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Department of Biochemistry

Publications 2017

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

Grotz, K., Nüesch, M., Holmstrom, E., Heinz, M., Stelzl, LS., Schuler, B. & Hummer, G. Dispersion correction alleviates dye stacking of single-stranded DNA and RNA in simulations of single-molecule fluorescence experiments. J Phys. Chem B. Oct [Epub ahead of print] (2018). PMID: 30285443.

Zheng, W., Hofmann, H., Schuler, B. & Best, RB. Origin of internal friction in disordered proteins depends on solvent quality. J Phys. Chem B. Oct [Epub ahead of print] (2018). PMID: 30277791.

Zhu, J., Dong, J., Batiste; L., Unzue, A., Dolbois, A., Pascanu, V., Śledź, P., Nevado, C. &  Caflisch, A. Binding motifs in the CBP bromodomain: an analysis of 20 crystal structures of complexes with small molecules. ACS Med Chem Lett. 9, 929-934 (2018). PMID: 39258543.

Langini C., Caflisch A. &  Vitalis A. The ATAD2 bromodomain binds different acetylation marks on the histone H4 in similar fuzzy complexes. J Biol Chem. 292, 19121 (2017). PMID: 29373865.

Clerici, M., Faini, M., Aebersold, R. & Jinek, M. Structural insights into the assembly and polyA signal recognition mechanism of the human CPSF complex. Elife e33111 (2017). PMID: 29274231.

Paulino, C., Kalienkova, V., Lam, AKM., Neldner, Y. & Dutzler, R. Activation mechanism of the calcium-activated chloride channel TMEM16A revealed by cryo-EM. Nature 552, 421-425 (2017). PMID: 29236691.

Abplanalp, J., Leutert, M., Frugier, E., Nowak, K., Feurer, R., Kato, J., Kistemaker, HVA., Filippov, DV., Moss, J., Caflisch, A. & Hottiger, MO. Proteomic analyses identify ARH3 as a serine mono-ADP-ribosylhydrolase. Nat Commun. 8, 2055 (2017). PMID: 29234005.

Hansen, S., Stüber, JC., Ernst, P., Koch, A., Bojar, D., Batyuk, A. & Plückthun, A. Design and applications of a clamp for Green Fluorescent Protein with picomolar affinity. Sci Rep 7, 16292 (2017). PMID: 29176615.

Bacci, M., Langini, C., Vymětal, J., Caflisch, A. & Vitalis, A. Focused conformational sampling in proteins. J Chem Phys 147, 195102 (2017). PMID: 29166086.

Garcia-Doval, C. & Jinek, M. Molecular architectures and mechanisms of Class 2 CRISPR-associated nucleases. Curr. Opin. Struct. Biol. 47, 157-166 (2017). PMID: 29107822.

Zosel, F.,Haenni, D., Soranno, A., Nettels, D. & Schuler, B. Combining short- and long-range fluorescence reporters with simulations to explore the intramolecular dynamics of an intrinsically disordered protein. J Chem Phys147, 152708 (2017). PMID: 29055320.

Verdurmen, WPR., Mazlami, M.& Plückthun, A. A quantitative comparison of cytosolic delivery via different protein uptake systems. Sci Rep. 7, 13194 (2017). PMID: 29038564.

Santoro, A., Ewa Wezynfeld, N., Vašák, M., Bal, W. & Faller , M. Cysteine and glutathione trigger the Cu-Zn swap between Cu(ii)-amyloid-β4-16 peptide and Zn7-metallothionein-3. Chem Commun (Camb) 53, 11634-11637 (2017). PMID: 28948272.

Niewoehner, O. & Jinek, M. Specialized Weaponry: How a Type III-A CRISPR-Cas System Excels at Combating Phages. Cell Host Microbe 22, 258-259 (2017). PMID: 28910631.

Wu, Y. Batyuk, A., Honegger, M., Brandl, F., Mitt, PRE. & Plückthun. Rigidly connected multispecific artificial binders with adjustable geometries. Sci Rep. 1, 11217 (2017). PMID: 28894181.

