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Publications

2021

  • Adam, S., Wiebeler, C., and Schapiro, I. (2021). Structural factors determining the absorption spectrum of channelrhodopsins: A Case study of the chimera C1C2. J Chem Theory Comput, 17, 10, 6302-6313. doi: 10.1021/acs.jctc.1c00160.

  • Asido, M., Kar, R. K., Kriebel, C. N., Braun, M., Glaubitz, C., Schapiro, I., and Wachtveitl, J. (2021). Transient Near-UV Absorption of the Light-Driven Sodium Pump Krokinobacter eikastus Rhodopsin 2: A Spectroscopic Marker for Retinal Configuration. J Phys Chem Lett, 12, 27, 6284-6291. doi: 10.1021/acs.jpclett.1c01436.

  • Baserga, F., Dragelj, J., Kozuch, J., Mohrmann, H., Knapp, E.-W., Stripp, S. T., and Heberle, J. (2021). Quantification of local electric field changes at the active site of Cytochrome c Oxidase by Fourier transform infrared spectroelectrochemical titrations. Front Chem, 9, 669452. doi: 10.3389/fchem.2021.669452.

  • Bondar, A.-N. (2021). Proton-binding motifs of membrane-bound proteins: From bacteriorhodopsin to spike protein S. Front Chem, 9, 685761. doi: 10.3389/fchem.2021.685761.

  • Dong, P., Stellmacher, J., Bouchet, L.M., Nieke, M., Kumar, A., Osorio-Blanco, E.R., Nagel, G., Lohan, S.B., Teutloff, C., Patzelt, A., Schäfer-Korting, M., Calderón, M., Meinke, M.C., and Alexiev, U. (2021). A Dual Fluorescence-Spin Label Probe for Visualization and Quantification of Target Molecules in Tissue by Multiplexed FLIM – EPR Spectroscopy. Angew Chem Int Ed, 60, 14938. doi: 10.1002/ange.202012852.

  • Dragelj, J., Mroginski, M. A., and Knapp, E.W. (2021). Beating Heart of Cytochrome c Oxidase: The Shared Proton of Heme a3 Propionates. J Phys Chem B, 125, 9668-9677. doi: 10.1021/acs.jpcb.1c03619.

  • 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.

  • Glielmo, A., Husic, B.E., Rodriguez, A., Clementi, C., Noé, F., and Laio, A. (2021). Unsupervised Learning Methods for Molecular Simulation Data. Chem Rev, 121, 16, 9722–9758. doi: 10.1021/acs.chemrev.0c01195.

  • 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.

  • Gonella, G., Backus, E.H.G., Nagata, Y., Bonthuis, D.J., Loche, P., Schlaich, A., Netz, R.R., Kühnle, A., McCrum, I.T., Koper, M.T.M., Wolf, M., Winter, B., Meijer, G., Campen, R.K., and Bonn, M. (2021). Water at charged interfaces. Nat Rev Chem 5, 466–485. doi: 10.1038/s41570-021-00293-2.
  • Hontani, Y., Baloban, M., Escobar, F. V., Jansen, S. A., Shcherbakova, D. M., Weißenborn, J., Kloz, M., Mroginski, M.A., Verkhusha, V. V., and Kennis, J.T.M. (2021). Real-time observation of tetrapyrrole binding to an engineered bacterial phytochrome. Commun Chem, 4, 1-11. doi: 10.1038/s42004-020-00437-3.

  • 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.

  • Juarez, J.F.B., Judge, P.J., Adam, S., Axford, D., Vinals, J., Birch, J., Kwan, T.O.C., Hoi, K.K., Yen, H.-Y., Vial, A., Milhiet, P.-E., Robinson, C.V., Schapiro, I., Moraes, I., and Watts, A. (2021). Structures of the archaerhodopsin-3 transporter reveal that disordering of internal water networks underpins receptor sensitization. Nat Commun 12, 629. doi: 10.1038/s41467-020-20596-0.

