Abstract
Directed molecular evolution is a powerful strategy for investigating the structure and function of proteins. When a function, such as ligand binding, can only be carried out by the native state of the protein, the biological selection for this function can be used to improve structural properties of the protein. Thus, thermodynamic stability and folding efficiency, which is the ability to avoid aggregation during folding, can be optimized. Three methods of selection are reviewed: phage display, selectively infective phages (SIP) and ribosome display, a cell-free method. Examples for optimizing antibody stability are discussed. In one case, antibodies have been generated under evolutionary pressure, which are stable in the absence of any disulfide bond, in the other case, a kink in the first strand of the beta-sandwich of kappa domains has been optimized.
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References
Baca, M.. Scanlan, T. S., Stephenson, R. C. and Wells, J. A. (1997). Phage display of a catalytic antibody to optimize affinity for transition-state analog binding. Proc. Natl. Acad. Sci. USA 94, 10063–10068.
Bai, C. and Elledge, S. J. (1996). Gene identification using the yeast two-hybrid system. Methods Enzymol. 273, 331–347.
Goder, E. T. and Wittrup, K. D. (1997). Yeast surface display for screening combinatorial polypeptide libraries. Nature Biotechnol. 15, 553–557.
Biocca, S. and Cattaneo, A. (1995). Intracellular immunization: Antibody targeting to subcellular compartments. Trends Cell Biol. 5, 248–252.
Cadwell, R. C. and Joyce, G. F. (1994). Mutagenic PCR. PCR Methods Appl. 3, 136–140.
Cortese, R., Monaci, P., Luzzago, A., Santini, C., Bartoli, F., Cortese, I., Fortugno, P., Galfre, G., Nicosia, A. and Felici, F. (1996). Selection of biologically active peptides by phage display of random peptide libraries. Curt. Opin. Biotechnol. 7, 616–621.
Cull, M. G., Miller, J. F. and Schatz, P. J. (1992). Screening for receptor ligands using large libraries of peptides linked to the C terminus of the lac repressor. Proc. Natl. Acad. Sci. USA 89, 1865–1869.
Dower, W. J. and Cwirla, S. E. (1992) in Guide to Electroporalion and Electrofusion, Eds.: Chang, D. C., Chassy, B. M., Saunders, J. A. and Sowers, A. E., Academic Press, San Diego, 291–301.
Duenas, M. and Borrebaeck, C. A. (1994). Clonal selection and amplification of phage displayed antibodies by linking antigen recognition and phage replication. Bio/Technol. 12, 999–1002.
Dunn, I. S. (1996). Phage display of proteins. Cure Opin. Biotechnol. 7,547–553.
Fersht, A. R. (1995). Characterizing transition states in protein folding: an essential step in the puzzle. Cure Opin. Struct. Biol. 5, 79–84.
Fersht, A. R. (1997). Nucleation mechanisms in protein folding. Cure. Opin. Struct. Biol. 7,3–9.
Fersht, A. R. and Wells, T. N. (1991). Linear free energy relationships in enzyme binding interactions studied by protein engineering. Protein Eng. 4, 229–231.
Freedman, R. B., Hirst, T. R. and Tuite, M. F. (1994). Protein disulphide isomerase: building bridges in protein folding. Trends Biochem. Sci. 19, 331–336.
Frisch, C., Kolmar, H. and Fritz, H. J. (1994). A soluble. immunoglobulin variable domain without a disulfide bridge: Construction, accumulation in the cytoplasm of E. coli, purification and physicochemical characterization. Biol. Chem. Hoppe-Seiler 375, 353–356.
Frisch, C., Kolmar, H., Schmidt, A., Kleemann, G., Reinhardt, A., Pohl, E., Usón, I., Schneider, T. R. and Fritz H. J. (1996). Contribution of the intramolecular disulfide bridge to the folding stability of REI(v), the variable domain of a human immunoglobulin kappa light chain. Fold. Des. 1,431–440.
Georgiou, G., Stathopoulos, C., Daugherty, P. S., Nayak, A. R.. Iverson, B. L. and Curtiss, R,111 (1997). Nature Biotechnol. 15, 29–34.
Gilbert, H. F. (1990). Molecular and cellular aspects of thiol-disulfide exchange.Adv. Enzymol. 63, 69–172.
