메뉴 건너뛰기




Volumn 12, Issue 107, 2015, Pages

Rapid bursts and slow declines: On the possible evolutionary trajectories of enzymes

Author keywords

Activity threshold; Adaptive evolution; Ancestral sequence reconstruction; Catalytic efficiency

Indexed keywords

BIOLOGY; ENERGY EFFICIENCY; MOBILE SECURITY;

EID: 84930750921     PISSN: 17425689     EISSN: 17425662     Source Type: Journal    
DOI: 10.1098/rsif.2015.0036     Document Type: Review
Times cited : (25)

References (83)
  • 2
    • 0017058392 scopus 로고
    • Evolution of enzyme function and the development of catalytic efficiency
    • Albery WJ, Knowles JR. 1976 Evolution of enzyme function and the development of catalytic efficiency. Biochemistry 15, 5631-5640. (doi:10.1021/bi00670a032)
    • (1976) Biochemistry , vol.15 , pp. 5631-5640
    • Albery, W.J.1    Knowles, J.R.2
  • 3
    • 79955640296 scopus 로고    scopus 로고
    • Single-molecule paleoenzymology probes the chemistry of resurrected enzymes
    • Perez-Jimenez R et al. 2011 Single-molecule paleoenzymology probes the chemistry of resurrected enzymes. Nat. Struct. Mol. Biol. 18, 592-596. (doi:10.1038/nsmb.2020)
    • (2011) Nat. Struct. Mol. Biol. , vol.18 , pp. 592-596
    • Perez-Jimenez, R.1
  • 5
    • 84855870416 scopus 로고    scopus 로고
    • On the origin and evolution of thermophily: Reconstruction of functional Precambrian enzymes from ancestors of Bacillus
    • Hobbs JK, Shepherd C, Saul DJ, Demetras NJ, Haaning S, Monk CR, Daniel RM, Arcus VL. 2012 On the origin and evolution of thermophily: reconstruction of functional Precambrian enzymes from ancestors of Bacillus. Mol. Biol. Evol. 29, 825-835. (doi:10.1093/molbev/msr253)
    • (2012) Mol. Biol. Evol. , vol.29 , pp. 825-835
    • Hobbs, J.K.1    Shepherd, C.2    Saul, D.J.3    Demetras, N.J.4    Haaning, S.5    Monk, C.R.6    Daniel, R.M.7    Arcus, V.L.8
  • 6
    • 84922378481 scopus 로고    scopus 로고
    • Towards more accurate ancestral protein genotype-phenotype reconstructions with the use of species tree-aware gene trees
    • Groussin M, Hobbs JK, Szöllo{combining double acute accent}si GJ, Gribaldo S, Arcus VL, Gouy M. 2015 Towards more accurate ancestral protein genotype-phenotype reconstructions with the use of species tree-aware gene trees. Mol. Biol. Evol. 32, 13-22. (doi:10.1093/molbev/msu305)
    • (2015) Mol. Biol. Evol. , vol.32 , pp. 13-22
    • Groussin, M.1    Hobbs, J.K.2    Szöllosi, G.J.3    Gribaldo, S.4    Arcus, V.L.5    Gouy, M.6
  • 8
    • 0029671221 scopus 로고    scopus 로고
    • Angiotensin II-forming activity in a reconstructed ancestral chymase
    • Chandrasekharan UM, Sanker S, Glynias MJ, Karnik SS, Husain A. 1996 Angiotensin II-forming activity in a reconstructed ancestral chymase. Science 271, 502-505. (doi:10.1126/science.271.5248.502)
    • (1996) Science , vol.271 , pp. 502-505
    • Chandrasekharan, U.M.1    Sanker, S.2    Glynias, M.J.3    Karnik, S.S.4    Husain, A.5
  • 9
    • 84871697209 scopus 로고    scopus 로고
    • Reconstruction of ancestral metabolic enzymes reveals molecular mechanisms underlying evolutionary innovation through gene duplication
    • Voordeckers K, Brown CA, Vanneste K, van der Zande E, Voet A, Maere S, Verstrepen KJ. 2012 Reconstruction of ancestral metabolic enzymes reveals molecular mechanisms underlying evolutionary innovation through gene duplication. PLoS Biol. 10, e1001446. (doi:10.1371/journal.pbio.1001446)
    • (2012) PLoS Biol , vol.10
    • Voordeckers, K.1    Brown, C.A.2    Vanneste, K.3    Van Der Zande, E.4    Voet, A.5    Maere, S.6    Verstrepen, K.J.7
  • 11
    • 27144538817 scopus 로고    scopus 로고
    • The biochemical architecture of an ancient adaptive landscape
    • Lunzer M, Miller S, Felsheim R, Dean AM. 2005 The biochemical architecture of an ancient adaptive landscape. Science 310, 499-501. (doi:10.1126/science.1115649)
    • (2005) Science , vol.310 , pp. 499-501
    • Lunzer, M.1    Miller, S.2    Felsheim, R.3    Dean, A.M.4
  • 12
    • 0001260894 scopus 로고
    • On the evolution of biochemical syntheses
    • Horowitz N. 1945 On the evolution of biochemical syntheses. Proc. Natl Acad. Sci. USA 31, 153-157. (doi:10.1073/pnas.31.6.153)
    • (1945) Proc. Natl Acad. Sci. USA , vol.31 , pp. 153-157
    • Horowitz, N.1
  • 13
    • 0002224909 scopus 로고
    • Punctuated equilibria: An alternative to phyletic gradualism
    • ed. T Schopf San Francisco, CA: Freeman Cooper
    • Eldredge N, Gould SJ. 1972 Punctuated equilibria: an alternative to phyletic gradualism. In Models in paleobiology (ed. T Schopf), pp. 82-115. San Francisco, CA: Freeman Cooper.
