Publications 2025

ZORA Publication List

Publications

• Kolibius, J., Weiss, F., Freitag, P., & Plückthun, A. (2025). Genome-replicating HC-AdV: A novel high-capacity adenoviral vector class featuring enhanced payload expression Molecular Therapy - Methods & Clinical Development, 33, 101582. https://doi.org/10.1016/j.omtm.2025.101582
• Wimmer, B. H., Moraïs, S., Amit, I., Tovar-Herrera, O., Tatli, M., Trautwein-Schult, A., Pfister, B., Zalk, R., Tödtli, P., Simoni, S., Lisibach, M., Levin, L., Becher, D., Bayer, E. A., Medalia, O., & Mizrahi, I. (2025). Spatial constraints drive amylosome-mediated resistant starch degradation by Ruminococcus bromii in the human colon Nature Communications, 16, 10763. https://doi.org/10.1038/s41467-025-65800-1
• Ghosh, S., Chowdhury, A., Tomares, D., Schuler, B., Kundagrami, A., & Pappu, R. (2025). Interplay of distinct modes of charge regulation on poly-acid ionization and conformation Journal of Chemical Physics, 163, 194908. https://doi.org/10.1063/5.0297651
• Arndt, M., Schweri, A., & Dutzler, R. (2025). Structural basis for lipid transport at membrane contact sites by the IST2-OSH6 complex Nature Structural & Molecular Biology, 32, 2219–2230. https://doi.org/10.1038/s41594-025-01660-z
• Nüesch, M. F., Ivanović, M. T., Nettels, D., Best, R. B., & Schuler, B. (2025). Accuracy of distance distributions and dynamics from single-molecule FRET Biophysical Journal, 124, 3408–3427. https://doi.org/10.1016/j.bpj.2025.03.028
• Levin, T., Garcia-Seisdedos, H., Lobov, A., Wojtynek, M., Alexandrov, A., Jona, G., Levi, D., Medalia, O., & Levy, E. D. (2025). Mutation-induced filaments of folded proteins are inert and non-toxic in a cellular system Molecular Systems Biology, 21, 1306–1324. https://doi.org/10.1038/s44320-025-00144-y
• Vargas-rosales Pablo Andrés, Giangreco, G., & Caflisch, A. (2025). Disrupting Amyloid Filaments of Tau by Means of Electric Fields Journal of Physical Chemistry B, 129, 9124–9137. https://doi.org/10.1021/acs.jpcb.5c04393
• Umbaugh, C. S., Groth, M., Erkut, C., Lee, K.-S., Marinho, J., Linder, S., Iser, F., Kapp, J. N., Schroeter, P., Dolaner, S., Kayserili, A., Helm, D., Schneider, M., Hartmann, J., Walch, P., Barth, T. F. E., Mellert, K., Dreier, B., Schaefer, J. V., … Scholl, C. (2025). Selective targeting of TBXT with DARPins identifies regulatory networks and therapeutic vulnerabilities in chordoma Science Advances, 11, eadu2796. https://doi.org/10.1126/sciadv.adu2796
• Florez Ariza, A. J., Lue, N. Z., Grob, P., Kaeser, B., Fang, J., Kassube, S. A., & Nogales, E. (2025). Structural insights into transcriptional regulation by the helicase RECQL5 Nature Structural & Molecular Biology, 32, 1721–1730. https://doi.org/10.1038/s41594-025-01611-8
• Nakadate, M., Kojima, R., Seike, N., Tachibana, R., Fujita, K., Tsuchiya, R., Kamiya, M., Plückthun, A., & Urano, Y. (2025). Design of Antigen-Targeting Fluorogenic Probes Utilizing Intramolecular Addition Reaction of Protein-Dye Hybrids Journal of the American Chemical Society, 147, 30684–30693. https://doi.org/10.1021/jacs.5c04193
• Invernizzi, A., Nai, F., Bedi Rajiv Kumar, Vargas-rosales Pablo Andrés, Li, Y., Bochenkova, E., Herok, M., Zálešák, F., & Caflisch, A. (2025). Discovery of YTHDF2 Ligands by Fragment-Based Design ACS Bio & Med Chem Au, 5, 753–765. https://doi.org/10.1021/acsbiomedchemau.5c00099
• Sukalskaia, A., Karner, A., Pugnetti, A., Weber, F., Plochberger, B., & Dutzler, R. (2025). Interactions between TTYH2 and APOE facilitate endosomal lipid transfer Nature, 644, 273–279. https://doi.org/10.1038/s41586-025-09200-x
• Wang, B., Kronenberg-tenga Rafael, Rosti, V., Di Patrizio Soldateschi, E., Luo, Q., Iannacchero, U. M., Pinet, L., Eibauer, M., Boujemaa-paterski Rajaa, Schuler, B., Lanzuolo, C., & Medalia, O. (2025). The molecular basis of lamin-specific chromatin interactions Nature Structural & Molecular Biology, 32, 1999–2011. https://doi.org/10.1038/s41594-025-01622-5
