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Department of Biochemistry

Publications 2012

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

Adler-Abramovich, L., vaks, L., Carny, O., Trudler, D., Magno, A., Caflisch, A., Frenkel, D. & Gazit, E. Phenylalanine assembly into toxic fibrils suggests amyloid etiology in phenylkentonuria. Nat Chem Biol 8, 701-706 (2012).

Alfarano, P., Varadamsetty, G., Ewald, C., Parmeggiani, F., Pellarin, R., Zerbe, O., Plückthun, A. & Caflisch, A. Optimization of designed armadillo repeat proteins by molecular dynamics simulations and NMR spectroscopy. Protein Sci. 21, 1298-1314 (2012).

Bank, EM., Ben-Harush, K.,  Feinstein, N., Medalia, O. & Gruenbaum, Y. Structural and physiological phenotypes of disease-linked lamin mutations in C. elegans. J Struct. Biol. 177, 106-112 (2012).

Bloem, R., Koziol, K., Waldauer, SA., Buchli, B., Walser, R., Samatanga, B., Jelesarov, I. & Hamm, P. Ligand binding studied by 2D IR spectroscopy using the azidohomoalanine label. J Phys Chem B. 116, 13705-13712 (2012).

Bokstad, M., Sabanay, H., Dahan, I., Geiger, B. & Medalia, O. Reconstructing adhesion structures in tissues by cryo-electron tomography of vitrified frozen sections. J. Struct. Biol. 178, 76-83 (2012).

Borgia, A., Wensley, BG., Soranno, A., Nettels, D., Borgia, MB., Hoffmann, A., Pfeil, SH., Lipamn, EA., Clarke, J. & Schuler, B. Localizing internal friction along the reaction corrdinate of protein folding by combining ensemble and single-molecule fluorescence spectroscopy. Nat Commun. 3, 1195 (2012).

Caflisch, A. & Hamm, P. Complexity in protein folding: simulation meets experiment. Curr Phys Chem. 2, 4-11 (2012).

Chodorge, M., Züger, S., Stirnimann, C., Briand, C., Jermutus, L., Grütter, MG. & Minter, RR. A series of Fas receptor agonist antibodies that demonstrate an inverse correlation between affinity and potency. Cell Death Diff. 19, 1187-1195 (2012).

Crespo, MD., Puorger, C., Schärer, MA., Eidam, O., Grütter, MG., Capitani, G. & Glockshuber, R. Quality control of disulfide bond formation in pilus subunits by the chaperone FimC. Nat Chem Biol. 8, 707-713 (2012).

Dreier, B. & Plückthun, A. Rapid selection of high-affinity binders using ribosome display. Methods Mol. Biol. 805, 261-286 (2012).

Eicher,T., Cha, HJ., Seeger, MA., Brandstätter, L., El-Delik, J., Bohnert, JA., Kern WV., Verrey, F., Grütter, MG., Diederichs, K. & Pos, KM. Transport of drugs by the multidrug transporter AcrB involves an access and a deep binding pocket that are separated by a switch-loop. PNAS 109, 5687-5692 (2012). 

Fernandez, FJ., de Vries, D., Pena-Soler, E., Coll, M., Christen, P., Gehring, H. & Vega, MC. Structure and mechanism of a cysteine sulfinate desulfinase engineered on the aspartate aminotransferase scaffold. Biochim Biophys Acta. 1824, 339-349 (2012).

Frei, AP., Jeon, OY., Kilcher, S., Moest, H., Henning, LM., Jost, C., Plückthun, A., Mercer, J., Aebersold, R., Carreira, EM. & Wollscheid, B. Direct identification of ligand-receptor interactions on living cells and tissues. Nat Biotechnol. 30, 997-1001 (2012).

Fridmann, K., Mader, A., Zwerger, M., Elia, N. & Medalia, O. Advances in tomography: probing the molecular architecture of cells. Nat Rev. Mol Cell Biol. 13, 736-742 (2012).

Grossmann, E., Medalia, O. & Zwerger, M. Functional architecture of the nuclear pore complex. Annu Rev Biophys. 41, 557-584 (2012).

