메뉴 건너뛰기




Volumn 109, Issue 21, 2012, Pages

Amino acid coevolution induces an evolutionary Stokes shift

Author keywords

[No Author keywords available]

Indexed keywords

ACID PHOSPHATASE TARTRATE RESISTANT ISOENZYME; AMINO ACID;

EID: 84861422981     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1120084109     Document Type: Article
Times cited : (158)

References (46)
  • 1
    • 0033635920 scopus 로고    scopus 로고
    • Assessing an unknown evolutionary process: Effect of increasing site-specific knowledge through taxon addition
    • Pollock DD, Bruno WJ (2000) Assessing an unknown evolutionary process: Effect of increasing site-specific knowledge through taxon addition. Mol Biol Evol 17:1854-1858.
    • (2000) Mol Biol Evol , vol.17 , pp. 1854-1858
    • Pollock, D.D.1    Bruno, W.J.2
  • 2
    • 67049119180 scopus 로고    scopus 로고
    • Evidence for an ancient adaptive episode of convergent molecular evolution
    • Castoe TA, et al. (2009) Evidence for an ancient adaptive episode of convergent molecular evolution. Proc Natl Acad Sci USA 106:8986-8991.
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 8986-8991
    • Castoe, T.A.1
  • 3
    • 76749112068 scopus 로고    scopus 로고
    • Disentangling direct from indirect co-evolution of residues in protein alignments
    • Burger L, van Nimwegen E (2010) Disentangling direct from indirect co-evolution of residues in protein alignments. PLoS Comput Biol 6:e1000633.
    • (2010) PLoS Comput Biol , vol.6
    • Burger, L.1    Van Nimwegen, E.2
  • 4
    • 84860533518 scopus 로고    scopus 로고
    • Detecting coevolving amino acid sites using Bayesian mutational mapping
    • DOI 10.1093/bioinformatics/bti1032
    • Dimmic MW, Hubisz MJ, Bustamante CD, Nielsen R (2005) Detecting coevolving amino acid sites using Bayesian mutational mapping. Bioinformatics 21(Suppl 1):i126-i135. (Pubitemid 41794482)
    • (2005) Bioinformatics , vol.21 , Issue.SUPPL. 1
    • Dimmic, M.W.1    Hubisz, M.J.2    Bustamante, C.D.3    Nielsen, R.4
  • 6
    • 84856090271 scopus 로고    scopus 로고
    • PSICOV: Precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments
    • Jones DT, Buchan DW, Cozzetto D, Pontil M (2012) PSICOV: Precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments. Bioinformatics 28:184-190.
    • (2012) Bioinformatics , vol.28 , pp. 184-190
    • Jones, D.T.1    Buchan, D.W.2    Cozzetto, D.3    Pontil, M.4
  • 7
    • 82855163967 scopus 로고    scopus 로고
    • Protein 3D structure computed from evolutionary sequence variation
    • Marks DS, et al. (2011) Protein 3D structure computed from evolutionary sequence variation. PLoS One 6:e28766.
    • (2011) PLoS One , vol.6
    • Marks, D.S.1
  • 8
    • 0033582946 scopus 로고    scopus 로고
    • Coevolving protein residues: Maximum likelihood identification and relationship to structure
    • DOI 10.1006/jmbi.1998.2601
    • Pollock DD, Taylor WR, Goldman N (1999) Coevolving protein residues: Maximum likelihood identification and relationship to structure. J Mol Biol 287:187-198. (Pubitemid 29134806)
    • (1999) Journal of Molecular Biology , vol.287 , Issue.1 , pp. 187-198
    • Pollock, D.D.1    Taylor, W.R.2    Goldman, N.3
  • 9
    • 84863393203 scopus 로고    scopus 로고
    • Protein topology from predicted residue contacts
    • Taylor WR, Jones DT, Sadowski MI (2012) Protein topology from predicted residue contacts. Protein Sci 21:299-305.
    • (2012) Protein Sci , vol.21 , pp. 299-305
    • Taylor, W.R.1    Jones, D.T.2    Sadowski, M.I.3
  • 10
    • 19944406094 scopus 로고    scopus 로고
    • Context dependence and coevolution among amino acid residues in proteins
    • DOI 10.1016/S0076-6879(05)95040-4, PII S0076687905950404, Molecular Evolution: Producing the Biochemical Data
    • Wang ZO, Pollock DD (2005) Context dependence and coevolution among amino acid residues in proteins. Methods Enzymol 395:779-790. (Pubitemid 40754397)
