Selecting proteins with improved stability by a phage-based method

Nature Biotechnology

Volumn 16, Issue 10, 1998, Pages 955-960

  Sieber, Volker ^a   Plückthun, Andreas ^b   Schmid, Franz X ^a  

^a UNIVERSITY OF BAYREUTH   (Germany)

^b UNIVERSITY OF ZURICH   (Switzerland)

Author keywords

Directed evolution; Phage display; Protein stabilization; Proteolysis

Indexed keywords

BETA LACTAMASE; SOLVENT;

ARTICLE; EVOLUTION; LIGAND BINDING; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN DEGRADATION; PROTEIN STABILITY; PROTEIN VARIANT; SITE DIRECTED MUTAGENESIS;

BASE SEQUENCE; DNA PRIMERS; DNA-BINDING PROTEINS; HYDROLYSIS; INOVIRUS; MUTAGENESIS, SITE-DIRECTED; RIBONUCLEASE T1; THERMODYNAMICS; VIRAL FUSION PROTEINS;

EID: 0031729179     PISSN: 10870156     EISSN: None     Source Type: Journal    
DOI: 10.1038/nbt1098-955     Document Type: Article

References (45)

1. Rubingh, D.N. 1997. Protein engineering from a bioindustrial point of view. Curr. Opin. Biotechnol. 8:417-422.
2. Kast, P. and Hilvert, D. 1997. 3D structural information as a guide to protein engineering using genetic selection, Curr, Opin, Struct, Biol. 7:470-479.
3. Kuchner, O. and Arnold, F.H. 1997. Directed evolution of enzyme catalysts. Trends Biotechnol. 15:523-530.
4. Matsumura, M. and Alba, S. 1985. Screening for thermostable mutant of kanamycin nucleotidyltransferase by the use of a transformation system for a thermophile, Bacillus stearothermophilus. J. Biol. Chem. 260:15298-15303.
5. Dunn, I.S. Phage display of proteins. 1996. Curr Opin. Biotechnol. 7:547-553.
6. Jung, S. and Plückthun, A. 1997. Improving in vivo folding and stability of a single-chain Fv antibody fragment by loop grafting. Protein Eng. 10:959-966.
7. Bothmann, H. and Plückthun, A. 1998. Selection for a periplasmic factor improving phage display and functional periplasmic expression. Nat. Biotechnol. 18:376-380.
8. Deng, S.J., MacKenzie, C.R., Sadowska, J., Michniewicz, J., Young, N.M., Bundle, D.R. 1994. Selection of antibody single-chain variable fragments with improved carbohydrate binding by phage display. J. Biol. Chem. 269:9533-9538.
9. Jackson, J.R., Sathe, G., Rosenberg, M., and Sweet, R. 1995. In vitro antibody maturation. Improvement of a high affinity, neutralizing antibody against IL-1 beta. J. Immunol. 154:3310-3319.
10. Proba, K., Worn, A., Honegger, A., and Plückthun, A. 1998. Antibody scFv fragments without disulfide bonds made by molecular evolution. J. Mol. Biol. 275:245-253.
11. Spada, S., Honegger, A., and Plückthun, A. 1998. Reproducing the natural evolution of protein structural features with the selectively infective phage (SIP) technology. J. Mol. Biol. In press.
12. Parsell, D. and Sauer, R. 1989. The structural stability of a protein is an Important determinant of Its proteolytic susceptibiliy in Escherichia coli. J. Biol. Chem. 284:7590-7595.
13. Kolmar, H., Frisch, C., Götze, K., and Fritz, H.J. 1995. Immunoglobulin mutant library genetically screened for folding stability exploiting bacterial signal transduction. J. Mol. Biol. 251:471-476.
14. Sauer, R.T. 1996. Protein folding from a combinatorial perspective. Fold. Des. 1:R27-R30.
15. Fontana, A., Polverino de Laureto, P., De Fllippis, V., Scaramella, E., and Zambonin, M. 1997. Probing the partly folded states of proteins by limited proteolysis. Fold. Des. 2:R17-R26.
16. Crissman, J.W. and Smith, G.P. 1984. Gene-III protein of filamentous phage: evidence for a carboxyl-terminal domain with a role in morphogenesis. Virology 132:445-455.
17. Stengele, I., Brosa, P., Garces, X., Giray, J., and Rasched, I. 1990. Dissection Of functional domains in phage fd adsorption protein. Discrimination between attachment and penetration sites. J. Mol. Biol. 212:143-149.
18. Krebber, C., Spada, S., Desplancq, D., Krebber, A., Ge, L., and,Plückthun, A. 1997 Selectively-infective phage (SIP): a mechanistic dissection of a novel in Vivo selection for protein-ligand interactions. J. Mol. Biol. 268:607-618.
19. Spada, S. and Plückthun, A. 1997. Selectively infective phage (SIP) technology: a novel method for in vivo selection of interacting protein-ligand pairs. Nat. Med. 3:694-696.
20. Schwind, P., Kramer, H., Kremser, A., Ramsberger, U., and Rasched, I. 1992. Subtilisin removes the surface layer of the phage fd coat. Eur. J. Biochem. 210:431-436.
