Publications 2021

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

Dalle Vedove, A., Cazzanelli, G., Corsi, J., Sedykh, M., D'Agostino, VG., Caflisch, A. & Lolli, G. Identification of a BAZ2A Bromodomain Hit Compound by Fragment Joining. ACS Bio Med Chem Au 1, 5-10 (2021). PMID: 36147311.

Bieri, M., Hendrickx, R., Bauer, M., Yu, B., Jetzer, T., Dreier, B., Mittl, PRE., Sobek, J., Plückthun, A., Greber, UF. & Hemmi, S. The RGD-binding integrins αvβ6 and αvβ8 are receptors for mouse adenovirus-1 and -3 infection. PLoS Pathog 17, e1010083 (2021). PMID: 34910784.

Thom, C., Ehrenmann, J., Vacca, S., Waltenspühl, Y., Schöppe, J., Medalia, O. & Plückthun, A. s proteins reveal substance P binding mode and unique activation features. Sci Adv 7, eabk2872 (2021). PMID: 34878828.

Kroupova, A., Ackle, F., Asanović, I., Weitzer, S., Boneberg, FM., Faini, M., Leitner, A., Chui, A., Aebersold, R., Martinez, J. & Jinek, M. Molecular architecture of the human tRNA ligase complex. Elife 10, (2021) (2021). PMID: 34854379.

Friedrich, N., Stiegeler, E., Glögl, M., Lemmin, T., Hansen, S., Kadelka, C., Wu, Y., Ernst, P., Maliqi, L., Foulkes, C., Morin, M., Eroglu, M., Liechti, T., Ivan, B., Reinberg, T., Schaefer, JV., Karakus, U., Ursprung, S., Mann, A., Rusert, P., Kouyos, RD., Robinson, JA., Günthard, HF., Plückthun, A. & Trkola, A. Distinct conformations of the HIV-1 V3 loop crown are targetable for broad neutralization. Nat Commun 12, 6705 (2021). PMID: 34795280.

Querques, I., Schmitz, M., Oberli, S., Chanez, C. & Jinek, M. Target site selection and remodelling by type V CRISPR-transposon systems. Nature 599, 497-502 (2021). PMID: 34759315.

Matsuda, S., Schaefer, JV., Mii, Y., Hori, Y., Bieli, D., Taira, M., Plückthun, A. & Affolter, M. Asymmetric requirement of Dpp/BMP morphogen dispersal in the Drosophila wing disc. Nat Commun 12, 6435 (2021). PMID: 34750371.

Cucuzza, S., Güntert, P., Plückthun, A. & Zerbe, O. Correction to: An automated iterative approach for protein structure refinement using pseudocontact shifts.  J Biomol NMR 75, 429-430 (2021). PMID: 34647187.

Perica, T., Mathy, CJP., Xu, J., Jang, GΜ., Zhang, Y., Kaake, R., Ollikainen, N., Braberg, H., Swaney, DL., Lambright, DG., Kelly, MJS., Krogan, NJ. & Kortemme, T. Systems-level effects of allosteric perturbations to a model molecular switch. Nature 599, 152-157 (2021). PMID: 34646016.

Schuller, AP., Wojtynek, M., Mankus, D., Tatli, M., Kronenberg-Tenga, R., Regmi, SG., Dip, PV., Lytton-Jean, AKR., Brignole, EJ., Dasso, M., Weis, K., Medalia, O. & Schwartz, TU. The cellular environment shapes the nuclear pore complex architecture. Nature 598, 667-671 (2021). PMID: 34646014.

Mysore, VP., Zhou, ZW., Ambrogio, C., Li, L., Kapp, JN., Lu, C., Wang, Q., Tucker, MR., Okoro, JJ., Nagy-Davidescu, G., Bai, X., Plückthun, A., Jänne, PA., Westover, KD., Shan, Y. & Shaw, DE. A structural model of a Ras-Raf signalosome. Nat Struct Mol Biol 28, 847-857 (2021). PMID: 34625747.

