Publications of the Max Planck Institute of Biophysics 1947 – present

Journal Article (56)

2014

Journal Article

Paulino, C.; Wöhlert, D.; Kapotova, E.; Yildiz, Ö.; Kühlbrandt, W.: Structure and transport mechanism of the sodium/proton antiporter MjNhaP1. eLife 3, e03583 (2014)

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Wöhlert, D.; Kühlbrandt, W.; Yildiz, Ö.: Structure and substrate ion binding in the sodium/proton antiporter PaNhaP. eLife 3, e03579 (2014)

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Nedialkova, L. V.; Amat, M. A.; Kevrekidis, I. G.; Hummer, G.: Diffusion maps, clustering and fuzzy Markov modeling in peptide folding transitions. The Journal of Chemical Physics 141 (11), pp. 114102 - 114117 (2014)

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Busch, A. P.; Rhinow, D.; Yang, F.; Reinhardt, H.; Beyer, A.; Gölzhäuser, A.; Hampp, N.: Site-selective biomineralization of native biological membranes. Journal of Materials Chemistry B 2, pp. 6924 - 6930 (2014)

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Hummer, G.: Potassium ions line up. Do K⁺ ions move in single file through potassium channels? Science Magazine 346 (6207), p. 303 - 303 (2014)

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Patwardhan, A.; Ashton, A.; Brandt, R.; Butcher, S.; Carzaniga, R.; Chiu, W.; Collison, L.; Doux, P.; Duke, E.; Ellisman, M. H. et al.; Franken, E.; Grünewald, K.; Heriche, J.-K.; Koster, A.; Kühlbrandt, W.; Lagerstedt, I.; Larabell, C.; Lawson, C. L.; Saibil, H. R.; Sanz-García, E.; Subramaniam, S.; Verkade, P.; Swedlow, J. R.; Kleywegt, G. J.: A 3D cellular context for the macromolecular world. Nature Structural and Molecular Biology 21 (10), pp. 841 - 845 (2014)

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Johnson, M. E.; Hummer, G.: Free-Propagator Reweighting Integrator for Single-Particle Dynamics in Reaction-Diffusion Models of Heterogeneous Protein-Protein Interaction Systems. Physical Review X 4 (3), pp. 031037 - 031058 (2014)

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Mantsyzov, A. B.; Maltsev, A. S.; Ying, J.; Shen, Y.; Hummer, G.; Bax, A.: A maximum entropy approach to the study of residue-specific backbone angle distributions in α-synuclein, an intrinsically disordered protein. Protein Science 23 (9), pp. 1275 - 1290 (2014)

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Poppe, J.; Warkentin, E.; Demmer, U.; Kowalewski, B.; Dierks, T.; Schneider, K.; Ermler, U.: Structural diversity of polyoxomolybdate clusters along the three-fold axis of the molybdenum storage protein. Journal of Inorganic Biochemistry 138, pp. 122 - 128 (2014)

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Fenollar-Ferrer, C.; Stockner, T.; Schwarz, T. C.; Pal, A.; Gotovina, J.; Hofmaier, T.; Jayaraman, K.; Adhikary, S.; Kudlacek, O.; Mehdipour, A. R. et al.; Tavoulari, S.; Rudnick, G.; Singh, S. K.; Konrat, R.; Sitte, H. H.; Forrest, L. R.: Structure and Regulatory Interactions of the Cytoplasmic Terminal Domains of Serotonin Transporter. Biochemistry 53 (33), pp. 5444 - 5460 (2014)

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Calinescu, O.; Danner, E.; Böhm, M.; Hunte, C.; Fendler, K.: Species differences in bacterial NhaA Na⁺/H⁺ exchangers. FEBS Letters 588 (17), pp. 3111 - 3116 (2014)

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Fujishiro, T.; Ermler, U.; Shima, S.: A possible iron delivery function of the dinuclear iron center of HcgD in [Fe]-hydrogenase cofactor biosynthesis. FEBS Letters 588 (17), pp. 2789 - 2793 (2014)

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Kühlbrandt, W.: Microscopy: Cryo-EM enters a new era. eLife 3, e03678 (2014)

