Publications 2024

ZORA Publication List

Publications

• Newcombe, E. A., Due, A. D., Sottini, A., Elkjær, S., Theisen, F. F., Fernandes, C. B., Staby, L., Delaforge, E., Bartling, C. R. O., Brakti, I., Bugge, K., Schuler, B., Skriver, K., Olsen, J. G., & Kragelund, B. B. (2024). Stereochemistry in the disorder-order continuum of protein interactions Nature, 636, 762–768. https://doi.org/10.1038/s41586-024-08271-6
• Münick, P., Zielinski, J., Strubel, A., Gutfreund, N., Dreier, B., Schaefer, J. V., Schäfer, B., Gebel, J., Osterburg, C., Chaikuad, A., Knapp, S., Plückthun, A., & Dötsch, V. (2024). DARPins as a novel tool to detect and degrade p73 Cell Death and Disease, 15, 909. https://doi.org/10.1038/s41419-024-07304-2
• Quinodoz, M., Rutz, S., Peter, V., Garavelli, L., Innes, A. M., Lehmann, E. F., Kellenberger, S., Peng, Z., Barone, A., Campos-Xavier, B., Unger, S., Rivolta, C., Dutzler, R., & Superti-Furga, A. (2024). De novo variants in LRRC8C resulting in constitutive channel activation cause a human multisystem disorder The EMBO Journal, 44, 413–436. https://doi.org/10.1038/s44318-024-00322-y
• Kono, Y., Pack, C.-G., Ichikawa, T., Komatsubara, A., Adam, S. A., Miyazawa, K., Rolas, L., Nourshargh, S., Medalia, O., Goldman, R. D., Fukuma, T., Kimura, H., & Shimi, T. (2024). Roles of the lamin A-specific tail region in the localization to sites of nuclear envelope rupture PNAS Nexus, 3, pgae527. https://doi.org/10.1093/pnasnexus/pgae527
• Janke, C., & Medalia, O. (2024). Editorial: Modern approaches in cytoskeleton-related topics Current Opinion in Cell Biology, 91, 102423. https://doi.org/10.1016/j.ceb.2024.102423
• Notbohm, J., & Perica, T. (2024). Biochemistry and genetics are coming together to improve our understanding of genotype to phenotype relationships Current Opinion in Structural Biology, 89, 102952. https://doi.org/10.1016/j.sbi.2024.102952
• Widmer, J., Vitalis, A., & Caflisch, A. (2024). On the specificity of the recognition of m6A-RNA by YTH reader domains Journal of Biological Chemistry, 300, 107998. https://doi.org/10.1016/j.jbc.2024.107998
• Tarullo, M., Fernandez Rodriguez, G., Iaiza, A., Venezia, S., Macone, A., Incocciati, A., Masciarelli, S., Marchioni, M., Giorgis, M., Lolli, M. L., Fornaseri, F., Proietti, L., Grebien, F., Rosignoli, S., Paiardini, A., Rotili, D., Mai, A., Bochenkova, E., Caflisch, A., … Fatica, A. (2024). Off-Target Inhibition of Human Dihydroorotate Dehydrogenase (hDHODH) Highlights Challenges in the Development of Fat Mass and Obesity-Associated Protein (FTO) Inhibitors ACS Pharmacology & Translational Science, 7, 4096–4111. https://doi.org/10.1021/acsptsci.4c00533
• Henkin, G., Brito, C., Plückthun, A., & Surrey, T. (2024). Preparation of Polarity-Marked Microtubules Using a Plus-End Capping DARPin Bio-Protocol, 14, e5109. https://doi.org/10.21769/BioProtoc.5109
• Holla, A., Martin, E. W., Dannenhoffer-Lafage, T., Ruff, K. M., König, S. L. B., Nüesch, M. F., Chowdhury, A., Louis, J. M., Soranno, A., Nettels, D., Pappu, R. V., Best, R. B., Mittag, T., & Schuler, B. (2024). Identifying Sequence Effects on Chain Dimensions of Disordered Proteins by Integrating Experiments and Simulations JACS Au, 4, 4729–4743. https://doi.org/10.1021/jacsau.4c00673