• Guo, M., Wong, I. Y., Moore, A. S., Medalia, O., Lippincott-Schwartz, J., Weitz, D. A., & Goldman, R. D. (2025). Vimentin intermediate filaments as structural and mechanical coordinators of mesenchymal cells Nature Cell Biology, 27, 1210–1218. https://doi.org/10.1038/s41556-025-01713-x
• Vacca, S., Gragera, M., Buschiazzo, A., Herreros, D., Krieger, J. M., Bonn-Garcia, S., Melero, R., Sorzano, C. O., Carazo, J. M., Medalia, O., & Plückthun, A. (2025). Structural analysis of HER2-trastuzumab complex reveals receptor conformational adaptation Science Advances, 11, eadu9945. https://doi.org/10.1126/sciadv.adu9945
• Loeff, L., Kroupova, A., Asanović, I., Boneberg, F. M., Pfleiderer, M. M., Riermeier, L., Leitner, A., Ferdigg, A., Ackle, F., Martinez, J., & Jinek, M. (2025). Mechanistic basis for PYROXD1-mediated protection of the human tRNA ligase complex against oxidative inactivation Nature Structural & Molecular Biology, 32, 1205–1212. https://doi.org/10.1038/s41594-025-01516-6
• Bromberg, Y., & Schuler, B. (2025). Editorial overview: Protein folding and binding - With a little help from AI Current Opinion in Structural Biology, 94, 103068. https://doi.org/10.1016/j.sbi.2025.103068
• Winkelvoß, D., Vukovic, D., Hänny, A.-C., Riermeier, L., Udovcic, A., Kolibius, J., Honegger, A., Mittl, P. R. E., Michel, E., Hansen, S., & Plückthun, A. (2025). Molecular features defining the efficiency of bioPROTACs Communications Biology, 8, 946. https://doi.org/10.1038/s42003-025-08352-w
• Weiss, F., Kolibius, J., Freitag, P. C., Gantenbein, F., Kipar, A., & Plückthun, A. (2025). Dendritic cell targeting in lymph nodes with modular adapters boosts HAdV5 and HC-HAdV5 tumor vaccination by co-secretion of IL-2v and IL-21 Molecular Therapy. Oncology, 33, 200984. https://doi.org/10.1016/j.omton.2025.200984
• Kapp, J. N., Verdurmen, W. P. R., Schaefer, J. V., Kopra, K., Nagy-Davidescu, G., Richard, E., Nokin, M.-J., Ernst, P., Tamaskovic, R., Schwill, M., Degen, R., Scholl, C., Santamaría, D., & Plückthun, A. (2025). A nucleotide-independent, pan-RAS-targeted DARPin elicits anti-tumor activity in a multimodal manner Molecular Oncology, 19, 3266–3286. https://doi.org/10.1002/1878-0261.70061
• Galvanetto, N., Ivanović, M. T., Del Grosso, S. A., Chowdhury, A., Sottini, A., Nettels, D., Best, R. B., & Schuler, B. (2025). Material properties of biomolecular condensates emerge from nanoscale dynamics Proceedings of the National Academy of Sciences of the United States of America, 122, e2424135122. https://doi.org/10.1073/pnas.2424135122
• Zinsli, L. V., Sobieraj, A. M., Du, J., Ernst, P., Meile, S., Kilcher, S., Iseli, C., Keller, A. P., Dreier, B., Mittl, P. R. E., Plückthun, A., Loessner, M. J., Schmelcher, M., & Dunne, M. (2025). Heterodimerization of staphylococcal phage φ2638A endolysin isoforms and their functional role in bacterial lysis MicroLife, 6, uqaf011. https://doi.org/10.1093/femsml/uqaf011
• Gosselé, K. A., Latino, I., Laul, E., Kirillova, M. S., Pascanu, V., Carloni, E., Bedi, R. K., Pizzichetti, C., Caflisch, A., González, S. F., & Nevado, C. (2025). Selective CBP/EP300 Bromodomain Inhibitors: Novel Epigenetic Tools to Counter TNF-α-Driven Inflammation JACS Au, 5, 2491–2499. https://doi.org/10.1021/jacsau.5c00085
• Sequeira, D. P., Suomalainen, M., Freitag, P. C., Plückthun, A., Klingenbrunner, M., Fischer, L., Hemmi, S., Münz, C., Volle, R., & Greber, U. F. (2025). Activated blood-derived human primary T cells support replication of HAdV C5 and virus transmission to polarized human primary epithelial cells Journal of Virology, 99, e0182524. https://doi.org/10.1128/jvi.01825-24
• Münick, P., Strubel, A., Balourdas, D.-I., Funk, J. S., Mernberger, M., Osterburg, C., Dreier, B., Schaefer, J. V., Tuppi, M., Yüksel, B., Schäfer, B., Knapp, S., Plückthun, A., Stiewe, T., Joerger, A. C., & Dötsch, V. (2025). DARPin-induced reactivation of p53 in HPV-positive cells Nature Structural & Molecular Biology, 32, 790–801. https://doi.org/10.1038/s41594-024-01456-7
