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Volumn 112, Issue 25, 2015, Pages E3226-E3235

Contingency and entrenchment in protein evolution under purifying selection

Author keywords

Coevolution; Intragenic epistasis; Near neutrality; Protein stability

Indexed keywords

PROTEIN;

EID: 84934908389     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1412933112     Document Type: Article
Times cited : (135)

References (102)
  • 1
    • 33645666942 scopus 로고    scopus 로고
    • Darwinian evolution can follow only very few mutational paths to fitter proteins
    • Weinreich DM, Delaney NF, Depristo MA, Hartl DL (2006) Darwinian evolution can follow only very few mutational paths to fitter proteins. Science 312(5770):111-114.
    • (2006) Science , vol.312 , Issue.5770 , pp. 111-114
    • Weinreich, D.M.1    Delaney, N.F.2    Depristo, M.A.3    Hartl, D.L.4
  • 2
    • 34548040966 scopus 로고    scopus 로고
    • Crystal structure of an ancient protein: Evolution by conformational epistasis
    • Ortlund EA, Bridgham JT, Redinbo MR, Thornton JW (2007) Crystal structure of an ancient protein: Evolution by conformational epistasis. Science 317(5844):1544-1548.
    • (2007) Science , vol.317 , Issue.5844 , pp. 1544-1548
    • Ortlund, E.A.1    Bridgham, J.T.2    Redinbo, M.R.3    Thornton, J.W.4
  • 3
    • 45849093668 scopus 로고    scopus 로고
    • Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli
    • Blount ZD, Borland CZ, Lenski RE (2008) Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli. Proc Natl Acad Sci USA 105(23):7899-7906.
    • (2008) Proc Natl Acad Sci USA , vol.105 , Issue.23 , pp. 7899-7906
    • Blount, Z.D.1    Borland, C.Z.2    Lenski, R.E.3
  • 4
    • 70349464621 scopus 로고    scopus 로고
    • An epistatic ratchet constrains the direction of glucocorticoid receptor evolution
    • Bridgham JT, Ortlund EA, Thornton JW (2009) An epistatic ratchet constrains the direction of glucocorticoid receptor evolution. Nature 461(7263):515-519.
    • (2009) Nature , vol.461 , Issue.7263 , pp. 515-519
    • Bridgham, J.T.1    Ortlund, E.A.2    Thornton, J.W.3
  • 5
    • 77953262416 scopus 로고    scopus 로고
    • Permissive secondary mutations enable the evolution of influenza oseltamivir resistance
    • Bloom JD, Gong LI, Baltimore D (2010) Permissive secondary mutations enable the evolution of influenza oseltamivir resistance. Science 328(5983):1272-1275.
    • (2010) Science , vol.328 , Issue.5983 , pp. 1272-1275
    • Bloom, J.D.1    Gong, L.I.2    Baltimore, D.3
  • 7
    • 84878935899 scopus 로고    scopus 로고
    • Epistasis among adaptive mutations in deer mouse hemoglobin
    • Natarajan C, et al. (2013) Epistasis among adaptive mutations in deer mouse hemoglobin. Science 340(6138):1324-1327.
    • (2013) Science , vol.340 , Issue.6138 , pp. 1324-1327
    • Natarajan, C.1
  • 8
    • 84879064073 scopus 로고    scopus 로고
    • Stability-mediated epistasis constrains the evolution of an influenza protein
    • Gong LI, Suchard MA, Bloom JD (2013) Stability-mediated epistasis constrains the evolution of an influenza protein. eLife 2:e00631.
    • (2013) eLife , vol.2
    • Gong, L.I.1    Suchard, M.A.2    Bloom, J.D.3
  • 9
    • 84906217983 scopus 로고    scopus 로고
    • Historical contingency and its biophysical basis in glucocorticoid receptor evolution
    • Harms MJ, Thornton JW (2014) Historical contingency and its biophysical basis in glucocorticoid receptor evolution. Nature 512(7513):203-207.
    • (2014) Nature , vol.512 , Issue.7513 , pp. 203-207
    • Harms, M.J.1    Thornton, J.W.2
  • 11
    • 0025526526 scopus 로고
    • Mutational order: A major stochastic process in evolution
    • Mani GS, Clarke BC (1990) Mutational order: A major stochastic process in evolution. Proc R Soc Lond B Biol Sci 240(1297):29-37.
    • (1990) Proc R Soc Lond B Biol Sci , vol.240 , Issue.1297 , pp. 29-37
    • Mani, G.S.1    Clarke, B.C.2
  • 12
    • 0028977087 scopus 로고
    • Experimental tests of the roles of adaptation, chance, and history in evolution
    • Travisano M, Mongold JA, Bennett AF, Lenski RE (1995) Experimental tests of the roles of adaptation, chance, and history in evolution. Science 267(5194):87-90.
    • (1995) Science , vol.267 , Issue.5194 , pp. 87-90
    • Travisano, M.1    Mongold, J.A.2    Bennett, A.F.3    Lenski, R.E.4
  • 13
    • 46149093073 scopus 로고    scopus 로고
    • Replaying life's tape
    • Beatty J (2006) Replaying life's tape. J Philos 103(7):336-362.