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Meyer, T.; Melin, F.; Xie, H.; von der Hocht, I.; Choi, S. K.; Noor, M. R.; Michel, H.; Gennis, R. B.; Soulimane, T.; Hellwig, P.: Evidence for Distinct Electron Transfer Processes in Terminal Oxidases from Different Origin by Means of Protein Film Voltammetry. Journal of the American Chemical Society 136 (31), pp. 10821 - 11196 (2014)

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Aktas, M.; Köster, S.; Kizilirmak, S.; Casanova, J. C.; Betz, H.; Fritz, C.; Moser, R.; Yildiz, Ö.; Narberhaus, F.: Enzymatic properties and substrate specificity of a bacterial phosphatidylcholine synthase. The FEBS Journal 281 (15), pp. 3523 - 3541 (2014)

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Salzer, R.; Kern, T.; Joos, F.; Averhoff, B.: Environmental factors affecting the expression of type IV pilus genes as well as piliation of Thermus thermophilus. FEMS Microbiology Letters 357 (1), pp. 56 - 62 (2014)

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Vitt, S.; Ma, K.; Warkentin, E.; Moll, J.; Pierik, A. J.; Shima, S.; Ermler, U.: The F₄₂₀-Reducing [NiFe]-Hydrogenase Complex from Methanothermobacter marburgensis, the First X-ray Structure of a Group 3 Family Member. Journal of Molecular Biology (London) 426 (15), pp. 2813 - 2826 (2014)

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Perez, C.; Faust, B.; Mehdipour, A. R.; Francesconi, K. A.; Forrest, L. R.; Ziegler, C.: Substrate-bound outward-open state of the betaine transporter BetP provides insights into Na⁺ coupling. Nature Communications 5, 4231 (2014)

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Lentes, C. J.; Mir, S. H.; Boehm, M.; Ganea, C.; Fendler, K.; Hunte, C.: Molecular Characterization of the Na⁺H⁺-Antiporter NhaA from Salmonella Typhimurium. PLoS One 9 (7), pp. 1 - 8 (2014)

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Gold, V. A. M.; Ieva, R.; Walter, A.; Pfanner, N.; van der Laan, M.; Kühlbrandt, W.: Visualizing active membrane protein complexes by electron cryotomography. Nature Communications 5, 4129 (2014)

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Naß, B.; Pöll, U.; Langer, J. D.; Kreuter, L.; Küper, U.; Flechsler, J.; Heimerl, T.; Rachel, R.; Huber, H.; Kletzin, A.: Three multihaem cytochromes c from the hyperthermophilic archaeon Ignicoccus hospitalis: purification, properties and localization. Microbiology/SGM 160 (6), pp. 1278 - 1289 (2014)

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Preiss, L.; Langer, J. D.; Hicks, D. B.; Liu, J.; Yildiz, Ö.; Krulwich, T. A.; Meier, T.: The c-ring ion binding site of the ATP synthase from Bacillus pseudofirmus OF4 is adapted to alkaliphilic lifestyle. Molecular Microbiology 92 (5), pp. 973 - 984 (2014)

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Sand, M.; Stahl, J.; Waclawska, I.; Ziegler, C.; Averhoff, B.: Identification of an osmo-dependent and an osmo-independent choline transporter in Acinetobacter baylyi: implications in osmostress protection and metabolic adaptation. Environmental Microbiology 16 (6), pp. 1490 - 1502 (2014)

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Kaila, V. R.I.; Wikström, M.; Hummer, G.: Electrostatics, hydration, and proton transfer dynamics in the membrane domain of respiratory complex I. Proceedings of the National Academy of Sciences of the United States of America 111 (19), pp. 6988 - 6993 (2014)

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Journal Article

Călinescu, O.; Paulino, C.; Kühlbrandt, W.; Fendler, K.: Keeping It Simple, Transport Mechanism and pH Regulation in Na⁺/H⁺. The Journal of Biological Chemistry 289, pp. 13168 - 13176 (2014)

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Bamann, C.; Bamberg, E.; Wachtveitl, J.; Glaubitz, C.: Proteorhodopsin. Biochimica et Biophysica Acta, Bioenergetics 1837 (5), pp. 614 - 625 (2014)

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Tufar, P.; Rahighi, S.; Kraas, F. I.; Kirchner, D. K.; Löhr, F.; Henrich, E.; Koepke, J.; Dikic, I.; Güntert, P.; Marahiel, M. A. et al.; Dötsch, V.: Crystal Structure of a PCP/Sfp Complex Reveals the Structural Basis for Carrier Protein Posttranslational Modification. Chemistry & Biology 21 (4), pp. 431 - 562 (2014)

