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Volumn 21, Issue , 2014, Pages 73-80

Accuracy-rate tradeoffs: How do enzymes meet demands of selectivity and catalytic efficiency?

Author keywords

[No Author keywords available]

Indexed keywords

DNA METHYLTRANSFERASE; ENZYME; POLYDEOXYRIBONUCLEOTIDE SYNTHASE; PROTEIN; DNA (CYTOSINE 5) METHYLTRANSFERASE;

EID: 84902670142     PISSN: 13675931     EISSN: 18790402     Source Type: Journal    
DOI: 10.1016/j.cbpa.2014.05.008     Document Type: Review
Times cited : (106)

References (47)
  • 2
    • 77956925998 scopus 로고    scopus 로고
    • Messy biology and the origins of evolutionary innovations
    • Tawfik D.S. Messy biology and the origins of evolutionary innovations. Nat Chem Biol 2010, 6:692-696.
    • (2010) Nat Chem Biol , vol.6 , pp. 692-696
    • Tawfik, D.S.1
  • 3
    • 77953623874 scopus 로고    scopus 로고
    • Enzyme promiscuity: a mechanistic and evolutionary perspective
    • Khersonsky O., Tawfik D.S. Enzyme promiscuity: a mechanistic and evolutionary perspective. Annu Rev Biochem 2010, 79:471-505.
    • (2010) Annu Rev Biochem , vol.79 , pp. 471-505
    • Khersonsky, O.1    Tawfik, D.S.2
  • 4
    • 84869212334 scopus 로고    scopus 로고
    • Evolutionary layering and the limits to cellular perfection
    • Lynch M. Evolutionary layering and the limits to cellular perfection. Proc Natl Acad Sci U S A 2012, 109:18851-18856.
    • (2012) Proc Natl Acad Sci U S A , vol.109 , pp. 18851-18856
    • Lynch, M.1
  • 5
    • 2942639702 scopus 로고    scopus 로고
    • Survival versus maintenance of genetic stability: a conflict of priorities during stress
    • Matic I., Taddei F., Radman M. Survival versus maintenance of genetic stability: a conflict of priorities during stress. Res Microbiol 2004, 155:337-341.
    • (2004) Res Microbiol , vol.155 , pp. 337-341
    • Matic, I.1    Taddei, F.2    Radman, M.3
  • 6
    • 14844325784 scopus 로고    scopus 로고
    • Robustness, evolvability, and neutrality
    • Wagner A. Robustness, evolvability, and neutrality. FEBS Lett 2005, 579:1772-1778.
    • (2005) FEBS Lett , vol.579 , pp. 1772-1778
    • Wagner, A.1
  • 7
    • 84874193830 scopus 로고    scopus 로고
    • Evaluating evolutionary models of stress-induced mutagenesis in bacteria
    • MacLean R.C., Torres-Barcelo C., Moxon R. Evaluating evolutionary models of stress-induced mutagenesis in bacteria. Nat Rev Genet 2013, 14:221-227.
    • (2013) Nat Rev Genet , vol.14 , pp. 221-227
    • MacLean, R.C.1    Torres-Barcelo, C.2    Moxon, R.3
  • 8
    • 31144465690 scopus 로고    scopus 로고
    • Quasispecies diversity determines pathogenesis through cooperative interactions in a viral population
    • Vignuzzi M., Stone J.K., Arnold J.J., Cameron C.E., Andino R. Quasispecies diversity determines pathogenesis through cooperative interactions in a viral population. Nature 2006, 439:344-348.
    • (2006) Nature , vol.439 , pp. 344-348
    • Vignuzzi, M.1    Stone, J.K.2    Arnold, J.J.3    Cameron, C.E.4    Andino, R.5
  • 10
    • 84864341793 scopus 로고    scopus 로고
    • Speed, dissipation, and error in kinetic proofreading
    • Murugan A., Huse D.A., Leibler S. Speed, dissipation, and error in kinetic proofreading. Proc Natl Acad Sci U S A 2012, 109:12034-12039.
    • (2012) Proc Natl Acad Sci U S A , vol.109 , pp. 12034-12039
    • Murugan, A.1    Huse, D.A.2    Leibler, S.3
  • 11
    • 79958097953 scopus 로고    scopus 로고
    • The moderately efficient enzyme: evolutionary and physicochemical trends shaping enzyme parameters
    • Bar-Even A., Noor E., Savir Y., Liebermeister W., Davidi D., Tawfik D.S., Milo R. The moderately efficient enzyme: evolutionary and physicochemical trends shaping enzyme parameters. Biochemistry 2011, 50:4402-4410.
    • (2011) Biochemistry , vol.50 , pp. 4402-4410
