A Method for Rapid Directed Evolution

Protein Engineering Handbook, Volume 1 & Volume 2

Volumn 2, Issue , 2011, Pages 409-439

  Reetz, Manfred T ^a  

^a MAX PLANCK INSTITUT FÜR KOHLENFORSCHUNG   (Germany)

Author keywords

Amino acid alphabet; Codon degeneracy; Directed evolution; Enzyme enantioselectivity; Enzyme thermostability; Focused libraries; Saturation mutagenesis

Indexed keywords

EID: 80052444296     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9783527634026.ch16     Document Type: Chapter

References (147)

1. Arnold, F.H. and Georgiou, G. (eds) (2003) Directed Enzyme Evolution: Screening and Selection Methods, Vol. 230, Humana Press, Totowa, New Jersey .
2. Brakmann, S. and Johnsson, K. (eds) (2002) Directed Molecular Evolution of Proteins or How to Improve Enzymes for Biocatalysis, Wiley-VCH Verlag GmbH, Weinheim, Germany .
3. Brakmann, S. and Schwienhorst, A. (eds) (2004) Evolutionary Methods in Biotechnology Clever Tricks for Directed Evolution, Wiley-VCH Verlag GmbH, Weinheim, Germany .
4. Taylor, S.V., Kast, P. and Hilvert, D. (2001) Investigating and engineering enzymes by genetic selection . Angewandte Chemie,113,3408-36 ; Angewandte Chemie-International Edition,40,3310-35 .
5. Powell, K.A., Ramer, S.W., Del Cardayré, S.B., Stemmer, W.P.C., Tobin, M.B., Longchamp, P.F. and Huisman, G.W. (2001) Directed evolution and biocatalysis . Angewandte Chemie,113,4068-80 ; Angewandte Chemie-International Edition,40,3948-59 .
6. Rubin-Pitel, S.B. and Zhao, H. (2006) Recent advances in biocatalysis by directed enzyme evolution . Combinatorial Chemistry and High Throughput Screening,9,247-57 .
7. Kaur, J. and Sharma, R. (2006) Directed evolution: An approach to engineer enzymes . Critical Reviews in Biotechnology,26,165-99 .
8. Wang, T.-W., Zhu, H., Ma, X.-Y., Zhang, T., Ma, Y.-S. and Wei, D.-Z. (2006) Mutant library construction in directed molecular evolution . Molecular Biotechnology,34,55-68 .
9. Yuan, L., Kurek, I., English, J. and Keenan, R. (2005) Laboratory-directed protein evolution . Microbiology and Molecular Biology Reviews,69,373-92 .
10. Ling, M.M. and Robinson, B.H. (1997) Approaches to DNA mutagenesis: An overview . Analytical Biochemistry,254,157-78 .
11. Stevenson, J.D. and Benkovic, S.J. (2002) Combinatorial approaches to engineering hybrid enzymes . Journal of the Chemical Society-Perkin Transactions,2,1483-93 .
12. Hibbert, E.G., Baganz, F., Hailes, H. C., Ward, J.M., Lye, G.J., Woodley, J.M. and Dalby, P.A. (2005) Directed evolution of biocatalytic processes . Biomolecular Engineering,22,11-19 .
13. Bershtein, S. and Tawfik, D. (2008) Advances in laboratory evolution of enzymes . Current Opinion in Chemistry and Biology,12,1-8 .
14. Fox, R.J. and Huisman, G.W. (2008) Enzyme optimization: moving from blind evolution to statistical exploration of sequence-function space . T rends in Biotechnology,26,132-8 .
15. Wintrode, P.L. and Arnold, F.H. (2001) Temperature adaptation of enzymes: Lessons from laboratory evolution . Advances in Protein Chemistry,55,161-225 .
16. Eijsink, V.G.H., Gåseidnes, S., Borchert, T.V. and van den Burg, B. (2005) Directed evolution of enzyme stability . Biomolecular Engineering,22,21-30 .
17. Arnold, F.H. (1998) Design by directed evolution . Accounts of Chemical Research,31,125-31 .
18. Reviews of directed evolution of enantioselective enzymes: (a) Reetz, M.T. (2002) Directed evolution of selective enzymes and hybrid catalysts . Tetrahedron,58,6595-602 .