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Stamm, M.; Staritzbichler, R.; Khafizov, K.; Forrest, L. R.: AlignMe-a membrane protein sequence alignment web server. Nucleic Acids Research 42 (W1), pp. W246 - W251 (2014)

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Alkoby, D.; Rimon, A.; Burdak, M.; Patino-Ruiz, M.; Calinescu, O.; Fendler, K.; Padan, E.: NhaA Na⁺/H⁺ Antiporter Mutants That Hardly React to the Membrane Potential. PLoS One 9 (4), p. e93200 - e93200 (2014)

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Buschmann, S.; Richers, S.; Ermler, U.; Michel, H.: A decade of crystallization drops: Crystallization of the cbb₃ cytochrome c oxidase from Pseudomonas stutzeri. Protein Science 23 (4), pp. 411 - 422 (2014)

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Kaila, V. R.I.; Schotte, F.; Cho, H. S.; Hummer, G.; Anfinrud, P. A.: Contradictions in X-ray structures of intermediates in the photocycle of photoactive yellow protein. Nature Chemistry 6 (4), pp. 258 - 259 (2014)

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Kühlbrandt, W.: The Resolution Revolution. Science 343 (6178), pp. 1443 - 1444 (2014)

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Fenollar-Ferrer, C.; Patti, M.; Knöpfel, T.; Werner, A.; Forster, I. C.; Forrest, L. R.: Structural Fold and Binding Sites of the Human Na⁺-Phosphate Cotransporter NaPi-II. Biophysical Journal 106 (6), pp. 1268 - 1279 (2014)

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Journal Article

Hernandez, V. H.; Gehrt, A.; Reuter, K.; Jing, Z.; Jeschke, M.; Mendoza Schulz, A.; Hoch, G.; Bartels, M.; Vogt, G.; Garnham, C. W. et al.; Yawo, H.; Fukazawa, Y.; Augustine, G. J.; Bamberg, E.; Kügler, S.; Salditt, T.; de Hoz, L.; Strenzke, N.; Moser, T.: Optogenetic stimulation of the auditory pathway. The Journal of Clinical Investigation 124 (3), pp. 1114 - 1129 (2014)

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Rosta, E.; Yang, W.; Hummer, G.: Calcium Inhibition of Ribonuclease H1 Two-Metal Ion Catalysis. Journal of the American Chemical Society 136 (8), pp. 3137 - 3144 (2014)

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Journal Article

Allegretti, M.; Mills, D. J.; McMullen, G.; Kühlbrandt, W.; Vonck, J.: Atomic model of the F₄₂₀-reducing [NiFe] hydrogenase by electron cryo-microscopy using a direct electron detector. eLife 3, e01963 (2014)

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Chowdhury, N. P.; Mowafy, A. M.; Demmer, J. K.; Upadhyay, V.; Koelzer, S.; Jayamani, E.; Kahnt, J.; Hornung, M.; Demmer, U.; Ermler, U. et al.; Buckel, W.: Studies on the Mechanism of Electron Bifurcation Catalyzed by Electron Transferring Flavoprotein (Etf) and Butyryl-CoA Dehydrogenase (Bcd) of Acidaminococcus fermentans. The Journal of Biological Chemistry 289 (8), pp. 5145 - 5157 (2014)

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Journal Article

Murphy, B. J.; Sargent, F.; A. Armstrong, F.: Transforming an oxygen-tolerant [NiFe] uptake hydrogenase into a proficient, reversible hydrogen producer. Energy & Environmental Science 7 (4), pp. 1426 - 1433 (2014)

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Full

Journal Article

Paulino, C.; Kühlbrandt, W.: pH- and sodium-induced changes in a sodium/proton antiporter. eLife 3, e01412 (2014)

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Journal Article

Kaur, J.; Olkhova, E.; Malviya, V. N.; Grell, E.; Michel, H.: A L-Lysine Transporter of High Stereoselectivity of the Amino Acid-Polyamine-Organocation (APC) Superfamily PRODUCTION, FUNCTIONAL CHARACTERIZATION, AND STRUCTURE MODELING. The Journal of Biological Chemistry 289 (3), pp. 1377 - 1387 (2014)

