메뉴 건너뛰기




Volumn 18, Issue 11, 2011, Pages 1743-1756

Optimization of combinatorial mutagenesis

Author keywords

combinatorial mutagenesis; combinatorial optimization; experiment planning; library diversity; protein engineering

Indexed keywords

BACTERIAL PROTEIN; BETA LACTAMASE; CYTOCHROME P450; GREEN FLUORESCENT PROTEIN;

EID: 80955123971     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2011.0152     Document Type: Article
Times cited : (29)

References (48)
  • 2
    • 85045502002 scopus 로고
    • Randomization of genes by PCR mutagenesis
    • Cadwell, R. C., and Joyce, G. F. 1992. Randomization of genes by PCR mutagenesis. PCR Methods Appl. 2, 28-33.
    • (1992) PCR Methods Appl. , vol.2 , pp. 28-33
    • Cadwell, R.C.1    Joyce, G.F.2
  • 3
    • 62649153772 scopus 로고    scopus 로고
    • Computational structure-based redesign of enzyme activity
    • Chen, C.-Y., Georgiev, I., Anderson, A. C., et al. 2009. Computational structure-based redesign of enzyme activity. Proc. Natl. Acad. Sci. USA 106, 3764-3769.
    • (2009) Proc. Natl. Acad. Sci. USA , vol.106 , pp. 3764-3769
    • Chen, C.-Y.1    Georgiev, I.2    Anderson, A.C.3
  • 5
    • 0028308402 scopus 로고
    • Reconstitution of the isobutene-forming reaction catalyzed by cytochrome P450 and P450 reductase from Rhodotorula minuta: Decarboxylation with the formation of isobutene
    • DOI 10.1006/bbrc.1994.1732
    • Fukuda, H., Fuiji, T., Sukita, E., et al. 1994. Reconstitution of the isobitene-forming reaction catalyzed by cytochrome p450 and p450 reductase from Rhodotorula minuta: decarboxylation with the formation of isobutene. Biochem. Biophys. Res. Commun. 201, 516-522. (Pubitemid 24206903)
    • (1994) Biochemical and Biophysical Research Communications , vol.201 , Issue.2 , pp. 516-522
    • Fukuda, H.1    Fujii, T.2    Sukita, E.3    Tazaki, M.4    Nagahama, S.5    Ogawa, T.6
  • 6
    • 33750800395 scopus 로고    scopus 로고
    • The Evolution of Catalytic Efficiency and Substrate Promiscuity in Human Theta Class 1-1 Glutathione Transferase
    • DOI 10.1016/j.jmb.2006.09.012, PII S0022283606011855
    • Griswold, K. E., Aiyappan, N. S., Iverson, B. L., et al. 2006. The evolution of catalytic efficiency and substrate promiscuity in human theta class 1-1 glutathione transferase. J. Mol. Biol. 364, 400-410. (Pubitemid 44715931)
    • (2006) Journal of Molecular Biology , vol.364 , Issue.3 , pp. 400-410
    • Griswold, K.E.1    Aiyappan, N.S.2    Iverson, B.L.3    Georgiou, G.4
  • 9
    • 0028580734 scopus 로고
    • Wavelength mutations and posttranslational autoxidation of green fluorescent protein
    • Heim, R., Prasher, D. C., and Tsien, R. Y. 1994. Wavelength mutations and posttranslational autoxidation of green fluorescent protein. Proc. Natl. Acad. Sci. USA 91, 12501-12504.
    • (1994) Proc. Natl. Acad. Sci. USA , vol.91 , pp. 12501-12504
    • Heim, R.1    Prasher, D.C.2    Tsien, R.Y.3
  • 10
    • 34548014497 scopus 로고    scopus 로고
    • Incorporating Synthetic Oligonucleotides via Gene Reassembly (ISOR): A versatile tool for generating targeted libraries
    • DOI 10.1093/protein/gzm014
    • Herman, A., and Tawfik, D. S. 2007. Incorporating synthetic oligonucleotides via gene reassembly (ISOR): a versatile tool for generating targeted libraries. Protein Eng. Des. Sel. 20, 219-226. (Pubitemid 351321303)
