메뉴 건너뛰기




Volumn 7, Issue 7, 2012, Pages

An automated flow for directed evolution based on detection of promiscuous scaffolds using spatial and electrostatic properties of catalytic residues

Author keywords

[No Author keywords available]

Indexed keywords

BETA LACTAMASE; LEUKOCYTE ELASTASE; PENICILLIN BINDING PROTEIN;

EID: 84863836923     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0040408     Document Type: Article
Times cited : (13)

References (81)
  • 1
    • 3042784274 scopus 로고    scopus 로고
    • Generating mutant libraries using error-prone PCR
    • Cirino PC, Mayer KM, Umeno D, (2003) Generating mutant libraries using error-prone PCR. Methods Mol Biol 231: 3-9.
    • (2003) Methods Mol Biol , vol.231 , pp. 3-9
    • Cirino, P.C.1    Mayer, K.M.2    Umeno, D.3
  • 2
    • 0018967477 scopus 로고
    • Evolution of a new enzymatic function by recombination within a gene
    • Hall BG, Zuzel T, (1980) Evolution of a new enzymatic function by recombination within a gene. Proc Natl Acad Sci USA 77: 3529-3533.
    • (1980) Proc Natl Acad Sci USA , vol.77 , pp. 3529-3533
    • Hall, B.G.1    Zuzel, T.2
  • 3
    • 0028050350 scopus 로고
    • Rapid evolution of a protein in vitro by DNA shuffling
    • Stemmer WP, (1994) Rapid evolution of a protein in vitro by DNA shuffling. Nature 370: 389-391.
    • (1994) Nature , vol.370 , pp. 389-391
    • Stemmer, W.P.1
  • 4
    • 0031909113 scopus 로고    scopus 로고
    • Molecular evolution by staggered extension process (StEP) in vitro recombination
    • Zhao H, Giver L, Shao Z, A holter JA, Arnold FH, (1998) Molecular evolution by staggered extension process (StEP) in vitro recombination. Nat Biotechnol 16: 258-261.
    • (1998) Nat Biotechnol , vol.16 , pp. 258-261
    • Zhao, H.1    Giver, L.2    Shao, Z.3    Aholter, J.A.4    Arnold, F.H.5
  • 5
    • 0035014185 scopus 로고    scopus 로고
    • Directed evolution of proteins by exon shuffling
    • Kolkman JA, Stemmer WP, (2001) Directed evolution of proteins by exon shuffling. Nat Biotechnol 19: 423-428.
    • (2001) Nat Biotechnol , vol.19 , pp. 423-428
    • Kolkman, J.A.1    Stemmer, W.P.2
  • 6
    • 65849183178 scopus 로고    scopus 로고
    • Golden gate shuffling: a one-pot DNA shuffling method based on type IIs restriction enzymes
    • Engler C, Gruetzner R, Kandzia R, Marillonnet S, (2009) Golden gate shuffling: a one-pot DNA shuffling method based on type IIs restriction enzymes. PLoS ONE 4: e5553.
    • (2009) PLoS ONE , vol.4
    • Engler, C.1    Gruetzner, R.2    Kandzia, R.3    Marillonnet, S.4
  • 7
    • 79955534060 scopus 로고    scopus 로고
    • A system for the continuous directed evolution of biomolecules
    • Esvelt KM, Carlson JC, Liu DR, (2011) A system for the continuous directed evolution of biomolecules. Nature 472: 499-503.
    • (2011) Nature , vol.472 , pp. 499-503
    • Esvelt, K.M.1    Carlson, J.C.2    Liu, D.R.3
  • 8
    • 24744453533 scopus 로고    scopus 로고
    • The promise and peril of continuous in vitro evolution
    • Johns GC, Joyce GF, (2005) The promise and peril of continuous in vitro evolution. J Mol Evol 61: 253-263.
    • (2005) J Mol Evol , vol.61 , pp. 253-263
    • Johns, G.C.1    Joyce, G.F.2
  • 9
    • 0029859408 scopus 로고    scopus 로고
    • Random circular permutation of genes and expressed polypeptide chains: application of the method to the catalytic chains of aspartate transcarbamoylase
    • Graf R, Schachman HK, (1996) Random circular permutation of genes and expressed polypeptide chains: application of the method to the catalytic chains of aspartate transcarbamoylase. Proc Natl Acad Sci USA 93: 11591-11596.
