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Department of Biochemistry

Publications of the Plückthun Group 1995-1999 (in alphabetical order)

Berger, C., Weber-Bornhauser, S., Eggenberger, J., Hanes, J., Plückthun, A. & Bosshard, H. R. Antigen recognition by conformational selection. FEBS Lett. 450, 149-153 (1999).    
Forrer, P., Jung, S. & Plückthun, A. Beyond binding: using phage display to select for structure, folding and enzymatic activity in proteins. Curr. Opin. Struct. Biol. 9, 514-520 (1999).    
Hanes, J., Jermutus, L., Schaffitzel, C. & Plückthun, A. Comparison of Escherichia coli and rabbit reticulocyte ribosome display systems. FEBS Lett. 450, 105-110 (1999).    
Hanes, J. &Plückthun, A. in Combinatorial Chemistry in Biology (eds. Famulok, M., Winnacker, E.-L. & Wong, C.-H.) 107-122 (Springer Verlag, Berlin Heidelberg, 1999).    
Iwai, H. & Plückthun, A. Circular ?-lactamase: Stability enhancement by cyclizing the backbone. FEBS Lett. 459, 166-172 (1999).    
Jäger, M. & Plückthun, A. Domain interactions in antibody Fv and scFv fragments: effects on unfolding kinetics and equilibria. FEBS Lett. 462, 307-312 (1999).    
Jäger, M. & Plückthun, A. Folding and assembly of an antibody Fv fragment, a heterodimer stabilized by antigen. J. Mol. Biol. 285, 2005-2019 (1999).    
Jung, S., Arndt, K. M., Müller, K. M. & Plückthun, A. Selectively infective phage (SIP) technology: scope and limitations. J. Immunol. Methods 231, 93-104 (1999).    
Jung, S., Honegger, A. & Plückthun, A. Selection for improved protein stability by phage display. J. Mol. Biol. 294, 163-80 (1999).    
Langedijk, A. C., Spinelli, S., Anguille, C., Hermans, P., Nederlof, J., Butenandt, J., Honegger, A., Cambillau, C. & Plückthun, A. Insight into odorant perception: The crystal structure and binding characteristics of antibody fragments directed against the musk odorant traseolide. J. Mol. Biol. 292, 855-869 (1999).    
Lubkowski, J., Hennecke, F., Plückthun, A. & Wlodawer, A. Filamentous phage infection: crystal structure of g3p in complex with its coreceptor, the C-terminal domain of TolA. Structure 7, 711-722 (1999).    
Pecorari, F., Tissot, A. C. & Plückthun, A. Folding, heterodimeric association and specific peptide recognition of a murine ?? T-cell receptor expressed in Escherichia coli. J. Mol. Biol. 285, 1831-1843 (1999).    
Pelletier, J. N., Arndt, K. M., Plückthun, A. & Michnick, S. W. An in vivo library-versus-library selection of optimized protein-protein interactions. Nat. Biotechnol. 17, 683-690 (1999).    
Ramm, K., Gehrig, P. & Plückthun, A. Removal of the conserved disulfide bridges from the scFv fragment of an antibody: Effects on folding kinetics and aggregation. J. Mol. Biol. 290, 535-546 (1999).    
Schaffitzel, C., Hanes, J., Jermutus, L. & Plückthun, A. Ribosome display: an in vitro method for selection and evolution of antibodies from libraries. J. Immunol. Methods 231, 119-135 (1999).    
Waibel, R., Alberto, R., Willuda, J., Finnern, R., Schibli, R., Stichelberger, A., Egli, A., Abram, U., Mach, J. P., Plückthun, A. & Schubiger, P. A. Stable one-step technetium-99m labeling of His-tagged recombinant proteins with a novel Tc(I)-carbonyl complex. Nat. Biotechnol. 17, 897-901 (1999).    
