Publications of the Max Planck Institute of Biophysics 1947

2025

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Majtner, T.; Turoňová, B.: Automated removal of corrupted tilts in cryo-electron tomography. Journal of Structural Biology: X 12, 100130 (2025)

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Okuda, E. K.; Kessler, L. F.: A new rapid-degradation system combined with super-resolution microscopy. Nature Reviews Molecular Cell Biology 26 (12), p. 904 (2025)

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Berrevoets, E. S.; Kessler, L. F.; Balakrishnan, A.; Okuda, E. K.; Müller-McNicoll, M.; Rieger, B.; Stallinga, S.; Heilemann, M.: Smart 3D super-resolution microscopy reveals the architecture of the RNA scaffold in a nuclear body. Nature Communications 16, 10689 (2025)

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Babic, R.; Brenneisen, J.; Wilfling, F.; Kraft, C.: Autophagy regulation by phase separation, avidity, and wetting. Trends in Biochemical Sciences (2025)

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Müller-McNicoll, M.: Getting sticky: How nuclear speckles tune the condensation-prone proteome. Molecular Cell 85 (22), pp. 4116 - 4118 (2025)

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Germain, H.; Hoffmann, P. C.: The Arabidopsis thaliana nuclear pore complex structure reveals conserved and distinct features. Nature Plants 11, pp. 2198 - 2199 (2025)

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Rosenkranz, N.; Birtasu, A. N.; Wieland, K.; Rehm, L.; Sharma, R.; Vats, A.; Manger, S.; Srivastava, A.; Bhattacharya, A.; Hummer, G. et al.; Frangakis, A. S.; Gottschalk, A.: In situ structure of a gap junction-stomatin complex. Science Advances 11 (45), eaea8596 (2025)

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Glushkova, D.; Böhm, S.; Beck, M.: Systematic membrane thickness variation across cellular organelles revealed by cryo-ET. Journal of Cell Biology 225 (1), e202504053 (2025)

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Mondal, S.; Mukherjee, S.; Namitz, K. E. W.; Yennawar, N. H.; Boehr, D. D.: Multivalent Interactions Between the Picornavirus 3C(D) Main Protease and RNA Oligonucleotides Induce Liquid-Liquid Phase Separation. Viruses 17 (11), 1473 (2025)

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Sanchez Carrillo, I. B.; Hoffmann, P. C.; Obarska-Kosinska, A.; Fourcassié, V.; Beck, M.; Germain, H.: In situ architecture of the nuclear pore complex of the higher plant Arabidopsis thaliana. Nature Plants (2025)

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Yang, T.-J.; Mukherjee, S.; Langer, J. D.; Hummer, G.; McDowell, M. A.: SND3 is the membrane insertase within a distinct SEC61 translocon complex. Nature Communications 16, 9566 (2025)

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Lago-Maciel, A.; Soares, J. C.; Zarzycki, J.; Buchanan, C. J.; Reif-Trauttmansdorff, T.; Schmidt, F. V.; Lometto, S.; Paczia, N.; Schuller, J. M.; Hansen, D. F. et al.; Heller, G. T.; Prinz, S.; Hochberg, G. K. A.; Pierik, A. J.; Rebelein, J. G.: Methylthio-alkane reductases use nitrogenase metalloclusters for carbon-sulfur bond cleavage. Nature Catalysis 8 (10), pp. 1086 - 1099 (2025)

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Bresciani, V.; Rinaldi, F.; Franco, P.; Girotto, S.; Cavalli, A.; Langer, J. D.; Masetti, M.; Bernetti, M.: Dissecting the RAD51–BRC4 Interaction Landscape through Integrative Molecular Simulations and Experimental Biophysics. Journal of Chemical Information and Modeling (2025)

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Hasselbeck, S.; Wang, J.; Bai, Z.; Hüfner, T.; Hummer, G.; Grote, P.; Cheng, X.: A Chemically Induced CRISPR/dCas13^FCPF Platform for Precise and Programmable RNA Regulation. Journal of Medicinal Chemistry (2025)