    • (1972) Models in Paleobiology , pp. 82-115
    • Eldredge, N.1    Gould, S.J.2
  • 14
    • 4243164875 scopus 로고
    • Punctuated equilibrium and criticality in a simple model of evolution
    • Bak P, Sneppen K. 1993 Punctuated equilibrium and criticality in a simple model of evolution. Phys. Rev. Lett. 71, 4083-4086. (doi:10.1103/PhysRevLett.71.4083)
    • (1993) Phys. Rev. Lett. , vol.71 , pp. 4083-4086
    • Bak, P.1    Sneppen, K.2
  • 15
    • 78650716528 scopus 로고    scopus 로고
    • Modeling the complex dynamics of enzyme-pathway coevolution
    • Schütte M, Skupin A, Segrè D, Ebenhöh O. 2010 Modeling the complex dynamics of enzyme-pathway coevolution. Chaos 20, 045115. (doi:10.1063/1.3530440)
    • (2010) Chaos , vol.20
    • Schütte, M.1    Skupin, A.2    Segrè, D.3    Ebenhöh, O.4
  • 16
    • 0035543093 scopus 로고    scopus 로고
    • The depth of chemical time and the power of enzymes as catalysts
    • Wolfenden R, Snider MJ. 2001 The depth of chemical time and the power of enzymes as catalysts. Acc. Chem. Res. 34, 938-945. (doi:10.1021/ar000058i)
    • (2001) Acc. Chem. Res. , vol.34 , pp. 938-945
    • Wolfenden, R.1    Snider, M.J.2
  • 17
    • 84908638699 scopus 로고    scopus 로고
    • Massive thermal acceleration of the emergence of primordial chemistry, the incidence of spontaneous mutation, and the evolution of enzymes
    • Wolfenden R. 2014 Massive thermal acceleration of the emergence of primordial chemistry, the incidence of spontaneous mutation, and the evolution of enzymes. J. Biol. Chem. 289, 30 198-30 204. (doi:10.1074/jbc.R114.567081)
    • (2014) J. Biol. Chem. , vol.289 , pp. 30198-30204
    • Wolfenden, R.1
  • 18
    • 84904394163 scopus 로고    scopus 로고
    • Primordial chemistry and enzyme evolution in a hot environment
    • Wolfenden R. 2014 Primordial chemistry and enzyme evolution in a hot environment. Cell Mol. Life Sci. 71, 2909-2915. (doi:10.1007/s00018-014-1587-2)
    • (2014) Cell Mol. Life Sci. , vol.71 , pp. 2909-2915
    • Wolfenden, R.1
  • 19
    • 0029240393 scopus 로고
    • Evolution in action
    • Scanlan TS, Reid RC. 1995 Evolution in action. Chem. Biol. 2, 71-75. (doi:10.1016/1074-5521(95)90278-3)
    • (1995) Chem. Biol. , vol.2 , pp. 71-75
    • Scanlan, T.S.1    Reid, R.C.2
  • 20
    • 0024316913 scopus 로고
    • Purification and properties of the phophotriesterase from Pseudomonas diminuta
    • Dumas DP, Caldwell SR, Wild JR, Raushel FM. 1989 Purification and properties of the phophotriesterase from Pseudomonas diminuta. J. Biol. Chem. 264, 19 659-19 665.
