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Department of Biochemistry

Publications 2020

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

Casalino, L., Nierzwicki, Ł., Jinek, M. & Palermo, G. Ab Initio Molecular Dynamics. ACS Catal 10, 13596-13605 (2020). PMID: 33520346.

Unzue, A., Jessen-Trefzer, C., Spiliotopoulos, D., Gaudio, E., Tarantelli, C., Dong, J., Zhao, H., Pachmayr, J., Zahler, S., Bernasconi, E., Sartori, G., Cascione, L., Bertoni, F., Śledź, P., Caflisch, A. & Nevado, C. b]quinoxaline-derivatives as kinase inhibitors. RSC Med Chem 11, 665-675 (2020). PMID: 33479666.

Karakus, U., Sahin, D., Mittl, PRE., Mooij, P., Koopman, G. & Boyman, O. Receptor-gated IL-2 delivery by an anti-human IL-2 antibody activates regulatory T cells in three different species. Sci Transl Med 12, (2020). PMID: 33328333.

Sapra, KT., Qin, Z., Dubrovsky-Gaupp, A., Aebi, U., Müller, DJ., Buehler, MJ. & Medalia, O. Nonlinear mechanics of lamin filaments and the meshwork topology build an emergent nuclear lamina. Nat Commun 11, 6205 (2020). PMID: 33277502.

Boujemaa-Paterski, R., Martins, B., Eibauer, M., Beales, CT., Geiger, B. & Medalia, O. Talin-activated vinculin interacts with branched actin networks to initiate bundles. Elife 9, (2020). PMID: 33185186.

Sottini, A., Borgia, A., Borgia, MB., Bugge, K., Nettels, D., Chowdhury, A., Heidarsson, PO., Zosel, F., Best, RB., Kragelund, BB. & Schuler, B. Polyelectrolyte interactions enable rapid association and dissociation in high-affinity disordered protein complexes. Nat Commun 11, 5736 (2020). PMID: 33184256.

Saha, A., Arantes, PR., Hsu, RV., Narkhede, YB., Jinek, M. & Palermo, G. Molecular Dynamics Reveals a DNA-Induced Dynamic Switch Triggering Activation of CRISPR-Cas12a. J Chem Inf Model 60, 6427-6437 (2020). PMID: 33107304.

Li, Y., Bedi, RK., Moroz-Omori, EV. & Caflisch, A. Structural and Dynamic Insights into Redundant Function of YTHDF Proteins. J Chem Inf Model 60, 5932-5935 (2020). PMID: 33073985.

Zijlstra, N., Nettels, D., Satija, R., Makarov, DE. & Schuler, B. Transition Path Dynamics of a Dielectric Particle in a Bistable Optical Trap. Phys Rev Lett 125, 146001 (2020). PMID: 33064519.

Nowak, K., Rosenthal, F., Karlberg, T., Bütepage, M., Thorsell, AG., Dreier, B., Grossmann, J., Sobek, J., Imhof, R., Lüscher, B., Schüler, H., Plückthun, A., Leslie Pedrioli, DM. & Hottiger, MO. Engineering Af1521 improves ADP-ribose binding and identification of ADP-ribosylated proteins. Nat Commun 11, 5199 (2020). PMID: 33060572.

Gray, A., Bradbury, ARM., Knappik, A., Plückthun, A., Borrebaeck, CAK. & Dübel, S. Animal-free alternatives and the antibody iceberg. Nat Biotechnol 38, 1234-1239 (2020). PMID: 33046876.

Khayat, M., Deri, S., Wolf, D., Trigano, T., Medalia, O. & Ben-Harush, K. Biomimetic nuclear lamin fibers with remarkable toughness and stiffness. Int. J. Biol. Macromol.163, 2060-2067 (2020). PMID: 32961198.

Cocina, F., Vitalis, A. & Caflisch, A. Sapphire-Based Clustering. J Chem Theory Comput 16, 6383-6396 (2020). PMID: 32905698.

Marchand, JR., Knehans, T., Caflisch, A. & Vitalis, A. An ABSINTH-Based Protocol for Predicting Binding Affinities between Proteins and Small Molecules. J Chem Inf Model 60, 5188-5202 (2020). PMID: 32897071.

Waltenspühl, Y., Schöppe, J., Ehrenmann, J., Kummer, L. & Plückthun, A. Crystal structure of the human oxytocin receptor. Sci Adv 6, eabb5419 (2020). PMID: 32832646.

Dolbois, A., Batiste, L., Wiedmer, L., Dong, J., Brütsch, M., Huang, D., Deerain, NM., Spiliotopoulos, D., Cheng-Sánchez, I., Laul, E., Nevado, C., Śledź, P. & Caflisch, A. Hitting a Moving Target: Simulation and Crystallography Study of ATAD2 Bromodomain Blockers. ACS Med Chem Lett 11, 1573-1580 (2020). PMID: 32832026.