  • 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, 11,1 , 1-14. doi: 10.1038/s41598-021-00236-3.

  • Kozuch, J., Schneider, S.H., Zheng, C., Ji, Z., Bradshaw, R.T., and Boxer, S.G. (2021). Testing the limitations of MD-based local electric fields using the vibrational Stark effect in solution: pencillin G as a test case. J Phys Chem B, 125, 4415-4427. doi: 10.1021/acs.jpcb.1c00578.

  • Kraskov, A., Buhrke, D., Scheerer, P., Shaef, I., Sanchez, J.C., Carrillo, M., Noda, M., Feliz, D., Stojković, E.A., and Hildebrandt, P. (2021). On the Role of the Conserved Histidine at the Chromophore Isomerization Site in Phytochromes. J Phys Chem B, 125, 50, 13696-13709. doi: 10.1021/acs.jpcb.1c08245.

  • Kraskov, A., von Sass, J., Nguyen, A.D., Hoang, T.O., Buhrke, D., Katz, S., Michael, N., Kozuch, J., Zebger, I., Siebert, F., Scheerer, P., Mroginski, M.A., Budisa, N., and Hildebrandt P. (2021). Local Electric Field Changes during the Photoconversion of the Bathy Phytochrome Agp2. Biochemistry, 60, 40, 2967-2977. doi: 10.1021/acs.biochem.1c00426.

  • Kruse, F., Nguyen, A.D., Dragelj, J., Heberle, J., Hildebrandt, P., Mroginski, M.A., and Weidinger, I.M. (2021). A Resonance Raman Marker Band Characterizes the Slow and Fast Form of Cytochrome c Oxidase. J Am Chem Soc, 143, 2769-2776. doi: 10.1021/jacs.0c10767.

  • Lamparter, T., Xue, P., Elkurdi, A., Kaeser, G., Sauthof, L., Scheerer, P., and Krauß, N. (2021). Phytochromes in Agrobacterium fabrum. Front Plant Sci, 12, 642801. doi: 10.3389/fpls.2021.642801.

  • Lin, X., George, J.T., Schafer, N.P., Chau, K.N., Birnbaum, M.E., Clementi, C., Onuchic, J.N. and Levine, H. (2021). Rapid assessment of T-cell receptor specificity of the immune repertoire. Nat Comput Sci 1, 362–373. doi: 10.1038/s43588-021-00076-1.

  • Maia, R.N., Ehrenberg, D., Oldemeyer, S., Knieps-Grünhagen, E., Krauss, U., and Heberle, J. (2021). Real-Time Tracking of Proton Transfer from the Reactive Cysteine to the Flavin Chromophore of a Photosensing Light Oxygen Voltage Protein. J Am Chem Soc, 143, 32, 12535–12542. doi: 10.1021/jacs.1c03409.

  • Merga, G., Lopez, M.F., Fischer, P., Piwowarski, P., Nogacz, Ż., Kraskov, A., Buhrke, D., Escobar, F.V., Michael, N., Siebert, F., Scheerer, P., Bartl, F., and Hildebrandt, P. (2021). Light- and temperature-dependent dynamics of chromophore and protein structural changes in bathy phytochrome Agp2. Phys Chem Chem Phys, 23, 33, 18197-18205. doi: 10.1039/d1cp02494a.

  • Mroginski, M.A., Adam, S., Amoyal, G.S., Barnoy, A., Bondar, A.-N., Borin, V.A., Church, J.R., Domratcheva, T., Ensing, B., Fanelli, F., Ferré, N., Filiba, O., Pedraza-González, L., González, R., González-Espinoza, C.E., Kar, R.K., Kemmler, L., Kim, S.S., Kongsted, J., Krylov, A.I., Lahav, Y., Lazaratos, M., NasserEddin, Q., Navizet, I., Nemukhin, A., Olivucci, M., Olsen, J.M.H., Pérez de Alba Ortíz, A., Pieri, E., Rao, A.G., Rhee, Y.M., Ricardi, N., Sen, S., Solov'yov, I.A., De Vico, L., Wesolowski, T.A., Wiebeler, C., Yang, X., and Schapiro, I. (2021). Frontiers in Multiscale Modeling of Photoreceptor Proteins. Photochem Photobiol, 97, 243-269. doi: 10.1111/php.13372.