Glockshuber, R., Schmidt, T. and Plückthun, A. (1992). The disulfide bonds in antibody variable domains: effects on stability, folding in vitro, and functional expression in Escherichia coil. Biochernisny 31, 1270–1279.
Goto, Y. and Hamaguchi, K. (1979). The role of the intrachain disulfide bond in the conformation and stability of the constant fragment of the immunoglobulin light chain. J. Biochem. 86, 1433–1441.
Gramatikoff, K., Georgiev, O. and Schaffner, W. (1994). Direct interaction rescue, a novel filamentous phage technique to study protein-protein interactions. Nucleic Acids Res. 22, 5761–5762.
Hall, A. and Knowles, J. R. (1976). Directed selective pressure on a beta-lactamase to analyse molecular changes involved in development of enzyme function. Nature 264, 803–804.
Hanes, J. and Plückthun, A. (1997). In vitro selection and evolution of functional proteins using ribosome display. Proc. Natl. Acad. Sci. USA 94, 4937–4942.
Horovitz, A. (1996). Double-mutant cycles: a powerful tool for analyzing protein structure and function. Fold. Des. 1, 121–126.
Huston, J. S., McCartney, J., Tai, M. S., Mottola-Hartshorn, C., Jin, D., Warren, F., Keck, P. and Oppermann, H. (1993). Medical applications of single-chain antibodies. Intern. Rev. Ionunol. 10, 195–217.
Jin, L., Fendly, B. M. and Wells, J. A. (1992). High resolution functional analysis of antibody-antigen interactions. J. Mot. Blot. 226, 851–865.
Jung, S. and Plückthun, A. (1997). Improving in vivo folding and stability of a single-chain Fv antibody fragment by loop grafting. Prot. Eng. 10, 959–966.
Kabat, E. A., Wu, T. T., Perry, H. M.,,Gottesman, K. S. and Foeller, C. (1991). Sequences of Proteins of Immunological Interest, 5th Ed., National Institutes of Health, Bethesda, MD.
Kayushin, A. L., Korosteleva, M. D., Miroshnikov, A. I., Kosch, W., Zubov, D. and Piel, N. (1996). A convenient approach to the synthesis of trinucleotide phosphoramidites--synthons for the generation of oligonucleotide/peptide libraries. Nucleic Acids Res. 24, 3748–3755.
Keiler, K. C., Waller, P. R. and Sauer, R. T. (1996). Role of a peptide tagging system in degradation of proteins synthesized from damaged messenger RNA. Science 271, 990–993.
Keohavong, P. and Thilly, W. G. (1989). Fidelity of DNA polymerases in DNA amplification. Proc. Natl. Acad. Sci. USA 86, 9253–9257.
Knappik, A. and Plückthun, A. (1995). Engineered turns of an antibody improve its in vivo folding. Protein Eng. 8. 81–89.
Krebber, C., Moroney, S., Plückthun, A. and Schneider, C. (1993). European Patent Application EP 93102484.
Krebber, C., Spada, S., Desplancq, D. and Plückthun, A. (1995). Coselection of cognate antibody-antigen pairs by selectively-infective phages. FEBS Lett. 377, 227–231.
Krebber, C., Spada, S., Desplancq, D., Krebber, A., Ge, L. and Plückthun, A. (1997). Selectively infective phage (SIP): a mechanistic dissection of a novel method to select for protein-ligand interactions. J. Mol. Biol. 268, 619–630.
Lerner, R. A., Benkovic, S. J. and Schultz, P. G. (1991). At the crossroads of chemistry and immunology: catalytic antibodies. Science 252, 659–667.
Low, N. M., Holliger, P. H. and Winter, G. (1996). Mimicking somatic hypermutation: affinity maturation of antibodies displayed on bacteriophage using a bacterial mutator strain. J. Mol. Biol. 260, 359–368.
Lubkowski, J., Hennecke, F., Plückthun, A. and Wlodawer A. (1998). The structural basis of phage display: The crystal structure of the N-tenninal domains of g3p at 1.46 Å resolution. Nature Structural Biology, 5, 140–147.
Mattheakis, L. C., Bhatt, R. R. and Dower, W. J. (1994). An in vitro polysome display system for identifying ligands from very large peptide libraries. Proc. Natl. Acad. Sci. USA 91, 9022–9026.
