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Volumn 586, Issue 19, 2012, Pages 3330-3335

Sequence-function-stability relationships in proteins from datasets of functionally annotated variants: The case of TEM β-lactamases

Author keywords

Antibiotic resistance; Function stability tradeoff; Lactamase; Protein evolution; Structure function relationship; TEM

Indexed keywords

AMINO ACID; BETA LACTAMASE; BETA LACTAMASE TEM; CEFOTAXIME; CLAVULANIC ACID; ENZYME VARIANT; UNCLASSIFIED DRUG;

EID: 84866602137     PISSN: 00145793     EISSN: 18733468     Source Type: Journal    
DOI: 10.1016/j.febslet.2012.07.010     Document Type: Article
Times cited : (25)

References (42)
  • 1
    • 80053393229 scopus 로고    scopus 로고
    • Protein design in metabolic engineering and synthetic biology
    • J. Pleiss Protein design in metabolic engineering and synthetic biology Curr. Opin. Biotechnol. 22 2011 611 617
    • (2011) Curr. Opin. Biotechnol. , vol.22 , pp. 611-617
    • Pleiss, J.1
  • 4
    • 0031449442 scopus 로고    scopus 로고
    • Beta-Lactamases: Quality and resistance
    • A.A. Medeiros Beta-Lactamases: quality and resistance Clin. Microbiol. Infect. 3 Suppl 4 1997 S2 S9
    • (1997) Clin. Microbiol. Infect. , vol.3 , Issue.SUPPL. 4
    • Medeiros, A.A.1
  • 5
    • 0032032930 scopus 로고    scopus 로고
    • Catalytic properties of class A beta-lactamases: Efficiency and diversity
    • A. Matagne, J. Lamotte-Brasseur, and J.M. FrŠre Catalytic properties of class A beta-lactamases: efficiency and diversity Biochem. J. 330 1998 581 598
    • (1998) Biochem. J. , vol.330 , pp. 581-598
    • Matagne, A.1    Lamotte-Brasseur, J.2    Fršre, J.M.3
  • 6
    • 77957770819 scopus 로고    scopus 로고
    • Alarming β-lactamase-mediated resistance in multidrug-resistant Enterobacteriaceae
    • K. Bush Alarming β-lactamase-mediated resistance in multidrug-resistant Enterobacteriaceae Curr. Opin. Microbiol. 13 2010 558 564
    • (2010) Curr. Opin. Microbiol. , vol.13 , pp. 558-564
    • Bush, K.1
  • 7
    • 27144490073 scopus 로고    scopus 로고
    • Extended-spectrum beta-lactamases: A clinical update
    • D.L. Paterson, and R.A. Bonomo Extended-spectrum beta-lactamases: a clinical update Clin. Microbiol. Rev. 18 2005 657 686
    • (2005) Clin. Microbiol. Rev. , vol.18 , pp. 657-686
    • Paterson, D.L.1    Bonomo, R.A.2
  • 8
    • 33645666942 scopus 로고    scopus 로고
    • Darwinian evolution can follow only very few mutational paths to fitter proteins
    • D.M. Weinreich, N.F. Delaney, M.A. Depristo, and D.L. Hartl Darwinian evolution can follow only very few mutational paths to fitter proteins Science 312 2006 111 114
    • (2006) Science , vol.312 , pp. 111-114
    • Weinreich, D.M.1    Delaney, N.F.2    Depristo, M.A.3    Hartl, D.L.4
  • 10
    • 0034607420 scopus 로고    scopus 로고
    • Rapid in vivo evolution of a beta-lactamase using phagemids
    • J. Long-McGie, A.D. Liu, and V. Schellenberger Rapid in vivo evolution of a beta-lactamase using phagemids Biotechnol. Bioeng. 68 2000 121 125
    • (2000) Biotechnol. Bioeng. , vol.68 , pp. 121-125
    • Long-Mcgie, J.1    Liu, A.D.2    Schellenberger, V.3
  • 11
    • 0036295508 scopus 로고    scopus 로고
    • Evolution of an antibiotic resistance enzyme constrained by stability and activity trade-offs
