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Department of Biochemistry

Publications 2022

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

Manatschal, C. & Dutzler, R. The Structural Basis for Metal Ion Transport in the SLC11/NRAMP Family. Chimia (Aarau) 76, 1005-1010 (2022). PMID: 38069795.

Nierzwicki, Ł., East, KW., Binz, JM., Hsu, RV., Ahsan, M., Arantes, PR., Skeens, E., Pacesa, M., Jinek, M., Lisi, GP. & Palermo, G. Principles of target DNA cleavage and the role of Mg2+ in the catalysis of CRISPR-Cas9. Nat Catal 5, 912-922 (2022). PMID: 36778082.

Buholzer, KJ., McIvor, J., Zosel, F., Teppich, C., Nettels, D., Mercadante, D. & Schuler, B. Multilayered allosteric modulation of coupled folding and binding by phosphorylation, peptidyl-prolyl cis/trans isomerization, and diversity of interaction partners. J Chem Phys 157, 235102 (2022). PMID: 36550025.

Chung, WL., Eibauer, M., Li, W., Boujemaa-Paterski, R., Geiger, B. & Medalia, O. A network of mixed actin polarity in the leading edge of spreading cells. Commun Biol 5, 1338 (2022). PMID: 36473943.

Kiss, C., Gall, FM., Dreier, B., Adams, M., Riedl, R., Plückthun, A. & Mittl, PRE. Structure of a hydrophobic leucinostatin derivative determined by host lattice display. Acta Crystallogr D Struct Biol 78, 1439-1450 (2022). PMID: 36458615.

Schmitz, M., Querques, I., Oberli, S., Chanez, C. & Jinek, M. Structural basis for the assembly of the type V CRISPR-associated transposon complex. Cell 185, 4999-5017.e17 (2022). PMID: 36435179.

Cocina, F., Vitalis, A. & Caflisch, A. Spiking burstiness and working memory in the human medial temporal lobe. Cereb Cortex Commun 3, tgac039 (2022). PMID: 36415307.

Arndt, M., Alvadia, C., Straub, MS., Clerico Mosina, V., Paulino, C. & Dutzler, R. Structural basis for the activation of the lipid scramblase TMEM16F. Nat Commun 13, 6692 (2022). PMID: 36335104.

Campbell, BFN., Dittmann, A., Dreier, B., Plückthun, A. & Tyagarajan, SK. A DARPin-based molecular toolset to probe gephyrin and inhibitory synapse biology. Elife 11, (2022). PMID: 36314779.

Pacesa, M., Lin, CH., Cléry, A., Saha, A., Arantes, PR., Bargsten, K., Irby, MJ., Allain, FH., Palermo, G., Cameron, P., Donohoue, PD. & Jinek, M. Structural basis for Cas9 off-target activity. Cell 185, 4067-4081.e21 (2022). PMID: 36306733.

Kipnis, Y., Chaib, AO., Vorobieva, AA., Cai, G., Reggiano, G., Basanta, B., Kumar, E., Mittl, PRE., Hilvert, D. & Baker, D. Design and optimization of enzymatic activity in a de novo β-barrel scaffold. Protein Sci 31, e4405 (2022). PMID: 36305767.

Kono, Y., Adam, SA., Sato, Y., Reddy, KL., Zheng, Y., Medalia, O., Goldman, RD., Kimura, H. & Shimi, T. Nucleoplasmic lamin C rapidly accumulates at sites of nuclear envelope rupture with BAF and cGAS. J Cell Biol 221,(2022). PMID: 36301259.

Anand, U., Shteinfer-Kuzmine, A., Sela, G., Santhanam, M., Gottschalk, B., Boujemaa-Paterski, R., Medalia, O., Graier, WF. & Shoshan-Barmatz, V. The Multicellular Effects of VDAC1 N-Terminal-Derived Peptide. Biomolecules 12, (2022). PMID: 36291596.

Philippi, M., Richter, CP., Kappen, M., Watrinet, I., Miao, Y., Runge, M., Jorde, L., Korneev, S., Holtmannspötter, M., Kurre, R., Holthuis, JCM., Garcia, KC., Plückthun, A., Steinhart, M., Piehler, J. & You, C. Biofunctional Nanodot Arrays in Living Cells Uncover Synergistic Co-Condensation of Wnt Signalodroplets. Small 18,e2203723 (2022). PMID: 36266931.

