New strategies of protein engineering - Directed evolution of enzyme in vitro

Chinese Science Bulletin

Volumn 44, Issue 18, 1999, Pages 1641-1648

  Zhang, Hongying ^a   Kong, Xiangduo ^a   Zhang, Jin ^a  

^a JILIN UNIVERSITY   (China)

Author keywords

Directed evolution; Enzyme; Protein engineering

Indexed keywords

EID: 0003398810     PISSN: 10016538     EISSN: None     Source Type: Journal    
DOI: 10.1007/BF03183480     Document Type: Review

References (54)

1. You, L., Arnold, F. H., Directed evolution of subtilisin E in Bacillus subtilis to enhance total activity in aqueous dimethylformamide, Protein Eng., 1996, 9: 77.
2. Leung, D. W., Chen, E., Goeddel, D. V., A method for random mutagenesis of a defined DNA segment using a modified polymerase chain reaction, Technique, 1989, 1: 11.
3. Cadwell, R. C., Joyce, G. F., Mutagenic PCR, New York: Cold Spring Harbor Laboratory Press, 1994.
4. Chen, K., Arnold, F. H., Enzyme engineering for nonaqueous solvents: random mutagenesis to enhance activity of subtilisin E inpolar organic media, Bio/Technology, 1991, 9: 1073.
5. Chen, K., Arnold, F. H., Tuning the activity of an enzyme for unusual environments: sequential random mutagenesis of subtilisin E for catalysis in dimethylformamide, Proc. Natl. Acad. Sci. USA, 1993, 90: 5618.
6. Stemmer, W. P. C., DNA shuffling by random fragmentation and reassembly-in vitro recombination for molecular evolution, Proc. Natl. Acad. Sci. USA, 1994a, 91: 10747.
7. Stemmer, W. P. C., Rapid evolution of a protein in vitro by DNA shuffling, Nature, 1994b, 340: 389.
8. Fisch, I., Kontermann, R. E., Finnern, R. et al., A strategy of exon shuffling for making large peptide repertories displayed on filamentous bacteriophage, Proc. Natl. Acad. Sci. USA, 1996, 93: 7761.
9. Stemmer, W. P. C., Searching sequence space using recombination to search more efficiently and thoroughly instead of making bigger combinational libraries, Bio/Technology, 1995, 13: 549.
10. Crameri, A. C., Raillard, S., Stemmer, W. P. C., DNA shuffling of a family of genes from diverse species accelerates directed evolution, Nature, 1997, 391: 288.
11. Zhang, J., Dawes, G., Stemmer, W. P. C., Evolution of an effective fucosidase from a galactosidase by DNA shuffling, Proc. Natl. Acad. Sci. USA, 1997, 94: 4504.
12. Moore, J. C., Arnold, F. H., Directed evolution of a para-nitrobenzyl esterase, Nature Biotechnol., 1996, 14: 458.
13. Moore, J. C., Jin, H. M., Kuchner, O. et al., Strategies for the in vitro evolution of protein function: enzyme evolution by random recombination of improved sequences, J. Mol. Biol., 1997, 272: 336.
14. Arnold, F. H., Directed evolution: creating biocatalysis for the future, Chemical. Eng. Sci., 1996, 51: 5091.
15. 2+, Nucleic Acids Research, 1995, 23: 3067.
16. Zhao, H. M., Arnold, F. H., Optimization of DNA shuffling for high-fidelity recombination, Nucleic Acids Research, 1997, 25: 1307.
17. Nixon, A. E., Ostermeier, M., Benkovic, S. J. et al., Hybrid enzyme: manipulating enzyme design, Trends Biotech., 1998, 16: 258.
18. Venekei, I., Szilagyi, L., Graf, L. et al., Attempt to convert chymotrypsin to trypsin, FEBS Lett., 1996, 379: 143.
19. Ballinger, M. D., Tom, J., Wells, J. A., Furilisin: a variant of subtilisin BPN' engineering for cleaving tribasic substrates, Biochem., 1996, 35: 13579.
20. Hecht, M. H., Strategies for the design of novel proteins in Protein Engineering and Design (ed. Carey, P. R.), San Diego: Academic Press, 1996.
21. Nixon, A. E., Werren, M. S., Benkovic, S. J., Assembly of an active enzyme by the linkage of two protein modules, Proc. Natl. Acad. Sci. USA, 1997, 94: 1069.
22. Kimura, N., Nishi, A., Goto, M. et al., Functional analyses of a variety of chimeric dioxygenases constructed from two biphenyl dioxygenases that are similar structurally but different functionally, J. Bacteriol., 1997, 179(12): 3936.
23. Cahhon, E. B., Lindqvist, Y., Schneider, G. et al., Resign of soluble fatty acid desaturases from plants for altered substrate specificity and double bond position, Proc. Natl. Acad. Sci. USA., 1997, 94: 4872.
24. Back, K., Chappell, J., Identifying functional domains within terpene cyclases using a domain-swapping strategy, Proc. Natl. Acad. Sci. USA., 1996, 93: 6841.
25. Cerdan, P., Rekik, M., Harayama, S., Substrate specificity differences between two catechl 2,3-dioxygenses encoded by the TOL and NAH plasmids from Psendomonas putida, Eur. J. Biochem., 1995, 229: 113.
