Publications 2024

ZORA Publication List

Publications

• Janke, Carsten; Medalia, Ohad (2024). Editorial: Modern approaches in cytoskeleton-related topics. Current Opinion in Cell Biology, 91:102423.
• Mahran, Randa; Kapp, Jonas N; Valtonen, Salla; Champagne, Allison; Ning, Jinying; Gillette, William; Stephen, Andrew G; Hao, Feng; Plückthun, Andreas; Härmä, Harri; Pantsar, Tatu; Kopra, Kari (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(10):2152-2164.
• Hwang, Wonmuk; Austin, Steven L; Blondel, Arnaud; Boittier, Eric D; Boresch, Stefan; Buck, Matthias; Buckner, Joshua; Caflisch, Amedeo; Chang, Hao-Ting; Cheng, Xi; Choi, Yeol Kyo; Chu, Jhih-Wei; Crowley, Michael F; Cui, Qiang; Damjanovic, Ana; Deng, Yuqing; Devereux, Mike; Ding, Xinqiang; Feig, Michael F; Gao, Jiali; Glowacki, David R; Gonzales, James E; Hamaneh, Mehdi Bagerhi; Harder, Edward D; Hayes, Ryan L; Huang, Jing; Huang, Yandong; Hudson, Phillip S; Im, Wonpil; Islam, Shahidul M; et al (2024). CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed. Journal of Physical Chemistry B, 128(41):9976-10042.
• Raimondi, Federica; Siow, Kah Mun; Wrona, Dominik; Fuster-García, Carla; Pastukhov, Oleksandr; Schmitz, Michael; Bargsten, Katja; Kissling, Lucas; Swarts, Daan C; Andrieux, Geoffroy; Cathomen, Toni; Modlich, Ute; Jinek, Martin; Siler, Ulrich; Reichenbach, Janine (2024). Gene editing of NCF1 loci is associated with homologous recombination and chromosomal rearrangements. Communications Biology, 7(1):1291.
• Zhou, Zhiwei; Nguyen, Tra Ly; Li, Xingxiao; Poujol, Christel; Berlinska, Ewa; Michelina, Sandra Vietti; Kapp, Jonas N; Plückthun, Andreas; Winslow, Monte M; Ambrogio, Chiara; Shan, Yibing; Santamaría, David; Westover, Kenneth D (2024). Experimental variables determine the outcome of RAS-RAS interactions. Journal of Biological Chemistry, 300(11):107859.
• Cheng-Sánchez, Iván; Gosselé, Katherine; Palaferri, Leonardo; Laul, Eleen; Riccabella, Gionata; Bedi, Rajiv K; Li, Yaozong; Müller, Anna; Corbeski, Ivan; Caflisch, Amedeo; Nevado, Cristina (2024). Structure-Based Design of CBP/EP300 Degraders: When Cooperativity Overcomes Affinity. JACS Au, 4(9):3466-3474.
• Freitag, Patrick C; Kolibius, Jonas; Wieboldt, Ronja; Weber, Remi; Hartmann, K Patricia; van Gogh, Merel; Brücher, Dominik; Läubli, Heinz; Plückthun, Andreas (2024). DARPin-fused T cell engager for adenovirus-mediated cancer therapy. Molecular therapy. Oncology, 32(3):200821.
• Siow, Kah Mun; Güngör, Merve; Wrona, Dominik; Raimondi, Federica; Pastukhov, Oleksandr; Tsapogas, Panagiotis; Menzi, Timon; Schmitz, Michael; Kulcsár, Péter István; Schwank, Gerald; Schulz, Ansgar; Jinek, Martin; Modlich, Ute; Siler, Ulrich; Reichenbach, Janine (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(3):102229.
• Zhou, Jiangtao; Assenza, Salvatore; Tatli, Meltem; Tian, Jiawen; Ilie, Ioana M; Starostin, Eugene L; Caflisch, Amedeo; Knowles, Tuomas P J; Dietler, Giovanni; Ruggeri, Francesco S; Stahlberg, Henning; Sekatskii, Sergey K; Mezzenga, Raffaele (2024). Hierarchical Protofilament Intertwining Rules the Formation of Mixed-Curvature Amyloid Polymorphs. Advanced Science, 11(32):e2402740.
