Optimization of Industrial Enzymes by Molecular Engineering

Industrial Biotransformations, Second Edition

Volumn , Issue , 2006, Pages 93-114

  Eggert, Thorsten ^a  

^a HEINRICH HEINE UNIVERSITY   (Germany)

Author keywords

Enzyme production using bacterial expression hosts; Identification of improved enzyme variants; Improvements to enzymes by molecular engineering techniques; Optimization of industrial enzymes by molecular engineering

Indexed keywords

EID: 84889380707     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9783527608188.ch4     Document Type: Chapter

References (126)

1. Amann, R.I., Ludwig, W., Schleifer, K.H. 1995, (Phylogenetic Identification and In Situ Detection of Individual Microbial-cells Without Cultivation), Microbiol. Rev. 59, 143-169.
2. Handelsman, J., Rondon, M.R., Brady, S.F., Clardy, J., R. Goodman, M. 1998, (Molecular Biological Access to the Chemistry of Unknown Soil Microbes: A New Frontier for Natural Products), Chem. Biol. 5, 245-249.
3. Patel, R.N. 2003, (Microbial/Enzymatic Synthesis of Chiral Pharmaceutical Intermediates), Curr. Opin. Drug Discov. 6, 902-920.
4. Straathof, A.J.J., Panke, S., Schmid, A. 2002, (The Production of Fine Chemicals by Biotransformations), Curr. Opin. Biotechnol. 13, 548-556.
5. Watson, J.D., Crick, F.H.C. 1953, (Molecular Structure of Nucleic Acids-a Structure for Deoxyribose Nucleic Acid), Nature 171, 737-738.
6. Smith, H.O., Wilcox, K.W. 1970, (A Restriction Enzyme from Hemophilus influenzae. 1. Purification and General Properties), J. Mol. Biol. 51, 379-391.
7. Kelly, T.J., Smith, H.O. 1970, (A Restriction Enzyme from Hemophilus influenzae. 2. Base Sequence of Recognition Site. J. Mol. Biol. 51, 393-409.
8. Mullis, K., Faloona, F., Scharf, S., Saiki, R., Horn, G., Erlich, H. 1986, (Specific Enzymatic Amplification of DNA In Vitro-the Polymerase Chain-reaction), Cold Spring Harbor Symposia on Quantitative Biology 51, 263-273.
9. Kunst, F., Ogasawara, N., Moszer, I., Albertini, A.M., Alloni, G., Azevedo, V., Bertero, M.G., Bessieres, P., Bolotin, A., Borchert, S., Borriss, R., Boursier, L., Brans, A., Braun, M., Brignell, S.C., Bron, S., Brouillet, S., Bruschi, C.V., Caldwell, B., Capuano, V., Carter, N.M., Choi, S.K., Codani, J.J., Connerton, I.F., Cummings, N.J., Daniel, R.A., Denizot, F., Devine, K.M., Dusterhoft, A., Ehrlich, S.D., Emmerson, P.T., Entian, K.D., Errington, J., Fabret, C., Ferrari, E., Foulger, D., Fritz, C., Fujita, M., Fujita, Y., Fuma, S., Galizzi, A., Galleron, N., Ghim, S.Y., Glaser, P., Goffeau, A., Golightly, E.J., Grandi, G., Guiseppi, G., Guy, B.J., Haga, K., Haiech, J., Harwood, C.R., Henaut, A., Hilbert, H., Holsappel, S., Hosono, S., Hullo, M.F., Itaya, M., Jones, L., Joris, B., Karamata, D., Kasahara, Y., KlaerrBlanchard, M., Klein, C., Kobayashi, Y., Koetter, P., Koningstein, G., Krogh, S., Kumano, M., Kurita, K., Lapidus, A., Lardinois, S., Lauber, J., Lazarevic, V., Lee, S.M., Levine, A., Liu, H., Masuda, S., Mauel, C., Medigue, C., Medina, N., Mellado, R.P., Mizuno, M., Moestl, D., Nakai, S., Noback, M., Noone, D., Oreilly, M., Ogawa, K., Ogiwara, A., Oudega, B., Park, S.H., Parro, V., Pohl, T.M., Portetelle, D., Porwollik, S., Prescott, A.M., Presecan, E., Pujic, P., Purnelle, B., Rapoport, G., Rey, M., Reynolds, S., Rieger, M., Rivolta, C., Rocha, E., Roche, B., Rose, M., Sadaie, Y., Sato, T., Scanlan, E., Schleich, S., Schroeter, R., Scoffone, J., Sekiguchi, F., Sekowska, A., Seror, S.J., Serror, P., Shin, B.S., Soldo, B., Sorokin, A., Tacconi, E., Takagi, T., Takahashi, H., Takemaru, K., Takeuchi, M., Tamakoshi, A., Tanaka, T., Terpstra, P., Tognoni, A., Tosato, V., Uchiyama, S., Vandenbol, M., Vannier, F., Vassarotti, A., Viari, A., Wambutt, R., Wedler, E., Wedler, H., Weitzenegger, T., Winters, P., Wipat, A., Yamamoto, H., Yamane, K., Yasumoto, K., Yata, K., Yoshida, K., Yoshikawa, H.F., Zumstein, E., Yoshikawa, H., Danchin, A. 1997, (The Complete Genome Sequence of the Gram-positive Bacterium Bacillus subtilis) Nature 390, 249-256.