Makasheva, K., Bryan, LC., Anders, C., Panikulam, S., Jinek, M. & Fierz, B. Multiplexed Single-Molecule Experiments Reveal Nucleosome Invasion Dynamics of the Cas9 Genome Editor. J Am Chem Soc 143, 16313-16319 (2021). PMID: 34597515.

Cocina, F., Vitalis, A. & Caflisch, A. Unsupervised methods for detection of neural states: case study of hippocampal-amygdala interactions. eNeuro 8, (2021). PMID: 34544761.

Klose, D., Holla, A., Gmeiner, C., Nettels, D., Ritsch, I., Bross, N., Yulikov, M., Allain, FH., Schuler, B. & Jeschke, G. Resolving small distance variations by single-molecule FRET & EPR spectroscopy using rotamer libraries. Biophys J 120, 4842-4858 (2021). PMID: 34536387.

Deneka, D., Rutz, S., Hutter, CAJ., Seeger, MA., Sawicka, M. & Dutzler, R. Allosteric modulation of LRRC8 channels by targeting their cytoplasmic domains. Nat Commun 12, 5435 (2021). PMID: 34521847.

Sorrentino, S., Conesa, JJ., Cuervo, A., Melero, R., Martins, B., Fernandez-Gimenez, E., de Isidro-Gomez, FP., de la Morena, J., Studt, JD., Sorzano, COS., Eibauer, M., Carazo, JM. & Medalia, O. Structural analysis of receptors and actin polarity in platelet protrusions. Proc Natl Acad Sci U S A 118, (2021). PMID: 34504018.

Donohoue, PD., Pacesa, M., Lau, E., Vidal, B., Irby, MJ., Nyer, DB., Rotstein, T., Banh, L., Toh, MS., Gibson, J., Kohrs, B., Baek, K., Owen, ALG., Slorach, EM., van Overbeek, M., Fuller, CK., May, AP., Jinek, M. & Cameron, P. Conformational control of Cas9 by CRISPR hybrid RNA-DNA guides mitigates off-target activity in T cells. Mol Cell 81, 3637-3649.e5 (2021). PMID: 34478654.

Dingfelder, F., Macocco, I., Benke, S., Nettels, D., Faccioli, P. & Schuler, B. Slow Escape from a Helical Misfolded State of the Pore-Forming Toxin Cytolysin A. JACS Au 1, 1217-1230 (2021). PMID: 34467360.

Becker, L., Singh Badwal, J., Brandl, F., Verdurmen, WPR. & Plückthun, A. Thermodynamic Stability Is a Strong Predictor for the Delivery of DARPins to the Cytosol via Anthrax Toxin. Pharmaceutics 13, (2021). PMID: 34452246.

Sapra, KT. & Medalia, O. Bend, Push, Stretch: Remarkable Structure and Mechanics of Single Intermediate Filaments and Meshworks. Cells 10, (2021). PMID: 34440729.

Dolbois, A., Bedi, RK., Bochenkova, E., Müller, A., Moroz-Omori, EV., Huang, D. & Caflisch, A. 1,4,9-Triazaspiro[5.5]undecan-2-one Derivatives as Potent and Selective METTL3 Inhibitors. J Med Chem 64, 12738-12760 (2021). PMID: 34431664.

Stephens, EA., Ludwicki, MB., Meksiriporn, B., Li, M., Ye, T., Monticello, C., Forsythe, KJ., Kummer, L., Zhou, P., Plückthun, A. & DeLisa, MP. Engineering Single Pan-Specific Ubiquibodies for Targeted Degradation of All Forms of Endogenous ERK Protein Kinase. ACS Synth Biol 10, 2396-2408 (2021). PMID: 34399052.

Sukalskaia, A., Straub, MS., Deneka, D., Sawicka, M. & Dutzler, R. Cryo-EM structures of the TTYH family reveal a novel architecture for lipid interactions. Nat Commun 12, 4893 (2021). PMID: 34385445.

