarty, N.W., Young, I.D., Blaschke, J.P., de Lichtenberg, C., Chernev, P., Cheah, M.H., Park, S., Park, G., Kim, J., Lee, S.J., Park, J., Tono, K., Owada, S., Hunter, M.S., Batyuk, A., Oggenfuss, R., Sander, M., Zerdane, S., Ozerov, D., Nass, K., Lemke, H., Mankowsky, R., Brewster, A.S., Messinger, J., Sauter, N.K., Yachandra, V.K., Yano, J., Zouni, A., and Kern, J. (2021). Room temperature XFEL crystallography reveals asymmetry in the vicinity of the two phylloquinones in photosystem I. Sci Rep, 11, 21787. doi: 10.1038/s41598-021-00236-3.

Morlock, S., Subramanian, S.K., Zouni, A. and Lisdat, F. (2023). Closing the green gap of photosystem I with synthetic fluorophores for enhanced photocurrent generation in photobiocathodes. Chem. Sci. doi: 10.1039/D2SC05324A.

Morlock, S., Subramanian, S. K., Zouni, A., and Lisdat, F. (2021). Scalable Three-Dimensional Photobioelectrodes Made of Reduced Graphene Oxide Combined with Photosystem I. ACS Applied Materials & Interfaces, 13, 9: 11237-11246. doi: 10.1021/acsami.1c01142.

Müh, F., Bothe, A. and Zouni, A. (2024). Towards understanding the crystallization of photosystem II: influence of poly(ethylene glycol) of various molecular sizes on the micelle formation of alkyl maltosides. Photosynth Res. doi:10.1007/s11120-024-01079-5.

Simon, P.S., Makita, H., Bogacz, I., Fuller, F., Bhowmick, A., Hussein, R., Ibrahim, M., Zhang, M., Chatterjee, R., Cheah, M.H., Chernev, P., Doyle, M.D., Brewster, A.S., Alonso-Mori, R., Sauter, N.K., Bergmann, U., Dobbek, H., Zouni, A., Messinger, J., Kern, J., Yachandra, V.K. and Yano, J. (2022). Capturing the sequence of events during the water oxidation reaction in photosynthesis using XFELs. FEBS Letters. doi: 10.1002/1873-3468.14527.

2017-2020

Chatterjee, R., Lasalle, L., Gul, S., Fuller, F.D., Young, I.D., Ibrahim, M., de Lichtenberg, C., Cheah, M.H., Zouni, A., Messinger, J., Yachandra, V.K., Kern, J., and Yano, J. (2019). Structural isomers of the S2 state in photosystem II: do they exist at room temperature and are they important for function? Physiol Plant. 166(1):60-72, doi: doi.org/10.1111/ppl.12947.

Fuller, F. D., Gul, S., Chatterjee, R., Burgie, E. S., Young, I. D., Lebrette, H., Srinivas, V., Brewster, A.S., Michels-Clark, T., Clinger, J. A., Andi, B., Ibrahim, M., Pastor, E., de Lichtenberg, C., Hussein, R., Pollock, C. J., Zhang, M., Stan, C. A., Kroll, T., Fransson, T., Weninger, C., Kubin, M., Aller, P., Lassalle, L., Brauer, P., Miller, M. D., Amin, M., Koroidov, S., Roessler, C. G., Allaire, M., Sierra, R. G., Docker, P. T., Glownia, J. M., Nelson, S., Koglin, J. E., Zhu, D., Chollet, M., Song, S., Lemke, H., Liang, M., Sokaras, D., Alonso-Mori, R., Zouni, A., Messinger, J., Bergmann, U., Boal, A. K., Bollinger Jr, J. M., Krebs, C., Hogbom, M., Phillips Jr, G. N., Vierstra, R. D., Sauter, N. K., Orville, A. M., Kern, J., Yachandra, V. K., and Yano, J. (2017). Drop-on-demand sample delivery for studying biocatalysts in action at X-ray free-electron lasers. Nature Meth. 4, 443-449; doi: 10.1038/nmeth.4195

Gerland, L.M., Friedrich, D., Hopf, L., Donovan, E., Wallmann, A., Erdmann, N., Diehl, A., Bommer, M., Buzar, K., Ibrahim, M., Schmieder, P., Dobbek, H., Zouni, A., Bondar, A.-N., Dau, H., and Oschkinat, H. (2020). pH‐Dependent Protonation of Surface Carboxylates in PsbO Enables Local Buffering and Triggers Structural Changes. ChemBioChem 21, 1597-1604. doi: 10.1002/cbic.201900739.