10. Istrail, S., Sutton, G.G., Florea, L., Halpern, A.L., Mobarry, C.M., Lippert, R., Walenz, B., Shatkay, H., Dew, I., Miller, J.R., Flanigan, M.J., Edwards, N.J., Bolanos, R., Fasulo, D., Halldorsson, B.V., Hannenhalli, S., Turner, R., Yooseph, S., Lu, F., Nusskern, D.R., Shue, B.C., Zheng, X.Q.H., Zhong, F., Delcher, A.L., Huson, D.H., Kravitz, S.A., Mouchard, L., Reinert, K., Remington, K.A., Clark, A.G., Waterman, M.S., Eichler, E.E., Adams, M.D., Hunkapiller, M.W., Myers, E.W., Venter, J.C. 2004, (Whole-genome Shotgun Assembly and Comparison of Human Genome Assemblies), Proc. Natl. Acad. Sci. USA 101, 1916-1921.
11. Fleischmann, R.D., Adams, M.D., White, O., Clayton, R.A., Kirkness, E.F., Kerlavage, A.R., Bult, C.J., Tomb, J.F., Dougherty, B.A., Merrick, J.M., McKenney, K., Sutton, G., Fitzhugh, W., Fields, C., Gocayne, J.D., Scott, J., Shirley, R., Liu, L.I., Glodek, A., Kelley, J.M., Weidman, J.F., Phillips, C.A., Spriggs, T., Hedblom, E., Cotton, M.D., Utterback, T.R., Hanna, M.C., Nguyen, D.T., Saudek, D.M., Brandon, R.C., Fine, L.D., Fritchman, J.L., Fuhrmann, J.L., Geoghagen, N.S.M., Gnehm, C.L., McDonald, L.A., Small, K.V., Fraser, C.M., Smith, H.O., Venter, J.C., 1995, (Whole-genome Random Sequencing and Assembly of Haemophilus influenzae Rd.) Science 269, 496-512.
12. Bult, C.J., White, O., Olsen, G.J., Zhou, L.X., Fleischmann, R.D., Sutton, G.G., Blake, J.A., Fitzgerald, L.M., Clayton, R.A., Gocayne, J.D., Kerlavage, A.R., Dougherty, B.A., Tomb, J.F., Adams, M.D., Reich, C.I., Overbeek, R., Kirkness, E.F., Weinstock, K.G., Merrick, J.M., Glodek, A., Scott, J.L., Geoghagen, N.S.M., Weidman, J.F., Fuhrmann, J.L., Nguyen, D., Utterback, T.R., Kelley, J.M., Peterson, J.D., Sadow, P.W., Hanna, M.C., Cotton, M.D., Roberts, K.M., Hurst, M.A., Kaine, B.P., Borodovsky, M., Klenk, H.P., Fraser, C.M., Smith, H.O., Woese, C.R., Venter, J.C. 1996, (Complete Genome Sequence of the Methanogenic Archaeon, Methanococcus jannaschii), Science 273, 1058-1073.
13. Blattner, F.R., Plunkett, G., Bloch, C.A., Perna, N.T., Burland, V., Riley, M., ColladoVides, J., Glasner, J.D., Rode, C.K., Mayhew, G.F., Gregor, J., Davis, N.W., Kirkpatrick, H.A., Goeden, M.A., Rose, D.J., Mau, B., Shao, Y. 1997, (The Complete Genome Sequence of Escherichia coli K-12), Science 277, 1453-1474.
14. Venter, J.C., Remington, K., Heidelberg, J.F., Halpern, A.L., Rusch, D., Eisen, J.A., Wu, D.Y., Paulsen, I., Nelson, K.E., Nelson,W., Fouts, D.E., Levy, S., Knap, A.H., Lomas, M.W., Nealson, K., White, O., Peterson, J., Hoffman, J., Parsons, R., Baden-Tillson, H., Pfannkoch, C., Rogers, Y.H., Smith, H.O. 2004, (Environmental Genome Shotgun Sequencing of the Sargasso Sea), Science 304, 66-74.