    • (2007) Protein Engineering, Design and Selection , vol.20 , Issue.5 , pp. 219-226
    • Herman, A.1    Tawfik, D.S.2
  • 11
    • 0038799745 scopus 로고    scopus 로고
    • General method for sequence-independent site-directed chimeragenesis
    • DOI 10.1016/S0022-2836(03)00590-4
    • Hiraga, K., and Arnold, F. H. 2003. General method for sequence-independent site-directed chimeragenesis. J. Mol. Biol. 330, 287-296. (Pubitemid 36773702)
    • (2003) Journal of Molecular Biology , vol.330 , Issue.2 , pp. 287-296
    • Hiraga, K.1    Arnold, F.H.2
  • 13
    • 77954762143 scopus 로고    scopus 로고
    • Consensus protein design without phylogenetic bias
    • Jackel, C., Bloom, J. D., Kast, P., et al. 2010. Consensus protein design without phylogenetic bias. J. Mol. Biol. 399, 541-546.
    • (2010) J. Mol. Biol. , vol.399 , pp. 541-546
    • Jackel, C.1    Bloom, J.D.2    Kast, P.3
  • 15
  • 17
    • 27944437517 scopus 로고    scopus 로고
    • Automated design of degenerate codon libraries
    • DOI 10.1093/protein/gzi061
    • Marco, A. M., and Daugherty, P. S. 2005. Automated design of degenerate codon libraries. Protein Eng. Des. Sel. 18, 559-561. (Pubitemid 41668821)
    • (2005) Protein Engineering, Design and Selection , vol.18 , Issue.12 , pp. 559-561
    • Mena, M.A.1    Daugherty, P.S.2
  • 18
    • 33845624902 scopus 로고    scopus 로고
    • Structure-guided SCHEMA recombination of distantly related β-lactamases
    • DOI 10.1093/protein/gzl045
    • Meyer, M. M., Hochrein, L., and Arnold, F. H. 2006. Structure-guided SCHEMA recombination of distantly related beta-lactamases. Protein Eng. Des. Sel. 19, 563-570. (Pubitemid 44950462)
    • (2006) Protein Engineering, Design and Selection , vol.19 , Issue.12 , pp. 563-570
    • Meyer, M.M.1    Hochrein, L.2    Arnold, F.H.3
  • 21
    • 64349107630 scopus 로고    scopus 로고
    • Development trends for therapeutic antibody fragments
    • Nelson, A. L., and Reichert, J. M. 2009. Development trends for therapeutic antibody fragments. Nat. Biotech. 27, 331-337.
    • (2009) Nat. Biotech. , vol.27 , pp. 331-337
    • Nelson, A.L.1    Reichert, J.M.2
  • 22
    • 33646753362 scopus 로고    scopus 로고
    • Structure-guided recombination creates an artificial family of cytochromes P450
    • Otey, C. R., Landwehr, M., Endelman, J. B., et al. 2006. Structure-guided recombination creates an artificial family of cytochromes P450. PLoS Biol. 4, e112.
    • (2006) PLoS Biol. , vol.4
    • Otey, C.R.1    Landwehr, M.2    Endelman, J.B.3
  • 23
    • 4043109994 scopus 로고    scopus 로고
    • Functional evolution and structural conservation in chimeric cytochromes P450: Calibrating a structure-guided approach
    • DOI 10.1016/j.chembiol.2004.02.018, PII S1074552104000572
    • Otey, C. R., Silberg, J. J., Voigt, C. A., et al. 2004. Functional evolution and structural conservation in chimeric cytochromes P450: calibrating a structure-guided approach. Chem. Biol. 11, 309-318. (Pubitemid 39403870)
    • (2004) Chemistry and Biology , vol.11 , Issue.3 , pp. 309-318
    • Otey, C.R.1    Silberg, J.J.2    Voigt, C.A.3    Endelman, J.B.4    Bandara, G.5    Arnold, F.H.6
  • 24
    • 34548803632 scopus 로고    scopus 로고