19. Reetz, M.T. (2004) Changing the enantioselectivity of enzymes of directed evolution, in Methods in Enzymology (eds D.E. Robertson and J.P. Noel), Elsevier Academic Press, San Diego, California,388, pp. 238-56 .
20. Reetz, M.T. (2004) Controlling the enantioselectivity of enzymes by directed evolution: Practical and theoretical ramifi cations . Proceedings of the National Academy of Sciences of the United States of America,101,5716-22 .
21. Reetz, M.T. (2006) Directed evolution of enantioselective enzymes as catalysts for organic synthesis, in Advances in Catalysis, Vol. 49 (eds B.C. Gates and H. Knözinger), Elsevier, San Diego, pp. 1-69 .
22. Turner, N.J. (2003) Directed evolution of enzymes for applied biocatalysis . Trends in Biotechnology,21,474-8 .
23. Reviews of high-throughput e e-screens: Reetz, M.T. (2002) New methods for the high-throughput screening of enantioselective catalysts and biocatalysts . Angewandte Chemie,114,1391-94 ; Angewandte Chemie-International Edition,41,1335-8 .
24. Reetz, M.T. (2003) Select protocols of high-throughput ee-screening for assaying enantioselective enzymes, in Methods in Molecular Biology, Vol. 230 (eds F.H. Arnold and G. Georgiou), Humana Press, Totowa, New Jersey, pp. 283-90 .
25. Reetz, M.T. (2004) Screening for enantioselective enzymes, in Enzyme Functionality-Design, Engineering and Screening (ed A. Svendsen), Marcel Dekker, New York, USA, pp. 559-98 .
26. Reetz, M.T. (2004) High-throughput screening of enantioselective industrial biocatalysts, in Evolutionary Methods in Biotechnology, vol. (eds S. Brakmann and A. Schwienhorst), Wiley-VCH Verlag GmbH, Weinheim, pp. 113-41 .
27. Reetz, M.T. (2006) High-throughput screening systems for assaying the enantioselectivity of enzymes, in Enzyme Assays-High-throughput Screening, Genetic Selection and Fingerprinting (ed J.-L. Reymond), Wiley-VCH Verlag GmbH, Weinheim, pp. 41-76 .
28. Reymond, J.-L. (2005) Enzyme Assays-High-throughput Screening, Genetic Selection and Fingerprinting, Wiley-VCH Verlag GmbH, Weinheim .
29. Leung, D.W., Chen, E. and Goeddel, D.V. (1989) A method for random mutagenesis of a defi ned DNA segment using a modifi ed polymerase chain reaction . Technique (Philadelphia),1,11-15 .
30. Cadwell, R.C. and Joyce, G.F. (1992) Randomization of genes by PCR mutagenesis . PCR Methods and Applications,2,28-33 .
31. Numerous different molecular biological approaches to saturation (or cassette) mutagenesis are known, in addition to the currently most often used QuikChange protocol by Stratagene [17], e.g.: Dominy, C.N. and Andrews, D.W. (2003) Site-directed mutagenesis by inverse PCR, in Methods in Molecular Biology, Vol. 235 (eds N. Casali and A. Preston), Humana Press, Totowa, New Jersey, pp. 209-23 .
32. Vandeyar, M.A., Weiner, M.P., Hutton, C.J. and Batt, C.A. (1988) A simple and rapid method for the selection of oligodeoxynucleotide-directed mutants . Gene,65,129-33 .
33. Kirsch, R.D. and Joly, E. (1998) An improved PCR-mutagenesis strategy for two-site mutagenesis or sequence swapping between related genes . Nucleic Acids Research,26,1848-50 .
34. Zheng, L., Baumann, U. and Reymond, J.-L. (2004) An effi cient one-step site-directed and site-saturation mutagenesis protocol . Nucleic Acids Research,32, e115 .
35. Smith, M. (1985) In vitro mutagenesis . Annual Review of Genetics,19,423-62 .
36. Georgescu, R., Bandara, G. and Sun, L. (2003) Saturation Mutagenesis, in Directed Evolution Library Creation (eds F.H. Arnold and G. Georgiou), Humana Press, Totowa, New Jersey, pp. 75-84 .
37. Wells, J.A., Vasser, M. and Powers, D. B. (1985) Cassette mutagenesis: an effi cient method for generation of multiple mutations at defi ned sites . Gene,34,315-23 .