15. Bolivar, F., Rodriguez, R.L., Greene, P.J., Betlach, M.C., Heyneker, H.L., Boyer, H.W., Crosa, J.H., Falkow, S. 1977, (Construction and Characterization of New Cloning Vehicles. 2. Multipurpose Cloning System), Gene 2, 95-113.
16. Yanisch-Perron, C., Vieira, J., Messing, J. 1985, (Improved M13Phage Cloning Vectors and Host Strains-Nucleotidesequences of the M13mp18 and pUC19-Vectors), Gene 33, 103-119.
17. Jaeger, K.E., Rosenau, F. 2004, (Overexpression and Secretion of Pseudomonas Lipases), in Pseudomonas-Biosynthesis of Macromolecules and MolecularMetabolism, (vol. 3), ed. Ramos, J.-L., Kluwer Academic/Plenum Publishers, New York, (pp.) 491-508.
18. Rosenau, F., Jaeger, K.E., 2004, (Overexpression and Secretion of Biocatalysts in Pseudomonas), in Enzyme Functionality: Design, Engineering, and Screening, ed. Svendsen, A., Marcel Dekker, New York, (pp.) 617-631.
19. Makrides, S.C. 1996, (Strategies for Achieving High-level Expression of Genes in Escherichia coli), Microbiol. Rev. 60, 512-538.
20. Baneyx, F. 1999, (Recombinant Protein Expression in Escherichia coli), Curr. Opin. Biotechnol. 10, 411-421.
21. Watson, A.A., Alm, R.A., Mattick, J.S. 1996, (Construction of Improved Vectors for Protein Production in Pseudomonas aeruginosa), Gene 172, 163-164.
22. Kovach, M.E., Phillips, R.W., Elzer, P.H., Roop, R.M., Peterson, K.M. 1994, (pBBR1MCS-a Broad-host-range Cloning Vector), Biotechniques 16, 800-802.
23. Kendrew, J.C., Dickerson, R.E., Strandberg, B.E., Hart, R.G., Davies, D.R., Phillips, D.C., Shore, V.C. 1960, (Structure of Myoglobin-3-Dimensional Fourier Synthesis at 2 Å Resolution), Nature 185, 422-427.
24. Kendrew, J.C., Bodo, G., Dintzis, H.M., Parrish, R.G., Wyckoff, H., Phillips, D.C. 1958, (3-Dimensional Model of the Myoglobin Molecule Obtained by X-ray Analysis), Nature 181, 662-666.
25. Westbrook, J., Feng, Z.K., Chen, L., Yang, H.W., Berman, H.M. 2003, (The Protein Data Bank and Structural Genomics), Nucleic Acids Res. 31, 489-491.
26. Saiki, R.K., Gelfand, D.H., Stoffel, S., Scharf, S.J., Higuchi, R., Horn, G.T., Mullis, K.B., Erlich, H.A. 1988, (Primerdirected Enzymatic Amplification of DNA with a Thermostable DNA-polymerase), Science 239, 487-491.
27. Matsumura, M., Becktel, W.J., Levitt, M., Matthews, B.W. 1989, (Stabilization of Phage-T4 Lysozyme by Engineered Disulfide Bonds), Proc. Natl. Acad. Sci. USA 86, 6562-6566.
28. Matsumura, M., Becktel, W.J., Matthews, B.W. 1988, (Hydrophobic Stabilization in T4 Lysozyme Determined Directly by Multiple Substitutions of Ile-3), Nature 334, 406-410.
29. Matsumura, M., Signor, G., Matthews, B.W. 1989, (Substantial Increase of Protein Stability by Multiple Disulfide Bonds), Nature 342, 291-293.
30. Bornscheuer, U.T., Pohl, M. 2001, (Improved Biocatalysts by Directed Evolution and Rational Protein Design), Curr. Opin. Chem. Biol. 5, 137-143.
31. Henke, E., Bornscheuer, U.T., Schmid, R.D., Pleiss, J. 2003, (A Molecular Mechanism of Enantiorecognition of Tertiary Alcohols by Carboxylesterases), Chembiochem. 4, 485-493.
32. Rotticci, D., Haeffner, F., Orrenius, C., Norin, T., Hult, K. 1998, (Molecular Recognition of sec-Alcohol Enantiomers by Candida antarctica Lipase B), J. Mol. Catal. BEnzymatic 5, 267-272.