Wall, J. G. & Plückthun, A. The hierarchy of mutations influencing the folding of antibody domains in Escherichia coli. Protein Eng. 12, 605-611 (1999).    
Willuda, J., Honegger, A., Waibel, R., Schubiger, P. A., Stahel, R., Zangemeister-Wittke, U. & Plückthun, A. High thermal stability is essential for tumor targeting of antibody fragments: Engineering of a humanized anti-epithelial glycoprotein-2 (epithelial cell adhesion molecule) single-chain Fv fragment. Cancer Res. 59, 5758-5767 (1999).    
Wörn, A. & Plückthun, A. Different equilibrium stability behavior of scFv fragments: Identification, classification, and improvement by protein engineering. Biochemistry 38, 8739-8750 (1999).    
zur Mühlen, E., Koschinski, P., Gehring, S., Ros, R., Tiefenauer, L., Haltner, E., Lehr, C.-M., Hartmann, U., Schwesinger, F. & Plückthun, A. in Bioadhesive Drug Delivery Systems (eds. Mathiowitz, E., Chickering III, D. E. & Lehr, C.-M.) 197-221 (Marcel Dekker Inc., New York, 1999).    
Apostolakis, J., Plückthun, A. & Caflisch, A. Docking small ligands in flexible binding sites. J. Comput. Chem. 19, 21-37 (1998).    
Arndt, K. M., Müller, K. M. & Plückthun, A. Factors influencing the dimer to monomer transition of an antibody single-chain Fv fragment. Biochemistry 37, 12918-12926 (1998).    
Bothmann, H. & Plückthun, A. Selection for a periplasmic factor improving phage display and functional periplasmic expression. Nat. Biotechnol. 16, 376-380 (1998).    
Gallimore, A., Glithero, A., Godkin, A., Tissot, A. C., Plückthun, A., Elliott, T., Hengartner, H. & Zinkernagel, R. Induction and exhaustion of lymphocytic choriomeningitis virus-specific cytotoxic T lymphocytes visualized using soluble tetrameric major histocompatibility complex class I-peptide complexes. J. Exp. Med. 187, 1383-1393 (1998).    
Gervasoni, P., Gehrig, P. & Plückthun, A. Two conformational states of ?-lactamase bound to GroEL: A biophysical characterization. J. Mol. Biol. 275, 663-675 (1998).    
Gervasoni, P., Staudenmann, W., James, P. & Plückthun, A. Identification of the binding surface on ?-lactamase for GroEL by limited proteolysis and MALDI-mass spectrometry. Biochemistry 37, 11660-11669 (1998).    
Hanes, J., Jermutus, L., Weber-Bornhauser, S., Bosshard, H. R. & Plückthun, A. Ribosome display efficiently selects and evolves high-affinity antibodies in vitro from immune libraries. Proc. Natl. Acad. Sci. USA 95, 14130-14135 (1998).    
Hennecke, F., Krebber, C. & Plückthun, A. Non-repetitive single-chain Fv linkers selected by selectively infective phage (SIP) technology. Protein Eng. 11, 405-410 (1998).    
Jermutus, L., Ryabova, L. A. & Plückthun, A. Recent advances in producing and selecting functional proteins by using cell-free translation. Curr. Opin. Biotechnol. 9, 534-548 (1998).    
Langedijk, A. C., Honegger, A., Maat, J., Planta, R. J., van Schaik, R. C. & Plückthun, A. The nature of antibody heavy chain residue H6 strongly influences the stability of a VH domain lacking the disulfide bridge. J. Mol. Biol. 283, 95-110 (1998).

