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Extremely high mutation rates were applied to subtilisin to determine whether it enables better evolution of function for directed evolution than more conventional (and less severe) mutagenesis. It does, as rare amino acid changes that require multiple base substitutions in a single codon are accessed by saturation mutagenesis, allowing the exploration of broader sequence space. This works towards a 'codon-based' mutagenesis approach.
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Miyazaki K., Arnold F.H. Exploring nonnatural evolutionary pathways by saturation mutagenesis: rapid improvement of protein function. J Mol Evol. 49:1999;716-720. Extremely high mutation rates were applied to subtilisin to determine whether it enables better evolution of function for directed evolution than more conventional (and less severe) mutagenesis. It does, as rare amino acid changes that require multiple base substitutions in a single codon are accessed by saturation mutagenesis, allowing the exploration of broader sequence space. This works towards a 'codon-based' mutagenesis approach.
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Hypermutation resulted in the isolation of enzymes with exceptionally higher activity. The use of triphosphate nucleotide analogs afforded good control over mutational load.
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Zaccolo M., Gherardi E. The effect of high-frequency random mutagenesis on in vitro protein evolution: a study on TEM-1 beta-lactamase. J Mol Biol. 285:1999;775-783. Hypermutation resulted in the isolation of enzymes with exceptionally higher activity. The use of triphosphate nucleotide analogs afforded good control over mutational load.
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This review affords a reasonably thorough treatment of the field, including a discussion of the myriad techniques that fall under the guise of 'directed evolution'. It also includes a discussion of screening methods and accentuates the general caveat to all evolutionary experiments: you get what you screen for.
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Stemmer W.P.C., Soong N.W. Molecular breeding of viruses for targeting and other clinical properties. Tumour Target. 4:1999;59-62.
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Patten P.A., Howard R.J., Stemmer W.P. Applications of DNA shuffling to pharmaceuticals and vaccines. Curr Opin Biotechnol. 8:1997;724-733.
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Patten, P.A.1
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Stemmer W.P. DNA shuffling by random fragmentation and reassembly: in vitro recombination for molecular evolution. Proc Natl Acad Sci USA. 91:1994;10 747-10 751.
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Stemmer, W.P.1
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The authors describe the evolution of an interferon-α with broadened specificity by family shuffling of over 20 human genes. Using a modest number of assays, shuffled variants that are more active than the native cytokine were identified. Very different, yet highly active solutions to functional problems were obtained. Many higher activity solutions appear to exist in the virtual genome (i.e. sequence space), making the high premium on the human genomic sequence seem somewhat over-rated.
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Chang C.C., Chen T.T., Cox B.W., Dawes G.N., Stemmer W.P., Punnonen J., Patten P.A. Evolution of a cytokine using DNA family shuffling. Nat Biotechnol. 17:1999;793-797. The authors describe the evolution of an interferon-α with broadened specificity by family shuffling of over 20 human genes. Using a modest number of assays, shuffled variants that are more active than the native cytokine were identified. Very different, yet highly active solutions to functional problems were obtained. Many higher activity solutions appear to exist in the virtual genome (i.e. sequence space), making the high premium on the human genomic sequence seem somewhat over-rated.
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Nat Biotechnol
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Chang, C.C.1
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Stemmer, W.P.5
Punnonen, J.6
Patten, P.A.7
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18
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0030989062
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Directed evolution of a fucosidase from a galactosidase by DNA shuffling and screening
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Zhang J.H., Dawes G., Stemmer W.P. Directed evolution of a fucosidase from a galactosidase by DNA shuffling and screening. Proc Natl Acad Sci USA. 94:1997;4504-4509.
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Proc Natl Acad Sci USA
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Zhang, J.H.1
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Improved green fluorescent protein by molecular evolution using DNA shuffling
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Crameri A., Whitehorn E.A., Tate E., Stemmer W.P. Improved green fluorescent protein by molecular evolution using DNA shuffling. Nat Biotechnol. 14:1996;315-319.
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Nat Biotechnol
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Crameri, A.1
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20
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0030951186
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Molecular evolution of an arsenate detoxification pathway by DNA shuffling
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Crameri A., Dawes G., Rodriguez E. Jr., Silver S., Stemmer W.P. Molecular evolution of an arsenate detoxification pathway by DNA shuffling. Nat Biotechnol. 15:1997;436-438.
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Nat Biotechnol
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Crameri, A.1
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21
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0032518266
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DNA shuffling of a family of genes from diverse species accelerates directed evolution
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Crameri A., Raillard S.A., Bermudez E., Stemmer W.P. DNA shuffling of a family of genes from diverse species accelerates directed evolution. Nature. 391:1998;288-291.