Lee, JH., Wang, R., Xiong, F., Krakowiak, J., Liao, Z., Nguyen, PT., Moroz-Omori, EV., Shao, J., Zhu, X., Bolt, MJ., Wu, H., Singh, PK., Bi, M., Shi, CJ., Jamal, N., Li, G., Mistry, R., Jung, SY., Tsai, KL., Ferreon, JC., Stossi, F., Caflisch, A., Liu, Z., Mancini, MA. & Li, W. Enhancer RNA m6A methylation facilitates transcriptional condensate formation and gene activation. Mol Cell 81, 3368-3385.e9 (2021). PMID: 34375583.

Cucuzza, S., Güntert, P., Plückthun, A. & Zerbe, O. An automated iterative approach for protein structure refinement using pseudocontact shifts. J Biomol NMR 75, 319-334(2021). PMID: 34338940.

Weber, MS., Eibauer, M., Sivagurunathan, S., Magin, TM., Goldman, RD. & Medalia, O. Structural heterogeneity of cellular K5/K14 filaments as revealed by cryo-electron microscopy. Elife 10, (2021). PMID: 34323216.

Pohl, MO., Busnadiego, I., Marrafino, F., Wiedmer, L., Hunziker, A., Fernbach, S., Glas, I., Moroz-Omori, EV., Hale, BG., Caflisch, A. & Stertz, S. Combined computational and cellular screening identifies synergistic inhibition of SARS-CoV-2 by lenvatinib and remdesivir. J Gen Virol 102, (2021). PMID: 34319869.

Merten, H., Brandl, F., Zimmermann, M., Schaefer, JV., Irpinio, L., M K Sand, K., Nilsen, J., Andersen, JT., Zangemeister-Wittke, U. & Plückthun, A. Half-life extension of efficiently produced DARPin serum albumin fusions as a function of FcRn affinity and recycling. Eur J Pharm Biopharm 167, 104-113 (2021). PMID: 34303832.

Nemergut, M., Škrabana, R., Berta, M., Plückthun, A. & Sedlák, E. Purification of MBP fusion proteins using engineered DARPin affinity matrix. Int J Biol Macromol  187, 105-112 (2021). PMID: 34298044.

 Bradbury, ARM., Dübel, S., Knappik, A. & Plückthun, A. in vitro-derived antibodies: avoiding the extremes. MAbs 13, 1950265 (2021). PMID: 34281490.

Straub, MS., Alvadia, C., Sawicka, M. & Dutzler, R. Cryo-EM structures of the caspase-activated protein XKR9 involved in apoptotic lipid scrambling. Elife 10, (2021). PMID: 34263724.

Dalle Vedove, A., Cazzanelli, G., Corsi, J., Sedykh, M., D'Agostino, V.G., Caflisch, A., Lolli, G. Identification of a BAZ2A bromodomain hit compound by fragment joining.  ACS Bio Med Chem Au (2021)

Moroz-Omori, EV., Huang, D., Bedi, RK., Cheriyamkunnel, SJ., Bochenkova, E., Dolbois, A., Rzeczkowski, MD., Li, Y., Wiedmer, L. & Caflisch, A. METTL3 inhibitors for epitranscriptomic modulation of cellular processes. ChemMedChem 16, 3035-3043 (2021). PMID: 34237194.

Radom, F., Vonrhein, C., Mittl, PRE. & Plückthun, A. Crystal structures of HER3 extracellular domain 4 in complex with the designed ankyrin-repeat protein D5. Acta Crystallogr F Struct Biol Commun 77, 192-201 (2021). PMID: 34196609.

Stüber, JC., Richter, CP., Bellón, JS., Schwill, M., König, I., Schuler, B., Piehler, J. & Plückthun, A. Apoptosis-inducing anti-HER2 agents operate through oligomerization-induced receptor immobilization. Commun Biol 4, 762 (2021). PMID: 34155320.

Bawankar, P., Lence, T., Paolantoni, C., Haussmann, IU., Kazlauskiene, M., Jacob, D., Heidelberger, JB., Richter, FM., Nallasivan, MP., Morin, V., Kreim, N., Beli, P., Helm, M., Jinek, M., Soller, M. & Roignant, JY. 6A mRNA methylation machinery. Nat Commun 12, 3778 (2021). PMID: 34145251.