Han, R., Rempfer, K., Zhang, M., Dobbek, H., Zouni, A., Dau, H., Luber, S. (2019) Investigating the Structure and Dynamics of Apo‑Photosystem II. ChemCatChem 11, 4072–4080.doi: 10.1002/cctc.201900351.

Hussein, R., Ibrahim, M., Chatterjee, R., Coates, L., Muh, F., Yachandra, V. K., Yano, J., Kern, J., Dobbek, H., Zouni, A. (2018). Optimizing Crystal Size of Photosystem II by Macroseeding: Toward Neutron Protein Crystallography. Cryst Growth Des 18, 85-94; doi: 10.1021/acs.cgd.7b00878

Ibrahim, M., Fransson, T., Chatterjee, R., Cheah, M. H., Hussein, R., Lassalle, L., Sutherlin, K. D., Young, I. D., Fuller, F. D., Gul, S., Kim, I.-S., Simon, P. S., de Lichtenberg, C., Chernev, P., Bogacz, I., Pham, C. C., Orville, A. M., Saichek, N., Northen, T., Batyuk, A., Carbajo, S., Alonso-Mori, R., Tono, K., Owada, S., Bhowmick, A., Bolotovsky, R., Mendez, D., Moriarty, N. W., Holton, J. M., Dobbek, H., Brewster, A. S., Adams, P. D., Sauter, N. K., Bergmann, U., Zouni, A., Messinger, J., Kern, J., Yachandra, V. K., and Yano, J. (2020). Untangling the sequence of events during the S2 → S3 transition in photosystem II and implications for the water oxidation mechanism. PNAS 117, 12624-12635. doi: 10.1073/pnas.2000529117

Kemmler, L., Ibrahim, M., Dobbek, H., Zouni, A., and Bondar, A.-N. (2019). Dynamic water bridging and proton transfer at a surface carboxylate cluster of photosystem II. Physical Chemistry Chemical Physics 21(45), 25449-25466, doi: 10.1039/C9CP03926k.

Kern, J., Chatterjee, R., Young, I. D., Fuller, F. D., Lassalle, L., Ibrahim, M., Gul, S., Fransson, T., Brewster, A. S., Alonso-Mori, R., Hussein, R., Zhang, M., Douthit, L., de Lichtenberg, C., Cheah, M. H., Shevela, D., Wersig, J., Seuffert, I., Sokaras, D., Pastor, E., Weninger, C., Kroll, T., Sierra, R. G., Aller, P., Butryn, A., Orville, A. M., Liang, M., Batyuk, A., Koglin, J. E., Carbajo, S., Boutet, S., Moriarty, N. W., Holton, J. M., Dobbek, H., Adams, P. D., Bergmann, U., Sauter, N. K., Zouni, A., Messinger, J., Yano, J., and Yachandra, V. K. (2018). Structures of the intermediates of Kok's photosynthetic water oxidation clock. Nature 563, 421-425; doi:10.1038/s41586-018-0681-2.

Kern, J., Müh, F., Zouni, A. (2019). Structural studies on tetrapyrrole containing proteins enabled by femtosecond X-ray pulses. In: Grimm B, Ed (2019). Metabolsm, structure and function of plant tetrapyrroles: Control mechanisms of chlorophyll biosynthesis and analysis of chlorophyll-binding proteins. Advances in Botanical Research, vol 91. pp. 33-67; doi: 10.1016/bs.abr.2019.04.003

Kielb, P., Utesch, T., Kozuch, J., Jeoung, J.-H., Dobbek, H., Mroginski, M.A., Hildebrandt, P., and Weidinger, I. (2017). Switchable Redox Chemistry of the Hexameric Tyrosine-Coordinated Heme Protein. Journal of Physical Chemistry B 121, 3955-3964; doi: 10.1021/acs.jpcb.7b01286

Müh, F., and Zouni, A. (2020). Structural basis of the light-harvesting in the photosystem II core complex. Protein Sci. 29(5):1090-1119; doi: 10.1002/pro.3841.