21. Kremser, A. and Rasched, I. 1994. The adsorption protein of filamentous phage fd: assignment of its disulfide fridges and identification of the domain incorporated in the coat. Biochemistry 33:13954-13958.
22. 22: Salivar, W.O., Tzagoloff, H., and Pratt D. 1964. Some physical-chemical and biological properties of the rod-shaped coliphage M13. Virology 24:359-371.
23. Willimsky, G., Bang, H., Fischer, G., and Marahiel, M.A. 1992. Characterization of cspB, a Bacillus subtilis inducible cold shock gene affecting cell viability at low temperature. J. Bacteriol. 174:6326-6335.
24. Schindler, T. and Schmid, F.X. 1995. Thermodynamic properties of an extremely rapid protein folding reaction. Biochemistry 36:16833-16842.
25. Frech, C., Wunderlich, M., Glockshuber, R., and Schmid, F.X. 1996. Competition between DsbA-mediated oxidation and conformational folding of RTEM1 beta-lactamase. Biochemistry 36:11386-11395.
26. Oobatake, M., Takahashi, S., and Ooi, T. 1979. Conformational stability of ribonuclease T1. I. Thermal denaturation and effects of salts. J. Biochem. 86:55-63.
27. Pace, C.N., Grimsley, G.R., Thomson, J.A., and Barnett, B.J. 1988. Conformational stability and activity of ribonuclease T1 with zero, one, and two Intact disulfide bonds. J. Biol. Chem. 263:11820-11825.
28. Mücke, M. and Schmid, F.X. 1994. Intact disulfide bonds decelerate the folding of ribonuclease T1. J. Mol. Biol. 239:713-725.
29. Shirley, B.A., Stanssens, P., Hahn, U., and Pace, C.N. 1992. Contribution of hydrogen bonding to the Conformational stability of ribonuclease T1. Biochemistry 31:725-732.
30. Walter, S., Hubner, B., Hahn, U., and Schmid, F.X. 1995. Destabilization of a protein helix by electrostatic interactions. J. Mol. Biol. 252:133-143.
31. Kiefhaber, T., Grunert, H.-P., Hahn, U., and Schmid, F.X. 1990. Replacement of a cis proline simplifies the mechanism of ribonuclease T1 folding, Biochemistry 29:6475-6480.
32. Ikehara, M., Ohtsuka, E., Tokunaga, T. Nishikawa, S., Uesugi, S., Tanaka, T. et al. 1986. Inquiries into the structure-function relationship of ribonuclease T1 using chemically synthesized coding sequences. Proc. Natl. Acad. Sci. USA 83:4695-4699.
33. Smith, G.P. and Scott, J.K. 1993. Libraries of peptides and proteins displayed on filamentous phage. Methods Enzymol, 217:228-257.
34. Greener, A., Callahan, M., and Jerpseth, B. 1997. An efficient random mutagenesis technique using an E. coli mutator strain. Mol. Biotechnol. 7:189-195.
35. Geiger, T. and Clarke, S. 1987. Deamidation, isomerization, and racemization at asparaginyl and aspartyl residues in peptides. Succinimide-linked reactions that contribute to protein degradation. J. Biol. Chem. 282:785-794.
36. Stemmer, W.R 1994. DNA shuffling by random fragmentation and reassembly: in vitro recombination for molecular evolution. Proc. Natl. Acad. Sci. USA 91:10747-10751.
37. Crameri, A., Cwirla, S., and Stemmer, W.R 1996. Construction and evolution of antibody-phage libraries by DNA shuffling. Nat. Med. 2:100-102.
38. Zhao, H., Giver, L., Shao, Z., Affholter, J.A., and Arnold, F.H. 1998. Molecular evolution by staggered extension process (StEP) in vitro recombination. Nat Biotechnol. 16:258-261.
39. Zhou, H.X., Hoess, R.H., and DeGrado, W.F, 1996. In vitro evolution of thermodynamically stable turns. Nat. Struct. Biol. 3:446-451.
40. Skinner, M.M. and Terwilliger, T.C. 1996. Potential use of additivity of mutational effects in simplifying protein engineering. Proc. Natl. Acad. Sci. USA 93:10753-10757.
41. Quaas, R., Grunert, H.-P., Kimura, M., and Hahn, U. 1988. Expression of ribonuclease T1 in Escherichia coli and rapid purification of the enzyme. Nucleosides & Nucleotides 7:619-623.
42. Sambrook, J., Fritsch, E.F., and Maniatis, T. 1989. Molecular cloning - a laboratory manual. Cold Spring Harbor Laboratory press, Cold Spring Harbor, New York.
43. Horton, R.M, and Pease, L.R. 1991. Recombination and mutagenesis of DNA sequences using PCR, pp. 217-247 in Directed mutagenesis - a practical approach. McPherson, M.J. (ed). IRL Press, Oxford, UK.
44. Mayr, L.M. and Schmid, F.X. 1993. A purification method for labile variants of ribonuclease T1. Protein Expr. Purif. 4:52-58.
45. Santoro, M.M. and Bolen, D.W. 1988. Unfolding free energy changes determined by the linear extrapolation method. 1. Unfolding of phenylmethanesulfonyl α-chymotrypsin using different denaturants. Biochemistry 27:8063-8068.