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Nature
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Crameri, A.1
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0033037012
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Directed evolution of thymidine kinase for AZT phosphorylation using DNA family shuffling
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The breeding of two herpes simplex virus thymidine kinase genes resulted in the creation of two novel chimaeric enzymes with increased affinity for AZT and decreased affinity for thymidine. The two progeny contained different solutions to the change in binding, inherited from different parents.
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Christians F.C., Scapozza L., Crameri A., Folkers G., Stemmer W.P. Directed evolution of thymidine kinase for AZT phosphorylation using DNA family shuffling. Nat Biotechnol. 17:1999;259-264. The breeding of two herpes simplex virus thymidine kinase genes resulted in the creation of two novel chimaeric enzymes with increased affinity for AZT and decreased affinity for thymidine. The two progeny contained different solutions to the change in binding, inherited from different parents.
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Nat Biotechnol
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Christians, F.C.1
Scapozza, L.2
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23
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0032885231
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DNA shuffling of subgenomic sequences of subtilisin
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An important paper on multiple levels. The authors describe the simultaneous evolution of multiple properties of an enzyme. The paper also contains interesting data illustrating that the 'best parent' (in desired activity) is not necessarily the 'closest parent' (in sequence identity) to the best-evolved progeny. This provides a caveat to those inclined to employ extremely rational constraints on the choice of identification of 'best' parent genes. It also shows that family shuffling enables a screening scenario in which a relatively small number of progeny need to be screened to find desirable improvements in activity.
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Ness J.E., Welch M., Giver L., Bueno M., Cherry J.R., Borchert T.V., Stemmer W.P., Minshull J. DNA shuffling of subgenomic sequences of subtilisin. Nat Biotechnol. 17:1999;893-896. An important paper on multiple levels. The authors describe the simultaneous evolution of multiple properties of an enzyme. The paper also contains interesting data illustrating that the 'best parent' (in desired activity) is not necessarily the 'closest parent' (in sequence identity) to the best-evolved progeny. This provides a caveat to those inclined to employ extremely rational constraints on the choice of identification of 'best' parent genes. It also shows that family shuffling enables a screening scenario in which a relatively small number of progeny need to be screened to find desirable improvements in activity.
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Nat Biotechnol
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Ness, J.E.1
Welch, M.2
Giver, L.3
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Borchert, T.V.6
Stemmer, W.P.7
Minshull, J.8
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24
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0033605826
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Evolution of differential substrate specificities in Mu class glutathione transferases probed by DNA shuffling
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Hansson L.O., Bolton-Grob R., Massoud T., Mannervik B. Evolution of differential substrate specificities in Mu class glutathione transferases probed by DNA shuffling. J Mol Biol. 287:1999;265-276.
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J Mol Biol
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Hansson, L.O.1
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25
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0032814117
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One way to improve the ability to shuffle dissimilar parental genes is to use restriction endonuclease cleavage to fragment the DNA.
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Kikuchi M., Ohnishi K., Harayama S. Novel family shuffling methods for the in vitro evolution of enzymes. Gene. 236:1999;159-167. One way to improve the ability to shuffle dissimilar parental genes is to use restriction endonuclease cleavage to fragment the DNA.
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Gene
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Kikuchi, M.1
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Kikuchi M., Ohnishi K., Harayama S. An effective family shuffling method using single-stranded DNA. Gene. 243:2000;133-137.
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Incremental truncation as a strategy in the engineering of novel biocatalysts
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Ostermeier M., Nixon A.E., Benkovic S.J. Incremental truncation as a strategy in the engineering of novel biocatalysts. Bioorg Med Chem. 7:1999;2139-2144.
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A combinatorial approach to hybrid enzymes independent of DNA homology
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This paper describes iterative truncation for the creation of hybrid enzymes ('ITCHY'). Two genes are progressively truncated, followed by ligation, to make recombined, single-crossover chimaeras. This enables the formation of hybrids from two essentially nonhomologous sequences. ITCHY generates a large amount of diversity from the two parents; however, a large amount of this sequence space is nonfunctional.
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Ostermeier M., Shim J.H., Benkovic S.J. A combinatorial approach to hybrid enzymes independent of DNA homology. Nat Biotechnol. 17:1999;1205-1209. This paper describes iterative truncation for the creation of hybrid enzymes ('ITCHY'). Two genes are progressively truncated, followed by ligation, to make recombined, single-crossover chimaeras. This enables the formation of hybrids from two essentially nonhomologous sequences. ITCHY generates a large amount of diversity from the two parents; however, a large amount of this sequence space is nonfunctional.
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Nat Biotechnol
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Ostermeier, M.1
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Valenzuela C.Y. Non random DNA evolution. Biol Res. 30:1997;117-123.
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Chothia C. Proteins. One thousand families for the molecular biologist. Nature. 357:1992;543-544.
