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Department of Biochemistry

Publications 2006

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

Accardi, A. Lobet, S. Williams, C. Miller, C. & Dutzler, R. Synergism between halide binding and proton transport in a CLC-type exchanger. J. Mol. Biol. 362, 691-699 (2006).

Amstutz, P., Binz, H. K., Zahnd, C. & Plückthun, A. in Cell Biology - A Laboratory Handbook (ed. Celis, J.) 497–509 (Elsevier Academic Press, 2006).

Amstutz, P., Koch, H., Binz, H. K., Deuber, S. A. & Plückthun, A. Rapid selection of specific MAP kinase-binders from designed ankyrin repeat protein libraries. Protein Eng. Des. Sel. 19, 219–229 (2006).

Baici, A. Enzyme kinetics: the velocity of reactions. The Biochemist 28, 36–39 (2006).

Baici, A., Müntener, K., Willimann, A. & Zwicky, R. Regulation of human cathepsin B by alternative  m RNA splicing: homeostasis, fatal errors and cell death. Biol. Chem. 387, 1017-1021 (2006).  

Bès, C. T., S. Chentouf, M. Breton, H. Lajoix, A. D. Heitz, F. Gross, R. Plückthun, A. & Chardès, T. PIN-bodies: a new class of antibody-like proteins with CD4 specificity derived from the protein inhibitor of neuronal nitric oxide synthase. Biochem. Biophys. Res. Commun. 343, 334–44 (2006).

Binz, H., Kohl, A., Plückthun, A. & Grütter, M. Crystal structure of a consensus-designed ankyrin repeat protein: Implications for stability. Proteins (2006).

Bjelic, S., Karshikoff, A. & Jelesarov, I. Stability and folding/unfolding kinetics of the homotrimeric coiled coil Lpp-56. Biochemistry 45, 8931-8939 (2006).

Caflisch, A. Computational models for the prediction of polypeptide aggregation propensity. Curr. Opin. Chemic. Biol. 10, 437-444 (2006).

Caflisch, A. Network and graph analyses of folding free energy surfaces. Curr. Opin. Struct. Biol. 16, 71–78 (2006).

Camenisch, U., Dip, R., Schumacher, S. B., Schuler, B. & Naegeli, H. Recognition of helical kinks by xeroderma pigmentosum group A protein triggers DNA excision repair. Nat. Struct. Mol. Biol. 13, 278–284 (2006).

Capitani, G., Eidam, O. & Grütter, M.G. Evidence for a novel domain of bacterial outer membrane ushers. Proteins 65, 816-823 (2006).

Capitani G., Eidam O., Glockshuber R. & Grütter M.G. Structural and functional insights into the assembly of type 1 pili from Escherichia coli. Microbes Infect. 8, 2284-2290 (2006).

Cecchini, M., Curcio, R., Pappalardo, M., Melki, R. & Caflisch, A. A molecular dynamics approach to the structural characterization of amyloid aggregation. J. Mol. Biol. 357, 1306–1321 (2006).

Deller, S., Sollner, S., Trenker-El-Toukhy, R., Jelesarov, I., Gubitz, G. M., Macheroux, P. Characterization of a thermostable NADPH:FMN oxidoreductase from the mesophilic bacterium Bacillus subtilisBiochemistry 45, 7083-7091(2006).

Devi, V. S., Sprecher, C. B., Hunziker, P., Mittl, P. R. E., Bosshard, H. R. & Jelesarov, I. Disulfide formation and stability of a cysteine-rich repeat protein from Helicobacter pylori. Biochemistry 45, 1599–1607 (2006).

Dutzler R. The ClC family of chloride channels and transporters. Curr. Opin. Struct. Biol. 16, 439-446 (2006).

Ekici O.D., Li Z.Z., Campbell A.J., James K.E., Asgian J.L., Mikolajczyk J., Salvesen G.S., Ganesan R., Jelakovic S., Grütter M.G. & Powers J.C. Design, synthesis, and evaluation of aza-peptide Michael acceptors as selective and potent inhibitors of caspases-2, -3, -6, -7, -8, -9, and -10. J. Med. Chem. 49, 5728-5749 (2006).

Fasan, R., Dias, RL., Moehle, K., Zerbe, O., Obrecht, D., Mittl, P. R. E., Grütter, M. G. & Robinson, J.A. Structure-activity studies in a family of beta-hairpin protein epitope mimetic inhibitors of the p53-HDM2 protein-protein interaction. Chembiochem 7, 515–526 (2006).

Frey, D., Braun, O., Briand, C., Vasak, M. & Grütter, M. G. Structure of the mammalian NOS regulator dimethylarginine dimethylaminohydrolase: A basis for the design of specific inhibitors. Structure 14, 901–911 (2006).

Galliciotti, G. & Sonderegger, P. Neuroserpin. Frontiers in Bioscience 11, 33–45 (2006).

