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Department of Biochemistry

Publications of the Plückthun Group 2000-2005 (in alphabetical order)

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. PNAS U.S.A. 102, 14587-14592 (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).    
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. Protein Sci. 14, 2537-2549 (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).    
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).    
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).    
Moroney, S. & Plückthun, A. in Modern Biopharmaceuticals (ed. Knäblein, J.) 1147-1186 (Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, 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).    
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).    
Binz, H. K., Amstutz, P., Kohl, A., Stumpp, M. T., Briand, C., Forrer, P., Grütter, M. G. & Plückthun, A. High-affinity binders selected from designed ankyrin repeat protein libraries. Nat. Biotechnol. 22, 575-582 (2004).    
Chang, C., Plückthun, A. & Wlodawer, A. Crystal structure of a truncated version of the phage ? protein gpD. Proteins 57, 866-868 (2004).    
Devi, V. S., Binz, H. K., Stumpp, M. T., Plückthun, A., Bosshard, H. R. & Jelesarov, I. Folding of a designed simple ankyrin repeat protein. Protein Sci. 13, 2864-2870 (2004).    
Ewert, S., Honegger, A. & Plückthun, A. Stability improvement of antibodies for extracellular and intracellular applications: CDR grafting to stable frameworks and structure-based framework engineering. Methods 34, 184-199 (2004).    
Forrer, P., Binz, H. K., Stumpp, M. T. & Plückthun, A. Consensus design of repeat proteins. Chembiochem. 5, 183-189 (2004).    
Forrer, P., Chang, C., Ott, D., Wlodawer, A. & Plückthun, A. Kinetic stability and crystal structure of the viral capsid protein SHP. J. Mol. Biol. 344, 179-193 (2004).    
Hu, K., Plückthun, A. & Pervushin, K. Backbone HN, N, C?, C' and C? chemical shift assignments and secondary structure of FkpA, a 245-residue peptidyl-prolyl cis/trans isomerase with chaperone activity. J. Biomol. NMR 28, 405-406 (2004).    
Iwai, H., Forrer, P., Plückthun, A. & Güntert, P. Assignments of 1H and 15N resonances of the bacteriophage ? capsid stabilizing protein gpD. J. Biomol. NMR 28, 89-90 (2004).    
Lipovsek, D. & Plückthun, A. In-vitro protein evolution by ribosome display and mRNA display. J. Immunol. Methods 290, 51-67 (2004).

Matsuura, T., Ernst, A., Zechel, D. L. & Plückthun, A. Combinatorial approaches to novel proteins. Chembiochem. 5, 177-182 (2004).

Matsuura, T. & Plückthun, A. Strategies for selection from protein libraries composed of de novo designed secondary structure modules. Origins of Life and Evolution of the Biosphere 34, 151-157 (2004).

Ott, D., Frischknecht, R. & Plückthun, A. Construction and characterization of a kappa opioid receptor devoid of all free cysteines. Protein Eng. Des. Sel. 17, 37-48 (2004).

Röthlisberger, D., Pos, K. M. & Plückthun, A. An antibody library for stabilizing and crystallizing membrane proteins - selecting binders to the citrate carrier CitS. FEBS Lett. 564, 340-348 (2004).

Zahnd, C., Spinelli, S., Luginbühl, B., Amstutz, P., Cambillau, C. & Plückthun, A. Directed in vitro evolution and crystallographic analysis of a peptide-binding single chain antibody fragment (scFv) with low picomolar affinity. J. Biol. Chem. 279, 18870-18877 (2004).

Binz, H. K., Stumpp, M. T., Forrer, P., Amstutz, P. & Plückthun, A. Designing repeat proteins: Well-expressed, soluble and stable proteins from combinatorial libraries of consensus ankyrin repeat proteins. J. Mol. Biol. 332, 489-503 (2003).

Cesaro-Tadic, S., Lagos, D., Honegger, A., Rickard, J. H., Partridge, L. J., Blackburn, G. M. & Plückthun, A. Turnover-based in vitro selection and evolution of biocatalysts from a fully synthetic antibody library. Nat. Biotechnol. 21, 679-685 (2003).