    • (1996) Proc Natl Acad Sci USA , vol.93 , pp. 11591-11596
    • Graf, R.1    Schachman, H.K.2
  • 10
    • 84859833076 scopus 로고    scopus 로고
    • Circular Permutation in the Ω-Loop of TEM-1 β-lactamase Results in Improved Activity and Altered Substrate Specificity
    • Guntas G, Kanwar M, Ostermeier M, (2012) Circular Permutation in the Ω-Loop of TEM-1 β-lactamase Results in Improved Activity and Altered Substrate Specificity. PLoS ONE 7: e35998.
    • (2012) PLoS ONE , vol.7
    • Guntas, G.1    Kanwar, M.2    Ostermeier, M.3
  • 11
    • 3543116602 scopus 로고    scopus 로고
    • Enzyme assays for high-throughput screening
    • Goddard JP, Reymond JL, (2004) Enzyme assays for high-throughput screening. Curr Opin Biotechnol 15: 314-322.
    • (2004) Curr Opin Biotechnol , vol.15 , pp. 314-322
    • Goddard, J.P.1    Reymond, J.L.2
  • 12
    • 78650121749 scopus 로고    scopus 로고
    • Development of an in vitro compartmentalization screen for high-throughput directed evolution of [FeFe] hydrogenases
    • Stapleton JA, Swartz JR, (2010) Development of an in vitro compartmentalization screen for high-throughput directed evolution of [FeFe] hydrogenases. PLoS ONE 5: e15275.
    • (2010) PLoS ONE , vol.5
    • Stapleton, J.A.1    Swartz, J.R.2
  • 13
    • 0035807809 scopus 로고    scopus 로고
    • Enzyme-like proteins by computational design
    • Bolon DN, Mayo SL, (2001) Enzyme-like proteins by computational design. Proc Natl Acad Sci USA 98: 14274-14279.
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 14274-14279
    • Bolon, D.N.1    Mayo, S.L.2
  • 16
    • 77954811495 scopus 로고    scopus 로고
    • Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction
    • Siegel JB, Zanghellini A, Lovick HM, Kiss G, Lambert AR, et al. (2010) Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction. Science 329: 309-313.
    • (2010) Science , vol.329 , pp. 309-313
    • Siegel, J.B.1    Zanghellini, A.2    Lovick, H.M.3    Kiss, G.4    Lambert, A.R.5
  • 18
    • 34248567845 scopus 로고    scopus 로고
    • Iterative saturation mutagenesis (ISM) for rapid directed evolution of functional enzymes
    • Reetz MT, Carballeira JD, (2007) Iterative saturation mutagenesis (ISM) for rapid directed evolution of functional enzymes. Nat Protoc 2: 891-903.
    • (2007) Nat Protoc , vol.2 , pp. 891-903
    • Reetz, M.T.1    Carballeira, J.D.2
  • 20
    • 33747234745 scopus 로고    scopus 로고
    • Expanding the substrate scope of enzymes: combining mutations obtained by CASTing
    • Reetz MT, Carballeira JD, Peyralans J, Hobenreich H, Maichele A, et al. (2006) Expanding the substrate scope of enzymes: combining mutations obtained by CASTing. Chemistry 12: 6031-6038.
    • (2006) Chemistry , vol.12 , pp. 6031-6038
    • Reetz, M.T.1    Carballeira, J.D.2    Peyralans, J.3    Hobenreich, H.4    Maichele, A.5
  • 22
    • 36749042777 scopus 로고    scopus 로고
    • Latent evolutionary potentials under the neutral mutational drift of an enzyme
    • Amitai G, Gupta RD, Taw k DS, (2007) Latent evolutionary potentials under the neutral mutational drift of an enzyme. HFSP J 1: 67-78.
    • (2007) HFSP J , vol.1 , pp. 67-78
    • Amitai, G.1    Gupta, R.D.2    Taw k, D.S.3
  • 23
    • 41649116075 scopus 로고    scopus 로고
    • A structural model of latent evolutionary potentials underlying neutral networks in proteins
    • Wroe R, Chan HS, Bornberg-Bauer E, (2007) A structural model of latent evolutionary potentials underlying neutral networks in proteins. HFSP J 1: 79-87.
