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Department of Biochemistry

Publications 2014

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

Anders, C. & Jinek, M. In vitro enzymology of cas9. Meth. Enzymol. 546, 1-20 (2014). PMID: 25398333.

Anders, C., Niewoehner, O., Duerst, A. & Jinek, M. Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease. Nature 513, 569-73 (2014). PMID: 25079318.

Beyer, C., Christen, P., Jelesarov, I. & Fröhlich, J. Real-time assessment of possible electromagnetic-field-induced changes in protein conformation and thermal stability. Bioelectromagnetics 35, 470-8 (2014). PMID: 25123495.

Bischofberger, I., Calzolari, DC., De Los Rios, P., Jelezarov, I. & Trappe, V. Hydrophobic hydration of poly-N-isopropyl acrylamide: a matter of the mean energetic state of water. Sci Rep 4, 4377 (2014). PMID: 24625553.

Blöchliger, N., Vitalis, A. & Caflisch, A. High-resolution visualisation of the States and pathways sampled in molecular dynamics simulations. Sci Rep 4, 6264 (2014). PMID: 25179558.

Brauchle, M., Hansen, S., Caussinus, E., Lenard, A., Ochoa-Espinosa, A., Scholz, O., Sprecher, SG., Plückthun, A. & Affolter, M. Protein interference applications in cellular and developmental biology using DARPins that recognize GFP and mCherry. Biol Open 3, 1252-61 (2014). PMID: 25416061.

Brucale, M., Schuler, B. & Samorì, B. Single-Molecule Studies of Intrinsically Disordered Proteins. Chem. Rev. 114, 3281-317 (2014). PMID: 24432838.

Brunner, JD., Lim, NK., Schenck, S., Duerst, A. & Dutzler, R. X-ray structure of a calcium-activated TMEM16 lipid scramblase.  Nature 516, 207-12 (2014). PMID: 25383531.

Egloff, P., Hillenbrand, M., Klenk, C., Batyuk, A., Heine, P., Balada, S., Schlinkmann, KM., Scott, DJ., Schütz, M. & Plückthun, A. Structure of signaling-competent neurotensin receptor 1 obtained by directed evolution in Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 111, E655-62 (2014). PMID: 24453215.

Ehrnstorfer, IA., Geertsma, ER., Pardon, E., Steyaert, J. & Dutzler, R. Crystal structure of a SLC11 (NRAMP) transporter reveals the basis for transition-metal ion transport. Nat. Struct. Mol. Biol.21, 990-6 (2014). PMID: 25326704.

Flütsch, A., Schroeder, T., Barandun, J., Ackermann, R., Bühlmann, M. & Grütter, MG. Specific targeting of human caspases using designed ankyrin repeat proteins. Biol. Chem. 395, 1243-52 (2014). PMID: 25153593.

Flütsch, A., Ackermann, R., Schroeder, T., Lukarska, M., Hausammann, GJ., Weinert, C., Briand, C. & Grütter, MG. Combined inhibition of caspase-3 and caspase-7 by two highly selective DARPins slows down cellular demise. Biochem. J. 461, 279-90 (2014). PMID: 24779913.

Friedman, R. & Caflisch, A. Wild type and mutants of the HET-s(218-289) prion show different flexibility at fibrillar ends: A simulation study. Proteins 82, 399-404 (2014). PMID: 24038616.

Fu, B., Sahakyan, AB., Camilloni, C., Tartaglia, GG., Paci, E., Caflisch, A., Vendruscolo, M. & Cavalli, A. ALMOST: An all atom molecular simulation toolkit for protein structure determination. J Comput Chem 35, 1101-5 (2014). PMID: 24676684.

Gruenbaum, Y. & Medalia, O. Lamins: the structure and protein complexes. Curr. Opin. Cell Biol. [Epub ahead of print] (2014). PMID: 25460776.

Grütter, MG. Biocrystallography in Switzerland: achievements and future perspectives. Chimia (Aarau) 68, 54-9 (2014). PMID: 24801698.

