-
2
-
-
77956925998
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
9
-
-
84868599895
-
Drift-barrier hypothesis and mutation-rate evolution
-
Sung W., Ackerman M.S., Miller S.F., Doak T.G., Lynch M. Drift-barrier hypothesis and mutation-rate evolution. Proc Natl Acad Sci U S A 2012, 109:18488-18492.
-
(2012)
Proc Natl Acad Sci U S A
, vol.109
, pp. 18488-18492
-
-
Sung, W.1
Ackerman, M.S.2
Miller, S.F.3
Doak, T.G.4
Lynch, M.5
-
10
-
-
84864341793
-
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
-
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
-
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
-
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
-
14
-
-
84871755504
-
Diminishing returns and tradeoffs constrain the laboratory optimization of an enzyme
-
Tokuriki N., Jackson C.J., Afriat-Jurnou L., Wyganowski K.T., Tang R., Tawfik D.S. Diminishing returns and tradeoffs constrain the laboratory optimization of an enzyme. Nat Commun 2012, 3:1257.
-
(2012)
Nat Commun
, vol.3
, pp. 1257
-
-
Tokuriki, N.1
Jackson, C.J.2
Afriat-Jurnou, L.3
Wyganowski, K.T.4
Tang, R.5
Tawfik, D.S.6
-
16
-
-
84865571240
-
Network context and selection in the evolution to enzyme specificity
-
Nam H., Lewis N.E., Lerman J.A., Lee D.H., Chang R.L., Kim D., Palsson B.O. Network context and selection in the evolution to enzyme specificity. Science 2012, 337:1101-1104.
-
(2012)
Science
, vol.337
, pp. 1101-1104
-
-
Nam, H.1
Lewis, N.E.2
Lerman, J.A.3
Lee, D.H.4
Chang, R.L.5
Kim, D.6
Palsson, B.O.7
-
17
-
-
79953310914
-
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
-
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
-
19
-
-
70349832423
-
Following evolutionary paths to protein-protein interactions with high affinity and selectivity
-
Levin K.B., Dym O., Albeck S., Magdassi S., Keeble A.H., Kleanthous C., Tawfik D.S. Following evolutionary paths to protein-protein interactions with high affinity and selectivity. Nat Struct Mol Biol 2009, 16:1049-1055.
-
(2009)
Nat Struct Mol Biol
, vol.16
, pp. 1049-1055
-
-
Levin, K.B.1
Dym, O.2
Albeck, S.3
Magdassi, S.4
Keeble, A.H.5
Kleanthous, C.6
Tawfik, D.S.7
-
20
-
-
84860211901
-
Trigger loop dynamics mediate the balance between the transcriptional fidelity and speed of RNA polymerase II
-
Larson M.H., Zhou J., Kaplan C.D., Palangat M., Kornberg R.D., Landick R., Block S.M. Trigger loop dynamics mediate the balance between the transcriptional fidelity and speed of RNA polymerase II. Proc Natl Acad Sci U S A 2012, 109:6555-6560.
-
(2012)
Proc Natl Acad Sci U S A
, vol.109
, pp. 6555-6560
-
-
Larson, M.H.1
Zhou, J.2
Kaplan, C.D.3
Palangat, M.4
Kornberg, R.D.5
Landick, R.6
Block, S.M.7
-
21
-
-
0003481596
-
-
W H Freeman & Co, Fersht AR:
-
Fersht AR: Enzyme Structure and Mechanism 1985, W H Freeman & Co. edn 2.
-
(1985)
Enzyme Structure and Mechanism
-
-
-
22
-
-
77951226274
-
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
-
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
-
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
-
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
-
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
-
27
-
-
84868350970
-
The molecular basis of phosphate discrimination in arsenate-rich environments
-
Elias M., Wellner A., Goldin-Azulay K., Chabriere E., Vorholt J.A., Erb T.J., Tawfik D.S. The molecular basis of phosphate discrimination in arsenate-rich environments. Nature 2012, 491:134-137.
-
(2012)
Nature
, vol.491
, pp. 134-137
-
-
Elias, M.1
Wellner, A.2
Goldin-Azulay, K.3
Chabriere, E.4
Vorholt, J.A.5
Erb, T.J.6
Tawfik, D.S.7
-
28
-
-
79951622275
-
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
-
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
-
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
-
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
-
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
-
33
-
-
84874973544
-
Enzyme-promoted base flipping controls DNA methylation fidelity
-
Matje D.M., Zhou H., Smith D.A., Neely R.K., Dryden D.T., Jones A.C., Dahlquist F.W., Reich N.O. Enzyme-promoted base flipping controls DNA methylation fidelity. Biochemistry 2013, 52:1677-1685.
-
(2013)
Biochemistry
, vol.52
, pp. 1677-1685
-
-
Matje, D.M.1
Zhou, H.2
Smith, D.A.3
Neely, R.K.4
Dryden, D.T.5
Jones, A.C.6
Dahlquist, F.W.7
Reich, N.O.8
-
34
-
-
84862963791
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
45
-
-
84861663597
-
Evolutionary trade-offs Pareto optimality, and the geometry of phenotype space
-
Shoval O., Sheftel H., Shinar G., Hart Y., Ramote O., Mayo A., Dekel E., Kavanagh K., Alon U. Evolutionary trade-offs Pareto optimality, and the geometry of phenotype space. Science 2012, 336:1157-1160.
-
(2012)
Science
, vol.336
, pp. 1157-1160
-
-
Shoval, O.1
Sheftel, H.2
Shinar, G.3
Hart, Y.4
Ramote, O.5
Mayo, A.6
Dekel, E.7
Kavanagh, K.8
Alon, U.9
-
46
-
-
84890860784
-
The universality of enzymatic rate-temperature dependency
-
Elias M., Wieczorek G., Rosenne S., Tawfik D.S. The universality of enzymatic rate-temperature dependency. Trends Biochem Sci 2014, 39:1-7.
-
(2014)
Trends Biochem Sci
, vol.39
, pp. 1-7
-
-
Elias, M.1
Wieczorek, G.2
Rosenne, S.3
Tawfik, D.S.4
-
47
-
-
0034719142
-
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
|