Moore, J. C., Jin, H. M., Kuchner, O. and Arnold, F. H. (1997). Strategies for the in vitro evolution of protein func- tion: enzyme evolution by random recombination of improved sequences. J. Mol. Biol. 272, 336–347.
Nieba, L., Honegger, A., Krebber C. and Plückthun, A. (1997). 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.
Padlan, E. A. (1996). X-ray crystallography of antibodies. Adv. Protein Chem. 49, 57–133.
Phizicky, E. M. and Fields, S. (1995). Protein-protein interactions: methods for detection and analysis. Microbiol. Rev. 59, 94–123.
Proba, K., Wörn, A., Honegger, A. and Plückthun, A. (1998). Antibody fragments without disulfide bonds, made by molecular evolution. J. col. Biol. 275, 245–253.
Richardson, J. H. and Marasco, W. A. (1995). Intracellular antibodies: development and therapeutic potential. Trends Biotechnol. 13, 306–310.
Rudikoff, S. and Pumphrey, J. G. (1986). Functional antibody lacking a variable-region disulfide bridge. Proc. Natl. Acad. Sci. USA 83, 7875–7878.
Ryabova, L., Desplancq, D., Spirin, S. and Plückthun, A. (1997). Making antibodies in vitro: the effect of molecular chaperones and disulfide isomerase on the functional expression of single-chain fragments by in vitro translation. Nat. Biotechnol.15, 79–84.
Scott, J. K. and Smith, G. P. (1990). Searching for peptide ligands with an epitope library. Science 249, 386–390.
Smith, G. P. (1985). Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface. Science 228, 1315–1317.
Spada, S. and Plückthun, A. (1997). Selectively infective phage (SIP) technology: a novel method for the in vivo selection of interacting protein-ligand pairs. Nature Med. 6, 694–696.
Spada, S., Krebber, C. and Plückthun, A. (1997). Selectively infective phages. Biol. Chem. 378, 445–456.
Stemmer, W. P. (1994a). Rapid evolution of a protein in vitro by DNA shuffling. Nature 370,389–391.
Stemmer, W. P. (1994b). DNA shuffling by random fragmentation and reassembly: in vitro recombination for mo-lecular evolution. Proc. Natl. Acad. Sci. USA 91, 10747–10751.
Usón, I., Bes, M. T., Sheldrick, G. M., Schneider, T. R., Hartsch, T. and Fritz, H. J. (1997). X-ray crystallography reveals stringent conservation of protein fold after removal of the only disulfide bridge from a stabilized immunoglobulin variable domain. Fold. Des. 2, 357–361.
Virnekäs, B., Ge, L., Plückthun, A., Schneider, K. C., Wellnhofer, G. and Moroney, S. E. (1994). Trinucleotide phosphoramidites: ideal reagents for the synthesis of mixed oligonucleotides for random mutagenesis. Noel. Acids Res. 22, 5600–5607.
Wagner, S. D. and Neuberger, M. S. (1996), Somatic hypermutation of immunoglobulin genes. Annu. Rev. Immunol. 14, 441–457.
Warbrick, E. (1997). Two’s company, three’s crowd: the yeast two hybrid system for mapping molecular interactions. Structure 5, 13–17.
Ward, W. H., Timms, D. and Fersht, A. R. (1990). Protein engineering and the study of structure-function relationships in receptors. Trends Pharmacol. Sci. 11, 280–284.
Wells, J. A., Cunningham, B. C., Fuh, G., Lowman, H. B., Bass, S. H., Mulkerrin, M. G., Ultsch, M. and deVos, A. M. (1993). The molecular basis for growth hormone-receptor interactions. Recent Prog. Horn. Res. 48, 253–275.
Winter, G., Griffiths, A. D., Hawkins, R. E. and Hoogenboom, H. R. (1994). Making antibodies by phage display technology. Annu. Rev. Immunol. 12, 433–455.
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Plückthun, A. (1998). Studying Protein Structure and Function by Directed Evolution. In: Jardetzky, O., Lefèvre, JF., Holbrook, R.E. (eds) Protein Dynamics, Function, and Design. NATO ASI Series, vol 301. Springer, Boston, MA. https://doi.org/10.1007/978-1-4615-4895-9_4
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