    • (2005) Methods in Enzymology , vol.395 , pp. 779-790
    • Wang, Z.O.1    Pollock, D.D.2
  • 11
    • 36148966864 scopus 로고    scopus 로고
    • Coevolutionary patterns in cytochrome c oxidase subunit I depend on structural and functional context
    • DOI 10.1007/s00239-007-9018-8
    • Wang ZO, Pollock DD (2007) Coevolutionary patterns in cytochrome c oxidase subunit I depend on structural and functional context. J Mol Evol 65:485-495. (Pubitemid 350115431)
    • (2007) Journal of Molecular Evolution , vol.65 , Issue.5 , pp. 485-495
    • Wang, Z.O.1    Pollock, D.D.2
  • 12
    • 15544374861 scopus 로고    scopus 로고
    • Site interdependence attributed to tertiary structure in amino acid sequence evolution
    • DOI 10.1016/j.gene.2004.12.011
    • Rodrigue N, Lartillot N, Bryant D, Philippe H (2005) Site interdependence attributed to tertiary structure in amino acid sequence evolution. Gene 347:207-217. (Pubitemid 40403760)
    • (2005) Gene , vol.347 , Issue.2 SPEC. ISS. , pp. 207-217
    • Rodrigue, N.1    Lartillot, N.2    Bryant, D.3    Philippe, H.4
  • 13
    • 33748126145 scopus 로고    scopus 로고
    • Assessing site-interdependent phylogenetic models of sequence evolution
    • DOI 10.1093/molbev/msl041
    • Rodrigue N, Philippe H, Lartillot N (2006) Assessing site-interdependent phylogenetic models of sequence evolution. Mol Biol Evol 23:1762-1775. (Pubitemid 44309770)
    • (2006) Molecular Biology and Evolution , vol.23 , Issue.9 , pp. 1762-1775
    • Rodrigue, N.1    Philippe, H.2    Lartillot, N.3
  • 14
    • 0000228203 scopus 로고
    • A model of evolutionary change in proteins
    • ed Dayhoff M(National Biomedical Research Foundation, Silver Spring, MD)
    • Dayhoff M, Schwartz R, Orcutt B (1978) A model of evolutionary change in proteins. Atlas of Protein Sequence and Structure, ed Dayhoff M(National Biomedical Research Foundation, Silver Spring, MD), pp 345-352.
    • (1978) Atlas of Protein Sequence and Structure , pp. 345-352
    • Dayhoff, M.1    Schwartz, R.2    Orcutt, B.3
  • 15
    • 0026691182 scopus 로고
    • The rapid generation of mutation data matrices from protein sequences
    • Jones DT, Taylor WR, Thornton JM (1992) The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 8:275-282.
    • (1992) Comput Appl Biosci , vol.8 , pp. 275-282
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 16
    • 0035031966 scopus 로고    scopus 로고
    • A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach
    • Whelan S, Goldman N (2001) A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol 18:691-699. (Pubitemid 32372940)
    • (2001) Molecular Biology and Evolution , vol.18 , Issue.5 , pp. 691-699
    • Whelan, S.1    Goldman, N.2
  • 17
    • 0027062943 scopus 로고
    • Environment-specific amino acid substitution tables: Tertiary templates and prediction of protein folds
    • Overington J, Donnelly D, Johnson MS, Sali A, Blundell TL (1992) Environment-specific amino acid substitution tables: Tertiary templates and prediction of protein folds. Protein Sci 1:216-226. (Pubitemid 23007288)
    • (1992) Protein Science , vol.1 , Issue.2 , pp. 216-226
    • Overington, J.1    Donnelly, D.2    Johnson, M.S.3    Sali, A.4    Blundell, T.L.5
  • 18
    • 0028808763 scopus 로고
    • Context-dependent optimal substitution matrices
    • Koshi JM, Goldstein RA (1995) Context-dependent optimal substitution matrices. Protein Eng 8:641-645.
    • (1995) Protein Eng , vol.8 , pp. 641-645
    • Koshi, J.M.1    Goldstein, R.A.2
  • 20
    • 0032529584 scopus 로고    scopus 로고
    • Models of natural mutations including site heterogeneity
    • DOI 10.1002/(SICI)1097-0134(19980815)32:3<289::AID-PROT4>3.0.CO;2-D
    • Koshi JM, Goldstein RA (1998) Models of natural mutations including site heterogeneity. Proteins 32:289-295. (Pubitemid 28360825)
    • (1998) Proteins: Structure, Function and Genetics , vol.32 , Issue.3 , pp. 289-295
    • Koshi, J.M.1    Goldstein, R.A.2
