Publikationen

2023

Zeitschriftenartikel

Thielmann, Y.; Luft, T.; Zint, N.; Koepke, J.: Crystal search - feasibility study of a real-time deep learning process for crystallization well images. Acta Crystallographica Section A: Foundations and Advances A79 (Part 4) (2023)

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Winiarska, A.; Ramírez-Amador, F.; Hege, D.; Gemmecker, Y.; Prinz, S.; Hochberg, G.; Heider, J.; Szaleniec, M.; Schuller, J. M.: A bacterial tungsten-containing aldehyde oxidoreductase forms an enzymatic decorated protein nanowire. Science Advances 9, eadg6689 (2023)

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Bullerjahn, J. T.; von Bülow, S.; Heidari, M.; Hénin, J.; Hummer, G.: Unwrapping NPT Simulations to Calculate Diffusion Coefficients. Journal of Chemical Theory and Computation (2023)

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Sun, C.; Desch, K.; Nassim-Assir, B.; Giandomenico, S. L.; Nemcova, P.; Langer, J. D.; Schuman, E. M.: An abundance of free regulatory (19S) proteasome particles regulates neuronal synapses. Science 380 (6647), eadf2018 (2023)

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Valko, A.; Fracchiolla, D.: “Autophagic landscapes: on the paradox of survival through self-degradation” – A science-inspired exhibition. Autophagy (2023)

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Foronda, H.; Fu, Y.; Covarrubias-Pinto, A.; Bocker, H. T.; González, A.; Seemann, E.; Franzka, P.; Bock, A.; Bhaskara, R. M.; Liebmann, L. et al.; Hoffmann, M. E.; Katona, I.; Koch, N.; Weis, J.; Kurth, I.; Gleeson, J. G.; Reggiori, F.; Hummer, G.; Kessels, M. M.; Qualmann, B.; Mari, M.; Dikić, I.; Hübner, C. A.: Heteromeric clusters of ubiquitinated ER-shaping proteins drive ER-phagy. Nature (2023)

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González, A.; Covarrubias-Pinto, A.; Bhaskara, R. M.; Glogger, M.; Kuncha, S. K.; Xavier, A.; Seemann, E.; Misra, M.; Hoffmann, M. E.; Bräuning, B. et al.; Balakrishnan, A.; Qualmann, B.; Dötsch, V.; Schulman, B. A.; Kessels, M. M.; Hübner, C. A.; Heilemann, M.; Hummer, G.; Dikić, I.: Ubiquitination regulates ER-phagy and remodelling of endoplasmic reticulum. Nature, S. 1 - 8 (2023)

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Last, M. G. F.; Tuijtel, M.; Voortman, L. M.; Sharp, T. H.: Selecting optimal support grids for super-resolution cryogenic correlated light and electron microscopy. Scientific Reports 13, 8270 (2023)

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Lettl, C.; Schindele, F.; Mehdipour, A. R.; Steiner, T.; Ring, D.; Brack-Werner, R.; Stecher, B.; Eisenreich, W.; Bilitewski, U.; Hummer, G. et al.; Witschel, M.; Fischer, W.; Haas, R.: Selective killing of the human gastric pathogen Helicobacter pylori by mitochondrial respiratory complex I inhibitors. Cell Chemical Biology 30 (5), S. 499 - 512 (2023)

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Kim, E.; Barth, R.; Dekker, C.: Looping the Genome with SMC Complexes. Annual Review of Biochemistry (2023)

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Okhrimenko, I. S.; Kovalev, K.; Petrovskaya, L. E.; Ilyinsky, N. S.; Alekseev, A. A.; Marin, E.; Rokitskaya, T. I.; Antonenko, Y. N.; Siletsky, S. A.; Popov, P. A. et al.; Zagryadskaya, Y. A.; Soloviov, D. V.; Chizhov, I. V.; Zabelskii, D. V.; Ryzhykau, Y. L.; Vlasov, A. V.; Kuklin, A. I.; Bogorodskiy, A. O.; Mikhailov, A. E.; Sidorov, D. V.; Bukhalovich, S.; Tsybrov, F.; Bukhdruker, S.; Vlasova, A. D.; Borshchevskiy, V. I.; Dolgikh, D. A.; Kirpichnikov, M. P.; Bamberg, E.; Gordeliy, V. I.: Mirror proteorhodopsins. Communications Chemistry 6, 88 (2023)