• Vukovic, D., Winkelvoss, D., Kapp, J. N., Hänny, A.-C., Bürgisser, H., Riermeier, L., Udovcic, A., Tiefenboeck, P., & Plückthun, A. (2024). Protein degradation kinetics measured by microinjection and live-cell fluorescence microscopy Scientific Reports, 14, 27153. https://doi.org/10.1038/s41598-024-76224-0
• Cazzanelli, G., Dalle Vedove, A., Sbardellati, N., Valer, L., Caflisch, A., & Lolli, G. (2024). Enhanced cellular death in liver and breast cancer cells by dual BET/BRPF1 inhibitors Protein Science, 33, e5191. https://doi.org/10.1002/pro.5191
• Mahran, R., Kapp, J. N., Valtonen, S., Champagne, A., Ning, J., Gillette, W., Stephen, A. G., Hao, F., Plückthun, A., Härmä, H., Pantsar, T., & Kopra, K. (2024). Beyond KRAS(G12C): Biochemical and Computational Characterization of Sotorasib and Adagrasib Binding Specificity and the Critical Role of H95 and Y96 ACS Chemical Biology, 19, 2152–2164. https://doi.org/10.1021/acschembio.4c00315
• Hwang, W., Austin, S. L., Blondel, A., Boittier, E. D., Boresch, S., Buck, M., Buckner, J., Caflisch, A., Chang, H.-T., Cheng, X., Choi, Y. K., Chu, J.-W., Crowley, M. F., Cui, Q., Damjanovic, A., Deng, Y., Devereux, M., Ding, X., Feig, M. F., … et al. (2024). CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed Journal of Physical Chemistry B, 128, 9976–10042. https://doi.org/10.1021/acs.jpcb.4c04100
• Raimondi, F., Siow, K. M., Wrona, D., Fuster-García, C., Pastukhov, O., Schmitz, M., Bargsten, K., Kissling, L., Swarts, D. C., Andrieux, G., Cathomen, T., Modlich, U., Jinek, M., Siler, U., & Reichenbach, J. (2024). Gene editing of NCF1 loci is associated with homologous recombination and chromosomal rearrangements Communications Biology, 7, 1291. https://doi.org/10.1038/s42003-024-06959-z
• Zhou, Z., Nguyen, T. L., Li, X., Poujol, C., Berlinska, E., Michelina, S. V., Kapp, J. N., Plückthun, A., Winslow, M. M., Ambrogio, C., Shan, Y., Santamaría, D., & Westover, K. D. (2024). Experimental variables determine the outcome of RAS-RAS interactions Journal of Biological Chemistry, 300, 107859. https://doi.org/10.1016/j.jbc.2024.107859
• Cheng-Sánchez, I., Gosselé, K., Palaferri, L., Laul, E., Riccabella, G., Bedi, R. K., Li, Y., Müller, A., Corbeski, I., Caflisch, A., & Nevado, C. (2024). Structure-Based Design of CBP/EP300 Degraders: When Cooperativity Overcomes Affinity JACS Au, 4, 3466–3474. https://doi.org/10.1021/jacsau.4c00292
• Freitag, P. C., Kolibius, J., Wieboldt, R., Weber, R., Hartmann, K. P., van Gogh, M., Brücher, D., Läubli, H., & Plückthun, A. (2024). DARPin-fused T cell engager for adenovirus-mediated cancer therapy Molecular Therapy. Oncology, 32, 200821. https://doi.org/10.1016/j.omton.2024.200821
• Nettels, D., Galvanetto, N., Ivanović, M. T., Nüesch, M., Yang, T., & Schuler, B. (2024). Single-molecule FRET for probing nanoscale biomolecular dynamics Nature Reviews. Physics, 6, 587–605. https://doi.org/10.1038/s42254-024-00748-7
• Siow, K. M., Güngör, M., Wrona, D., Raimondi, F., Pastukhov, O., Tsapogas, P., Menzi, T., Schmitz, M., Kulcsár, P. I., Schwank, G., Schulz, A., Jinek, M., Modlich, U., Siler, U., & Reichenbach, J. (2024). Targeted knock-in of NCF1 cDNA into the NCF2 locus leads to myeloid phenotypic correction of p47 $^{phox}$ -deficient chronic granulomatous disease Molecular Therapy : Nucleic Acids, 35, 102229. https://doi.org/10.1016/j.omtn.2024.102229
• Zhou, J., Assenza, S., Tatli, M., Tian, J., Ilie, I. M., Starostin, E. L., Caflisch, A., Knowles, T. P. J., Dietler, G., Ruggeri, F. S., Stahlberg, H., Sekatskii, S. K., & Mezzenga, R. (2024). Hierarchical Protofilament Intertwining Rules the Formation of Mixed-Curvature Amyloid Polymorphs Advanced Science, 11, e2402740. https://doi.org/10.1002/advs.202402740
• Weibel, N., Curcio, M., Schreiber, A., Arriaga, G., Mausy, M., Mehdy, J., Brüllmann, L., Meyer, A., Roth, L., Flury, T., Pecina, V., Starlinger, K., Dernič, J., Jungfer, K., Ackle, F., Earp, J., Hausmann, M., Jinek, M., Rogler, G., & Antunes Westmann, C. (2024). Engineering a Novel Probiotic Toolkit in Escherichia coli Nissle 1917 for Sensing and Mitigating Gut Inflammatory Diseases ACS Synthetic Biology, 13, 2376–2390. https://doi.org/10.1021/acssynbio.4c00036
• Coelho-Rato, L. S., Parvanian, S., Andrs Salajkova, S., Medalia, O., & Eriksson, J. E. (2024). Intermediate filaments at a glance Journal of Cell Science, 137, jcs261386. https://doi.org/10.1242/jcs.261386
• Kechagia, Z., Eibauer, M., & Medalia, O. (2024). Structural determinants of intermediate filament mechanics Current Opinion in Cell Biology, 89, 102375. https://doi.org/10.1016/j.ceb.2024.102375
• Auger, S. A., Venkatachalapathy, S., Suazo, K. F. G., Wang, Y., Sarkis, A. W., Bernhagen, K., Justyna, K., Schaefer, J. V., Wollack, J. W., Plückthun, A., Li, L., & Distefano, M. D. (2024). Broadening the Utility of Farnesyltransferase-Catalyzed Protein Labeling Using Norbornene-Tetrazine Click Chemistry Bioconjugate Chemistry, 35, 922–933. https://doi.org/10.1021/acs.bioconjchem.4c00072
• Nüesch, M. F., Pietrek, L., Holmstrom, E. D., Nettels, D., von Roten, V., Kronenberg-Tenga, R., Medalia, O., Hummer, G., & Schuler, B. (2024). Nanosecond chain dynamics of single-stranded nucleic acids Nature Communications, 15, 6010. https://doi.org/10.1038/s41467-024-50092-8
• Loeff, L., Adams, D. W., Chanez, C., Stutzmann, S., Righi, L., Blokesch, M., & Jinek, M. (2024). Molecular mechanism of plasmid elimination by the DdmDE defense system Science, 385, 188–194. https://doi.org/10.1126/science.adq0534
• Reginato, G., Dello Stritto, M. R., Wang, Y., Hao, J., Pavani, R., Schmitz, M., Halder, S., Morin, V., Cannavo, E., Ceppi, I., Braunshier, S., Acharya, A., Ropars, V., Charbonnier, J.-B., Jinek, M., Nussenzweig, A., Ha, T., & Cejka, P. (2024). HLTF disrupts Cas9-DNA post-cleavage complexes to allow DNA break processing Nature Communications, 15, 5789. https://doi.org/10.1038/s41467-024-50080-y
• Stark, Y., Menard, F., Jeliazkov, J. R., Ernst, P., Chembath, A., Ashraf, M., Hine, A. V., & Plückthun, A. (2024). Modular binder technology by NGS-aided, high-resolution selection in yeast of designed armadillo modules Proceedings of the National Academy of Sciences of the United States of America, 121, e2318198121. https://doi.org/10.1073/pnas.2318198121