Ciatto, C., Capitani, G., Tissot, A. C., Pécorari, F., Plückthun, A. & Grütter, M. G. Structural analysis of mycobacterial and murine hsp60 epitopes in complex with the class I MHC molecule H-2Db. FEBS Lett. 543, 11-15 (2003).

Deyev, S. M., Waibel, R., Lebedenko, E. N., Schubiger, A. P. & Plückthun, A. Design of multivalent complexes using the barnase*barstar module. Nat. Biotechnol. 21, 1486-1492 (2003).

Di Paolo, C., Willuda, J., Kubetzko, S., Lauffer, I., Tschudi, D., Waibel, R., Plückthun, A., Stahel, R. A. & Zangemeister-Wittke, U. A recombinant immunotoxin derived from a humanized epithelial cell adhesion molecule-specific single-chain antibody fragment has potent and selective antitumor activity ERRATUM: Vol. 10, 2004, 2579. Clin. Cancer Res. 9, 2837-2848 (2003).

Ewert, S., Honegger, A. & Plückthun, A. Structure-based improvement of the biophysical properties of immunoglobulin Vh domains with a generalizable approach. Biochemistry 42, 1517-1528 (2003).

Ewert, S., Huber, T., Honegger, A. & Plückthun, A. Biophysical properties of human antibody variable domains. J. Mol. Biol 325, 531-553 (2003).

Forrer, P., Stumpp, M. T., Binz, H. K. & Plückthun, A. A novel strategy to design binding molecules harnessing the modular nature of repeat proteins. FEBS Lett. 539, 2-6 (2003).

Kohl, A., Binz, H. K., Forrer, P., Stumpp, M. T., Plückthun, A. & Grütter, M. G. Designed to be stable: Crystal structure of a consensus ankyrin repeat protein. Proc. Natl. Acad. Sci. USA 100, 1700-1705 (2003).

Matsuura, T. & Plückthun, A. Selection based on the folding properties of proteins with ribosome display. FEBS Lett. 539, 24-28 (2003).

Stumpp, M. T., Forrer, P., Binz, H. K. & Plückthun, A. Designing repeat proteins: Modular leucine-rich repeat protein libraries based on the mammalian ribonuclease inhibitor family. J. Mol. Biol332, 471-487 (2003).

Amstutz, P., Pelletier, J. N., Guggisberg, A., Jermutus, L., Cesaro-Tadic, S., Zahnd, C. & Plückthun, A. In vitro selection for catalytic activity with ribosome display. J. Am. Chem. Soc. 124, 9396-9403 (2002).

Arndt, K., Pelletier, J., Muller, K., Plückthun, A. & Alber, T. Comparison of in vivo selection and rational design of heterodimeric coiled coils. Structure (Camb) 10, 1235-1248 (2002).

Auf Der Maur, A., Zahnd, C., Fischer, F., Spinelli, S., Honegger, A., Cambillau, C., Escher, D., Plückthun, A. & Barberis, A. Direct in vivo screening of intrabody libraries constructed on a highly stable single-chain framework. J. Biol. Chem277, 45075-45086 (2002).

Betley, J. R., Cesaro-Tadic, S., Mekhalfia, A., Rickard, J. H., Denham, H., Partridge, L. J., Plückthun, A. & Blackburn, G. M. Direct screening for phosphatase activity by turnover-based capture of protein catalysts. Angewandte Chemie-International Edition 41, 775-777 (2002).

Blank, K., Lindner, P., Diefenbach, B. & Plückthun, A. Self-immobilizing recombinant antibody fragments for immunoaffinity chromatography: Generic, parallel, and scalable protein purification. Protein Express. Purif24, 313-322 (2002).

Ewert, S., Cambillau, C., Conrath, K. & Plückthun, A. Biophysical properties of camelid VHH domains compared to those of human VH3 domains. Biochemistry 41, 3628-3636 (2002).