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Gehl, M.; Demmer, U.; Ermler, U.; Shima, S.: Crystal structure of FAD-independent methylene-tetrahydrofolate reductase from Mycobacterium hassiacum. Proteins: Structure, Function, and Bioinformatics (2023)

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Yu, M.; Heidari, M.; Mikhaleva, S.; Tan, P. S.; Mingu, S.; Ruan, H.; Reinkemeier, C. D.; Obarska-Kosinska, A.; Siggel, M.; Beck, M. et al.; Hummer, G.; Lemke, E. A.: Visualizing the disordered nuclear transport machinery in situ. Nature (2023)

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Jung, H.; Covino, R.; Arjun, A.; Leitold, C.; Dellago, C.; Bolhuis, P. G.; Hummer, G.: Machine-guided path sampling to discover mechanisms of molecular self-organization. Nature Computational Science 3 (4), S. 334 - 345 (2023)

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Wu, D.; Mehdipour, A. R.; Finke, F.; Goojani, H. G.; Groh, R. R.; Grund, T. N.; Reichhart, T. M. B.; Zimmermann, R.; Welsch, S.; Bald, D. et al.; Shepherd, M.; Hummer, G.; Safarian, S.: Dissecting the conformational complexity and mechanism of a bacterial heme transporter. Nature Chemical Biology 10, S. 1 - 12 (2023)

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Pradhan, B.; Kanno, T.; Umeda Igarashi, M.; Loke, M. S.; Baaske, M. D.; Wong, J. S. K.; Jeppsson, K.; Björkegren, C.; Kim, E.: The Smc5/6 complex is a DNA loop-extruding motor. Nature (2023)

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Gorriti, M. F.; Bamann, C.; Alonso-Reyes, D. G.; Wood, P. G.; Bamberg, E.; Farías, M. E.; Gärtner, W.; Albarracín, V. H.: Functional characterization of xanthorhodopsin in Salinivibrio socompensis, a novel halophile isolated from modern stromatolites. Photochemical & Photobiological Sciences (2023)

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Bhattacharya, A.; Mukherjee, R.; Kuncha, S. K.; Brunstein, M. E.; Rathore, R.; Junek, S.; Münch, C.; Đikić, I.: A lysosome membrane regeneration pathway depends on TBC1D15 and autophagic lysosomal reformation proteins. Nature Cell Biology (2023)

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Kalavacherla, T.; Buschmann, S.; Schleker, E. S. M.; Michel, H.; Reinhart, C.: Purification and characterization of eukaryotic ATP-dependent transporters homologously expressed in Pichia pastoris for structural studies by cryo-electron microscopy. Protein Expression and Purification 204, 106230 (2023)

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Lambertz, J.; Meier-Credo, J.; Kucher, S.; Bordignon, E.; Langer, J. D.; Nowaczyk, M. M.: Isolation of a novel heterodimeric PSII complex via strep-tagged PsbO. Biochimica et Biophysica Acta, Bioenergetics 1864 (2), 148953 (2023)

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Cai, W.; Jäger, M.; Bullerjahn, J. T.; Hugel, T.; Wolf, S.; Balzer, B. N.: Anisotropic Friction in a Ligand-Protein Complex. Nano Letters (2023)

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Fábián, B.; Thallmair, S.; Hummer, G.: Optimal Bond Constraint Topology for Molecular Dynamics Simulations of Cholesterol. Journal of Chemical Theory and Computation 19 (5), S. 1592 - 1601 (2023)

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Li, M.; Tripathi-Giesgen, I.; Schulman, B. A.; Baumeister, W.; Wilfling, F.: In situ snapshots along a mammalian selective autophagy pathway. Proceedings of the National Academy of Sciences of the United States of America 120 (12), e2221712120 (2023)