Riedel, M., Wersig, J., Ruff, A., Schuhmann, W., Zouni, A., and Lisdat, F. (2019). A Z‐scheme‐inspired photobioelectrochemical H₂O/O₂ cell with a 1 V open‐circuit voltage combining photosystem II and PbS quantum dots. Angewandte Chemie - International Edition 58, 801-805; doi: 10.1002/anie.201811172

Sidabras, J. W., Duan, J. Winkler, M., Happe, T., Hussein, R., Zouni, A., Suter, D., Schnegg, A., Lubitz, W., Reijerse, E. J. (2019). Extending electron paramagnetic resonance to nanoliter volume protein single crystals using a self-resonant microhelix. Sci. Adv 5, No 10; doi: 10.1126/sciadv.aay1394.

Sullivan, B., Archibald, R., Langan, P. S., Dobbek, H., Bommer, M., McFeeters, R. L., Coates, L., Wang, X., Gallmeier, F., Carpenter, J. M., Lynch, V., and Langan, P. (2018). Improving the accuracy and resolution of neutron crystallographic data by three-dimensional profile fitting of Bragg peaks in reciprocal space. Acta Crystallogr D Struct Biol 74, 1085-1095; doi: 10.1107/S2059798318013347

Zhang, M., Bommer, M., Chatterjee, R., Hussein, R., Yano, J., Dau, H., Kern, J., Dobbek, H., and Zouni, A. (2017). Structural insights into the light-driven auto-assembly process of the wateroxidizing Mn₄CaO₅- cluster in photosystem II. eLife 6; doi: 10.7554/eLife.26933

2013 - 2016

Alonso-Mori, R., Asa, K., Bergmann, U., Brewster, A.S., Chatterjee, R., Cooper, J.K., Frei, M., Fuller, F.D., Goggins, E., Gul, S., Fukuzawa, H., Iablonsky, D., Ibrahim, M., Katayamaj, T., Kroll, T., Kumagai, Y., McClure, B.A., Messinger, J., Motomura, K., Nagaya, K., Nishiyama, T., Saracini, C., Sato, Y., Sauter, N.K., Sokaras, D., Takanashi, T., Togashi, T., Ueda, K., Weare, W.W., Weng, T.-C., Yabashi, M., Yachandra, V.K., Young, I.D., Zouni, A., Kern, J.F. and Yano, J. (2016). Towards Characterization of Photo-Excited Electron Transfer and Catalysis in Natural and Artificial Systems Using XFELs. Faraday Discussions, The Royal Society of Chemistry 194, 621-638.

Bommer, M., Bondar, A.-N., Zouni, A., Dobbek, H., and Dau, H. (2016). Crystallographic and computational analysis of the barrel part of the PsbO protein of photosystem II - carboxylate-water clusters as putative proton transfer relays and structural switches. Biochemistry 55, 4626-4635.

Brecht, M., Skandary, S., Hellmich, J., Gloeckner, C., Konrad, A., Hussels, M., Meixner, A.J., Zouni, A., and Schlodder, E. (2014). Spectroscopic properties of photosystem II core complexes from Thermosynechococcus elongatus revealed by single-molecule experiments. Biochimica et Biophysica Acta (BBA) - Bioenergetics 1837, 773-781.

Glockner, C., Kern, J., Broser, M., Zouni, A., Yachandra, V., and Yano, J. (2013). Structural Changes of the Oxygen-evolving Complex in Photosystem II during the Catalytic Cycle. Journal of Biological Chemistry 288, 22607-22620.

Hellmich, J., Bommer, M., Burkhardt, A., Ibrahim, M., Kern, J., Meents, A., Müh, F., Dobbek, H., and Zouni, A. (2014). Native-like Photosystem II Superstructure at 2.44 Å Resolution through Detergent Extraction from the Protein Crystal. Structure 22, 1607-1615. [Link to news section.]

Ibrahim, M., Chatterjee, R., Hellmich, J., Tran, R., Bommer, M., Yachandra, V.K., Yano, J., Kern, J., and Zouni, A. (2015). Improvements in serial femtosecond crystallography of photosystem II by optimizing crystal uniformity using microseeding procedures. Structural Dynamics 2, 041705.