    • (1989) J. Biol. Chem. , vol.264 , pp. 19659-19665
    • Dumas, D.P.1    Caldwell, S.R.2    Wild, J.R.3    Raushel, F.M.4
  • 21
    • 33751221972 scopus 로고    scopus 로고
    • The latent promiscuity of newly identified microbial lactonases is linked to a recently diverged phosphotriesterase
    • Afriat L, Roodveldt C, Manco G, Tawfik DS. 2006 The latent promiscuity of newly identified microbial lactonases is linked to a recently diverged phosphotriesterase. Biochemistry 45, 13 677-13 686. (doi:10.1021/bi061268r)
    • (2006) Biochemistry , vol.45 , pp. 13677-13686
    • Afriat, L.1    Roodveldt, C.2    Manco, G.3    Tawfik, D.S.4
  • 22
    • 0027241801 scopus 로고
    • Mineralization of the s-triazine ring of atrazine by stable bacterial mixed cultures
    • Mandelbaum R, Wackett LP, Allan DL. 1993 Mineralization of the s-triazine ring of atrazine by stable bacterial mixed cultures. Appl. Environ. Microbiol. 59, 1695-1701.
    • (1993) Appl. Environ. Microbiol. , vol.59 , pp. 1695-1701
    • Mandelbaum, R.1    Wackett, L.P.2    Allan, D.L.3
  • 23
    • 0028153319 scopus 로고
    • Mineralization of the herbicide atrazine as a carbon source by a Pseudomonas strain
    • Yanze-Kontchou C, Gschwind N. 1994 Mineralization of the herbicide atrazine as a carbon source by a Pseudomonas strain. Appl. Environ. Microbiol. 60, 4297-4302.
    • (1994) Appl. Environ. Microbiol. , vol.60 , pp. 4297-4302
    • Yanze-Kontchou, C.1    Gschwind, N.2
  • 24
    • 0028922453 scopus 로고
    • Isolation and characterization of a Pseudomonas sp. that mineralizes the s-triazine herbicide atrazine
    • Mandelbaum R, Allan DL, Wackett LP. 1995 Isolation and characterization of a Pseudomonas sp. that mineralizes the s-triazine herbicide atrazine. Appl. Environ. Microbiol. 61, 1451-1457.
    • (1995) Appl. Environ. Microbiol. , vol.61 , pp. 1451-1457
    • Mandelbaum, R.1    Allan, D.L.2    Wackett, L.P.3
  • 25
    • 0035980264 scopus 로고    scopus 로고
    • Rapid evolution of bacterial catabolic enzymes: A case study with atrazine
    • Seffernick JL, Wackett LP. 2001 Rapid evolution of bacterial catabolic enzymes: a case study with atrazine. Biochemistry 40, 12 747-12 753. (doi:10.1021/bi011293r)
    • (2001) Biochemistry , vol.40 , pp. 12747-12753
    • Seffernick, J.L.1    Wackett, L.P.2
  • 26
    • 0029784331 scopus 로고    scopus 로고
    • Atrazine chlorohydrolase from Pseudomonas sp. strain ADP: Gene sequence, enzyme purification, and protein characterization
    • De Souza M, Sadowsky M, Wackett L. 1996 Atrazine chlorohydrolase from Pseudomonas sp. strain ADP: gene sequence, enzyme purification, and protein characterization. J. Bacteriol. 178, 4894-4900.
    • (1996) J. Bacteriol. , vol.178 , pp. 4894-4900
    • De Souza, M.1    Sadowsky, M.2    Wackett, L.3
  • 27
    • 0035091008 scopus 로고    scopus 로고
    • Melamine deaminase and atrazine chlorohydrolase: 98 percent identical but functionally different
    • Seffernick J, de Souza M. 2001 Melamine deaminase and atrazine chlorohydrolase: 98 percent identical but functionally different. J. Bacteriol. 183, 2405-2410. (doi:10.1128/JB.183.8.2405-2410.2001)
    • (2001) J. Bacteriol. , vol.183 , pp. 2405-2410
    • Seffernick, J.1    De Souza, M.2
  • 28
    • 79958097953 scopus 로고    scopus 로고
    • The moderately efficient enzyme: Evolutionary and physicochemical trends shaping enzyme parameters
    • Bar-Even A, Noor E, Savir Y, Leibermeister W, Davidi D, Tawfik DS, Milo R. 2011 The moderately efficient enzyme: evolutionary and physicochemical trends shaping enzyme parameters. Biochemistry 50, 4402-4410. (doi:10.1021/bi2002289)
    • (2011) Biochemistry , vol.50 , pp. 4402-4410
    • Bar-Even, A.1    Noor, E.2    Savir, Y.3    Leibermeister, W.4    Davidi, D.5    Tawfik, D.S.6    Milo, R.7
  • 29
    • 84867651617 scopus 로고    scopus 로고
    • Real time evolution of new genes by innovation, amplification and divergence
    • Näsvall J, Sun L, Roth JR, Andersson DI. 2012 Real time evolution of new genes by innovation, amplification and divergence. Science 338, 384-387. (doi:10.1126/science.1226521)
    • (2012) Science , vol.338 , pp. 384-387
    • Näsvall, J.1    Sun, L.2    Roth, J.R.3    Andersson, D.I.4
  • 30