    • (2006) J Philos , vol.103 , Issue.7 , pp. 336-362
    • Beatty, J.1
  • 14
    • 84979134212 scopus 로고
    • Reversibility in evolution considered from the standpoint of genetics
    • Muller HJ (1939) Reversibility in evolution considered from the standpoint of genetics. Biol Rev Camb Philos Soc 14:261-280.
    • (1939) Biol Rev Camb Philos Soc , vol.14 , pp. 261-280
    • Muller, H.J.1
  • 15
    • 0017728436 scopus 로고
    • A systems-analytical approach to macro-evolutionary phenomena
    • Riedl R (1977) A systems-analytical approach to macro-evolutionary phenomena. Q Rev Biol 52(4):351-370.
    • (1977) Q Rev Biol , vol.52 , Issue.4 , pp. 351-370
    • Riedl, R.1
  • 17
    • 79956314177 scopus 로고    scopus 로고
    • Path dependence and historical contingency in biology
    • Palgrave Macmillan, New York
    • Szathmáry E (2006) Path dependence and historical contingency in biology. Understanding Change: Models, Methodologies, and Metaphors (Palgrave Macmillan, New York), pp 140-157.
    • (2006) Understanding Change: Models, Methodologies, and Metaphors , pp. 140-157
    • Szathmáry, E.1
  • 18
    • 84861422981 scopus 로고    scopus 로고
    • Amino acid coevolution induces an evolutionary Stokes shift
    • Pollock DD, Thiltgen G, Goldstein RA (2012) Amino acid coevolution induces an evolutionary Stokes shift. Proc Natl Acad Sci USA 109(21):E1352-E1359.
    • (2012) Proc Natl Acad Sci USA , vol.109 , Issue.21 , pp. E1352-E1359
    • Pollock, D.D.1    Thiltgen, G.2    Goldstein, R.A.3
  • 19
    • 0014935646 scopus 로고
    • Natural selection and the concept of a protein space
    • Smith JM (1970) Natural selection and the concept of a protein space. Nature 225(5232):563-564.
    • (1970) Nature , vol.225 , Issue.5232 , pp. 563-564
    • Smith, J.M.1
  • 22
    • 0036797562 scopus 로고    scopus 로고
    • Epistasis: What it means, what it doesn't mean, and statistical methods to detect it in humans
    • Cordell HJ (2002) Epistasis: What it means, what it doesn't mean, and statistical methods to detect it in humans. Hum Mol Genet 11(20):2463-2468.
    • (2002) Hum Mol Genet , vol.11 , Issue.20 , pp. 2463-2468
    • Cordell, H.J.1
  • 23
    • 54149088214 scopus 로고    scopus 로고
    • Epistasis - The essential role of gene interactions in the structure and evolution of genetic systems
    • Phillips PC (2008) Epistasis - the essential role of gene interactions in the structure and evolution of genetic systems. Nat Rev Genet 9(11):855-867.
    • (2008) Nat Rev Genet , vol.9 , Issue.11 , pp. 855-867
    • Phillips, P.C.1
  • 24
    • 84902775598 scopus 로고    scopus 로고
    • Empirical fitness landscapes and the predictability of evolution
    • de Visser JAGM, Krug J (2014) Empirical fitness landscapes and the predictability of evolution. Nat Rev Genet 15(7):480-490.
    • (2014) Nat Rev Genet , vol.15 , Issue.7 , pp. 480-490
    • De Visser, J.A.G.M.1    Krug, J.2
  • 25
    • 0037069428 scopus 로고    scopus 로고
    • Dobzhansky-Muller incompatibilities in protein evolution
    • Kondrashov AS, Sunyaev S, Kondrashov FA (2002) Dobzhansky-Muller incompatibilities in protein evolution. Proc Natl Acad Sci USA 99(23):14878-14883.
    • (2002) Proc Natl Acad Sci USA , vol.99 , Issue.23 , pp. 14878-14883
    • Kondrashov, A.S.1    Sunyaev, S.2    Kondrashov, F.A.3
  • 26
    • 23944490117 scopus 로고    scopus 로고
    • Missense meanderings in sequence space: A biophysical view of protein evolution
    • DePristo MA, Weinreich DM, Hartl DL (2005) Missense meanderings in sequence space: a biophysical view of protein evolution. Nat Rev Genet 6(9):678-687.
    • (2005) Nat Rev Genet , vol.6 , Issue.9 , pp. 678-687
    • DePristo, M.A.1    Weinreich, D.M.2    Hartl, D.L.3
  • 27
    • 78449233935 scopus 로고    scopus 로고
    • Pervasive cryptic epistasis in molecular evolution
    • Lunzer M, Golding GB, Dean AM (2010) Pervasive cryptic epistasis in molecular evolution. PLoS Genet 6(10):e1001162.
    • (2010) PLoS Genet , vol.6 , Issue.10
    • Lunzer, M.1    Golding, G.B.2    Dean, A.M.3
  • 28
    • 77957346489 scopus 로고    scopus 로고
    • Genome-wide analysis of a long-term evolution experiment with Drosophila
    • Burke MK, et al. (2010) Genome-wide analysis of a long-term evolution experiment with Drosophila. Nature 467(7315):587-590.