Kast, F., Schwill, M., Stüber, JC., Pfundstein, S., Nagy-Davidescu, G., Rodríguez, JMM., Seehusen, F., Richter, CP., Honegger, A., Hartmann, KP., Weber, TG., Kroener, F., Ernst, P., Piehler, J. & Plückthun, A. Engineering an anti-HER2 biparatopic antibody with a multimodal mechanism of action. Nat Commun 12, 3790 (2021). PMID: 34145240.

Kosareva, A., Punjabi, M., Ochoa-Espinosa, A., Xu, L., Schaefer, JV., Dreier, B., Plückthun, A. & Kaufmann, BA. Designed Ankyrin Repeat Proteins as Novel Binders for Ultrasound Molecular Imaging. Ultrasound Med Biol  47, 2664-2675 (2021). PMID: 34144832.

Hartmann, J., Münch, RC., Freiling, RT., Schneider, IC., Dreier, B., Samukang, W., Koch, J., Seeger, MA., Plückthun, A. & Buchholz, CJ. Erratum: A Library-Based Screening Strategy for the Identification of DARPins as Ligands for Receptor-Targeted AAV and Lentiviral Vectors. Mol Ther Methods Clin Dev 21, 728 (2021). PMID: 34141827.

Benke, S., Holla, A., Wunderlich, B., Soranno, A., Nettels, D. & Schuler, B. Combining Rapid Microfluidic Mixing and Three-Color Single-Molecule FRET for Probing the Kinetics of Protein Conformational Changes. J Phys Chem B 125, 6617-6628 (2021). PMID: 34125545.

Vulovic, I., Yao, Q., Park, YJ., Courbet, A., Norris, A., Busch, F., Sahasrabuddhe, A., Merten, H., Sahtoe, DD., Ueda, G., Fallas, JA., Weaver, SJ., Hsia, Y., Langan, RA., Plückthun, A., Wysocki, VH., Veesler, D., Jensen, GJ. & Baker, D. Generation of ordered protein assemblies using rigid three-body fusion. Proc Natl Acad Sci U S A 118, (2021). PMID: 34074752.

Rothgangl, T., Dennis, MK., Lin, PJC., Oka, R., Witzigmann, D., Villiger, L., Qi, W., Hruzova, M., Kissling, L., Lenggenhager, D., Borrelli, C., Egli, S., Frey, N., Bakker, N., Walker, JA., Kadina, AP., Victorov, DV., Pacesa, M., Kreutzer, S., Kontarakis, Z., Moor, A., Jinek, M., Weissman, D., Stoffel, M., van Boxtel, R., Holden, K., Pardi, N., Thöny, B., Häberle, J., Tam, YK., Semple, SC. & Schwank, G. In vivo adenine base editing of PCSK9 in macaques reduces LDL cholesterol levels. Nat Biotechnol 39, 949-957 (2021). PMID: 34012094.

Smith, SN., Schubert, R., Simic, B., Brücher, D., Schmid, M., Kirk, N., Freitag, PC., Gradinaru, V. & Plückthun, A. The SHREAD gene therapy platform for paracrine delivery improves tumor localization and intratumoral effects of a clinical antibody. Proc Natl Acad Sci U S A 118, (2021). PMID: 34001602.

Asanović, I., Strandback, E., Kroupova, A., Pasajlic, D., Meinhart, A., Tsung-Pin, P., Djokovic, N., Anrather, D., Schuetz, T., Suskiewicz, MJ., Sillamaa, S., Köcher, T., Beveridge, R., Nikolic, K., Schleiffer, A., Jinek, M., Hartl, M., Clausen, T., Penninger, J., Macheroux, P., Weitzer, S. & Martinez, J. + as an antioxidant to sustain tRNA ligase activity in pre-tRNA splicing and unfolded protein response. Mol Cell 81, 2520-2532.e16 (2021). PMID: 33930333.