    • Optimal protein library design using recombination or point mutations based on sequence-based scoring functions
    • DOI 10.1093/protein/gzm030
    • Pantazes, R. J., Saraf, M. C., and Maranas, C. D. 2007. Optimal protein library design using recombination or point mutations based on sequence-based scoring functions. Protein Eng. Des. Sel. 20, 361-373. (Pubitemid 47428963)
    • (2007) Protein Engineering, Design and Selection , vol.20 , Issue.8 , pp. 361-373
    • Pantazes, R.J.1    Saraf, M.C.2    Maranas, C.D.3
  • 25
    • 80052071931 scopus 로고    scopus 로고
    • Optimization of therapeutic proteins to delete T-cell epitopes while maintaining beneficial residue interactions
    • Parker, A. S., Griswold, K., and Bailey-Kellogg, C. 2011. Optimization of therapeutic proteins to delete T-cell epitopes while maintaining beneficial residue interactions. J. Bioinform. Comput. Biol. 207-229.
    • (2011) J. Bioinform. Comput. Biol. , pp. 207-229
    • Parker, A.S.1    Griswold, K.2    Bailey-Kellogg, C.3
  • 26
    • 77950673538 scopus 로고    scopus 로고
    • Optimization algorithms for functional deimmunization of therapeutic proteins
    • Parker, A. S., Zheng, W., Griswold, K., et al. 2010. Optimization algorithms for functional deimmunization of therapeutic proteins. BMC Bioinform. 11, 180.
    • (2010) BMC Bioinform. , vol.11 , pp. 180
    • Parker, A.S.1    Zheng, W.2    Griswold, K.3
  • 27
    • 0037412183 scopus 로고    scopus 로고
    • Protein design is NP-hard
    • Pierce, N., and Winfree, E. 2002. Protein design is NP-hard. Protein Eng. 15, 779-782. (Pubitemid 36043220)
    • (2002) Protein Engineering , vol.15 , Issue.10 , pp. 779-782
    • Pierce, N.A.1    Winfree, E.2
  • 28
    • 34248567845 scopus 로고    scopus 로고
    • Iterative saturation mutagenesis (ISM) for rapid directed evolution of functional enzymes
    • DOI 10.1038/nprot.2007.72, PII NPROT.2007.72
    • Reetz, M. T., and Carballira, J. D. 2007. Iterative saturation mutagenesis (ISM) for rapid directed evolution of functional enzymes. Nat. Protocols 2, 891-903. (Pubitemid 46758808)
    • (2007) Nature Protocols , vol.2 , Issue.4 , pp. 891-903
    • Reetz, M.T.1    Carballeira, J.D.2
  • 29
    • 54349090614 scopus 로고    scopus 로고
    • Addressing the numbers problem in directed evolution
    • Reetz, M. T., Kahakeaw, D., and Lohmer, R. 2008. Addressing the numbers problem in directed evolution. Chem-BioChem 9, 1797-1804.
    • (2008) Chem-BioChem. , vol.9 , pp. 1797-1804
    • Reetz, M.T.1    Kahakeaw, D.2    Lohmer, R.3
  • 30
    • 25644442464 scopus 로고    scopus 로고
    • Natural-like function in artificial WW domains
    • DOI 10.1038/nature03990, PII N03990
    • Russ, W. P., Lowery, D. M., Mishra, P., et al. 2005. Natural-like function in artificial WW domains. Nature 437, 579-583. (Pubitemid 41613558)
    • (2005) Nature , vol.437 , Issue.7058 , pp. 579-583
    • Russ, W.P.1    Lowery, D.M.2    Mishra, P.3    Yaffe, M.B.4    Ranganathan, R.5
  • 33
    • 14644393547 scopus 로고    scopus 로고
    • Green fluorescent protein is a quantitative reporter of gene expression in individual eukaryotic cells
    • DOI 10.1096/fj.04-3180fje
    • Soboleski, M. R., Oaks, J., and Halford, W. P. 2005. Green fluorescent protein is a quantitative reporter of gene expression in individual eukaryotic cells. FASEB J. 19, 440-442. (Pubitemid 40316543)