    • (2010) Nature , vol.467 , Issue.7315 , pp. 587-590
    • Burke, M.K.1
  • 29
    • 79952270576 scopus 로고    scopus 로고
    • Prevalence of epistasis in the evolution of influenza A surface proteins
    • Kryazhimskiy S, Dushoff J, Bazykin GA, Plotkin JB (2011) Prevalence of epistasis in the evolution of influenza A surface proteins. PLoS Genet 7(2):e1001301.
    • (2011) PLoS Genet , vol.7 , Issue.2
    • Kryazhimskiy, S.1    Dushoff, J.2    Bazykin, G.A.3    Plotkin, J.B.4
  • 30
    • 79957948242 scopus 로고    scopus 로고
    • Negative epistasis between beneficial mutations in an evolving bacterial population
    • Khan AI, Dinh DM, Schneider D, Lenski RE, Cooper TF (2011) Negative epistasis between beneficial mutations in an evolving bacterial population. Science 332(6034):1193-1196.
    • (2011) Science , vol.332 , Issue.6034 , pp. 1193-1196
    • Khan, A.I.1    Dinh, D.M.2    Schneider, D.3    Lenski, R.E.4    Cooper, T.F.5
  • 31
    • 79957958115 scopus 로고    scopus 로고
    • Diminishing returns epistasis among beneficial mutations decelerates adaptation
    • Chou HH, Chiu HC, Delaney NF, Segrè D, Marx CJ (2011) Diminishing returns epistasis among beneficial mutations decelerates adaptation. Science 332(6034):1190-1192.
    • (2011) Science , vol.332 , Issue.6034 , pp. 1190-1192
    • Chou, H.H.1    Chiu, H.C.2    Delaney, N.F.3    Segrè, D.4    Marx, C.J.5
  • 33
    • 84866944595 scopus 로고    scopus 로고
    • Genomic analysis of a key innovation in an experimental Escherichia coli population
    • Blount ZD, Barrick JE, Davidson CJ, Lenski RE (2012) Genomic analysis of a key innovation in an experimental Escherichia coli population. Nature 489(7417):513-518.
    • (2012) Nature , vol.489 , Issue.7417 , pp. 513-518
    • Blount, Z.D.1    Barrick, J.E.2    Davidson, C.J.3    Lenski, R.E.4
  • 34
    • 84890116570 scopus 로고    scopus 로고
    • Long-term dynamics of adaptation in asexual populations
    • Wiser MJ, Ribeck N, Lenski RE (2013) Long-term dynamics of adaptation in asexual populations. Science 342(6164):1364-1367.
    • (2013) Science , vol.342 , Issue.6164 , pp. 1364-1367
    • Wiser, M.J.1    Ribeck, N.2    Lenski, R.E.3
  • 35
    • 0032571568 scopus 로고    scopus 로고
    • Contingency and determinism in replicated adaptive radiations of island lizards
    • Losos JB, Jackman TR, Larson A, Queiroz K, Rodriguez-Schettino L (1998) Contingency and determinism in replicated adaptive radiations of island lizards. Science 279(5359):2115-2118.
    • (1998) Science , vol.279 , Issue.5359 , pp. 2115-2118
    • Losos, J.B.1    Jackman, T.R.2    Larson, A.3    Queiroz, K.4    Rodriguez-Schettino, L.5
  • 36
    • 79953738501 scopus 로고    scopus 로고
    • Initial mutations direct alternative pathways of protein evolution
    • Salverda MLM, et al. (2011) Initial mutations direct alternative pathways of protein evolution. PLoS Genet 7(3):e1001321.
    • (2011) PLoS Genet , vol.7 , Issue.3
    • Salverda, M.L.M.1
  • 37
    • 84863393863 scopus 로고    scopus 로고
    • Repeatability and contingency in the evolution of a key innovation in phage lambda
    • Meyer JR, et al. (2012) Repeatability and contingency in the evolution of a key innovation in phage lambda. Science 335(6067):428-432.
    • (2012) Science , vol.335 , Issue.6067 , pp. 428-432
    • Meyer, J.R.1
  • 38
    • 84878427504 scopus 로고    scopus 로고
    • Experimental interrogation of the path dependence and stochasticity of protein evolution using phage-assisted continuous evolution
    • Dickinson BC, Leconte AM, Allen B, Esvelt KM, Liu DR (2013) Experimental interrogation of the path dependence and stochasticity of protein evolution using phage-assisted continuous evolution. Proc Natl Acad Sci USA 110(22):9007-9012.
    • (2013) Proc Natl Acad Sci USA , vol.110 , Issue.22 , pp. 9007-9012
    • Dickinson, B.C.1    Leconte, A.M.2    Allen, B.3    Esvelt, K.M.4    Liu, D.R.5
  • 39
    • 84866697042 scopus 로고    scopus 로고
    • Fitness conferred by replaced amino acids declines with time
    • Naumenko SA, Kondrashov AS, Bazykin GA (2012) Fitness conferred by replaced amino acids declines with time. Biol Lett 8(5):825-828.
