Comparison of random mutagenesis and semi-rational designed libraries for improved cytochrome P450 BM3-catalyzed hydroxylation of small alkanes

Protein Engineering, Design and Selection

Volumn 25, Issue 4, 2012, Pages 171-178

  Chen, Mike M Y ^a   Snow, Christopher D ^b   Vizcarra, Christina L ^a,c   Mayo, Stephen L ^a,d   Arnold, Frances H ^a  

^a California Institute of Technology   (United States)

^b Department of Chemical and Biological Engineering and School of Biomedical Engineering   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

alkane hydroxylation; CH activation; directed evolution; P450 enzymes; semi rational library design

Indexed keywords

ACTIVE SITE RESIDUES; AMINO ACID SUBSTITUTION; BINDING POCKETS; C-H ACTIVATION; CATALYTIC TURNOVER; COMPUTATIONAL DESIGN; CYTOCHROME P450 BM3; DIMETHYL ETHERS; DIRECTED EVOLUTION; RANDOM MUTAGENESIS; SEMI-RATIONAL LIBRARY DESIGN; SEQUENCE SPACE;

ALGORITHMS; AMINO ACIDS; CHEMICAL ACTIVATION; DIAGNOSIS; ETHANE; FUELS; HYDROXYLATION; LIBRARIES; MUTAGENESIS; PROPANE;

RATIONAL FUNCTIONS;

ALKANE; AMINO ACID; CYTOCHROME P450 BM3; ENZYME VARIANT; ETHANE; PROPANE;

ALGORITHM; AMINO ACID SUBSTITUTION; ARTICLE; COMBINATORIAL SITE SATURATION MUTAGENESIS; COMPARATIVE STUDY; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME ENGINEERING; HYDROXYLATION; MOLECULAR LIBRARY; MUTAGENESIS; PRIORITY JOURNAL;

ALKANES; CATALYSIS; CATALYTIC DOMAIN; CYTOCHROME P-450 ENZYME SYSTEM; GENE LIBRARY; HYDROXYLATION; MODELS, MOLECULAR; MUTAGENESIS, SITE-DIRECTED;

EID: 84863337761     PISSN: 17410126     EISSN: 17410134     Source Type: Journal    
DOI: 10.1093/protein/gzs004     Document Type: Article

References (40)