    • 0021251828 scopus 로고
    • A large increase in enzyme-substrate affinity by protein engineering
    • Wilkinson AJ, Fersht AR, Blow DM, Carter P, Winter G. 1984 A large increase in enzyme-substrate affinity by protein engineering. Nature 307, 187-188. (doi:10.1038/307187a0)
    • (1984) Nature , vol.307 , pp. 187-188
    • Wilkinson, A.J.1    Fersht, A.R.2    Blow, D.M.3    Carter, P.4    Winter, G.5
  • 32
    • 0024356362 scopus 로고
    • The neutral theory of molecular evolution and the world view of the neutralists
    • Kimura M. 1989 The neutral theory of molecular evolution and the world view of the neutralists. Genome 31, 24-31. (doi:10.1139/g89-009)
    • (1989) Genome , vol.31 , pp. 24-31
    • Kimura, M.1
  • 33
    • 0037559407 scopus 로고    scopus 로고
    • The EBG system of E. coli: Origin and evolution of a novel β-galactosidase for the metabolism of lactose
    • Hall BG. 2003 The EBG system of E. coli: origin and evolution of a novel β-galactosidase for the metabolism of lactose. Genetica 118, 143-156. (doi:10.1023/A:1024149508376)
    • (2003) Genetica , vol.118 , pp. 143-156
    • Hall, B.G.1
  • 34
    • 0017844361 scopus 로고
    • Experimental evolution of a new enzymatic function. II. Evolution of multiple functions for EBG enzyme in E. coli
    • Hall BG. 1978 Experimental evolution of a new enzymatic function. II. Evolution of multiple functions for EBG enzyme in E. coli. Genetics 89, 453-465.
    • (1978) Genetics , vol.89 , pp. 453-465
    • Hall, B.G.1
  • 35
    • 77953115788 scopus 로고    scopus 로고
    • Cost of unneeded proteins in E. coli is reduced after several generations in exponential growth
    • Shachrai I, Zaslaver A, Alon U, Dekel E. 2010 Cost of unneeded proteins in E. coli is reduced after several generations in exponential growth. Mol. Cell 38, 758-767. (doi:10.1016/j.molcel.2010.04.015)
    • (2010) Mol. Cell , vol.38 , pp. 758-767
    • Shachrai, I.1    Zaslaver, A.2    Alon, U.3    Dekel, E.4
  • 36
    • 40049106856 scopus 로고    scopus 로고
    • A study in molecular contingency: Glutamine phosphoribosylpyrophosphate amidotransferase is a promiscuous and evolvable phosphoribosylanthranilate isomerase
    • Patrick WM, Matsumura I. 2008 A study in molecular contingency: glutamine phosphoribosylpyrophosphate amidotransferase is a promiscuous and evolvable phosphoribosylanthranilate isomerase. J. Mol. Biol. 377, 323-336. (doi:10.1016/j.jmb.2008.01.043)
    • (2008) J. Mol. Biol. , vol.377 , pp. 323-336
    • Patrick, W.M.1    Matsumura, I.2
  • 37
    • 84883249614 scopus 로고    scopus 로고
    • Substrate ambiguous enzymes within the Escherichia coli proteome offer different evolutionary solutions to the same problem
    • Yip SH-C, Matsumura I. 2013 Substrate ambiguous enzymes within the Escherichia coli proteome offer different evolutionary solutions to the same problem. Mol. Biol. Evol. 30, 2001-2012. (doi:10.1093/molbev/mst105)
    • (2013) Mol. Biol. Evol. , vol.30 , pp. 2001-2012
    • Yip, S.H.-C.1    Matsumura, I.2
  • 38
    • 2542594077 scopus 로고    scopus 로고
    • Identifying latent enzyme activities: Substrate ambiguity within modern bacterial sugar kinases
    • Miller BG, Raines RT. 2004 Identifying latent enzyme activities: substrate ambiguity within modern bacterial sugar kinases. Biochemistry 43, 6387-6392. (doi:10.1021/bi049424m)
    • (2004) Biochemistry , vol.43 , pp. 6387-6392
    • Miller, B.G.1    Raines, R.T.2
  • 39
    • 51649110669 scopus 로고    scopus 로고
    • A compromise required by gene sharing enables survival: Implications for evolution of new enzyme activities
    • McLoughlin SY, Copley SD. 2008 A compromise required by gene sharing enables survival: implications for evolution of new enzyme activities. Proc. Natl Acad. Sci. USA 105, 13 497-13 502. (doi:10.1073/pnas.0804804105)
    • (2008) Proc. Natl Acad. Sci. USA , vol.105 , pp. 13497-13502
    • McLoughlin, S.Y.1    Copley, S.D.2
  • 40
    • 0002437481 scopus 로고    scopus 로고
    • Chemical composition of Escherichia coli
    • ed. F Neidhardt Washington, DC: ASM Press
    • Neidhardt F, Umbarger H. 1996 Chemical composition of Escherichia coli. In Escherichia coli and Salmonella (ed. F Neidhardt), pp. 13-16. Washington, DC: ASM Press.
