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Department of Biochemistry

Publications 2019

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

Jínek, M. Uncut but Primed for Change. CRISPR J 2, 352-354 (2019). PMID: 31860347.

Stüber, JC. & Plückthun, A. Labeling surface proteins with high specificity: Intrinsic limitations of phosphopantetheinyl transferase systems. PLoS ONE 14, e0226579 (2019). PMID: 31856184.

Assenza, S., Sassi, AS., Kellner, R., Schuler, B., De Los Rios, P. & Barducci, A. Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones. Elife 8, e4891 (2019). PMID: 31845888.

Davey, NE., Babu, MM., Blackledge, M., Bridge, A., Capella-Gutierrez, S., Dosztanyi, Z., Drysdale, R., Edwards, RJ., Elofsson, A., Felli, IC., Gibson, TJ., Gutmanas, A., Hancock, JM., Harrow, J., Higgins, D., Jeffries, CM., Le Mercier, P., Mészáros, B., Necci, M., Notredame, C., Orchard, S., Ouzounis, CA., Pancsa, R., Papaleo, E., Pierattelli, R., Piovesan, D., Promponas, VJ., Ruch, P., Rustici, G., Romero, P., Sarntivijai, S., Saunders, G., Schuler, B., Sharan, M., Shields, DC., Sussman, JL., Tedds, JA., Tompa, P., Turewicz, M., Vondrasek, J., Vranken, WF., Wallace, BA., Wichapong, K. & Tosatto, SCE. An intrinsically disordered proteins community for ELIXIR. F1000Res 8, (2019). PMID: 31824649.

Chernyavska, M., Schmid, M., Freitag, PC., Palacio-Castañeda, V., Piruska, A., Huck, WTS., Plückthun, A. & Verdurmen, WPR. Unravelling Receptor and RGD Motif Dependence of Retargeted Adenoviral Vectors using Advanced Tumor Model Systems. Sci Rep 9, 18568 (2019). PMID: 31811202.

Manatschal, C., Pujol-Giménez, J., Poirier, M., Reymond, JL., Hediger, MA. & Dutzler, R. Mechanistic basis of the inhibition of SLC11/NRAMP-mediated metal ion transport by bis-isothiourea substituted compounds. Elife 8, (2019). PMID: 31804182.

Ernst, P., Honegger, A., van der Valk, F., Ewald, C., Mittl, PRE. & Plückthun, A. Rigid fusions of designed helical repeat binding proteins efficiently protect a binding surface from crystal contacts. Sci Rep 9, 16162 (2019). PMID: 31700118.

Li, Y., Bedi, RK., Wiedmer, L., Huang, D., Sledz, P. & Caflisch, A. 6A reader protein YTHDC1 to its preferred RNA motif. J Chem Theory Comput 15, 7004-7014 (2019). PMID: 31670957.

Ehrenmann, J., Schöppe, J., Klenk, C. & Plückthun, A. New views into class B GPCRs from the crystal structure of PTH1R. FEBS J. 286, 4852-4860 (2019). PMID: 31670461.

Dunne, M., Rupf, B., Tala, M., Qabrati, X., Ernst, P., Shen, Y., Sumrall, E., Heeb, L., Plückthun, A., Loessner, MJ. & Kilcher, S. Reprogramming Bacteriophage Host Range through Structure-Guided Design of Chimeric Receptor Binding Proteins. Cell Rep 29, 1336-1350.e4 (2019). PMID: 31665644.

Ernst, P., Plückthun, A. & Mittl, PRE. Structural analysis of biological targets by host:guest crystal lattice engineering. Sci Rep 9, 15199 (2019). PMID: 31645583.

Allain, FH. & Jinek, M. Editorial overview: Protein-nucleic acid interactions - cryo-EM, what else?. Curr. Opin. Struct. Biol. 59, vi-viii (2019). PMID: 31635992.

Boneberg, FM., Brandmann, T., Kobel, L., van den Heuvel, J., Bargsten, K., Bammert, L., Kutay, U. & Jinek, M. Corrigendum: Molecular mechanism of the RNA helicase DHX37 and its activation by UTP14A in ribosome biogenesis. RNA 25, 1576 (2019). PMID: 31619564.