• Bobadilla Ugarte, P., Halter, S., Mutte, S. K., Heijstek, C., Niault, T., Terenin, I., Barendse, P., Koopal, B., Roosjen, M., Boeren, S., Hauryliuk, V., Jinek, M., Westphal, A. H., & Swarts, D. C. (2025). Cyanobacterial Argonautes and Cas4 family nucleases cooperate to interfere with invading DNA Molecular Cell, 85, 1920-1937.e10. https://doi.org/10.1016/j.molcel.2025.03.025
• Bugge, K., Sottini, A., Ivanović, M. T., Buus, F. S., Saar, D., Fernandes, C. B., Kocher, F., Martinsen, J. H., Schuler, B., Best, R. B., & Kragelund, B. B. (2025). Role of charges in a dynamic disordered complex between an IDP and a folded domain Nature Communications, 16, 3242. https://doi.org/10.1038/s41467-025-58374-5
• Miró-Vinyals, C., Emmert, S., Grammbitter, G., Jud, A., Kockmann, T., & Rivera Fuentes, P. (2025). Characterization of the glutathione redox state in the Golgi apparatus Redox Biology, 81, 103560. https://doi.org/10.1016/j.redox.2025.103560
• Vitalis, A., Parker, D., Radler, F., Vargas-Rosales, P. A., Zhang, Y., Marchand, J.-R., & Caflisch, A. (2025). Parallelized Tools for the Preparation and Curation of Large Libraries for Virtual Screening Journal of Computational Chemistry, 46, e70074. https://doi.org/10.1002/jcc.70074
• Vitalis, A., Winkler, S., Zhang, Y., Widmer, J., & Caflisch, A. (2025). A FAIR-Compliant Management Solution for Molecular Simulation Trajectories Journal of Chemical Information and Modeling, 65, 2443–2455. https://doi.org/10.1021/acs.jcim.4c01301
• Tröster, V., Wong, R. P., Börgel, A., Cakilkaya, B., Renz, C., Möckel, M. M., Eifler-Olivi, K., Marinho, J., Reinberg, T., Furler, S., Schaefer, J. V., Plückthun, A., Wolf, E., & Ulrich, H. D. (2025). Custom affinity probes reveal DNA-damage-induced, ssDNA-independent chromatin SUMOylation in budding yeast Cell Reports, 44, 115353. https://doi.org/10.1016/j.celrep.2025.115353
• Finocchio, G., Querques, I., Chanez, C., Speichert, K. J., & Jinek, M. (2025). Structural basis of TnsC oligomerization and transposase recruitment in type I-B CRISPR-associated transposons Nucleic Acids Research, 53, gkaf149. https://doi.org/10.1093/nar/gkaf149
• Muhar, M. F., Farnung, J., Cernakova, M., Hofmann, R., Henneberg, L. T., Pfleiderer, M. M., Denoth-Lippuner, A., Kalčic, F., Nievergelt, A. S., Peters Al-Bayati, M., Sidiropoulos, N. D., Beier, V., Mann, M., Jessberger, S., Jinek, M., Schulman, B. A., Bode, J. W., & Corn, J. E. (2025). C-terminal amides mark proteins for degradation via SCF-FBXO31 Nature, 638, 519–527. https://doi.org/10.1038/s41586-024-08475-w
• Loeff, L., Walter, A., Rosalen, G. T., & Jinek, M. (2025). DNA end sensing and cleavage by the Shedu anti-phage defense system Cell, 188, 721-733.e17. https://doi.org/10.1016/j.cell.2024.11.030
• Vargas-Rosales, P. A., & Caflisch, A. (2025). The physics-AI dialogue in drug design RSC Medicinal Chemistry, 16, 1499–1515. https://doi.org/10.1039/d4md00869c
• Liziczai, M., Fuchs, A., Manatschal, C., & Dutzler, R. (2025). Structural basis for metal ion transport by the human SLC11 proteins DMT1 and NRAMP1 Nature Communications, 16, 761. https://doi.org/10.1038/s41467-024-54705-0
• Jungfer, K., Moravčík, Š., Garcia-Doval, C., Knörlein, A., Hall, J., & Jinek, M. (2025). Mechanistic determinants and dynamics of cA6 synthesis in type III CRISPR-Cas effector complexes Nucleic Acids Research, 53, gkae1277. https://doi.org/10.1093/nar/gkae1277
• Wang, B., Luo, Q., & Medalia, O. (2025). Lamins and chromatin join forces Advances in Biological Regulation, 95, 101059. https://doi.org/10.1016/j.jbior.2024.101059
• Zhang, Y., & Vitalis, A. (2025). Benchmarking the robustness of the correct identification of flexible 3D objects using common machine learning models Patterns, 6, 101147. https://doi.org/10.1016/j.patter.2024.101147