Grossman, E., Dahan, I., Stick, R., Goldberg, MW., Gruenbaum, Y. & Medalia, O. Filament assembly of ectopically expressed Caenorhabditis elegans lamin within Xenopus oocytes. J. Struct. Biol. 177, 113-118 (2012).

Grütter, MG & Luban, J.TRIM5 structure, HIV-1 capsid recognition, and innate immune signaling. Curr Opin Virol. 2, 142-150 (2012).

Heck,T., Merz, T., Reimer, A., Seebach, D., Rentsch, D., Briand, C., Grütter, MG., Kohler, HP. & Geueke, B. Crytsal structure of BapA complexes with beta-lactam-derived inhibitors illustrate substrate specificity and enantioselectivity of beta-aminopeptidases. Chembiochem. 13, 2137-2145 (2012).

Henderson, R, Sali, A, Baker, ML, Carragher B, Devkota B, Downing KH, Egelman EH, Feng Z, Frank J, Grigorieff N, Jiang W, Ludtke SJ, Medalia O, Penczek PA, Rosenthal PB, Rossmann MG, Schmid MF, Schröder GF, Steven AC, Stokes DL, Westbrook JD, Wriggers W, Yang H, Young J, Berman HM, Chiu W, Kleywegt GJ & Lawson CL. Outcome of the first electron microscopy validation task force meeting. Structure 20, 205-2014 (2012).

Hofmann, H., Soranno, A., Borgia, A., Gast, K., Nettels, D. & Schuler, B. Polymer scaling laws of unfolded and intrinsically disordered proteins quantified with single-molecule spectroscopy. PNAS USA 109, 16155-16160 (2012).

Hohl, M., Briand, C., Grütter, MG. & Seeger, M. Crystal structure of a heterodimeric ABC transporter in its inward-facing conformation. Nat Struct Mol Biol. 19, 395-402 (2012).

Huang, D. & Caflisch, A. How does Darunavir prevent HIV-1 protease dimerization? J Chem Theory Comput. 8, 1786-1794 (2012).

Kebbel, F., Kurz, M., Grütter, M. & Stahlberg, H. Projection structure of the secondary citrate/sodium symporter CitSat 6 Angstroem resolution by electron crystallography. J Mol Biol. 418, 117-126 (2012).

Kummer, L.,Parizek, P., Rube, P., Millgramm, B., Prinz, A., Mittl, PR., Kaufholz, M., Zimmermann, B., Herberg, FW. & Plückthun, A. Structural and functional analysis of phosphorylation-specific binders of the kinase ERK from designed ankyrin repeat protein libraries. PNAS USA109, E2248-2257 (2012).

Madhurantakam, C., Varadamsetty, G., Grütter, MG., Plückthun, A. & Mittl, PR. Structure-based optimization of designed Armadillo-repeat proteins. Protein Sci. 21, 1015-1028 (2012).

Magno, A,, Pellarin, R. & Caflisch, A. Mechanisms and kinetics of amyloid aggregation investigated by a phenomenological coarse-grained model. In: Computational Modelling of Biological Systems, eds. N. Dokholyan, Springer 2012, pp. 191 ff.

Maimon, T., Elad, N., Dahan, I. & Medalia, O. The human nuclear pore complex as revealed by cryo-electron tomography. Structure 20, 998-1006 (2012).

Manso,Y., Carrasco, J., Comes, G., Meloni, G., Adlard, PA., Bush, AI, Vasak, M. & Hidalgo, J. Characterization of the role of metallothionein-3 in an animal model of Alzheimer's disease.  Cell Mol Life Sci. 69, 3683-3700 (2012).

Marino, J., Geertsma, ER. & Zerbe, O. Topogenesis of heterologously expressed fragments of the human Y4 GPCR. Biochim Biophys Acta. 1818, 3055-3063 (2012).

Medalia, O., & Frangakis, A. Special issue on electron tomography. J Struct Biol. 178, 75 (2012).

Meloni, G., Crameri, A., Fritz, G., Davies, P., Brown, DR., Kroneck, PM. & Vasak, M. The catalytic redox activity of prion protein-Cu(II) is controlled by metal exchange with the Zn(II)-thiolate clusters of Zn(7) metallothionein-3. Chembiochem13, 1261-1265 (2012).