    • (2012) Biol Lett , vol.8 , Issue.5 , pp. 825-828
    • Naumenko, S.A.1    Kondrashov, A.S.2    Bazykin, G.A.3
  • 40
    • 84874768052 scopus 로고    scopus 로고
    • Estimating the rate of irreversibility in protein evolution
    • Soylemez O, Kondrashov FA (2012) Estimating the rate of irreversibility in protein evolution. Genome Biol Evol 4(12):1213-1222.
    • (2012) Genome Biol Evol , vol.4 , Issue.12 , pp. 1213-1222
    • Soylemez, O.1    Kondrashov, F.A.2
  • 41
    • 33845864966 scopus 로고    scopus 로고
    • Robustness-epistasis link shapes the fitness landscape of a randomly drifting protein
    • Bershtein S, Segal M, Bekerman R, Tokuriki N, Tawfik DS (2006) Robustness-epistasis link shapes the fitness landscape of a randomly drifting protein. Nature 444(7121):929-932.
    • (2006) Nature , vol.444 , Issue.7121 , pp. 929-932
    • Bershtein, S.1    Segal, M.2    Bekerman, R.3    Tokuriki, N.4    Tawfik, D.S.5
  • 42
    • 36148966864 scopus 로고    scopus 로고
    • Coevolutionary patterns in cytochrome c oxidase subunit I depend on structural and functional context
    • Wang ZO, Pollock DD (2007) Coevolutionary patterns in cytochrome c oxidase subunit I depend on structural and functional context. J Mol Evol 65(5):485-495.
    • (2007) J Mol Evol , vol.65 , Issue.5 , pp. 485-495
    • Wang, Z.O.1    Pollock, D.D.2
  • 43
    • 77953718211 scopus 로고    scopus 로고
    • Sequence space and the ongoing expansion of the protein universe
    • Povolotskaya IS, Kondrashov FA (2010) Sequence space and the ongoing expansion of the protein universe. Nature 465(7300):922-926.
    • (2010) Nature , vol.465 , Issue.7300 , pp. 922-926
    • Povolotskaya, I.S.1    Kondrashov, F.A.2
  • 44
    • 84903742512 scopus 로고    scopus 로고
    • Why human disease-associated residues appear as the wild-type in other species: Genome-scale structural evidence for the compensation hypothesis
    • Xu J, Zhang J (2014) Why human disease-associated residues appear as the wild-type in other species: Genome-scale structural evidence for the compensation hypothesis. Mol Biol Evol 31(7):1787-1792.
    • (2014) Mol Biol Evol , vol.31 , Issue.7 , pp. 1787-1792
    • Xu, J.1    Zhang, J.2
  • 45
    • 0033582946 scopus 로고    scopus 로고
    • Coevolving protein residues: Maximum likelihood identification and relationship to structure
    • Pollock DD, Taylor WR, Goldman N (1999) Coevolving protein residues: Maximum likelihood identification and relationship to structure. J Mol Biol 287(1):187-198.
    • (1999) J Mol Biol , vol.287 , Issue.1 , pp. 187-198
    • Pollock, D.D.1    Taylor, W.R.2    Goldman, N.3
  • 46
    • 1542642309 scopus 로고    scopus 로고
    • Protein evolution with dependence among codons due to tertiary structure
    • Robinson DM, Jones DT, Kishino H, Goldman N, Thorne JL (2003) Protein evolution with dependence among codons due to tertiary structure. Mol Biol Evol 20(10):1692-1704.
    • (2003) Mol Biol Evol , vol.20 , Issue.10 , pp. 1692-1704
    • Robinson, D.M.1    Jones, D.T.2    Kishino, H.3    Goldman, N.4    Thorne, J.L.5
  • 47
    • 33748126145 scopus 로고    scopus 로고
    • Assessing site-interdependent phylogenetic models of sequence evolution
    • Rodrigue N, Philippe H, Lartillot N (2006) Assessing site-interdependent phylogenetic models of sequence evolution. Mol Biol Evol 23(9):1762-1775.
    • (2006) Mol Biol Evol , vol.23 , Issue.9 , pp. 1762-1775
    • Rodrigue, N.1    Philippe, H.2    Lartillot, N.3
  • 48
    • 34547809931 scopus 로고    scopus 로고
    • Quantifying the impact of protein tertiary structure on molecular evolution
    • Choi SC, Hobolth A, Robinson DM, Kishino H, Thorne JL (2007) Quantifying the impact of protein tertiary structure on molecular evolution. Mol Biol Evol 24(8):1769-1782.
    • (2007) Mol Biol Evol , vol.24 , Issue.8 , pp. 1769-1782
    • Choi, S.C.1    Hobolth, A.2    Robinson, D.M.3    Kishino, H.4    Thorne, J.L.5
  • 49
    • 84890067204 scopus 로고    scopus 로고
    • Protein evolution along phylogenetic histories under structurally constrained substitution models
    • Arenas M, Dos Santos HG, Posada D, Bastolla U (2013) Protein evolution along phylogenetic histories under structurally constrained substitution models. Bioinformatics 29(23):3020-3028.
    • (2013) Bioinformatics , vol.29 , Issue.23 , pp. 3020-3028
    • Arenas, M.1    Dos Santos, H.G.2    Posada, D.3    Bastolla, U.4
  • 51
    • 0028168856 scopus 로고
    • A codon-based model of nucleotide substitution for protein-coding DNA sequences
    • Goldman N, Yang Z (1994) A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol Biol Evol 11(5):725-736.