Zhang, Y., Wang, Y., Uslu, S., Venkatachalapathy, S., Rashidian, M., Schaefer, JV., Plückthun, A. & Distefano, MD. Enzymatic Construction of DARPin-Based Targeted Delivery Systems Using Protein Farnesyltransferase and a Capture and Release Strategy. Int J Mol Sci 23, (2022). PMID: 36232839.

Dehabadi, MH., Caflisch, A., Ilie, IM. & Firouzi, R. 42 Dimer: A Computational Study. J Phys Chem B 126, 7627-7637 (2022). PMID: 36148988.

Nai, F., Nachawati, R., Zálešák, F., Wang, X., Li, Y. & Caflisch, A. 6A-RNA Reader YTHDF2. ACS Med Chem Lett 13, 1500-1509 (2022). PMID: 36110386.

Dalle Vedove, A., Cazzanelli, G., Batiste, L., Marchand, JR., Spiliotopoulos, D., Corsi, J., D'Agostino, VG., Caflisch, A. & Lolli, G. Identification of a BAZ2A-Bromodomain Hit Compound by Fragment Growing. ACS Med Chem Lett 13, 1434-1443 (2022). PMID: 36105334.

Muckenfuss, LM., Migenda Herranz, AC., Boneberg, FM., Clerici, M. & Jinek, M. Fip1 is a multivalent interaction scaffold for processing factors in human mRNA 3' end biogenesis. Elife 11, (2022). PMID: 36073787.

Camus, A., Truong, G., Mittl, PRE., Markert, G. & Hilvert, D. Reprogramming Nonribosomal Peptide Synthetases for Site-Specific Insertion of α-Hydroxy Acids. J Am Chem Soc 144, 17567-17575 (2022). PMID: 36070491.

Pacesa, M., Loeff, L., Querques, I., Muckenfuss, LM., Sawicka, M. & Jinek, M. R-loop formation and conformational activation mechanisms of Cas9. Nature 609, 191-196 (2022). PMID: 36002571

Kralt, A., Wojtynek, M., Fischer, JS., Agote-Aran, A., Mancini, R., Dultz, E., Noor, E., Uliana, F., Tatarek-Nossol, M., Antonin, W., Onischenko, E., Medalia, O. & Weis, K. S. cerevisiae. Elife 11, (2022). PMID: 36000978.

Giordano, D., Langini, C., Caflisch, A., Marabotti, A. & Facchiano, A. Streptomyces mobaraensis. Comput Struct Biotechnol J 20, 3924-3934 (2022). PMID: 35950183.

Freitag, PC., Brandl, F., Brücher, D., Weiss, F., Dreier, B. & Plückthun, A. Modular Adapters Utilizing Binders of Different Molecular Types Expand Cell-Targeting Options for Adenovirus Gene Delivery. Bioconjug Chem 33, 1595-1601 (2022). PMID: 35944553.

Strittmatter, T., Wang, Y., Bertschi, A., Scheller, L., Freitag, PC., Ray, PG., Stuecheli, P., Schaefer, JV., Reinberg, T., Tsakiris, D., Plückthun, A., Ye, H. & Fussenegger, M. Programmable DARPin-based receptors for the detection of thrombotic markers.Nat Chem Biol 18, 1125-1134 (2022). PMID: 35941237. .

Ilie, IM. & Caflisch, A. Antibody binding increases the flexibility of the prion protein. Biochim Biophys Acta Proteins Proteom 1870,140827 (2022). PMID: 35931365.

Waltenspühl, Y., Ehrenmann, J., Vacca, S., Thom, C., Medalia, O. & Plückthun, A. Structural basis for the activation and ligand recognition of the human oxytocin receptor. Nat Commun 13, 4153 (2022). PMID: 35851571.

Kirchhammer, N., Trefny, MP., Natoli, M., Brücher, D., Smith, SN., Werner, F., Koch, V., Schreiner, D., Bartoszek, E., Buchi, M., Schmid, M., Breu, D., Hartmann, KP., Zaytseva, P., Thommen, DS., Läubli, H., Böttcher, JP., Stanczak, MA., Kashyap, AS., Plückthun, A. & Zippelius, A. NK cells with tissue-resident traits shape response to immunotherapy by inducing adaptive antitumor immunity. Sci Transl Med 14, eabm9043 (2022). PMID: 35857639.

Beales, CT. & Medalia, O. Gold nanomaterials and their potential use as cryo-electron tomography labels. J Struct Biol 214, 107880 (2022). PMID: 35809758.

