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Project C4 - terminated 2020

Coupling between protein, water, and protonation dynamics in channelrhodopsin-2 and photosystem II

Principal Investigator: Prof. Dr. Ana-Nicoleta Bondar (FU)

Functionally crucial processes in channelrhodopsin-2 (ChR2) and photosystem II (PSII) involve changes in the protonation states of specific amino acid residues of the protein. The key open question of how changes in protonation couple with both protein conformational dynamics and water dynamics is addressed in C4. Theoretical biophysics techniques are used to study the dynamics of ChR2 and PSII in hydrated lipid membrane environments, probe the response of protein and water dynamics to changes in protonation or mutations, dissect hydrogen-bonded networks and compute proton-transfer pathways.


2017 - 2020

Adam, S., and Bondar A.-N. (2018). Mechanism by which water and protein electrostatic interactions control proton transfer at the active site of channelrhodopsin. PLoS One. 13(8), e0201298. doi: 10.1371/journal.pone.0201298.

Adam S., Knapp-Mohammady M., Yi J., and Bondar A-N. (2017). Revised CHARMM force-field parameters for iron-containing cofactors of photosystem II. Journal of Computational Chemistry 39(1):7-20. doi: 10.1002/jcc.24918

Bondar, A.-N. and Lemieux, J. (2019). Reactions at membrane interfaces. Chemical Reviews. 119, 6162-6183. doi: doi.org/10.1021/acs.chemrev.8b00596.

Bondar A.-N. and Smith J.C. (2017). Protonation-state coupled conformational dynamics in reaction mechanisms of channel and pump rhodopsins. Photochemistry and Photobiology 93, 1336-1344. doi: 10.1111/php.12790

del Val, C. and Bondar, A.-N. (2017). Charged groups at binding interfaces of the PsbO subunit of photosystem II: a combined bioinformatics and simulation study. Biochimica et Biophysica Acta (BBA) - Bioenergetics 1858, 432-441; doi: 10.1016/j.bbabio.2017.03.004

Elghobashi-Meinhardt, N., Phatak, P., Bondar, A.-N., Elstner, M., and Smith, J. C. (2018). Catalysis of ground state cis-trans isomerization of bacteriorhodopsin’s retinal chromophore by a hydrogen-bond network. Journal of Membrane Biology (Topical Collection) 251:315-327. doi:10.1007/s00232-018-0027-x.

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.

Guerra, F., Siemers, M., Mielack, C., and Bondar, A.-N. (2018). Dynamics of Long-Distance Hydrogen-Bond Networks in Photosystem II. Journal of Physical Chemistry B 122, 4625-4641. doi: 10.1021/acs.jpcb.8b00649

Harris, A., Lazaratos, M., Siemers, M., Watt, E., Hoang, A., Tomida, S., Schubert, L., Saita, M., Heberle, J., Furutani, Y., Kandori, H., Bondar, A. N., and Brown, L. S. (2020). Mechanism of Inward Proton Transport in an Antarctic Microbial Rhodopsin. Journal of Physical Chemistry B 124, 4851-4872. doi: 10.1021/acs.jpcb.0c02767

Harris, A., Saita, M., Resler, T., Hughes-Visentin, A., Maia, R., Pranga-Sellnau, F., Bondar, A.-N., Heberle, J., and Brown, L. S. (2018). Molecular details of the unique mechanism of chloride transport by a cyanobacterial rhodopsin. Physical Chemistry Chemical Physics 20, 3184-3199. doi: 10.1039/C7CP06068H

Karathanou, K. and Bondar, A.-N. (2019). Using graphs of dynamic hydrogen bonds to dissect conformational coupling in a protein motor. Journal of Chemical Information and Modeling 59(5), 1882-1896. doi: 10.1021/acs.jcim.8b00979.

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.

Siemers, M., Lazaratos, M., Karathanou, K., Brown, L.S., and Bondar, A.-N. (2019). Bridge: A graph-based algorithm to analyze dynamic H-bond networks in membrane proteins. Journal of Chemical Theory and Computation 15(12), 6781-6798. doi: 10.1021/acs.jctc.9b00697.

2014 - 2016

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.

del Val, C., Bondar, L., and Bondar, A.-N. (2014). Coupling between inter-helical hydrogen bonding and water dynamics in a proton transporter. Journal of Structural Biology 186, 95-111.

del Val, C., Royuela-Flor, J., Milenkovic, S., and Bondar, A.-N. (2014). Channelrhodopsins: A bioinformatics perspective. Biochimica et Biophysica Acta (BBA) - Bioenergetics 1837, 643-655.

Guerra, F., Adam, S., and Bondar, A.-N. (2015). Revised force-field parameters for chlorophyll-a, pheophytin-a and plastoquinone-9. Journal of Molecular Graphics & Modelling 58, 30-39.

Guerra, F., and Bondar, A.-N. (2015). Dynamics of the Plasma Membrane Proton Pump. Journal of Membrane Biology 248, 443-453.

Karge, O., Bondar, A.-N., and Dau, H. (2014). Cationic screening of charged surface groups (carboxylates) affects electron transfer steps in photosystem-II water oxidation and quinone reduction. Biochimica et Biophysica Acta (BBA) - Bioenergetics 1837, 1625-1634.

Lorch, S., Capponi, S., Pieront, F., and Bondar, A.-N. (2015). Dynamic Carboxylate/Water Networks on the Surface of the PsbO Subunit of Photosystem II. Journal of Physical Chemistry B 119, 12172-12181.

Nango A., Royant A., Kubo M., Nakane T., Wickstrand C., Kimura T., Tanaka T., Tono K., Song C., Tanaka R., Arima T., Yamashita A., Kobayashi J., Hosaka T., Mizohata E., Nogly P., Sugahara M., Nam D., Nomura T., Shimamura T., Im D., Fujiwara T., Yamanaka Y., Jeon B., Nishizawa T., Oda K., Fukuda M., Andersson R., Båth P., Dods R., Davidsson J., Matsuoka S., Kawatake S., Murata M., Nureki O., Owada S., Kameshima T., Hatsui T., Joti Y., Schertler G., Yabashi M., Bondar A.-N., Standfuss J., Neutze R., and Iwata S. (2016). A three-dimensional movie of structural changes in bacteriorhodopsin. Science 354, 1552-1557.

Sugihara, M., Suwa, M., and Bondar, A.-N. (2014). Dynamics of bovine opsin bound to G-protein fragments. Journal of Structural Biology 188, 79-86