    • (1994) Mol Biol Evol , vol.11 , Issue.5 , pp. 725-736
    • Goldman, N.1    Yang, Z.2
  • 52
    • 34547675965 scopus 로고    scopus 로고
    • An empirical codon model for protein sequence evolution
    • Kosiol C, Holmes I, Goldman N (2007) An empirical codon model for protein sequence evolution. Mol Biol Evol 24(7):1464-1479.
    • (2007) Mol Biol Evol , vol.24 , Issue.7 , pp. 1464-1479
    • Kosiol, C.1    Holmes, I.2    Goldman, N.3
  • 53
    • 39749161509 scopus 로고    scopus 로고
    • Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage
    • Yang Z, Nielsen R (2008) Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage. Mol Biol Evol 25(3):568-579.
    • (2008) Mol Biol Evol , vol.25 , Issue.3 , pp. 568-579
    • Yang, Z.1    Nielsen, R.2
  • 54
    • 77949536563 scopus 로고    scopus 로고
    • Mutation-selection models of coding sequence evolution with site-heterogeneous amino acid fitness profiles
    • Rodrigue N, Philippe H, Lartillot N (2010) Mutation-selection models of coding sequence evolution with site-heterogeneous amino acid fitness profiles. Proc Natl Acad Sci USA 107(10):4629-4634.
    • (2010) Proc Natl Acad Sci USA , vol.107 , Issue.10 , pp. 4629-4634
    • Rodrigue, N.1    Philippe, H.2    Lartillot, N.3
  • 55
    • 84858184390 scopus 로고    scopus 로고
    • Estimating the distribution of selection coefficients from phylogenetic data using sitewise mutation-selection models
    • Tamuri AU, dos Reis M, Goldstein RA (2012) Estimating the distribution of selection coefficients from phylogenetic data using sitewise mutation-selection models. Genetics 190(3):1101-1115.
    • (2012) Genetics , vol.190 , Issue.3 , pp. 1101-1115
    • Tamuri, A.U.1    Dos Reis, M.2    Goldstein, R.A.3
  • 56
    • 84905001681 scopus 로고    scopus 로고
    • An experimentally determined evolutionary model dramatically improves phylogenetic fit
    • Bloom JD (2014) An experimentally determined evolutionary model dramatically improves phylogenetic fit. Mol Biol Evol 31(8):1956-1978.
    • (2014) Mol Biol Evol , vol.31 , Issue.8 , pp. 1956-1978
    • Bloom, J.D.1
  • 57
    • 0036291145 scopus 로고    scopus 로고
    • Predicting changes in the stability of proteins and protein complexes: A study of more than 1000 mutations
    • Guerois R, Nielsen JE, Serrano L (2002) Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J Mol Biol 320(2):369-387.
    • (2002) J Mol Biol , vol.320 , Issue.2 , pp. 369-387
    • Guerois, R.1    Nielsen, J.E.2    Serrano, L.3
  • 58
    • 0025082684 scopus 로고
    • Additivity of mutational effects in proteins
    • Wells JA (1990) Additivity of mutational effects in proteins. Biochemistry 29(37):8509-8517.
    • (1990) Biochemistry , vol.29 , Issue.37 , pp. 8509-8517
    • Wells, J.A.1
  • 59
    • 0027441807 scopus 로고
    • Step-wise mutation of barnase to binase. A procedure for engineering increased stability of proteins and an experimental analysis of the evolution of protein stability
    • Serrano L, Day AG, Fersht AR (1993) Step-wise mutation of barnase to binase. A procedure for engineering increased stability of proteins and an experimental analysis of the evolution of protein stability. J Mol Biol 233(2):305-312.
    • (1993) J Mol Biol , vol.233 , Issue.2 , pp. 305-312
    • Serrano, L.1    Day, A.G.2    Fersht, A.R.3
  • 60
    • 79959992592 scopus 로고    scopus 로고
    • A biophysical protein folding model accounts for most mutational fitness effects in viruses
    • Wylie CS, Shakhnovich EI (2011) A biophysical protein folding model accounts for most mutational fitness effects in viruses. Proc Natl Acad Sci USA 108(24):9916-9921.
    • (2011) Proc Natl Acad Sci USA , vol.108 , Issue.24 , pp. 9916-9921
    • Wylie, C.S.1    Shakhnovich, E.I.2
  • 61
    • 84891364264 scopus 로고    scopus 로고
    • Mutational effects on stability are largely conserved during protein evolution
    • Ashenberg O, Gong LI, Bloom JD (2013) Mutational effects on stability are largely conserved during protein evolution. Proc Natl Acad Sci USA 110(52):21071-21076.
    • (2013) Proc Natl Acad Sci USA , vol.110 , Issue.52 , pp. 21071-21076
    • Ashenberg, O.1    Gong, L.I.2    Bloom, J.D.3
  • 62
    • 0014296201 scopus 로고
    • Genetic variability maintained in a finite population due to mutational production of neutral and nearly neutral isoalleles
    • Kimura M (1968) Genetic variability maintained in a finite population due to mutational production of neutral and nearly neutral isoalleles. Genet Res 11(3):247-269.