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. The NSL complex maintains nuclear architecture stability via lamin A/C acetylation. Nat. Cell Biol. 21, 1248-1260 (2019). PMID: 31576060.

Renko, M., Fiedler, M., Rutherford, TJ., Schaefer, JV., Plückthun, A. & Bienz, M. Rotational symmetry of the structured Chip/LDB-SSDP core module of the Wnt enhanceosome. Proc. Natl. Acad. Sci. U.S.A. 116, 20977-20983 (2019). PMID: 31570581.

Balakrishnan, A., Rajan, A., Salter, AI., Kosasih, PL., Wu, Q., Voutsinas, J., Jensen, MC., Plückthun, A. & Riddell, S. Multispecific targeting with synthetic ankyrin repeat motif chimeric antigen receptors. Clin. Cancer Res. 25, 7506-7516 (2019). PMID: 31548346.

Kumar, A., Clerici, M., Muckenfuss, LM., Passmore, LA. & Jinek, M. Mechanistic insights into mRNA 3'-end processing. Curr. Opin. Struct. Biol. 59, 143-150 (2019). PMID: 31499460.

Dumeau, CE., Monfort, A., Kissling, L., Swarts, DC., Jinek, M. & Wutz, A. Introducing gene deletions by mouse zygote electroporation of Cas12a/Cpf1. Transgenic Res. 28, 525-535 (2019). PMID: 31482512.

Stivala, S., Sorrentino, S., Gobbato, S., Bonetti, NR., Camici, GG., Lüscher, TF., Medalia, O. & Beer, JH. Glycoprotein Ib clustering in platelets can be inhibited by α-linolenic acid as revealed by cryo-electron tomography. Haematologica 105, 1660-1666 (2020). PMID: 31439672.

Walter, JD., Sawicka, M. & Dutzler, R. Cryo-EM structures and functional characterization of murine Slc26a9 reveal mechanism of uncoupled chloride transport. Elife 8, (2019). PMID: 31339488.

Merten, H., Schaefer, JV., Brandl, F., Zangemeister-Wittke, U. & Plückthun, A. Facile Site-Specific Multiconjugation Strategies in Recombinant Proteins Produced in Bacteria. Methods Mol. Biol. 2033, 253-273 (2019). PMID: 31332759.

Zhang, Y., Auger, S., Schaefer, JV., Plückthun, A. & Distefano, MD. Site-Selective Enzymatic Labeling of Designed Ankyrin Repeat Proteins Using Protein Farnesyltransferase. Methods Mol. Biol. 2033, 207-219 (2019). PMID: 31332756.

Bunzel, HA., Kries, H., Marchetti, L., Zeymer, C., Mittl, PRE., Mulholland, AJ. & Hilvert, D. Emergence of a Negative Activation Heat Capacity during Evolution of a Designed Enzyme. J. Am. Chem. Soc. 141, 11745-11748 (2019).  PMID: 31282667.

Brandl, F., Merten, H., Zimmermann, M., Béhé, M., Zangemeister-Wittke, U. & Plückthun, A. Influence of size and charge of unstructured polypeptides on pharmacokinetics and biodistribution of targeted fusion proteins.  J Control Release 307, 379-392 (2019). PMID: 31252038.

Gutte, B. & Klauser, S. Design of catalytic polypeptides and proteins. Protein Eng. Des. Sel. 31, 457-470 (2018). PMID: 31241746.

Holmstrom, ED., Liu, Z., Nettels, D., Best, RB. & Schuler, B. Disordered RNA chaperones can enhance nucleic acid folding via local charge screening. Nat Commun 10, 2453 (2019). PMID: 31165735.

Lorenzer, C., Streußnig, S., Tot, E., Winkler, AM., Merten, H., Brandl, F., Sayers, EJ., Watson, P., Jones, AT., Zangemeister-Wittke, U., Plückthun, A. & Winkler, J. Targeted delivery and endosomal cellular uptake of DARPin-siRNA bioconjugates: Influence of linker stability on gene silencing. Eur J Pharm Biopharm  141, 37-50 (2019). PMID: 31103742.

