Chapter 27: In Vitro Selection and Evolution of Protein–Ligand Interactions by Ribosome Display—References
Amstutz P., Pelletier J.N., Guggisberg A., Jermutus L., Cesaro-Tadic S., Zahnd C., and Plückthun A. 2002. In vitro selection for catalytic activity with ribosome display. J. Am. Chem. Soc. 124: 9396–9403.
Bass S., Gu Q., and Christen A. 1996. Multicopy suppressors of prc mutant Escherichia coli include two HtrA (DegP) protease homologs (HhoAB), DksA, and a truncated R1pA. J. Bacteriol. 178: 1154–1161.
Binz H.K., Stumpp M.T., Forrer P., Amstutz P., and Plückthun A. 2003. Designing repeat proteins: Well-expressed, soluble and stable proteins from combinatorial libraries of consensus ankyrin repeat proteins. J. Mol. Biol. 332: 489–503.
Binz H.K., Amstutz P., Kohl A., Stumpp M.T., Briand C., Forrer P., Grütter M.G., and Plückthun A. 2004. High-affinity binders selected from designed ankyrin repeat protein libraries. Nat. Biotechnol. 22: 575–582.
Boder E.T. and Wittrup K.D. 1997. Yeast surface display for screening combinatorial polypeptide libraries. Nat. Biotechnol. 15: 553–557.
Cadwell R.C. and Joyce G.F. 1992. Randomization of genes by PCR mutagenesis. PCR Methods Appl. 2: 28–33.
Chen H.Z. and Zubay G. 1983. Prokaryotic coupled transcription-translation. Methods Enzymol. 101: 674–690.
Chen Y., Wiesmann C., Fuh G., Li B., Christinger H.W., McKay P., de Vos A.M., and Lowman H.B. 1999. Selection and analysis of an optimized anti-VEGF antibody: Crystal structure of an affinity-matured Fab in complex with antigen. J. Mol. Biol. 293: 865–881.
Chien C.T., Bartel P.L., Sternglanz R., and Fields S. 1991. The two-hybrid system: A method to identify and clone genes for proteins that interact with a protein of interest. Proc. Natl. Acad. Sci. 88: 9578–9582.
Cull M.G. and Schatz P.J. 2000. Biotinylation of proteins in vivo and in vitro using small peptide tags. Methods Enzymol. 326: 430–440.
Dower W.J. and Cwirla S.E. 1992. Creating vast peptide expression libraries: Electroporation as a tool to construct plasmid libraries of greater than 109 recombinants. In Guide to electroporation and electrofusion (ed. D.C. Chang et al.), pp. 291–301. Academic Press, San Diego, California.
Fields S. and Song O. 1989. A novel genetic system to detect protein-protein interactions. Nature 340: 245–246.
Freedman R.B., Hawkins H.C., and McLaughlin S.H. 1995. Protein disulfide-isomerase. Methods Enzymol. 251: 397–406.
Georgiou G., Poetschke H.L., Stathopoulos C., and Francisco J.A. 1993. Practical applications of engineering gram-negative bacterial cell surfaces. Trends Biotechnol. 11: 6–10.
Gersuk G.M., Corey M.J., Corey E., Stray J.E., Kawasaki G.H., and Vessella R.L. 1997. High-affinity peptide ligands to prostate-specific antigen identified by polysome selection. Biochem. Biophys. Res. Commun. 232: 578–582.
Hajnsdorf E., Braun F., Haugel-Nielsen J., Le Derout J., and Régnier P. 1996. Multiple degradation pathways of the rpsO mRNA of Escherichia coli. RNase E interacts with the 5´ and 3´ extremities of the primary transcript. Biochimie 78: 416–424.
Hanes J. and Plückthun A. 1997. In vitro selection and evolution of functional proteins by using ribosome display. Proc. Natl. Acad. Sci. 94: 4937–4942.
Hanes J., Jermutus L., Schaffitzel C., and Plückthun A. 1999. Comparison of Escherichia coli and rabbit reticulocyte ribosome display systems. FEBS Lett. 450: 105–110.
Hanes J., Schaffitzel C., Knappik A., and Plückthun A. 2000. Picomolar affinity antibodies from a fully synthetic naive library selected and evolved by ribosome display. Nat. Biotechnol. 18: 1287–1292.
Hanes J., Jermutus L., Weber-Bornhauser S., Bosshard H.R., and Plückthun A. 1998. Ribosome display efficiently selects and evolves high-affinity antibodies in vitro from immune libraries. Proc. Natl. Acad. Sci. 95: 14130–14135.
Hawkins R.E., Russell S.J., and Winter G. 1992. Selection of phage antibodies by binding affinity. Mimicking affinity maturation. J. Mol. Biol. 226: 889–896.
He M. and Taussig M.J. 1997. Antibody-ribosome-mRNA (ARM) complexes as efficient selection particles for in vitro display and evolution of antibody combining sites. Nucleic Acids Res. 25: 5132–5134.
He M., Menges M., Groves M.A., Corps E., Liu H., Brüggemann M., and Taussig M.J. 1999. Selection of a human anti-progesterone antibody fragment from a transgenic mouse library by ARM ribosome display. J. Immunol. Methods 231: 105–117.
Irving R.A., Kortt A.A., and Hudson P.J. 1996. Affinity maturation of recombinant antibodies using E. coli mutator cells. Immunotechnology 2: 127–143.