    • (2007) HFSP J , vol.1 , pp. 79-87
    • Wroe, R.1    Chan, H.S.2    Bornberg-Bauer, E.3
  • 24
    • 33751525692 scopus 로고    scopus 로고
    • New algorithms and an in silico benchmark for computational enzyme design
    • Zanghellini A, Jiang L, Wollacott AM, Cheng G, Meiler J, et al. (2006) New algorithms and an in silico benchmark for computational enzyme design. Protein Sci 15: 2785-2794.
    • (2006) Protein Sci , vol.15 , pp. 2785-2794
    • Zanghellini, A.1    Jiang, L.2    Wollacott, A.M.3    Cheng, G.4    Meiler, J.5
  • 25
    • 0030793767 scopus 로고    scopus 로고
    • De novo protein design: fully automated sequence selection
    • Dahiyat BI, Mayo SL, (1997) De novo protein design: fully automated sequence selection. Science 278: 82-87.
    • (1997) Science , vol.278 , pp. 82-87
    • Dahiyat, B.I.1    Mayo, S.L.2
  • 26
    • 70349330137 scopus 로고    scopus 로고
    • Automated scaffold selection for enzyme design
    • Malisi C, Kohlbacher O, Hocker B, (2009) Automated scaffold selection for enzyme design. Proteins 77: 74-83.
    • (2009) Proteins , vol.77 , pp. 74-83
    • Malisi, C.1    Kohlbacher, O.2    Hocker, B.3
  • 27
    • 46449106372 scopus 로고    scopus 로고
    • The minimized dead-end elimination criterion and its appli-cation to protein redesign in a hybrid scoring and search algorithm for computing partition functions over molecular ensembles
    • Georgiev I, Lilien RH, Donald BR, (2008) The minimized dead-end elimination criterion and its appli-cation to protein redesign in a hybrid scoring and search algorithm for computing partition functions over molecular ensembles. J Comput Chem 29: 1527-1542.
    • (2008) J Comput Chem , vol.29 , pp. 1527-1542
    • Georgiev, I.1    Lilien, R.H.2    Donald, B.R.3
  • 29
    • 82955246714 scopus 로고    scopus 로고
    • Active site detection by spatial conformity and electrostatic analysis-unravelling a proteolytic function in shrimp alkaline phosphatase
    • Chakraborty S, Minda R, Salaye L, Bhattacharjee SK, Rao BJ, (2011) Active site detection by spatial conformity and electrostatic analysis-unravelling a proteolytic function in shrimp alkaline phosphatase. PLoS ONE 6: e28470.
    • (2011) PLoS ONE , vol.6
    • Chakraborty, S.1    Minda, R.2    Salaye, L.3    Bhattacharjee, S.K.4    Rao, B.J.5
  • 30
    • 0029944652 scopus 로고    scopus 로고
    • The catalytic mechanism of beta-lactamases: NMR titration of an active-site lysine residue of the TEM-1 enzyme
    • Damblon C, Raquet X, Lian LY, Lamotte-Brasseur J, Fonze E, et al. (1996) The catalytic mechanism of beta-lactamases: NMR titration of an active-site lysine residue of the TEM-1 enzyme. Proc Natl Acad Sci USA 93: 1747-1752.
    • (1996) Proc Natl Acad Sci USA , vol.93 , pp. 1747-1752
    • Damblon, C.1    Raquet, X.2    Lian, L.Y.3    Lamotte-Brasseur, J.4    Fonze, E.5
  • 31
    • 84862682287 scopus 로고    scopus 로고
    • Enumerating pathways of proton abstraction based on a spatial and electrostatic analysis of residues in the catalytic site
    • Chakraborty S, (2012) Enumerating pathways of proton abstraction based on a spatial and electrostatic analysis of residues in the catalytic site. PLoS ONE, In Press.
    • (2012) PLoS ONE, In Press
    • Chakraborty, S.1
  • 32
    • 84857124305 scopus 로고    scopus 로고
    • A measure of the promiscuity of proteins and characteristics of residues in the vicinity of the catalytic site that regulate promiscuity
    • Chakraborty S, Rao BJ, (2012) A measure of the promiscuity of proteins and characteristics of residues in the vicinity of the catalytic site that regulate promiscuity. PLoS ONE 7: e32011.