    • (1996) Escherichia Coli and Salmonella , pp. 13-16
    • Neidhardt, F.1    Umbarger, H.2
  • 41
    • 68049100110 scopus 로고    scopus 로고
    • Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli
    • Bennett BD, Kimball EH, Gao M, Osterhout R, Van Dien SJ, Rabinowitz JD. 2009 Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli. Nat. Chem. Biol. 5, 593-599. (doi:10.1038/nchembio.186)
    • (2009) Nat. Chem. Biol. , vol.5 , pp. 593-599
    • Bennett, B.D.1    Kimball, E.H.2    Gao, M.3    Osterhout, R.4    Van Dien, S.J.5    Rabinowitz, J.D.6
  • 42
    • 84861588442 scopus 로고    scopus 로고
    • 8-barrel enzymes: Establishing phosphoribosylanthranilate isomerisation activity on the scaffold of the tryptophan synthase a-subunit
    • 8-barrel enzymes: establishing phosphoribosylanthranilate isomerisation activity on the scaffold of the tryptophan synthase a-subunit. Protein Eng. Des. Sel. 25, 285-293. (doi:10.1093/protein/gzs015)
    • (2012) Protein Eng. Des. Sel. , vol.25 , pp. 285-293
    • Evran, S.1    Telefoncu, A.2    Sterner, R.3
  • 44
    • 45149128433 scopus 로고    scopus 로고
    • The cost of expression of Escherichia coli lac operon proteins is in the process, not in the products
    • Stoebel DM, Dean AM, Dykhuizen DE. 2008 The cost of expression of Escherichia coli lac operon proteins is in the process, not in the products. Genetics 178, 1653-1660. (doi:10.1534/genetics.107.085399)
    • (2008) Genetics , vol.178 , pp. 1653-1660
    • Stoebel, D.M.1    Dean, A.M.2    Dykhuizen, D.E.3
  • 45
    • 79952166228 scopus 로고    scopus 로고
    • Artificial gene amplification reveals an abundance of promiscuous resistance determinants in Escherichia coli
    • Soo VWC, Hanson-Manful P, Patrick WM. 2011 Artificial gene amplification reveals an abundance of promiscuous resistance determinants in Escherichia coli. Proc. Natl Acad. Sci. USA 108, 1484-1489. (doi:10.1073/pnas.1012108108)
    • (2011) Proc. Natl Acad. Sci. USA , vol.108 , pp. 1484-1489
    • Soo, V.W.C.1    Hanson-Manful, P.2    Patrick, W.M.3
  • 46
    • 23844503225 scopus 로고    scopus 로고
    • Reconstitution of a defunct glycolytic pathway via recruitment of ambiguous sugar kinases
    • Miller BG, Raines RT. 2005 Reconstitution of a defunct glycolytic pathway via recruitment of ambiguous sugar kinases. Biochemistry 44, 10 776-10 783. (doi:10.1021/bi0506268)
    • (2005) Biochemistry , vol.44 , pp. 10776-10783
    • Miller, B.G.1    Raines, R.T.2
  • 47
    • 44349161622 scopus 로고    scopus 로고
    • Intense neutral drifts yield robust and evolvable consensus proteins
    • Bershtein S, Goldin K, Tawfik DS. 2008 Intense neutral drifts yield robust and evolvable consensus proteins. J. Mol. Biol. 379, 1029-1044. (doi:10.1016/j.jmb.2008.04.024)
    • (2008) J. Mol. Biol. , vol.379 , pp. 1029-1044
    • Bershtein, S.1    Goldin, K.2    Tawfik, D.S.3
  • 48
    • 78149293610 scopus 로고    scopus 로고
    • Mutational robustness of ribosomal protein genes
    • Lind PA, Berg OG, Andersson DI. 2010 Mutational robustness of ribosomal protein genes. Science 330, 825-828. (doi:10.1126/science.1194617)
    • (2010) Science , vol.330 , pp. 825-828
    • Lind, P.A.1    Berg, O.G.2    Andersson, D.I.3
  • 49
    • 0029962946 scopus 로고    scopus 로고
    • Amino acid sequence determinants of β-lactamase structure and activity
    • Huang W, Petrosino J, Hirsch M, Shenkin PS, Palzkill T. 1996 Amino acid sequence determinants of β-lactamase structure and activity. J. Mol. Biol. 258, 688-703. (doi:10.1006/jmbi.1996.0279)