    • (1968) Genet Res , vol.11 , Issue.3 , pp. 247-269
    • Kimura, M.1
  • 63
    • 84905454017 scopus 로고    scopus 로고
    • Modeling evolution using the probability of fixation: History and implications
    • McCandlish DM, Stoltzfus A (2014) Modeling evolution using the probability of fixation: History and implications. Q Rev Biol 89(3):225-252.
    • (2014) Q Rev Biol , vol.89 , Issue.3 , pp. 225-252
    • McCandlish, D.M.1    Stoltzfus, A.2
  • 64
    • 74549207309 scopus 로고    scopus 로고
    • Assessing computational methods for predicting protein stability upon mutation: Good on average but not in the details
    • Potapov V, Cohen M, Schreiber G (2009) Assessing computational methods for predicting protein stability upon mutation: Good on average but not in the details. Protein Eng Des Sel 22(9):553-560.
    • (2009) Protein Eng Des Sel , vol.22 , Issue.9 , pp. 553-560
    • Potapov, V.1    Cohen, M.2    Schreiber, G.3
  • 65
    • 79551470095 scopus 로고    scopus 로고
    • Role of conformational sampling in computing mutation-induced changes in protein structure and stability
    • Kellogg EH, Leaver-Fay A, Baker D (2011) Role of conformational sampling in computing mutation-induced changes in protein structure and stability. Proteins 79(3):830-838.
    • (2011) Proteins , vol.79 , Issue.3 , pp. 830-838
    • Kellogg, E.H.1    Leaver-Fay, A.2    Baker, D.3
  • 66
    • 0028949615 scopus 로고
    • Proteins and temperature
    • Somero GN (1995) Proteins and temperature. Annu Rev Physiol 57:43-68.
    • (1995) Annu Rev Physiol , vol.57 , pp. 43-68
    • Somero, G.N.1
  • 69
    • 84893786232 scopus 로고    scopus 로고
    • Understanding thermal adaptation of enzymes through the multistate rational design and stability prediction of 100 adenylate kinases
    • Howell SC, Inampudi KK, Bean DP, Wilson CJ (2014) Understanding thermal adaptation of enzymes through the multistate rational design and stability prediction of 100 adenylate kinases. Structure 22(2):218-229.
    • (2014) Structure , vol.22 , Issue.2 , pp. 218-229
    • Howell, S.C.1    Inampudi, K.K.2    Bean, D.P.3    Wilson, C.J.4
  • 70
    • 2942565781 scopus 로고    scopus 로고
    • The distribution of fitness effects caused by single-nucleotide substitutions in an RNA virus
    • Sanjuán R, Moya A, Elena SF (2004) The distribution of fitness effects caused by single-nucleotide substitutions in an RNA virus. Proc Natl Acad Sci USA 101(22):8396-8401.
    • (2004) Proc Natl Acad Sci USA , vol.101 , Issue.22 , pp. 8396-8401
    • Sanjuán, R.1    Moya, A.2    Elena, S.F.3
  • 71
    • 34447546660 scopus 로고    scopus 로고
    • The distribution of fitness effects of new mutations
    • Eyre-Walker A, Keightley PD (2007) The distribution of fitness effects of new mutations. Nat Rev Genet 8(8):610-618.
    • (2007) Nat Rev Genet , vol.8 , Issue.8 , pp. 610-618
    • Eyre-Walker, A.1    Keightley, P.D.2
  • 72
    • 84881408157 scopus 로고    scopus 로고
    • Capturing the mutational landscape of the beta-lactamase TEM-1
    • Jacquier H, et al. (2013) Capturing the mutational landscape of the beta-lactamase TEM-1. Proc Natl Acad Sci USA 110(32):13067-13072.
    • (2013) Proc Natl Acad Sci USA , vol.110 , Issue.32 , pp. 13067-13072
    • Jacquier, H.1
  • 73
    • 84895727363 scopus 로고    scopus 로고
    • A bayesian MCMC approach to assess the complete distribution of fitness effects of new mutations: Uncovering the potential for adaptive walks in challenging environments
    • Bank C, Hietpas RT, Wong A, Bolon DN, Jensen JD (2014) A bayesian MCMC approach to assess the complete distribution of fitness effects of new mutations: Uncovering the potential for adaptive walks in challenging environments. Genetics 196(3):841-852.
    • (2014) Genetics , vol.196 , Issue.3 , pp. 841-852
    • Bank, C.1    Hietpas, R.T.2    Wong, A.3    Bolon, D.N.4    Jensen, J.D.5
  • 76
    • 0036139093 scopus 로고    scopus 로고
    • Why are proteins marginally stable?
    • Taverna DM, Goldstein RA (2002) Why are proteins marginally stable? Proteins 46(1):105-109.
    • (2002) Proteins , vol.46 , Issue.1 , pp. 105-109
    • Taverna, D.M.1    Goldstein, R.A.2
  • 78
    • 34248674895 scopus 로고    scopus 로고
    • The stability effects of protein mutations appear to be universally distributed
    • Tokuriki N, Stricher F, Schymkowitz J, Serrano L, Tawfik DS (2007) The stability effects of protein mutations appear to be universally distributed. J Mol Biol 369(5):1318-1332.