Radom, F., Paci, E. & Plückthun, A. Computational Modeling of Designed Ankyrin Repeat Protein Complexes with their Targets. J. Mol. Biol. 431, 2852-2868 (2019). PMID: 31082438.

Wiedmer, L., Schärer, C., Spiliotopoulos, D., Hürzeler, M., Śledź, P. & Caflisch, A. Ligand retargeting by binding site analogy. Eur J Med Chem 175, 107-113 (2019). PMID: 31077996.

Hegge, JW., Swarts, DC., Chandradoss, SD., Cui, TJ., Kneppers, J., Jinek, M., Joo, C. & van der Oost, J. DNA-guided DNA cleavage at moderate temperatures by Clostridium butyricum Argonaute. Nucleic Acids Res.  47, 5809-5821 (2019). PMID: 31069393.

Stüber, JC., Kast, F. & Plückthun, A. High-Throughput Quantification of Surface Protein Internalization and Degradation. ACS Chem. Biol. 14, 1154-1163 (2019). PMID: 31050891.

Ricci, CG., Chen, JS., Miao, Y., Jinek, M., Doudna, JA., McCammon, JA. & Palermo, G. Deciphering Off-Target Effects in CRISPR-Cas9 through Accelerated Molecular Dynamics. ACS Cent Sci 5, 651-662 (2019). PMID: 31041385.

Campanacci, V., Urvoas, A., Cantos-Fernandes, S., Aumont-Nicaise, M., Arteni, AA., Velours, C., Valerio-Lepiniec, M., Dreier, B., Plückthun, A., Pilon, A., Poüs, C., Minard, P. & Gigant, B. Insight into microtubule nucleation from tubulin-capping proteins. Proc. Natl. Acad. Sci. U.S.A. 116, 9859-9864 (2019). PMID: 31036638.

Qi, C., Sorrentino, S., Medalia, O. & Korkhov, VM. The structure of a membrane adenylyl cyclase bound to an activated stimulatory G protein. Science 364, 389-394 (2019). PMID: 31023924.

Meksiriporn, B., Ludwicki, MB., Stephens, EA., Jiang, A., Lee, HC., Waraho-Zhmayev, D., Kummer, L., Brandl, F., Plückthun, A. & DeLisa, MP. A survival selection strategy for engineering synthetic binding proteins that specifically recognize post-translationally phosphorylated proteins. Nat Commun 10, 1830 (2019). PMID: 31015433.

Ilie, IM. & Caflisch, A. Simulation Studies of Amyloidogenic Polypeptides and Their Aggregates. Chem. Rev. 119, 6956-6993 (2019). PMID: 30973229

Andres, F., Iamele, L., Meyer, T., Stüber, JC., Kast, F., Gherardi, E., Niemann, HH. & Plückthun, A. Inhibition of the MET Kinase Activity and Cell Growth in MET-Addicted Cancer Cells by Bi-Paratopic Linking.  J. Mol. Biol. 431, 2020-2039 (2019). PMID: 30930049.

Heine, P., Witt, G., Gilardi, A., Gribbon, P., Kummer, L. & Plückthun, A. High-Throughput Fluorescence Polarization Assay to Identify Ligands Using Purified G Protein-Coupled Receptor. SLAS Discov 24, 915-927 (2019). PMID: 30925845.

Boneberg, F., Brandmann, T., Kobel, L., van den Heuvel, J., Bargsten, K., Bammert, L., Kutay, U. & Jinek, M. Molecular mechanism of the RNA helicase DHX37 and its activation by UTP14 in ribosome biogenesis. RNA 25, 685-701 (2019). PMID: 30910870.

Deprey, K., Becker, L., Kritzer, J. & Plückthun, A. Trapped! A Critical Evaluation of Methods for Measuring Total Cellular Uptake versus Cytosolic Localization. Bioconjug. Chem. 30, 1006-1027 (2019). PMID: 30882208.

Bacci, M., Caflisch, A. & Vitalis, A. On the removal of initial state bias from simulation data. J Chem Phys 150, 104105 (2019). PMID: 30876362.