• Houvast, R. D., Badr, N., March, T., de Muynck, L. D. A. N., Sier, V. Q., Schomann, T., Bhairosingh, S., Baart, V. M., Peeters, J. A. H. M., van Westen, G. J. P., Plückthun, A., Burggraaf, J., Kuppen, P. J. K., Vahrmeijer, A. L., & Sier, C. F. M. (2024). Preclinical evaluation of EpCAM-binding designed ankyrin repeat proteins (DARPins) as targeting moieties for bimodal near-infrared fluorescence and photoacoustic imaging of cancer European Journal of Nuclear Medicine and Molecular Imaging, 51, 2179–2192. https://doi.org/10.1007/s00259-023-06407-w
• Dederer, V., Sanz Murillo, M., Karasmanis, E. P., Hatch, K. S., Chatterjee, D., Preuss, F., Abdul Azeez, K. R., Nguyen, L. V., Galicia, C., Dreier, B., Plückthun, A., Versees, W., Mathea, S., Leschziner, A. E., Reck-Peterson, S. L., & Knapp, S. (2024). A designed ankyrin-repeat protein that targets Parkinson’s disease-associated LRRK2. Journal of Biological Chemistry, 300, 107469. https://doi.org/10.1016/j.jbc.2024.107469
• Bastiaanssen, C., Bobadilla Ugarte, P., Kim, K., Finocchio, G., Feng, Y., Anzelon, T. A., Köstlbacher, S., Tamarit, D., Ettema, T. J. G., Jinek, M., MacRae, I. J., Joo, C., Swarts, D. C., & Wu, F. (2024). RNA-guided RNA silencing by an Asgard archaeal Argonaute Nature Communications, 15, 5499. https://doi.org/10.1038/s41467-024-49452-1
• Cui, Z., Ayva, C. E., Liew, Y. J., Guo, Z., Mutschler, R., Dreier, B., Fiorito, M. M., Walden, P., Howard, C. B., Ely, F., Plückthun, A., Pretorius, C., Ungerer, J. P., Buckle, A. M., & Alexandrov, K. (2024). mRNA Display Pipeline for Protein Biosensor Construction ACS Sensors, 9, 2846–2857. https://doi.org/10.1021/acssensors.3c02471
• Drożdżyk, K., Peter, M., & Dutzler, R. (2024). Structural features of heteromeric channels composed of CALHM2 and CALHM4 paralogs ELife, 13, RP96138. https://doi.org/10.7554/eLife.96138
• Zálešák, F., Nai, F., Herok, M., Bochenkova, E., Bedi, R. K., Li, Y., Errani, F., & Caflisch, A. (2024). Structure-Based Design of a Potent and Selective YTHDC1 Ligand Journal of Medicinal Chemistry, 67, 9516–9535. https://doi.org/10.1021/acs.jmedchem.4c00599
• Eibauer, M., Weber, M. S., Kronenberg-Tenga, R., Beales, C. T., Boujemaa-Paterski, R., Turgay, Y., Sivagurunathan, S., Kraxner, J., Köster, S., Goldman, R. D., & Medalia, O. (2024). Vimentin filaments integrate low-complexity domains in a complex helical structure Nature Structural & Molecular Biology, 31, 939–949. https://doi.org/10.1038/s41594-024-01261-2
• Nai, F., Flores Espinoza, M. P., Invernizzi, A., Vargas-Rosales, P. A., Bobileva, O., Herok, M., & Caflisch, A. (2024). Small-Molecule Inhibitors of the m7G-RNA Writer METTL1 ACS Bio & Med Chem Au, 4, 100–110. https://doi.org/10.1021/acsbiomedchemau.3c00030
• Ivanova, J. R., Benk, A. S., Schaefer, J. V., Dreier, B., Hermann, L. O., Plückthun, A., Missirlis, D., & Spatz, J. P. (2024). Designed Ankyrin Repeat Proteins as Actin Labels of Distinct Cytoskeletal Structures in Living Cells ACS Nano, 18, 8919–8933. https://doi.org/10.1021/acsnano.3c12265
• Corbeski, I., Vargas-Rosales, P. A., Bedi, R. K., Deng, J., Coelho, D., Braud, E., Iannazzo, L., Li, Y., Huang, D., Ethève-Quelquejeu, M., Cui, Q., & Caflisch, A. (2024). The catalytic mechanism of the RNA methyltransferase METTL3 ELife, 12, RP92537. https://doi.org/10.7554/eLife.92537
• Weber, Y., Böck, D., Ivașcu, A., Mathis, N., Rothgangl, T., Ioannidi, E. I., Blaudt, A. C., Tidecks, L., Vadovics, M., Muramatsu, H., Reichmuth, A., Marquart, K. F., Kissling, L., Pardi, N., Jinek, M., & Schwank, G. (2024). Enhancing prime editor activity by directed protein evolution in yeast Nature Communications, 15, 2092. https://doi.org/10.1038/s41467-024-46107-z