    • (2005) FASEB Journal , vol.19 , Issue.3 , pp. 440-442
    • Soboleski, M.R.1    Oaks, J.2    Halford, W.P.3
  • 34
  • 38
    • 68149166344 scopus 로고    scopus 로고
    • Graphical models of protein-protein interaction specificity from correlated mutations and interaction data
    • Thomas, J., Ramakrishnan, N., and Bailey-Kellogg, C. 2009a. Graphical models of protein-protein interaction specificity from correlated mutations and interaction data. Proteins 76, 911-929.
    • (2009) Proteins. , vol.76 , pp. 911-929
    • Thomas, J.1    Ramakrishnan, N.2    Bailey-Kellogg, C.3
  • 43
    • 34547672873 scopus 로고    scopus 로고
    • Hypergraph model of multi-residue interactions in proteins: Sequentially-constrained partitioning algorithms for optimization of site-directed protein recombination
    • DOI 10.1089/cmb.2007.R016
    • Ye, X., Friedman, A. M., and Bailey-Kellogg, C. 2007. Hypergraph model of multi-residue interactions in proteins: sequentially-constrained partitioning algorithms for optimization of site-directed protein recombination. J. Comput. Biol. 14, 777-790. (Pubitemid 47221817)
    • (2007) Journal of Computational Biology , vol.14 , Issue.6 , pp. 777-790
    • Ye, X.1    Friedman, A.M.2    Bailey-Kellogg, C.3
  • 45
    • 0031909113 scopus 로고    scopus 로고
    • Molecular evolution by staggered extension process (StEP) in vitro recombination
    • DOI 10.1038/nbt0398-258
    • Zhao, H., Giver, L., Shao, Z., et al. 1998. Molecular evolution by staggered extension process (StEP) in vitro recombination. Nat. Biotech. 16, 258-261. (Pubitemid 28120104)
    • (1998) Nature Biotechnology , vol.16 , Issue.3 , pp. 258-261
    • Zhao, H.1    Giver, L.2    Shao, Z.3    Affholter, J.A.4    Arnold, F.H.5
  • 46
    • 70349221279 scopus 로고    scopus 로고
    • Algorithms for joint optimization of stability and diversity in planning combinatorial libraries of chimeric proteins
    • Zheng, W., Friedman, A. M., and Bailey-Kellogg, C. 2009. Algorithms for joint optimization of stability and diversity in planning combinatorial libraries of chimeric proteins. J. Comput. Biol. 16, 1151-1168.
    • (2009) J. Comput. Biol. , vol.16 , pp. 1151-1168
    • Zheng, W.1    Friedman, A.M.2    Bailey-Kellogg, C.3
  • 47
    • 77950803114 scopus 로고    scopus 로고
    • Protein fragment swapping: A method for asymmetric, selective site-directed recombination
    • Zheng, W., Griswold, K. E., and Bailey-Kellogg, C. 2010. Protein fragment swapping: a method for asymmetric, selective site-directed recombination. J. Comput. Biol. 17, 459-475.
    • (2010) J. Comput. Biol. , vol.17 , pp. 459-475
    • Zheng, W.1    Griswold, K.E.2    Bailey-Kellogg, C.3
  • 48
    • 38449090890 scopus 로고    scopus 로고
    • Algorithms for selecting breakpoint locations to optimize diversity in protein engineering by site-directed protein recombination
    • Zheng, W., Ye, X., Friedman, A. M., et al. 2007. Algorithms for selecting breakpoint locations to optimize diversity in protein engineering by site-directed protein recombination. Proc. CSB 31-40.
    • (2007) Proc. CSB , pp. 31-40
    • Zheng, W.1    Ye, X.2    Friedman, A.M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.