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Publications

Simulation snapshot for a nm-thick water layer

Simulation snapshot for a nm-thick water layer
Image Credit: APS: Schlaich et al., Phys. Rev. Lett. (2016)

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 Discuss 194, 621-638.

  • Berndt, A., Lee, S.Y., Wietek, J., Ramakrishnan, C., Steinberg, E.E., Rashid, A.J., Kim, H., Park, S., Santoro, A., Frankland, P.W., et al. (2016). Structural foundations of optogenetics: Determinants of channelrhodopsin ion selectivity. Proc Natl Acad Sci USA 113, 822-829.

  • 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.

  • Bonthuis, D.J., Mamatkulov, S., and Netz, R.R. (2016). Optimization of classical nonpolarizable force fields for OH- and H3O+. J Chem Phys 144, 104503.

  • Bonthuis, D.J., Uematsu, Y., and Netz, R.R. (2016). Interfacial layer effects on surface capacitances and electro-osmosis in electrolytes. Phil Trans R Soc A 374, 20150033.

  • Buhrke, D., Velazquez Escobar, F., Sauthof, L., Wilkening, S., Herder, N., Tavraz, N.N., Willoweit, M., Keidel, A., Utesch, T., Mroginski, M.A., Schmitt, F.J., Hildebrandt, P., and Friedrich, T. (2016). The role of local and remote amino acid substitutions for optimizing fluorescence in bacteriophytochromes: A case study on iRFP. Sci Rep 6, 28444.

  • Chernev, P., Zaharieva, I., Rossini, E., Galstyan, A., Dau, H., and Knapp, E.-W. (2016). Merging structural information from X-ray crystallography, quantum chemistry and EXAFS spectra: The oxygen-evolving complex in PSII. J Phys Chem B 120, 10899-10922.

  • Damrow, R., Maldener, I., and Zilliges, Y. (2016).The Multiple Functions of Common Microbial Carbon Polymers, Glycogen and PHB, during Stress Responses in the Non-Diazotrophic Cyanobacterium Synechocystis sp. PCC 6803. Front Microbiol 7, 966.

  • Daldrop, J.O., Kim, W.K., and Netz, R.R. (2016). Transition paths are hot. Europhys Lett 113, 18004.

  • Gerecke, M., Bierhance, G., Gutmann, M., Ernsting, N.P., and Rosspeintner, A. (2016). Femtosecond broadband fluorescence upconversion spectroscopy: spectral coverage versus efficiency. Rev Sci Instrum 87, 053115.

  • González-Flores, D., Zaharieva, I., Heidkamp, J., Chernev, P., Martinez-Moreno, E., Pasquini, C., Mohammadi, M.R., Klingan, K., Gernet, U., Fischer, A., and Dau, H. (2016). Electrosynthesis of biomimetic manganese-calcium oxides for water oxidation catalysis - atomic structure and functionality. ChemSusChem 9, 379-387.

  • Jagtap, A.P., Geiger, M.-A., Stöppler, D., Orwick-Rydmark., M, Oschkinat, H., and Sigurdsson, S.T. (2016). bcTol: A highly water-soluble biradical for efficient dynamic nuclear polarization of biomolecules. ChemComm 52, 7020-7023.

  • Mohrmann, H., Kube, I., Lórenz-Fonfría, V.A., Engelhard, M., and Heberle, J. (2016). Transient Conformational Changes of Sensory Rhodopsin II Investigated by Vibrational Stark Effect Probes. J Phys Chem B 120, 4383-4387.

  • 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.

  • Nagano, S., Scheerer, P., Zubow, K., Michael, N., Inomata, K., Lamparter, T., Krauß, N. (2016). The Crystal Structures of the N-terminal Photosensory Core Module of Agrobacterium Phytochrome Agp1 as Parallel and Anti-parallel Dimers. J Biol Chem 291, 20674-20691.

  • 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.

  • Otero, L.O., Klinke, S., Rinaldi, J., Velazquez Escobar, F., Mroginski, M.A., Fernandez Lopez, M., Malamud, F., Vojnov, A., Hildebrandt, P., Goldbaum, F.A., and Bonomi, H.R. (2016). Structure of the full-length bacteriophytochrome from the plant pathogen Xanthomonas campestris provides clues to its long-range signaling mechanism. J Mol Biol 428, 3702-3720.

  • Reidelbach, M., Betz, F., Mäusle, R. M., and Imhof, P. (2016). Proton transfer pathways in an aspartate-water cluster sampled by a network of discrete states. Chem Phys Lett 659, 169-175.

  • Richter, C., Ernsting, N.P., and Mahrwald, R. (2016). Operationally simple and selective one-pot synthesis of hydroxyl-phenones: a facile access to SNARF dyes. Synthesis 48, 1217-1225.

  • Rossini, E., and Knapp, E.-W. (2016). Proton Solvation in Protic and Aprotic Solvents. J Comput Chem 37, 1082-1091.

  • Rossini, E., and Knapp, E.-W. (2016). Erratum: Proton Solvation in Protic and Aprotic Solvents [J. Comput. Chem. 2015, 37, 1082–1091]. J Comput Chem 37, 2163-2164.