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The authors describe the conversion of an indole-3-glycerol-phosphate synthase (IGPS) to a phosphoribosylanthranilate isomerase (PRAI) using a combined structure-based and directed evolution approach. The IGPS α/β barrel was modified by the incorporation of the basic design of the loop system of PRAI. PRAI activity was evolved. The evolved PRAI enzyme obtained a different solution to that encoded by natural PRAI and lost all IGPS activity. This is an important demonstration that evolution occurs in modules and that structural criteria may be useful in choosing parental genes for directed evolution of new functions.
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Altamirano M.M., Blackburn J.M., Aguayo C., Fersht A.R. Directed evolution of a new catalytic activity using the alpha/beta-barrel scaffold. Nature. 403:2000;617-622. The authors describe the conversion of an indole-3-glycerol-phosphate synthase (IGPS) to a phosphoribosylanthranilate isomerase (PRAI) using a combined structure-based and directed evolution approach. The IGPS α/β barrel was modified by the incorporation of the basic design of the loop system of PRAI. PRAI activity was evolved. The evolved PRAI enzyme obtained a different solution to that encoded by natural PRAI and lost all IGPS activity. This is an important demonstration that evolution occurs in modules and that structural criteria may be useful in choosing parental genes for directed evolution of new functions.
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A demonstration that 'rational' and 'irrational' approaches may be combined to perform directed evolution. Site-directed mutagenesis was used to alter residues deemed important through structural analysis; this was followed by the randomization and combination of beneficial mutations, by the introduction of random mutations by error-prone PCR and by recombination of mutations by in vivo shuffling using the homologous recombination system of the host.
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Cherry J.R., Lamsa M.H., Schneider P., Vind J., Svendsen A., Jones A., Pedersen A.H. Directed evolution of a fungal peroxidase. Nat Biotechnol. 17:1999;379-384. A demonstration that 'rational' and 'irrational' approaches may be combined to perform directed evolution. Site-directed mutagenesis was used to alter residues deemed important through structural analysis; this was followed by the randomization and combination of beneficial mutations, by the introduction of random mutations by error-prone PCR and by recombination of mutations by in vivo shuffling using the homologous recombination system of the host.
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Nat Biotechnol
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Directed evolution of thermostable kanamycin-resistance gene: A convenient selection marker for Thermus thermophilus
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Increased thermostability was largely conferred by the accumulation of multiple mutations on the protein surface, obtained by DNA shuffling and antibiotic selection. The best progeny retained full activity, had a 20° increase in thermostability and contained 19 amino acid substitutions.
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Hoseki J., Yano T., Koyama Y., Kuramitsu S., Kagamiyama H. Directed evolution of thermostable kanamycin-resistance gene: a convenient selection marker for Thermus thermophilus. J Biochem (Tokyo). 126:1999;951-956. Increased thermostability was largely conferred by the accumulation of multiple mutations on the protein surface, obtained by DNA shuffling and antibiotic selection. The best progeny retained full activity, had a 20° increase in thermostability and contained 19 amino acid substitutions.
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Matsumura I., Wallingford J.B., Surana N.K., Vize P.D., Ellington A.D. Directed evolution of the surface chemistry of the reporter enzyme beta- glucuronidase. Nat Biotechnol. 17:1999;696-701.
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Improving the catalytic activity of a thermophilic enzyme at low temperatures
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A parent enzyme, indole glycerol phosphate synthase from Sulfolobus solfataricus, displayed poor activity at low temperatures, apparently because of structural rigidity. DNA shuffling for improved activity at low temperature can create an enzyme with improved turnover under those conditions.
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Merz A., Yee M., Szadkowski H., Pappenberger G., Crameri A., Stemmer W.P., Yanofsky C., Kirschner K. Improving the catalytic activity of a thermophilic enzyme at low temperatures. Biochemistry. 39:2000;880-889. A parent enzyme, indole glycerol phosphate synthase from Sulfolobus solfataricus, displayed poor activity at low temperatures, apparently because of structural rigidity. DNA shuffling for improved activity at low temperature can create an enzyme with improved turnover under those conditions.
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Merz, A.1
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A structural view of evolutionary divergence
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Crystallographic analyses of variants of p-nitrobenzyl esterases generated in a directed evolution experiment demonstrate the cooperative interplay among networks of mutations. This illustrates how directed evolution can access function via structural changes that result from unpredictable combinations of mutations.
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Spiller B., Gershenson A., Arnold F.H., Stevens R.C. A structural view of evolutionary divergence. Proc Natl Acad Sci USA. 96:1999;12 305-12 310. Crystallographic analyses of variants of p-nitrobenzyl esterases generated in a directed evolution experiment demonstrate the cooperative interplay among networks of mutations. This illustrates how directed evolution can access function via structural changes that result from unpredictable combinations of mutations.