33. Magnusson, A., Hult, K., Holmquist, M. 2001, (Creation of an Enantioselective Hydrolase by Engineered Substrate-assisted Catalysis), J. Am. Chem. Soc. 123, 4354-4355.
34. Orrenius, C., Haeffner, F., Rotticci, D., Ohrner, N., Norin, T., Hult, K. 1998, (Chiral Recognition of Alcohol Enantiomers in Acyl Transfer Reactions Catalysed by Candida antarctica Lipase B), Biocatal. Biotrans. 16, 1-15.
35. Rotticci, D., Rotticci-Mulder, J.C., Denman, S., Norin, T., Hult, K. 2001, (Improved Enantioselectivity of a Lipase by Rational Protein Engineering), Chembiochem. 2, 766-770.
36. Chen-Goodspeed, M., Sogorb, M.A., Wu, F.Y., Hong, S.B., Raushel, F.M. 2001, (Structural Determinants of the Substrate and Stereochemical Specificity of Phosphotriesterase), Biochemistry 40, 1325-1331.
37. Chen-Goodspeed, M., Sogorb, M.A., Wu, F.Y., Raushel, F.M. 2001, (Enhance ment, Relaxation, and Reversal of the Stereoselectivity for Phosphotriesterase by Rational Evolution of Active Site Residues), Biochemistry 40, 1332-1339.
38. Schoneboom, J.C., Lin, H., Reuter, N., Thiel, W., Cohen, S., Ogliaro, F., Shaik, S. 2002, (The Elusive Oxidant Species of Cytochrome P450 Enzymes: Characterization by Combined Quantum Mechanical/Molecular Mechanical (QM/MM) Calculations), J. Am. Chem. Soc. 124, 8142-8151.
39. Zhang, Y.X., Perry, K., Vinci, V.A., Powell, K., Stemmer, W.P.C., del Cardayre, S.B. 2002, (Genome Shuffling Leads to Rapid Phenotypic Improvement in Bacteria), Nature 415, 644-646.
40. Patnaik, R., Louie, S., Gavrilovic, V., Perry, K., Stemmer, W.P.C., Ryan, C.M., del Cardayre, S. 2002, (Genome Shuffling of Lactobacillus for Improved Acid Tolerance), Nat. Biotechnol. 20, 707-712.
41. Eckert, K.A., Kunkel, T.A. 1990, (High Fidelity DNA-synthesis by the Thermus aquaticus DNA-polymerase), Nucleic Acids Res. 18, 3739-3744.
42. Tindall, K.R., Kunkel, T.A. 1988, (Fidelity of DNA-synthesis by the Thermus aquaticus DNA-polymerase), Biochemistry 27, 6008-6013.
43. Cadwell, R.C., Joyce, G.F. 1992, Randomization of Genes by PCR Mutagenesis), PCR Methods Appl. 2, 28-33.
44. Cadwell, R.C., Joyce, G.F. 1995, (Mutagenic PCR), in PCR Primer: a Laboratory Manual, eds. Dieffenbach, C.H., Dveksler, G.S., CSHL Press, Cold Spring Harbor, (p.) 583.
45. Zaccolo, M., Williams, D.M., Brown, D.M., Gherardi, E. 1996, (An Approach to Random Mutagenesis of DNA Using Mixtures of Triphosphate Derivatives of Nucleoside Analogues), J. Mol. Biol. 255, 589-603.
46. Zhou, Y.H., Zhang, X.P., Ebright, R.H. 1991, (Random Mutagenesis of Gene-sized DNA-molecules by use of PCR with Taq DNA-polymerase), Nucleic Acids Res. 19, 6052-6052.
47. Jaeger, K.E., Eggert, T., Eipper, A., Reetz, M.T. 2001, (Directed Evolution and the Creation of Enantioselective Biocatalysts), Appl. Microbiol. Biotechnol. 55, 519-530.
48. Eggert, T., Reetz, M.T., Jaeger, K.E. 2004, (Directed Evolution by Random Mutagenesis: a Critical Evaluation), in Enzyme Functionality: Design, Engineering, and Screening, ed. Svendsen, A., Marcel Dekker, New York, 375-390.
49. Bessler, C., Schmitt, J., Maurer, K.H., Schmid, R.D. 2003, (Directed Evolution of a Bacterial Alpha-amylase: Toward Enhanced pH-performance and Higher Specific Activity), Protein Sci. 12, 2141-2149.
50. Chen, K., Arnold, F.H. 1993, (Tuning the Activity of an Enzyme for Unusual Environments: Sequential Random Mutagenesis of Subtilisin E for Catalysis in Dimethylformamide), Proc. Natl. Acad. Sci. USA 90, 5618-5622.