    • Bar-Even, A.1    Noor, E.2    Savir, Y.3    Liebermeister, W.4    Davidi, D.5    Tawfik, D.S.6    Milo, R.7
  • 12
    • 0017493504 scopus 로고
    • Efficiency and evolution of enzyme catalysis
    • Albery W.J., Knowles J.R. Efficiency and evolution of enzyme catalysis. Angew Chem Int Ed Engl 1977, 16:285-293.
    • (1977) Angew Chem Int Ed Engl , vol.16 , pp. 285-293
    • Albery, W.J.1    Knowles, J.R.2
  • 13
    • 0037032998 scopus 로고    scopus 로고
    • Efficiency of correct nucleotide insertion governs DNA polymerase fidelity
    • Beard W.A., Shock D.D., Vande Berg B.J., Wilson S.H. Efficiency of correct nucleotide insertion governs DNA polymerase fidelity. J Biol Chem 2002, 277:47393-47398.
    • (2002) J Biol Chem , vol.277 , pp. 47393-47398
    • Beard, W.A.1    Shock, D.D.2    Vande Berg, B.J.3    Wilson, S.H.4
  • 17
    • 79953310914 scopus 로고    scopus 로고
    • Optimizing non-natural protein function with directed evolution
    • Brustad E.M., Arnold F.H. Optimizing non-natural protein function with directed evolution. Curr Opin Chem Biol 2011, 15:201-210.
    • (2011) Curr Opin Chem Biol , vol.15 , pp. 201-210
    • Brustad, E.M.1    Arnold, F.H.2
  • 18
    • 84894101033 scopus 로고    scopus 로고
    • Negative selection and stringency modulation in phage-assisted continuous evolution
    • Carlson J.C., Badran A.H., Guggiana-Nilo D.A., Liu D.R. Negative selection and stringency modulation in phage-assisted continuous evolution. Nat Chem Biol 2014, 10:216-222.
    • (2014) Nat Chem Biol , vol.10 , pp. 216-222
    • Carlson, J.C.1    Badran, A.H.2    Guggiana-Nilo, D.A.3    Liu, D.R.4
  • 21
  • 22
    • 77951226274 scopus 로고    scopus 로고
    • At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis?
    • Kamerlin S.C., Warshel A. At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis?. Proteins 2010, 78:1339-1375.
    • (2010) Proteins , vol.78 , pp. 1339-1375
    • Kamerlin, S.C.1    Warshel, A.2
  • 23
    • 80052585808 scopus 로고    scopus 로고
    • Prechemistry versus preorganization in DNA replication fidelity
    • Ram Prasad B., Warshel A. Prechemistry versus preorganization in DNA replication fidelity. Proteins 2011, 79:2900-2919.
    • (2011) Proteins , vol.79 , pp. 2900-2919
    • Ram Prasad, B.1    Warshel, A.2
  • 24
    • 33845496747 scopus 로고    scopus 로고
    • Discovery of a substrate selectivity switch in tyrosine ammonia-lyase, a member of the aromatic amino acid lyase family
    • Watts K.T., Mijts B.N., Lee P.C., Manning A.J., Schmidt-Dannert C. Discovery of a substrate selectivity switch in tyrosine ammonia-lyase, a member of the aromatic amino acid lyase family. Chem Biol 2006, 13:1317-1326.
    • (2006) Chem Biol , vol.13 , pp. 1317-1326
    • Watts, K.T.1    Mijts, B.N.2    Lee, P.C.3    Manning, A.J.4    Schmidt-Dannert, C.5
  • 25
    • 84874416569 scopus 로고    scopus 로고
    • Mutagenesis of a specificity-determining residue in tyrosine hydroxylase establishes that the enzyme is a robust phenylalanine hydroxylase but a fragile tyrosine hydroxylase
    • Daubner S.C., Avila A., Bailey J.O., Barrera D., Bermudez J.Y., Giles D.H., Khan C.A., Shaheen N., Thompson J.W., Vasquez J., et al. Mutagenesis of a specificity-determining residue in tyrosine hydroxylase establishes that the enzyme is a robust phenylalanine hydroxylase but a fragile tyrosine hydroxylase. Biochemistry 2013, 52:1446-1455.
    • (2013) Biochemistry , vol.52 , pp. 1446-1455
    • Daubner, S.C.1    Avila, A.2    Bailey, J.O.3    Barrera, D.4    Bermudez, J.Y.5    Giles, D.H.6    Khan, C.A.7    Shaheen, N.8    Thompson, J.W.9    Vasquez, J.10
  • 26
    • 84857030795 scopus 로고    scopus 로고
    • Structural analyses clarify the complex control of mistranslation by tRNA synthetases