• Weibel, Nathalie; Curcio, Martina; Schreiber, Atilla; Arriaga, Gabriel; Mausy, Marine; Mehdy, Jana; Brüllmann, Lea; Meyer, Andreas; Roth, Len; Flury, Tamara; Pecina, Valerie; Starlinger, Kim; Dernič, Jan; Jungfer, Kenny; Ackle, Fabian; Earp, Jennifer; Hausmann, Martin; Jinek, Martin; Rogler, Gerhard; Antunes Westmann, Cauã (2024). Engineering a Novel Probiotic Toolkit in Escherichia coli Nissle 1917 for Sensing and Mitigating Gut Inflammatory Diseases. ACS Synthetic Biology, 13(8):2376-2390.
• Coelho-Rato, Leila S; Parvanian, Sepideh; Andrs Salajkova, Sarka; Medalia, Ohad; Eriksson, John E (2024). Intermediate filaments at a glance. Journal of Cell Science, 137(16):jcs261386.
• Kechagia, Zanetta; Eibauer, Matthias; Medalia, Ohad (2024). Structural determinants of intermediate filament mechanics. Current Opinion in Cell Biology, 89:102375.
• Auger, Shelby A; Venkatachalapathy, Sneha; Suazo, Kiall Francis G; Wang, Yiao; Sarkis, Alexander W; Bernhagen, Kaitlyn; Justyna, Katarzyna; Schaefer, Jonas V; Wollack, James W; Plückthun, Andreas; Li, Ling; Distefano, Mark D (2024). Broadening the Utility of Farnesyltransferase-Catalyzed Protein Labeling Using Norbornene-Tetrazine Click Chemistry. Bioconjugate Chemistry, 35(7):922-933.
• Nüesch, Mark F; Pietrek, Lisa; Holmstrom, Erik D; Nettels, Daniel; von Roten, Valentin; Kronenberg-Tenga, Rafael; Medalia, Ohad; Hummer, Gerhard; Schuler, Benjamin (2024). Nanosecond chain dynamics of single-stranded nucleic acids. Nature Communications, 15(1):6010.
• Loeff, Luuk; Adams, David W; Chanez, Christelle; Stutzmann, Sandrine; Righi, Laurie; Blokesch, Melanie; Jinek, Martin (2024). Molecular mechanism of plasmid elimination by the DdmDE defense system. Science, 385(6705):188-194.
• Reginato, Giordano; Dello Stritto, Maria Rosaria; Wang, Yanbo; Hao, Jingzhou; Pavani, Raphael; Schmitz, Michael; Halder, Swagata; Morin, Vincent; Cannavo, Elda; Ceppi, Ilaria; Braunshier, Stefan; Acharya, Ananya; Ropars, Virginie; Charbonnier, Jean-Baptiste; Jinek, Martin; Nussenzweig, Andrè; Ha, Taekjip; Cejka, Petr (2024). HLTF disrupts Cas9-DNA post-cleavage complexes to allow DNA break processing. Nature Communications, 15(1):5789.
• Stark, Yvonne; Menard, Faye; Jeliazkov, Jeliazko R; Ernst, Patrick; Chembath, Anupama; Ashraf, Mohammed; Hine, Anna V; Plückthun, Andreas (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(27):e2318198121.
• Houvast, Ruben D; Badr, Nada; March, Taryn; de Muynck, Lysanne D A N; Sier, Vincent Q; Schomann, Timo; Bhairosingh, Shadhvi; Baart, Victor M; Peeters, Judith A H M; van Westen, Gerard J P; Plückthun, Andreas; Burggraaf, Jacobus; Kuppen, Peter J K; Vahrmeijer, Alexander L; Sier, Cornelis 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(8):2179-2192.