Hofmann, A., Iwai, H., Hess, S., Plückthun, A. & Wlodawer, A. Structure of cyclized green fluorescent protein. Acta Crystallogr. D Biol. Crystallogr. 58, 1400-1406 (2002).

Hoyer, W., Ramm, K. & Plückthun, A. A kinetic trap is an intrinsic feature in the folding pathway of single-chain Fv fragments. Biophys. Chem. 96, 273-284 (2002).    
Jermutus, L., Kolly, R., Földes-Papp, Z., Hanes, J., Rigler, R. & Plückthun, A. Ligand binding of a ribosome-displayed protein detected in solution at the single molecule level by fluorescence correlation spectroscopy. Eur. Biophys. J. 31, 179-184 (2002).    
Kaufmann, M., Lindner, P., Honegger, A., Blank, K., Tschopp, M., Capitani, G., Plückthun, A. & Grütter, M. G. Crystal structure of the anti-His tag antibody 3D5 single-chain fragment complexed to its antigen. J. Mol. Biol. 318, 135-147 (2002).    
Lindner, P., Blank, K., Diefenbach, B. & Plückthun, A. in EUCHIS'02, 5th International Conference of the European Chitin Society (eds. Vårum, K. M., Domard, A. & Smidsrød, O.) 261-262 (NTNU Trondheim, Norway, Trondheim, Norway, 2002).    
Matsuura, T., Ernst, A. & Plückthun, A. Construction and characterization of protein libraries composed of secondary structure modules. Protein Sci. 11, 2631-2643 (2002).    
Valle, F., DeRose, J. A., Dietler, G., Kawe, M., Plückthun, A. & Semenza, G. AFM structural study of the molecular chaperone GroEL and its two-dimensional crystals: an ideal "living" calibration sample. Ultramicroscopy 93, 83-89 (2002).    
Amstutz, P., Forrer, P., Zahnd, C. & Plückthun, A. In vitro display technologies: Novel developments and applications. Curr. Opin. Biotechnol. 12, 400-405 (2001).    
Arndt, K. M., Müller, K. M. & Plückthun, A. Helix-stabilized Fv (hsFv) antibody fragments: Substituting the constant domains of a Fab fragment for a heterodimeric coiled-coil domain. J. Mol. Biol. 312, 221-228 (2001).    
Bothmann, H. & Plückthun, A. in Antibody Engineering (eds. Kontermann, R. & Dübel, S.) 307-317 (Springer-Verlag, Berlin Heidelberg, 2001).    
Burmester, J. & Plückthun, A. in Antibody Engineering (eds. Kontermann, R. & Dübel, S.) 19-40 (Springer-Verlag, Berlin Heidelberg, 2001).    
Burmester, J., Spinelli, S., Pugliese, L., Krebber, A., Honegger, A., Jung, S., Schimmele, B., Cambillau, C. & Plückthun, A. Selection, characterization and X-ray structure of anti-ampicillin single-chain Fv fragments from phage-displayed murine antibody libraries. J. Mol. Biol. 309, 671-685 (2001).    
Chang, C., Mooser, A., Plückthun, A. & Wlodawer, A. Crystal structure of the dimeric C-terminal domain of TonB reveals a novel fold. J. Biol. Chem. 276, 27535-27540 (2001).    
Ciatto, C., Tissot, A. C., Tschopp, M., Capitani, G., Pecorari, F., Plückthun, A. & Grütter, M. G. ERRATUM: Zooming in on the hydrophobic ridge of H-2Db: Implications for the conformational variability of bound peptides. J. Mol. Biol. 314, 1257 (2001).    