  • 21
    • 2442691520 scopus 로고    scopus 로고
    • A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process
    • DOI 10.1093/molbev/msh112
    • Lartillot N, Philippe H (2004) A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Mol Biol Evol 21:1095-1109. (Pubitemid 38658218)
    • (2004) Molecular Biology and Evolution , vol.21 , Issue.6 , pp. 1095-1109
    • Lartillot, N.1    Philippe, H.2
  • 22
    • 4243140058 scopus 로고    scopus 로고
    • A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data
    • DOI 10.1080/10635150490468675
    • Pagel M, Meade A (2004) A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data. Syst Biol 53:571-581. (Pubitemid 39290200)
    • (2004) Systematic Biology , vol.53 , Issue.4 , pp. 571-581
    • Pagel, M.1    Meade, A.2
  • 24
    • 0031875569 scopus 로고    scopus 로고
    • Evolutionary distances for protein-coding sequences: Modeling site- specific residue frequencies
    • Halpern AL, Bruno WJ (1998) Evolutionary distances for protein-coding sequences: Modeling site-specific residue frequencies. Mol Biol Evol 15:910-917. (Pubitemid 28321889)
    • (1998) Molecular Biology and Evolution , vol.15 , Issue.7 , pp. 910-917
    • Halpern, A.L.1    Bruno, W.J.2
  • 25
    • 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 107:4629-4634.
    • (2010) Proc Natl Acad Sci USA , vol.107 , pp. 4629-4634
    • Rodrigue, N.1    Philippe, H.2    Lartillot, N.3
  • 27
    • 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 190:1101-1115.
    • (2012) Genetics , vol.190 , pp. 1101-1115
    • Tamuri, A.U.1    Dos Reis, M.2    Goldstein, R.A.3
  • 29
    • 0000896629 scopus 로고
    • Some problems of stochastic processes in genetics
    • Kimura M (1957) Some problems of stochastic processes in genetics. Ann Math Stat 28:882-901.
    • (1957) Ann Math Stat , vol.28 , pp. 882-901
    • Kimura, M.1
  • 30
    • 0000800333 scopus 로고
    • On the probability of fixation of mutant genes in a population
    • Kimura M (1962) On the probability of fixation of mutant genes in a population. Genetics 47:713-719.
    • (1962) Genetics , vol.47 , pp. 713-719
    • Kimura, M.1
  • 31
    • 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 79:830-838.
    • (2011) Proteins , vol.79 , pp. 830-838
    • Kellogg, E.H.1    Leaver-Fay, A.2    Baker, D.3
  • 32
    • 0035029534 scopus 로고    scopus 로고
    • Maximum-likelihood phylogenetic analysis under a covarion-like model
    • Galtier N (2001) Maximum-likelihood phylogenetic analysis under a covarion-like model. Mol Biol Evol 18:866-873.
    • (2001) Mol Biol Evol , vol.18 , pp. 866-873
    • Galtier, N.1
  • 33
    • 0034777365 scopus 로고    scopus 로고
    • Mathematical elegance with biochemical realism: The covarion model of molecular evolution
    • DOI 10.1007/s002390010258
    • Penny D, McComish BJ, Charleston MA, Hendy MD (2001) Mathematical elegance with biochemical realism: The covarion model of molecular evolution. J Mol Evol 53:711-723. (Pubitemid 32989425)
    • (2001) Journal of Molecular Evolution , vol.53 , Issue.6 , pp. 711-723
    • Penny, D.1    McComish, B.J.2    Charleston, M.A.3    Hendy, M.D.4
  • 34
    • 0034207528 scopus 로고    scopus 로고
    • Probabilistic models of DNA sequence evolution with context dependent rates of substitution
    • Jensen JL, Pedersen AMK (2000) Probabilistic models of DNA sequence evolution with context dependent rates of substitution. Adv Appl Probab 32:499-517.
    • (2000) Adv Appl Probab , vol.32 , pp. 499-517
    • Jensen, J.L.1    Pedersen, A.M.K.2
  • 35
    • 1542510106 scopus 로고    scopus 로고
    • Phylogenetic Estimation of Context-Dependent Substitution Rates by Maximum Likelihood
    • DOI 10.1093/molbev/msh039
    • Siepel A, Haussler D (2004) Phylogenetic estimation of context-dependent substitution rates by maximum likelihood. Mol Biol Evol 21:468-488. (Pubitemid 38339664)