    • X. Wang, G. Minasov, and B.K. Shoichet Evolution of an antibiotic resistance enzyme constrained by stability and activity trade-offs J. Mol. Biol. 320 2002 85 95
    • (2002) J. Mol. Biol. , vol.320 , pp. 85-95
    • Wang, X.1    Minasov, G.2    Shoichet, B.K.3
  • 12
    • 0035122917 scopus 로고    scopus 로고
    • Predicting the emergence of antibiotic resistance by directed evolution and structural analysis
    • M.C. Orencia, J.S. Yoon, J.E. Ness, W.P. Stemmer, and R.C. Stevens Predicting the emergence of antibiotic resistance by directed evolution and structural analysis Nat. Struct. Biol. 8 2001 238 242
    • (2001) Nat. Struct. Biol. , vol.8 , pp. 238-242
    • Orencia, M.C.1    Yoon, J.S.2    Ness, J.E.3    Stemmer, W.P.4    Stevens, R.C.5
  • 14
    • 0028050350 scopus 로고
    • Rapid evolution of a protein in vitro by DNA shuffling
    • W.P. Stemmer Rapid evolution of a protein in vitro by DNA shuffling Nature 370 1994 389 391
    • (1994) Nature , vol.370 , pp. 389-391
    • Stemmer, W.P.1
  • 15
    • 14744267551 scopus 로고    scopus 로고
    • Evolution of transposons containing blaTEM genes
    • S.R. Partridge, and R.M. Hall Evolution of transposons containing blaTEM genes Antimicrob. Agents Chemother. 49 2005 1267 1268
    • (2005) Antimicrob. Agents Chemother. , vol.49 , pp. 1267-1268
    • Partridge, S.R.1    Hall, R.M.2
  • 16
    • 25644459220 scopus 로고    scopus 로고
    • Mimicking natural evolution in metallo-beta-lactamases through second-shell ligand mutations
    • P.E. Tomatis, R.M. Rasia, L. Segovia, and A.J. Vila Mimicking natural evolution in metallo-beta-lactamases through second-shell ligand mutations Proc. Natl. Acad. Sci. USA 102 2005 13761 13766
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 13761-13766
    • Tomatis, P.E.1    Rasia, R.M.2    Segovia, L.3    Vila, A.J.4
  • 17
    • 0037396711 scopus 로고    scopus 로고
    • Experimental prediction of the natural evolution of antibiotic resistance
    • M. Barlow, and B.G. Hall Experimental prediction of the natural evolution of antibiotic resistance Genetics 163 2003 1237 1241
    • (2003) Genetics , vol.163 , pp. 1237-1241
    • Barlow, M.1    Hall, B.G.2
  • 19
    • 0013850042 scopus 로고
    • Penicillinase synthesis controlled by infectious R factors in Enterobacteriaceae
    • N. Datta, and P. Kontomichalou Penicillinase synthesis controlled by infectious R factors in Enterobacteriaceae Nature 208 1965 239 241
    • (1965) Nature , vol.208 , pp. 239-241
    • Datta, N.1    Kontomichalou, P.2
  • 20
    • 78649360645 scopus 로고    scopus 로고
    • Natural evolution of TEM-1 beta-lactamase: Experimental reconstruction and clinical relevance
    • M.L.M. Salverda, G.M. Arjan, J. de Visser, and M. Barlow Natural evolution of TEM-1 beta-lactamase: experimental reconstruction and clinical relevance FEMS Microbiol. Lett. 2010 1015 1036
    • (2010) FEMS Microbiol. Lett. , pp. 1015-1036
    • Salverda, M.L.M.1    Arjan, G.M.2    De Visser, J.3    Barlow, M.4
  • 21
    • 70349567532 scopus 로고    scopus 로고
    • The Lactamase Engineering Database: A critical survey of TEM sequences in public databases
    • Q.K. Thai, F. Bos, and J. Pleiss The Lactamase Engineering Database: a critical survey of TEM sequences in public databases BMC Genomics 10 2009 390