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Spiller, B.1
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A cold-adapted protease engineered by experimental evolution system
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Taguchi S., Ozaki A., Nonaka T., Mitsui Y., Momose H. A cold-adapted protease engineered by experimental evolution system. J Biochem (Tokyo). 126:1999;689-693.
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Taguchi, S.1
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Characterization of a novel stable biocatalyst obtained by protein engineering
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Van den Burg B., de Kreij A., Van der Veek P., Mansfeld J., Venema G. Characterization of a novel stable biocatalyst obtained by protein engineering. Biotechnol Appl Biochem. 30:1999;35-40.
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Mansfeld, J.4
Venema, G.5
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50
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Directed evolution converts subtilisin E into a functional equivalent of thermitase
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Zhao H., Arnold F.H. Directed evolution converts subtilisin E into a functional equivalent of thermitase. Protein Eng. 12:1999;47-53.
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51
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Redesigning the substrate specificity of an enzyme by cumulative effects of the mutations of non-active site residues
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An impressive demonstration of the power of DNA shuffling, here used to change the substrate specificity of an aspartate aminotransferase to valine. Crystallographic analysis revealed cumulative and dispersed mutations, distant from the active site, that exert higher order structural changes affecting substrate and cofactor binding. The increase in catalytic efficiency for the valine was two-million-fold that of the parent enzyme.
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Oue S., Okamoto A., Yano T., Kagamiyama H. Redesigning the substrate specificity of an enzyme by cumulative effects of the mutations of non-active site residues. J Biol Chem. 274:1999;2344-2349. An impressive demonstration of the power of DNA shuffling, here used to change the substrate specificity of an aspartate aminotransferase to valine. Crystallographic analysis revealed cumulative and dispersed mutations, distant from the active site, that exert higher order structural changes affecting substrate and cofactor binding. The increase in catalytic efficiency for the valine was two-million-fold that of the parent enzyme.
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J Biol Chem
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Oue, S.1
Okamoto, A.2
Yano, T.3
Kagamiyama, H.4
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52
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0032167489
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Microbial lipases form versatile tools for biotechnology
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Jaeger K.E., Reetz M.T. Microbial lipases form versatile tools for biotechnology. Trends Biotechnol. 16:1998;396-403.
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Trends Biotechnol
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Jaeger, K.E.1
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Schulze B., Wubbolts M.G. Biocatalysis for industrial production of fine chemicals. Curr Opin Biotechnol. 10:1999;609-615.
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Schulze, B.1
Wubbolts, M.G.2
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Directed evolution of an esterase for the stereoselective resolution of a key intermediate in the synthesis of epothilones
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Bornscheuer U.T., Altenbuchner J., Meyer H.H. Directed evolution of an esterase for the stereoselective resolution of a key intermediate in the synthesis of epothilones. Biotechnol Bioeng. 58:1998;554-559.
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Bornscheuer, U.T.1
Altenbuchner, J.2
Meyer, H.H.3
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55
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Directed evolution of an esterase from Pseudomonas fluorescens. Random mutagenesis by error-prone PCR or a mutator strain and identification of mutants showing enhanced enantioselectivity by a resorufin-based fluorescence assay
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Henke E., Bornscheuer U.T. Directed evolution of an esterase from Pseudomonas fluorescens. Random mutagenesis by error-prone PCR or a mutator strain and identification of mutants showing enhanced enantioselectivity by a resorufin-based fluorescence assay. Biol Chem. 380:1999;1029-1033.
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Henke, E.1
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Creation of enantioselective biocatalysts for organic chemistry by in vitro evolution
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Reetz M.T., Zonta A., Schimossek K., Liebeton K., Jaeger K-E. Creation of enantioselective biocatalysts for organic chemistry by in vitro evolution. Agnew Chem Int Ed Engl. 36:1997;2830-2832.
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Reetz, M.T.1
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Jaeger, K.-E.5
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57
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0033578095
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Laboratory evolution of peroxide-mediated cytochrome P450 hydroxylation
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One of the major problems associated with the ex situ use of enzymes requiring cofactors is cofactor regeneration. This paper describes the evolution of P450 monooxygenases that hydroxylate naphthalene in the absence of cofactors by using a 'peroxide shunt' pathway (i.e. hydrogen peroxide as the source of oxygen).
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Joo H., Lin Z., Arnold F.H. Laboratory evolution of peroxide-mediated cytochrome P450 hydroxylation. Nature. 399:1999;670-673. One of the major problems associated with the ex situ use of enzymes requiring cofactors is cofactor regeneration. This paper describes the evolution of P450 monooxygenases that hydroxylate naphthalene in the absence of cofactors by using a 'peroxide shunt' pathway (i.e. hydrogen peroxide as the source of oxygen).
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(1999)
Nature
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Joo, H.1
Lin, Z.2
Arnold, F.H.3
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