Jermutus L., Honnegger A., Schwesinger F., Hanes J., and Plückthun A. 2001. Tailoring in vitro evolution for protein affinity or stability. Proc. Natl. Acad. Sci. 98: 75–80.
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.
Knappik A., Ge L., Honegger A., Pack P., Fischer M., Wellnhofer G., Hoess A., Wölle J., Plückthun A., and Virnekäs B. 2000. Fully synthetic human combinatorial antibody libraries (HuCAL) based on modular consensus frameworks and CDRs randomized with trinucleotides. J. Mol. Biol. 296: 57–86.
Krebber A., Bornhauser S., Burmester J., Honegger A., Willuda J., Bosshard H.R., and Plückthun A. 1997. 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.
Lamla T. and Erdmann V.A. 2003. Searching sequence space for high-affinity binding peptides using ribosome display. J. Mol. Biol. 329: 381–388.
Lee M.S., Kwon M.H., Kim K.H., Shin H.J., Park S., and Kim H.I. 2004. Selection of scFvs specific for HBV DNA polymerase using ribosome display. J. Immunol. Methods 284: 147–157.
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.
Matsuura T. and Plückthun A. 2003. Selection based on the folding properties of proteins with ribosome display. FEBS Lett. 539: 24–28.
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. 91: 9022–9026.
Mattheakis L.C., Dias J.M., and Dower W.J. 1996. Cell-free synthesis of peptide libraries displayed on polysomes. Methods Enzymol. 267: 195–207.
Plückthun A., Schaffitzel C., Hanes J., and Jermutus L. 2000. In vitro selection and evolution of proteins. Adv. Protein Chem. 55: 367–403.
Pokrovskaya I.D. and Gurevich V.V. 1994. In vitro transcription: Preparative RNA yields in analytical scale reactions. Anal. Biochem. 220: 420–423.
Pratt J.M. 1984. Coupled transcription-translation in prokaryotic cell-free systems. IRL Press, Oxford, United Kingdom.
Ramachandiran V., Kramer G., and Hardesty B. 2000. Expression of different coding sequences in cell-free bacterial and eukaryotic systems indicates translational pausing on Escherichia coli ribosomes. FEBS Lett. 482: 185–188.
Ryabova L.A., Desplancq D., Spirin A.S., and Plückthun A. 1997. Functional antibody production using cell-free translation: Effects of protein disulfide isomerase and chaperones. Nat. Biotechnol. 15: 79–84.
Sambrook J. and Russell D.W. 2001. Molecular cloning: A laboratory manual, 3rd edition. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
Schaffitzel C., Berger I., Postberg J., Hanes J., Lipps H.J., and Plückthun A. 2001. In vitro generated antibodies specific for telomeric guanine-quadruplex DNA react with Stylonychia lemnae macronuclei. Proc. Natl. Acad. Sci. 98: 8572–8577.
Schwesinger F., Ros R., Strunz T., Anselmetti D., Güntherodt H.J., Honegger A., Jermutus L., Tiefenauer L., and Plückthun A. 2000. Unbinding forces of single antibody-antigen complexes correlate with their thermal dissociation rates. Proc. Natl. Acad. Sci. 97: 9972–9977.
Smith G. P. 1985. Filamentous fusion phage: Novel expression vectors that display cloned antigens on the virion surface. Science 228: 1315–1317.
Stemmer W.P. 1994. Rapid evolution of a protein in vitro by DNA shuffling. Nature 370: 389–391.
Stumpp M.T., Forrer P., Binz H.K., and Plückthun A. 2003. Designing repeat proteins: Modular leucine-rich repeat protein libraries based on the mammalian ribonuclease inhibitor family. J. Mol. Biol. 332: 471–487.
Takahashi F., Ebihara T., Mie M., Yanagida Y., Endo Y., Kobatake E., and Aizawa M. 2002. Ribosome display for selection of active dihydrofolate reductase mutants using immobilized methotrexate on agarose beads. FEBS Lett. 514: 106–110.
Wade H.E. and Robinson H.K. 1966. Magnesium ion-independent ribonucleic acid depolymerases in bacteria. Biochem. J. 101: 467–479.
Weichhart T., Horky M., Sollner J., Gangl S., Henics T., Nagy E., Meinke A., von Gabain A., Fraser C.M., Gill S.R., Hafner M., and von Ahsen U. 2003. Functional selection of vaccine candidate peptides from Staphylococcus aureus whole-genome expression libraries in vitro. Infect. Immun. 71: 4633–4641.
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.
Yang W.P., Green K., Pinz-Sweeney S., Briones A.T., Burton D.R., and Barbas C.F., III. 1995. CDR walking mutagenesis for the affinity maturation of a potent human anti-HIV-1 antibody into the picomolar range. J. Mol. Biol. 254: 392–403.
Yau K.Y., Groves M.A., Li S., and Sheedy C. 2003. Selection of hapten-specific single-domain antibodies from a non-immunized llama ribosome display library. J. Immunol. Methods 281: 161–175.
Zaccolo M., Williams D.M., Brown D.M., and Gherardi E. 1996. An approach to random mutagenesis of DNA using mixtures of triphosphate derivatives of nucleoside analogues. J. Mol. Biol. 255: 589–603.
Zahnd C., Spinelli S., Luginbühl B., Amstutz P., Cambillau C., and Plückthun A. 2004. 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.
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