Lubkowski, J., Hennecke, F., Plückthun, A. & Wlodawer, A. The structural basis of phage display elucidated by the crystal structure of the N-terminal domains of g3p. Nat. Struct. Biol. 5, 140-147 (1998).

Müller, K. M., Arndt, K. M., Bauer, K. & Plückthun, A. Tandem immobilized metal-ion affinity chromatography/immunoaffinity purification of His-tagged proteins - evaluation of two anti-His-tag monoclonal antibodies. Anal. Biochem. 259, 54-61 (1998).

Müller, K. M., Arndt, K. M. & Plückthun, A. Model and simulation of multivalent binding to fixed ligands. Anal. Biochem. 261, 149-158 (1998).

Müller, K. M., Arndt, K. M. & Plückthun, A. A dimeric bispecific miniantibody combines two specificities with avidity. FEBS Lett. 432, 45-49 (1998).

Müller, K. M., Arndt, K. M., Strittmatter, W. & Plückthun, A. The first constant domain (CH1 and CL) of an antibody used as heterodimerization domain for bispecific miniantibodies. FEBS Lett. 422, 259-264 (1998).

Plückthun, A. in Protein Dynamics, Function and Design (eds. Jardetzky, O. & Lefèvre, J. F.) 37-57 (Plenum Press, New York, 1998).

Proba, K., Wörn, A., Honegger, A. & Plückthun, A. Antibody scFv fragments without disulfide bonds made by molecular evolution. J. Mol. Biol. 275, 245-253 (1998).

Ros, R., Schwesinger, F., Anselmetti, D., Kubon, M., Schäfer, R., Plückthun, A. & Tiefenauer, L. Antigen binding forces of individually addressed single-chain Fv antibody molecules. Proc. Natl. Acad. Sci. USA 95, 7402-7405 (1998).

Shusta, E. V., Raines, R. T., Plückthun, A. & Wittrup, K. D. Increasing the secretory capacity of Saccharomyces cerevisiae for production of single-chain antibody fragments. Nat. Biotechnol. 16, 773-777 (1998).

Sieber, V., Plückthun, A. & Schmid, F. X. Selecting proteins with improved stability by a phage-based method. Nat. Biotechnol. 16, 955-960 (1998).

Spada, S., Honegger, A. & Plückthun, A. Reproducing the natural evolution of protein structural features with the selectively infective phage (SIP) technology. The kink in the first strand of antibody kappa domains. J. Mol. Biol. 283, 395-407 (1998).

Stegmann, R., Manakova, E., Rössle, M., Heumann, H., Nieba-Axmann, S. E., Plückthun, A., Hermann, T., May, R. P. & Wiedenmann, A. Structural changes of the Escherichia coli GroEL-GroES chaperonins upon complex formation in solution: A neutron small angle scattering study. J. Struct. Biol. 121, 30-40 (1998).

