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Department of Biochemistry

Publications 2005

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

Amstutz, P., Binz, H. K., Parizek, P. Stumpp, M. T. Kohl, A. Grütter, M. G. Forrer, P. & Plückthun, A. Intracellular kinase inhibitors selected from combinatorial libraries of designed ankyrin repeat proteins. J. Biol. Chem. 280, 24715-24722 (2005).

Backmann, N., Zahnd, C. Huber, F., Bietsch, A., Plückthun, A., Lang, H. P., Güntherodt, H. J., Hegner, M. & Gerber, C. A label-free immunosensor array using single-chain antibody fragments. Proc. Natl. Acad. Sci. USA 102, 14587-14592 (2005).

Baici, A. in Myoarthropathien und orofaziale Schmerzen (ed. Palla, S.) in press (RC Libri, Milano, 2005).

Binz, H. K., Amstutz, P., Plückthun, A. Engineering novel binding proteins from nonimmunoglobulin domains. Nat. Biotechnol. 23, 1257-1268 (2005).

Binz, H. K. & Plückthun, A. Engineered proteins as specific binding reagents. Curr. Opin. Biotechnol. 16, 459-469 (2005).

Bockmann, R. A. & Caflisch, A. Spontaneous formation of detergent micelles around the outer membrane protein OmpX. Biophys. J. 88, 3191-3204 (2005).

Boiangeou, C. D., Jayamani, E. Brügel, D., Herrmann, G., Forzi, L., Hedderich, R., Vgenopoulou, I., Pierik, A. J., Steuber, J. & Buckel, W. Sodium ion pumps and hydrogen production in glutamate fermenting anaerobic bacteria. J. Mol. Microbiol. Biotechnol. 10, 105-119 (2005).

Caflisch, A. & Paci, E. in Protein Folding Handbook (eds. Buchner, J. & Kiefhaber, T.) (2005).

Capitani, G., De Biase, D., Gut, H., Ahmed, S. & Grütter, M. G. Structural model of human GAD65: Prediction and interpretation of biochemical and immunogenic features. Proteins 59, 7-14 (2005).

Capitani, G., Tschopp, M., Eliot, A. C., Kirsch, J. F. & Grütter, M. G. Structure of ACC synthase inactivated by the mechanism-based inhibitor L-vinylglycine. FEBS Lett. 579, 2458-2462 (2005).

Christen, P. C. & Jaussi, R. Biochemie (Eine Einführung mit 40 Lerneinheiten), Springer Verlag (2005) , Berlin, Heidelberg, New York.

Curcio, R., Caflisch, A. & Paci, E. Change of the unbinding mechanism upon a mutation: A molecular dynamics study of an antibody-hapten complex. Prot. Sci. 14, 2499-2514 (2005).

Gorfe, A. A. & Caflisch, A. Functional plasticity in the substrate binding site of beta-secretase. Structure 13, 1487-1498 (2005).

Grimshaw, J. P., Siegenthaler, R. K., Zuger, S., Schönfeld, H. J., Z'graggen, B. R. & Christen, P. The heat-sensitive Escherichia coli grpE280 phenotype: impaired interaction of GrpE(G122D) with DnaK. J. Mol. Biol. 353, 888-96 (2005).

Honegger, A., Spinelli, S., Cambillau, C. & Plückthun, A. A mutation designed to alter crystal packing permits structural analysis of a tight-binding fluorescein-scFv complex. Prot. Sci. 14, 2537-2549 (2005).

Huang, D. Z., Lüthi, U., Kolb, P., Edler, K., Cecchini, M., Audetat, S., Barberis, A. & Caflisch, A. Discovery of cell-permeable non-peptide inhibitors of beta-secretase by high-throughput docking and continuum electrostatics calculations. J. Med. Chem. 48, 5108-5111 (2005).

Iwai, H., Forrer, P., Plückthun, A. & Güntert, P. NMR solution structure of the monomeric form of the bacteriophage ? capsid stabilizing protein gpD. J. Biomol. NMR 31, 351-356 (2005).

Knipp, M., Braun, O. & Vasak, M. Searching for DDAH inhibitors: S-nitroso-L-homocysteine is a chemical lead. J. Am. Chem. Soc. 127, 2372-2373 (2005).

Knipp, M., Meloni, G., Roschitzki, B. & Vasak, M. Zn(7)metallothionein-3 and the synaptic vesicle cycle: Interaction of metallothionein-3 with the small GTPase Rab3A. Biochemistry 44, 3159-3165 (2005).

Kohl, A., Amstutz, P., Parizek, P., Binz, H. K., Briand, C., Capitani, G., Forrer, P., Plückthun, A. & Grütter, M. G. Allosteric inhibition of aminoglycoside phosphotransferase by a designed ankyrin repeat protein. Structure (Camb) 13, 1131-1141 (2005).

Kolb, P., Cecchini, M., Huang, D. & Caflisch, A. in Virtual Screening (eds. Shoichet, B. & Alvarez, J.) (2005).

Kubetzko, S., Sarkar, C. A. & Plückthun, A. Protein PEGylation decreases observed target association rates via a dual blocking mechanism. Mol. Pharmacol. 68, 1439-1454 (2005).

Lebeurrier, N., Liot, G., Lopez-Atalaya, J. P., Orset, C., Fernandez-Monreal, M., Sonderegger, P., Ali, C. & Vivien, D. The brain-specific tissue-type plasminogen activator inhibitor, neuroserpin, protects neurons against excitotoxicity both in vitro and in vivo. Mol. Cell. Neurosci. 30, 552-558 (2005).