51. Giver, L., Gershenson, A., Freskgard, P.O., Arnold, F.H. 1998, (Directed Evolution of a Thermostable Esterase), Proc. Natl. Acad. Sci. USA 95, 12809-12813.
52. Meyer, A., Schmid, A., Held, M., Westphal, A.H., Rothlisberger, M., Kohler, H.P., van Berkel, W.J., Witholt, B. 2002,(Changing the Substrate Reactivity of 2-Hydroxybiphenyl 3-Monooxygenase from Pseudomonas azelaica HBP1 by Directed Evolution), J. Biol. Chem. 277, 5575-5582.
53. Liebeton, K., Zonta, A., Schimossek, K., Nardini, M., Lang, D., Dijkstra, B.W., Reetz, M.T., Jaeger, K.E. 2000, (Directed Evolution of an Enantioselective Lipase), Chem. Biol. 7, 709-718.
54. Funke, S.A., Eipper, A., Reetz, M.T., Otte, N., Thiel, W., Van Pouderoyen, G., Dijkstra, B.W., Jaeger, K.E., Eggert, T. 2003, (Directed Evolution of an Enantioselective Bacillus subtilis Lipase), Biocatal. Biotrans. 21, 67-73.
55. Barettino, D., Feigenbutz, M., Valcarcel, R., Stunnenberg, H.G. 1994, (Improved Method for PCR-mediated Site-directedMutagenesis), Nucleic Acids Res. 22, 541-542.
56. Urban, A., Neukirchen, S., Jaeger, K.E. 1997, (A Rapid and Efficient Method for Site-directedMutagenesis Using One-step Overlap Extension PCR), Nucleic Acids Res. 25, 2227-2228.
57. Gray, K.A., Richardson, T.H., Kretz, K., Short, J.M., Bartnek, F., Knowles, R., Kan, L., Swanson, P.E., Robertson, D.E. 2001, (Rapid Evolution of Reversible Denaturation and Elevated Melting Temperature in a Microbial Haloalkane Dehalogenase), Adv. Synth. Catal. 343, 607-617.
58. DeSantis, G., Wong, K., Farwell, B., Chatman, K., Zhu, Z.L., Tomlinson, G., Huang, H.J., Tan, X.Q., Bibbs, L., Chen, P., Kretz, K., Burk, M.J. 2003, (Creation of a Productive, Highly Enantioselective Nitrilase Through Gene Site Saturation Mutagenesis (GSSM)), J. Am. Chem. Soc. 125, 11476-11477.
59. Stemmer, W.P.C. 1994, (DNA Shuffling by Random Fragmentation and Reassembly-In Vitro Recombination for Molecular Evolution), Proc. Natl. Acad. Sci. USA 91, 10747-10751.
60. Stemmer, W.P.C. 1994, (Rapid Evolution of a Protein In Vitro by DNA Shuffling), Nature 370, 389-391.
61. Farinas, E.T., Bulter, T., Arnold, F.H. 2001, (Directed Enzyme Evolution), Curr. Opin. Biotechnol. 12, 545-551.
62. Minshull, J., Stemmer, W.P.C. 1999, (Protein Evolution by Molecular Breeding) Curr. Opin. Chem. Biol. 3, 284-290.
63. Crameri, A., Dawes, G., Rodriguez, E., Silver, S., Stemmer, W.P.C. 1997, (Molecular Evolution of an Arsenate Detoxification Pathway DNA Shuffling. Nat. Biotechnol. 15, 436-438.
64. Stemmer, W.P.C., Soong, N.W. 1999, (Molecular Breeding of Viruses for Targeting and Other Clinical Properties), Tumor Target 4, 59-62.
65. Powell, S.K., Kaloss, M.A., Pinkstaff, A., McKee, R., Burimski, I., Pensiero, M., Otto, E., Stemmer, W.P.C., Soong, N.W. 2000, (Breeding of Retroviruses by DNA Shuffling for Improved Stability and Processing Yields), Nat. Biotechnol. 18, 1279-1282.
66. Soong, N.W., Nomura, L., Pekrun, K., Reed, M., Sheppard, L., Dawes, G., Stemmer, W.P.C. 2000, (Molecular Breeding of Viruses), Nat. Genet. 25, 436-439.
67. Zhao, H., Giver, L., Shao, Z., Affholter, J.A., Arnold, F.H. 1998, (Molecular Evolution by Staggered Extension Process (StEP) In Vitro Recombination), Nat. Biotechnol. 16, 258-261.
68. Zha, D.X., Eipper, A., Reetz, M.T. 2003, (Assembly of Designed Oligonucleotides as an Efficient Method for Gene Recombination: A New Tool in Directed Evolution), Chembiochem. 4, 34-39.