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Sprankel, L.; Vizaragga, D.; Martín, J.; Manger, S.; Meier-Credo, J.; Marcos, M.; Julve, J.; Rotllan, N.; Scheffer, M. P.; Escolà-Gil, J. C. et al.; Langer, J. D.; Piñol, J.; Fita, I.; Frangakis, A. S.: Essential protein P116 extracts cholesterol and other indispensable lipids for Mycoplasmas. Nature Structural and Molecular Biology 30 (3), S. 321 - 329 (2023)

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Lyratzakis, A.; Meier-Credo, J.; Langer, J. D.; Tsiotis, G.: Insights into the sulfur metabolism of Chlorobaculum tepidum by label-free quantitative proteomics. Proteomics n/a, 2200138 (2023)

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Pietrek, L. M.; Stelzl, L. S.; Hummer, G.: Structural ensembles of disordered proteins from hierarchical chain growth and simulation. Current Opinion in Structural Biology 78, 102501 (2023)

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Hegemann, P.; Michel, H.: Dieter Oesterhelt (1940–2022). Science 379 (6630), S. 337 (2023)

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von Bülow, S.; Sikora, M.; Blanc, F. E. C.; Covino, R.; Hummer, G.: Antibody accessibility determines location of spike surface mutations in SARS-CoV-2 variants. PLoS Computational Biology 19 (1), e1010822 (2023)

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Xie, H.; Lyratzakis, A.; Khera, R.; Koutantou, M.; Welsch, S.; Michel, H.; Tsiotis, G.: Cryo-EM structure of the whole photosynthetic reaction center apparatus from the green sulfur bacterium Chlorobaculum tepidum. Proceedings of the National Academy of Sciences of the United States of America 120 (5), e2216734120 (2023)

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Honti, B.; Fábián, B.; Idrissi, A.; Jedlovszky, P.: Surface Properties of N,N-Dimethylformamide-Water Mixtures, As Seen from Computer Simulations. The Journal of Physical Chemistry B 127 (4), S. 1050 - 1062 (2023)

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Hampoelz, B.; Baumbach, J.: Nuclear envelope assembly and dynamics during development. Seminars in Cell & Developmental Biology 133, S. 96 - 106 (2023)

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Grund, T. N.; Kabashima, Y.; Kusumoto, T.; Wu, D.; Welsch, S.; Sakamoto, J.; Michel, H.; Safarian, S.: The cryoEM structure of cytochrome bd from C. glutamicum provides novel insights into structural properties of actinobacterial terminal oxidases. Frontiers in Chemistry (2023)

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Klusch, N.; Dreimann, M.; Senkler, J.; Rugen, N.; Kühlbrandt, W.; Braun, H.-P.: Cryo-EM structure of the respiratory I + III₂ supercomplex from Arabidopsis thaliana at 2 Å resolution. Nature Plants 9, S. 142 - 156 (2023)

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Wieferig, J.-P.; Kühlbrandt, W.: Analysis of the conformational heterogeneity of the Rieske iron–sulfur protein in complex III₂ by cryo-EM. IUCrJ 10 (1), S. 27 - 37 (2023)

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2022

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Zhu, R.; Canena, D.; Sikora, M.; Klausberger, M.; Seferovic, H.; Mehdipour, A. R.; Hain, L.; Laurent, E.; Monteil, V.; Wirnsberger, G. et al.; Wieneke, R.; Tampé, R.; Kienzl, N. F.; Mach, L.; Mirazimi, A.; Oh, Y. J.; Penninger, J. M.; Hummer, G.; Hinterdorfer, P.: Force-tuned avidity of spike variant-ACE2 interactions viewed on the single-molecule level. Nature Communications 13 (1), 7926 (2022)

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Jensen, L. E.; Rao, S.; Schuschnig, M.; Cada, A. K.; Martens, S.; Hummer, G.; Hurley, J. H.: Membrane curvature sensing and stabilization by the autophagic LC3 lipidation machinery. Science Advances 8 (50), eadd1436 (2022)

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Hammarén, H. M.; Geissen, E.-M.; Potel, C. M.; Beck, M.; Savitski, M. M.: Protein-Peptide Turnover Profiling reveals the order of PTM addition and removal during protein maturation. Nature Communications 13, 7431 (2022)