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Journal Article

Herrmann, J.; Berberich, H.; Hartmann, J.; Beyer, S.; Davies, K.; Koch, J.: Homo-oligomerization of the Activating Natural Killer Cell Receptor NKp30 Ectodomain Increases Its Binding Affinity for Cellular Ligands. The Journal of Biological Chemistry 289 (2), pp. 765 - 777 (2014)

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Journal Article

Ceballos, J. A.; Giraldo, M. A.; Cossio, P.: Effects of a disulfide bridge prior to amyloid formation of the ABRI peptide. RSC Advances 4, pp. 36923 - 36928 (2014)

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Journal Article

Daum, B.; Quax, T. E. F.; Sachse, M.; Mills, D. J.; Reimann, J.; Yildiz, Ö.; Häder, S.; Saveanu, C.; Forterre, P.; Albers, S.-V. et al.; Kühlbrandt, W.; Prangishvili, D.: Self-assembly of the general membrane-remodeling protein PVAP into sevenfold virus-associated pyramids. Proceedings of the National Academy of Sciences of the United States of America 111 (10), pp. 3829 - 3834 (2014)

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Journal Article

Davies, K. M.; Daum, B.; Gold, V. A. M.; Mühleip, A. W.; Brandt, T.; Blum, T.; Mills, D. J.; Kühlbrandt, W.: Visualization of ATP Synthase Dimers in Mitochondria by Electron Cryo-tomography. Journal of Visualized Experiments (91 doi: 10.3791/51228), e51228 (2014)

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Journal Article

Hummer, G.; Dellago, C.: Computing Equilibrium Free Energies Using Non-Equilibrium Molecular Dynamics. Entropy 16 (1), pp. 41 - 61 (2014)

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Journal Article

Imhof, M.; Rhinow, D.; Hampp, N.: Two-photon polarization data storage in bacteriorhodopsin films and its potential use in security applications. Applied Physics Letters 104, 081921 (2014)

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Keller, R.; Ziegler, C.; Schneider, D.: When two turn into one: evolution of membrane transporters from half modules. Biological Chemistry 395 (12), pp. 1379 - 1388 (2014)

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Köster, S.; van Pee, K.; Hudel, M.; Leustik, M.; Rhinow, D.; Kühlbrandt, W.; Chakraborty, T.: Crystal structure of listeriolysin O reveals molecular details of oligomerization and pore formation. Nature Communications 5, 3690 (2014)

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Matthies, D.; Zhou, W.; Klyszejko, A. L.; Anselmi, C.; Yildiz, Ö.; Brandt, K.; Müller, V.; Faraldo-Gómez, J. D.; Faraldo-Gómez, J. D.; Meier, T.: High-resolution structure and mechanism of an F/V-hybrid rotor ring in a Na⁺-coupled ATP synthase. Nature Communications 5, 5286 (2014)

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Journal Article

Mourier, A.; Ruzzenente, B.; Brandt, T.; Kühlbrandt, W.; Larsson, N.-G.: Loss of LRPPRC causes ATP synthase deficiency. Human Molecular Genetics 23 (10), pp. 2580 - 2592 (2014)

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Journal Article

Salzer, R.; Herzberg, M.; Nies, D. H.; Joos, F.; Rathmann, B.; Thielmann, Y.; Averhoff, B.: Zinc and ATP Binding of the Hexameric AAA-ATPase PilF from Thermus thermophilus: ROLE IN COMPLEX STABILITY, PILIATION, ADHESION, TWITCHING MOTILITY, AND NATURAL TRANSFORMATION. The Journal of Biological Chemistry 289 (44), pp. 30343 - 30354 (2014)

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Journal Article

Salzer, R.; Joos, F.; Averhoff, B.: Type IV Pilus Biogenesis, Twitching Motility, and DNA Uptake in Thermus thermophilus: Discrete Roles of Antagonistic ATPases PilF, PilT1, and PilT2. Applied and Environmental Microbiology 80 (2), pp. 644 - 652 (2014)

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Journal Article

Schweikhard, E. S.; Kempson, S. A.; Ziegler, C.; Burckhardt, B. C.: Mutation of a single threonine in the cytoplasmic NH2 terminus disrupts trafficking of renal betaine-GABA transporter 1 during hypertonic stress. American Journal of Physiology - Renal Physiology 307 (1), pp. F107 - F115 (2014)