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Grabarczyk, D. B.; Aird, E. J.; Reznikow, V.; Kirchgatterer, P. C.; Ehrmann, J. F.; Kurzbauer, R.; Bell, L. E.; Kellner, M. J.; Aggarwal, R.; Schleiffer, A. et al.; Faas, V.; Deszcz, L.; Meinhart, A.; Versteeg, G. A.; Penninger, J. M.; Stelzl, L. S.; Gaidt, M. M.; Tessmer, I.; Corn, J. E.; Clausen, T.: A split-site E3 ligase mechanism enables ZNFX1 to ubiquitinate and cluster single-stranded RNA into ubiquitin-coated nucleoprotein particles. Cell 188 (21), pp. 5995 - 6011 (2025)

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Sachweh, J.; Börmel, M.; Klumpe, S.; Becker, A.; Taniguchi, R.; Kubańska, M. A.; Pintschovius, V.; Kaindl, E.; Plitzko, J. M.; Wilfling, F. et al.; Beck, M.; Hampoelz, B.: The small GTPase Ran defines nuclear pore complex asymmetry. Cell 188 (21), pp. 5931 - 5946 (2025)

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Langschied, F.; Iruegas, R.; Sikora, M.; Covino, R.; Ebersberger, I.: A Multi-level Perspective on the Evolution of Orthologs and Their Functions. Journal of Molecular Evolution (2025)

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Grothaus, I. L.; Spellerberg, P.; Rovira, C.; Colombi Ciacchi, L.: Shaping the Glycan Landscape: Hidden Relationships between Linkage and Ring Distortions Induced by Carbohydrate-Active Enzymes. Journal of the American Chemical Society 147 (42), pp. 38376 - 38389 (2025)

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Majtner, T.; Kreysing, J. P.; Tuijtel, M.; Cruz-León, S.; Liu, J.; Hummer, G.; Beck, M.; Turoňová, B.: cryoTIGER: deep-learning based tilt interpolation generator for enhanced reconstruction in cryo electron tomography. Communications Biology 8, 1443 (2025)

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Kumari, R.; Nath, T.; Pflaum, J.; R, I.; Vinay, S.; Wilfling, F.; Manjithaya, R.: The autophagy-specific exocyst subcomplex contributes to phagophore assembly site integrity by promoting phagophore expansion. Proceedings of the National Academy of Sciences of the United States of America 122 (41), e2426476122 (2025)

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Hohorst, L.; Ros, U.; Garcia-Saez, A. J.: Mitochondrial dynamics and pore formation in regulated cell death pathways. Trends in Biochemical Sciences (2025)

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Manger, S.; Arghittu, S. M.; Sprankel, L.; Meier-Credo, J.; Wieland, K.; Bublak, D.; Langer, J. D.; Covino, R.; Frangakis, A. S.: How does Mycoplasma pneumoniae scavenge lipids from its host membranes? Science Advances 11 (40), eady4746 (2025)

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Zaghbani, S.; Faber, L.; Garcia Saez, A. J.: Convolutional Neural Network approach to classify mitochondrial morphologies. Computational Biology and Chemistry 118, 108477 (2025)

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Majoul, A.; Garcia-Saez, A. J.: Dynamic regulation of cell death signaling. Current Opinion in Cell Biology 97, 102583 (2025)

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Ho-Xuan, H.; Bruckmann, A.; Natali, L.; Prieto-Garcia, C.; Stuke, J. F. M.; Brunello, L.; Vicente, A.; Pfab, A.; Wesseling, H.; Cano-Franco, S. et al.; Khatri, A.; Larivera, S.; Sanz-Martinez, P.; de la Cruz-Thea, B.; Jacomin, A.-C.; Prochazka, J.; Feederle, R.; Dötsch, V.; Sedlacek, R.; Hummer, G.; Kaiser, S.; Dikic, I.; Musri, M. M.; Meister, G.; Stolz, A.: YTHDF proteins and m⁶A-RNA clients undergo autophagic turnover during contact inhibition. Cell Reports 44 (9), 116188 (2025)

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Mineev, K. S.; Gande, S. L.; Wenzel, A.; Linhard, V.; Andrews-Clark, H.; Witt, K.; Köster, S.; Segarra, M.; McDowell, M. A.; Acker-Palmer, A. et al.; Schwalbe, H.: Structural Role of Conformational Heterogeneity and Juxtamembrane Regions in the Ephrin A1 Interactions With the EphA2 Receptor Ligand-binding Domain. Journal of Molecular Biology 437 (24), 169454 (2025)