38. Barettino, D., Feigenbutz, M., Valcarcel, R. and Stunnenberg, H.G. (1994) Improved method for PCR-mediated site-directed mutagenesis . Nucleic Acids Research,22,541-2 .
39. Horwitz, M.S.Z. and Loeb, L.A. (1986) Promoters selected from random DNA sequences . Proceedings of the National Academy of Sciences of the United States of America,83,7405-9 .
40. Oliphant, A.R., Nussbaum, A.L. and Struhl, K. (1986) Cloning of random-sequence oligodeoxynucleotides . Gene,44,177-83 .
41. Reidhaar-Olson, J.F. and Sauer, R.T. (1988) Combinatorial cassette mutagenesis as a probe of the informational content of protein sequences . Science (Washington, DC),241,53-7 .
42. Hermes, J.D., Parekh, S.M., Blacklow, S.C., Köster, H. and Knowles, J.R. (1989) A reliable method for random mutagenesis: The generation of mutant libraries using spiked oligodeoxyribonucleotide primers . Gene,84,143-51 .
43. Sarkar, G. and Sommer, S.S. (1990) The " megaprimer " method of site-directed mutagenesis . BioTechniques,8,404-7 .
44. Martin, A., Toselli, E., Rosier, M.-F., Auffray, C. and Devignes, M.-D. (1995) Rapid and high effi ciency site-directed mutagenesis by improvement of the homologous recombination technique . Nucleic Acids Research,23,1642-3 .
45. Stemmer, W.P.C. (1994) Rapid evolu tion of a protein in vitro by DNA shuffl ing . Nature (London, UK),370,389-91 .
46. Stemmer, W.P.C. (1994) DNA shuffl ing by random fragmentation and reassembly: In vitro recombination for molecular evolution . Proceedings of the National Academy of Sciences of the United States of America,91,10747-51 .
47. Crameri, A., Raillard, S.-A., Bermudez, E. and Stemmer, W.P.C. (1998) DNA shuffl ing of a family of genes from diverse species accelerates directed evolution . Nature,391,288-91 .
48. Lutz, S. and Patrick, W.M. (2004) Novel methods for directed evolution of enzymes: quality, not quantity . Current Opinion in Biotechnology,15,291-7 .
49. Neylon, C. (2004) Chemical and biochemical strategies for the randomization of protein encoding DNA sequences: Library construction methods for directed evolution . Nucleic Acids Research,32,1448-59 .
50. Polizzi, K.M., Parikh, M., Spencer, C. U., Matsumura, I., Lee, J.H., Realff, M.J. and Bommarius, A.S. (2006) Pooling for improved screening of combinatorial libraries for directed evolution . Biotechnology Progress,22,961-7 .
51. Reetz, M.T., Zonta, A., Schimossek, K., Liebeton, K. and Jaeger, K.-E. (1997) Creation of enantioselective biocatalysts for organic chemistry by in vitro evolution . Angewandte Chemie,109,2961-3 ; Angewandte Chemie-International Edition,36,2830-2 .
52. Reetz, M.T., Wilensek, S., Zha, D. and Jaeger, K.-E. (2001) Directed evolution of an enantioselective enzyme through combinatorial multiple cassette mutagenesis . Angewandte Chemie,113,3701-3 ; Angewandte Chemie-International Edition,40,3589-91 .
53. Zha, D., Wilensek, S., Hermes, M., Jaeger, K.-E. and Reetz, M.T. (2001) Complete reversal of enantioselectivity of an enzyme-catalyzed reaction by directed evolution . Chemical Communications,2664-5 .
54. Drummond, D.A., Iverson, B.L., Georgiou, G. and Arnold, F.H. (2005) Why high-error-rate random mutagenesis libraries are enriched in functional and improved proteins . Journal of Molecular Biology,350,806-16 .
55. Eggert, T., Reetz, M.T. and Jaeger, K.-E. (2004) Directed evolution by random mutagenesis: a critical evaluation, in Enzyme Functionality-Design, Engineering, and Screening (ed A. Svendsen), Marcel Dekker, New York, USA, pp. 375-90 .
56. Cirino, P.C., Mayer, K.M. and Umeno, D. (2003) Generating mutant libraries using error-prone PCR, in Directed Evolution Library Creation: Methods and Protocols, Vol. 231 (eds G. Georgiou and F.H. Arnold), Humana Press, Totowa, New Jersey, pp. 3-9 .