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Journal Article

Stockburger, C.; Gold, V. A. M.; Pallas, T.; Kolesova, N.; Miano, D.; Leuner, K.: A cell model for the initial phase of sporadic Alzheimer’s disease. Journal of Alzheimer's Disease 42 (2), pp. 395 - 411 (2014)

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Journal Article

Xie, H.; Buschmann, S.; Langer, J. D.; Ludwig, B.; Michel, H.: Biochemical and Biophysical Characterization of the Two Isoforms of cbb₃-Type Cytochrome c Oxidase from Pseudomonas stutzeri. Journal of Bacteriology (Washington, DC) 196 (2), pp. 472 - 482 (2014)

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Journal Article

Zhang, C.; Allegretti, M.; Vonck, J.; Langer, J.; Marcia, M.; Peng, G.; Michel, H.: Production of fully assembled and active Aquifex aeolicus F1FO ATP synthase in Escherichia coli. Biochimica et Biophysica Acta (BBA) - General Subjects 1840 (1), pp. 34 - 40 (2014)

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Thesis - PhD (15)

2014

Thesis - PhD

Paulino, C. B.: Structural and functional characterization of the Na⁺/H⁺antiporter MjNhap1. Dissertation, Goethe-Universität, Frankfurt am Main (2014)

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Thesis - PhD

Koshy, C.: Insights into the functional and regulatory mechanisms of the osmoregulated Na⁺/glycine betaine symporter BetP from Corynebacterium glutamicum: A structural and computational study. Dissertation, Goethe-Universität, Frankfurt am Main (2014)

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Thesis - PhD

Xie, H.: Characterization of the two isoforms of cbb₃-type cytochrome c oxidase from Pseudomonoas stutzeri ZoBell. Dissertation, 224 pp., Fachbereich 14, Biochemie, Chemie und Pharmazie der Johann Wolfgang Goethe Universität, Frankfurt am Main (2014)

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Thesis - PhD

Kapotova, E.: Three-dimensional crystallization of the sodium-proton antiporter NhaP1 from Methanocaldococcus jannaschii. Dissertation, Goethe university, Frankfurt am Main (2014)

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Thesis - PhD

Calinescu, O.: Investigation of electroneutral M. jannaschii NhaP1 and electrogenic H. pylori NhaA: A common transport mechanism for CPA1 and CPA2 Na⁺/H⁺ antiporters. Dissertation, 143 pp., Goethe Universität, Frankfurt (2014)

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Thesis - PhD

Ciccarelli, L.: Mycobacterium tuberculosis type-I fatty acid synthase: Structure and conformational variability of a protein complex by single-particle electron cryo-microscopy. Dissertation, 139 pp., Fachbereich 14 Biochemie, Chemie und Pharmazie der Johann Wolfgang Goethe Universität, Frankfurt am Main (2014)

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Thesis - PhD

Daum, B.: Electron cryo-tomography of bioenergetic membranes. Dissertation, 324 pp., Goethe-Universität, Frankfurt am Main (2014)

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Thesis - PhD

Janke, C.: Biophysikalische Analyse des eukaryotischen Proteorhodopsins OR1 aus Oxyrrhis marina. Dissertation, 141 pp., Fachbereich Biochemie, Chemie und Pharmazie, Goethe Universität Frankfurt, Deutschland, Frankfurt am Main (2014)

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Thesis - PhD

Malviya, V. N.: Heterologous Production, Isolation and Characterisation of MOP superfamily transporters from Pyrococcus furiosus, Aquifex aeolicus and Salmonella typhimurium. Dissertation, 218 pp., Goethe-Universität, Frankfurt am Main (2014)

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Thesis - PhD

Matthies, D.: Biochemical and structural analysis of F-type ATP synthases and its subcomplexes. Dissertation, Goethe-Universität, Frankfurt am Main (2014)

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Thesis - PhD

Müller, M.: Structure and function of channelrhodopsin-2 by cryo electron crystallography. Dissertation, 150 pp., Goethe-Universität, Frankfurt am Main (2014)