Garolini, D., Vitalis, A. & Caflisch, A. Unsupervised identification of states from voltage recordings of neural networks. J. Neurosci. Methods 318, 104-117 (2019). PMID: 30807781.

Tomatis, PE., Schütz, M., Umudumov, E. & Plückthun, A. Mutations in sigma 70 transcription factor improves expression of functional eukaryotic membrane proteins in Escherichia coli. Sci Rep 9, 2483 (2019). PMID: 30792443.

Alvadia, C., Lim, NK., Clerico Mosina, V., Oostergetel, GT., Dutzler, R. & Paulino, C. Cryo-EM structures and functional characterization of the murine lipid scramblase TMEM16F. Elife 8, (2019). PMID: 30785399.

Kalienkova, V., Clerico Mosina, V., Bryner, L., Oostergetel, GT., Dutzler, R. & Paulino, C. Stepwise activation mechanism of the scramblase nhTMEM16 revealed by cryo-EM. Elife 8, (2019). PMID: 30785398.

Wiedmer, L., Eberle, SA., Bedi, RK., Śledź, P. & Caflisch, A. 6A Writers and Erasers. Anal. Chem. 91, 3078-3084 (2019). PMID: 30715855.

Kissling, L., Monfort, A., Swarts, DC., Wutz, A. & Jinek, M. Preparation and electroporation of Cas12a/Cpf1-guide RNA complexes for introducing large gene deletions in mouse embryonic stem cells. Meth. Enzymol. 616, 241-263 (2019). PMID: 30691645.

Savić, N., Ringnalda, FC., Berk, C., Bargsten, K., Hall, J., Jinek, M. & Schwank, G. In vitro Generation of CRISPR-Cas9 Complexes with Covalently Bound Repair Templates for Genome Editing in Mammalian Cells. Bio Protoc 9, (2019). PMID: 30675496.

Schwill, M., Tamaskovic, R., Gajadhar, AS., Kast, F., White, FM. & Plückthun, A. Systemic analysis of tyrosine kinase signaling reveals a common adaptive response program in a HER2-positive breast cancer. Sci Signal 12, (2019). PMID: 30670633.

Weber, MS., Wojtynek, M. & Medalia, O. Cellular and Structural Studies of Eukaryotic Cells by Cryo-Electron Tomography. Cells 8, (2019). PMID: 30654455.

Swarts, DC. & Jinek, M. Mechanistic Insights into the cis- and trans-Acting DNase Activities of Cas12a. Mol. Cell 73, 589-600 (2019). PMID: 30639240.

Kumar, A. & Plückthun, A. In vivo assembly and large-scale purification of a GPCR - Gα fusion with Gβγ, and characterization of the active complex. PLoS ONE 14, e0210131 (2019). PMID: 30620756.

Gall, FM., Hohl, D., Frasson, D., Wermelinger, T., Mittl, PRE., Sievers, M. & Riedl, R. Drug Design Inspired by Nature: Crystallographic Detection of an Auto-Tailored Protease Inhibitor Template. Angew. Chem. Int. Ed. Engl. 58, 4051-4055 (2019). PMID: 30615822.

Schöppe, J., Ehrenmann, J., Klenk, C., Rucktooa, P., Schütz, M., Doré, AS. & Plückthun, A. Crystal structures of the human neurokinin 1 receptor in complex with clinically used antagonists. Nat Commun 10, 17 (2019). PMID: 30604743.

Gay, JC., Eckenroth, BE., Evans, CM., Langini, C., Carlson, S., Lloyd, JT., Caflisch, A. & Glass, KC. Disulfide bridge formation influences ligand recognition by the ATAD2 bromodomain. Proteins 87, 157-167 (2019). PMID: 30520161.

Michel, E., Plückthun, A. & Zerbe, O. Peptide binding affinity redistributes preassembled repeat protein fragments. Biol. Chem. 400, 395-404 (2019). PMID: 30517075.

Kroupova, A., Ivascu, A., Reimão-Pinto, MM., Ameres, SL. & Jinek, M. Structural basis for acceptor RNA substrate selectivity of the 3' terminal uridylyl transferase Tailor. Nucleic Acids Res. 47, 1030-1042 (2019). PMID: 30462292.