Publications 2025

ZORA Publication List

Publications

• Cruz, A. R., Wimmer, B. H., Teo, T. H., Pehau-Arnaudet, G., Winter, J.-M., Gazi, A. D., Lafaye, P., Brier, S., Legrand, A., Dubrovsky-Gaupp, A., Bérard, M., Aymé, G., Sartori-Rupp, A., Medalia, O., & Schnupf, P. (2025). Segmented filamentous bacteria undergo a structural transition at their adhesive tip during unicellular to filament development Nature Communications, online. https://doi.org/10.1038/s41467-025-66892-5
• 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(4), 101582. https://doi.org/10.1016/j.omtm.2025.101582
• Phillips, M., Holla, A., Wojtas, M., Chowdhury, A., Sottini, A., König, S. L. B., Mutter, N., Lamb, N., Huihui, J., Lopko, M., Soranno, A., Nettels, D., Ożyhar, A., Schuler, B., & Ghosh, K. (2025). Mapping Charge Interactions in Intrinsically Disordered Proteins Advanced Science, online. https://doi.org/10.1002/advs.202514056
• 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, online. 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(19), 194908. https://doi.org/10.1063/5.0297651
• Zhang, S., Liu, S., Lai, H.-F., Bender, K. W., Kim, G., Caflisch, A., & Zipfel, C. (2025). Author Correction: Reverse engineering of the pattern recognition receptor FLS2 reveals key design principles of broader recognition spectra against evading flg22 epitopes Nature Plants, 11(11), 2437. https://doi.org/10.1038/s41477-025-02166-8
• 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, Epub ahead of print. 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, 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
• 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
• 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, online. https://doi.org/10.1038/s41594-025-01660-z
• 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, Anastasiia; Karner, Andreas; Pugnetti, Anna; Weber, Florian; Plochberger, Birgit; Dutzler, Raimund (2025). Interactions between TTYH2 and APOE facilitate endosomal lipid transfer Nature, 644(8075):273-279.
• 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
• 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, online. https://doi.org/10.1038/s41594-025-01622-5
• Zhang, S., Liu, S., Lai, H.-F., Bender, K. W., Kim, G., Caflisch, A., & Zipfel, C. (2025). Reverse engineering of the pattern recognition receptor FLS2 reveals key design principles of broader recognition spectra against evading flg22 epitopes Nature Plants, 11, 1642–1657. https://doi.org/10.1038/s41477-025-02050-5
• 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
• 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, Epub ahead of print. https://doi.org/10.1038/s41594-025-01611-8
• Loeff, Luuk; Kroupova, Alena; Asanović, Igor; Boneberg, Franziska M; Pfleiderer, Moritz M; Riermeier, Luca; Leitner, Alexander; Ferdigg, Andrè; Ackle, Fabian; Martinez, Javier; Jinek, Martin (2025). Mechanistic basis for PYROXD1-mediated protection of the human tRNA ligase complex against oxidative inactivation Nature Structural & Molecular Biology, 32(7):1205-1212.
• Bromberg, Yana; Schuler, Benjamin (2025). Editorial overview: Protein folding and binding - With a little help from AI Current Opinion in Structural Biology, 94:103068.
• Winkelvoß, Dorothea; Vukovic, David; Hänny, Anna-Carina; Riermeier, Luca; Udovcic, Anto; Kolibius, Jonas; Honegger, Annemarie; Mittl, Peer R E; Michel, Erich; Hansen, Simon; Plückthun, Andreas (2025). Molecular features defining the efficiency of bioPROTACs Communications Biology, 8(1):946.
• Weiss, Fabian; Kolibius, Jonas; Freitag, Patrick C; Gantenbein, Felix; Kipar, Anja; Plückthun, Andreas (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(2):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, Epub ahead of print. https://doi.org/10.1002/1878-0261.70061
• Zinsli, Léa V; Sobieraj, Anna M; Du, Jiemin; Ernst, Patrick; Meile, Susanne; Kilcher, Samuel; Iseli, Cedric; Keller, Anja P; Dreier, Birgit; Mittl, Peer R E; Plückthun, Andreas; Loessner, Martin J; Schmelcher, Mathias; Dunne, Matthew (2025). Heterodimerization of staphylococcal phage φ2638A endolysin isoforms and their functional role in bacterial lysis microLife, 6:uqaf011.
• Galvanetto, Nicola; Ivanović, Miloš T; Del Grosso, Simone A; Chowdhury, Aritra; Sottini, Andrea; Nettels, Daniel; Best, Robert B; Schuler, Benjamin (2025). Material properties of biomolecular condensates emerge from nanoscale dynamics Proceedings of the National Academy of Sciences of the United States of America, 122(23):e2424135122.