    • Guo M., Schimmel P. Structural analyses clarify the complex control of mistranslation by tRNA synthetases. Curr Opin Struct Biol 2012, 22:119-126.
    • (2012) Curr Opin Struct Biol , vol.22 , pp. 119-126
    • Guo, M.1    Schimmel, P.2
  • 28
    • 79951622275 scopus 로고    scopus 로고
    • Arsenate replacing phosphate: alternative life chemistries and ion promiscuity
    • Tawfik D.S., Viola R.E. Arsenate replacing phosphate: alternative life chemistries and ion promiscuity. Biochemistry 2011, 50:1128-1134.
    • (2011) Biochemistry , vol.50 , pp. 1128-1134
    • Tawfik, D.S.1    Viola, R.E.2
  • 29
    • 21644487218 scopus 로고    scopus 로고
    • Structural basis for discrimination between oxyanion substrates or inhibitors in aspartate-beta-semialdehyde dehydrogenase
    • Faehnle C.R., Blanco J., Viola R.E. Structural basis for discrimination between oxyanion substrates or inhibitors in aspartate-beta-semialdehyde dehydrogenase. Acta Crystallogr D: Biol Crystallogr 2004, 60:2320-2324.
    • (2004) Acta Crystallogr D: Biol Crystallogr , vol.60 , pp. 2320-2324
    • Faehnle, C.R.1    Blanco, J.2    Viola, R.E.3
  • 30
    • 0842313326 scopus 로고    scopus 로고
    • Altering the sequence specificity of HaeIII methyltransferase by directed evolution using in vitro compartmentalization
    • Cohen H.M., Tawfik D.S., Griffiths A.D. Altering the sequence specificity of HaeIII methyltransferase by directed evolution using in vitro compartmentalization. Protein Eng Des Sel 2004, 17:3-11.
    • (2004) Protein Eng Des Sel , vol.17 , pp. 3-11
    • Cohen, H.M.1    Tawfik, D.S.2    Griffiths, A.D.3
  • 31
    • 84871226912 scopus 로고    scopus 로고
    • Evolutionary transitions to new DNA methyltransferases through target site expansion and shrinkage
    • Rockah-Shmuel L., Tawfik D.S. Evolutionary transitions to new DNA methyltransferases through target site expansion and shrinkage. Nucleic Acids Res 2012, 40:11627-11637.
    • (2012) Nucleic Acids Res , vol.40 , pp. 11627-11637
    • Rockah-Shmuel, L.1    Tawfik, D.S.2
  • 32
    • 84862338135 scopus 로고    scopus 로고
    • DNA interaction of the CcrM DNA methyltransferase: a mutational and modeling study
    • Albu R.F., Zacharias M., Jurkowski T.P., Jeltsch A. DNA interaction of the CcrM DNA methyltransferase: a mutational and modeling study. Chembiochem 2012, 13:1304-1311.
    • (2012) Chembiochem , vol.13 , pp. 1304-1311
    • Albu, R.F.1    Zacharias, M.2    Jurkowski, T.P.3    Jeltsch, A.4
  • 34
    • 84862963791 scopus 로고    scopus 로고
    • Genetic code translation displays a linear trade-off between efficiency and accuracy of tRNA selection
    • Johansson M., Zhang J., Ehrenberg M. Genetic code translation displays a linear trade-off between efficiency and accuracy of tRNA selection. Proc Natl Acad Sci U S A 2012, 109:131-136.
    • (2012) Proc Natl Acad Sci U S A , vol.109 , pp. 131-136
    • Johansson, M.1    Zhang, J.2    Ehrenberg, M.3
  • 35
    • 84886434125 scopus 로고    scopus 로고
    • Naked mole-rat has increased translational fidelity compared with the mouse, as well as a unique 28S ribosomal RNA cleavage
    • Azpurua J., Ke Z., Chen I.X., Zhang Q., Ermolenko D.N., Zhang Z.D., Gorbunova V., Seluanov A. Naked mole-rat has increased translational fidelity compared with the mouse, as well as a unique 28S ribosomal RNA cleavage. Proc Natl Acad Sci U S A 2013, 110:17350-17355.
    • (2013) Proc Natl Acad Sci U S A , vol.110 , pp. 17350-17355
    • Azpurua, J.1    Ke, Z.2    Chen, I.X.3    Zhang, Q.4    Ermolenko, D.N.5    Zhang, Z.D.6    Gorbunova, V.7    Seluanov, A.8
  • 36
    • 77954743785 scopus 로고    scopus 로고
    • Mutational effects and the evolution of new protein functions
    • Soskine M., Tawfik D.S. Mutational effects and the evolution of new protein functions. Nat Rev Genet 2010, 11:572-582.