Merz,T., Heck, T. Geueke, B., Mittl, PR., Briand, C., Seebach, D., Kohler, HP. & Grütter, MG. Autoproteolytic and catalytic mechanisms for the beta-aminopeptidase BapA- a member of the Ntn hydrolase family. Structure 20, 1850-1860 (2012).

Mignot,I., Pecqueur, L., Dorléans, A., Karuppasamy, M., Ravelli, RB., Dreier, B., Plückthun, A., Knossow, M. & Gigant, B. Design and characterization of modular scaffolds for tubulin assembly. J Biol Chem. 287, 31085-31094 (2012).

Mittal, A., Boehm, S., Grütter, MG., Bordignon, E. & Seeger, MA. Asymmetry in the homodimeric ABC transporter MsbA recognized by a DARPin. J Biol Chem. 287, 20395-20406 (2012).

Nettels, D., Hoffmann, A. & Schuler, B. Corrections to "Unfolded protein and peptide dynamics investigated with single-molecule FRET and correlation spectroscopy from picoseconds to seconds. J Phys Chem B. 112, 6137-6146 (2012).

Novinec, M.,  Lenar?i?, B. & Baici, A. Clusterin is a specific stabilizer and liberator of extracellular cathepsin K. FEBS Lett. 586, 1062-1066 (2012).

Parizek, P., Kummer, L., Rube, P., Prinz, A., Herberg, FW. & Plückthun, A. Ankyrin repeat proteins (DARPins) as novel isoform-specific intracellular inhibitors of c-jun-N-terminal kinases. ACS Chem Biol.  7, 1356-1366 (2012).

Pecqueur, L., Duellberg, C., Dreier, B., Jiang, Q., Wang, C., Plückthun, A., Surrey, T., Gigant, B. & Knossow, M. A designed ankyrin repeat protein selected to bind to tubulin caps at the microtubule plus end. Proc Natl Acad Sci U S A 109, 12011-12016 (2012).

Pedersen, JT., Hureau, C., Hemmingsen, L., Heegard, NH., Ostergaard, J., Vasak, M. & Faller, P. Rapid metal exchange between Zn7-metallothionein-3 and amyloid-beta peptide promotes amyloid related structural changes. Biochemistry 51, 1697-1706 (2012).

Petrera, A., Amstutz, B., Gioia, M., Hähnlein, J., Baici, A., Selchow, P., Ferraris, DM., Rizzi, M., Sbardella, D., Marini, S., Coletta, M. & Sander, P. Functional characterization of the Mycobacterium tuberculosis zinc metallopeptidase Zmp1 and identification of potential substrates. Biol Chem. 393, 631-640 (2012).

Plückthun, A. Ribosome display: a perspective. Methods Mol. Biol. 805, 3-28 (2012).

Radhakrishnan, A., Vitalis, A., Mao, AH., Steffen, AT. & Pappu, RV. Improved atomistic Monte Carlo simulations demonstrate that poly-l-proline adoptsc heterogeneous ensembles of conformations of semi-rigid segments interrupted by kinks. J Phys Chem B. 116, 6862-6871 (2012).

Rennebaum, S. & Caflisch, A. Inhibition of interdomain motion in G-actin by the natural product latrunculin: a molecular dynamics study. Proteins 80, 1998-2008 (2012). 

Rigort, A., Günther, D., Hegert, R., Baum, D., Weber, B., Prohaska, S., Medalia, O., Baumeister, W. & Hege, HC. Automated segmentation of electron tomograms for a quantitative description of actin filament networks. J Struct Biol. 177, 135-144 (2012).

Roschitzki-Voser, H., Schröder, T-. Lenherr, ED., Frölich, F., Schweizer, A., Donepudi, M., Ganesan, R., Mittl, PR., Baici, A. & Grütter, MG. Human caspases in vitro: expression, purification and kinetic characterization. Protein Expr Purif. 84, 236-246 (2012).

Scalco, R. & Caflisch, A. Ultrametricity in protein folding dynamics. J Chem Theory Comput. 8, 1580-1588 (2012).