Goossens, K., Wroblowski, B., Langini, C., Van Vlijmen, H., Caflisch, A. & De Winter, H. Assessment of the fragment docking program SEED. J Chem Inf Model 60, 4881-4893 (2020). PMID: 32820916.

Tenga, R. & Medalia, O. Structure and unique mechanical aspects of nuclear lamin filaments. Curr Opin Struct Biol 64, 152-159 (2020). PMID: 32810798.

Becker, L., Verdurmen, WPR. & Plückthun, A. Reengineering anthrax toxin protective antigen for improved receptor-specific protein delivery. BMC Biol. 18, 100 (2020). PMID: 32792013.

Brandl, F., Busslinger, S., Zangemeister-Wittke, U. & Plückthun, A. Optimizing the anti-tumor efficacy of protein-drug conjugates by engineering the molecular size and half-life. J Control Release 327, 186-197 (2020). PMID: 32768630.

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. [Epub ahead of print] (2020). PMID: 32768452.

Voskuil, JLA., Bandrowski, A., Begley, CG., Bradbury, ARM., Chalmers, AD., Gomes, AV., Hardcastle, T., Lund-Johansen, F., Plückthun, A., Roncador, G., Solache, A., Taussig, MJ., Trimmer, JS., Williams, C. & Goodman, SL. The Antibody Society's antibody validation webinar series. MAbs 12, 1794421 (2020). PMID: 32748696.

Pinto, PH., Kroupova, A., Schleiffer, A., Mechtler, K., Jinek, M., Weitzer, S. & Martinez, J. ANGEL2 is a member of the CCR4 family of deadenylases with 2',3'-cyclic phosphatase activity. Science 369, 524-530 (2020). PMID: 32732418.

Gray, AC., Bradbury, ARM., Knappik, A., Plückthun, A., Borrebaeck, CAK. & Dübel, S. Animal-derived-antibody generation faces strict reform in accordance with European Union policy on animal use. Nat. Methods 17, 755-756 (2020). PMID: 32719533.

Horev, MB., Zabary, Y., Zarka, R., Sorrentino, S., Medalia, O., Zaritsky, A. & Geiger, B. Differential dynamics of early stages of platelet adhesion and spreading on collagen IV- and fibrinogen-coated surfaces. F1000Res 9, (2020). PMID: 32566134.

Brücher, D., Franc, V., Smith, SN., Heck, AJR. & Plückthun, A. Malignant tissues produce divergent antibody glycosylation of relevance for cancer gene therapy effectiveness. MAbs 12, 1792084 (2020). PMID: 32643525.

Chabloz, A., Schaefer, JV., Kozieradzki, I., Cronin, SJF., Strebinger, D., Macaluso, F., Wald, J., Rabbitts, TH., Plückthun, A., Marlovits, TC. & Penninger, JM. Salmonella-based platform for efficient delivery of functional binding proteins to the cytosol. Commun Biol 3, 342 (2020). PMID: 32620833.

Zosel, F., Soranno, A., Buholzer, KJ., Nettels, D. & Schuler, B. Depletion interactions modulate the binding between disordered proteins in crowded environments. Proc. Natl. Acad. Sci. U.S.A. 117, 13480-13489 (2020). PMID: 32487732.

Wrona, D., Pastukhov, O., Pritchard, RS., Raimondi, F., Tchinda, J., Jinek, M., Siler, U. & Reichenbach, J. NCF1 Locus Is Challenged by Frequent Incidence of Chromosomal Deletions. Mol Ther Methods Clin Dev 17, 936-943 (2020). PMID: 32420407.

Gray, AC., Bradbury, A., Dübel, S., Knappik, A., Plückthun, A. & Borrebaeck, CAK. Reproducibility: bypass animals for antibody production. Nature 581, 262 (2020). PMID: 32415238.

Schuster, M., Deluigi, M., Pantić, M., Vacca, S., Baumann, C., Scott, DJ., Plückthun, A. & Zerbe, O. 1B-adrenergic receptor for solution NMR studies. Biochim Biophys Acta Biomembr 1862, 183354 (2020). PMID: 32413443.

Persson, BD., Lenman, A., Frängsmyr, L., Schmidt, M., Ahlm, C., Plückthun, A., Jenssen, H. & Arnberg, N. Lactoferrin-hexon interactions mediate CAR-independent adenovirus infection of human respiratory cells. J Virol 94, (2020). PMID: 32376620.

Drożdżyk, K., Sawicka, M., Bahamonde-Santos, MI., Jonas, Z., Deneka, D., Albrecht, C. & Dutzler, R. Cryo-EM structures and functional properties of CALHM channels of the human placenta. Elife 9, (2020). PMID: 32374262.