Ganesan R., Jelakovic S., Campbell A.J., Li Z.Z., Asgian J.L., Powers J.C. & Grütter M.G. Exploring the S4 and S1 prime subsite specificities in caspase-3 with aza-peptide epoxide inhibitors. Biochemistry 45, 9059-9067 (2006).

Ganesan R., Mittl P.R., Jelakovic S. & Grütter M.G. Extended substrate recognition in caspase-3 revealed by high resolution X-ray structure analysis. J Mol Biol. 359, 1378-1388 (2006).

Gilchrist, MA, Wagner, A. A model of protein translation including codon bias, nonsense errors,and ribosome recycling. J. Theor. Biol. 239, 417-434 (2006).

Golinelli-Pimpaneau, B., Lüthi, C. & Christen, P. Structural basis for d-amino acid transamination by the pyridoxal 5'-phosphate-dependent catalytic antibody 15A9. J. Biol. Chem. 281, 23969–77 (2006).

Grütter, Ch., Briand, Ch., Capitani, G., Mittl, P. R. E., Papin, S., Tschopp, J. & Grütter, M.G. Structure of the PRYSPRY-domain: Implications for autoinflammatory diseases. FEBS Lett. 580, 99–106 (2006).

Gut, H., Pennacchietti, E., John, R. A., Bossa, F., Capitani, G., De Biase, D. & Grütter, M. G. Escherichia coli acid resistance: pH-sensing, activation by chloride and autoinhibition in GadB. EMBO J. 25, 2643-2651 (2006).

Gutte, B. R. B. Merrifield (1921–2006). Angew. Chem. Int. Ed. Engl. 45, 5412–3 (2006).

Honnappa, S., Okhrimenko, O., Jaussi, R., Jawhari, H., Jelesarov, I., Winkler, F. K. & Steinmetz, M. O. Key interaction modes of dynamic plus TIP networks. Mol. Cell 23, 663-671 (2006).

Huang, D., Lüthi, U., Kolb, P., Cecchini, M., Barberis, A. & Caflisch, A. In silico discovery of beta-secretase inhibitors. J. Am. Chem Soc. 128, 5436–5443 (2006).

Interlandi, G., Settanni, G. & Caflisch, A. Unfolding transition state and intermediates of the tumor suppressor p16INK4a investigated by molecular dynamics simulations. Proteins 64, 178-192 (2006).

Kawe, M., Forrer, P., Amstutz, P.& Plückthun, A. Isolation of intracellular proteinase inhibitors derived from designed ankyrin repeat proteins by genetic screening. J Biol Chem. 281, 40252-63 (2006).

Kawe, M. & Plückthun, A. GroEL walks the fine line: The subtle balance of substrate and co-chaperonin binding by GroEL. A combinatorial investigation by design, selection and screening. J. Mol. Biol. 357, 411–426 (2006).

Koch, H., Gräfe, N., Schiess, R. & Plückthun, A. Direct selection of antibodies from complex libraries with the protein fragment complementation assay. J. Mol. Biol. 357, 427–441 (2006).

Kolb, P. & Caflisch, A. Automatic and efficient decomposition of two-dimensional structures of small molecules for fragment-based high-throughput docking. J. Med. Chem. 49, 7384-7392 (2006). 

Konecna, A., Frischknecht, R., Kinter, J., Ludwig, A., Steuble, M., Meskenaite, V., Indermühle, M., Engel, M., Cen, C., Mateos, J. M., Streit, P. & Sonderegger, P. Calsyntenin-1 docks vesicular cargo to Kinesin-1. Mol. Biol. Cell 17, 3651–3663 (2006).

Kubetzko, S., Balic, E., Waibel, R., Zangemeister-Wittke, U. & Plückthun, A. PEGylation and multimerization of the anti-p185HER-2 single chain Fv fragment 4D5: EFFECTS ON TUMOR TARGETING. J Biol Chem 281, 35186-35201 (2006).

Li, L., Wetzel, S., Plückthun, A. & Fernandez, J. M. Stepwise unfolding of ankyrin repeats in a single protein revealed by atomic force microscopy. Biophys. J. 90, L30–32 (2006).

Lobet, S. & Dutzler, R. Ion-binding properties of the ClC chloride selectivity filter. EMBO J. 25, 24–33 (2006).

Luginbühl, B., Kanyo, Z., Jones, R.M., Fletterick, R., Prusiner, S.B., Cohen, F.E., Williamson, R.A., Burton, D. R. & Plückthun, A. Directed evolution of an anti-prion protein scFv fragment to an affinity of 1 pM and its structural interpretation. J . Mol. Biol. 363, 75-97 (2006).

Meloni, G., Zovo, K., Kazantseva, J., Palumaa, P. & Vasak, M. Organization and assembly of metal-thiolate clusters in epithelium-specific metallothionein-4. J. Biol. Chem. 281, 14588–14595 (2006).