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Fábián, B.; Stuke, J. F. M.; Heinz, M.; Hummer, G.: AlphaFold modeling of polyubiquitin complexes and covalently linked proteins. Cell Reports Physical Science 6 (9), 102796 (2025)

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Sucharitakul, J.; Mangkalee, M.; Intasian, P.; Pornsuwan, S.; Ermler, U.; Buckel, W.; Chaiyen, P.: Kinetic mechanisms of electron bifurcation with electron transfer flavoprotein, NADH, butyryl-CoA dehydrogenase, and ferredoxin reveal a semiquinone cycle. Journal of Biological Chemistry 301 (10), 110727 (2025)

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King, L. E.; Faber, L.; García-Sáez, A. J.: Activator of apoptosis harakiri (HRK) localisation at mitochondria alters mitochondrial morphology independently of other BCL-2 proteins. The FEBS Journal (2025)

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Brdar, A.; Osterburg, C.; Münick, P.; Machel, A. C.; Rathore, R.; Osterburg, S.; Yüksel, B.; Schäfer, B.; Desch, K.; Langer, J. D. et al.; Dikic, I.; Dötsch, V.: p53 isoforms have a high aggregation propensity, interact with chaperones and lack binding to p53 interaction partners. eLife 13, RP103537 (2025)

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Shrestha, R.; Alessandri, R.; Vögele, M.; Hilpert, C.; Souza, P. C. T.; Marrink, S. J.; Monticelli, L.: Martini 3 Coarse-Grained Models for Carbon Nanomaterials. Journal of Chemical Theory and Computation 21 (18), pp. 9035 - 9053 (2025)

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Zietek, M.; Miguel, A.; Shi, H.; Khusainov, I.; Asmar, A. T.; Ram, S.; Wartel, M.; Sueki, A.; Schorb, M.; Goulian, M. et al.; Collet, J.-F.; Beck, M.; Huang, K. C.; Typas, A.: Bacterial cell widening alters periplasmic size and activates envelope stress responses. The EMBO Journal 44 (20), pp. 5816 - 5833 (2025)

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Blum, T. B.; Davies, K. M.; Kühlbrandt, W.: Subtomogram averages of mitochondrial ATP synthase dimers from plants show a conserved extra density at the peripheral stalk. IUCrJ 12, pp. 563 - 569 (2025)

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Zeinert, R.; Zhou, F.; Franco, P.; Zöller, J.; Madni, Z. K.; Lessen, H.; Aravind, L.; Langer, J. D.; Sodt, A. J.; Storz, G. et al.; Matthies, D.: P-type ATPase magnesium transporter MgtA acts as a dimer. Nature Structural & Molecular Biology 32 (9), pp. 1633 - 1643 (2025)

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Horvath, F.; Jung, H.; Grabmayr, H.; Fahrner, M.; Romanin, C.; Hummer, G.: STIM1 transmembrane helix dimerization captured by AI-guided transition path sampling. Proceedings of the National Academy of Sciences of the United States of America 122 (35), e2506516122 (2025)

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Kaulich, E.; Waselenchuk, Q.; Fürst, N.; Desch, K.; Mosbacher, J.; Ciirdaeva, E.; Juengling, M.; Ray, R.; Nassim-Assir, B.; Tushev, G. et al.; Langer, J. D.; Schuman, E. M.: An integrated transcriptomic and proteomic map of the mouse hippocampus at synaptic resolution. Nature Communications 16, 7942 (2025)

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Dikic, I.; Mayor-Ruiz, C.; Winter, G. E.; Koch, K.; Ciulli, A.; Thomä, N. H.: Opportunities in proximity modulation: Bridging academia and industry. Molecular Cell 85 (16), pp. 3012 - 3022 (2025)

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Franco, P. H. C.; Zeinert, R.; Meier-Credo, J.; Storz, G.; Langer, J. D.: Detection and Quantitation of Small Proteins Using Mass Spectrometry. Molecular & Cellular Proteomics 24 (9), 101052 (2025)

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Nomura, S.; San Segundo-Acosta, P.; Protasov, E.; Kaneko, M.; Kahnt, J.; Murphy, B. J.; Shima, S.: Electron flow in hydrogenotrophic methanogens under nickel limitation. Nature 644 (8076), pp. 490 - 496 (2025)

