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Department of Biochemistry

Publications 2011

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

Bank, EM., Ben-Harush, K., Wiesel-Motiuk, N., Barkan, R., Feinstein, N., Lotan, O., Medalia, O. & Gruenbaum, Y. A laminopathic mutation disrupting lamin filament assembly causes disease-like phenotypes in C. elegans. Mol Biol Cell. 22, 2716-2728 (2011).

Boenzli, E., Robert-Tissot,C., Sabatino, G., Cattori, V., Meli, ML., Gutte, B., Rovero, P., Flynn, N., Hofmann-Lehmann, R. & Lutz, H. In vitro inhibition of feline leukemia virus infection by synthetic peptides derived from the transmembrane domain. Antivir Ther. 16, 905-913 (2011).

Boersma, YL. & Plückthun, A. DARPins and other repeat protein scaffolds: advances in engineering and applications. Curr Opin Biotechnol. 22, 849-857 (2011).

Boersma, Y., Chao, G., Steiner, D., Wittrup, KD. & Plückthun, A. Bispecific Designed Ankyrin repeat Proteins (DARPins) targeting epidermal growth factor receptor inhibit A431 cell proliferation and receptor recycling. J Biol. Chem. 286, 41273-41285 (2011). 

Borgia, MB., Borgia, A., Best, RB., Steward, A., Nettels, D., Wunderlich, B., Schuler, B. & Clarke, J. Single-molecule fluorescence reveals sequence-specific misfolding in multidomain proteins. Nature 474, 662-665 (2011).

Bourquin, F., Capitani, G. & Grütter, MG. PLP-dependent enzymes as entry and exit gates of sphingolipid metabolism. Protein Sci. 20, 1492-1508 (2011). 

Bütikofer, L. Zurlinden , A., Bolliger, MF., Kunz, B. & Sonderegger, P. Destabilization of the neuromuscular junction by proteolytic cleavage of agrin results in precocious sarcopenia. FASEB J. 12, 4378-4393 (2011). 

Convertino, M., Vitalis, A. & Caflisch, A. Disordered binding of small molecules to A{beta}12-28. J Biol Chem. 414, 303-312 (2011).

Devi, VS, & Mittl. PR. Monitoring the disulfide bond formation of a cysteine-rich repeat proteine from Helicobacter pylori in the periplasm of escherichia coli. Curr Microbiol. 62, 903-907 (2011).

Dodevski, I. & Plückthun, A. Evolution of three human GPCRs for higher expression and stability. J Mol. Biol. 408, 599-615 (2011).

Dreier, B. & Plückthun, A. Ribosome display: a technology for selecting and evolving proteins from large libraries. Methods Mol. Biol. 687, 283-306 (2011).

Dreier, B., Mikheeva, G., Belousova, N., Parizek, P., Boczek, E., Jelesarov, I., Forrer, P., Plückthun, A. & Krasnykh, V. Her2-specific multivalent adapters confer designed tropism to adenovirus for gene targeting. J. Mol. Biol. 405, 410-426 (2011). 

Elad, N., Abramovitch, S., Sabanay, H. & Medalia, O. Microtubule organization in the final stages of cytokinesis as revealed by cryo-electron tomography. J Cell Sci. 124, 207-215 (2011). 

Flütsch, A., Schröder, T., Grütter MG. & Patzke, GR. HIV-1 protease inhibition potential of functionalized polyoxometalates. Bioorg. Med. Chem. Lett. 21, 1162-1166 (2011).

Friedman, R. & Caflisch, A. Surfactant effects of amyloid aggregation kinetics. J Mol. Biol. 414, 303-312 (2011).

Frydman-Marom, A., Convertino. M., Pellarin, R., Lampel, A., Shaltiel-Karyo, R., Segal, D., Caflisch, A., Shalev, DE. & Gazit, E. Structural basis for inhibiting beta amyloid oligomerization by a non-coded beta-breaker-substituted endomorphin analogue. ACS Chem Biol. 6, 1265-1276 (2011).