    • (2010) Nat Rev Genet , vol.11 , pp. 572-582
    • Soskine, M.1    Tawfik, D.S.2
  • 37
    • 84901408859 scopus 로고    scopus 로고
    • A comprehensive, high-resolution map of a gene's fitness landscape
    • Firnberg E., Labonte J.W., Gray J.J., Ostermeier M. A comprehensive, high-resolution map of a gene's fitness landscape. Mol Biol Evol 2014, 31:1581-1592.
    • (2014) Mol Biol Evol , vol.31 , pp. 1581-1592
    • Firnberg, E.1    Labonte, J.W.2    Gray, J.J.3    Ostermeier, M.4
  • 38
    • 65549084298 scopus 로고    scopus 로고
    • Potential role of phenotypic mutations in the evolution of protein expression and stability
    • Goldsmith M., Tawfik D.S. Potential role of phenotypic mutations in the evolution of protein expression and stability. Proc Natl Acad Sci U S A 2009, 106:6197-6202.
    • (2009) Proc Natl Acad Sci U S A , vol.106 , pp. 6197-6202
    • Goldsmith, M.1    Tawfik, D.S.2
  • 39
    • 84864281240 scopus 로고    scopus 로고
    • Temperature dependence of accuracy of DNA polymerase I from Geobacillus anatolicus
    • Caglayan M., Bilgin N. Temperature dependence of accuracy of DNA polymerase I from Geobacillus anatolicus. Biochimie 2012, 94:1968-1973.
    • (2012) Biochimie , vol.94 , pp. 1968-1973
    • Caglayan, M.1    Bilgin, N.2
  • 40
    • 0019333190 scopus 로고
    • Probing the limits of protein-amino acid side chain recognition with the aminoacyl-tRNA synthetases. Discrimination against phenylalanine by tyrosyl-tRNA synthetases
    • Fersht A.R., Shindler J.S., Tsui W.C. Probing the limits of protein-amino acid side chain recognition with the aminoacyl-tRNA synthetases. Discrimination against phenylalanine by tyrosyl-tRNA synthetases. Biochemistry 1980, 19:5520-5524.
    • (1980) Biochemistry , vol.19 , pp. 5520-5524
    • Fersht, A.R.1    Shindler, J.S.2    Tsui, W.C.3
  • 41
    • 84855892823 scopus 로고    scopus 로고
    • Quality control in aminoacyl-tRNA synthesis its role in translational fidelity
    • Yadavalli S.S., Ibba M. Quality control in aminoacyl-tRNA synthesis its role in translational fidelity. Adv Protein Chem Struct Biol 2012, 86:1-43.
    • (2012) Adv Protein Chem Struct Biol , vol.86 , pp. 1-43
    • Yadavalli, S.S.1    Ibba, M.2
  • 42
    • 0027497871 scopus 로고
    • Modification of the amino acid specificity of tyrosyl-tRNA synthetase by protein engineering
    • de Prat Gay G., Duckworth H.W., Fersht A.R. Modification of the amino acid specificity of tyrosyl-tRNA synthetase by protein engineering. FEBS Lett 1993, 318:167-171.
    • (1993) FEBS Lett , vol.318 , pp. 167-171
    • de Prat Gay, G.1    Duckworth, H.W.2    Fersht, A.R.3
  • 43
    • 0014219470 scopus 로고
    • D-Tyrosyl RNA formation, hydrolysis and utilization for protein synthesis
    • Calendar R., Berg P. d-Tyrosyl RNA formation, hydrolysis and utilization for protein synthesis. J Mol Biol 1967, 26:39-54.
    • (1967) J Mol Biol , vol.26 , pp. 39-54
    • Calendar, R.1    Berg, P.2
  • 44
    • 84861671055 scopus 로고    scopus 로고
    • Evolution. Efficiency in evolutionary trade-offs
    • Noor E., Milo R. Evolution. Efficiency in evolutionary trade-offs. Science 2012, 336:1114-1115.
    • (2012) Science , vol.336 , pp. 1114-1115
    • Noor, E.1    Milo, R.2
  • 47
    • 0034719142 scopus 로고    scopus 로고
    • DNA polymerase beta: contributions of template-positioning and dNTP triphosphate-binding residues to catalysis and fidelity
    • Kraynov V.S., Showalter A.K., Liu J., Zhong X., Tsai M.D. DNA polymerase beta: contributions of template-positioning and dNTP triphosphate-binding residues to catalysis and fidelity. Biochemistry 2000, 39:16008-16015.
    • (2000) Biochemistry , vol.39 , pp. 16008-16015
    • Kraynov, V.S.1    Showalter, A.K.2    Liu, J.3    Zhong, X.4    Tsai, M.D.5


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