    • (1996) J. Mol. Biol. , vol.258 , pp. 688-703
    • Huang, W.1    Petrosino, J.2    Hirsch, M.3    Shenkin, P.S.4    Palzkill, T.5
  • 50
    • 79956357160 scopus 로고    scopus 로고
    • Experimental illumination of a fitness landscape
    • Hietpas RT, Jensen JD, Bolon DNA. 2011 Experimental illumination of a fitness landscape. Proc. Natl Acad. Sci. USA 108, 7896-7901. (doi:10.1073/pnas.1016024108)
    • (2011) Proc. Natl Acad. Sci. USA , vol.108 , pp. 7896-7901
    • Hietpas, R.T.1    Jensen, J.D.2    Bolon, D.N.A.3
  • 51
    • 33748796613 scopus 로고    scopus 로고
    • Natural history as a predictor of protein evolvability
    • O'Loughlin TL, Patrick WM, Matsumura I. 2006 Natural history as a predictor of protein evolvability. Protein Eng. Des. Sel. 19, 439-442. (doi:10.1093/protein/gzl029)
    • (2006) Protein Eng. Des. Sel. , vol.19 , pp. 439-442
    • O'Loughlin, T.L.1    Patrick, W.M.2    Matsumura, I.3
  • 53
    • 79960601166 scopus 로고    scopus 로고
    • Slow protein evolutionary rates are dictated by surface-core association
    • Tóth-Petróczy Á, Tawfik DS. 2011 Slow protein evolutionary rates are dictated by surface-core association. Proc. Natl Acad. Sci. USA 108, 11 151-11 156. (doi:10.1073/pnas.1015994108)
    • (2011) Proc. Natl Acad. Sci. USA , vol.108 , pp. 11151-11156
    • Tóth-Petróczy, Á.1    Tawfik, D.S.2
  • 54
    • 84902670142 scopus 로고    scopus 로고
    • Accuracy-rate tradeoffs: How do enzymes meet demands of selectivity and catalytic efficiency?
    • Tawfik DS. 2014 Accuracy-rate tradeoffs: how do enzymes meet demands of selectivity and catalytic efficiency? Curr. Opin. Chem. Biol. 21, 73-80. (doi:10.1016/j.cbpa.2014.05.008)
    • (2014) Curr. Opin. Chem. Biol. , vol.21 , pp. 73-80
    • Tawfik, D.S.1
  • 55
    • 0037032998 scopus 로고    scopus 로고
    • Efficiency of correct nucleotide insertion governs DNA polymerase fidelity
    • Beard WA, Shock DD, Vande Berg BJ, Wilson SH. 2002 Efficiency of correct nucleotide insertion governs DNA polymerase fidelity. J. Biol. Chem. 277, 47 393-47 398. (doi:10.1074/jbc.M210036200)
    • (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
  • 57
    • 64849101493 scopus 로고    scopus 로고
    • Protein dynamism and evolvability
    • Tokuriki N, Tawfik DS. 2009 Protein dynamism and evolvability. Science 324, 203-207. (doi:10.1126/science.1169375)
    • (2009) Science , vol.324 , pp. 203-207
    • Tokuriki, N.1    Tawfik, D.S.2
  • 58
    • 33746237576 scopus 로고    scopus 로고
    • The quest for the universals of protein evolution
    • Rocha EPC. 2006 The quest for the universals of protein evolution. Trends Genet. 22, 412-416. (doi:10.1016/j.tig.2006.06.004)
    • (2006) Trends Genet , vol.22 , pp. 412-416
    • Rocha, E.P.C.1
  • 59
    • 84879604998 scopus 로고    scopus 로고
    • Three independent determinants of protein evolutionary rate
    • Choi SS, Hannenhalli S. 2013 Three independent determinants of protein evolutionary rate. J. Mol. Evol. 76, 98-111. (doi:10.1007/s00239-013-9543-6)
    • (2013) J. Mol. Evol. , vol.76 , pp. 98-111
    • Choi, S.S.1    Hannenhalli, S.2
  • 60
    • 0028926047 scopus 로고
    • Energetics of bacterial growth: Balance of anabolic and catabolic reactions
    • Russell J, Cook G. 1995 Energetics of bacterial growth: balance of anabolic and catabolic reactions. Microbiol. Rev. 59, 48-62.