Ciatto, C., Tissot, A. C., Tschopp, M., Capitani, G., Pecorari, F., Plückthun, A. & Grütter, M. G. Zooming in on the hydrophobic ridge of H-2Db: Implications for the conformational variability of bound peptides. J. Mol. Biol. 312, 1059-1071 (2001).    
Honegger, A. & Plückthun, A. Yet another numbering scheme for immunoglobulin variable domains: An automatic modeling and analysis tool. J. Mol. Biol. 309, 657-670 (2001).    
Honegger, A. & Plückthun, A. The influence of the buried glutamine or glutamate residue in position 6 on the structure of Immunoglobulin variable domains. J. Mol. Biol. 309, 687-699 (2001).    
Iwai, H., Lingel, A. & Plückthun, A. Cyclic green fluoroscent protein produced in vivo using and artifically Split PI-PfuI intein from Pyrococcus furiosus. J. Biol. Chem. 276, 16548-16554 (2001).    
Jäger, M., Gehrig, P. & Plückthun, A. The scFv fragment of the antibody hu4D5-8: Evidence for early premature domain interaction in refolding. J. Mol. Biol. 305, 1111-1129 (2001).    
Jermutus, L., Honegger, A., Schwesinger, F., Hanes, J. & Plückthun, A. Tailoring in vitro evolution for protein affinity or stability. Proc. Natl. Acad. Sci. USA 98, 75-80 (2001).    
Jung, S., Spinelli, S., Schimmele, B., Honegger, A., Pugliese, L., Cambillau, C. & Plückthun, A. The importance of framework residue H6, H7 and H10 in antibody heavy chains: Experimental evidence for a new structural subclassification of antibody VH domains. J. Mol. Biol. 309, 701-716 (2001).    
Lindner, P. & Plückthun, A. in Antibody Engineering (eds. Kontermann, R. & Dübel, S.) 637-647 (Springer-Verlag, Berlin Heidelberg, 2001).    
Mössner, E., Koch, H. & Plückthun, A. Fast selection of antibodies without antigen purification: Adaption of the protein fragment complementation assay to select antigen-antibody pairs. J. Mol. Biol. 308, 115-122 (2001).    
Mössner, E. & Plückthun, A. Directed evolution with fast and efficient selection technologies. Chimia 55, 325-329 (2001).    
Paci, E., Caflisch, A., Plückthun, A. & Karplus, M. Forces and energetics of hapten-antibody dissociation: A biased molecular dynamics simulation study. J. Mol. Biol. 314, 589-605 (2001).    
Ramm, K. & Plückthun, A. High enzymatic activity and chaperone function are mechanistically related features of the dimeric E. coli peptidyl-prolyl-isomerase FkpA. J. Mol. Biol. 310, 485-498 (2001).    
Schaffitzel, C., Berger, I., Postberg, J., Hanes, J., Lipps, H. J. & Plückthun, A. In vitro generated antibodies specific for telomeric guanine-quadruplex DNA react with Stylonychia lemnae macronuclei. Proc. Natl. Acad. Sci. USA 98, 8572-8577 (2001).    
Schaffitzel, C. & Plückthun, A. Protein-fold evolution in the test tube. Trends Biochem. Sci. 26, 577-579 (2001).