Waltenspühl, Y., Jeliazkov, JR., Kummer, L. & Plückthun, A. Directed evolution for high functional production and stability of a challenging G protein-coupled receptor. Sci Rep 11, 8630 (2021). PMID: 33883583.

Pott, M., Tinzl, M., Hayashi, T., Ota, Y., Dunkelmann, D., Mittl, PRE. & Hilvert, D. Noncanonical heme ligands steer carbene transfer reactivity in an artificial metalloenzyme. Angew Chem Int Ed Engl 60, 15063-15068 (2021).  PMID: 33880851.

Waltenspühl, Y., Ehrenmann, J., Klenk, C. & Plückthun, A. Engineering of Challenging G Protein-Coupled Receptors for Structure Determination and Biophysical Studies. Molecules 26, (2021). PMID: 33800379.

Lerner, E., Barth, A., Hendrix, J., Ambrose, B., Birkedal, V., Blanchard, SC., Börner, R., Sung Chung, H., Cordes, T., Craggs, TD., Deniz, AA., Diao, J., Fei, J., Gonzalez, RL., Gopich, IV., Ha, T., Hanke, CA., Haran, G., Hatzakis, NS., Hohng, S., Hong, SC., Hugel, T., Ingargiola, A., Joo, C., Kapanidis, AN., Kim, HD., Laurence, T., Lee, NK., Lee, TH., Lemke, EA., Margeat, E., Michaelis, J., Michalet, X., Myong, S., Nettels, D., Peulen, TO., Ploetz, E., Razvag, Y., Robb, NC., Schuler, B., Soleimaninejad, H., Tang, C., Vafabakhsh, R., Lamb, DC., Seidel, CA. & Weiss, S. FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices. Elife 10, (2021). PMID: 33779550.

Incaviglia, I., Frutiger, A., Blickenstorfer, Y., Treindl, F., Ammirati, G., Lüchtefeld, I., Dreier, B., Plückthun, A., Vörös, J. & Reichmuth, AM. An Approach for the Real-Time Quantification of Cytosolic Protein-Protein Interactions in Living Cells. ACS Sens  6, 1572-1582 (2021). PMID: 33759497.

Li, W., Sancho, A., Chung, WL., Vinik, Y., Groll, J., Zick, Y., Medalia, O., Bershadsky, AD. & Geiger, B. Differential cellular responses to adhesive interactions with galectin-8 and fibronectin coated substrates. J Cell Sci  134, (2021). PMID: 33722978.

Brücher, D., Kirchhammer, N., Smith, SN., Schumacher, J., Schumacher, N., Kolibius, J., Freitag, PC., Schmid, M., Weiss, F., Keller, C., Grove, M., Greber, UF., Zippelius, A. & Plückthun, A. iMATCH: an integrated modular assembly system for therapeutic combination high-capacity adenovirus gene therapy. Mol Ther Methods Clin Dev 20, 572-586 (2021). PMID: 33665227.

Zhang, M., Gui, M., Wang, ZF., Gorgulla, C., Yu, JJ., Wu, H., Sun, ZJ., Klenk, C., Merklinger, L., Morstein, L., Hagn, F., Plückthun, A., Brown, A., Nasr, ML. & Wagner, G. Cryo-EM structure of an activated GPCR-G protein complex in lipid nanodiscs. Nat Struct Mol Biol 28, 258-267 (2021). PMID: 33633398.

König, I., Soranno, A., Nettels, D. & Schuler, B. Impact of In-Cell and In-Vitro Crowding on the Conformations and Dynamics of an Intrinsically Disordered Protein. Angew Chem Int Ed Engl 60, 10724-10729 (2021). PMID: 33587794.

Deluigi, M., Klipp, A., Klenk, C., Merklinger, L., Eberle, SA., Morstein, L., Heine, P., Mittl, PRE., Ernst, P., Kamenecka, TM., He, Y., Vacca, S., Egloff, P., Honegger, A. & Plückthun, A. Complexes of the neurotensin receptor 1 with small-molecule ligands reveal structural determinants of full, partial, and inverse agonism. Sci Adv 7, (2021). PMID: 33571132.