    • (2012) PLoS ONE , vol.7
    • Chakraborty, S.1    Rao, B.J.2
  • 33
    • 0017272554 scopus 로고
    • Enzyme recruitment in evolution of new function
    • Jensen RA, (1976) Enzyme recruitment in evolution of new function. Annu Rev Microbiol 30: 409-425.
    • (1976) Annu Rev Microbiol , vol.30 , pp. 409-425
    • Jensen, R.A.1
  • 35
    • 77956925998 scopus 로고    scopus 로고
    • Messy biology and the origins of evolutionary innovations
    • Taw k DS, (2010) Messy biology and the origins of evolutionary innovations. Nat Chem Biol 6: 692-696.
    • (2010) Nat Chem Biol , vol.6 , pp. 692-696
    • Taw k, D.S.1
  • 36
    • 79953326533 scopus 로고    scopus 로고
    • Exploiting models of molecular evolution to efficiently direct protein engineering
    • Cole MF, Gaucher EA, (2011) Exploiting models of molecular evolution to efficiently direct protein engineering. J Mol Evol 72: 193-203.
    • (2011) J Mol Evol , vol.72 , pp. 193-203
    • Cole, M.F.1    Gaucher, E.A.2
  • 37
    • 0026049801 scopus 로고
    • Serine beta-lactamases and penicillin-binding proteins
    • Ghuysen JM, (1991) Serine beta-lactamases and penicillin-binding proteins. Annu Rev Microbiol 45: 37-67.
    • (1991) Annu Rev Microbiol , vol.45 , pp. 37-67
    • Ghuysen, J.M.1
  • 38
    • 2942562249 scopus 로고    scopus 로고
    • Evolution of the serine beta-lactamases: past, present and future
    • Hall BG, Barlow M, (2004) Evolution of the serine beta-lactamases: past, present and future. Drug Resist Updat 7: 111-123.
    • (2004) Drug Resist Updat , vol.7 , pp. 111-123
    • Hall, B.G.1    Barlow, M.2
  • 39
    • 0033082703 scopus 로고    scopus 로고
    • The beta-lactamase cycle: a tale of selective pressure and bacterial ingenuity
    • Matagne A, Dubus A, Galleni M, Frere JM, (1999) The beta-lactamase cycle: a tale of selective pressure and bacterial ingenuity. Nat Prod Rep 16: 1-19.
    • (1999) Nat Prod Rep , vol.16 , pp. 1-19
    • Matagne, A.1    Dubus, A.2    Galleni, M.3    Frere, J.M.4
  • 40
    • 0032985224 scopus 로고    scopus 로고
    • Escherichia coli mutants lacking all possible combinations of eight penicillin binding proteins: viability, characteristics, and implications for peptidoglycan synthesis
    • Denome SA, Elf PK, Henderson TA, Nelson DE, Young KD, (1999) Escherichia coli mutants lacking all possible combinations of eight penicillin binding proteins: viability, characteristics, and implications for peptidoglycan synthesis. J Bacteriol 181: 3981-3993.
    • (1999) J Bacteriol , vol.181 , pp. 3981-3993
    • Denome, S.A.1    Elf, P.K.2    Henderson, T.A.3    Nelson, D.E.4    Young, K.D.5
  • 42
    • 0036227417 scopus 로고    scopus 로고
    • Increase of the deacylation rate of PBP2x from Streptococcus pneumoniae by single point mutations mimicking the class A beta-lactamases
    • Chesnel L, Zapun A, Mouz N, Dideberg O, Vernet T, (2002) Increase of the deacylation rate of PBP2x from Streptococcus pneumoniae by single point mutations mimicking the class A beta-lactamases. Eur J Biochem 269: 1678-1683.
    • (2002) Eur J Biochem , vol.269 , pp. 1678-1683
    • Chesnel, L.1    Zapun, A.2    Mouz, N.3    Dideberg, O.4    Vernet, T.5
  • 43
    • 58549119937 scopus 로고    scopus 로고
    • Structure of PBP-A from Ther-mosynechococcus elongatus, a penicillin-binding protein closely related to class A beta-lactamases
    • Urbach C, Evrard C, Pudzaitis V, Fastrez J, Soumillion P, et al. (2009) Structure of PBP-A from Ther-mosynechococcus elongatus, a penicillin-binding protein closely related to class A beta-lactamases. J Mol Biol 386: 109-120.
