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Department of Biochemistry

Publications 2013

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

Attanasio, F., Convertino, M., Magno, A., Caflisch, A., Corazza, A., Haridas, H., Esposito, G., Cataldo, S., Pignataro, B., Milardi, D. & Rizzarelli, E. Carnosine inhibits ABeta(42) aggregation by perturbing the H-bond network in and around the central hydrophobic cluster. Chembiochem 14, 583-592 (2013).

Aznauryan, M., Nettels, D., Holla, A., Hofmann, H. & Schuler, B. Single-molecule spectroscopy of cold denaturation and the temperature-induced collapse of unfolded proteins. J. Am. Chem. Soc. 135, 14040-3 (2013).

Beyer, C, Christen, P., Jelesarov, I. & Fröhlich, J. Experimental system for real-time assessment of potential changes in protein conformation induced by electromagnetic fields. Bioelectromagnetics 34, 419-428 (2013). 

Bjelic, S. & Jelesarov, I. Probing the energetic and kinetic impact of topologically conserved interactions in the SIV gp41 six-helix bundle. Biophys Chem. 171, 54-62 (2013).

Blöchlinger, N., Vitalis, A. & Caflisch, A. A scalable algorithm to order ad annotate continuous observations reveals the metastable states visited by dynamical systems. Computer Phys. Comm. 184, 2446-2453 (2013).

Blomberg, R., Kries, H., Pinkas, DM., Mittl, PR., Grütter, MG., Privett, HK., Mayo, SL. & Hilvert, D. Precision is essential for efficient catalysis in an evolved Kemp eliminase. Nature 503, 418-21 (2013).

Bonnet, M., Kurz, M., Mesa, S., Briand, C., Hennecke, H. & Grütter, MG. Structure of Bradyrhizobium japonicum transcription factor FixK2 unveils sites of DNA binding and oxidation. J Biol.Chem. 288, 14238-14246 (2013).

Buchli, B., Waldauer, SA., Walser, R., Donten, ML., Pfister, R., Blöchliger, N., Steiner, S., Caflisch, A., Zerbe, O. & Hamm, P. Kinetic response of a photoperturbed allosteric protein. PNAS 110, 11725-11730 (2013).

Bukowska, MA. & Grütter, MG. New concepts and aids to facilitate crystallization. Curr Opin Struct Biol23, 409-416 (2013).

Dreier, B., Honegger, A., Hess, C., Nagy-Davidescu, G., Mittl, PR., Grütter, MG., Belousova, N., Mekheeva, G., Krasnykh, V. & Plückthun, A. Development of a generic adenovirus delivery system based on structure-guided design of bispecific trimeric DARPin adapters. PNAS USA 110, E869-877 (2013).

Elad, N, Volberg, T., Patla, I., Hirschfeld-Warneken, V., Grashoff, C., Spatz, JP., Fässler, R., Geiger, B. & Medalia, O. The role of integrin-linked kinase in the molecular architecture of focal adhesions. J Cell Sci. 126, 4099-4107 (2013).

Epa, VC., Dolezal, O., Doughthy, L., Xiao, X., Jost, C., Plückthun. A. & Adams, TE. Structural model for the interaction of a designed ankyrin repeat protein with the human epidermal growth factor receptor 2. PLoS One. 8(3): e59163 (2013).

Freisinger, E. & Vasak, M. Cadmium in metallothioneins. Met Ions Life Sci. 11, 339-371 (2013).

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 [Epub ahead of print] (2013).

Friedrich, K., Hanauer, JR., Prüfer, S., Münch, RC., Völker, I., Filippis, C., Jost, C., Hanschmann, KM., Cattaneo, R., Peng, KW., Plückthun, A., Buchholz, CJ., Cichutek, K. & Mühlebach, MD. DARPin-targeting of measles virus: unique bispecificity, effective oncolysis, and enhanced safety. Mol Ther. 21, 849-859 (2013).

Garcia-Celma, J., Szydelko, A. & Dutzler, R. Functional characterization of a CIC transporter by solid-supported membrane electrophysiology. J Gen Physiol. 141479-491 (2013).

Gigant, B., Wang, W., Dreier, B., Jiang, Q., Pecqueur, L., Plückthun, A., Wang, C. & Knossow, M. Structure of a kinesin-tubulin complex and implications for kinesin motility. Nat Struct Mol Biol. 20, 1001-1007 (2013).

Gisler, C., Lüscher, D., Schätzle, P., Dürr, S., Baici, A., Gallicotti, G., Reif, R., Bolliger, MF., Kunz, B. & Sonderegger, P. Zymogen activation of neurotrypsin-dependent agrin cleavage on the cell surface are enhanced by glycosaminoglycans. Biochem J. 453, 83-100 (2013).