Ganesan, R., Jelakovic, S., Mittl, PR., Caflisch, A. & Grütter, MG. In silico identification and crystal structure validation of procaspase-3 inhibitors without a P1 aspartic acid moiety. Acta Crystallogr SectF Struct Biol Cryst Commun. 67(Pt8), 842-850 (2011). 

Geertsma, E. & Dutzler, R. A versatile and efficient high-throughput cloning tool for structural biology. Biochemistry 50, 3272-3278 (2011). 

Hoefling, M., Lima, N., Haenni, D., Seidel, CA., Schuler, B. & Grubmüller, H. Structural heterogeneity and quantitative FRET efficiency distributions of polyprolines through a hybrid atomistic simulation and Monte Carlo approach. PloS one6(5):e 19791 (2011).

Hoffmann, A., Nettels, D., Clark, J., Borgia, A., Radford, SE., Clarke, J. & Schuler, B. Quantifying heterogeneity and conformational dynamics from single molecule FRET of diffusing molecules: recurrence analysis of single particles. Phys Chem Chem Phys. 13, 1857-1871 (2011).

Huang, D. & Caflisch, A. The free energy landscape of small molecule unbinding. PLoS Comput. Biol. 7 (2): e1002002 (2011). 

Huang, D. & Caflisch, A. Small molecule binding to proteins: affinity and binding/unbinding dynamics from atomistic simulations. Chem Med Chem. 6, 1578-1580(2011).

Huwiler,A., Bourquin, F., Kotelevets, N., Pastukhov, O., Capitani, G., Grütter, MG. & Zangemeister-Wittke, U. A prokaryotic S1P lyase degrades extracellular S1P in vitro and in vivo: implication for treating hyperproliferative disorders. PLoS One. 6(8): e22436 (2011). 

Leemann-Zakaryan, R., Pahlich, S., Grossenbacher, D. & Gehring, H. Tyrosine phosphorylation in the C-terminal nuclear localization and retention signal (C-NLS) of the EWS protein. Sarcoma 2011, ID 218483 (2011).

Manso, Y., Adlard, PA., Carrasco, J., Vasak, M. & Hidalgo, J. Metallothionein and brain inflammation. J Biol Inorg Chem. 16, 1103-1113 (2011).

Martin-Killias, P., Stefan, N., Rothschild, S., Plückthun, A. & Zangemeister-Wittke, U. A novel fusion toxin derived from an EpCAM-specific designed ankyrin repeat protein has potent anti-tumor activity. Clin Cancer Res. 17, 100-110 (2011). 

Meloni, G. & Vasak, M. Redox activity of a alpha-synuclein-Cu is silenced by Zn(7)-metallothionrin-3. Free Radic Biol Med50, 1471-1479 (2011).

Mishra, S. & Caflisch, A .Dynamics in the active site of beta secretase: a network analysis of atomistic simulations. Biochemistry 50, 9328-9339 ( 2011).

Monroe, N., Sennhauser, G., Seeger, M., Briand, C. & Grütter, MG. Designed ankyrin repeat protein binders for the crystallization of AcrB: Plasticity of the dominant interface. J. Struct. Biol. 174, 269-281 (2011).

Münch, RC., Mühlebach, MC., Schaser, T., Kneissl, S., Jost, C., Plückthun, A., Cichutek, K. & Buchholz, CJ. DARPins: an efficient targeting domain for lentiviral vectors. Mol Ther. 19, 686-693 (2011). 

Oufir, M., Bisset, LR., Hoffmann, SRK., Xue, G., Klauser, S., Bergamaschi, B., Gervaix, A., Böni, J., Schüpbach, J. & Gutte, B. Artificial 64-residue HIV-1 enhancer-binding peptide is a potent inhibitor of viral replication in HIV-infected cells. Advances in Virol. ID 165871 (2011). 