Vinckier, A., Gervasoni, P., Zaugg, F., Ziegler, U., Lindner, P., Groscurth, P., Plückthun, A. & Semenza, G. Atomic force microscopy detects changes in the interaction forces between GroEL and substrate proteins. Biophys. J. 74, 3256-3263 (1998).    
Wörn, A. & Plückthun, A. Mutual stabilization of VL and VH in single-chain antibody fragments, investigated with mutants engineered for stability. Biochemistry 37, 13120-13127 (1998).    
Wörn, A. & Plückthun, A. An intrinsically stable antibody scFv fragment can tolerate the loss of both disulfide bonds and fold correctly. FEBS Lett. 427, 357-361 (1998).
Freund, C., Gehrig, P., Baici, A., Holak, T. A. & Plückthun, A. Parallel pathways in the folding of a short-term denatured scFv fragment of an antibody. Fold. Des. 3, 39-49 (1997).    
Freund, C., Gehrig, P., Holak, T. A. & Plückthun, A. Comparison of the amide proton exchange behavior of the rapidly formed folding intermediate and the native state of an antibody scFv fragment. FEBS Lett. 407, 42-46 (1997).    
Gervasoni, P. & Plückthun, A. Folding intermediates of ?-lactamase recognized by GroEL. FEBS Lett. 401, 138-142 (1997).    
Hanes, J. & Plückthun, A. In vitro selection and evolution of functional proteins by using ribosome display. Proc. Natl. Acad. Sci. USA 94, 4937-4942 (1997).    
Hottenrott, S., Schumann, T., Plückthun, A., Fischer, G. & Rahfeld, J. U. The Escherichia coli SlyD is a metal ion-regulated peptidyl-prolyl cis/trans-isomerase. J. Biol. Chem. 272, 15697-15701 (1997).    
Jäger, M. & Plückthun, A. The rate-limiting steps for the folding of an antibody scFv fragment. FEBS Lett. 418, 106-110 (1997).    
Jung, S. & Plückthun, A. Improving in vivo folding and stability of a single-chain Fv antibody fragment by loop grafting. Protein Eng. 10, 959-966 (1997).    
Krebber, A., Bornhauser, S., Burmester, J., Honegger, A., Willuda, J., Bosshard, H. R. & Plückthun, A. Reliable cloning of functional antibody variable domains from hybridomas and spleen cell repertoires employing a reengineered phage display system. J. Immunol. Methods 201, 35-55 (1997).    
Krebber, C., Spada, S., Desplancq, D., Krebber, A., Ge, L. & Plückthun, A. Selectively-infective phage (SIP): A mechanistic dissection of a novel in vivo selection for protein-ligand interactions. J. Mol. Biol. 268, 607-618 (1997).    
Lindner, P., Bauer, K., Krebber, A., Nieba, L., Kremmer, E., Krebber, C., Honegger, A., Klinger, B., Mocikat, R. & Plückthun, A. Specific detection of His-tagged proteins with recombinant anti-His tag scFv-phosphatase or scFv-phage fusions. Biotechniques 22, 140-149 (1997).    
Nieba, L., Honegger, A., Krebber, C. & Plückthun, A. Disrupting the hydrophobic patches at the antibody variable/constant domain interface: Improved in vivo folding and physical characterization of an engineered scFv fragment. Protein Eng. 10, 435-444 (1997).    
Nieba, L., Nieba-Axmann, S. E., Persson, A., Hämäläinen, M., Edebratt, F., Hansson, A., Lidholm, J., Magnusson, K., Karlsson, A. F. & Plückthun, A. BIACORE analysis of histidine-tagged proteins using a chelating NTA sensor chip. Anal. Biochem. 252, 217-228 (1997).    
Nieba, S. E. & Plückthun, A. Chaperone-mediated protein folding. BIOforum International 1, 20-24 (1997).    
Nieba-Axmann, S. E., Ottiger, M., Wüthrich, K. & Plückthun, A. Multiple cycles of global unfolding of GroEL-bound cyclophilin A evidenced by NMR. J. Mol. Biol. 271, 803-818 (1997).    
Pedrazzi, G., Schwesinger, F., Honegger, A., Krebber, C. & Plückthun, A. Affinity and folding properties both influence the selection of antibodies with the selectively infective phage (SIP) methodology. FEBS Lett. 415, 289-293 (1997).    
Plückthun, A. & Cortese, R. New developments in combinatorial libraries. Biol. Chem. 378, 443 (1997).    
Plückthun, A. & Pack, P. New protein engineering approaches to multivalent and bispecific antibody fragments. Immunotechnology 3, 83-105 (1997).    
Proba, K., Honegger, A. & Plückthun, A. A natural antibody missing a cysteine in VH: Consequences for thermodynamic stability and folding. J. Mol. Biol. 265, 161-172 (1997).    
Ryabova, L. A., Desplancq, D., Spirin, A. S. & Plückthun, A. Functional antibody production using cell-free translation: Effects of protein disulfide isomerase and chaperones. Nat. Biotechnol. 15, 79-84 (1997).    
Slootstra, J. W., Kuperus, D., Plückthun, A. & Meloen, R. H. Identification of new tag sequences with differential and selective recognition properties for the anti-FLAG monoclonal antibodies M1, M2 and M5. Mol. Divers. 2, 156-164 (1997).    
Spada, S., Krebber, C. & Plückthun, A. Selectively infective phages (SIP). Biol. Chem. 378, 445-456 (1997).    
Spada, S. & Plückthun, A. Selectively infective phage (SIP) technology: A novel method for in vivo selection of interacting protein-ligand pairs. Nat. Med. 3, 694-696 (1997).    
Stegmann, R., Manakova, E., Axmann, S., Rößle, M., Hermann, T., May, R. P., Wiedenmann, A., Plückthun, A. & Heumann, H. Conformational changes and spatial arrangement of the E. coli chaperones GroEL and GroES. Physica B: Condensed Matter 234-236, 220-222 (1997).    