Kittisopikul, M., Shimi, T., Tatli, M., Tran, JR., Zheng, Y., Medalia, O., Jaqaman, K., Adam, SA. & Goldman, RD. Computational analyses reveal spatial relationships between nuclear pore complexes and specific lamins. J Cell Biol 220, (2021). PMID: 33570570.

Lam, AKM. & Dutzler, R. Mechanism of pore opening in the calcium-activated chloride channel TMEM16A. Nat Commun 12, 786 (2021). PMID: 33542228.

Lam, AKM., Rheinberger, J., Paulino, C. & Dutzler, R. Gating the pore of the calcium-activated chloride channel TMEM16A. Nat Commun 12, 785 (2021). PMID: 33542223.

Kronenberg-Tenga, R., Tatli, M., Eibauer, M., Wu, W., Shin, JY., Bonne, G., Worman, HJ. & Medalia, O. A lamin A/C variant causing striated muscle disease provides insights into filament organization. J Cell Sci 134, (2021). PMID: 33536248.

Martins, B., Sorrentino, S., Chung, WL., Tatli, M., Medalia, O. & Eibauer, M. Unveiling the polarity of actin filaments by cryo-electron tomography. Structure 29, 488-498.e4 (2021). PMID: 33476550.

Li, Y., Bedi, RK., Wiedmer, L., Sun, X., Huang, D. & Caflisch, A. 6A) Recognition by the Reader Domain of YTHDC1.J Chem Theory Comput 17, 1240-1249 (2021). PMID: 33472367.

Milardi, D., Gazit, E., Radford, SE., Xu, Y., Gallardo, RU., Caflisch, A., Westermark, GT., Westermark, P., Rosa, C. & Ramamoorthy, A. Proteostasis of Islet Amyloid Polypeptide: A Molecular Perspective of Risk Factors and Protective Strategies for Type II Diabetes.  Chem Rev 121, 1845-1893 (2021). PMID: 33427465.

Cappelletti, V., Hauser, T., Piazza, I., Pepelnjak, M., Malinovska, L., Fuhrer, T., Li, Y., Dörig, C., Boersema, P., Gillet, L., Grossbach, J., Dugourd, A., Saez-Rodriguez, J., Beyer, A., Zamboni, N., Caflisch, A., de Souza, N. & Picotti, P. Dynamic 3D proteomes reveal protein functional alterations at high resolution in situ. Cell Cell 184, 545-559.e22 (2021). PMID: 33357446.

Mallona, I., Ilie, IM., Karemaker, ID., Butz, S., Manzo, M., Caflisch, A. & Baubec, T. Flanking sequence preference modulates de novo DNA methylation in the mouse genome. Nucleic Acids Res 49, 145-157 (2021). PMID: 33290556.

Teale, WD., Pasternak, T., Dal Bosco, C., Dovzhenko, A., Kratzat, K., Bildl, W., Schwörer, M., Falk, T., Ruperti, B., Schaefer, JV., Shahriari, M., Pilgermayer, L., Li, X., Lübben, F., Plückthun, A., Schulte, U. & Palme, K. Flavonol-mediated stabilization of PIN efflux complexes regulates polar auxin transport. EMBO J 40(1):e104416 (2021). PMID: 33185277.

Goba, I., Goricanec, D., Schum, D., Hillenbrand, M., Plückthun, A. & Hagn, F. Probing the Conformation States of Neurotensin Receptor 1 Variants by NMR Site-Directed Methyl Labeling. Chembiochem 22, 139-146 (2021). PMID: 32881260.

Pinto, MF., Baici, A., Pereira, PJB., Macedo-Ribeiro, S., Pastore, A., Rocha, F. & Martins, PM. interferENZY: A Web-Based Tool for Enzymatic Assay Validation and Standardized Kinetic Analysis. J Mol Biol 433, 166613 (2021). PMID: 32768452.