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Department of Biochemistry

Publications 2023

by date of publication in PubMed, most recent at the top:


Leka, O., Wu, Y., Zanetti, G., Furler, S., Reinberg, T., Marinho, J., Schaefer, JV., Plückthun, A., Li, X., Pirazzini, M. & Kammerer, RA. A DARPin promotes faster onset of botulinum neurotoxin A1 action. Nat Commun 14, 8317 (2023). PMID: 38110403.

Jungfer, K., Sigg, A. & Jinek, M. Substrate selectivity and catalytic activation of the type III CRISPR ancillary nuclease Can2. Nucleic Acids Res 52, 462-473 (2023). PMID: 38033326.

Cucuzza, S., Sitnik, M., Jurt, S., Michel, E., Dai, W., Müntener, T., Ernst, P., Häussinger, D., Plückthun, A. & Zerbe, O. Unexpected dynamics in femtomolar complexes of binding proteins with peptides. Nat Commun 14, 7823 (2023). PMID: 38016954.

Lam, AK. & Dutzler, R. Mechanistic basis of ligand efficacy in the calcium-activated chloride channel TMEM16A. EMBO J 42, e115030 (2023). PMID: 37984335.

Pacesa, M., Loeff, L., Querques, I., Muckenfuss, LM., Sawicka, M. & Jinek, M. Publisher Correction: R-loop formation and conformational activation mechanisms of Cas9. Nature 623, E10  (2023). PMID: 37903882.

Eichenberger, M., Schwander, T., Hüppi, S., Kreuzer, J., Mittl, PRE., Peccati, F., Jiménez-Osés, G., Naesby, M. & Buller, RM. The catalytic role of glutathione transferases in heterologous anthocyanin biosynthesis. Nat Catal 6, 927-938 (2023). PMID: 37881531.

Strubel, A., Münick, P., Hartmann, O., Chaikuad, A., Dreier, B., Schaefer, JV., Gebel, J., Osterburg, C., Tuppi, M., Schäfer, B., Buck, V., Rosenfeldt, M., Knapp, S., Plückthun, A., Diefenbacher, ME. & Dötsch, V. DARPins detect the formation of hetero-tetramers of p63 and p73 in epithelial tissues and in squamous cell carcinoma. Cell Death Dis 14, 674 (2023). PMID: 37828008.

Buxboim, A., Kronenberg-Tenga, R., Salajkova, S., Avidan, N., Shahak, H., Thurston, A. & Medalia, O. Scaffold, mechanics and functions of nuclear lamins. FEBS Lett 597, 2791-2805 (2023). PMID: 37813648.

Baumann, C., Chiang, WC., Valsecchi, R., Jurt, S., Deluigi, M., Schuster, M., Rosengren, KJ., Plückthun, A. & Zerbe, O. Side-chain dynamics of the α1B -adrenergic receptor determined by NMR via methyl relaxation. Protein Sci 32, e4801 (2023). PMID: 37805830.

Bobrovs, R., Drunka, L., Kanepe, I., Jirgensons, A., Caflisch, A., Salvalaglio, M. & Jaudzems, K. Exploring the Binding Pathway of Novel Nonpeptidomimetic Plasmepsin V Inhibitors. J Chem Inf Model 63, 6890-6899  (2023). PMID: 37801405.

Chowdhury, A., Borgia, A., Ghosh, S., Sottini, A., Mitra, S., Eapen, RS., Borgia, MB., Yang, T., Galvanetto, N., Ivanović, MT., Łukijańczuk, P., Zhu, R., Nettels, D., Kundagrami, A. & Schuler, B. Driving forces of the complex formation between highly charged disordered proteins. Proc Natl Acad Sci U S A 120, e2304036120 (2023). PMID: 37796987.

Zhao, L., Koseki, SRT., Silverstein, RA., Amrani, N., Peng, C., Kramme, C., Savic, N., Pacesa, M., Rodríguez, TC., Stan, T., Tysinger, E., Hong, L., Yudistyra, V., Ponnapati, MR., Jacobson, JM., Church, GM., Jakimo, N., Truant, R., Jinek, M., Kleinstiver, BP., Sontheimer, EJ. & Chatterjee, P. PAM-flexible genome editing with an engineered chimeric Cas9. Nat Commun 14, 6175 (2023). PMID: 37794046.

Vargas-Rosales, PA., D'Addio, A., Zhang, Y. & Caflisch, A. Disrupting Dimeric β-Amyloid by Electric Fields. ACS Phys Chem Au 3, 456-466 (2023). PMID: 37780539.