    • (2009) J Mol Biol , vol.386 , pp. 109-120
    • Urbach, C.1    Evrard, C.2    Pudzaitis, V.3    Fastrez, J.4    Soumillion, P.5
  • 44
    • 0032032930 scopus 로고    scopus 로고
    • Catalytic properties of class A beta-lactamases: efficiency and diversity
    • Matagne A, Lamotte-Brasseur J, Frere JM, (1998) Catalytic properties of class A beta-lactamases: efficiency and diversity. Biochem J 330 (Pt 2): 581-598.
    • (1998) Biochem J , vol.330 , Issue.2 , pp. 581-598
    • Matagne, A.1    Lamotte-Brasseur, J.2    Frere, J.M.3
  • 45
    • 0347362788 scopus 로고    scopus 로고
    • Crystal structure of wild-type penicillin-binding protein 5 from Escherichia coli: implications for deacylation of the acyl-enzyme complex
    • Nicholas RA, Krings S, Tomberg J, Nicola G, Davies C, (2003) Crystal structure of wild-type penicillin-binding protein 5 from Escherichia coli: implications for deacylation of the acyl-enzyme complex. J Biol Chem 278: 52826-52833.
    • (2003) J Biol Chem , vol.278 , pp. 52826-52833
    • Nicholas, R.A.1    Krings, S.2    Tomberg, J.3    Nicola, G.4    Davies, C.5
  • 46
    • 0032502332 scopus 로고    scopus 로고
    • Role of the omega-loop in the activity, substrate specificity, and structure of class A beta-lactamase
    • Banerjee S, Pieper U, Kapadia G, Pannell LK, Herzberg O, (1998) Role of the omega-loop in the activity, substrate specificity, and structure of class A beta-lactamase. Biochemistry 37: 3286-3296.
    • (1998) Biochemistry , vol.37 , pp. 3286-3296
    • Banerjee, S.1    Pieper, U.2    Kapadia, G.3    Pannell, L.K.4    Herzberg, O.5
  • 47
    • 77954797329 scopus 로고    scopus 로고
    • Biocatalytic asymmetric synthesis of chiral amines from ketones applied to sitagliptin manufacture
    • Savile CK, Janey JM, Mundor EC, Moore JC, Tam S, et al. (2010) Biocatalytic asymmetric synthesis of chiral amines from ketones applied to sitagliptin manufacture. Science 329: 305-309.
    • (2010) Science , vol.329 , pp. 305-309
    • Savile, C.K.1    Janey, J.M.2    Mundor, E.C.3    Moore, J.C.4    Tam, S.5
  • 49
    • 84856021987 scopus 로고    scopus 로고
    • Combinatorial reshaping of the Candida antarctica lipase A substrate pocket for enantioselectivity using an extremely condensed library
    • Sandstrom AG, Wikmark Y, Engstrom K, Nyhlen J, Backvall JE, (2012) Combinatorial reshaping of the Candida antarctica lipase A substrate pocket for enantioselectivity using an extremely condensed library. Proc Natl Acad Sci USA 109: 78-83.
    • (2012) Proc Natl Acad Sci USA , vol.109 , pp. 78-83
    • Sandstrom, A.G.1    Wikmark, Y.2    Engstrom, K.3    Nyhlen, J.4    Backvall, J.E.5
  • 50
    • 0037194629 scopus 로고    scopus 로고
    • Discovery of further pyrrolidine trans-lactams as inhibitors of human neutrophil elastase (HNE) with potential as development candidates and the crystal structure of HNE complexed with an inhibitor (GW475151)
    • Macdonald SJ, Dowle MD, Harrison LA, Clarke GD, Inglis GG, et al. (2002) Discovery of further pyrrolidine trans-lactams as inhibitors of human neutrophil elastase (HNE) with potential as development candidates and the crystal structure of HNE complexed with an inhibitor (GW475151). J Med Chem 45: 3878-3890.
    • (2002) J Med Chem , vol.45 , pp. 3878-3890
    • Macdonald, S.J.1    Dowle, M.D.2    Harrison, L.A.3    Clarke, G.D.4    Inglis, G.G.5
  • 53
    • 0027490930 scopus 로고
    • Plant 'pathogenesis-related' proteins and their role in defense against pathogens
    • Stintzi A, Heitz T, Prasad V, Wiedemann-Merdinoglu S, Kau mann S, et al. (1993) Plant 'pathogenesis-related' proteins and their role in defense against pathogens. Biochimie 75: 687-706.