Kern, J., Alonso-Mori, R., Tran, R., Hattne, J., Gildea, R.J., Echols, N., Gloeckner, C., Hellmich, J., Laksmono, H., Sierra, R.G., et al. (2013). Simultaneous Femtosecond X-ray Spectroscopy and Diffraction of Photosystem II at Room Temperature. Science 340, 491-495.

Kern, J., Tran, R., Alonso-Mori, R., Koroidov, S., Echols, N., Hattne, J., Ibrahim, M., Gul, S., Laksmono, H., Sierra, R.G., et al. (2014). Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy. Nature Communications 5, 4371.

Müh, F., DiFiore, D., and Zouni, A. (2015). The influence of poly(ethylene glycol) on the micelle formation of alkyl maltosides used in membrane protein crystallization. Physical Chemistry Chemical Physics 17, 11678-11691.

Müh, F., and Zouni, A. (2016). Cytochrome b₅₅₉ in photosystem II. In: William A. Cramer, Toivo Kallas (ed.) Cytochrome Complexes: Evolution, Structures, Energy Transduction, and Signaling. Volume 41 of the series Advances in Photosynthesis and Respiration, 143-175.

Müh, F., and Zouni, A. (2013). The nonheme iron in photosystem II. Photosynthesis Research 116, 295-314.

Sierra, R.G., Gati, C., Laksmono, H., Dao, E.H., Gul, S., Fuller, F., Kern, J., Chatterjee, R., Ibrahim, M., Brewster, A.S., Young, I.D., Michels-Clark, T., Aquila, A., Liang, M., Hunter, M.S., Koglin, J.E., Boutet, S., Junco, E.A., Hayes, B., Bogan, M.J., Hampton, C.Y., Puglisi, E.V., Sauter, N.K., Stan, C.A., Zouni, A., Yano, J., Yachandra, V.K., Soltis, S.M., Puglisi, J.D., and DeMirci, H. (2016). Concentric-flow electrokinetic injector enables serial crystallography of ribosome and photosystem II. Nat. Methods 13, 59-62.

Skandary, S., Hussels, M., Konrad, A., Renger, T., Müh, F., Bommer, M., Zouni, A., Meixner, A.J., and Brecht, M. (2015). Variation of Exciton-Vibrational Coupling in Photosystem II Core Complexes from Thermosynechococcus elongatus As Revealed by Single-Molecule Spectroscopy. Journal of Physical Chemistry B 119, 4203-4210.

Tran, R., Kern, J., Hattne, J., Koroidov, S., Hellmich, J., Alonso-Mori, R., Sauter, N.K., Bergmann, U., Messinger, J., Zouni, A., et al. (2014). The Mn4Ca photosynthetic water-oxidation catalyst studied by simultaneous X-ray spectroscopy and crystallography using an X-ray free-electron laser. Philosophical Transactions of the Royal Society B-Biological Sciences 369, 20130324.

Young, I.D., Ibrahim, M., Chatterjee, R., Gul, S., Fuller, F.D., Koroidov, S., Brewster, A.S., Tran, R., Alonso-Mori, R., Kroll, T., Michels-Clark, T., Laksmono, H., Sierra, R.G., Stan, C.A., Hussein, R., Zhang, M., Douthit, L., Kubin, M., de Lichtenberg, C., Vo Pham, L., Nilsson, H., Hon Cheah, M., Shevela, D., Saracini, C., Bean, M.A., Seuffert, I., Sokaras, D., Weng, T.-C., Pastor, E., Weninger, C., Fransson, T., Lassalle, L., Bräuer, P., Aller, P., Docker, P.T., Andi, B., Orville, A.M., Glownia, J.M., Nelson, S., Sikorski, M., Zhu, D., Hunter, M.S., Lane, T.J., Aquila, A., Koglin, J.E., Robinson, J., Liang, M., Boutet, S., Lyubimov, A.Y., Uervirojnangkoorn, M., Moriarty, N.W., Liebschner, D., Afonine, P.V., Waterman, D.G., Evans, G., Wernet, P., Dobbek, H., Weis, W.I., Brunger, A.T., Zwart, P.H., Adams, P.D., Zouni, A., Messinger, J., Bergmann, U., Sauter, N.K., Kern, J., Yachandra, V.K., and Yano, J. (2016). Structure of photosystem II and substrate binding at room temperature. Nature 540, 453-457.