• Dederer, Verena; Sanz Murillo, Marta; Karasmanis, Eva P; Hatch, Kathryn S; Chatterjee, Deep; Preuss, Franziska; Abdul Azeez, Kamal R; Nguyen, Landon Vu; Galicia, Christian; Dreier, Birgit; Plückthun, Andreas; Versees, Wim; Mathea, Sebastian; Leschziner, Andres E; Reck-Peterson, Samara L; Knapp, Stefan (2024). A designed ankyrin-repeat protein that targets Parkinson's disease-associated LRRK2. Journal of Biological Chemistry, 300(7):107469.
• Bastiaanssen, Carolien; Bobadilla Ugarte, Pilar; Kim, Kijun; Finocchio, Giada; Feng, Yanlei; Anzelon, Todd A; Köstlbacher, Stephan; Tamarit, Daniel; Ettema, Thijs J G; Jinek, Martin; MacRae, Ian J; Joo, Chirlmin; Swarts, Daan C; Wu, Fabai (2024). RNA-guided RNA silencing by an Asgard archaeal Argonaute. Nature Communications, 15(1):5499.
• Cui, Zhenling; Ayva, Cagla Ergun; Liew, Yi Jin; Guo, Zhong; Mutschler, Roxane; Dreier, Birgit; Fiorito, Maria M; Walden, Patricia; Howard, Christopher B; Ely, Fernanda; Plückthun, Andreas; Pretorius, Carel; Ungerer, Jacobus Pj; Buckle, Ashley M; Alexandrov, Kirill (2024). mRNA Display Pipeline for Protein Biosensor Construction. ACS Sensors, 9(6):2846-2857.
• Drożdżyk, Katarzyna; Peter, Martina; Dutzler, Raimund (2024). Structural features of heteromeric channels composed of CALHM2 and CALHM4 paralogs. eLife, 13:RP96138.
• Zálešák, František; Nai, Francesco; Herok, Marcin; Bochenkova, Elena; Bedi, Rajiv K; Li, Yaozong; Errani, Francesco; Caflisch, Amedeo (2024). Structure-Based Design of a Potent and Selective YTHDC1 Ligand. Journal of Medicinal Chemistry, 67(11):9516-9535.
• Eibauer, Matthias; Weber, Miriam S; Kronenberg-Tenga, Rafael; Beales, Charlie T; Boujemaa-Paterski, Rajaa; Turgay, Yagmur; Sivagurunathan, Suganya; Kraxner, Julia; Köster, Sarah; Goldman, Robert D; Medalia, Ohad (2024). Vimentin filaments integrate low-complexity domains in a complex helical structure. Nature Structural & Molecular Biology, 31(6):939-949.
• Nai, Francesco; Flores Espinoza, Maria Paula; Invernizzi, Annalisa; Vargas-Rosales, Pablo Andrés; Bobileva, Olga; Herok, Marcin; Caflisch, Amedeo (2024). Small-Molecule Inhibitors of the m7G-RNA Writer METTL1. ACS Bio & Med Chem Au, 4(2):100-110.
• Ivanova, Julia R; Benk, Amelie S; Schaefer, Jonas V; Dreier, Birgit; Hermann, Leon O; Plückthun, Andreas; Missirlis, Dimitris; Spatz, Joachim P (2024). Designed Ankyrin Repeat Proteins as Actin Labels of Distinct Cytoskeletal Structures in Living Cells. ACS Nano, 18(12):8919-8933.
• Corbeski, Ivan; Vargas-Rosales, Pablo Andrés; Bedi, Rajiv Kumar; Deng, Jiahua; Coelho, Dylan; Braud, Emmanuelle; Iannazzo, Laura; Li, Yaozong; Huang, Danzhi; Ethève-Quelquejeu, Mélanie; Cui, Qiang; Caflisch, Amedeo (2024). The catalytic mechanism of the RNA methyltransferase METTL3. eLife, 12:RP92537.
• Weber, Yanik; Böck, Desirée; Ivașcu, Anastasia; Mathis, Nicolas; Rothgangl, Tanja; Ioannidi, Eleonora I; Blaudt, Alex C; Tidecks, Lisa; Vadovics, Máté; Muramatsu, Hiromi; Reichmuth, Andreas; Marquart, Kim F; Kissling, Lucas; Pardi, Norbert; Jinek, Martin; Schwank, Gerald (2024). Enhancing prime editor activity by directed protein evolution in yeast. Nature Communications, 15(1):2092.