Freund, C., Honegger, A., Hunziker, P., Holak, T. A. & Plückthun, A. Folding nuclei of the scFv fragment of an antibody. Biochemistry 35, 8457-8464 (1996).    
Gervasoni, P., Staudenmann, W., James, P., Gehrig, P. & Plückthun, A. ?-Lactamase binds to GroEL in a conformation highly protected against hydrogen/deuterium exchange. Proc. Natl. Acad. Sci. USA 93, 12189-12194 (1996).    
Horn, U., Strittmatter, W., Krebber, A., Knüpfer, U., Kujau, M., Wenderoth, R., Müller, K. M., Matzku, S., Plückthun, A. & Riesenberg, D. High volumetric yields of functional dimeric miniantibodies in Escherichia coli, using an optimized expression vector and high-cell-density fermentation under non-limited growth conditions. Appl. Microbiol. Biotechnol. 46, 524-532 (1996).    
Kalinke, U., Krebber, A., Krebber, C., Bucher, E., Plückthun, A., Zinkernagel, R. M. & Hengartner, H. Monovalent single-chain Fv fragments and bivalent miniantibodies bound to vesicular stomatitis virus protect against lethal infection. Eur. J. Immunol. 26, 2801-2806 (1996).    
Krebber, A., Burmester, J. & Plückthun, A. Inclusion of an upstream transcriptional terminator in phage display vectors abolishes background expression of toxic fusions with coat protein g3p. Gene 178, 71-74 (1996).    
Nieba, L., Krebber, A. & Plückthun, A. Competition BIAcore for measuring true affinities: Large differences from values determined from binding kinetics. Anal. Biochem. 234, 155-165 (1996).    
Plückthun, A., Krebber, A., Krebber, C., Horn, U., Knüpfer, U., Wenderoth, R., Nieba, L., Proba, K. & Riesenberg, D. in Antibody Engineering (eds. McCafferty, J., Hoogenboom, H. R. & Chiswell, D. J.) 203-252 (IRL Press, Oxford, 1996).    
Rheinnecker, M., Hardt, C., Ilag, L. L., Kufer, P., Gruber, R., Hoess, A., Lupas, A., Rottenberger, C., Plückthun, A. & Pack, P. Multivalent antibody fragments with high functional affinity for a tumor-associated carbohydrate antigen. J. Immunol. 157, 2989-2997 (1996).    
Zahn, R., Lindner, P., Axmann, S. E. & Plückthun, A. Effect of single point mutations in citrate synthase on binding to GroEL. FEBS Lett. 380, 152-156 (1996).    
Ge, L., Knappik, A., Pack, P., Freund, C. & Plückthun, A. in Antibody Engineering (ed. Borrebaeck, C. A. K.) 229-266 (Oxford University Press, Inc., New York, 1995).    
Ge, L., Lupas, A., Peraldi-Roux, S., Spada, S. & Plückthun, A. A mouse Ig ? domain of very unusual framework structure loses function when converted to the consensus. J. Biol. Chem. 270, 12446-12451 (1995).    
Harris, J. R., Zahn, R. & Plückthun, A. Electron microscopy of the GroEL-GroES filament. J. Struct. Biol. 115, 68-77 (1995).

Haunschild, J., Faro, H.-P., Pack, P. & Plückthun, A. Pharmacokinetic properties of bivalent miniantibodies and comparison to other immunoglobulin forms. Antibody, Immunoconjugates and Radiopharmaceuticals 8, 111-128 (1995).

Knappik, A. & Plückthun, A. Engineered turns of a recombinant antibody improve its in vivo folding. Protein Eng. 8, 81-89 (1995).    
Krebber, C., Spada, S., Desplancq, D. & Plückthun, A. Co-selection of cognate antibody-antigen pairs by selectively-infective phages. FEBS Lett. 377, 227-231 (1995).    
Pack, P., Müller, K. M., Zahn, R. & Plückthun, A. Tetravalent miniantibodies with high avidity assembling in Escherichia coli. J. Mol. Biol. 246, 28-34 (1995).    
Proba, K., Ge, L. & Plückthun, A. Functional antibody single-chain fragments from the cytoplasm of Escherichia coli: Influence of thioredoxin reductase (TrxB). Gene 159, 203-207 (1995).    
Wall, J. G. & Plückthun, A. Effects of overexpressing folding modulators on the in vivo folding of heterologous proteins in Escherichia coli. Curr. Opin. Biotechnol. 6, 507-516 (1995).    
Wülfing, C. & Plückthun, A. T-cell receptor signal sequences. Immunol. Today 16, 405-406 (1995).    
Wülfing, C. & Plückthun, A. Soluble T-cell receptor fragments - guidance of folding and assembly. The Immunologist 3, 59-66 (1995).