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North, B. J.; Fracchiolla, D.; Ragusa, M. J.; Martens, S.; Shoemaker, C. J.: The rapidly expanding role of LC3-interacting regions in autophagy. Journal of Cell Biology 224 (8), e202504076 (2025)

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Adriaenssens, E.; Schaar, S.; Cook, A. S. I.; Stuke, J. F. M.; Sawa-Makarska, J.; Nguyen, T. N.; Ren, X.; Schuschnig, M.; Romanov, J.; Khuu, G. et al.; Uoselis, L.; Lazarou, M.; Hummer, G.; Hurley, J. H.; Martens, S.: Reconstitution of BNIP3/NIX-mitophagy initiation reveals hierarchical flexibility of the autophagy machinery. Nature Cell Biology 27 (8), pp. 1272 - 1287 (2025)

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Mukherjee, R.; Bhattacharya, A.; Tomaskovic, I.; Mello-Vieira, J.; Brunstein, M. E.; Başoğlu, M.; Veenendaal, T.; Bailey, H.; Colby, T.; Misra, M. et al.; Eimer, S.; Klumperman, J.; Münch, C.; Matic, I.; Dikic, I.; Đikić, I.: Phosphoribosyl ubiquitination of SNARE proteins regulates autophagy during Legionella infection. The EMBO Journal 44 (15), pp. 4252 - 4279 (2025)

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Zabelskii, D.; Bukhdruker, S.; Bukhalovich, S.; Tsybrov, F.; Lamm, G. H. U.; Astashkin, R.; Doroginin, D.; Matveev, G.; Sudarev, V.; Kuzmin, A. et al.; Zinovev, E.; Vlasova, A.; Ryzhykau, Y.; Ilyinsky, N.; Gushchin, I.; Bourenkov, G.; Alekseev, A.; Round, A.; Wachtveitl, J.; Bamberg, E.; Gordeliy, V.: Ion-conducting and gating molecular mechanisms of channelrhodopsin revealed by true-atomic-resolution structures of open and closed states. Nature Structural & Molecular Biology 32 (8), pp. 1347 - 1357 (2025)

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Zaghbani, S.; Pranti, R. K.; Faber, L.; Garcia-Saez, A. J.: MitoSkel: AI tool for semantic segmentation and quantification of mitochondria from light microscopy images. Biomedical Signal Processing and Control 106, 107762 (2025)

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Pedersen, K. B.; Ingólfsson, H. I.; Ramirez-Echemendia, D. P.; Borges-Araújo, L.; Andreasen, M. D.; Empereur-mot, C.; Melcr, J.; Ozturk, T. N.; Bennett, W. F. D.; Kjølbye, L. R. et al.; Brasnett, C.; Corradi, V.; Khan, H. M.; Cino, E. A.; Crowley, J.; Kim, H.; Fábián, B.; Borges-Araújo, A. C.; Pavan, G. M.; Launay, G.; Lolicato, F.; Wassenaar, T. A.; Melo, M. N.; Thallmair, S.; Carpenter, T. S.; Monticelli, L.; Tieleman, D. P.; Schiøtt, B.; Souza, P. C. T.; Marrink, S. J.: The Martini 3 Lipidome: Expanded and Refined Parameters Improve Lipid Phase Behavior. ACS Central Science 11 (9), pp. 1598 - 1610 (2025)

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Rose, K.; Herrmann, E.; Kakudji, E.; Lizarrondo, J.; Celebi, A. Y.; Wilfling, F.; Lewis, S. C.; Hurley, J. H.: In situ cryo-ET visualization of mitochondrial depolarization and mitophagic engulfment. Proceedings of the National Academy of Sciences of the United States of America 122 (31), e2511890122 (2025)

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Agip, A.-N. A.; Ornelas, P.; Yang, T.-J.; Uboldi, E.; Häder, S.; McDowell, M.; Kühlbrandt, W.: Structures of Chaetomium thermophilum TOM complexes with bound preproteins. Proceedings of the National Academy of Sciences of the United States of America 122 (29), e2507279122 (2025)