    • (1993) Biochimie , vol.75 , pp. 687-706
    • Stintzi, A.1    Heitz, T.2    Prasad, V.3    Wiedemann-Merdinoglu, S.4    Kau mann, S.5
  • 54
    • 0017280367 scopus 로고
    • Distribution of elastase-like enzyme activity among snake venoms
    • Bernick JJ, Simpson W, (1976) Distribution of elastase-like enzyme activity among snake venoms. Comp Biochem Physiol, B 54: 51-54.
    • (1976) Comp Biochem Physiol, B , vol.54 , pp. 51-54
    • Bernick, J.J.1    Simpson, W.2
  • 55
    • 0041731780 scopus 로고    scopus 로고
    • Isolation and characterization of a cone snail protease with homology to CRISP proteins of the pathogenesis-related protein superfamily
    • Milne TJ, Abbenante G, Tyndall JD, Halliday J, Lewis RJ, (2003) Isolation and characterization of a cone snail protease with homology to CRISP proteins of the pathogenesis-related protein superfamily. J Biol Chem 278: 31105-31110.
    • (2003) J Biol Chem , vol.278 , pp. 31105-31110
    • Milne, T.J.1    Abbenante, G.2    Tyndall, J.D.3    Halliday, J.4    Lewis, R.J.5
  • 56
    • 38849143983 scopus 로고    scopus 로고
    • Neutrophil elastase, proteinase 3 and cathepsin G: physic-ochemical properties, activity and physiopathological functions
    • Korkmaz B, Moreau T, Gauthier F, (2008) Neutrophil elastase, proteinase 3 and cathepsin G: physic-ochemical properties, activity and physiopathological functions. Biochimie 90: 227-242.
    • (2008) Biochimie , vol.90 , pp. 227-242
    • Korkmaz, B.1    Moreau, T.2    Gauthier, F.3
  • 58
    • 0027428548 scopus 로고
    • Evolution of an enzyme activity: crystallographic structure at 2-A resolution of cephalosporinase from the ampC gene of Enterobacter cloacae P99 and comparison with a class A penicillinase
    • Lobkovsky E, Moews PC, Liu H, Zhao H, Frere JM, et al. (1993) Evolution of an enzyme activity: crystallographic structure at 2-A resolution of cephalosporinase from the ampC gene of Enterobacter cloacae P99 and comparison with a class A penicillinase. Proc Natl Acad Sci USA 90: 11257-11261.
    • (1993) Proc Natl Acad Sci USA , vol.90 , pp. 11257-11261
    • Lobkovsky, E.1    Moews, P.C.2    Liu, H.3    Zhao, H.4    Frere, J.M.5
  • 59
    • 56749154097 scopus 로고    scopus 로고
    • Unconventional serine proteases: variations on the catalytic Ser/His/Asp triad configuration
    • Ekici OD, Paetzel M, Dalbey RE, (2008) Unconventional serine proteases: variations on the catalytic Ser/His/Asp triad configuration. Protein Sci 17: 2023-2037.
    • (2008) Protein Sci , vol.17 , pp. 2023-2037
    • Ekici, O.D.1    Paetzel, M.2    Dalbey, R.E.3
  • 60
    • 0035808477 scopus 로고    scopus 로고
    • Crystal structure of a deacylation-defective mutant of penicillin-binding protein 5 at 2.3-A resolution
    • Davies C, White SW, Nicholas RA, (2001) Crystal structure of a deacylation-defective mutant of penicillin-binding protein 5 at 2.3-A resolution. J Biol Chem 276: 616-623.
    • (2001) J Biol Chem , vol.276 , pp. 616-623
    • Davies, C.1    White, S.W.2    Nicholas, R.A.3
  • 61
    • 49149090311 scopus 로고    scopus 로고
    • Directed evolution generates a novel oncolytic virus for the treatment of colon cancer
    • Kuhn I, Harden P, Bauzon M, Chartier C, Nye J, et al. (2008) Directed evolution generates a novel oncolytic virus for the treatment of colon cancer. PLoS ONE 3: e2409.