Schaefer, JV. & Plückthun, A. Engineering aggregation resistance in IgG by two independent mechanisms: lessons from comparison of pichia pastoris and mammalian cell expression. J Mol Biol. 417, 309-335 (2012).

Schaefer, JV. & Plückthun, A. Transfer of engineered biophysical properties between different antibody formats and expression systems. Protein Eng Des Sel. 25, 485-506 (2012).

Schätzle, P., Wuttke, R., Ziegler, U. & Sonderegger, P. Automated quantification of synapses by fluorescence microscopy. J. Neurosci. Methods 204, 144-149 (2012).

Schlinkmann, KM., Honegger, A., Türeci, E., Robison, KE., Lipovsek, D. & Plückthun, A. Critical features for biosynthesis, stability, and functionality of a G protein-coupled receptor. PNAS U S A 109, 9810-9815 (2012).

Schlinkmann, KM., Hillenbrand, M., Rittner, A., Künz, M., Strohner, R. & Plückthun, A. Maximizing detergent stability and functional expression of a GPCR by exhaustive recombination and evolution. J Mol Biol. 422, 414-428 (2012).

Schuler, B., Müller-Späth, S., Soranno, A. & Nettels, D. Application of confocal single-molecule FRET to intrinsically disordered proteins. Methods Mol Biol 896, 21-45 (2012).

Seeger, MA., Mittal, A., Velamakanni, S., Hohl, M., Schauer, S., Salaa, I., Grütter, MG. & van Veen, HW. Tuning the drug efflux activity of an ABC transporter in vivo by in vitro selected DARPin binders. PLoS One 7(6):e37845 (2012).

Simon, M., Zangemeister-Wittke, U. & Plückthun, A. Facile double-functionalization of designed Ankyrin repeat proteins using click and thiol chemistries. Bioconjug Chem. 23, 279-286 (2012).

Steiner, S. & Caflisch, A. Peptide binding to the PDZ3 domain by conformational selection. Proteins. 80, 2562-2572 (2012).

Steuble, M., Diep, TM., Schätzle, P., Ludwig, A., Tagaya, M., Kunz, B. & Sonderegger, P. Calsyntenin-1 shelters APP from proteolytic processing during anterograde axonal transport. Biol Open. 1, 761-774 (2012).

Tamaskovic, R., Simon, M., Stefan, N., Schwill, M. & Plückthun, A. Designed Ankyrin Repeat Proteins (DARPins): From Research to Therapy. Methods Enzymol. 503, 101-134 (2012). 

Varadamsetty, G., Tremmel, D., Hansen, S., Parmeggiani, F. & Plückthun, A. Designed armadillo repeat proteins: library generation, characterization and selection of peptide binders with high specificity. J Mol Biol424, 68-87 (2012).

Vitalis, A. & Caflisch, A. 50 years of Lifson-Roig models: applications to molecular simulation data. J Chem Theory Comput. 8, 363-373 (2012).

Vitalis, A. & Caflisch, A. Efficient construction of mesostate networks from molecular dynamics trajectories.  J Chem Theory Comput. 8, 1108-1120 (2012).

Waldauer,SA., Hassan, S., Paoli, B., Donaldson, PM, Pfister, R., Hamm, P., Caflisch, A. & Pellarin, R. Photocontrol of reversible amyloid formation with a minimal-design peptide. J. Phys. Chem. B. 116, 8961-8973 (2012).

Zhou, Q., Schneider, IC., Edes, I., Honegger, A., Bach, P., Schönfeld, K., Schambach, A., Wels, WS., Kneissl, S., Uckert, W. & Buchholz, CJ. T cell receptor gene transfer exclusively to human CD8+ cells enhances tumor cell killing. Blood 120, 4334-4442 (2012).

Zimmermann, I, Marabelli, A., Bertozzi, C., Sivilotti, LG. & Dutzler, R. Inhibition of the prokaryotic pentameric ligand-gated ion channel ELIC by divalent cations. PLOS Biol. 10, e1001429 (2012).

Zwerger, M. & Medalia, O. Unravelling the lamina network. Nat. Rev. Mol. Cell Biol. 13, 140 (2012).