  • 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.

  • Oda, K., Nomura, T., Nakane, T., Yamashita, K., Inoue, K., Ito, S., Vierock, J., Hirata, K., Maturana, A.D., Katayama, K., Ikuta, T., Ishigami, I., Izume, T., Umeda, R., Eguma, R., Oishi, S., Kasuya, G., Kato, T., Kusakizako, T., Shihoya, W., Shimada, H., Takatsuji, T., Takemoto, M., Taniguchi, R., Tomita, A., Nakamura, R., Fukuda, M., Miyauchi, H., Lee, Y., Nango, E., Tanaka, R., Tanaka, T., Sugahara, M., Kimura, T., Shimamura, T., Fujiwara, T., Yamanaka, Y., Owada, S., Joti, Y., Tono, K., Ishitani, R., Hayashi, S., Kandori, H., Hegemann, P., Iwata, S., Kubo, M., Nishizawa, T., and Nureki, O. (2021). Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin. Elife, 10, e62389. doi: 10.7554/eLife.62389.

  • Riebe, S., Adam, S., Roy, B., Maisuls, I., Daniliuc, C. G., Dubbert, J., Strassert, C.A., Schapiro, I., and Voskuhl, J. (2021). Bridged Aromatic Oxo‐and Thioethers with Intense Emission in Solution and the Solid State. Chem Asian J, 16, 2307-2313. doi: 10.1002/asia.202100492.

  • Siemers, M., and Bondar, A.-N. (2021). Interactive interface for graph-based analyses of dynamic H-bond networks: Application to spike protein S. J Chem Inf Model, 61, 6, 2998–3014. doi: 10.1021/acs.jcim.1c00306.

  • Sokolovski, S.G., Zherebtsov, E.A., Kar, R.K., Golonka, D., Stabel, R., Chichkov, N.B., Gorodetsky, A., Schapiro, I., Möglich, A, and Rafailov, E. U. (2021). Two-photon conversion of a bacterial phytochrome. Biophys J, 120, 5, 964-974. doi: 10.1016/j.bpj.2021.01.028.

  • Theiß, M., Grupe, M., Lamparter, T., Mroginski, M.A., and Diller, R. (2021). Ultrafast proton release reaction and primary photochemistry of phycocyanobilin in solution observed with fs-time-resolved mid-IR and UV/Vis spectroscopy. Photochem Photobiol Sci, 1-18. doi: 10.1007/s43630-021-00045-7.

  • Walter, M., and Schlesinger, R. (2021). Nanodisc Reconstitution of Channelrhodopsins Heterologously Expressed in Pichia pastoris for Biophysical Investigations. In: Dempski R. (eds) Channelrhodopsin. Methods Mol Biol, 2191. Humana, New York, NY. doi: 10.1007/978-1-0716-0830-2_3.

  • Wang, J., Charron, N., Husic, B., Olsson, S., Noé, F., and Clementi, C. (2021). Multi-body effects in a coarse-grained protein force field. J Chem Phys, 154, 164113. doi: 10.1063/5.0041022.

  • Xue, P., Bai, Y., Rottwinkel, G., Averbukh, E., Ma, Y., Roeder, T., Scheerer, P., Krauß, N., and Lamparter, T. (2021). Phytochrome mediated responses in Agrobacterium fabrum: Growth, motility and plant infection. Curr Microbiol, 78, 2708-2719. doi: 10.1007/s00284-021-02526-5.