69. Lutz, S., Patrick, W.M. 2004, (Novel Methods for Directed Evolution of Enzymes: Quality, not Quantity), Curr. Opin. Biotechnol. 15, 291-297.
70. Neylon, C. 2004, (Chemical and Biochemical Strategies for the Randomization of Protein Encoding DNA Sequences: Library Construction Methods for Directed Evolution), Nucleic Acids Res. 32, 1448-1459.
71. Ostermeier, M., Nixon, A.E., Shim, J.H., Benkovic, S.J. 1999, (Combinatorial Protein Engineering by Incremental Truncation), Proc. Natl. Acad. Sci. USA 96, 3562-3567.
72. Lutz, S., Benkovic, S.J. 2000, (Homologyindependent Protein Engineering), Curr. Opin. Biotechnol. 11, 319-324.
73. Lutz, S., Ostermeier, M., Moore, G.L., Maranas, C.D., Benkovic, S.J. 2001, (Creating Multiple-crossover DNA Libraries Independent of Sequence Identity), Proc. Natl. Acad. Sci. USA 98, 11248-11253.
74. Smith, G.P. 1985, (Filamentous Fusion Phage-Novel Expression Vectors that Display Cloned Antigens on the Virion Surface), Science 228, 1315-1317.
75. Fernandez-Gacio, A., Uguen, M., Fastrez, J. 2003, (Phage Display as a Tool for the Directed Evolution of Enzymes), Trends Biotechnol. 21, 408-414.
76. Lin, H.N., Cornish, V.W. 2002, (Screening and Selection Methods for Large-scale Analysis of Protein Function), Angew. Chem., Int. Ed. Engl. 41, 4403-4425.
77. Sieber, V., Plückthun, A., Schmid, F.X. 1998, (Selecting Proteins with Improved Stability by a Phage-based Method), Nat. Biotechnol. 16, 955-960.
78. Verhaert, R.M.D., Beekwilder, J., Olsthoorn, R., van Duin, J., Quax, W.J. 2002, (Phage Display Selects for Amylases with Improved Low pH Starch-binding), J Biotechnol. 96, 103-118.
79. Dröge, M.J., Rüggeberg, C.J., van der Sloot, A.M., Schimmel, J., Dijkstra, D.S., Verhaert, R.M.D., Reetz, M.T., Quax, W.J. 2003, (Binding of Phage Displayed Bacillus subtilis Lipase A to a Phosphonate Suicide Inhibitor), J. Biotechnol. 101, 19-28.
80. Reetz, M.T., Rüggeberg, C.J., Dröge, M.J., Quax, W.J. 2002, (Immobilization of Chiral Enzyme Inhibitors on Solid Supports by Amide-forming Coupling and Olefin Metathesis), Tetrahedron 58, 8465-8473.
81. Goddard, J.-P., Reymond, J.-L. 2004, (Enzyme Assays forHigh-throughput Screening), Curr. Opin. Biotechnol. 15, 314-322.
82. Reymond, J.L., Wahler, D., 2002, (Substrate Arrays as Enzyme Fingerprinting Tools), Chembiochem. 3, 701-708.
83. Wahler, D., Reymond, J.L. 2001, (Highthroughput Screening for Biocatalysts), Curr. Opin. Biotechnol. 12, 535-544.
84. Arnold, F.H.,Georgiou,G. 2003, Directed Enzyme Evolution: Screening and Selection Methods,Humana Press, Totowa, NewJersey.
85. Eisenthal, R., Danson, M. 2002, Enzyme Assays: A Practical Approach, Oxford University Press, Oxford.
86. Reetz, M.T. 2003, (An Overview of Highthroughput Screening Systems for Enantioselective Enzymatic Transformations), in Directed Enzyme Evolution: Screening and Selection Methods, eds. Arnold, F.H., Georgiou, G., (vol. 230), Humana Press, Totowa, New Jersey, (pp.) 59-282.
87. Reetz, M.T. 2002, (New Methods for the High-throughput Screening of Enantioselective Catalysts and Biocatalysts), Angew. Chem., Int. Ed. Engl. 41, 1335-1338.
88. Svendsen, A. 2004, Enzyme Functionality: Design, Engineering, and Screening, Marcel Dekker, New York.
89. Arnold, F.H., Georgiou, G. 2003, Directed Evolution Library Creation: Methods and Protocols, Humana Press, Totowa, New Jersey.
90. Hughes, M.D., Nagel, D.A., Santos, A.F., Sutherland, A.J., Hine, A.V. 2003, (Removing the Redundancy from Randomised Gene Libraries), J. Mol. Biol. 331, 973-979.
