메뉴 건너뛰기




Volumn 24, Issue 8, 2007, Pages 1769-1782

Quantifying the impact of protein tertiary structure on molecular evolution

Author keywords

Bayes factor; