Learning from directed evolution: Further lessons from theoretical investigations into cooperative mutations in lipase enantioselectivity

ChemBioChem

Volumn 8, Issue 1, 2007, Pages 106-112

  Reetz, Manfred T ^a   Puls, Michael ^b   Carballeira, José Daniel ^a   Vogel, Andreas ^a   Jaeger, Karl Erich ^b   Eggert, Thorsten ^b   Thiel, Walter ^a   Bocola, Marco ^a   Otte, Nikolaj ^a  

^a MAX PLANCK INSTITUT FÜR KOHLENFORSCHUNG   (Germany)

^b HEINRICH HEINE UNIVERSITY   (Germany)

Author keywords

Directed evolution; Enantioselectivity; Kinetic resolution; Lipases; Molecular modeling

Indexed keywords

ENZYME VARIANT; TRIACYLGLYCEROL LIPASE;

ARTICLE; CHEMICAL STRUCTURE; ENANTIOSELECTIVITY; ENZYME KINETICS; EVOLUTION; MUTATION; PRIORITY JOURNAL; PSEUDOMONAS AERUGINOSA;

CATALYSIS; CRYSTALLOGRAPHY, X-RAY; DIRECTED MOLECULAR EVOLUTION; DNA PRIMERS; ESTERS; GENETIC TECHNIQUES; KINETICS; LIPASE; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR CONFORMATION; MUTATION; PSEUDOMONAS AERUGINOSA; SOFTWARE; STEREOISOMERISM;

PSEUDOMONAS AERUGINOSA;

EID: 33846302851     PISSN: 14394227     EISSN: 14397633     Source Type: Journal    
DOI: 10.1002/cbic.200600359     Document Type: Article

References (68)