57. Wong, T.S., Tee, K.L., Hauer, B. and Schwaneberg, U. (2004) Sequence saturation mutagenesis (SeSaM): a novel method for directed evolution . Nucleic Acids Research,32, e26 .
58. Kikuchi, H., Ohnishi, K. and Harayama, S. (1999) An effective family shuffl ing method using single-stranded DNA . Gene,243,133-7 .
59. Rowe, L.A., Geddie, M.L., Alexander, O.B. and Matsumura, I. (2003) A comparison of directed evolution approaches using the β-glucuronidase model system . Journal of Molecular Biology,332,851-60 .
60. Parikh, M.R. and Matsumura, I. (2005) Site-saturation mutagenesis is more effi cient than DNA shuffl ing for the directed evolution of β-fucosidase from β-galactosidase . Journal of Molecular Biology,352,621-8 .
61. Coco, W.M., Levinson, W.E., Crist, M.J., Hektor, H.J., Darzins, A., Pienkos, P.T., Squires, C.H. and Monticello, D.J. (2001) DNA shuffl ing method for generating highly recombined genes and evolved enzymes . Nature Biotechnology,19,354-9 .
62. Coco, W.M. (2003) RACHITT: Gene family shuffl ing by random chimeragenesis on transient templates, in Directed Evolution Library Creation: Methods and Protocols, Vol. 231 (eds F.H. Arnold and G. Georgiou), Humana Press, Totowa, New Jersey, pp. 111-27 .
63. Ness, J.E., Kim, S., Gottman, A., Pak, R., Krebber, A., Borchert, T.V., Govindarajan, S., Mundorff, E.C. and Minshull, J. (2002) Synthetic shuffl ing expands functional protein diversity by allowing amino acids to recombine independently . Nature Biotechnology,20,1251-5 .
64. Coco, W.M., Encell, L.P., Levinson, W.E., Crist, M.J., Loomis, A.K., Licato, L.L., Arensdorf, J.J., Sica, N., Pienkos, P.T. and Monticello, D.J. (2002) Growth factor engineering by degenerate homoduplex gene family recombination . Nature Biotechnology,20,1246-50 .
65. Zha, D., Eipper, A. and Reetz, M.T. (2003) Assembly of designed oligonucleotides as an effi cient method for gene recombination: A new tool in directed evolution . ChemBioChem,4,34-9 .
66. Hogrefe, H.H., Cline, J., Youngblood, G.L. and Allen, R.M. (2002) Creating randomized amino acid libraries with the QuikChange ® multi site-directed mutagenesis kit . BioTechniques,33,1158-65 .
67. Horsman, G.P., Liu, A.M.F., Henke, E., Bornscheuer, U.T. and Kazlauskas, R.J. (2003) Mutations in distant residues moderately increase the enantioselectivity of Pseudomonas fl uorescens esterase towards methyl 3-bromo-2-methylpropanoate and ethyl 3-phenylbutyrate . Chemistry-A European Journal,9,1933-9 .
68. Schmidt, M., Hasenpusch, D., Kähler, M., Kirchner, U., Wiggenhorn, K., Langel, W. and Bornscheuer, U.T. (2006) Directed evolution of an esterase from Pseudomonas fl uorescens yields a mutant with excellent enantioselectivity and activity for the kinetic resolution of a chiral building block . ChemBioChem,7,805-9 .
69. Reetz, M.T., Wang, L.-W. and Bocola, M. (2006) Directed evolution of enantioselective enzymes: Iterative cycles of CASTing for probing protein-sequence space . Angewandte Chemie,118,1258-63 ; Erratum,2556 ; Angewandte Chemie-International Edition (2006) 45,1236-41 ; Erratum,2494 .
70. Reetz, M.T. and Carballeira, J.D. (2007) Iterative Saturation Mutagenesis (ISM) for rapid directed evolution of functional enzymes . Nature Protocols,2,891-903 .
71. Bosley, A.D. and Ostermeier, M. (2005) Mathematical expressions useful in the construction, description and evaluation of protein libraries . Biomolecular Engineering,22,57-61 .
72. Patrick, W.M. and Firth, A.E. (2005) Strategies and computational tools for improving randomized protein libraries . Biomolecular Engineering,22,105-12 .