91. Murakami, H., Hohsaka, T., Sisido, M. 2002, (Random Insertion and Deletion of Arbitrary Number of Bases for Codon-based Random Mutation of DNAs), Nat. Biotechnol. 20, 76-81.
92. Pikkemaat, M.G., Janssen,D.B. 2002, (Generating SegmentalMutations inHaloalkane Dehalogenase:A Novel Part in the Directed Evolution Toolbox),NucleicAcids Res. 30, e35.
93. Zhao, H., Arnold, F.H. 1997, (Optimization of DNA Shuffling for High Fidelity Recombination), Nucleic Acids Res. 25, 1307-1308.
94. Crameri, A., Raillard, S.A., Bermudez, E., Stemmer, W.P.C. 1998, (DNA Shuffling of a Family of Genes from Diverse Species Accelerates Directed Evolution), Nature 391, 288-291.
95. Shao, Z., Zhao, H., Giver, L., Arnold, F.H. 1998, (Random-priming In Vitro Recombination: an Effective Tool for Directed Evolution), Nucleic Acids Res. 26, 681-683.
96. Volkov, A.A., Shao, Z., Arnold, F.H. 1999, (Recombination and Chimeragenesis by In Vitro Heteroduplex Formation and In Vivo Repair), Nucleic Acids Res. 27, e18.
97. Kikuchi, M., Ohnishi, K., Harayama, S. 1999, (Novel Family Shuffling Methods for the In Vitro Evolution of Enzymes), Gene 236, 159-167.
98. Kikuchi, M., Ohnishi, K., Harayama, S. 2000, (An Effective Family Shuffling Method using Single-stranded DNA), Gene 243, 133-137.
99. Gibbs, M.D., Nevalainen, K.M., Bergquist, P.L. 2001, (Degenerate Oligonucleotide Gene Shuffling (DOGS): A Method for Enhancing the Frequency of Recombination with Family Shuffling), Gene 271, 13-20.
100. Coco,W.M., Levinson, W.E., Crist, M.J., Hektor, H.J., Darzins, A., Pienkos, P.T., Squires, C.H., Monticello, D.J. 2001, (DNA Shuffling Method for Generating Highly Recombined Genes and Evolved Enzymes), Nat. Biotechnol. 19, 354-359.
101. Song, J.K., Chung, B., Oh, Y.H., Rhee, J.S. 2002, (Construction of DNA-shuffled and Incrementally Truncated Libraries by a Mutagenic and Unidirectional Reassembly Method: Changing from a Substrate Specificity of Phospholipase to that of Lipase), Appl. Environ. Microbiol. 68, 6146-6151.
102. Ostermeier, M., Shim, J.H., Benkovic, S.J. 1999, (A Combinatorial Approach to Hybrid Enzymes Independent of DNA Homology), Nat. Biotechnol. 17, 1205-1209.
103. Sieber, V., Martinez, C.A., Arnold, F.H. 2001, (Libraries of Hybrid Proteins from Distantly Related Sequences), Nat. Biotechnol. 19, 456-460.
104. Kawarasaki, Y.,Griswold,K.E., Stevenson, J.D., Selzer, T., Benkovic, S.J., Iverson, B.L., Georgiou,G. 2003, (EnhancedCrossover SCRATCHY: Construction andHighthroughput Screening of a Combinatorial LibraryContainingMultipleNon-homologousCrossovers), NucleicAcidsRes. 31, e126.
105. Reetz, M.T., Zonta, A., Schimossek, K., Liebeton, K., Jaeger, K.E. 1997, (Creation of Enantioselective Biocatalysts for Organic Chemistry by In Vitro Evolution), Angew. Chem., Int. Ed. Engl. 36, 2830-2832.
106. Farinas, E.T. 2003, (Colorimetric Screen for Aliphatic Hydroxylation by Cytochrome P450 using p-Nitrophenyl-substituted Alkanes), in Directed Enzyme Evolution: Screening and Selection Methods, (vol. 230), eds. Arnold, F.H., Georgiou, G., Humana Press, Totowa, New Jersey, (pp.) 149-155.
107. Badalassi, F., Wahler, D., Klein, G., Crotti, P., Reymond, J.L. 2000, (A Versatile Periodate-coupled Fluorogenic Assay for Hydrolytic Enzymes), Angew. Chem., Int. Ed. Engl. 39, 4067-4070.
108. Leroy, E., Bensel, N., Reymond, J.L. 2003, (Fluorogenic Cyanohydrin Esters as Chiral Probes for Esterase and Lipase Activity), Adv. Synth. Catal. 345, 859-865.