    • (2008) PLoS ONE , vol.3
    • Kuhn, I.1    Harden, P.2    Bauzon, M.3    Chartier, C.4    Nye, J.5
  • 62
    • 79958708794 scopus 로고    scopus 로고
    • Assessing directed evolution methods for the generation of biosynthetic enzymes with potential in drug biosynthesis
    • Nannemann DP, Birmingham WR, Scism RA, Bachmann BO, (2011) Assessing directed evolution methods for the generation of biosynthetic enzymes with potential in drug biosynthesis. Future Med Chem 3: 809-819.
    • (2011) Future Med Chem , vol.3 , pp. 809-819
    • Nannemann, D.P.1    Birmingham, W.R.2    Scism, R.A.3    Bachmann, B.O.4
  • 63
    • 80052102623 scopus 로고    scopus 로고
    • Strategy and success for the directed evolution of enzymes
    • Dalby PA, (2011) Strategy and success for the directed evolution of enzymes. Curr Opin Struct Biol 21: 473-480.
    • (2011) Curr Opin Struct Biol , vol.21 , pp. 473-480
    • Dalby, P.A.1
  • 64
    • 78349313517 scopus 로고    scopus 로고
    • Beyond directed evolution-semi-rational protein engineering and design
    • Lutz S, (2010) Beyond directed evolution-semi-rational protein engineering and design. Curr Opin Biotechnol 21: 734-743.
    • (2010) Curr Opin Biotechnol , vol.21 , pp. 734-743
    • Lutz, S.1
  • 65
    • 15244340939 scopus 로고    scopus 로고
    • Altering protein specificity: techniques and applications
    • Antikainen NM, Martin SF, (2005) Altering protein specificity: techniques and applications. Bioorg Med Chem 13: 2701-2716.
    • (2005) Bioorg Med Chem , vol.13 , pp. 2701-2716
    • Antikainen, N.M.1    Martin, S.F.2
  • 66
    • 0038148710 scopus 로고    scopus 로고
    • Conformational diversity and protein evolution-a 60-year-old hypothesis revisited
    • James LC, Taw k DS, (2003) Conformational diversity and protein evolution-a 60-year-old hypothesis revisited. Trends Biochem Sci 28: 361-368.
    • (2003) Trends Biochem Sci , vol.28 , pp. 361-368
    • James, L.C.1    Taw k, D.S.2
  • 67
    • 49349085897 scopus 로고    scopus 로고
    • The subtle benefits of being promiscuous: adaptive evolution potentiated by enzyme promiscuity
    • Depristo MA, (2007) The subtle benefits of being promiscuous: adaptive evolution potentiated by enzyme promiscuity. HFSP J 1: 94-98.
    • (2007) HFSP J , vol.1 , pp. 94-98
    • Depristo, M.A.1
  • 68
    • 84855440297 scopus 로고    scopus 로고
    • Functional evolution of dupli-cated odorant-binding protein genes, Obp57d and Obp57e, in Drosophila
    • Harada E, Nakagawa J, Asano T, Taoka M, Sorimachi H, et al. (2012) Functional evolution of dupli-cated odorant-binding protein genes, Obp57d and Obp57e, in Drosophila. PLoS ONE 7: e29710.
    • (2012) PLoS ONE , vol.7
    • Harada, E.1    Nakagawa, J.2    Asano, T.3    Taoka, M.4    Sorimachi, H.5
  • 69
    • 37049099038 scopus 로고
    • Studies on the oxidase activity of copper(ii) carboxypeptidase a
    • Yamamura K, Kaiser ET, (1976) Studies on the oxidase activity of copper(ii) carboxypeptidase a. J Chem Soc, Chem Commun pp. 830-831.
    • (1976) J Chem Soc, Chem Commun , pp. 830-831
    • Yamamura, K.1    Kaiser, E.T.2
  • 70
    • 84860234014 scopus 로고    scopus 로고
    • Many pathways in laboratory evolution can lead to improved enzymes: how to escape from local minima
    • Gumulya Y, Sanchis J, Reetz MT, (2012) Many pathways in laboratory evolution can lead to improved enzymes: how to escape from local minima. Chembiochem 13: 1060-1066.