Gu, GJ., Friedman, M., Jost, C., Johnsson, K., Kamali-Moghaddam, M., Plückthun, A., Landegren, U. & Söderberg, O. Protein tag-mediated conjugation of oligonucleotides to recombinant affinity binders for proximity ligation. N Biotechnol 30, 144-52 (2013).

Haenni, D.,Zosel, F., Reymond, L., Nettels, D. & Schuler, B. Intramolecular distances and dynamics from the combined photon statistics of single-molecule FRET and photoinduced electron transfer. J Phys Che B117, 13015-23028 (2013).

Harapin,J., Eibauer, M. & Medalia, O. Structural analysis of supramolecular assemblies by cryo-electron tomography. Structure 21, 1522-1530 (2013).

Hausammann, GJ., Heitkamp, T., Matile, H., Gsell, B., Thoma, R., Schmid, G., Frasson, D., Sievers, M., Hennig, M. & Grütter, MG. Generation of an antibody toolbox to characterize hERG. Biochem Biophys Res Commun431, 70-75 (2013).

Hausammann, GJ. & Grütter, MG. Chimeric hERG Channels Containing a Tetramerization Domain are Functional and Stable. Biochemistry 52, 9237-45 (2013).

Hofmann, H., Nettels, D. & Schuler, B. Single-molecule spectroscopy of the unexpected collapse of an unfolded protein at low pH. J Chem Phys 139, 121930 (2013).

Huang, D., Rossini, E., Steiner, S. & Caflisch, A. Structured Water Molecules in the Binding Site of Bromodomains Can Be Displaced by Cosolvent. ChemMedChem [Epub ahead of print] (2013).

Jinek, M., East, A., Cheng, A., Lin, S., Ma, E. & Doudna, J. RNA-programmed genome editing in human cells. elife. 2:e00471 (2013).

Jost, C., Schilling, J., Tamaskovic, R., Schwill, M., Honegger, A. & Plückthun, A. Structural basis for eliciting a cytotoxic effect in HER2-overexpressing cancer cells via binding to the extracellular domain of HER2. Structure 21, 1979-91 (2013).

Kalgin, IV., Caflisch, A., Chekmarev,SF. & Karplus, M. New insights into the folding of a beta sheet miniprotein in a reduced space of collective hydrogen bond variables: application to a hydrodynamic analysis of the folding flow. J Phys Chem B. 117, 6092-6105 (2013).

Kassube, SA., Jinek, M., Fang, J., Tsutakawa, S. & Nogales, E. Structural mimicry in transcription regulation of human RNA polymerase II by the DNA helicase RECQL5. Nat Struct Mol Biol. 20, 892-899 (2013).

Kebbel, F., Kurz, M., Arheit, M., Grütter, MG. & Stahlberg, H.Structure and substrate-induced conformational changes of the secondary citrate/ sodium symporter CitS revealed by electron crystallography. Structure 21, 1243-1250 (2013).

Kummer, L., Hsu, CW., Dagliyan, O., Macnevin, C., Kaufholz, M., Zimmermann, B., Dokholyan, NV., Hahn, KM. & Plückthun, A. Knowledge-based design of a biosensor to quantify localized ERK activation in living cells. Chem Biol. 20, 847-856 (2013).

Lafleur, K., Dong, J., Huang, D., Caflisch, A. & Nevado, C. Optimization of inhibitors of the tyrosine kinase EphB4.2. cellular potency improvement and binding mode validation by X-ray crystallography.  J Med Chem. 56, 84-96 (2013).

Lavelin, I., Wolfenson, H., Patla, I., Henis, YI., Medalia, O., Volberg, T., Livne, A., Kam, Z. & Geiger, B. Differential effect of actomyosin relaxation on the dynamic properties of focal adhesion proteins. PLoS ONE 8, e73549 (2013).

Magno, A., Steiner, S. & Caflisch, A. Mechanism and kinetics of acetyl-lysine binding bromodomains. J. Chem. Theor. Comput. 9, 4225-4232 (2013).

Mann, A., Friedrich, N., Krarup, A., Weber, J., Stiegeler, E., Dreier, B., Pugach, P., Robbiani, M., Riedel, T., Moehle, K., Robinson, JA., Rusert, P., Plückthun, A. & Trkola, A. Conformation-dependent recognition of HIV gp 120 by designed ankyrin repeat proteins provides access to novel HIV entry inhibitors. J Virol. 87, 5868-5881 (2013).

Putty, K., Marcus, SA., Mittl, PR., Bogadi, LE., Hunter, AM., Arur, S., Berg, DE., Sethu, P. & Kalia, A. Robustness of Helicobacter pylori infection conferred by context-variable redundancy among cysteine-rich paralogs. PLoS One 8(3): e59560 (2013).