Davies, K. & Jínek, M. The CRISPR-RNA World: An Interview with Martin Jínek. CRISPR J 3, 68-72 (2020). PMID: 32315230.

Arnold, FM., Weber, MS., Gonda, I., Gallenito, MJ., Adenau, S., Egloff, P., Zimmermann, I., Hutter, CAJ., Hürlimann, LM., Peters, EE., Piel, J., Meloni, G., Medalia, O. & Seeger, MA. The ABC exporter IrtAB imports and reduces mycobacterial siderophores. Nature 580, 413-417 (2020). PMID: 32296173.

Pretze, M., Neuber, C., Kinski, E., Belter, B., Köckerling, M., Caflisch, A., Steinbach, J., Pietzsch, J. & Mamat, C. 18F-labelled xanthine derivatives for PET imaging of Eph receptors. Org. Biomol. Chem. 18, 3104-3116 (2020). PMID: 32253415.

Bertrand, AT., Brull, A., Azibani, F., Benarroch, L., Chikhaoui, K., Stewart, CL., Medalia, O., Ben Yaou, R. & Bonne, G. LMNA-Congenital Muscular Dystrophy Is Responsible for the Increased Severity of the Disease Compared with Emery-Dreifuss Muscular Dystrophy. Cells 9, (2020). PMID: 32244403.
Gosavi, S. & Schuler, B. Editorial overview: Molecular interactions that drive folding and binding: new challenges and opportunities. Curr. Opin. Struct. Biol. 60, iii-iv (2020). PMID: 32228883.

Garcia-Doval, C., Schwede, F., Berk, C., Rostøl, JT., Niewoehner, O., Tejero, O., Hall, J., Marraffini, LA. & Jinek, M. Activation and self-inactivation mechanisms of the cyclic oligoadenylate-dependent CRISPR ribonuclease Csm6. Nat Commun 11, 1596 (2020). PMID: 32221291.

Bedi, RK., Huang, D., Eberle, SA., Wiedmer, L., Śledź, P. & Caflisch, A. Small-Molecule Inhibitors of METTL3, the Major Human Epitranscriptomic Writer. ChemMedChem 15, 744-748 (2020). PMID: 32159918.

Petrenčáková, M., Filandr, F., Hovan, A., Yassaghi, G., Man, P., Kožár, T., Schwer, MS., Jancura, D., Plückthun, A., Novák, P., Miškovský, P., Bánó, G. & Sedlák, E. Photoinduced damage of AsLOV2 domain is accompanied by increased singlet oxygen production due to flavin dissociation. Sci Rep 10, 4119 (2020). PMID: 32139757.

Bedi, RK., Huang, D., Wiedmer, L., Li, Y., Dolbois, A., Wojdyla, JA., Sharpe, ME., Caflisch, A. & Sledz, P. 6A-Dependent Protein-RNA Interactions with Fragments. ACS Chem. Biol. 15, 618-625 (2020). PMID: 32101404.

Ernst, P., Zosel, F., Reichen, C., Nettels, D., Schuler, B. & Plückthun, A. Structure-Guided Design of a Peptide Lock for Modular Peptide Binders. ACS Chem. Biol. 15, 457-468 (2020). PMID: 31985201.

Mittl, PR., Ernst, P. & Plückthun, A. Chaperone-assisted structure elucidation with DARPins. Curr. Opin. Struct. Biol.60, 93-100 (2020). PMID: 31918361.

Caflisch, A. Kinetic Control of Amyloidogenesis Calls for Unconventional Drugs To Fight Alzheimer's Disease. ACS Chem Neurosci 11, 103-104 (2020). PMID: 31904213.

Andres, F., Schwill, M., Boersma, YL. & Plückthun, A. High-Throughput Generation of Bispecific Binding Proteins by Sortase A-Mediated Coupling for Direct Functional Screening in Cell Culture. Mol. Cancer Ther. 19, 1080-1088 (2020). PMID: 31871271.

Salutari, I., Martin, R. & Caflisch, A. The 3A6-TCR/superagonist/HLA-DR2a complex shows similar interface and reduced flexibility compared to the complex with self-peptide. Proteins 88, 31-46 (2020). PMID: 31237711.

Quesada, R. & Dutzler, R. Alternative chloride transport pathways as pharmacological targets for the treatment of cystic fibrosis. J. Cyst. Fibros. 19 Suppl 1, S37-S41 (2020). PMID: 31662238.

Schuler, B., Borgia, A., Borgia, MB., Heidarsson, PO., Holmstrom, ED., Nettels, D. & Sottini, A. Binding without folding - the biomolecular function of disordered polyelectrolyte complexes. Curr. Opin. Struct. Biol. 60, 66-76 (2020). PMID: 31874413.