• Thalmann, L., Martín-González, N., Brücher, D., Plückthun, A., de Pablo, P. J., Suomalainen, M., & Greber, U. (2024). Gutless helper-dependent and first generation HAdV5 vectors have similar mechanical properties and common transduction mechanisms Human Gene Therapy, 35, 163–176. https://doi.org/10.1089/hum.2023.221
• Schmidheini, L., Mathis, N., Marquart, K. F., Rothgangl, T., Kissling, L., Böck, D., Chanez, C., Wang, J. P., Jinek, M., & Schwank, G. (2024). Continuous directed evolution of a compact CjCas9 variant with broad PAM compatibility Nature Chemical Biology, 20, 333–343. https://doi.org/10.1038/s41589-023-01427-x
• Klinnert, S., Schenkel, C. D., Freitag, P. C., Günthard, H. F., Plückthun, A., & Metzner, K. J. (2024). Targeted shock-and-kill HIV-1 gene therapy approach combining CRISPR activation, suicide gene tBid and retargeted adenovirus delivery Gene Therapy, 31, 74–84. https://doi.org/10.1038/s41434-023-00413-1
• Pacesa, M., Pelea, O., & Jinek, M. (2024). Past, present, and future of CRISPR genome editing technologies Cell, 187, 1076–1100. https://doi.org/10.1016/j.cell.2024.01.042
• Finocchio, G., Koopal, B., Potocnik, A., Heijstek, C., Westphal, A. H., Jinek, M., & Swarts, D. C. (2024). Target DNA-dependent activation mechanism of the prokaryotic immune system SPARTA Nucleic Acids Research, 52, 2012–2029. https://doi.org/10.1093/nar/gkad1248
• Errani, F., Invernizzi, A., Herok, M., Bochenkova, E., Stamm, F., Corbeski, I., Romanucci, V., Di Fabio, G., Zálešák, F., & Caflisch, A. (2024). Proteolysis Targeting Chimera Degraders of the METTL3-14 m$^{6}$A-RNA Methyltransferase JACS Au, 4, 713–729. https://doi.org/10.1021/jacsau.4c00040
• Saha, A., Ahsan, M., Arantes, P. R., Schmitz, M., Chanez, C., Jinek, M., & Palermo, G. (2024). An alpha-helical lid guides the target DNA toward catalysis in CRISPR-Cas12a Nature Communications, 15, 1473. https://doi.org/10.1038/s41467-024-45762-6
• Grabenhorst, L., Sturzenegger, F., Hasler, M., Schuler, B., & Tinnefeld, P. (2024). Single-Molecule FRET at 10 MHz Count Rates Journal of the American Chemical Society, 146, 3539–3544. https://doi.org/10.1021/jacs.3c13757
• Abdul-Ridha, A., de Zhang, L. A., Betrie, A. H., Deluigi, M., Vaid, T. M., Whitehead, A., Zhang, Y., Davis, B., Harris, R., Simmonite, H., Hubbard, R. E., Gooley, P. R., Plückthun, A., Bathgate, R. A. D., Chalmers, D. K., & Scott, D. J. (2024). Identification of a Novel Subtype-Selective α$_{1B}$-Adrenoceptor Antagonist ACS Chemical Neuroscience, 15, 671–684. https://doi.org/10.1021/acschemneuro.3c00767
• Tinzl, M., Diedrich, J. V., Mittl, P. R. E., Clémancey, M., Reiher, M., Proppe, J., Latour, J.-M., & Hilvert, D. (2024). Myoglobin-Catalyzed Azide Reduction Proceeds via an Anionic Metal Amide Intermediate Journal of the American Chemical Society, 146, 1957–1966. https://doi.org/10.1021/jacs.3c09279
• Jungfer, K., Sigg, A., & Jinek, M. (2024). Substrate selectivity and catalytic activation of the type III CRISPR ancillary nuclease Can2 Nucleic Acids Research, 52, 462–473. https://doi.org/10.1093/nar/gkad1102