Gutte, PG., Jurt, S., Grütter, MG. & Zerbe, O. Unusual Structural Features Revealed by the Solution NMR Structure of the NLRC5 Caspase Recruitment Domain. Biochemistry 53, 3106-17 (2014). PMID: 24815518.

Hanenberg, M., McAfoose, J., Kulic, L., Welt, T., Wirth, F., Parizek, P., Strobel, L., Cattepoel, S., Späni, C., Derungs, R., Maier, M., Plückthun, A. & Nitsch, RM. Aβ-specific DARPins as a novel class of potential therapeutics for Alzheimer's disease. J. Biol. Chem. 289, 27080-9 (2014). PMID: 25118284.

Hofmann, H., Hillger, F., Delley, C., Hoffmann, A., Pfeil, SH., Nettels, D., Lipman, EA. & Schuler, B. Role of denatured-state properties in chaperonin action probed by single-molecule spectroscopy. Biophys. J. 107, 2882-93 (2014). PMID: 25517154.

Hohl, M., Hürlimann, LM., Böhm, S., Schöppe, J., Grütter, MG., Bordignon, E. & Seeger, MA. Structural basis for allosteric cross-talk between the asymmetric nucleotide binding sites of a heterodimeric ABC exporter. Proc. Natl. Acad. Sci. U.S.A. 111, 11025-30 (2014). PMID: 25030449.

Jinek, M., Jiang, F., Taylor, DW., Sternberg, SH., Kaya, E., Ma, E., Anders, C., Hauer, M., Zhou, K., Lin, S., Kaplan, M., Iavarone, AT., Charpentier, E., Nogales, E. & Doudna, JA. Structures of Cas9 Endonucleases Reveal RNA-Mediated Conformational Activation. Science 343. 1247997 (2014). PMID: 24505130.

Jost, C. & Plückthun, A. Engineered proteins with desired specificity: DARPins, other alternative scaffolds and bispecific IgGs. Curr. Opin. Struct. Biol. 27C, 102-112 (2014). PMID: 25033247.

Kellner, R., Hofmann, H., Barducci, A., Wunderlich, B., Nettels, D. & Schuler, B. Single-molecule spectroscopy reveals chaperone-mediated expansion of substrate protein. Proc. Natl. Acad. Sci. U.S.A. 111, 13355-60 (2014). PMID: 25165400.

Kiuchi, T., Ortiz-Zapater, E., Monypenny, J., Matthews, DR., Nguyen, LK., Barbeau, J., Coban, O., Lawler, K., Burford, B., Rolfe, DJ., de Rinaldis, E., Dafou, D., Simpson, MA., Woodman, N., Pinder, S., Gillett, CE., Devauges, V., Poland, SP., Fruhwirth, G., Marra, P., Boersma, YL., Plückthun, A., Gullick, WJ., Yarden, Y., Santis, G., Winn, M., Kholodenko, BN., Martin-Fernandez, ML., Parker, P., Tutt, A., Ameer-Beg, SM. & Ng, T. The ErbB4 CYT2 variant protects EGFR from ligand-induced degradation to enhance cancer cell motility. Sci Signal 7, ra78 (2014). PMID: 25140053.

Larrick, JW., Parren, PW., Huston, JS., Plückthun, A., Bradbury, A., Tomlinson, IM., Chester, KA., Burton, DR., Adams, GP., Weiner, LM., Scott, JK., Alfenito, MR., Veldman, T. & Reichert, JM. Antibody engineering and therapeutics conference. MAbs 6, 1115-23 (2014). PMID: 25517297.

Niewoehner, O., Jinek, M. & Doudna, JA. Evolution of CRISPR RNA recognition and processing by Cas6 endonucleases. Nucleic Acids Res. 42, 1341-53 (2014). PMID: 24150936.

Novinec, M., Lenarčič, B. & Baici, A. Probing the activity modification space of the cysteine peptidase cathepsin k with novel allosteric modifiers. PLoS ONE 9, e106642 (2014). PMID: 25184245.