1. Reviews: a) Methods in Molecular Biology, Vol. 231: Directed Evolution Library Creation: Methods and Protocols (Eds.: F. H. Arnold, G. Georgiou), Humana, Totowa, 2003;
2. b) Methods in Molecular Biology, Vol. 230: Directed Enzyme Evolution: Screening and Selection Methods (Eds.: F. H. Arnold, G. Georgiou), Humana, Totowa, 2003;
3. c) Directed Molecular Evolution of Proteins (Eds.: S. Brakmann, K. Johnsson), Wiley-VCH, Weinheim, 2002;
4. d) Enzyme Functionality-Design, Engineering, and Screening (Ed.: A. Svendsen), Marcel Dekker, New York, 2004;
5. e) K. A. Powell, S. W. Ramer, S. B. del Cardayré, W. P. C. Stemmer, M. B. Tobin, P. F. Longchamp, G. W. Huisman, Angew. Chem. 2001, 113, 4068-4080;
6. Angew. Chem. Int. Ed. 2001, 40, 3948-3959;
7. f) M. T. Reetz, K.-E. Jaeger, Top. Curr. Chem. 1999, 200, 31-57;
8. g) S. V. Taylor, P. Kast, D. Hilvert, Angew. Chem. 2001, 113, 3408-3436;
9. Angew. Chem. Int. Ed. 2001, 40, 3310-3335;
10. h) N. J. Turner, Trends Biotechnol. 2003, 21, 474-478;
11. i) S. Lutz, W. M. Patrick, Curr. Opin. Biotechnol. 2004, 15, 291-297.
12. Comprehensive review of directed evolution of enantioselective enzymes: M. T. Reetz in Advances in Catalysis, Vol. 49 (Eds.: B. C. Gates, H. Knözinger), Elsevier, San Diego, 2006, pp. 1-69.
13. a) M. T. Reetz, A. Zonta, K. Schimossek, K. Liebeton, K.-E. Jaeger, Angew. Chem. 1997, 109, 2961-2963;
14. Angew. Chem. Int. Ed. Engl. 1997, 36, 2830-2832;
15. b) K. Liebeton, A. Zonta, K. Schimossek, M. Nardini, D. Lang, B. W. Dijkstra, M. T. Reetz, K.-E. Jaeger, Chem. Biol. 2000, 7, 709-718;
16. c) M. T. Reetz, S. Wilensek, D. Zha, K.-E. Jaeger, Angew. Chem. 2001, 113, 3701-3703;
17. Angew. Chem. Int. Ed. 2001, 40, 3589-3591;
18. d) D. Zha, S. Wilensek, M. Hermes, K.-E. Jaeger, M. T. Reetz, Chem. Commun. 2001, 2664-2665;
19. e) M. T. Reetz, Tetrahedron 2002, 58, 6595-6602;
20. f) M. T. Reetz, Proc. Natl. Acad. Sci. USA 2004, 101, 5716-5722.
21. A. Crameri, W. P. C. Stemmer, BioTechniques 1995, 18, 194-196.
22. M. Nardini, D. A. Lang, K. Liebeton, K.-E. Jaeger, B. W. Dijkstra, J. Biol. Chem. 2000, 275, 31 219-31 225.
23. Examples of remote effects: a) S. Oue, A. Okamoto, T. Yano, H. Kagamiyama, J. Biol. Chem. 1999, 274, 2344-2349;
24. b) H. Zhao, F. H. Arnold, Protein Eng. 1999, 12, 47-53;
25. c) A. Iffland, P. Tafelmeyer, C. Saudan, K. Johnsson, Biochemistry 2000, 39, 10790-10798;
26. d) M. Kumar, K. K. Kannan, M. V. Hosur, N. S. Bhavesh, A. Chatterjee, R. Mittal, R. V. Hosur, Biochem. Biophys. Res. Commun. 2002, 294, 395-401;
27. e) P. K. Agarwal, S. R. Billeter, P. T. R. Rajagopalan, S. J. Benkovic, S. Hammes-Schiffer, Proc. Natl. Acad. Sci. USA 2002, 99, 2794-2799;
28. f) F. H. Arnold, P. L. Wintrode, K. Miyazaki, A. Gershenson, Trends Biochem. Sci. 2001, 26, 100-106;
29. g) G. P. Horsman, A. M. F. Liu, E. Henke, U. T. Bornscheuer, R. J. Kazlauskas, Chem. Eur. J. 2003, 9, 1933-1939.
30. M. Bocola, N. One, K.-E. Jaeger, M. T. Reetz, W. Thiel, ChemBioChem 2004, 5, 214-223.
31. a) R. D. Schmid, R. Verger, Angew. Chem. 1998, 110, 1694-1720;
32. Angew. Chem. Int. Ed. 1998, 37, 1608-1633;
33. b) Enzyme Catalysis in Organic Synthesis: A Comprehensive Handbook, Vols. I-III (Eds.: K. Drauz, H. Waldmann), 2nd ed., Wiley-VCH, Weinheim, 2002;
34. c) Biotransformations in Organic Chemistry (Ed.: K. Faber), 4th ed., Springer, Berlin, 2000;
35. d) S. H. Krishna, N. G. Karanth, Catal. Rev. Sci Eng. 2002, 44, 499-591;
36. e) P. Berglund, K. Huit in Stereoselective Biocatalysis (Eds.: R. N Patel, N. Ramesh), Marcel Dekker, New York, 2000, pp. 633-657;