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Hoffmann, P. C.; Kreysing, J. P.; Khusainov, I.; Tuijtel, M.; Welsch, S.; Beck, M.: Structures of the eukaryotic ribosome and its translational states in situ. Nature Communications 13, 7435 (2022)

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Krause, D. S.; Dikic, I.: Mycobacterium tuberculosis hijacks ubiquitin to inhibit pyroptosis. Molecular Cell 82 (24), S. 4588 - 4590 (2022)

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Linke, M.; Quoika, P. K.; Bramas, B.; Köfinger, J.; Hummer, G.: Complexes++: Efficient and versatile coarse-grained simulations of protein complexes and their dense solutions. The Journal of Chemical Physics 157 (20), 204802 (2022)

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Schmitt, D.; Bozkurt, S.; Henning-Domres, P.; Huesmann, H.; Eimer, S.; Bindila, L.; Behrends, C.; Boyle, E.; Wilfling, F.; Tascher, G. et al.; Münch, C.; Behl, C.; Kern, A.: FACS-mediated isolation of native autophagic vesicles. Autophagy (2022)

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Laube, E.; Meier-Credo, J.; Langer, J. D.; Kühlbrandt, W.: Conformational changes in mitochondrial complex I of the thermophilic eukaryote Chaetomium thermophilum. Science Advances 8 (47), eadc9952 (2022)

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Schiller, J.; Laube, E.; Wittig, I.; Kühlbrandt, W.; Vonck, J.; Zickermann, V.: Insights into complex I assembly: Function of NDUFAF1 and a link with cardiolipin remodeling. Science Advances 8 (46), eadd3855 (2022)

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Oo, J. A.; Pálfi, K.; Warwick, T.; Wittig, I.; Prieto-Garcia, C.; Matkovic, V.; Tomašković, I.; Boos, F.; Izquierdo Ponce, J.; Teichmann, T. et al.; Petriukov, K.; Haydar, S.; Maegdefessel, L.; Wu, Z.; Pham, M. D.; Krishnan, J.; Baker, A. H.; Günther, S.; Ulrich, H. D.; Đikić, I.; Leisegang, M. S.; Brandes, R. P.: Long non-coding RNA PCAT19 safeguards DNA in quiescent endothelial cells by preventing uncontrolled phosphorylation of RPA2. Cell Reports: Methods 41 (7), 111670 (2022)

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Schaefer, S. L.; Hummer, G.: Sublytic gasdermin-D pores captured in atomistic molecular simulations. eLife 11, e81432 (2022)

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Kühlbrandt, W.: Concluding remarks: Challenges and future developments in biological electron cryo-microscopy. Faraday Discussions 240, S. 323 - 335 (2022)

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Siggel, M.; Kehl, S.; Reuter, K.; Köfinger, J.; Hummer, G.: TriMem: A parallelized hybrid Monte Carlo software for efficient simulations of lipid membranes. The Journal of Chemical Physics 157 (17), 174801 (2022)

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Astashkin, R.; Kovalev, K.; Bukhdruker, S.; Vaganova, S.; Kuzmin, A.; Alekseev, A.; Balandin, T.; Zabelskii, D.; Gushchin, I.; Royant, A. et al.; Volkov, D.; Bourenkov, G.; Koonin, E.; Engelhard, M.; Bamberg, E.; Gordeliy, V.: Structural insights into light-driven anion pumping in cyanobacteria. Nature Communications 13, 6460 (2022)

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Vitt, S.; Prinz, S.; Eisinger, M. L.; Ermler, U.; Buckel, W.: Purification and structural characterization of the Na⁺-translocating ferredoxin: NAD⁺ reductase (Rnf) complex of Clostridium tetanomorphum. Nature Communications 13, 6315 (2022)

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Shah, V. J.; Đikić, I.: Localization matters in targeted protein degradation. Cell Chemical Biology 29 (10), S. 1465 - 1466 (2022)

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Cruz-León, S.; Schwierz, N.: RNA Captures More Cations than DNA: Insights from Molecular Dynamics Simulations. The Journal of Physical Chemistry B (2022)