Schaffitzel, C., Zahnd, C., Amstutz, P., Luginbühl, B. & Plückthun, A. in Protein-Protein Interactions, A Molecular Cloning Manual (ed. Golemis, E.) 535-567 (Cold Spring Harbor Laboratory Press, New York, 2001).

Valle, F., Derose, J. A., Dietler, G., Kawe, M., Semenza, G. & Plückthun, A. Imaging the native structure of the charperone protein GroEL without fixation using atomic force microscopy. J. Microsc. 203, 195-198 (2001).

Willuda, J., Kubetzko, S., Waibel, R., Schubiger, P. A., Zangemeister-Wittke, U. & Plückthun, A. Tumor targeting of mono-, di- and tetravalent Anti-p185HER-2 miniantibodies multimerized by self-associating peptides. J. Biol. Chem. 276, 14385-14392 (2001).

Wörn, A. & Plückthun, A. Stability engineering of antibody single-chain Fv fragments. J. Mol. Biol. 305, 989-1010 (2001).

Arndt, K. M., Jung, S., Krebber, C. & Plückthun, A. Selectively infective phage technology. Methods Enzymol. 328, 364-388 (2000).

Arndt, K. M., Pelletier, J. N., Müller, K. M., Alber, T., Michnick, S. W. & Plückthun, A. A heterodimeric coiled-coil peptide pair selected in vivo from a designed library-versus-library ensemble. J. Mol. Biol. 295, 627-639 (2000).

Bothmann, H. & Plückthun, A. The periplasmic Escherichia coli peptidylprolyl cis,trans-isomerase FkpA: I. Increased functional expression of antibody fragments with and without cis-prolines. J. Biol. Chem. 275, 17100-17105 (2000).

Hanes, J., Jermutus, L. & Plückthun, A. Selecting and evolving functional proteins in vitro by ribosome display. Methods Enzymol. 328, 404-430 (2000).

Hanes, J., Schaffitzel, C., Knappik, A. & Plückthun, A. Picomolar affinity antibodies from a fully synthetic naive library selected and evolved by ribosome display. Nat. Biotechnol. 18, 1287-1292 (2000).

Jäger, M. & Plückthun, A. Direct evidence by H/D exchange and ESI-MS for transient unproductive domain interaction in the refolding of an antibody scFv fragment. Protein Sci. 9, 552-563 (2000).

Knappik, A., Ge, L., Honegger, A., Pack, P., Fischer, M., Wellnhofer, G., Hoess, A., Wölle, J., Plückthun, A. & Virnekäs, B. Fully synthetic human combinatorial antibody libraries (HuCAL) based on modular consensus frameworks and CDRs randomized with trinucleotides. J. Mol. Biol. 296, 57-86 (2000).

Linke, R. P., Schäeffer, J., Gielow, P., Lindner, P., Lottspeich, F., Plückthun, A. & Weiss, E. H. Production of recombinant human ?2-microglobulin for scintigraphic diagnosis of amyloidosis in uremia and hemodialysis. Eur. J. Biochem. 267, 627-633 (2000).

Plückthun, A., Schaffitzel, C., Hanes, J. & Jermutus, L. In vitro selection and evolution of proteins. Adv. Protein Chem55, 367-403 (2000).

Ramm, K. & Plückthun, A. The periplasmic Escherichia coli peptidylprolyl cis,trans-isomerase FkpA: II. Isomerase-independent chaperone activity in vitro. J. Biol. Chem. 275, 17106-17113 (2000).

Schwesinger, F., Ros, R., Strunz, T., Anselmetti, D., Güntherodt, H.-J., Honegger, A., Jermutus, L., Tiefenauer, L. & Plückthun, A. Unbinding forces of single antibody-antigen complexes correlate with their thermal dissociation rates. Proc. Natl. Acad. Sci. USA 97, 9972-9977 (2000).    
Tissot, A. C., Ciatto, C., Mittl, P. R. E., Grütter, M. G. & Plückthun, A. ERRATUM: Viral escape at the molecular level explained by quantitative T-cell receptor/peptide/MHC interactions and the crystal structure of a peptide/MHC complex. J. Mol. Biol. 304, 683 (2000).    
Tissot, A. C., Ciatto, C., Mittl, P. R. E., Grütter, M. G. & Plückthun, A. Viral escape at the molecular level explained by quantitative T-cell receptor/peptide/MHC interactions and the crystal structure of a peptide/MHC complex. J. Mol. Biol. 302, 873-885 (2000).    
Tissot, A. C., Pecorari, F. & Plückthun, A. Characterizing the functionality of recombinant T-cell receptors in vitro: A pMHC tetramer based approach. J. Immunol. Methods 236, 147-165 (2000).    
Wörn, A., Auf der Maur, A., Escher, D., Honegger, A., Barberis, A. & Plückthun, A. Correlation between in vitro stability and in vivo performance of anti-GCN4 intrabodies as cytoplasmic inhibitors. J. Biol. Chem. 275, 2795-2803 (2000).    
Yang, F., Forrer, P., Dauter, Z., Conway, J. F., Cheng, N., Cerritelli, M. E., Steven, A. C., Plückthun, A. & Wlodawer, A. Novel fold and capsid-binding properties of the ?-phage display platform protein gpD. Nat. Struct. Biol. 7, 230-237 (2000).