    • (2012) Chembiochem , vol.13 , pp. 1060-1066
    • Gumulya, Y.1    Sanchis, J.2    Reetz, M.T.3
  • 71
    • 33746891446 scopus 로고    scopus 로고
    • Penicillin binding proteins: key players in bacterial cell cycle and drug resistance processes
    • Macheboeuf P, Contreras-Martel C, Job V, Dideberg O, Dessen A, (2006) Penicillin binding proteins: key players in bacterial cell cycle and drug resistance processes. FEMS Microbiol Rev 30: 673-691.
    • (2006) FEMS Microbiol Rev , vol.30 , pp. 673-691
    • Macheboeuf, P.1    Contreras-Martel, C.2    Job, V.3    Dideberg, O.4    Dessen, A.5
  • 72
    • 77149165713 scopus 로고    scopus 로고
    • Updated functional classification of beta-lactamases
    • Bush K, Jacoby GA, (2010) Updated functional classification of beta-lactamases. Antimicrob Agents Chemother 54: 969-976.
    • (2010) Antimicrob Agents Chemother , vol.54 , pp. 969-976
    • Bush, K.1    Jacoby, G.A.2
  • 73
    • 57749084589 scopus 로고    scopus 로고
    • A new family of cyanobacterial penicillin-binding proteins. A missing link in the evolution of class A beta-lactamases
    • Urbach C, Fastrez J, Soumillion P, (2008) A new family of cyanobacterial penicillin-binding proteins. A missing link in the evolution of class A beta-lactamases. J Biol Chem 283: 32516-32526.
    • (2008) J Biol Chem , vol.283 , pp. 32516-32526
    • Urbach, C.1    Fastrez, J.2    Soumillion, P.3
  • 74
    • 0037378572 scopus 로고    scopus 로고
    • Sequences near the active site in chimeric penicillin binding proteins 5 and 6 a ect uniform morphology of Escherichia coli
    • Ghosh AS, Young KD, (2003) Sequences near the active site in chimeric penicillin binding proteins 5 and 6 a ect uniform morphology of Escherichia coli. J Bacteriol 185: 2178-2186.
    • (2003) J Bacteriol , vol.185 , pp. 2178-2186
    • Ghosh, A.S.1    Young, K.D.2
  • 75
    • 80052356047 scopus 로고    scopus 로고
    • PBP5, PBP6 and DacD play different roles in intrinsic β-lactam resistance of Escherichia coli
    • Sarkar SK, Dutta M, Chowdhury C, Kumar A, Ghosh AS, (2011) PBP5, PBP6 and DacD play different roles in intrinsic β-lactam resistance of Escherichia coli. Microbiology (Reading, Engl) 157: 2702-2707.
    • (2011) Microbiology (Reading, Engl) , vol.157 , pp. 2702-2707
    • Sarkar, S.K.1    Dutta, M.2    Chowdhury, C.3    Kumar, A.4    Ghosh, A.S.5
  • 76
    • 46249130782 scopus 로고    scopus 로고
    • Physiological functions of D-alanine carboxypeptidases in Escherichia coli
    • Ghosh AS, Chowdhury C, Nelson DE, (2008) Physiological functions of D-alanine carboxypeptidases in Escherichia coli. Trends Microbiol 16: 309{317.
    • (2008) Trends Microbiol , vol.16 , pp. 309-317
    • Ghosh, A.S.1    Chowdhury, C.2    Nelson, D.E.3
  • 77
  • 78
    • 3242886771 scopus 로고    scopus 로고
    • PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations
    • Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA, (2004) PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res 32: W665-667.
    • (2004) Nucleic Acids Res , vol.32
    • Dolinsky, T.J.1    Nielsen, J.E.2    McCammon, J.A.3    Baker, N.A.4
  • 80
    • 0034201441 scopus 로고    scopus 로고
    • EMBOSS: the European Molecular Biology Open Software Suite
    • Rice P, Longden I, Bleasby A, (2000) EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 16: 276-277.
    • (2000) Trends Genet , vol.16 , pp. 276-277
    • Rice, P.1    Longden, I.2    Bleasby, A.3
  • 81
    • 38849092210 scopus 로고    scopus 로고
    • A note on difficult structure alignment problems
    • Sippl MJ, Wiederstein M, (2008) A note on difficult structure alignment problems. Bioinformatics 24: 426-427.
    • (2008) Bioinformatics , vol.24 , pp. 426-427
    • Sippl, M.J.1    Wiederstein, M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.