    • (1995) Microbiol. Rev. , vol.59 , pp. 48-62
    • Russell, J.1    Cook, G.2
  • 61
    • 84899550455 scopus 로고    scopus 로고
    • Quantifying absolute protein synthesis rates reveals principles underlying allocation of cellular resources
    • Li G-W, Burkhardt D, Gross C, Weissman JS. 2014 Quantifying absolute protein synthesis rates reveals principles underlying allocation of cellular resources. Cell 157, 624-635. (doi:10.1016/j.cell.2014.02.033)
    • (2014) Cell , vol.157 , pp. 624-635
    • Li, G.-W.1    Burkhardt, D.2    Gross, C.3    Weissman, J.S.4
  • 62
    • 1942531303 scopus 로고    scopus 로고
    • Resurrecting ancient genes: Experimental analysis of extinct molecules
    • Thornton JW. 2004 Resurrecting ancient genes: experimental analysis of extinct molecules. Nat. Rev. Genet. 5, 366-375. (doi:10.1038/nrg1324)
    • (2004) Nat. Rev. Genet. , vol.5 , pp. 366-375
    • Thornton, J.W.1
  • 63
    • 77955584075 scopus 로고    scopus 로고
    • Analyzing protein structure and function using ancestral gene reconstruction
    • Harms MJ, Thornton JW. 2010 Analyzing protein structure and function using ancestral gene reconstruction. Curr. Opin. Struct. Biol. 20, 360-366. (doi:10.1016/j.sbi.2010.03.005)
    • (2010) Curr. Opin. Struct. Biol. , vol.20 , pp. 360-366
    • Harms, M.J.1    Thornton, J.W.2
  • 64
    • 84880862788 scopus 로고    scopus 로고
    • Evolutionary biochemistry: Revealing the historical and physical causes of protein properties
    • Harms MJ, Thornton JW. 2013 Evolutionary biochemistry: revealing the historical and physical causes of protein properties. Nat. Rev. Genet. 14, 559-571. (doi:10.1038/nrg3540)
    • (2013) Nat. Rev. Genet. , vol.14 , pp. 559-571
    • Harms, M.J.1    Thornton, J.W.2
  • 65
    • 0141431993 scopus 로고    scopus 로고
    • Resurrecting the ancestral steroid receptor: Ancient origin of estrogen signaling
    • Thornton JW, Need E, Crews D. 2003 Resurrecting the ancestral steroid receptor: ancient origin of estrogen signaling. Science 301, 1714-1717. (doi:10.1126/science.1086185)
    • (2003) Science , vol.301 , pp. 1714-1717
    • Thornton, J.W.1    Need, E.2    Crews, D.3
  • 66
    • 0141828152 scopus 로고    scopus 로고
    • Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins
    • Gaucher EA, Thomson JM, Burgan MF, Benner SA. 2003 Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins. Nature 425, 285-288. (doi:10.1038/nature01977)
    • (2003) Nature , vol.425 , pp. 285-288
    • Gaucher, E.A.1    Thomson, J.M.2    Burgan, M.F.3    Benner, S.A.4
  • 67
    • 0025270813 scopus 로고
    • Ancestral lysozymes reconstructed, neutrality tested, and thermostability linked to hydrocarbon packing
    • Malcolm BA, Wilson KP, Matthews BW, Kirsch JF, Wilson AC. 1990 Ancestral lysozymes reconstructed, neutrality tested, and thermostability linked to hydrocarbon packing. Nature 345, 86-89. (doi:10.1038/345086a0)
    • (1990) Nature , vol.345 , pp. 86-89
    • Malcolm, B.A.1    Wilson, K.P.2    Matthews, B.W.3    Kirsch, J.F.4    Wilson, A.C.5
  • 68
    • 38949093003 scopus 로고    scopus 로고
    • Palaeotemperature trend for precambrian life inferred from resurrected proteins
    • Gaucher EA, Govindarajan S, Ganesh O. 2008 Palaeotemperature trend for precambrian life inferred from resurrected proteins. Nature 451, 704-708. (doi:10.1038/nature06510)
    • (2008) Nature , vol.451 , pp. 704-708
    • Gaucher, E.A.1    Govindarajan, S.2    Ganesh, O.3
  • 69
    • 84874602326 scopus 로고    scopus 로고
    • Hyperstability and substrate promiscuity in laboratory resurrections of Precambrian β-lactamases
    • Risso V, Gavira J, Mejia-Carmona D, Gaucher EA, Sanchez-Ruiz J. 2013 Hyperstability and substrate promiscuity in laboratory resurrections of Precambrian β-lactamases. J. Am. Chem. Soc. 135, 2899-2902. (doi:10.1021/ja311630a)
    • (2013) J. Am. Chem. Soc. , vol.135 , pp. 2899-2902
    • Risso, V.1    Gavira, J.2    Mejia-Carmona, D.3    Gaucher, E.A.4    Sanchez-Ruiz, J.5