Maliqi, L., Friedrich, N., Glögl, M., Schmutz, S., Schmidt, D., Rusert, P., Schanz, M., Zaheri, M., Pasin, C., Niklaus, C., Foulkes, C., Reinberg, T., Dreier, B., Abela, I., Peterhoff, D., Hauser, A., Kouyos, RD., Günthard, HF., van Gils, MJ., Sanders, RW., Wagner, R., Plückthun, A. & Trkola, A. Assessing immunogenicity barriers of the HIV-1 envelope trimer. NPJ Vaccines 8, 148 (2023). PMID: 37777519.

Yang, T., Buholzer, KJ., Sottini, A., Cao, X., deMello, A., Nettels, D. & Schuler, B. Rapid droplet-based mixing for single-molecule spectroscopy. Nat Methods 20, 1479-1482 (2023). PMID: 37749213.

Schmidheini, L., Mathis, N., Marquart, KF., Rothgangl, T., Kissling, L., Böck, D., Chanez, C., Wang, JP., Jinek, M. & Schwank, G. Continuous directed evolution of a compact CjCas9 variant with broad PAM compatibility. Nat Chem Biol [Epub ahead of print] (2023). PMID: 37735239.

Sottini, A., Borgia, A., Borgia, MB., Bugge, K., Nettels, D., Chowdhury, A., Heidarsson, PO., Zosel, F., Best, RB., Kragelund, BB. & Schuler, B. Author Correction: Polyelectrolyte interactions enable rapid association and dissociation in high-affinity disordered protein complexes. Nat Commun 14, 5864 (2023). PMID: 37735166.

Houvast, RD., Badr, N., March, T., de Muynck, LDAN., Sier, VQ., Schomann, T., Bhairosingh, S., Baart, VM., Peeters, JAHM., van Westen, GJP., Plückthun, A., Burggraaf, J., Kuppen, PJK., Vahrmeijer, AL. & Sier, CFM. Preclinical evaluation of EpCAM-binding designed ankyrin repeat proteins (DARPins) as targeting moieties for bimodal near-infrared fluorescence and photoacoustic imaging of cancer. Eur J Nucl Med Mol Imaging [Epub ahead of print] (2023). PMID: 37642704.

Hartmann, KP., van Gogh, M., Freitag, PC., Kast, F., Nagy-Davidescu, G., Borsig, L. & Plückthun, A. FAP-retargeted Ad5 enables in vivo gene delivery to stromal cells in the tumor microenvironment. Mol Ther 31, 2914-2928 (2023). PMID: 37641405.

Glögl, M., Friedrich, N., Cerutti, G., Lemmin, T., Kwon, YD., Gorman, J., Maliqi, L., Mittl, PRE., Hesselman, MC., Schmidt, D., Weber, J., Foulkes, C., Dingens, AS., Bylund, T., Olia, AS., Verardi, R., Reinberg, T., Baumann, NS., Rusert, P., Dreier, B., Shapiro, L., Kwong, PD., Plückthun, A. & Trkola, A. Trapping the HIV-1 V3 loop in a helical conformation enables broad neutralization. Nat Struct Mol Biol 30, 1323-1336 (2023). PMID: 37605043.

Becker, J., Peters, JS., Crooks, I., Helmi, S., Synakewicz, M., Schuler, B. & Kukura, P. A Quantitative Description for Optical Mass Measurement of Single Biomolecules. ACS Photonics 10, 2699-2710 (2023). PMID: 37602293.

Bedi, RK., Huang, D., Li, Y. & Caflisch, A. Structure-Based Design of Inhibitors of the m6 A-RNA Writer Enzyme METTL3. ACS Bio Med Chem Au 3, 359-370 (2023). PMID: 37599794.

Cazzanelli, G., Vedove, AD., Parolin, E., D'Agostino, VG., Unzue, A., Nevado, C., Caflisch, A. & Lolli, G. Reevaluation of bromodomain ligands targeting BAZ2A. Protein Sci 32, e4752 (2023). PMID: 37574751.

Klinnert, S., Schenkel, CD., Freitag, PC., Günthard, HF., Plückthun, A. & Metzner, KJ. Targeted shock-and-kill HIV-1 gene therapy approach combining CRISPR activation, suicide gene tBid and retargeted adenovirus delivery. Gene Ther [Epub ahead of print] (2023). PMID: 37558852.

Galvanetto, N., Ivanović, MT., Chowdhury, A., Sottini, A., Nüesch, MF., Nettels, D., Best, RB. & Schuler, B. Extreme dynamics in a biomolecular condensate. Nature 619, 876-883 (2023). PMID: 37468629.