  • Rossini, E., Netz, R.R., and Knapp, E.W. (2016). Computing pKa values in different solvents by electrostatic transformation. J Chem Theory and Comput 12, 3360-3369.

  • Schlaich, A., Knapp, E.W., and Netz, R.R. (2016). Water Dielectric Effects in Planar Confinement. Phys Rev Lett 117, 048001.

  • Schnedermann, C., Muders, V., Ehrenberg, D., Schlesinger, R., Kukura, P., and Heberle, J. (2016). Vibronic Dynamics of the Ultrafast all-trans to 13-cis Photoisomerization of Retinal in Channelrhodopsin-1. J Am Chem Soc 138, 4757-4762.

  • Schwierz, N., Horinek, D., Sivan, U.,and Netz, R.R. (2016). Reversed Hofmeister series - The rule rather than the exception. Curr Opin Colloid Interface Sci. 23, 10-18.

  • Sierra, R.G., Gati, C., Laksmono, H., Dao, E.H., Gul, S., Fuller, F., Kern, J., Chatterjee, R., Ibrahim, M., Brewster, A.S., et al. (2016). Concentric-flow electrokinetic injector enables serial crystallography of ribosome and photosystem II. Nat Methods 13, 59-62.

  • Stensitzki, T., Yang, Y., Berg, A., Mahammed, A., Gross, Z., and Heyne, K. (2016). Ultrafast electronic and vibrational dynamics in brominated aluminum corroles: Energy relaxation and triplet formation. Struct Dyn 3, 043210.

  • Stensitzki, T., Yang, Y., Muders, V., Schlesinger, R., Heberle, J., and Heyne, K. (2016). Femtosecond infrared spectroscopy of channelrhodopsin-1 chromophore isomerization. Struct Dyn 3, 043208.

  • Stöppler, D., Song, C., van Rossum, B.-J., Geiger, M.-A., Lang, C., Mroginski, M.-A., Jagtap, A.P., Sigurdsson, S.T., Matysik, J., Hughes, J., and Oschkinat, H. (2016). Dynamic nuclear polarization provides new insights into chromophore structure in phytochrome photoreceptors. Angew Chem Int Ed 55, 16017–16020, doi: doi: 10.1002/anie.201608119.

  • Süss, B., Ringleb, F., and Heberle, J. (2016). New ultrarapid-scanning interferometer for FT-IR spectroscopy with microsecond time-resolution. Rev Sci Instrum 87, 063113.

  • Volz, P., Krause, N., Balke, J., Schneider, C., Walter, M., Schneider, F., Schlesinger, R., and Alexiev, U. (2016). Light and pH-induced changes in structure and accessibility of transmembrane helix B and its immediate environment in Channelrhodopsin-2. J Biol Chem 291, 17382-17393.

  • Wietek, J., Broser, M., Krause, B.S., and Hegemann, P. (2016). Identification of a Natural Green Light Absorbing Chloride Conducting Channelrhodopsin from Proteomonas sulcata. J Biol Chem 291, 4121-4127.

  • Wolf, A., Schneider, C., Kim, T.Y., Kirchberg, K., Volz, P., and Alexiev, U. (2016). A simulation-guided fluorescence correlation spectroscopy tool to investigate to protonation dynamics of cytrochrome c oxidase. Phys Chem Chem Phys 18, 12877-12885.

  • Yang, Y., Heyne, K., Mathies, R.A., and Dasgupta, J. (2016). Non-Bonded Interactions Drive the Sub-Picosecond Bilin Photoisomerization in the Pfr State of Phytochrome Cph1. ChemPhysChem 17, 369-374.

  • 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.

  • Zaharieva, I., Chernev, P., Berggren, G., Anderlund, M., Styring, S., Dau, H., and Haumann, M. (2016). Room-Temperature Energy-Sampling Kbeta X-ray Emission Spectroscopy of the Mn4Ca Complex of Photosynthesis Reveals Three Manganese-Centered Oxidation Steps and Suggests a Coordination Change Prior to O2 Formation. Biochemistry 55, 4197-4211.

  • Zaharieva, I., Dau, H., and Haumann, M. (2016). Sequential and Coupled Proton and Electron Transfer Events in the S2 --> S3 Transition of Photosynthetic Water Oxidation Revealed by Time-Resolved X-ray Absorption Spectroscopy. Biochemistry 55, 6996-7004.

  • Zaharieva, I., González-Flores, D., Asfari, B., Pasquini, C., Mohammadi, M.R., Klingan, K., Zizak, I., Loos, S., Chernev, P., and Dau, H. (2016). Water oxidation catalysis – role of redox and structural dynamics in biological photosynthesis and inorganic manganese oxides. Energy Environ Sci 9, 2433-2443.

  • Zilliges, Y. and Dau, H. (2016). Unexpected capacity for organic carbon assimilation by Thermosynechococcus elongatus, a crucial photosynthetic model organism. FEBS Lett 590, 962-970.