Bacci, M., Vymětal, J., Mihajlovic, M., Caflisch. A. & Vitalis, A. Amyloid beta fibril elongation by monomers involves disorder a the tip. J Chem Theory Comput. 13, 5117-5130 (2017). PMID: 28870064.

Marchand, JR., Vedove, AD., Lollo, G. & Caflisch, A. Discovery of inhibitors of four bromodomains by fragment-anchored ligand docking. J Chem Inf Model. 57, 2584-2597 (2017). PMID: 28862840.

Spiliotopoulos, D., Wamhoff, EC., Lolli, G., Rademacher, C. & Caflisch, A. Discovery of BAZ2A bromodomain ligands. Eur J Med Chem 139, 564-572  (2017). PMID: 28837921.

Nemergut, M., Žoldák, G., Schaefer, JV., Kast, F., Miškovský, P., Plückthun, A. & Sedlák, E. Analysis of IgG kinetic stability by differential scanning calorimetry, probe fluorescence and light scattering. Protein Sci 11, 2229-2239 (2017). PMID: 28833802.

Kramer, L., Renko, M., Završnik, J., Turk, D., Seeger, MA., Vasiljeva, O., Grütter, MG., Turk, V. & Turk, B. Non-invasive in vivo imaging of tumour-associated cathepsin B by a highly selective inhibitory DARPin. Theranostics 7, 2806-2821 (2017). PMID: 28824717.

Langini, C.,Caflisch, A. & Vitalis, A. The ATAD2 bromodomain binds different acetytation marks on the histone H4 in similar fuzzy complexes. J Biol Chem 292, 16734-16745 (2017). PMID: 28798233 .

Peón, A., Robles, A., Blanco, B., Convertino, M., Thompson, P., Hawkins, AR., Caflisch, A. & Gonzalez-Bello, C. Reducing the flexibility of type II dehydroquinase enzyme for inhibition - a fragment-base approach and molecular dynamics simulation study.  ChemMedChem. 12, 1512-1524 (2017). PMID: 28791799 .

Marino, J., Holzhüter, K., Kuhn, B. & Geertsma, ER. Efficient Screening and Optimization of Membrane Protein Production in Escherichia coli. Meth. Enzymol. 594, 139-164 (2017). PMID: 28779839.

Palermo, G., Miao, Y., Walker, RC., Jinek, M. & McCammon, JA. CRISPR-Cas9 conformational activation as elucidated from enhanced molecular simulations. Proc. Natl. Acad. Sci. U.S.A. 114, 7260-7265 (2017). PMID: 28652374.

Plitzko, JM., Schuler, B. & Selenko, P. Structural Biology outside the box-inside the cell. Curr. Opin. Struct. Biol. 46, 110-121 (2017). PMID: 28735108.

Schenck, S., Kunz, L., Sahlender, D., Pardon, E., Geertsma, ER., Savtchouk, I., Suzuki, T., Neldner, Y., Štefanić, S., Steyaert, J., Volterra, A. & Dutzler, R. Generation and Characterization of Anti-VGLUT Nanobodies Acting as Inhibitors of Transport. Biochemistry 56, 3962-3971 (2017). PMID: 28731329.

Niewoehner, O., Garcia-Doval, C.,  Rostøl, JT., Berk, C., Schwede, F., Bigler. L., Hall, J., Marraffini, LA. & Jinek, M. Type III CRISPR-Cas systems produce cyclic oligoadenylate second messengers. Nature 548, 543-548 (2017).  28722012.

Hansen, S., Kiefer, JD.,Madhurantakam, C., Mittl, PRE. & Plückthun, A. Structures of designed armadillo repeat proteins binding to peptides fused to globular proteins. Protein Sci. 26, 1942-1952 (2017). PMID: 28691351.