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Okuda, E. K.; Kessler, L. F.; Arnold, B.; Riegger, R. J.; Hernández Cañás, M. C.; Zebrowska, E.; Bakisoglu, C.; Rudigier, M.; Krost, C.; Nagasse, H. Y. et al.; Keiten-Schmitz, J.; Müller, S.; Stanek, D.; Dormann, D.; Zarnack, K.; Heilemann, M.; Müller-McNicoll, M.: Rapid depletion and super-resolution microscopy reveal dual roles of SRSF5 in coordinating nuclear speckle-paraspeckle crosstalk during cellular stress. Nucleic Acids Research 53, gkaf713 (2025)

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Singh, M. K.; Cavellini, L.; Morcillo-Parra, M. A.; Kunz, C.; Lelek, M.; Bomme, P.; Barascu, A.; Alsayyah, C.; Teixeira, M. T.; Belgareh-Touzé, N. et al.; Mallet, A.; Dietrich, L.; Zimmer, C.; Cohen, M. M.: A constricted mitochondrial morphology formed during respiration. Nature Communications 16, 5314 (2025)

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Buckel, W.; Ermler, U.; Vonck, J.; Fritz, G.; Steuber, J.: The RNF/NQR redox pumps: a versatile system for energy transduction in bacteria and archaea. Applied Microbiology and Biotechnology 109, 148 (2025)

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Lafargue, E.; Duneau, J.-P.; Buzhinsky, N.; Ornelas, P.; Ortega, A.; Ravishankar, V.; Sturgis, J.; Casuso, I.; Bergdoll, L.: Membrane lipid composition modulates the organization of VDAC1, a mitochondrial gatekeeper. Communications Biology 8, 936 (2025)

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Perez-Rivera, E.; Plasencia, C.; Ros, U.: The Multifaceted Role of Calcium Signaling in Regulated Necrosis. Biomolecules 15 (6), 854 (2025)

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Introini, B.; Hahn, A.; Kühlbrandt, W.: Cryo-EM structure of the NDH-PSI-LHCI supercomplex from Spinacia oleracea. Nature Structural & Molecular Biology 32 (6), pp. 968 - 978 (2025)

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Mondal, S.; Mukherjee, S.; Bagchi, B.: Dipolar Cross-Correlations in Aqueous Systems: How Surfaces Influence Water's Action at a Distance. Journal of Chemical Theory and Computation 21, pp. 5686 - 5696 (2025)

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Garcia-Saez, A. J.; McBride, H.: Special Issue – Cell Biology of Mitochondria. Journal of Cell Science 138 (9), jcs264067 (2025)

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Stautz, J.; Griwatz, D.; Kaltwasser, S.; Mehdipour, A. R.; Ketter, S.; Thiel, C.; Wunnicke, D.; Schrecker, M.; Mills, D. J.; Hummer, G. et al.; Vonck, J.; Hänelt, I.: A short intrinsically disordered region at KtrB’s N-terminus facilitates allosteric regulation of K⁺ channel KtrAB. Nature Communications 16, 4252 (2025)

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Stuke, J. F. M.; Hummer, G.: AlphaFold2 SLiM screen for LC3-LIR interactions in autophagy. Autophagy 21 (10), pp. 2192 - 2212 (2025)

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Carra, S.; Fabian, B.; Taghavi, H.; Milanetti, E.; Giliberti, V.; Ruocco, G.; Shepherd, J.; Vendruscolo, M.; Fuxreiter, M.: Virus-like particles of retroviral origin in protein aggregation and neurodegenerative diseases. Molecular Aspects of Medicine 103, 101369 (2025)

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Kühlbrandt, W.; Carreira, L. A. M.; Yildiz, Ö.: Cryo-EM of Mitochondrial Complex I and ATP Synthase. Annual Review of Biophysics 54, pp. 209 - 226 (2025)

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Münick, P.; Strubel, A.; Balourdas, D.-I.; Funk, J. S.; Mernberger, M.; Osterburg, C.; Dreier, B.; Schaefer, J. V.; Tuppi, M.; Yüksel, B. et al.; Schäfer, B.; Knapp, S.; Plückthun, A.; Stiewe, T.; Joerger, A. C.; Dötsch, V.: DARPin-induced reactivation of p53 in HPV-positive cells. Nature Structural & Molecular Biology 32 (5), pp. 790 - 801 (2025)