Kopra, K., Valtonen, S., Mahran, R., Kapp, JN., Hassan, N., Gillette, W., Dennis, B., Li, L., Westover, KD., Plückthun, A. & Härmä, H. Thermal Shift Assay for Small GTPase Stability Screening: Evaluation and Suitability. Int J Mol Sci 23, (2022). PMID: 35806100.

Strubel, A., Münick, P., Chaikuad, A., Dreier, B., Schaefer, J., Gebel, J., Osterburg, C., Tuppi, M., Schäfer, B., Knapp, S., Plückthun, A. & Dötsch, V. Designed Ankyrin Repeat Proteins as a tool box for analyzing p63. Cell Death Differ 29, 2445-2458 (2022). PMID: 35717504.

Ilie, IM., Bacci, M., Vitalis, A. & Caflisch, A. Antibody binding modulates the dynamics of the membrane bound prion protein. Biophys J 121, 2813-2825 (2022). PMID: 35672948.

Andrés Vargas-Rosales, P. & Caflisch, A. Domino effect in allosteric signaling of peptide binding. J Mol Biol 434, 167661 (2022). PMID: 35640719.

Tatli, M., Moraïs, S., Tovar-Herrera, OE., Bomble, YJ., Bayer, EA., Medalia, O. & Mizrahi, I. Nanoscale resolution of microbial fiber degradation in action. Elife 11 (2022). PMID: 35638899.

Lam, AKM., Rutz, S. & Dutzler, R. Inhibition mechanism of the chloride channel TMEM16A by the pore blocker 1PBC. Nat Commun 13, 2798 (2022). PMID: 35589730.

Guimaraes Koch, SS., Thorpe, R., Kawasaki, N., Lefranc, MP., Malan, S., Martin, ACR., Mignot, G., Plückthun, A., Rizzi, M., Shubat, S., Weisser, K. & Balocco, R. International nonproprietary names for monoclonal antibodies: an evolving nomenclature system. MAbs 14, 2075078 (2022). PMID: 35584276.

Dultz, E., Wojtynek, M., Medalia, O. & Onischenko, E. The Nuclear Pore Complex: Birth, Life, and Death of a Cellular Behemoth. Cells 11, (2022). PMID: 35563762.

Sawicka, M. & Dutzler, R. Regulators of cell volume: The structural and functional properties of anion channels of the LRRC8 family. Curr Opin Struct Biol 74, 102382 (2022). PMID: 35504105.

Lone, MA., Bourquin, F. & Hornemann, T. Serine Palmitoyltransferase Subunit 3 and Metabolic Diseases. Adv Exp Med Biol 1372, 47-56 (2022). PMID: 35503173.

Wang, L., Moreira, EA., Kempf, G., Miyake, Y., Oliveira Esteves, BI., Fahmi, A., Schaefer, JV., Dreier, B., Yamauchi, Y., Alves, MP., Plückthun, A. & Matthias, P. Disrupting the HDAC6-ubiquitin interaction impairs infection by influenza and Zika virus and cellular stress pathways. Cell Rep 39, 110736 (2022). PMID: 35476995.

Fay, R., Törő, I., Schinke, AL., Simic, B., Schaefer, JV., Dreier, B., Plückthun, A. & Holland, JP. 89Zr-Radiolabeling of Designed Ankyrin Repeat Proteins for PET. Mol Pharm 19, 3576-3585 (2022). PMID: 35434995.

Stelzl, LS., Pietrek, LM., Holla, A., Oroz, J., Sikora, M., Köfinger, J., Schuler, B., Zweckstetter, M. & Hummer, G. Global Structure of the Intrinsically Disordered Protein Tau Emerges from Its Local Structure. JACS Au 2, 673-686 (2022). PMID: 35373198.

García-Viñuales, S., Ilie, IM., Santoro, AM., Romanucci, V., Zarrelli, A., Di Fabio, G., Caflisch, A. & Milardi, D. Silybins inhibit human IAPP amyloid growth and toxicity through stereospecific interactions. Biochim Biophys Acta Proteins Proteom 1870, 140772 (2022). PMID: 35307557.  

Wu, H., Shen, Y., Sivagurunathan, S., Weber, MS., Adam, SA., Shin, JH., Fredberg, JJ., Medalia, O., Goldman, R. & Weitz, DA. Vimentin intermediate filaments and filamentous actin form unexpected interpenetrating networks that redefine the cell cortex. Proc Natl Acad Sci U S A 119, e2115217119 (2022). PMID: 35235449.

