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Department of Biochemistry

Publications of the Plückthun Group 2006-2010 (in alphabetical order)

Brient-Litzler, E., Plückthun, A. & Bedouelle, H. Knowledge-based design of reagentless fluorescent biosensors from a designed ankyrin repeat protein. Protein Eng. Des. Sel. 23, 229-241 (2010). 

Kramer, MA., Wetzel, SK., Plückthun, A., Mittl, PR. & Grütter, MG. Structural determinants for improved stability of designed ankyrin repeat proteins with a redesigned c-capping module. J Mol Biol. 404, 381-391 (2010).

Plückthun, A. HIV: antibodies with a split personality. Nature 467, 537-538 (2010). 

Theurillat JP, Dreier B, Nagy-Davidescu G, Seifert B, Behnke S, Zürrer-Härdi U, Ingold F, Plückthun A & Moch H. Designed ankyrin repeat proteins: a novel tool for testing epidermal growth factor receptor 2 expression in breast cancer. Mod Pathol. 23, 1289-1297 (2010).

Wetzel, SK., Ewald, C., Settanni, G., Jurt, S., Plückthun, A. & Zerbe, O. Residue-resolved stability of full-consensus ankyrin repeat proteins probed by NMR. J Mol Biol. 402, 241-258 (2010).

Zahnd, C., Sarkar, CA. & Plückthun, A. Computational analysis of off-rate selection experiments to optimize affinity maturation by directed evolution. Protein Eng Des Sel. 23, 175-184 (2010).

Zahnd C, Kawe M, Stumpp MT, de Pasquale C, Tamaskovic R, Nagy-Davidescu G, Dreier B, Schibli R, Binz HK, Waibel R, Plückthun A. Efficient tumor targeting with high-affinity designed ankyrin repeat proteins: effects of affinity and molecular size. Cancer Res. 70, 1595-1605 (2010).

Honegger, A., Malebranche, AD., Röthlisberger, D. & Plückthun, A. The influence of the framework core residues on the biophysical properties of immunoglobulin heavy chain variable domains. Protein Eng. Des. Sel. 22, 121-134 (2009).

Kawe, M., Horn, U. & Plückthun, A. Facile promotor deletion in Escherichia coli in response to leaky expression of very robust and benign proteins from common expression vectors. Microb. Cell. Fact. 8, 8 (2009).

Kügler, M., Stein C., Schwenkert M., Saul D., Vockentanz L., Huber T., Wetzel SK., Scholz O., Plückthun A., Honegger A. &  Fey GH. Stabilization and humanization of a single-chain Fv antibody fragment specific for human lymphocyte antigen CD19 by designed point mutations and CDR-grafting onto a human framework. Protein Eng. Des. Sel. 22, 135-147 (2009).

Milovnik P, Ferrari D, Sarkar CA & Plückthun A. Selection and characterization of DARPins specific for the neurotensin receptor 1. Protein Eng Des Sel. 22, 357-66 (2009). 

Plückthun, A. Alternative scaffolds: expanding the options of antibodies. In: Little, M (ed.), Recombinant antibodies for immunotherapy. New York, USA, Cambridge University Press, 243-271  (2009).

Veesler, D., Dreier, B., Blangy, S., Lichiere, J., Tremblay, D., Moineau, S., Spinelli, S., Tegoni, M., Plückthun, A., Campanacci, V. & Cambillau, C. Crystal structure and function of a DARPin neutralizing inhibitor of lactococcal phage TP901-1: comparison of DARPin and camelid VHH binding mode. J Biol Chem. 284, 30718-30726 (2009).

Winkler, J., Martin-Kilias,P., Plückthun, A. & Zangemeister-Wittke, U. EpCAM-targeted delivery of nanocomplexed siRNA to tumor cells with designed ankyrin repeat proteins. Mol Cancer Ther. 8, 2674-2683 (2009). 

Frey, D., Huber, T., Plückthun, A. & Grütter, MG. Structure of the recombinant antibody Fab fragment f3p4. Acta Crystallogr D Biol Crystallogr64, 636-643 (2008).

Honegger, A. Engineering antibodies for stability and efficient folding. in: Handb. Exp. Pharmacol. 181, 47-68 (2008).  

Interlandi, G., Wetzel, S.K., Settani, G. , Plückthun, A. & Caflisch, A. Characterization and further stabilization of designed ankyrin repeat proteins by combining molecular dynamics simulations and experiments. J. Mol. Biol375, 837-854 (2008).

Merz, T., Wetzel, SK., Firbank, S., Plückthun, A., Grütter, MG. & Mittl, PR. Stabilizing Ionic Interactions in a Full-Consensus Ankyrin Repeat Protein. J.Mol. Biol. 376, 232-240 (2008). 

Parmeggiani, F., Pellarin, R., Larsen, AP:, Varadamsetty, G., Stumpp, MT., Zerbe, O., Caflisch, A. & Plückthun, A. Designed Armadillo Repeat Proteins as general peptide-binding scaffolds: consensus design and computational optimization of hydrophobic core. J. Mol. Biol. 376, 1282-1304 (2008).