Novinec, M., Korenč, M., Caflisch, A., Ranganathan, R., Lenarčič, B. & Baici, A. A novel allosteric mechanism in the cysteine peptidase cathepsin K discovered by computational methods. Nat Commun 5, 3287 (2014). PMID: 24518821.

Pevzner, Y., Frugier, E., Schalk, V., Caflisch, A. & Woodcock, HL. Fragment-Based Docking: Development of the CHARMMing Web User Interface as a Platform for Computer-Aided Drug Design. J Chem Inf Model 54, 2612-20 (2014). PMID: 25151852.

Pochorovski, I., Knehans, T., Nettels, D., Müller, AM., Schweizer, WB., Caflisch, A., Schuler, B. & Diederich, F. Experimental and Computational Study of BODIPY Dye-Labeled Cavitand Dynamics. J. Am. Chem. Soc. 136, 2441-9 (2014). PMID: 24490940.

Reichen, C., Hansen, S. & Plückthun, A. Modular peptide binding: From a comparison of natural binders to designed armadillo repeat proteins. J. Struct. Biol. 185, 147-62 (2014). PMID: 23916513.

Reichen, C., Madhurantakam, C., Plückthun, A. & Mittl, PR. Crystal structures of designed armadillo repeat proteins: Implications of construct design and crystallization conditions on overall structure. Protein Sci.  23, 1572-83 (2014). PMID: 25132085.

Roderer, D., Benke, S., Müller, M., Fäh-Rechsteiner, H., Ban, N., Schuler, B. & Glockshuber, R. Characterization of Variants of the Pore-Forming Toxin ClyA from Escherichia coli Controlled by a Redox Switch. Biochemistry  53, 6357-69 (2014). PMID: 25222267.

Schilling, J., Schöppe, J. & Plückthun, A. From DARPins to LoopDARPins: Novel LoopDARPin design allows the selection of low picomolar binders in a single round of ribosome display. J. Mol. Biol. 426, 691-721 (2014). PMID: 24513107.

Schilling, J., Schöppe, J., Sauer, E. & Plückthun, A. Co-crystallization with conformation-specific designed ankyrin repeat proteins explains the conformational flexibility of BCL-W. J. Mol. Biol. 426, 2346-62 (2014). PMID: 24747052.

Scholz, O., Hansen, S. & Plückthun, A. G-quadruplexes are specifically recognized and distinguished by selected designed ankyrin repeat proteins.  Nucleic Acids Res. 42, 9182-94 (2014). PMID: 25053846.

Scott, DJ., Kummer, L., Egloff, P., Bathgate, RA. & Plückthun, A. Improving the apo-state detergent stability of NTS1 with CHESS for pharmacological and structural studies. Biochim. Biophys. Acta 1838, 2817-24 (2014). PMID: 25064156.

Simon, M., Stefan, N., Borsig, L., Plückthun, A. & Zangemeister-Wittke, U. Increasing the Antitumor Effect of an EpCAM-Targeting Fusion Toxin by Facile Click PEGylation. Mol. Cancer Ther. 13, 375-85 (2014). PMID: 24184633.

Sonderegger, P. & Matsumoto-Miyai, K. Activity-controlled proteolytic cleavage at the synapse. Trends Neurosci. 37, 413-23 (2014). PMID: 24969462.

Soranno, A., Koenig, I., Borgia, MB., Hofmann, H., Zosel, F., Nettels, D. & Schuler, B. Single-molecule spectroscopy reveals polymer effects of disordered proteins in crowded environments. Proc. Natl. Acad. Sci. U.S.A. 111, 4874-9 (2014). PMID: 24639500.

Stefan, N., Zimmermann, M., Simon, M., Zangemeister-Wittke, U. & Plückthun, A. A novel prodrug-like fusion toxin with protease-sensitive bioorthogonal PEGylation for tumor targeting. Bioconjug. Chem. 25, 2144-56 (2014). PMID: 25350699.