  • 70
    • 84896730564 scopus 로고    scopus 로고
    • Reconstructed ancestral myo-inositol-3-phosphate synthases indicate that ancestors of the Thermococcales and Thermotoga species were more thermophilic than their descendants
    • Butzin NC, Lapierre P, Green AG, Swithers KS, Gogarten JP, Noll KM. 2013 Reconstructed ancestral myo-inositol-3-phosphate synthases indicate that ancestors of the Thermococcales and Thermotoga species were more thermophilic than their descendants. PLoS ONE 8, e84300. (doi:10.1371/journal.pone.0084300)
    • (2013) PLoS ONE , vol.8
    • Butzin, N.C.1    Lapierre, P.2    Green, A.G.3    Swithers, K.S.4    Gogarten, J.P.5    Noll, K.M.6
  • 72
    • 0041317258 scopus 로고    scopus 로고
    • More than the sum of their parts: On the evolution of proteins from peptides
    • Söding J, Lupas AN. 2003 More than the sum of their parts: on the evolution of proteins from peptides. BioEssays 25, 837-846. (doi:10.1002/bies.10321)
    • (2003) BioEssays , vol.25 , pp. 837-846
    • Söding, J.1    Lupas, A.N.2
  • 74
    • 34547170043 scopus 로고    scopus 로고
    • The origin of modern metabolic networks inferred from phylogenomic analysis of protein architecture
    • Caetano-Anollés G, Kim HS, Mittenthal JE. 2007 The origin of modern metabolic networks inferred from phylogenomic analysis of protein architecture. Proc. Natl Acad. Sci. USA 104, 9358-9363. (doi:10.1073/pnas.0701214104)
    • (2007) Proc. Natl Acad. Sci. USA , vol.104 , pp. 9358-9363
    • Caetano-Anollés, G.1    Kim, H.S.2    Mittenthal, J.E.3
  • 75
    • 80051923523 scopus 로고    scopus 로고
    • Computational reconstruction of primordial prototypes of elementary functional loops in modern proteins
    • Goncearenco A, Berezovsky IN. 2011 Computational reconstruction of primordial prototypes of elementary functional loops in modern proteins. Bioinformatics 27, 2368-2375. (doi:10.1093/bioinformatics/btr396)
    • (2011) Bioinformatics , vol.27 , pp. 2368-2375
    • Goncearenco, A.1    Berezovsky, I.N.2
  • 77
    • 0017272554 scopus 로고
    • Enzyme recruitment in evolution of new function
    • Jensen R. 1976 Enzyme recruitment in evolution of new function. Annu. Rev. Microbiol. 30, 409-425. (doi:10.1146/annurev.mi.30.100176.002205)
    • (1976) Annu. Rev. Microbiol. , vol.30 , pp. 409-425
    • Jensen, R.1
  • 79
    • 84894174799 scopus 로고    scopus 로고
    • Enzyme recruitment and its role in metabolic expansion
    • Schulenburg C, Miller BG. 2014 Enzyme recruitment and its role in metabolic expansion. Biochemistry 53, 836-845. (doi:10.1021/bi401667f)
    • (2014) Biochemistry , vol.53 , pp. 836-845
    • Schulenburg, C.1    Miller, B.G.2
  • 80
    • 11844299096 scopus 로고    scopus 로고
    • When Earth started blooming: Insights from the fossil record
    • Friis EM, Pedersen KR, Crane PR. 2005 When Earth started blooming: insights from the fossil record. Curr. Opin. Plant Biol. 8, 5-12. (doi:10.1016/j.pbi.2004.11.006)
    • (2005) Curr. Opin. Plant Biol. , vol.8 , pp. 5-12
    • Friis, E.M.1    Pedersen, K.R.2    Crane, P.R.3
  • 82
    • 84881637825 scopus 로고    scopus 로고
    • A branchheterogeneous model of protein evolution for efficient inference of ancestral sequences
    • Groussin M, Boussau B, Gouy M. 2013 A branchheterogeneous model of protein evolution for efficient inference of ancestral sequences. Syst. Biol. 62, 523-538. (doi:10.1093/sysbio/syt016)
    • (2013) Syst. Biol. , vol.62 , pp. 523-538
    • Groussin, M.1    Boussau, B.2    Gouy, M.3
  • 83
    • 34548018528 scopus 로고    scopus 로고
    • Mechanistic approaches to the study of evolution: The functional synthesis
    • Dean AM, Thornton JW. 2007 Mechanistic approaches to the study of evolution: the functional synthesis. Nat. Rev. Genet. 8, 675-688. (doi:10.1038/nrg2160)
    • (2007) Nat. Rev. Genet. , vol.8 , pp. 675-688
    • Dean, A.M.1    Thornton, J.W.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.