73. Denault, M. and Pelletier, J.N. (2007) Protein library design and screening. Working out the probabilities, in Protein Engineering Protocols (eds K.M. Arndt and K.M. Müller), Humana Press, Totowa, New Jersey, pp. 127-54 .
74. Kamtekar, S., Schiffer, J.M., Xiong, H.Y., Babik, J.M. and Hecht, M.H. (1993) Protein design by binary patterning of polar and nonpolar amino-acids . Science,262,1680-5 .
75. Davidson, A.R., Lumb, K.J. and Sauer, R.T. (1995) Cooperative folded proteins in random sequence libraries . Nature Structural Biology,2,856-64 .
76. Walter, K.U., Vamvaca, K. and Hilvert, D. (2005) An active enzyme constructed from a nine amino acid alphabet . The Journal of Biological Chemistry,280,37742-6 .
77. Reetz, M.T. (1999) Strategies for the development of enantioselective catalysts . Pure and Applied Chemistry,71,1503-9 .
78. Liebeton, K., Zonta, A., Schimossek, K., Nardini, M., Lang, D., Dijkstra, B.W., Reetz, M.T. and Jaeger, K.-E. (2000) Directed evolution of an enantioselective lipase . Chemistry and Biology,7,709-18 .
79. Reetz, M.T. (2000) Application of directed evolution in the development of enantioselective enzymes . Pure and Applied Chemistry,72,1615-22 .
80. Fersht, A. (1999) Structure and Mechanism in Protein Science, W.H Freeman, New York .
81. Bocola, M., Otte, N., Jaeger, K.-E., Reetz, M.T. and Thiel, W. (2004) Learning from directed evolution: Theoretical investigations into cooperative mutations in lipase enantioselectivity . ChemBioChem,5,214-23 .
82. Reetz, M.T., Puls, M., Carballeira, J.D., Vogel, A., Jaeger, K.-E., Eggert, T., Thiel, W., Bocola, M. and Otte, N. (2007) Learning from directed evolution: Further 436 16 A Method for Rapid Directed Evolution lessons from theoretical investigations into cooperative mutations in lipase enantioselectivity . ChemBioChem,8,106-12 .
83. Miyazaki, K. and Arnold, F.H. (1999) Exploring nonnatural evolutionary pathways by saturation mutagenesis: Rapid improvement of protein function . Journal of Molecular Evolution,49,716-20 .
84. Arnold, F.H., Wintrode, P.L., Miyazaki, K. and Gershenson, A. (2001) How enzymes adapt: Lessons from directed evolution . Trends in Biochemical Sciences,26,100-6 .
85. Desantis, G., Wong, K., Farwell, B., Chatman, K., Zhu, Z., Tomlinson, G., Huang, H., Tan, X., Bibbs, L., Chen, P., Kretz, K. and Burk, M.J. (2003) Creation of a productive, highly enantioselective nitrilase through Gene Site Saturation Mutagenesis (GSSM) . Journal of the American Chemical Society,125,11476-7 .
86. Funke, S.A., Eipper, A., Reetz, M.T., Otte, N., Thiel, W., Van Pouderoyen, G., Dijkstra, B.W., Jaeger, K.-E. and Eggert, T. (2003) Directed evolution of an enantioselective Bacillus subtilis lipase . Biocatalysis and Biotransformation,21,67-73 .
87. Brissos, V., Eggert, T., Cabral, J.M.S. and Jaeger, K.-E. (2008) Improving activity and stability of cutinase towards the anionic detergent AOT by complete saturation mutagenis . Protein Engineering, Design & Selection,21,387-93 .
88. Nardini, M., Lang, D.A., Liebeton, K., Jaeger, K.-E. and Dijkstra, B.W. (2000) Crystal structure of Pseudomonas aeruginosa lipase in the open conformation . The Journal of Biological Chemistry,275,31219-25 .
89. Fong, S., Machajewski, T.D., Mak, C.C. and Wong, C.-H. (2000) Directed evolution of D-2-keto-3-deoxy-6-phosphogluconate aldolase to new variants for the effi cient synthesis of D-and L-sugars . Chemistry and Biology,7,873-83 .
90. Wang, L.-F., Goodey, N.M., Benkovic, S.J. and Kohen, A. (2006) Coordinated effects of distal mutations on environmentally coupled tunneling in dihydrofolate reductase . Proceedings of the National Academy of Sciences of the United States of America,103,15753-8 .