26. Shao, Z., Zhao, H., Giver, L. et al., Random-priming in vitro recombination: an effective tool for directed evolution, Nucl. Acids Res., 1998, 26: 681.
27. Zhao, H., Giver, L., Shao, Z. et al., Molecular evolution by staggered extension process (StEP) in vitro recombination, Nature Biotech, 1998, 16: 258.
28. Hu, W. S., Bowman, E. H., Delviks, K. A., Homologous recombination occurs in a distinct retroviral subpopulation and exhibits high negative interference, J. Virol., 1997, 71: 6028.
29. Zhang, J., Li, Z. Q., Zhang, H. Y., An enzymatic method for random-(site-specific) mutagenesis of ginseng peptide gene in vitro, Chinese Biochem. J. (in Chinese), 1992, 8(1): 115.
30. Zhang, H. Y., Li, Z. Q., Zhang, J. et al., Enzymatic generation of libraries in vitro for random mutagenesis of the aspartase gene, Chinese Science Buletin, 1992, 37: 598
31. Zhang, H. Y., Zhang, J., Lin, L. et al., Enhancement of the stability and activity of aspartase by random and site-directed mutagenesis, BBRC, 1993, 192(1): 15.
32. Zhang, J., Zhang, H. Y., Xiao, P. W. et al., Studies and application of aspartase, Progress of Natural Science, 1997, 7(3): 266.
33. Zhao, H., Arnold, F. H., Functional and nonfunctional mutations distinguished by random recombination of homologous genes, Proc. Natl. Acad. Sci. USA, 1997, 94: 7997.
34. Zhao, H., Arnold, F. H., Combinatorial protein design: strategies for screening protein libraries, Curr. Opin. Struct. Biol., 1997, 7: 480.
35. Kast, P., Hilvert, D., 3D structural information as a guide to protein engineering using genetic selection, Curr. Opin. Struct. Biol., 1997, 7: 470.
36. Venekei, I., Hedstrom, L., Rutter, W. J., A rapid and effective procedure for screening protease mutants, Protein Eng., 1996, 9: 85.
37. O'Neil, K. T., Hoess, R. H., Phage display: protein engineering by directed evolution, Curr. Opin. Struct. Biol., 1995, 5: 443.
38. Roberts, B. L., Markland, W., Arthur, C. et al., Directed evolution of a protein: selection of potent neutrophil elastase inhibitors displayed on M13 fusion phage, Proc. Natl. Acad. Sci. USA, 1992, 89: 2429.
39. Manes, J., Pluckthun, A., In vitro selection and evolution of functional proteins by using ribosome display, Proc. Natl. Acad. Sci. USA, 1997, 94: 4937.
40. Warren, M. S., Marolewski, A. E., Beukovic, S. J., A rapid screen of active site mutants in glycinamide ribonucleotide, Biochem., 1996, 35: 8855.
41. Crameri, A., Whitehorn, E. A., Tale, E. et al., Improved green fluorescent protein by molecular evolution using DNA shuffling, Nature Biotechnol, 1996, 14: 315.
42. Harayama, S., Artificial evolution by DNA shuffling, Trends Biotech., 1998, 16: 76.
43. Shao, Z., Arnold, F. H., Engineering new function and altering existing functions, Curr. Opin. Struct. Biol., 1996, 6: 513.
44. Kuchner, O., Arnold, F. H., Directed evolution of enzyme catalysts, Trends Biotech., 1997, 15: 523.
45. Crameri, A., Dawes, G., Rodrigues, E. J. et al., Molecular evolution of an arsenate detoxification pathway by DNA shuffling, Nature Biotechnol., 1997, 15: 436.
46. Ewing, D., The directed evolution of radiation resistance in E. coli, Biochem. Biophys. Res. Commun., 1995, 216: 549.
47. Richaud, C., Mengin-Lecreulx, D., Pochet, S. et al., Directed evolution of biosynthetic pathways, J. Biol. Chem., 1993, 268: 26827.
48. Matcham, G. W., Bowen, A. R. S., Biocatalysis for chiral intermediates: meeting commercial and technical challenges, Chem. Today, 1996, 14: 20.
49. Crameri, A., Cwirla, S., Stemmer, W. P. C., Construction and evolution of antibody-phage libraries by DNA shuffling, Nature Med., 1996, 2: 100.
50. He, Y. Y., Stockley, P. G., Gold, L. In vitro evolution of the DNA binding site of Escherichia coli methionine repressor, Met. J. J. Mol. Biol., 1996, 255: 55.
51. Strausberg, S. L., Alexander, P. A., Gallagher, D. T. et al., Directed evolution of subtilisin with calcium-independent stability, Biotechnology, 1995, 13: 669.
52. Black, M. E., Newcomb, T. G., Wilson, H. M. P. et al., Creation of drug specific HSV-1 thymidine kinase mutants for gene therapy, Proc. Natl. Acad. Sci. USA, 1996, 93: 3525.
53. Beaudry, A. A., Joyce, G. F., Directed evolution of an RNA enzyme, Science, 1992, 257: 635641.
54. Patten, P. A., Howard, R. J., Stemmer, W. P. C., Application of DNA shuffling to pharmaceuticals and vaccines, Curr. Opin. Biotech., 1997 8: 724.