Pertel, T.,Hausmann, S., Morger, D., Züger, S., Guerra, J., Lascano, J., Reinhard, C., Santoni, FA., Uchil, PD., Chatel, L., Bisiaux, A., Albert, ML., Strambio-De-Castillia, C., Mothes, W., Pizzato, M., Grutter, MG. & Luban, J. TRIM5 is an innate immune sensor for the retrovirus capsid lattice. Nature 472, 361-365 (2011). 

Roschitzki, B.,Schauer, S. & Mittl, PR. Recognition of host proteins by Helicobacter cysteine-rich proteine C. Curr Microbiol. 63, 239-249 (2011).

Scalco, R. & Caflisch, A. Equilibrium distribution from distributed computing (simulations of protein folding). J. Phys. Chem B. 115, 6358-6365 (2011). 

Schärer, MA., Eliot, AC., Grütter, MG. & Capitani, G. Structural basis for reduced activity of 1-aminocyclopropane-1-carboxylate synthase affected by a mutation linked to andromonoecy . FEBS Lett. 585, 111-114 (2011).  

Schätzle, P., Ster J., Verbich, D., Mc Kinney, RA., Gerber, U., Sonderegger, P. & Mateos, JM. Rapid and reversible formation of spine head filopodia in response to muscarinic receptor activation in CA 1 pyramidal cells. J Physiol. 589, 4353-4364 (2011). 

Seeber, M., Felline, A., Raimondi, F., Muff, S., Friedmann, R., Rao, F., Caflisch, A. & Fanelli, F. Wordom: a user-friendly program for the analysis of molecular structures, trajectories and free energy surfaces. J Comput Chem. 32, 1183-1194 (2011).

Sharma, SK., Goloubinoff, P. & Christen, P. Non-native proteins as newly-identified targets of heavy metals and metalloids. In: Cellular Effects of Heavy Metal Ions. Banfalvi, G. (Ed.), Springer, Heidelberg, p. 263-274 (2011).

Stefan, N., Martin-Killias, P., Wyss-Stoeckle, S., Honegger, A., Zangemeister-Wittke, U. & Plückthun, A. DARPins recognizing the tumor-associated antigen EpCAM selected by phage and ribosome display and engineered for multivalency. J Mol Biol. 413, 826-843 (2011). 

Stevens, GB., Krüger, M., Latychevskaia, T., Lindner, P., Plückthun, A. & Fink, HW. Individual filamentous phage imaged by electron holography. Eur Biophys J. 40, 1197-1201 (2011).

Tamir, A., Elad, N. & Medalia, O. Assembly and breakdown of microtubules within the midbody. Commun Integr. Biol. 5, 552-553 (2011). 

Vasak, M. & Meloni, G. Chemistry and biology of mammalian metallothioneins. Biol Inorg Chem 16, 1067-1078 (2011).

Vasak, M. Metallothioneins: chemical and biological challenges. J Biol Inorg Chem. 16, 975-976 (2011). 

Wu, F., Christen, P. & Gehring, H. A novel approach to inhibit intracellular vitamin B6-dependent enzymes: proof of principle with human and plasmodium ornithine decarboxylase and human histidine decarboxylase. FASEB J. 25, 2109-2122 (2011).

Yahav, T., Maimon, T., Grossman, E., Dahan, I. & Medalia, O. Cryo-electron tomography: gaining insight into cellular processes by strcutural approaches. Curr Opin Struct Biol. 21, 670-677 (2011).

Yuan, H., Xia, T., Schuler, B. & Orrit, M. Temperature-cycle single-molecule FRET microscopy on polyprolines. Phys Chem Chem Phys. 13, 1762-1769 (2011).

Zhao, H. & Huang, D. Hydrogen bond penalty upon ligand binding. PLoS One 6(6): e19923 (2011).

Zheng, W., Qi, B., Rohrdanz, MA., Caflisch, A., Dinner, AR. & Clementi, C. Delineation of folding pathways of a beta-sheet mini-protein. J Phys Chem B. 115, 13065-13074 (2011).

Zimmermann, I. & Dutzler, R. Ligand activation of the prokaryotic pentameric ligand-gated ion channel ELIC. PLoS Biol. 9(6): e 1001101 (2011).