Afroz, T., Hock, EM., Ernst, P., Foglieni, C., Jambeau, M., Gilhespy, LAB., Laferriere, F., Maniecka, Z., Plückthun, A., Mittl, P., Paganetti, P., Allain, FHT. & Polymenidou, M. Functional and dynamic polymerization of the ALS-linked protein TDP-43 antagonizes its pathologic aggregation. Nat Commun 8, 45 (2017). PMID: 28663553.

Palermo, G., Ricci, CG., Fernando, A., Basak, R., Jinek, M., Rivalta, I., Batista, VS. & McCammon, JA. Protospacer Adjacent Motif-Induced Allostery Activates CRISPR-Cas9. J. Am. Chem. Soc. 139, 16028-16031 (2017). PMID: 28764328.

Jost C., Stüber, JC., Honegger, A., Wu, Y., Batyuk, A. & Plückthun, A.  Rigidity of the ewxtracellular part of HER2: Evidence from engineering subdomain interfaces and shared-helix DARPin-DARPin fusions. Protein Sci 26, 1796-1806 (2017). PMID: 28639341.

Turgay, Y. & Medalia, O. The structure of lamin filaments in somatic cells as revealed by cryo-electron tomography. Nucleus 8, 475-481 (2017). PMID: 28635493.

Parren, PWHI., Carter, PJ. & Plückthun, A. Changes to International Nonproprietary Names for antibody therapeutics 2017 and beyond: of mice, men and more. MAbs 9, 898-906 (2017). PMID: 28621572.

Paulino C, Neldner Y, Lam AK, Kalienkova V, Brunner JD, Schenck S &  Dutzler R. Structural basis for anion conduction in the calcium-activated chloride channel TMEM16A. Elife. May 31;6. pii: e26232 (2017). PMID: 28561733.

Vašák M, Meloni G. Mammalian methallothionein-3: new functional and structural insights. Int J Mol Sci18(6), pii: E1117 (2017). PMID: 28538697.

Huber, S., Casagrande, F., Hug, MN., Wang, L., Heine, P., Kummer, L., Plückthun, A. & Hennig, M. SPR-based fragment screening with neurotensin receptor 1 generates novel small molecule ligands. PLoS ONE 12, e0175842 (2017). PMID: 28510609.

Zijlstra, N., Dingfelder, F., Wunderlich, B., Zosel, F., Benke, S., Nettels, D. & Schuler, B. Rapid Microfluidic Dilution for Single-Molecule Spectroscopy of Low-Affinity Biomolecular Complexes. Angew. Chem. Int. Ed. Engl. 56, 7126-7129 (2017). PMID: 28510311.

Skegro, D., Stutz, C., Ollier, R, Svensson, E., Wassmann P., Bourquin, F., Monney, T., Gn, S. & Blein, S. Immunoglobulin domain interface exchange as a platform technology for the generation of Fc heterodimers and bispecific antibodies. J Biol Chem. 292, 9745-9759 (2017).PMID: 28450393.

Swarts, DC., van der Oost, J. & Jinek, M. Structural Basis for Guide RNA Processing and Seed-Dependent DNA Targeting by CRISPR-Cas12a. Mol. Cell 66, 221-233.e4 (2017). PMID: 28431230.

Spiliotopoulos, D., Zhu, J., Wamhoff, EC., Deerain, N., Marchand, JR., Aretz, J., Rademacher, C. & Caflisch, A. Virtual screen to NMR (VS2NMR): Discovery of fragment hits for the CBP bromodomain. Bioorg. Med. Chem. Lett. 27, 2472-2478 (2017). PMID: 28410781.

Dingfelder, F., Wunderlich, B., Benke, S., Zosel, F., Zijlstra, N., Nettels, D. & Schuler, B. Rapid Microfluidic Double-Jump Mixing Device for Single-Molecule Spectroscopy. J. Am. Chem. Soc. 139, 6062-6065 (2017). PMID: 28394601.

Samatanga, B., Cléry, A., Barraud, P., Allain, FH. & Jelesarov, I. Comparative analyses of the thermodynamic RNA binding signatures of different types of RNA recognition motifs. Nucleic Acids Res. 45, 6037-6050 (2017). PMID: 28334819.