Qi, C., Lavriha, P., Mehta, V., Khanppnavar, B., Mohammed, I., Li, Y., Lazaratos, M., Schaefer, JV., Dreier, B., Plückthun, A., Bondar, AN., Dessauer, CW. & Korkhov, VM. Structural basis of adenylyl cyclase 9 activation. Nat Commun 13, 1045 (2022). PMID: 35210418.

Vahabikashi, A., Adam, SA., Medalia, O. & Goldman, RD. Nuclear lamins: Structure and function in mechanobiology. APL Bioeng 6, 011503 (2022). PMID: 35146235.

Schöppe, J., Ehrenmann, J., Waltenspühl, Y. & Plückthun, A. Universal platform for the generation of thermostabilized GPCRs that crystallize in LCP. Nat Protoc 17, 698-726 (2022). PMID: 35140409.

de Leeuw, R., Kronenberg-Tenga, R., Eibauer, M. & Medalia, O. C. elegans lamin in the absence of helix 1A. Nucleus 13, 49-57 (2022). PMID: 35130129.

Salutari, I. & Caflisch, A. Dynamics of the Histone Acetyltransferase Lysine-Rich Loop in the Catalytic Core of the CREB-Binding Protein. J Chem Inf Model 62, 1014-1024 (2022). PMID: 35119862.

Gisdon, FJ., Kynast, JP., Ayyildiz, M., Hine, AV., Plückthun, A. & Höcker, B. Modular peptide binders - development of a predictive technology as alternative for reagent antibodies. Biol Chem 403, 535-543 (2022). PMID: 35089661.

Martinsen, JH., Saar, D., Fernandes, CB., Schuler, B., Bugge, K. & Kragelund, BB. Structure, Dynamics and Stability of the Globular Domain of Human Linker Histone H1.0 and the Role of Positive Charges. Protein Sci 31, 918-932 (2022). PMID: 35066947.

Deluigi, M., Morstein, L., Schuster, M., Klenk, C., Merklinger, L., Cridge, RR., de Zhang, LA., Klipp, A., Vacca, S., Vaid, TM., Mittl, PRE., Egloff, P., Eberle, SA., Zerbe, O., Chalmers, DK., Scott, DJ. & Plückthun, A. 1B-adrenergic receptor reveals molecular determinants of selective ligand recognition. Nat Commun 13, 382 (2022). PMID: 35046410.

Matsuda, S., Schaefer, JV., Mii, Y., Hori, Y., Bieli, D., Taira, M., Plückthun, A. & Affolter, M. Author Correction: Asymmetric requirement of Dpp/BMP morphogen dispersal in the Drosophila wing disc. Nat Commun 13, 389 (2022). PMID: 35031605

Ramanadane, K., Straub, MS., Dutzler, R. & Manatschal, C. Structural and functional properties of a magnesium transporter of the SLC11/NRAMP family. Elife 11, (2022). PMID: 35001872.

Heidarsson, PO., Mercadante, D., Sottini, A., Nettels, D., Borgia, MB., Borgia, A., Kilic, S., Fierz, B., Best, RB. & Schuler, B. Release of linker histone from the nucleosome driven by polyelectrolyte competition with a disordered protein. Nat Chem 14, 224-231 (2022). PMID: 34992286.

Nüesch, MF., Ivanović, MT., Claude, JB., Nettels, D., Best, RB., Wenger, J. & Schuler, B. Single-molecule Detection of Ultrafast Biomolecular Dynamics with Nanophotonics. J Am Chem Soc 144, 52-56 (2022). PMID: 34970909.

Nass, KJ., Ilie, IM., Saller, MJ., Driessen, AJM., Caflisch, A., Kammerer, RA. & Li, X. The role of the N-terminal amphipathic helix (N-AH) in bacterial YidC: Insights from functional studies, the crystal structure and molecular dynamics simulations. Biochim Biophys Acta Biomembr  1864, 183825 (2022). PMID: 34871574.

Zosel, F., Holla, A. & Schuler, B. Labeling of Proteins for Single-Molecule Fluorescence Spectroscopy. Methods Mol Biol 2376, 207-233 (2022). PMID: 34845612.

Schilling, J., Jost, C., Ilie, IM., Schnabl, J., Buechi, O., Eapen, RS., Truffer, R., Caflisch, A. & Forrer, P. Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. J Biol Chem 298(1), 101403 (2022). PMID: 34793836.