Franz, F., Tapia-Rojo, R., Winograd-Katz, S., Boujemaa-Paterski, R., Li, W., Unger, T., Albeck, S., Aponte-Santamaria, C., Garcia-Manyes, S., Medalia, O., Geiger, B. & Gräter, F. Allosteric activation of vinculin by talin. Nat Commun 14, 4311 (2023). PMID: 37463895.

Gut, M., Dreier, B., Furler, S., Sobek, J., Plückthun, A. & Holland, JP. Designed ankyrin repeat proteins for detecting prostate-specific antigen expression in vivo. RSC Chem Biol 4, 494-505 (2023). PMID: 37415866.

Widmer, J., Langini, C., Vitalis, A. & Caflisch, A. Optimized reaction coordinates for analysis of enhanced sampling. J Chem Phys 159, (2023). PMID: 37403854.

Shi, J., Hauschulte, K., Mikicic, I., Maharjan, S., Arz, V., Strauch, T., Heidelberger, JB., Schaefer, JV., Dreier, B., Plückthun, A., Beli, P., Ulrich, HD. & Wollscheid, HP. Nuclear myosin VI maintains replication fork stability. Nat Commun 14, 3787 (2023). PMID: 37355687.

Tippett, DN., Breen, C., Butler, SJ., Sawicka, M. & Dutzler, R. Structural and functional properties of the transporter SLC26A6 reveal mechanism of coupled anion exchange. Elife 12, (2023). PMID: 37351578.

Lone, MA., Zeng, S., Bourquin, F., Wang, M., Huang, S., Lin, Z., Tang, B., Zhang, R. & Hornemann, T. SPTLC1 p.Leu38Arg, a novel mutation associated with childhood ALS. Biochim Biophys Acta Mol Cell Biol Lipids 1868, 159359 (2023). PMID: 37348646.

Ilie, IM., Ehrhardt, C., Caflisch, A. & Weitz-Schmidt, G. Decrypting Integrins by Mixed-Solvent Molecular Dynamics Simulations. J Chem Inf Model 63, 3878-3891 (2023). PMID: 37310029.

Li, W., Chung, WL., Kozlov, MM., Medalia, O., Geiger, B. & Bershadsky, AD. Chiral growth of adherent filopodia. Biophys J  122, 3704-3721 (2023). PMID: 37301982.

Wimmer, BH., Moraïs, S., Zalk, R., Mizrahi, I. & Medalia, O. Phylogenetic diversity of core rumen microbiota as described by cryo-ET. Microlife 4, uqad010 (2023). PMID: 37223726.

Becker, L. & Plückthun, A. DARPins bind their cytosolic targets after having been translocated through the protective antigen pore of anthrax toxin. Sci Rep 13, 8048 (2023). PMID: 37198284.

Blanc, M., Lettl, C., Guérin, J., Vieille, A., Furler, S., Briand-Schumacher, S., Dreier, B., Bergé, C., Plückthun, A., Vadon-Le Goff, S., Fronzes, R., Rousselle, P., Fischer, W. & Terradot, L. Designed Ankyrin Repeat Proteins provide insights into the structure and function of CagI and are potent inhibitors of CagA translocation by the Helicobacter pylori type IV secretion system. PLoS Pathog 19, e1011368 (2023). PMID: 37155700.

Ramanadane, K., Liziczai, M., Markovic, D., Straub, MS., Rosalen, GT., Udovcic, A., Dutzler, R. & Manatschal, C. Structural and functional properties of a plant NRAMP-related aluminum transporter. Elife 12, (2023). PMID: 37074929.

Schubert, R., Bae, T., Simic, B., Smith, SN., Park, SH., Nagy-Davidescu, G., Gradinaru, V., Plückthun, A. & Hur, JK. CRISPR-clear imaging of melanin-rich B16-derived solid tumors. Commun Biol 6, 370 (2023). PMID: 37016073.

Freitag, PC., Kaulfuss, M., Flühler, L., Mietz, J., Weiss, F., Brücher, D., Kolibius, J., Hartmann, KP., Smith, SN., Münz, C., Chijioke, O. & Plückthun, A. Targeted adenovirus-mediated transduction of human T cells in vitro and in vivo. Mol Ther Methods Clin Dev 29, 120-132 (2023). PMID: 37007608.

Klenk, C., Scrivens, M., Niederer, A., Shi, S., Mueller, L., Gersz, E., Zauderer, M., Smith, ES., Strohner, R. & Plückthun, A. A Vaccinia-based system for directed evolution of GPCRs in mammalian cells. Nat Commun 14, 1770 (2023). PMID: 36997531.