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Murphy, B. J.; Kaila, V. R. I.; Roessler, M. M.; Chukhutsina, V.; Fadini, A.; Hanson, S. M.; Maia, F. R. N. C.; Kovalev, K.: Introducing Bonnie Murphy, Ville Kaila, Maxie Roessler, Volha Chukhutsina, Alisia Fadini, Sonya Hanson, Filipe Maia, and Kirill Kovalev. Structure 33 (5), pp. 829 - 835 (2025)

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Taniguchi, R.; Orniacki, C.; Kreysing, J. P.; Zila, V.; Zimmerli, C. E.; Böhm, S.; Turoňová, B.; Kräusslich, H.-G.; Doye, V.; Beck, M.: Nuclear pores safeguard the integrity of the nuclear envelope. Nature Cell Biology 27 (5), pp. 762 - 775 (2025)

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Gutfreund, N.; Tuppi, M.; Schäfer, B.; Klinger, F. G.; Kirchhof, A.; Hofmann, A.; Đikić, I.; Dötsch, V.: Mechanisms of chemotherapy-induced oocyte death through activation of TAp63α. Reproduction: the Journal of the Society for Reproduction and Fertility 169 (5), e240225 (2025)

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Bukhdruker, S.; Gushchin, I.; Shevchenko, V.; Kovalev, K.; Polovinkin, V.; Tsybrov, F.; Astashkin, R.; Alekseev, A.; Mikhaylov, A.; Bukhalovich, S. et al.; Bratanov, D.; Ryzhykau, Y.; Kuklina, D.; Caramello, N.; Rokitskaya, T.; Antonenko, Y.; Rulev, M.; Stoev, C.; Zabelskii, D.; Round, E.; Rogachev, A.; Borshchevskiy, V.; Ghai, R.; Bourenkov, G.; Zeghouf, M.; Cherfils, J.; Engelhard, M.; Chizhov, I.; Rodriguez-Valera, F.; Bamberg, E.; Gordeliy, V.: Proteorhodopsin insights into the molecular mechanism of vectorial proton transport. Science Advances 11 (16), eadu5303 (2025)

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Klumpe, S.; Senti, K. A.; Beck, F.; Sachweh, J.; Hampoelz, B.; Ronchi, P.; Oorschot, V.; Brandstetter, M.; Yeroslaviz, A.; Briggs, J. A. G. et al.; Brennecke, J.; Beck, M.; Plitzko, J. M.: In-cell structure and snapshots of copia retrotransposons in intact tissue by cryoelectron tomography. Cell 188 (8), pp. 2094 - 2110.e18 (2025)

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Ros, U.; Martinez-Osorio, V.; Valiente, P. A.; Abdelwahab, Y.; Gojkovic, M.; Shalaby, R.; Zanna, S.; Saggau, J.; Wachsmuth, L.; Nemade, H. N. et al.; Zoeller, J.; Lottermoser, H.; Chen, Y.-G.; Ibrahim, M.; Kelepouras, K.; Vasilikos, L.; Bedoya, P.; Espiritu, R. A.; Müller, S.; Altmannova, V.; Tieleman, D. P.; Weir, J.; Langer, J. D.; Adam, M.; Walczak, H.; Wong, W. W.-L.; Liccardi, G.; Mollenhauer, M.; Pasparakis, M.; Peltzer, N.; García-Sáez, A. J.: MLKL activity requires a splicing-regulated, druggable intramolecular interaction. Molecular Cell 85 (8), pp. 1589 - 1605 (2025)

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Cook, A. S. I.; Chen, M.; Nguyen, T. N.; Cabezudo, A. C.; Khuu, G.; Rao, S.; Garcia, S. N.; Yang, M.; Iavarone, A. T.; Ren, X. et al.; Lazarou, M.; Hummer, G.; Hurley, J. H.: Structural pathway for PI3-kinase regulation by VPS15 in autophagy. Science 388 (6743), eadl3787 (2025)

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Fuchs, J.; Fernández-Arévalo, U.; Demmer, U.; Díaz, E.; Ullmann, G. M.; Pierik, A. J.; Ermler, U.; Boll, M.: Enzymatic Birch reduction via hydrogen atom transfer at [4Fe-4S]-OH₂ and [8Fe-9S] clusters. Nature Communications 16, 3236 (2025)

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