• Gosselé, Katherine A; Latino, Irene; Laul, Eleen; Kirillova, Mariia S; Pascanu, Vlad; Carloni, Emanuele; Bedi, Rajiv K; Pizzichetti, Chiara; Caflisch, Amedeo; González, Santiago F; Nevado, Cristina (2025). Selective CBP/EP300 Bromodomain Inhibitors: Novel Epigenetic Tools to Counter TNF-α-Driven Inflammation JACS Au, 5(6):2491-2499.
• Sequeira, Daniela Policarpo; Suomalainen, Maarit; Freitag, Patrick C; Plückthun, Andreas; Klingenbrunner, Michael; Fischer, Lucy; Hemmi, Silvio; Münz, Christian; Volle, Romain; Greber, Urs 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(5):e0182524.
• Münick, Philipp; Strubel, Alexander; Balourdas, Dimitrios-Ilias; Funk, Julianne S; Mernberger, Marco; Osterburg, Christian; Dreier, Birgit; Schaefer, Jonas V; Tuppi, Marcel; Yüksel, Büşra; Schäfer, Birgit; Knapp, Stefan; Plückthun, Andreas; Stiewe, Thorsten; Joerger, Andreas C; Dötsch, Volker (2025). DARPin-induced reactivation of p53 in HPV-positive cells Nature Structural & Molecular Biology, 32(5):790-801.
• Bobadilla Ugarte, Pilar; Halter, Stefanie; Mutte, Sumanth K; Heijstek, Clint; Niault, Theophile; Terenin, Ilya; Barendse, Patrick; Koopal, Balwina; Roosjen, Mark; Boeren, Sjef; Hauryliuk, Vasili; Jinek, Martin; Westphal, Adrie H; Swarts, Daan C (2025). Cyanobacterial Argonautes and Cas4 family nucleases cooperate to interfere with invading DNA Molecular Cell, 85(10):1920-1937.e10.
• Bugge, Katrine; Sottini, Andrea; Ivanović, Miloš T; Buus, Freia S; Saar, Daniel; Fernandes, Catarina B; Kocher, Fabienne; Martinsen, Jacob H; Schuler, Benjamin; Best, Robert B; Kragelund, Birthe B (2025). Role of charges in a dynamic disordered complex between an IDP and a folded domain Nature Communications, 16(1):3242.
• Vitalis, Andreas; Parker, David; Radler, Fabian; Vargas-Rosales, Pablo Andrés; Zhang, Yang; Marchand, Jean-Rémy; Caflisch, Amedeo (2025). Parallelized Tools for the Preparation and Curation of Large Libraries for Virtual Screening Journal of Computational Chemistry, 46(7):e70074.
• Vitalis, Andreas; Winkler, Steffen; Zhang, Yang; Widmer, Julian; Caflisch, Amedeo (2025). A FAIR-Compliant Management Solution for Molecular Simulation Trajectories Journal of Chemical Information and Modeling, 65(5):2443-2455.
• Tröster, Vera; Wong, Ronald P; Börgel, Arne; Cakilkaya, Baris; Renz, Christian; Möckel, Martin M; Eifler-Olivi, Karolin; Marinho, Joana; Reinberg, Thomas; Furler, Sven; Schaefer, Jonas V; Plückthun, Andreas; Wolf, Eva; Ulrich, Helle D (2025). Custom affinity probes reveal DNA-damage-induced, ssDNA-independent chromatin SUMOylation in budding yeast Cell Reports, 44(3):115353.
• Finocchio, Giada; Querques, Irma; Chanez, Christelle; Speichert, Katarzyna J; Jinek, Martin (2025). Structural basis of TnsC oligomerization and transposase recruitment in type I-B CRISPR-associated transposons Nucleic Acids Research, 53(5):gkaf149.
• Muhar, Matthias F; Farnung, Jakob; Cernakova, Martina; Hofmann, Raphael; Henneberg, Lukas T; Pfleiderer, Moritz M; Denoth-Lippuner, Annina; Kalčic, Filip; Nievergelt, Ajse S; Peters Al-Bayati, Marwa; Sidiropoulos, Nikolaos D; Beier, Viola; Mann, Matthias; Jessberger, Sebastian; Jinek, Martin; Schulman, Brenda A; Bode, Jeffrey W; Corn, Jacob E (2025). C-terminal amides mark proteins for degradation via SCF-FBXO31 Nature, 638(8050):519-527.
• Loeff, Luuk; Walter, Alexander; Rosalen, Gian Tizio; Jinek, Martin (2025). DNA end sensing and cleavage by the Shedu anti-phage defense system Cell, 188(3):721-733.e17.
• Vargas-Rosales, Pablo Andrés; Caflisch, Amedeo (2025). The physics-AI dialogue in drug design RSC Medicinal Chemistry, 16(4):1499-1515.
• Liziczai, Márton; Fuchs, Ariane; Manatschal, Cristina; Dutzler, Raimund (2025). Structural basis for metal ion transport by the human SLC11 proteins DMT1 and NRAMP1 Nature Communications, 16(1):761.
• Jungfer, Kenny; Moravčík, Štefan; Garcia-Doval, Carmela; Knörlein, Anna; Hall, Jonathan; Jinek, Martin (2025). Mechanistic determinants and dynamics of cA6 synthesis in type III CRISPR-Cas effector complexes Nucleic Acids Research, 53(2):gkae1277.
• Zhang, Yang; Vitalis, Andreas (2025). Benchmarking the robustness of the correct identification of flexible 3D objects using common machine learning models Patterns, 6(1):101147.
• Wang, Baihui; Luo, Qiang; Medalia, Ohad (2025). Lamins and chromatin join forces Advances in Biological Regulation, 95:101059.