Lehmann, EF., Liziczai, M., Drożdżyk, K., Altermatt, P., Langini, C., Manolova, V., Sundstrom, H., Dürrenberger, F., Dutzler, R. & Manatschal, C. Structures of ferroportin in complex with its specific inhibitor vamifeport. Elife 12, (2023). PMID: 36943194.

Karoutas, A., Szymanski, W., Rausch, T., Guhathakurta, S., Rog-Zielinska, EA., Peyronnet, R., Seyfferth, J., Chen, HR., de Leeuw, R., Herquel, B., Kimura, H., Mittler, G., Kohl, P., Medalia, O., Korbel, JO. & Akhtar, A. Author Correction: The NSL complex maintains nuclear architecture stability via lamin A/C acetylation. Nat Cell Biol 25,  626 (2023). PMID: 36849559.

Geiger, B., Boujemaa-Paterski, R., Winograd-Katz, SE., Balan Venghateri, J., Chung, WL. & Medalia, O. The Actin Network Interfacing Diverse Integrin-Mediated Adhesions. Biomolecules 13, (2023). PMID: 36830665.

Schellhorn, S., Brücher, D., Wolff, N., Schröer, K., Sallard, E., Mese, K., Zhang, W., Ehrke-Schulz, E., Thevenod, F., Plückthun, A. & Ehrhardt, A. Targeting Oncolytic Adenoviruses to Cancer Cells Using a Designed Ankyrin Repeat Protein (DARPin) Lipocalin-2 (LCN2) Fusion Protein. Hum Gene Ther 34, 203-216 (2023). PMID: 36802735.

Mathy, CJP., Mishra, P., Flynn, JM., Perica, T., Mavor, D., Bolon, DNA. & Kortemme, T. A complete allosteric map of a GTPase switch in its native cellular network. Cell Syst 14, 237-246.e7 (2023). PMID: 36801015.

Spalinger, MR., Kasper, S., Gottier, C., Lang, S., Atrott, K., Vavricka, SR., Scharl, S., Gutte, PM., Grütter, MG., Beer, HD., Contassot, E., Chan, AC., Dai, X., Rawlings, DJ., Mair, F., Becher, B., Falk, W., Fried, M., Rogler, G. & Scharl, M. NLRP3 tyrosine phosphorylation is controlled by protein tyrosine phosphatase PTPN22. J Clin Invest 133, (2023). PMID: 36787260.

Chowdhury, A., Nettels, D. & Schuler, B. Interaction Dynamics of Intrinsically Disordered Proteins from Single-Molecule Spectroscopy. Annu Rev Biophys 52, 18.1-18.30 (2023). PMID: 36750251.

Tapia-Rojo, R., Mora, M., Board, S., Walker, J., Boujemaa-Paterski, R., Medalia, O. & Garcia-Manyes, S. Enhanced statistical sampling reveals microscopic complexity in the talin mechanosensor folding energy landscape. Nat Phys 19, 52-60 (2023). PMID: 36660164.

Rutz, S., Deneka, D., Dittmann, A., Sawicka, M. & Dutzler, R. Structure of a volume-regulated heteromeric LRRC8A/C channel. Nat Struct Mol Biol 30, 52-61 (2023). PMID: 36522427

Xiang, Y., Zhai, G., Li, Y., Wang, M., Chen, X., Wang, R., Xie, H., Zhang, W., Ge, G., Zhang, Q., Xu, Y., Caflisch, A., Xu, J., Chen, H. & Chen, L. Ginkgolic acids inhibit SARS-CoV-2 and its variants by blocking the spike protein/ACE2 interplay. Int J Biol Macromol 226, 780-792 (2023). PMID: 36521705

Michel, E., Cucuzza, S., Mittl, PRE., Zerbe, O. & Plückthun, A. Improved Repeat Protein Stability by Combined Consensus and Computational Protein Design. Biochemistry 62,318-329 (2023). PMID: 35657362

Reimann, RR., Puzio, M., Rosati, A., Emmenegger, M., Schneider, BL., Valdés, P., Huang, D., Caflisch, A. & Aguzzi, A. Rapid ex vivo reverse genetics identifies the essential determinants of prion protein toxicity. Brain Pathol 33, e13130 (2023). PMID: 36329611.

Wang, C., Wojtynek, M. & Medalia, O. Structural investigation of eukaryotic cells: From the periphery to the interior by cryo-electron tomography. Adv Biol Regul 87, 100923 (2023). PMID: 36280452.