    • (2007) J Mol Biol , vol.369 , Issue.5 , pp. 1318-1332
    • Tokuriki, N.1    Stricher, F.2    Schymkowitz, J.3    Serrano, L.4    Tawfik, D.S.5
  • 79
    • 33846515095 scopus 로고    scopus 로고
    • Thermodynamics of neutral protein evolution
    • Bloom JD, Raval A, Wilke CO (2007) Thermodynamics of neutral protein evolution. Genetics 175(1):255-266.
    • (2007) Genetics , vol.175 , Issue.1 , pp. 255-266
    • Bloom, J.D.1    Raval, A.2    Wilke, C.O.3
  • 80
    • 36049027813 scopus 로고    scopus 로고
    • Protein stability imposes limits on organism complexity and speed of molecular evolution
    • Zeldovich KB, Chen P, Shakhnovich EI (2007) Protein stability imposes limits on organism complexity and speed of molecular evolution. Proc Natl Acad Sci USA 104(41):16152-16157.
    • (2007) Proc Natl Acad Sci USA , vol.104 , Issue.41 , pp. 16152-16157
    • Zeldovich, K.B.1    Chen, P.2    Shakhnovich, E.I.3
  • 81
    • 0028808763 scopus 로고
    • Context-dependent optimal substitution matrices
    • Koshi JM, Goldstein RA (1995) Context-dependent optimal substitution matrices. Protein Eng 8(7):641-645.
    • (1995) Protein Eng , vol.8 , Issue.7 , pp. 641-645
    • Koshi, J.M.1    Goldstein, R.A.2
  • 82
    • 0345062357 scopus 로고    scopus 로고
    • Universally conserved positions in protein folds: Reading evolutionary signals about stability, folding kinetics and function
    • Mirny LA, Shakhnovich EI (1999) Universally conserved positions in protein folds: Reading evolutionary signals about stability, folding kinetics and function. J Mol Biol 291(1):177-196.
    • (1999) J Mol Biol , vol.291 , Issue.1 , pp. 177-196
    • Mirny, L.A.1    Shakhnovich, E.I.2
  • 83
    • 33748143748 scopus 로고    scopus 로고
    • Structural determinants of the rate of protein evolution in yeast
    • Bloom JD, Drummond DA, Arnold FH, Wilke CO (2006) Structural determinants of the rate of protein evolution in yeast. Mol Biol Evol 23(9):1751-1761.
    • (2006) Mol Biol Evol , vol.23 , Issue.9 , pp. 1751-1761
    • Bloom, J.D.1    Drummond, D.A.2    Arnold, F.H.3    Wilke, C.O.4
  • 84
    • 84988239865 scopus 로고    scopus 로고
    • Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history
    • Risso VA, et al. (2015) Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history. Mol Biol Evol 32(2):440-455.
    • (2015) Mol Biol Evol , vol.32 , Issue.2 , pp. 440-455
    • Risso, V.A.1
  • 86
    • 84886298744 scopus 로고    scopus 로고
    • Selection biases the prevalence and type of epistasis along adaptive trajectories
    • Draghi JA, Plotkin JB (2013) Selection biases the prevalence and type of epistasis along adaptive trajectories. Evolution 67(11):3120-3131.
    • (2013) Evolution , vol.67 , Issue.11 , pp. 3120-3131
    • Draghi, J.A.1    Plotkin, J.B.2
  • 87
    • 84901650146 scopus 로고    scopus 로고
    • The changing geometry of a fitness landscape along an adaptive walk
    • Greene D, Crona K (2014) The changing geometry of a fitness landscape along an adaptive walk. PLOS Comput Biol 10(5):e1003520.
    • (2014) PLOS Comput Biol , vol.10 , Issue.5
    • Greene, D.1    Crona, K.2
  • 88
    • 70649097086 scopus 로고    scopus 로고
    • Lethal mutagenesis in viruses and bacteria
    • Chen P, Shakhnovich EI (2009) Lethal mutagenesis in viruses and bacteria. Genetics 183(2):639-650.
    • (2009) Genetics , vol.183 , Issue.2 , pp. 639-650
    • Chen, P.1    Shakhnovich, E.I.2
  • 89
    • 84898811791 scopus 로고    scopus 로고
    • Strong evidence for protein epistasis, weak evidence against it
    • Pollock DD, Goldstein RA (2014) Strong evidence for protein epistasis, weak evidence against it. Proc Natl Acad Sci USA 111(15):E1450.
    • (2014) Proc Natl Acad Sci USA , vol.111 , Issue.15
    • Pollock, D.D.1    Goldstein, R.A.2
  • 91
    • 84878410814 scopus 로고    scopus 로고
    • The role of epistasis in protein evolution
    • discussion E2-E3
    • McCandlish DM, Rajon E, Shah P, Ding Y, Plotkin JB (2013) The role of epistasis in protein evolution. Nature 497(7451):E1-E2, discussion E2-E3.
    • (2013) Nature , vol.497 , Issue.7451 , pp. E1-E2
    • McCandlish, D.M.1    Rajon, E.2    Shah, P.3    Ding, Y.4    Plotkin, J.B.5
  • 92
    • 77953287348 scopus 로고    scopus 로고
    • Mechanistic revisions of phenomenological modeling strategies in molecular evolution
    • Rodrigue N, Philippe H (2010) Mechanistic revisions of phenomenological modeling strategies in molecular evolution. Trends Genet 26(6):248-252.