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Thesis - PhD

Preiß, L.: Structural and functional characterization of the rotor rings from a Bacillus and a Mycobacterium F₁F₀ ATP synthase. Dissertation, 219 pp., Goethe-Universität, Frankfurt am Main (2014)

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Thesis - PhD

Sattig, T.: Selektion und Charakterisierung funktioneller Channelrhodopsin-2-Mutanten zur Studie von lichtinduzierten Konformationsänderungen. Dissertation, 137 pp., Fachbereich Biochemie, Goethe-Universität, Frankfurt am Main (2014)

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Thesis - PhD

Schweikhard, E. S.: Na⁺-coupled betaine symporters involved in osmotic stress response in prokaryotes and eukaryotes. Dissertation, Johannes Gutenberg-Universität, Mainz (2014)

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Thesis - PhD

Walter, A.: Development, implementation and practical aspects of phase plates in electron cryo-microscopy. Dissertation, Goethe-Universität, Frankfurt am Main (2014)

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Thesis - Habilitation (1)

2014

Thesis - Habilitation

Rhinow, D.: Biological and Artificial Membranes - Structural Analysis and Nanotechnological Applications. Habilitation, Philipps-Universität, Marburg (2014)

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Thesis - Diploma (2)

2014

Thesis - Diploma

Eller, A. K. L.: Strukturelle und funktionelle Charakterisierung von Kation/Proton-Antiportern. Diploma, 91 pp., Goethe-Universität, Frankfurt am Main (2014)

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Thesis - Diploma

Grötzinger, M.: Biochemical Characterization of the Secondary Transporter SeCits from Salmonella Enterica. Diploma, 61 pp., Goethe-Universität, Frankfurt am Main (2014)

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Thesis - Master (4)

2014

Thesis - Master

Jost-Lopez, A.: Coarse-Grained Molecular Simulations of Weak Protein Complexes. Master, 66 pp., Goethe Universität, Frankfurt am Main (2014)

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Thesis - Master

Kaufmann, D.: Modelling Alternate States of Membrane Transporters Utilizing their Inverted-Fold Characteristics. Master, 67 pp., Fachbereich Informatik und Mathematik, Goethe Universität, Frankfurt am Main (2014)

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Thesis - Master

Schneider, M.: Untersuchungen zur pH-Gradientenstabilität an Proteoliposomen in Hinblick auf SSM-Messungen. Master, 105 pp., Hochschule Darmstadt, Darmstadt (2014)

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Thesis - Master

Jung, S.: Charakterisierung der thermischen Stabilität des Na⁺/H⁺- Antiporters NhaA und seiner Varianten. Master, 93 pp., Johannes Gutenberg Universität, Mainz (2014)

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Thesis - Bachelor (6)

2014

Thesis - Bachelor

Zabadne, A. J.: SSM-Messungen an funktionsrelevanten Mutanten des Glukose-Protonen-Symporters aus Staphylococcus epidermidis (GlcPSe). Bachelor, 67 pp., Goethe Universität, Frankfurt (2014)

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Thesis - Bachelor

Dörr, M.: Konstruktion und biochemische Charakterisierung der Phosphatidylserin-Synthase von Methanococcus jannaschii. Bachelor, 71 pp., Fachbereich Biowissenschaften, Goethe-University Frankfurt, Frankfurt am Main (2014)

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Thesis - Bachelor

Kappenstein, M. R.: Elektrophysiologische Charakterisierung des Transportverhaltens der XylE Mutante I172A. Bachelor, 44 pp., Goethe University, Frankfurt (2014)

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Thesis - Bachelor

Litschel, T.: Morphologische Charakterisierung und Oberflächenanalyse von Mitochondrien aus Drosophila melanogaster mittels Elektronen-Kryotomographie. Bachelor, 49 pp., Goethe Universität, Institut für Biophysik, Frankurt (2014)

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Thesis - Bachelor

Schäfer, J.: Funktionelle Charakterisierung des cholesterolabhängigen Cytolysins Pneumolysin. Bachelor, 71 pp., Fachbereich Biowissenschaften, Goethe-University Frankfurt, Frankfurt am Main (2014)

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Thesis - Bachelor

Devant, J. M.: Cholin-Transporter der BCCT-Familie. Bachelor, 85 pp., Fachbereich Biowissenschaften, Goethe-University Frankfurt, Frankfurt am Main (2014)

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