91. Oelschlaeger, P., Schmid, R.D. and Pleiss, J. (2003) Modeling domino effects in enzymes: molecular basis of the substrate specifi city of the bacterial metallo-β-lactamases IMP-1 and IMP-6 . Biochemistry,42,8945-56 .
92. Fowler, S.M., Taylor, J.M., Friedberg, T., Wolf, C.R. and Riley, R.J. (2002) CYP3A4 active site volume modifi cation by mutagenesis of leucine 211 . Drug Metabolism and Disposition,30,452-6 .
93. Chin, J.K. and Klinman, J.P. (2000) Probes of a role for remote binding interactions on hydrogen tunnelling in the horse liver alcohol dehydrogenase reaction . Biochemistry,39,1278-84 .
94. Reetz, M.T., Carballeira, J.D. and Vogel, A. (2006) Iterative saturation mutagenesis on the basis of B factors as a strategy for increasing protein thermostability . Angewandte Chemie,118,7909-15 ; Angewandte Chemie-International Edition,45,7745-51 .
95. Rui, L., Cao, L., Chen, W., Reardon, K.F. and Wood, T.K. (2004) Active site engineering of the epoxide hydrolase from Agrobacterium radiobacter AD1 to enhance aerobic mineralization of cis-1,2-dichloroethylene in cells expressing an evolved toluene ortho-monooxygenase . The Journal of Biological Chemistry,279,46810-17 .
96. Greisman, H.A. and Pabo, C.O. (1997) A general strategy for selecting high-affi nity zinc fi nger proteins for diverse DNA target sites . Science,275,657-61 .
97. Reetz, M.T., Bocola, M., Carballeira, J.D., Zha, D. and Vogel, A. (2005) Expanding the range of substrate acceptance of enzymes: Combinatorial active-site saturation test . Angewandte Chemie,117,4264-8 ; Angewandte Chemie-International Edition,44,4192-6 .
98. Dartois, V., Baulard, A., Schanck, K. and Colson, C. (1992) Cloning, nucleotide-sequence and expression in Escherichia coli of a lipase gene from Bacillus subtilis 168 . Biochimica et Biophysica Acta,1131,253-60 .
99. Jaeger, K.-E., Dijkstra, B.W. and Reetz, M.T. (1999) Bacterial biocatalysts: molecular biology, three-dimensional structures, and biotechnological applications of lipases . Annual Review of Microbiology,53,315-51 .
100. Reetz, M.T., Carballeira, J.D., Peyralans, J.J.-P., Höbenreich, H., Maichele, A. and Vogel, A. (2006) Expanding the substrate scope of enzymes: combining mutations obtained by CASTing . Chemistry-A European Journal,12,6031-8 .
101. Reetz, M.T., Torre, C., Eipper, A., Lohmer, R., Hermes, M., Brunner, B., Maichele, A., Bocola, M., Arand, M., Cronin, A., Genzel, Y., Archelas, A. and Furstoss, R. (2004) Enhancing the enantioselectivity of an epoxide hydrolase by directed evolution . Organic Letters,6,177-80 .
102. Zou, J.Y., Hallberg, B.M., Bergfors, T., Oesch, F., Arand, M., Mowbray, S.L. and Jones, T.A. (2000) Structure of Aspergillus niger epoxide hydrolase at 1.8åresolution: implications for the structure and function of the mammalian microsomal class of epoxide hydrolases . Structure,8,111-22 .
103. Weinreich, D.M., Delaney, N.F., Depristo, M.A. and Hartl, D.L. (2006) Darwinian evolution can follow only very few mutational paths to fi tter proteins . Science,312,111-14 .
104. Faber, K. and Orru, R.V.A. (2002) Hydrolysis of Epoxides, in Enzyme Catalysis in Organic Synthesis: A Comprehensive Handbook (eds K. Drauz and H. Waldmann), Vol. II, Wiley-VCH Verlag GmbH, Weinheim, pp. 579-608 .
105. Morisseau, C. and Hammock, B.D. (2005) Epoxide hydrolases: mechanisms, inhibitor designs, and biological roles . Annual Review of Pharmacology and Toxicology,45,311-33 .
106. Archelas, A. and Furstoss, R. (2001) Synthetic applications of epoxide hydrolases . Current Opinion in Chemical Biology,5,112-19 .
107. Bruice, T.C. (2002) A view at the millennium: the effi ciency of enzymatic catalysis . Accounts of Chemical Research,35,139-48 .