• Thalmann, Lars; Martín-González, Natalia; Brücher, Dominik; Plückthun, Andreas; de Pablo, Pedro J; Suomalainen, Maarit; Greber, Urs (2024). Gutless helper-dependent and first generation HAdV5 vectors have similar mechanical properties and common transduction mechanisms. Human Gene Therapy, 35(5-6):163-176.
• Schmidheini, Lukas; Mathis, Nicolas; Marquart, Kim Fabiano; Rothgangl, Tanja; Kissling, Lucas; Böck, Desirée; Chanez, Christelle; Wang, Jingrui Priscilla; Jinek, Martin; Schwank, Gerald (2024). Continuous directed evolution of a compact CjCas9 variant with broad PAM compatibility. Nature Chemical Biology, 20(3):333-343.
• Klinnert, Sarah; Schenkel, Corinne D; Freitag, Patrick C; Günthard, Huldrych F; Plückthun, Andreas; Metzner, Karin J (2024). Targeted shock-and-kill HIV-1 gene therapy approach combining CRISPR activation, suicide gene tBid and retargeted adenovirus delivery. Gene Therapy, 31(3-4):74-84.
• Pacesa, Martin; Pelea, Oana; Jinek, Martin (2024). Past, present, and future of CRISPR genome editing technologies. Cell, 187(5):1076-1100.
• Finocchio, Giada; Koopal, Balwina; Potocnik, Ana; Heijstek, Clint; Westphal, Adrie H; Jinek, Martin; Swarts, Daan C (2024). Target DNA-dependent activation mechanism of the prokaryotic immune system SPARTA. Nucleic Acids Research, 52(4):2012-2029.
• Errani, Francesco; Invernizzi, Annalisa; Herok, Marcin; Bochenkova, Elena; Stamm, Fiona; Corbeski, Ivan; Romanucci, Valeria; Di Fabio, Giovanni; Zálešák, František; Caflisch, Amedeo (2024). Proteolysis Targeting Chimera Degraders of the METTL3-14 m$^{6}$A-RNA Methyltransferase. JACS Au, 4(2):713-729.
• Saha, Aakash; Ahsan, Mohd; Arantes, Pablo R; Schmitz, Michael; Chanez, Christelle; Jinek, Martin; Palermo, Giulia (2024). An alpha-helical lid guides the target DNA toward catalysis in CRISPR-Cas12a. Nature Communications, 15(1):1473.
• Abdul-Ridha, Alaa; de Zhang, Lazarus A; Betrie, Ashenafi Haileyesus; Deluigi, Mattia; Vaid, Tasneem M; Whitehead, Alice; Zhang, Yifan; Davis, Ben; Harris, Richard; Simmonite, Heather; Hubbard, Roderick E; Gooley, Paul R; Plückthun, Andreas; Bathgate, Ross A D; Chalmers, David K; Scott, Daniel J (2024). Identification of a Novel Subtype-Selective α$_{1B}$-Adrenoceptor Antagonist. ACS Chemical Neuroscience, 15(3):671-684.
• Grabenhorst, Lennart; Sturzenegger, Flurin; Hasler, Moa; Schuler, Benjamin; Tinnefeld, Philip (2024). Single-Molecule FRET at 10 MHz Count Rates. Journal of the American Chemical Society, 146(5):3539-3544.
• Tinzl, Matthias; Diedrich, Johannes V; Mittl, Peer R E; Clémancey, Martin; Reiher, Markus; Proppe, Jonny; Latour, Jean-Marc; Hilvert, Donald (2024). Myoglobin-Catalyzed Azide Reduction Proceeds via an Anionic Metal Amide Intermediate. Journal of the American Chemical Society, 146(3):1957-1966.
• Jungfer, Kenny; Sigg, Annina; Jinek, Martin (2024). Substrate selectivity and catalytic activation of the type III CRISPR ancillary nuclease Can2. Nucleic Acids Research, 52(1):462-473.