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Schleker, E. S. M.; Buschmann, S.; Xie, H.; Welsch, S.; Michel, H.; Reinhart, C.: Structural and functional investigation of ABC transporter STE6-2p from Pichia pastoris reveals unexpected interaction with sterol molecules. Proceedings of the National Academy of Sciences of the United States of America 126 (43), S. 8646 - 8654 (2022)

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Mathioudaki, E.; Alifragis, Y.; Fouskaki, M.; Chochlakis, D.; Xie, H.; Psaroulaki, A.; Tsiotis, G.; Chaniotakis, N.: Electrochemical Antigenic Sensor for the Diagnosis of Chronic Q Fever. Current Research in Biotechnology 4, S. 537 - 543 (2022)

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Lee, Y.; Haapanen, O.; Altmeyer, A.; Kühlbrandt, W.; Sharma, V.; Zickermann, V.: Ion transfer mechanisms in Mrp-type antiporters from high resolution cryoEM and molecular dynamics simulations. Nature Communications 13 (1), 6091 (2022)

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Schmitt, D.; Bozkurt, S.; Henning-Domres, P.; Huesmann, H.; Eimer, S.; Bindila, L.; Behrends, C.; Boyle, E.; Wilfling, F.; Tascher, G. et al.; Münch, C.; Behl, C.; Kern, A.: Lipid and protein content profiling of isolated native autophagic vesicles. EMBO Reports, e53065 (2022)

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Schulz, L.; Guo, Z.; Zarzycki, J.; Steinchen, W.; Schuller, J. M.; Heimerl, T.; Prinz, S.; Mueller-Cajar, O.; Erb, T. J.; Hochberg, G. K. A.: Evolution of increased complexity and specificity at the dawn of form I Rubiscos. Science 378 (6616), S. 155 - 160 (2022)

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Bieber, A.; Capitanio, C.; Erdmann, P. S.; Fiedler, F.; Beck, F.; Lee, C.-W.; Li, D.; Hummer, G.; Schulman, B. A.; Baumeister, W. et al.; Wilfling, F.: In situ structural analysis reveals membrane shape transitions during autophagosome formation. Proceedings of the National Academy of Sciences of the United States of America 119 (39), e2209823119 (2022)

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Zöller, J.; Hong, S.; Eisinger, M. L.; Anderson, M.; Radloff, M.; Desch, K.; Gennis, R.; Langer, J. D.: Ligand binding and conformational dynamics of the E. coli nicotinamide nucleotide transhydrogenase revealed by hydrogen/deuterium exchange mass spectrometry. Computational and Structural Biotechnology Journal 20, S. 5430 - 5439 (2022)

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Khera, R.; Mehdipour, A. R.; Bolla, J. R.; Kahnt, J.; Welsch, S.; Ermler, U.; Münke, C.; Robinson, C. V.; Hummer, G.; Xie, H. et al.; Michel, H.: Cryo-EM structures of pentameric autoinducer-2 exporter from Escherichia coli reveal its transport mechanism. The EMBO Journal 41 (18), e109990 (2022)

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Steinhilper, R.; Höff, G.; Heider, J.; Murphy, B. J.: Structure of the membrane-bound formate hydrogenlyase complex from Escherichia coli. Nature Communications 13, 5395 (2022)

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Mukherjee, R.; Dikic, I.: Regulation of Host-Pathogen Interactions via the Ubiquitin System. Annual Review of Microbiology 76, S. 211 - 233 (2022)

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Vögele, M.; Köfinger, J.; Hummer, G.: Nanoporous Membranes of Densely Packed Carbon Nanotubes Formed by Lipid-Mediated Self-Assembly. ACS applied bio materials (2022)

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Kafkia, E.; Andres-Pons, A.; Ganter, K.; Seiler, M.; Smith, T. S.; Andrejeva, A.; Jouhten, P.; Pereira, F.; Franco, C.; Kuroshchenkova, A. et al.; Leone, S.; Sawarkar, R.; Boston, R.; Thaventhiran, J.; Zaugg, J. B.; Lilley, K. S.; Lancrin, C.; Beck, M.; Patil, K. R.: Operation of a TCA cycle subnetwork in the mammalian nucleus. Science Advances 8 (35), eabq5206 (2022)