108. Wang, L.-W. (2006) Directed evolution of the Aspergillus niger epoxide hydrolase . Dissertation, Ruhr-Universität Bochum, Germany.
109. Clouthier, C.M., Kayser, M.M. and Reetz, M.T. (2006) Designing new Baeyer-Villiger monooxygenases using restricted CASTing . The Journal of Organic Chemistry,71,8431-7 .
110. Reetz, M.T. (2001) Patent DE-A 101 29 187.6 .
111. Reetz, M.T. (2002) Directed evolution of selective enzymes and hybrid catalysts . Tetrahedron,58,6595-602 .
112. Reetz, M.T., Peyralans, J.J.-P., Maichele, A., Fu, Y. and Maywald, M. (2006) Directed evolution of hybrid enzymes: evolving enantioselectivity of an achiral Rh-complex anchored to a protein . Chemical Communications,4318-20 .
113. Reetz, M.T., Rentzsch, M., Pletsch, A., Maywald, M., Maiwald, P., Peyralans, J.J.-P., Maichele, A., Fu, Y., Jiao, N., Hollmann, F., Mondière, R. and Taglieber, A. (2007) Directed evolution of enantioselective hybrid catalysts: a novel concept in asymmetric catalysis . Tetrahedron,63,6404-14 .
114. Reetz, M.T., Rentzsch, M., Pletsch, A., Taglieber, A., Hollmann, F., Mondière, R. J.G., Dickmann, N., Höcker, B., Cerrone, S., Haeger, M.C. and Sterner, R. (2008) A robust protein host for anchoring chelating ligands and organocatalysts . ChemBioChem,9,552-64 .
115. Bartsch, S., Kourist, R. and Bornscheuer, U.T. (2008) Complete inversion of enantioselectivity towards acetylated tertiary alcohols by a double mutant of a Bacillus subtilis esterase . Angewandte Chemie,120,1531-4 ; Angewandte Chemie-International Edition,47,1508-11 .
116. Liang, L., Zhang, J. and Lin, Z. (2007) Altering coenzyme specifi city of Pichia stipitis xylose reductase by the semi-rational approach CASTing . Microbial Cell Factories,6,36 .
117. Oshima, T. (1994) Stabilization of proteins by evolutionary molecular engineering techniques . Current Opinion in Structural Biology,4,623-8 .
118. Ó'Fágáin, C. (2003) Enzyme stabilization-recent experimental progress . Enzyme and Microbial Technology,33,137-49 .
119. Eijsink, V.G.H., Bjørk, A., Gåseidnes, S., Sirevåg, R., Synstad, B., van den Burg, B. and Vriend, G. (2004) Rational engineering of enzyme stability . Journal of Biotechnology,113,105-20 .
120. Palackal, N., Brennan, Y., Callen, W.N., Dupree, P., Frey, G., Goubet, F., Hazlewood, G.P., Healey, S., Kang, Y.E., Kretz, K.A., Lee, E., Tan, X., Tomlinson, G.L., Verruto, J., Wong, V.W.K., Mathur, E.J., Short, J.M., Robertson, D.E. and Steer, B.A. (2004) An evolutionary route to xylanase process fi tness . Protein Science,13,494-503 .
121. Giver, L., Gershenson, A., Freskgard, P.O. and Arnold, F.H. (1998) Directed evolution of a thermostable esterase . Proceedings of the National Academy of Sciences of the United States of America,95,12809-13 .
122. Valinger, G., Hermann, M., Wagner, U.G. and Schwab, H. (2007) Stability and activity improvement of cephalosporin esterase EstB from Burkholderia gladioli by directed evolution and structural interpretation of muteins . Journal of Biotechnology,129,98-108 .
123. Matthews, B.W. (1993) Structural and genetic analysis of protein stability . Annual Review of Biochemistry,62,139-60 .
124. Jaenicke, R. and Böhm, G. (1998) The stability of proteins in extreme environments . Current Opinion in Structural Biology,8,738-48 .
125. Vieille, C. and Zeikus, G.J. (2001) Hyperthermophilic enzymes: sources, uses, and molecular mechanisms for thermostability . Microbiology and Molecular Biology Reviews,65,1-43 .
126. Sterner, R. and Liebl, W. (2001) Thermophilic adaption of proteins . Critical Reviews in Biochemistry and Molecular Biology,36,39-106 .