Ster, J., Steuble, M., Orlando, C., Diep, TM., Akhmedov, A., Raineteau, O., Pernet, V., Sonderegger, P. & Gerber, U. Calsyntenin-1 regulates targeting of dendritic NMDA receptors and dendritic spine maturation in CA1 hippocampal pyramidal cells during postnatal development. J. Neurosci. 34, 8716-27 (2014). PMID: 24966372.

Sternberg, SH., Redding, S., Jinek, M., Greene, EC. & Doudna, JA. DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature 507, 62-7 (2014). PMID: 24476820.

Tamás, MJ., Sharma, SK., Ibstedt, S., Jacobson, T. & Christen, P. Heavy metals and metalloids as a cause for protein misfolding and aggregation. Biomolecules 4, 252-67 (2014). PMID: 24970215.

Unzue, A., Dong, J., Lafleur, K., Zhao, H., Frugier, E., Caflisch, A. & Nevado, C. Pyrrolo[3,2-b]quinoxaline Derivatives as Types I1/2 and II Eph Tyrosine Kinase Inhibitors: Structure-Based Design, Synthesis, and in Vivo Validation. J. Med. Chem. 57, 6834-44 (2014). PMID: 25076195.

Vitalis, A. & Caflisch, A. Equilibrium sampling approach to the interpretation of electron density maps. Structure 22, 156-67 (2014). PMID: 24316403.

Walczak, MJ., Samatanga, B., van Drogen, F., Peter, M., Jelesarov, I. & Wider, G. The RING Domain of the Scaffold Protein Ste5 Adopts a Molten Globular Character with High Thermal and Chemical Stability. Angew. Chem. Int. Ed. Engl. 53, 1320-3 (2014). PMID: 24356903.

Watson, RP., Christen, MT., Ewald, C., Bumbak, F., Reichen, C., Mihajlovic, M., Schmidt, E., Güntert, P., Caflisch, A., Plückthun, A. & Zerbe, O. Spontaneous Self-Assembly of Engineered Armadillo Repeat Protein Fragments into a Folded Structure. Structure 22, 985-995 (2014). PMID: 24931467.

Weisenburger, S., Jing, B., Hänni, D., Reymond, L., Schuler, B., Renn, A. & Sandoghdar, V. Cryogenic Colocalization Microscopy for Nanometer-Distance Measurements. Chemphyschem 15, 763-70 (2014). PMID: 24677759.

Wunderlich, B., Nettels, D. & Schuler, B. Taylor dispersion and the position-to-time conversion in microfluidic mixing devices. Lab Chip 14, 219-28 (2014). PMID: 24195996.

Wuttke, R., Hofmann, H., Nettels, D., Borgia, MB., Mittal, J., Best, RB. & Schuler, B. Temperature-dependent solvation modulates the dimensions of disordered proteins. Proc. Natl. Acad. Sci. U.S.A. 111, 5213-8 (2014). PMID: 24706910.

Yan, J., Gu, GJ., Jost, C., Hammond, M., Plückthun, A., Landegren, U. & Kamali-Moghaddam, M. A Universal Approach to Prepare Reagents for DNA-Assisted Protein Analysis. PLoS ONE 9, e108061 (2014). PMID: 25233463.

Zhao, H. & Caflisch, A. Discovery of dual ZAP70 and Syk kinases inhibitors by docking into a rare C-helix-out conformation of Syk. Bioorg. Med. Chem. Lett. 24, 1523-7 (2014). PMID: 24569110.

Zhao, H., Gartenmann, L., Dong, J., Spiliotopoulos, D. & Caflisch, A. Discovery of BRD4 bromodomain inhibitors by fragment-based high-throughput docking. Bioorg. Med. Chem. Lett. 24, 2493-6 (2014). PMID: 24767840.

Zhou, T., Georgeon, S., Moser, R., Moore, DJ., Caflisch, A. & Hantschel, O. Specificity and mechanism-of-action of the JAK2 tyrosine kinase inhibitors ruxolitinib and SAR302503 (TG101348). Leukemia 28, 471-2 (2014). PMID: 24496285.