109. Sevestre, A., Helaine, V., Guyot, G., Martin, C., Hecquet, L. 2003, (A Fluorogenic Assay for Transketolase from Saccharomyces cerevisiae), Tetrahedron Lett. 44, 827-830.
110. Gonzalez-Garcia, E., Helaine, V., Klein, G., Schuermann, M., Sprenger, G.A., Fessner, W.D., Reymond, J.L. 2003, (Fluorogenic Stereochemical Probes for Transaldolases), Chem. Eur. J. 9, 893-899.
111. Zocher, F., Enzelberger, M.M., Bornscheuer, U.T., Hauer, B., Schmid, R.D. 1999, (A Colorimetric Assay Suitable for Screening Epoxide Hydrolase Activity), Anal. Chim. Acta 391, 345-351.
112. Beisson, F., Ferte, N., Nari, J., Noat, G., Arondel, V., Verger, R. 1999, (Use of Naturally Fluorescent Triacylglycerols from Parinari glaberrimum to Detect Low Lipase Activities from Arabidopsis thaliana Seedlings), J. Lipid Res. 40, 2313-2321.
113. Beisson, F., Tiss, A., Riviere, C., Verger, R. 2000, (Methods for Lipase Detection and Assay: A Critical Review), Eur. J. Lipid Sci. Technol. 102, 133-153.
114. Henke, E., Bornscheuer, U.T. 2003, (Fluorophoric Assay for the High-throughput Determination of Amidase Activity), Anal. Chem. 75, 255-260.
115. Konarzycka-Bessler, M., Bornscheuer, U.T. 2003, (A High-throughput-screening Method for Determining the Synthetic Activity of Hydrolases), Angew. Chem., Int. Ed. Engl. 42, 1418-1420.
116. Banerjee, A., Sharma, R., Banerjee, U.C. 2003, (A Rapid and Sensitive Fluorometric Assay Method for the Determination of Nitrilase Activity), Biotech. Appl. Biochem. 37, 289-293.
117. Li, Z., Bütikofer, L., Witholt, B. 2004, (Highthroughput Measurement of the Enantiomeric Excess of Chiral Alcohols by using Two Enzymes), Angew. Chem., Int. Ed. Engl. 43, 1698-1702.
118. Moris-Varas, F., Shah, A., Aikens, J., Nadkarni, N.P., Rozzell, J.D., Demirjian, D.C. 1999, (Visualization of Enzyme-catalyzed Reactions using pH Indicators: Rapid Screening of Hydrolase Libraries and Estimation of the Enantioselectivity), Bioorg. Med. Chem. 7, 2183-2188.
119. Janes, L.E., Löwendahl, A.C., Kazlauskas, R.J. 1998, (Quantitative Screening of Hydrolase Libraries using pH Indicators: Identifying Active and Enantioselective Hydrolases), Chem. Eur. J. 4, 2324-2331.
120. Zhao. H. 2003, (A pH-indicator-based Screen for Hydrolytic Haloalkane Dehalogenase), in Directed Enzyme Evolution: Screening and Selection Methods, (vol. 230), eds. Arnold, F.H., Georgiou, G., Humana Press, Totowa, New Jersey, (pp.) 213-221.
121. Breuer, M., Pohl, M., Hauer, B., Lingen, B. 2002, (High-throughput Assay of (R)-phenylacetylcarbinol Synthesized by Pyruvate Decarboxylase), Anal. Bioanal. Chem. 374, 1069-1073.
122. Lingen, B., Kolter-Jung, D., Dünkelmann, P., Feldmann, R., Grotzinger, J., Pohl, M., Müller, M. 2003, (Alteration of the Substrate Specificity of Benzoylformate Decarboxylase from Pseudomonas putida by Directed Evolution), Chembiochem. 4, 721-726.
123. Doderer, K., Lutz-Wahl, S., Hauer, B., Schmid, R.D. 2003, (Spectrophotometric Assay for Epoxide Hydrolase Activity Toward any Epoxide), Anal. Biochem. 321, 131-134.
124. Marchesi, J.R. 2003, (A Microplate Fluorimetric Assay for Measuring Dehalogenase Activity), J. Microbiol. Meth. 55, 325-329.
125. Wahler, D., Reymond, J.L. 2001, (Novel Methods for Biocatalyst Screening), Curr. Opin. Chem. Biol. 5, 152-158.
126. Eggert, T., Funke, S.A., Rao, O.M., Acharya, P., Krumm, H., Reetz, M.T., Jaeger, K.-E. 2005 (Multiplex-PCR-based recombination as a novel high fidelity method for directed evolution), Chembiochem 6, 1-6.