127. Lazaridis, T., Lee, I. and Karplus, M. (1997) Dynamics and unfolding pathways of a hyperthermophilic and a mesophilic rubredoxin . Protein Science,6,2589-605 .
128. Kumar, S. and Nussinov, R. (2001) How do thermophilic proteins deal with heat? Cellular and Molecular Life Sciences,58,1216-33 .
129. Podar, M. and Reysenbach, A.-L. (2006) New opportunities revealed by biotechnological explorations of extremophiles . Current Opinion in Biotechnology,17,1-6 .
130. Demirjian, D.C., Morís-Varas, F. and Cassidy, C.S. (2001) Enzymes from extremophiles . Current Opinion in Chemical Biology,5,144-51 .
131. Rodriguez-Larrea, D., Minning, S., Borchert, T.V. and Sanchez-Ruiz, J.M. (2006) Role of solvation barriers in protein kinetic stability . Journal of Molecular Biology,360,715-24 .
132. Atomi, H. (2005) Recent progress towards the application of hyperthermophiles and their enzymes . Current Opinion in Biotechnology,9,166-73 .
133. Vogt, G., Woell, S. and Argos, P. (1997) Protein thermal stability, hydrogen bonds, and ion pairs . Journal of Molecular Biology,269,631-43 .
134. Buchner, J. and Kiefhaber, T. (2005) Protein Folding Handbook, Wiley-VCH Verlag GmbH, Weinheim .
135. Schlessinger, A. and Rost, B. (2005) Protein flexibility and rigidity predicted from sequence . Proteins: Structure, Function, and Bioinformatics,61,115-26 .
136. Wang, C., Karpowich, N., Hunt, J.F., Rance, M. and Palmer, A.G. (2004) Dynamics of ATP-binding cassette contribute to allosteric control, nucleotide binding and energy transduction in ABC transporters . Journal of Molecular Biology,342,525-37 .
137. Schlessinger, A., Yachdav, G. and Rost, B. (2006) PROFbval: predict flexible and rigid residues in proteins . Bioinformatics,22,891-3 .
138. Jin, Y. and Dunbrack, R.L. Jr (2005) Assessment of disorder predictions in CASP6 . Proteins: Structure, Function, and Bioinformatics,61,167-75 .
139. Karplus, P.A. and Schulz, G.E. (1985) Prediction of chain flexibility in proteins . Naturwissenschaften,72,212-13 .
140. Vihinen, M. (1987) Relationship of protein flexibility of thermostability . Protein Engineering,1,477-80 .
141. Parthasarathy, S. and Murthy, M.R.N. (2000) Protein thermal stability: insights from atomic displacement parameters (B values) . Protein Engineering,13,9-13 .
142. Yuan, Z., Zhao, J. and Wang, Z.-X. (2003) Flexibility analysis of enzyme active sites by crystallographic temperature factors . Protein Engineering,16,109-14 .
143. Radivojac, P., Obradovic, Z., Smith, D.K., Zhu, G., Vucetic, S., Brown, C.J., Lawson, J.D. and Dunker, A.K. (2004) Protein flexibility and intrinsic disorder . Protein Science,13,71-80 .
144. Trueblood, K.N., Bürgi, H.-B., Burzlaff, H., Dunitz, J.D., Gramaccioli, C.M., Schulz, H.H., Shmueli, U. and Abrahams, S.C. (1996) Atomic displacement parameter nomenclature report of a subcommittee on atomic displacement parameter nomenclature . Acta Crystallographica, A52,770-81 .
145. Van Pouderoyen, G., Eggert, T., Jaeger, K.-E. and Dijkstra, B.W. (2001) The crystal structure of Bacillus subtilis lipase: a minimal a/ β hydrolase fold enzyme . Journal of Molecular Biology,309,215-26 .
146. Kawasaki, K., Kondo, H., Suzuki, M., Ohgiya, S. and Tsuda, S. (2002) Alternative conformations observed in catalytic serine of Bacillus subtilis lipase determined at 1.3åresolution . Acta Crystallographica Section D. Biological Crystallography,58,1168-74 .
147. Bloom, J.D., Labthavikul, S.T., Otey, C.R. and Arnold, F.H. (2006) Protein stability promotes evolvability . Proceedings of the National Academy of Sciences of the United States of America,103,5869-74 .