37. f) M. T. Reetz, Curr. Opin. Chem. Biol. 2002, 6, 145-150;
38. g) QM-Studies of serine hydrolases: C.-H. Hu, T. Brinck, K. Hult, Int. J. Quantum Chem. 1997, 89-103;
39. h) J. Pleiss in Enzyme Functionality (Ed.: A. Svendsen), Marcel Dekker, New York, 2003, pp. 59-77;
40. i) Mechanism of serine proteases: L. Hedstrom, Chem. Rev. 2002, 102, 4501-4523.
41. S. Wilensek, PhD Dissertation, Ruhr-Universität Bochum (Germany), 2001.
42. M. T. Reetz, M. Bocola, J. D. Carballeira, D. Zha, A. Vogel, Angew. Chem. 2005, 117, 4264-4268;
43. Angew. Chem. Int. Ed. 2005, 44, 4192-4196.
44. All E values were derived by applying the formula of Sih et al.: C.-S. Chen, Y. Fujimoto, G. Girdaukas, C. J. Sih, J. Am. Chem. Soc. 1982, 104, 7294-7299.
45. a) M. R. Parikh, I. Matsumura, J. Mol. Biol. 2005, 352, 621-628;
46. b) W. M. Coco, W. E. Levinson, M. J. Crist, H. J. Hektor, A. Darzins, P. T. Pienkos, C. H. Squires, D. J. Monticello, Nat. Biotechnol. 2001, 19, 354-359;
47. c) M. Kikuchi, K. Ohnishi, S. Harayama, Gene 2000, 243, 133-137;
48. d) T. Eggert, M. T. Reetz, K.-E. Jaeger in Enzyme Functionality- Design, Engineering, and Screening (Ed.: A. Svendsen), Marcel Dekker, New York, 2004, pp. 375-390;
49. e) M. Kikuchi, K. Ohnishi, S. Harayama, Gene 2000, 243, 133-137;
50. f) D. A. Drummond, B. L. Iverson, G. Georgiou, F. H. Arnold, J. Mol. Biol. 2005, 350, 806-816;
51. g) M. Zaccolo, E. Gherardi, J. Mol. Biol. 1999, 285, 775-783;
52. h) T. S. Wong, D. Roccatano, M. Zacharias, U. Schwaneberg, J. Mol. Biol. 2006, 355, 858-871;
53. i) F. H. Arnold, Nat. Biotechnol. 2006, 24, 328-330.
54. Recent example of rational design in improving the enantioselectivity of a lipase: a) T. Ema, T. Fujii, M. Ozaki, T. Korenaga, T. Sakai, Chem. Commun. 2005, 4650-4651.
55. For reviews of rational design of enzymes based on site-specific mutagenesis, see: b) F. Cedrone, A. Ménez, E. Quéméneur, Curr. Opin. Struct. Biol. 2000, 10, 405-410;
56. c) J. L. Harris, C. S. Craik, Curr. Opin. Chem. Biol. 1998, 2, 127-132;
57. d) R. J. Kazlauskas, Curr. Opin. Chem. Biol. 2000, 4, 81-88;
58. e) Q.-S. Li, U. Schwaneberg, M. Fischer, J. Schmitt, J. Pleiss, S. Lutz-Wahl, R. D. Schmid, Biochim. Biophys. Acta 2001, 1545, 114-121.
59. M. T. Reetz, L.-W. Wang, M. Bocola, Angew. Chem. 2006, 118, 1258-1263; Erratum, 2556;
60. Angew. Chem. Int. Ed. 2006, 45, 1236-1241; Erratum, 2494.
61. A. D. MacKerell, Jr., D. Bashford, M. Bellott, R. L. Dunbrack, Jr., J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher III, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, M. Karplus, J. Phys. Chem. B 1998, 102, 3586-3616.
62. B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, M. Karplus, J. Comput. Chem. 1983, 4, 187-217.
63. The widely used QuikChange protocol (QuikChange Site-Directed Mutagenesis Kit, Instruction Manual, 2003, Stratagene, La JoIIa, CA) is based on a number of previous publications. These and other developments have been reviewed in: a) C. N. Dominy, D. W. Andrews in Methods in Molecular Biology, Vol. 235: E. coli Plasmid Vectors (Eds.: N. Casali, A. Preston), Humana, Totowa, 2003, pp. 209-223;
64. see also: b) M. A. Vandeyar, M. P. Weiner, C. J. Hutton, C. A. Batt, Gene 1988, 65, 129-133;
65. c) R. D. Kirsch, E. Joly, Nucleic Acids Res. 1998, 26, 1848-1850.
66. G. Sarkar, S. S. Sommer, BioTechniques 1990, 8, 404-407.
67. A. A. Watson, R. A. Alm, J. S. Mattick, Gene 1996, 172, 163-164.
68. K.-E. Jaeger, B. Schneidinger, F. Rosenau, M. Werner, D. Lang, B. W. Dijkstra, K. Schimossek, A. Zonta, M. T. Reetz, J. Mol. Catal. B 1997, 3, 3-12.