    • (2004) Molecular Biology and Evolution , vol.21 , Issue.3 , pp. 468-488
    • Siepel, A.1    Haussler, D.2
  • 36
    • 21044435697 scopus 로고    scopus 로고
    • Perspective: Sign epistasis and genetic constraint on evolutionary trajectories
    • Weinreich DM, Watson RA, Chao L (2005) Perspective: Sign epistasis and genetic constraint on evolutionary trajectories. Evolution 59:1165-1174. (Pubitemid 40870413)
    • (2005) Evolution , vol.59 , Issue.6 , pp. 1165-1174
    • Weinreich, D.M.1    Watson, R.A.2    Chao, L.3
  • 37
    • 0034920057 scopus 로고    scopus 로고
    • The evolution of postzygotic isolation: Accumulating Dobzhansky-Muller incompatibilities
    • Orr HA, Turelli M (2001) The evolution of postzygotic isolation: Accumulating Dobzhansky-Muller incompatibilities. Evolution 55:1085-1094. (Pubitemid 32665219)
    • (2001) Evolution , vol.55 , Issue.6 , pp. 1085-1094
    • Orr, H.A.1    Turelli, M.2
  • 38
    • 0034093093 scopus 로고    scopus 로고
    • Dominance, epistasis and the genetics of postzygotic isolation
    • Turelli M, Orr HA (2000) Dominance, epistasis and the genetics of postzygotic isolation. Genetics 154:1663-1679. (Pubitemid 30211249)
    • (2000) Genetics , vol.154 , Issue.4 , pp. 1663-1679
    • Turelli, M.1    Orr, H.A.2
  • 39
    • 60549084864 scopus 로고    scopus 로고
    • Dobzhansky-Muller incompatibilities and adaptation to a shared environment
    • Unckless RL, Orr HA (2009) Dobzhansky-Muller incompatibilities and adaptation to a shared environment. Heredity (Edinb) 102:214-217.
    • (2009) Heredity (Edinb) , vol.102 , pp. 214-217
    • Unckless, R.L.1    Orr, H.A.2
  • 40
    • 9444269272 scopus 로고    scopus 로고
    • Compensated deleterious mutations in insect ganomes
    • DOI 10.1126/science.1100522
    • Kulathinal RJ, Bettencourt BR, Hartl DL (2004) Compensated deleterious mutations in insect genomes. Science 306:1553-1554. (Pubitemid 39564950)
    • (2004) Science , vol.306 , Issue.5701 , pp. 1553-1554
    • Kulathinal, R.J.1    Bettencourt, B.R.2    Hartl, D.L.3
  • 41
    • 79954542203 scopus 로고    scopus 로고
    • The evolution and evolutionary consequences of marginal thermostability in proteins
    • Goldstein RA (2011) The evolution and evolutionary consequences of marginal thermostability in proteins. Proteins 79:1396-1407.
    • (2011) Proteins , vol.79 , pp. 1396-1407
    • Goldstein, R.A.1
  • 43
    • 33845377127 scopus 로고
    • Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation
    • Miyazawa S, Jernigan RL (1985) Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation. Macromolecules 18:534-552.
    • (1985) Macromolecules , vol.18 , pp. 534-552
    • Miyazawa, S.1    Jernigan, R.L.2
  • 44
    • 0345151820 scopus 로고    scopus 로고
    • Three-dimensional structure of a mammalian purple acid phosphatase at 2.2 A resolution with a mu-(hydr)oxo bridged di-iron center
    • DOI 10.1006/jmbi.1999.2962
    • Lindqvist Y, Johansson E, Kaija H, Vihko P, Schneider G (1999) Three-dimensional structure of a mammalian purple acid phosphatase at 2.2 A resolution with a mu-(hydr)oxo bridged di-iron center. J Mol Biol 291:135-147. (Pubitemid 29391410)
    • (1999) Journal of Molecular Biology , vol.291 , Issue.1 , pp. 135-147
    • Lindqvist, Y.1    Johansson, E.2    Kaija, H.3    Vihko, P.4    Schneider, G.5
  • 45
    • 0019296687 scopus 로고
    • A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
    • Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111-120.
    • (1980) J Mol Evol , vol.16 , pp. 111-120
    • Kimura, M.1
  • 46
    • 0001100522 scopus 로고
    • On the relationship among three theories of relaxation in disordered systems
    • Klafter J, Shlesinger MF (1986) On the relationship among three theories of relaxation in disordered systems. Proc Natl Acad Sci USA 83:848-851.
    • (1986) Proc Natl Acad Sci USA , vol.83 , pp. 848-851
    • Klafter, J.1    Shlesinger, M.F.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.