    • (2009) BMC Genomics , vol.10 , pp. 390
    • Thai, Q.K.1    Bos, F.2    Pleiss, J.3
  • 22
    • 0036320784 scopus 로고    scopus 로고
    • Predicting Evolutionary Potential. in vitro evolution accurately reproduces natural evolution of the tem beta-lactamase
    • M. Barlow, and B.G. Hall Predicting Evolutionary Potential. In vitro evolution accurately reproduces natural evolution of the tem beta-lactamase Genetics 161 2002 1355B 1355
    • (2002) Genetics , vol.161
    • Barlow, M.1    Hall, B.G.2
  • 24
    • 0036721168 scopus 로고    scopus 로고
    • Predicting evolution by in vitro evolution requires determining evolutionary pathways
    • B.G. Hall Predicting evolution by in vitro evolution requires determining evolutionary pathways Antimicrob. Agents Chemother. 46 2002 3035 3038
    • (2002) Antimicrob. Agents Chemother. , vol.46 , pp. 3035-3038
    • Hall, B.G.1
  • 25
    • 0029071785 scopus 로고
    • A functional classification scheme for beta-lactamases and its correlation with molecular structure
    • K. Bush, G.A. Jacoby, and A.A. Medeiros A functional classification scheme for beta-lactamases and its correlation with molecular structure Antimicrob. Agents Chemother. 39 1995 1211 1233
    • (1995) Antimicrob. Agents Chemother. , vol.39 , pp. 1211-1233
    • Bush, K.1    Jacoby, G.A.2    Medeiros, A.A.3
  • 26
    • 77149165713 scopus 로고    scopus 로고
    • Updated functional classification of -lactamases
    • K. Bush, and G.A. Jacoby Updated functional classification of -lactamases Antimicrob. Agents Chemother. 54 2010 969 976
    • (2010) Antimicrob. Agents Chemother. , vol.54 , pp. 969-976
    • Bush, K.1    Jacoby, G.A.2
  • 28
    • 85043220576 scopus 로고    scopus 로고
    • A standard numbering scheme for the Class Abeta-lactamases
    • R.P. Ambler A standard numbering scheme for the Class Abeta-lactamases Biochem. J. 276 2011 269 270
    • (2011) Biochem. J. , vol.276 , pp. 269-270
    • Ambler, R.P.1
  • 29
    • 70450242805 scopus 로고    scopus 로고
    • Exploring protein fitness landscapes by directed evolution
    • P.A. Romero, and F.H. Arnold Exploring protein fitness landscapes by directed evolution Nat. Rev. Mol. Cell Biol. 10 2009 866 876
    • (2009) Nat. Rev. Mol. Cell Biol. , vol.10 , pp. 866-876
    • Romero, P.A.1    Arnold, F.H.2
  • 31
    • 0036384211 scopus 로고    scopus 로고
    • Structural bases of stability-function tradeoffs in enzymes
    • B.M. Beadle, and B.K. Shoichet Structural bases of stability-function tradeoffs in enzymes J. Mol. Biol. 321 2002 285 296
    • (2002) J. Mol. Biol. , vol.321 , pp. 285-296
    • Beadle, B.M.1    Shoichet, B.K.2
  • 32
    • 67650287695 scopus 로고    scopus 로고
    • In the light of directed evolution: Pathways of adaptive protein evolution
    • J.D. Bloom, and F.H. Arnold In the light of directed evolution: pathways of adaptive protein evolution Proc. Natl. Acad. Sci. USA 2009 9995 10000
    • (2009) Proc. Natl. Acad. Sci. USA , pp. 9995-10000
    • Bloom, J.D.1    Arnold, F.H.2
  • 33
    • 0030788941 scopus 로고    scopus 로고
    • A natural polymorphism in b-lactamase is a global suppressor
    • W. Huang, and T. Palzkill A natural polymorphism in b-lactamase is a global suppressor Proc. Nat. Acad. Sci. USA 94 1997 8801 8806
    • (1997) Proc. Nat. Acad. Sci. USA , vol.94 , pp. 8801-8806