Rosenthal, F., Feijs, KL., Frugier, E., Bonalli, M., Forst, AH., Imhof, R., Winkler, HC., Fischer, D., Caflisch, A., Hassa, PO., Lüscher, B. & Hottiger, MO. Macrodomain-containing proteins are new mono-ADP-ribosylhydrolases. Nat Struct. Mol. Biol. 20, 502-507 (2013).

Sandler, I., Medalia, O. & Aharoni, A. Experimental analysis of co-evolution within protein complexes: the yeast exosome as a model. Proteins 81, 1997-2006 (2013)

Samatanga, B., Dominguez, C., Jelesarov, I. & Allain, FH. The high kinetic stability of a G-quadruplex limits hn RNP F qRRM3 binding to G-tract RNA. Nucleic Acids Res. 41, 2505-2516 (2013).

Scherzer-Attali, R., Convertino, M., Pellarin, R., Caflisch, A., Gazit, E. & Segal, D. Methylations of tryptophan modified naphtoquinone affect its inhibitory potential towards Abeta aggregation. J Phys Chem B117, 1780-1789 (2013).

Schlinkmann, KM. & Plückthun. A. Directed evolution of g-coupled receptors for high functional expression and detergent stability. Methods Enzymol. 520, 67-97 (2013).

Schröder, T., Barandun, J., flütsch, A., Briand, C., Mittl, PR. & Grütter, MG. Specific inhibition of caspase-3 by a competitive DARPin: molecular mimicry between native and designed inhibitors. Structure 21, 277-289 (2013).

Schuler, B. Single-molecule FRET of protein structure and dynamics - a primer. J Nanobiotechnology 11 Suppl 1, S2 (2013).

Schuler, B. & Hofmann, H. Single-molecule spectroscopy of protein folding dynamics-expanding scope and timescales. Curr Opin Struct Biol. 23, 36-47 (2013).

Schuler, B. & Clarke, J. Biophysics: rough passage across a barrier. Nature 502, 632-633 (2013).

Scott, D. & Plückthun, A. Direct molecular evolution of detergent-stable G protein-coupled receptors using polymer encapsulated cells. J Mol Biol 425, 662-677 (2013).

Scott, D., Kummer, L., Tremmel, D. & Plückthun, A. Stabilizing membrane proteins through protein engineering. Curr Opin Chem Biol. 17, 427-435 (2013).

Seeger, MA., Zbinden, R., Flütsch, A., Gutte, PG., Engeler, S., Roschitzki-Voser, H. & Grütter, MG. Design, construction and characterization of a second-generation DARPin library with reduced hydrophobicity. Protein Sci. 22, 1239-1257 (2013). 

Simon, M., Stefan. N., Plückthun, A. & Zangemesiter-Wittke, U. Epithelial cell adhesion molecule-targeted drug delivery for cancer therapy. Expert Opin Drug Deliv. 10, 451-468 (2013).

Simon, M., Frey, R., Zangemeister-Wittke, U. & Plückthun, A. Orthogonal assembly of a designed ankyrin repeat protein-cytotoxin conjugate with a clickable serum albumin module for half-life extension. Bioconjug. Chem. 24, 1955-66 (2013)

Steiner, S, Magno, A., Huang, D. & Caflisch, A. Does bromodomain flexibility influence histone recognition? FEBS Lett. 587, 2158-2163 (2013).

Tschirren,B., Andersson, M., Scherman, K., Westerdahl, H., Mittl, PR. & Raberg, L. Polymorphisms at the innate immune receptor TLR2 are associated with Borrelia infection in a wild rodent population. Proc Biol Sci. 280, 20130364 (2013).

Wunderlich, B., Nettels, D., Benke, S., Clark, J., Weidner, S., Hofmann, H., Pfeil, SH. & Schuler, B. Microfluidic mixer designed for performing single-molecule kinetics with confocal detection on timescales from milliseconds to minutes. Nat Protocols 8, 1459-1474 (2013).

Zhao, H. & Caflisch, A. Discovery of ZAP70 inhibitors by high-throughput docking into a conformation of its kinase domain generated by molecular dynamics. Bioorg. Med. Chem. Lett. 23, 5721-6 (2013).

Zhou, Y., Yu, J., Lei, X., Niu, Q., Zhang, Y., Liu, H., Christen, P., Gehring , H. & Wu, F. High-throughput tandem-microwell assay identifies inhibitors of the hydrogen sulfide signaling pathway. Chem Comm (Camb.) 49, 11782-11784 (2013).

Zwerger, M. & Medalia, O. From lamins to lamina: a structural perspective. Histochem Cell Biol. 140, 3-12 (2013).