    • (2010) Trends Genet , vol.26 , Issue.6 , pp. 248-252
    • Rodrigue, N.1    Philippe, H.2
  • 93
    • 84938520945 scopus 로고    scopus 로고
    • Codon models as a vehicle for reconciling population genetics with inter-specific sequence data
    • eds Cannarozzi GM, Schneider A (Oxford Univ Press, Oxford)
    • Thorne JL, Lartillot N, Rodrigue N, Choi SC (2012) Codon models as a vehicle for reconciling population genetics with inter-specific sequence data. Codon Evolution: Mechanisms and Models, eds Cannarozzi GM, Schneider A (Oxford Univ Press, Oxford), pp 97-110.
    • (2012) Codon Evolution: Mechanisms and Models , pp. 97-110
    • Thorne, J.L.1    Lartillot, N.2    Rodrigue, N.3    Choi, S.C.4
  • 94
    • 84864029746 scopus 로고    scopus 로고
    • Bringing molecules back into molecular evolution
    • Wilke CO (2012) Bringing molecules back into molecular evolution. PLOS Comput Biol 8(6):e1002572.
    • (2012) PLOS Comput Biol , vol.8 , Issue.6
    • Wilke, C.O.1
  • 95
    • 84864697376 scopus 로고    scopus 로고
    • Inferring species trees directly from biallelic genetic markers: Bypassing gene trees in a full coalescent analysis
    • Bryant D, Bouckaert R, Felsenstein J, Rosenberg NA, RoyChoudhury A (2012) Inferring species trees directly from biallelic genetic markers: Bypassing gene trees in a full coalescent analysis. Mol Biol Evol 29(8):1917-1932.
    • (2012) Mol Biol Evol , vol.29 , Issue.8 , pp. 1917-1932
    • Bryant, D.1    Bouckaert, R.2    Felsenstein, J.3    Rosenberg, N.A.4    RoyChoudhury, A.5
  • 96
    • 84888597013 scopus 로고    scopus 로고
    • Linking great apes genome evolution across time scales using polymorphism-aware phylogenetic models
    • De Maio N, Schlötterer C, Kosiol C (2013) Linking great apes genome evolution across time scales using polymorphism-aware phylogenetic models. Mol Biol Evol 30(10):2249-2262.
    • (2013) Mol Biol Evol , vol.30 , Issue.10 , pp. 2249-2262
    • De Maio, N.1    Schlötterer, C.2    Kosiol, C.3
  • 97
    • 84883240912 scopus 로고    scopus 로고
    • A phylogenetic model for the detection of epistatic interactions
    • Nasrallah CA, Huelsenbeck JP (2013) A phylogenetic model for the detection of epistatic interactions. Mol Biol Evol 30(9):2197-2208.
    • (2013) Mol Biol Evol , vol.30 , Issue.9 , pp. 2197-2208
    • Nasrallah, C.A.1    Huelsenbeck, J.P.2
  • 98
    • 52449148668 scopus 로고
    • The role of compensatory neutral mutations in molecular evolution
    • Kimura M (1985) The role of compensatory neutral mutations in molecular evolution. J Genet 64:7-19.
    • (1985) J Genet , vol.64 , pp. 7-19
    • Kimura, M.1
  • 99
    • 0037035388 scopus 로고    scopus 로고
    • Evolution of functionally conserved enhancers can be accelerated in large populations: A population-genetic model
    • Carter AJR, Wagner GP (2002) Evolution of functionally conserved enhancers can be accelerated in large populations: A population-genetic model. Proc Biol Sci 269(1494):953-960.
    • (2002) Proc Biol Sci , vol.269 , Issue.1494 , pp. 953-960
    • Carter, A.J.R.1    Wagner, G.P.2
  • 100
    • 1942453330 scopus 로고    scopus 로고
    • Stochastic tunnels in evolutionary dynamics
    • Iwasa Y, Michor F, Nowak MA (2004) Stochastic tunnels in evolutionary dynamics. Genetics 166(3):1571-1579.
    • (2004) Genetics , vol.166 , Issue.3 , pp. 1571-1579
    • Iwasa, Y.1    Michor, F.2    Nowak, M.A.3
  • 101
    • 83455238341 scopus 로고    scopus 로고
    • Biophysical and structural considerations for protein sequence evolution
    • Grahnen JA, Nandakumar P, Kubelka J, Liberles DA (2011) Biophysical and structural considerations for protein sequence evolution. BMC Evol Biol 11:361.
    • (2011) BMC Evol Biol , vol.11 , pp. 361
    • Grahnen, J.A.1    Nandakumar, P.2    Kubelka, J.3    Liberles, D.A.4
  • 102
    • 84861434946 scopus 로고    scopus 로고
    • The interface of protein structure, protein biophysics, and molecular evolution
    • Liberles DA, et al. (2012) The interface of protein structure, protein biophysics, and molecular evolution. Protein Sci 21(6):769-785.
    • (2012) Protein Sci , vol.21 , Issue.6 , pp. 769-785
    • Liberles, D.A.1


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