Meyer, S. & Dutzler, R. Crystal structure of the cytoplasmic domain of the chloride channel ClC-0. Structure 14, 299–307 (2006).

Meyer S., Savaresi S., Forster I.C. & Dutzler R. Nucleotide recognition by the cytoplasmic domain of the human chloride transporter ClC-5. Nat. Struct. Mol. Biol. 14, 60-67 (2006).

Mittl, P.R., & Grütter, M.G. Opportunities for sructure-based design of protease -directed drugs. Curr. Opin. Struct. Biol. 16, 769-775 (2006)

Pahlich, S., Zakaryan, R. P. & Gehring, H. (2006) Protein arginine methylation: Cellular functions and methods of analysis. Biochimica et Biophysica Acta 1764, 1890-1903 (2006).

Penkowa, M., Tio, L., Giralt, M., Quintana, A., Molinero, A., Atrian, S., Vasak, M. & Hidalgo, J. Specificity and divergence in the neurobiologic effects of different metallothioneins after brain injury. J. Neurosci. Res. 83, 974–984 (2006).

Pellarin, R. & Caflisch,A. Interpreting the aggregation kinetics of amyloid peptides. J. Mol. Biol. 360, 882 - 892 (2006).

Schuler, B., Application of Single Molecule Förster Resonance Energy Transfer to Protein Folding. in: Protein Folding Protocols (Humana Press; Bai, Nussinov, Eds.), 366 (2006).

Seeber, M., Fanelli, F., Paci, E. & Caflisch, A. Sequential unfolding of individual helices of bacterioopsin observed in molecular dynamics simulations of extraction from the purple membrane. Biophys. J. 91, 3276-3284 (2006). 

Siegenthaler, R. K. & Christen, P. Tuning of DnaK chaperone action by non-native-protein sensor DnaJ and thermosensor GrpE. J. Biol. Chem. 281, 34448-34456 (2006).

Simonin, Y., Charron, Y., Sonderegger, P., Vassalli, JD. & Kato AC. An inhibitor of serine proteases, neuroserpin, acts as a neuroprotective agent in a mouse model of neurodegenerative disease. J Neurosci. 26, 10614-9 (2006).

Steiner, D., Forrer, P., Stumpp, M. T. & Plückthun, A. Signal sequences directing cotranslational translocation expand the range of proteins amenable to phage display. Nat. Biotechnol. 24, 823-831 (2006).

Stirnimann, C. U.,  Rozhkova, A., Grauschopf, U., Bockmann, R. A., Glockshuber, R., Capitani G. & Grütter M. G. High-resolution structures of Escherichia coli cDsbD in different redox states: A combined crystallographic, biochemical and computational study. J. Mol. Biol. 358, 829–45 (2006).

Stirnimann C.U., Grütter M.G., Glockshuber R. & Capitani G. nDsbD: a redox interaction hub in the Escherichia coli periplasm. Cell. Mol. Life Sci. 63, 1642-1648 (2006).

Tao, M., Türk, K., Diez, J., Grütter, M. G. & Fritz, G. Steuber, J. Crystallization of the NADH-oxidizing domain of the Na+ -translocating NADH:ubiquinone oxidoreductase from Vibrio cholerae. Acta Cryst. F62, 110–112 (2006).

Vitkup, D, Kharchenko, P. & Wagner, A. Influence of metabolic network structure and function on enzyme evolution. Genome Biol. 7, R39 (2006).

Vgenopoulou, I., Gemperli, A. C. & Steuber, J. Specific modification of a Na+ binding site in the NADH:quinone oxidoreductase (NDH-1) from Klebsiella pneumoniae with dicyclohexylcarbodiimide. J. Bacteriol. 188, 3264-3272 (2006).

Wagner, A. Cooperation is Fleeting in the World of Transposable Elements. PLoS Computational Biology 2(12): e162 (2006).

Wagner, A. Periodic extinctions of transposable elements in bacterial lineages: Evidence from intragenomic variation in multiple genomes. Mol. Biol. Evol. 23, 723-733(2006).

Yu H., Kohl A., Binz H.K., Plückthun A., Grütter M.G. & van Gunsteren W.F. Molecular dynamics study of the stabilities of consensus designed ankyrin repeat proteins. Proteins 65, 285-295 (2006).

Zahnd, C., Pécorari, F., Straumann, N., Wyler, E. & Plückthun, A. Selection and Characterization of Her2 Binding-designed Ankyrin Repeat Proteins. J. Biol. Chem. 281, 35167-35175 (2006).

Zakaryan, R. P. & Gehring, H. Identification and Characterization of the Nuclear Localization/Retention Signal in the EWS Proto-oncoprotein. J. Mol. Biol. 363, 27–38 (2006).