    • Huang, W.1    Palzkill, T.2
  • 35
    • 78649529303 scopus 로고    scopus 로고
    • Multiple global suppressors of protein stability defects facilitate the evolution of extended-spectrum TEM -lactamases
    • N.G. Brown, J.M. Pennington, W. Huang, T. Ayvaz, and T. Palzkill Multiple global suppressors of protein stability defects facilitate the evolution of extended-spectrum TEM -lactamases J. Mol. Biol. 404 2010 832 846
    • (2010) J. Mol. Biol. , vol.404 , pp. 832-846
    • Brown, N.G.1    Pennington, J.M.2    Huang, W.3    Ayvaz, T.4    Palzkill, T.5
  • 37
    • 80053445930 scopus 로고    scopus 로고
    • Network Models of TEM β-Lactamase Mutations Coevolving under Antibiotic Selection Show Modular Structure and Anticipate Evolutionary Trajectories
    • V.B. Guthrie, J. Allen, M. Camps, and R. Karchin Network Models of TEM β-Lactamase Mutations Coevolving under Antibiotic Selection Show Modular Structure and Anticipate Evolutionary Trajectories PLoS Comp. Biol. 7 2011 e1002184
    • (2011) PLoS Comp. Biol. , vol.7 , pp. 1002184
    • Guthrie, V.B.1    Allen, J.2    Camps, M.3    Karchin, R.4
  • 38
    • 36549064186 scopus 로고    scopus 로고
    • Accurate prediction of enzyme mutant activity based on a multibody statistical potential
    • M. Masso, and I.I. Waisman Accurate prediction of enzyme mutant activity based on a multibody statistical potential Bioinformatics 23 2007 3155 3161
    • (2007) Bioinformatics , vol.23 , pp. 3155-3161
    • Masso, M.1    Waisman, I.I.2
  • 39
    • 0035937259 scopus 로고    scopus 로고
    • Predicting the functional consequences of non-synonymous single nucleotide polymorphisms
    • D. Chasman, and R.M. Adams Predicting the functional consequences of non-synonymous single nucleotide polymorphisms J. Mol. Biol. 307 2001 683 706
    • (2001) J. Mol. Biol. , vol.307 , pp. 683-706
    • Chasman, D.1    Adams, R.M.2
  • 40
    • 9644283060 scopus 로고    scopus 로고
    • Predicting enzyme class from protein structure without alignments
    • P.D. Dobson, and A.J. Doig Predicting enzyme class from protein structure without alignments J. Mol. Biol. 345 2005 187 199
    • (2005) J. Mol. Biol. , vol.345 , pp. 187-199
    • Dobson, P.D.1    Doig, A.J.2
  • 41
    • 0036130770 scopus 로고    scopus 로고
    • Classification of G-protein coupled receptors by alignment-independent extraction of principal chemical properties of primary amino acid sequences
    • M. Lapinsh, A. Gutcaits, P. Prusis, C. Post, L. Torbjörn, and J.E.S. Wikberg Classification of G-protein coupled receptors by alignment-independent extraction of principal chemical properties of primary amino acid sequences Protein Sci. 11 2002 795 805
    • (2002) Protein Sci. , vol.11 , pp. 795-805
    • Lapinsh, M.1    Gutcaits, A.2    Prusis, P.3    Post, C.4    Torbjörn, L.5    Wikberg, J.E.S.6
  • 42
    • 0022385890 scopus 로고
    • A multivariate study of the relationship between the genetic code and the physical-chemical properties of amino acids
    • M. Sjöstrom, and S. Wold A multivariate study of the relationship between the genetic code and the physical-chemical properties of amino acids J. Mol. Evol. 22 1985 272 277
    • (1985) J. Mol. Evol. , vol.22 , pp. 272-277
    • Sjöstrom, M.1    Wold, S.2


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