Malka-Gibor, E., Kornreich, M., Laser-Azogui, A., Doron, O., Zingerman-Koladko, I., Harapin, J., Medalia, O. & Beck, R. Phosphorylation-Induced Mechanical Regulation of Intrinsically Disordered Neurofilament Proteins. Biophys. J. 112, 892-900 (2017). PMID: 28297648.

Ruggeri, F., Zosel, F., Mutter, N., Różycka, M., Wojtas, M., Ożyhar, A., Schuler, B. & Krishnan, M. Single-molecule electrometry. Nat Nanotechnol 12, 488-495 (2017). PMID: 28288117.

Verdurmen, WP., Mazlami, M. & Plückthun, A. A Biotin Ligase-Based Assay for the Quantification of the Cytosolic Delivery of Therapeutic Proteins. Methods Mol. Biol. 1575, 223-236 (2017). PMID: 28255884.

Turgay, Y., Eibauer, M., Goldman, AE., Shimi, T., Khayat, M., Ben-Harush, K., Dubrovsky-Gaupp, A., Sapra, KT., Goldman, RD. & Medalia, O. The molecular architecture of lamins in somatic cells. Nature 543, 261-264 (2017). PMID: 28241138.

Soranno, A., Holla, A., Dingfelder, F., Nettels, D., Makarov, DE. & Schuler, B. Integrated view of internal friction in unfolded proteins from single-molecule FRET, contact quenching, theory, and simulations. Proc. Natl. Acad. Sci. U.S.A. 114, E1833-E1839 (2017). PMID: 28223518.

Ghayor, C., Gjoksi, B., Dong, J., Siegenthaler, B., Caflisch, A. & Weber, FE. N,N Dimethylacetamide a drug excipient that acts as bromodomain ligand for osteoporosis treatment. Sci Rep 7, 42108 (2017). PMID: 28176838.

Benke, S., Nettels, D., Hofmann, H. & Schuler, B. Quantifying kinetics from time series of single-molecule Förster resonance energy transfer efficiency histograms. Nanotechnology 28, 114002 (2017). PMID: 28103588.

Ehrnstorfer IA, Manatschal C, Arnold FM, Laederach J, Dutzler R. Structural and mechanistic basic of proton-coupled metal ion transport in the SLC11/NRAMP family. Nat Commun. 8:140343 (2017). PMID: 28059071.

Syafrizayanti, Lueong SS, Di C, Schaefer JV, Plückthun A, Hoheisel JD. Personalised proteome analysis by means of protein microarrays made from individual patient samples. Sci Rep. 7, 39756 (2017). PMID: 28045055.

Ranganathan, A., Heine, P., Rudling, A., Plückthun, A., Kummer, L. & Carlsson, J. Ligand Discovery for a Peptide-Binding GPCR by Structure-Based Screening of Fragment- and Lead-Like Chemical Libraries. ACS Chem. Biol. 12, 735-745 (2017). PMID: 28032980.

Obexer R, Godina A, Garrabou X, Mittl PR, Baker D, Griffiths AD, Hilvert D. Emergence of a catalytic tetrad during evolution of a highly active artificial aldolase. Nat Chem.9, 50-56 (2017). PMID: 27995916.

Ernst, P. & Plückthun, A. Advances in the design and engineering of peptidebinding repeat proteins. Biol. Chem. 398, 23-29 (2017). PMID: 27636831.

Anders U, Schaefer JV, Hibti FE, Frydman C, Suckau D, Plückthun A, Zenobi R.SPRi-MALDI MS: characterization and identification of a kinase from cell lysate by specific interaction with different designed ankyrin repeat proteins. Anal Bioanal Chem 409, 1827-1836 (2017). PMID: 27987025.

Nasr ML, Baptista D, Strauss M, Sun ZJ, Grigoriu S, Huser S, Plückthun A, Hagn F, Walz T, Hogle JM, Wagner G. Covalently circularized nanodiscs for studying membrane proteins and viral entry. Nat Methods14, 49-52 (2017). PMID: 27869813.