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Mikolajczyk, K.; Sikora, M.; Hanus, C.; Kaczmarek, R.; Czerwinski, M.: One of the two N-glycans on the human Gb3/CD77 synthase is essential for its activity and allosterically regulates its function. Biochemical and Biophysical Research Communications (Orlando, FL) 617, S. 36 - 41 (2022)

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Palacio-Rodriguez, K.; Vroylandt, H.; Stelzl, L. S.; Pietrucci, F.; Hummer, G.; Cossio, P.: Transition Rates and Efficiency of Collective Variables from Time-Dependent Biased Simulations. The Journal of Physical Chemistry Letters 13 (32), S. 7490 - 7496 (2022)

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Sušac, L.; Vuong, M. T.; Thomas, C.; von Bülow, S.; O'Brien-Ball, C.; Santos, A. M.; Fernandes, R. A.; Hummer, G.; Tampé, R.; Davis, S. J.: Structure of a fully assembled tumor-specific T cell receptor ligated by pMHC. Cell 185 (17), S. 3201 - 3213 (2022)

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Bullerjahn, J. T.; Hummer, G.: Reversible bond kinetics from single-molecule force spectroscopy experiments close to equilibrium. Physical Review Research 4 (3), 033097 (2022)

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Sinning, I.; McDowell, M. A.: Cryo-EM insights into tail-anchored membrane protein biogenesis in eukaryotes. Current Opinion in Structural Biology 75, 102428 (2022)

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Fábián, B.; Thallmair, S.; Hummer, G.: Small ionic radii limit time step in Martini 3 molecular dynamics simulations. The Journal of Chemical Physics 157 (3), 034101 (2022)

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Meier-Credo, J.; Preiss, L.; Wüllenweber, I.; Resemann, A.; Nordmann, C.; Zabret, J.; Suckau, D.; Michel, H.; Nowacyk, M. M.; Meier, T. et al.; Langer, J. D.: Top-Down Identification and Sequence Analysis of Small Membrane Proteins Using MALDI-MS/MS. Journal of the American Society for Mass Spectrometry 33 (7), S. 1293 - 1302 (2022)

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Enenkel, C.; Kang, R. W.; Wilfling, F.; Ernst, O. P.: Intracellular localization of the proteasome in response to stress conditions. The Journal of Biological Chemistry 298 (7), 102083 (2022)

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Hollenstein, D. M.; Veis, J.; Romanov, N.; Gérecová, G.; Ogris, E.; Hartl, M.; Ammerer, G.; Reiter, W.: PP2A^Rts1 antagonizes Rck2-mediated hyperosmotic stress signaling in yeast. Microbiological Research 260, 127031 (2022)

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Heinz, V.; Jäckel, W.; Kaltwasser, S.; Cutugno, L.; Bedrunka, P.; Graf, A.; Reder, A.; Michalik, S.; Dhople, V. M.; Madei, M. G. et al.; Conway, M.; Lechner, M.; Riedel, K.; Bange, G.; Boyd, A.; Völker, U.; Lewis, R. J.; Marles-Wright, J.; Ziegler, C.; Pané-Farré, J.: The Vibrio vulnificus stressosome is an oxygen-sensor involved in regulating iron metabolism. Communications Biology 5, 622 (2022)

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Miksys, A.; Fu, L.; Madej, M. G.; Guerreiro, D. N.; Kaltwasser, S.; Conway, M.; Ejder, S.; Bruckmann, A.; Marles-Wright, J.; Lewis, R. J. et al.; O'Byrne, C.; Pané-Farré, J.; Ziegler, C.: Molecular insights into intra-complex signal transmission during stressosome activation. Communications Biology 5, 621 (2022)

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Kayastha, K.; Katsyv, A.; Himmrich, C.; Welsch, S.; Schuller, J. M.; Ermler, U.; Müller, V.: Structure-based electron-confurcation mechanism of the Ldh-EtfAB complex. eLife 11, e77095 (2022)

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Aziz, I.; Kaltwasser, S.; Kayastha, K.; Khera, R.; Vonck, J.; Ermler, U.: The molybdenum storage protein forms and deposits distinct polynuclear tungsten oxygen aggregates. Journal of Inorganic Biochemistry 234, 111904 (2022)

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