Rothe, C., Urlinger, S., Löhning, C., Prassler, J., Stark, Y., Jäger, U., Hubner, B., Bardroff, M., Pradel, I., Boss, M., Bittlingmaier, R., Bataa, T., Frisch, C., Brocks, B., Honegger, A. & Urban, M. The human combinatorial antibody library HuCAL GOLD combines diversification of all six CDRs according to the natural immune system with a novel display method for efficient selection of high-affinity antibodies. J Mol Biol 376, 1182-1200 (2008). 

Sarkar, CA., Dodevski, I.,Kenig, M., Dudli, S., Mohr, A., Hermans, E. & Plückthun, A. Directed evolution of a G protein-coupled receptor for expression, stability, and binding selectivity. PNAS USA 105, 14808-14813 (2008). 

Steiner, D., Forrer, P. & Plückthun, A. Efficient selection of DARPins with sub-nanomolar affinities using SRP phage display. J Mol Biol 382, 1211-1227(2008). 

Wetzel SK., Settani, G., Kenig. M., Binz, HK. & Plückthun, A. Folding and unfolding mechanism of highly stable full-consensus ankyrin repeat proteins. J. Mol. Biol376, 241-257 (2008).  

Huber, T., Steiner, D., Röthlisberger, D., Plückthun, A. In vitro selection and characterization of DARPins and Fab fragments for the co-crystallization of membrane proteins: The Na(+)-citrate symporter CitS as an example. J. Struct. Biol. 159, 206-211 (2007).

Hussain, S., Plückthun, A., Allen, TM. & Zangemeister-Wittke, U. Antitumor activity of an epithelial cell adhesion molecule targeted nanovesicular drug delivery system. Mol. Cancer Ther. 6, 3019-3027 (2007).

Kolly,R., Thiel, M.A., Herrmann, T. & Plückthun, A. Monovalent antibody scFv fragments selected to modulate T-cell activation by inhibition of CD86-CD28 interaction. Protein Eng. Des. Sel. 20, 91-98 (2007). 

Morfill, J., Blank, K.,  Zahnd, C., Luginbühl, B., Kuhner, F., Gottschalk, K.E., Plückthun, A. & Gaub, H.E. Affinity-matured recombinant antibody fragments analyzed by single force spectroscopy. Biophys. J. Aug. 93, 3583-3490 (2007).

Schweizer, A., Roschitzki-Voser, H., Amstutz, P., Briand, C., Gulotti-Georgieva, M., Prenosil, E., Binz, HK., Capitani, G., Baici, A., Plückthun, A. & Grütter MG. Inhibition of caspase-2 by a designed ankyrin repeat protein: specificity, structure, and inhibition mechanism. Structure 15,625-636 (2007).

Taussig, M. J., Stoevesandt, O., Borrebaeck, C. A., Bradbury, A. R., Cahill, D., Cambillau, C., de Daruvar, A., Dubel, S., Eichler, J., Frank, R., Gibson, T. J., Gloriam, D., Gold, L., Herberg, F. W., Hermjakob, H., Hoheisel, J. D., Joos, T. O., Kallioniemi, O., Koegll, M., Konthur, Z., Korn, B., Kremmer, E., Krobitsch, S., Landegren, U., van der Maarel, S., McCafferty, J., Muyldermans, S., Nygren, P. A., Palcy, S., Plückthun, A., Polic, B., Przybylski, M., Saviranta, P., Sawyer, A., Sherman, D. J., Skerra, A., Templin, M., Ueffing, M., & Uhlen, M. ProteomeBinders: planning a European resource of affinity reagents for analysis of the human proteome. Nat. Methods 4, 13-17 (2007).

Zahnd, C., Wyler, E., Schwenk, JM., Steiner, D., Lawrence, MC., McKern, NM., Pecorari, F., Ward, CW., Joss, TO. & Plückthun, A. A designed ankyrin repeat protein evolved to picomolar affinity to her2. J. Mol. Biol. 369, 1015-1028 (2007). 

Zahnd, C., Amstutz, P. & Plückthun A. Ribosome display: selecting and evolving proteins in vitro that specifically bind to a target. Nat. Methods 4, 269-279 (2007). 

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).

Bès, C., Troadec, 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. K., Kohl, A., Plückthun, A. & Grütter, M. G. Crystal structure of a consensus-designed ankyrin repeat protein: implications for stability. Proteins 65, 280-284 (2006).

Hussain, S., Plückthun, A., Allen, T. M. & Zangemeister-Wittke, U. Chemosensitization of carcinoma cells using epithelial cell adhesion molecule-targeted liposomal antisense against bcl-2/bcl-xL. Mol. Cancer Ther. 5, 3170-80 (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).

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).  

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).

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).

Yu, H. et al. 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).