Lin, P.-C., Puhar, A., Türk, K., Piligkos, S., Bill, E., Neese, F. & Steuber, J. A vertebrate-type ferredoxin domain in the Na+ -translocating NADH dehydrogenase from Vibrio cholerae. J. Biol. Chem. 280, 22560 - 22563 (2005).

Meh, P., Pav?ic, M., Turk, V., Baici, A. & Lenarcic, B. Dual concentration-dependent activity of thyroglobulin type-1 domain of testican: specific inhibitor and substrate of cathepsin L. Biol. Chem. 386, 75-83 (2005).

Meloni, G., Knipp, M., Roschitzki, B. & Vasak, M. Metallothionein-3 and the synaptic vesicle cycle: interaction of metallothionein-3 with the small GTPase Rab3A. FEBS J. 272, 332-332 (2005).

Meloni, G., Knipp, M. & Vasak, M. Detection of neuronal growth inhibitory factor (metallothionein-3) in polyacrylamide gels and by Western blot analysis. J. Biochem. Biophys. Meth. 64, 76-81 (2005).

Milev, S., Bosshard, H. R. & Jelesarov, I. Enthalpic and entropic effects of salt and polyol osmolytes on site-specific protein-DNA association: The integrase Tn916-DNA complex. Biochemistry 44, 285-293 (2005).

Moroney, S. & Plückthun, A. in Modern Biopharmaceuticals (ed. Knäblein, J.) 1147-1186 (Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, 2005).

Muff, S., Rao, F. & Caflisch, A. Local modularity measure for network clusterizations. Physi. Rev. E 72 (2005).

Müntener, K., Willimann, A., Zwicky, R., Svoboda, B., Mach, L. & Baici, A. Folding competence of N-terminally truncated forms of human procathepsin B. J. Biol. Chem. 280, 11973-11980 (2005).

Nishiyama, M., Horst, R. Eidam, O. Herrmann, T. Ignatov, O. Vetsch, M. Bettendorff, P. Jelesarov, I. Grütter, M. G. Wüthrich, K. Glockshuber, R. & Capitani, G. Structural basis of chaperone-subunit complex recognition by the type 1 pilus assembly platform FimD. EMBO J. 24, 2075-2086 (2005).

Ott, D., Neldner, Y., Cèbe, R., Dodevski, I. & Plückthun, A. Engineering and functional immobilization of opioid receptors. Protein Eng. Des. Sel. 18, 153-160 (2005).

Pahlich, S., Bschir, K., Chiavi, C., Belyanskaya, L. & Gehring, H. Different methylation characteristics of protein arginine methyltransferase 1 and 3 toward the Ewing sarcoma protein and a peptide. Proteins 61, 164-175 (2005).

Rao, F., Settanni, G., Guarnera, E. & Caflisch, A. Estimation of protein folding probability from equilibrium simulations. J. Chem. Physics 122 (2005).

Röthlisberger, D., Honegger, A. & Plückthun, A. Domain interactions in the Fab fragment: a comparative evaluation of the single-chain Fv and Fab format engineered with variable domains of different stability. J. Mol. Biol. 347, 773-789 (2005).

Schaffitzel, C., Zahnd, C., Amstutz, P., Luginbühl, B. & Plückthun, A. in Protein-Protein Interactions: A Molecular Cloning Manual (eds. Golemis, E. & Adams, P.) 517-548 (Cold Spring Harbor Laboratory Press, NY, New York, 2005).

Schimmele, B., Gräfe, N. & Plückthun, A. Ribosome display of mammalian receptor domains. Protein Eng. Des. Sel. 18, 285-294 (2005).

Schimmele, B. & Plückthun, A. in Protein Folding Handbook (eds. Buchner, J. & Kiefhaber, T.) 1281-1333 (Wiley Verlag GmbH & Co. KGaA., Weinheim, Germany, 2005).

Schimmele, B. & Plückthun, A. Identification of a functional epitope of the Nogo receptor by a combinatorial approach using ribosome display. J. Mol. Biol. 352, 229-241 (2005).

Schrimpf, S. P., Meskenaite, V., Brunner, E., Rutishauser, D., Walther, P., Eng, J., Aebersold, R. & Sonderegger, P. Proteomic analysis of synaptosomes using isotope-coded affinity tags and mass spectrometry. Proteomics 5, 2531-2541 (2005).

Schuler, B. Single-molecule fluorescence spectroscopy of protein folding. Chemphyschem 6, 1206-1220 (2005).

Schuler, B., Lipman, E. A., Steinbach, P. J., Kumke, M. & Eaton, W. A. Polyproline and the "spectroscopic ruler" revisited with single molecule fluorescence. Proc. Natl. Acad. Sci. USA 102, 2754-2759 (2005).

Settanni, G., Rao, F. & Caflisch, A. phi-Value analysis by molecular dynamics simulations of reversible folding. Proc. Natl. Acad. Sci. USA 102, 628-633 (2005).

Siegenthaler, R. K. & Christen, P. The importance of having thermosensor control in the DnaK chaperone system. J. Biol. Chem. 280, 14395-401 (2005).

Tartaglia, G. G., Cavalli, A., Pellarin, R. & Caflisch, A. Prediction of aggregation rate and aggregation-prone segments in polypeptide sequences. Protein Sci. 14, 2723-2734 (2005).

Tartaglia, G. G., Pellarin, R., Cavalli, A. & Caflisch, A. Organism complexity anti-correlates with proteomic beta-aggregation propensity. Protein Sci. 14, 2735-2740 (2005).

Vasak, M. Advances in metallothionein structure and functions. J. Trace Elements Med. Biol. 19, 13-17 (2005).