1. Arnold, F. H. (1998) Acc. Chem. Res., 31, 125-131.
2. Arnold, G. E. and Ornstein, R. L. (1997) Biophys. J., 73, 1147-1159.
3. Cadwell, R. C. and Joyce, G. F. (1994) PCR-Methods Appl., 3, S136-S140.
4. Chefson, A. and Auclair, K. (2006) Mol. Biosyst., 2, 462-469.
5. Damborsky, J. and Brezovsky, J. (2009) Curr. Opin. Chem. Biol., 13, 26-34.
6. de Montellano, P. R. O. (1986) Cytochrome P450, 1st edn, Plenum Publishing Corp., New York.
7. de Montellano, P. R. O. (2010) Chem. Rev., 110, 932-948.
8. Denisov, I. G., Makris, T. M., Sligar, S. G. and Schlichting, I. (2005) Chem. Rev., 105, 2253-2277.
9. Drummond, D. A., Iverson, B. L., Georgiou, G. and Arnold, F. H. (2005) J. Mol. Biol., 350, 806-816.
10. Fasan, R., Chen, M. M., Crook, N. C. and Arnold, F. H. (2007) Angew. Chem. Int. Ed., 46, 8414-8418.
11. Fasan, R., Meharenna, Y. T., Snow, C. D., Poulos, T. L. and Arnold, F. H. (2008) J. Mol. Biol., 383, 1069-1080.
12. Geddie, M. and Matsumura, I. (2004) J. Mol. Biol., 279, 26462-26468.
13. Glieder, A., Farinas, E. T. and Arnold, F. H. (2002) Nat. Biotechnol., 20, 1135-1139.
14. Haines, D. C., Tomchick, D. R., Machius, M. and Peterson, J. A. (2001) Biochemistry, 40, 13456-13465.
15. Hayes, R. J., Bentzien, J., Ary, M. L., Hwang, M. Y., Jacinto, J. M., Vielmetter, J., Kundu, A. and Dahiyat, B. I. (2002) Proc. Natl Acad. Sci. USA, 99, 15926-15931.
16. Isin, E. M. and Guengerich, F. P. (2007) Biochim. Biophys. Acta-Gen Subj., 1770, 314-329.
17. Kadkhodayan, S., Coulter, E. D., Maryniak, D. M., Bryson, T. A. and Dawson, J. H. (1995) J. Biol. Chem., 270, 28042-28048.
18. Kunkel, T. A., Roberts, J. D. and Zakour, R. A. (1987) Methods Enzymol., 154, 367-382.
19. Lassila, J. K. (2010) Curr. Opin. Chem. Biol., 14, 676-682.
20. Lewis, J. C., Bastian, S., Bennett, C. S., Fu, Y., Mitsuda, Y., Chen, M. M., Greenberg, W. A., Wong, C. H. and Arnold, F. H. (2009) Proc. Natl Acad. Sci. USA, 106, 16550-16555.
21. Lewis, J. C., Mantovani, S. M., Fu, Y., Snow, C. D., Komor, R. S., Wong, C. H. and Arnold, F. H. (2010) Chembiochem, 11, 2502-2505.
22. Li, Q. S., Ogawa, J., Schmid, R. D. and Shimizu, S. (2001) Appl. Environ. Microbiol., 67, 5735-5739.
23. Meinhold, P., Peters, M. W., Hartwick, A., Hernandez, A. R. and Arnold, F. H. (2006) Adv. Synth. Catal., 348, 763-772.
24. Morant, M., Bak, S., Moller, B. L. and Werck-Reichhart, D. (2003) Curr. Opin. Biotechnol., 14, 151-162.
25. O'Maille, P. E., Bakhtina, M. and Tsai, M. D. (2002) J. Mol. Biol., 321, 677-691.
26. Omura, T. and Sato, R. (1964) J. Biol. Chem., 239, 2370-2374.
27. Ost, T. W. B., Miles, C. S., Murdoch, J., Cheung, Y. F., Reid, G. A., Chapman, S. K. and Munro, A. W. (2000) FEBS Lett., 486, 173-177.
28. Otey, C. and Joern, J. M. (2003) In Arnold, F. H. and Georgiou, G. (eds), Methods in Molecular Biology. Humana Press, Totowa, pp. 141-148.
29. Patrick, W. M., Firth, A. E. and Blackburn, J. M. (2003) Protein Eng., 16, 451-457.
30. Peters, M. W., Meinhold, P., Glieder, A. and Arnold, F. H. (2003) J. Am. Chem. Soc., 125, 13442-13450.
31. Pylypenko, O. and Schlichting, I. (2004) Annu. Rev. Biochem., 73, 991-1018.
32. Reidhaarolson, J. F. and Sauer, R. T. (1988) Science, 241, 53-57.
33. Rohl, C. A., Strauss, C. E. M., Misura, K. M. S. and Baker, D. (2004) Numerical Computer Methods, Partt D, Academic Press Inc, San Diego, p. 66.
34. Schlichting, I., Berendzen, J., Chu, K., et al. (2000) Science, 287, 1615-1622.
35. Schwaneberg, U., Sprauer, A., Schmidt-Dannert, C. and Schmid, R. D. (1999) J. Chromatogr. A, 848, 149-159.
36. Treynor, T. P., Vizcarra, C. L., Nedelcu, D. and Mayo, S. L. (2007) Proc. Natl Acad. Sci. USA, 104, 48-53.
37. Urlacher, V. B. and Eiben, S. (2006) Trends Biotechnol., 24, 324-330.
38. Widersten, M., Hansson, L. O., Tronstad, L. and Mannervik, B. (2000) Methods Enzymol., 328, 389-404.
39. You, L. and Arnold, F. H. (1996) Protein Eng., 9, 77-83.
40. Zhang, K. D., El Damaty, S. and Fasan, R. (2011) J. Am. Chem. Soc., 133, 3242-3245.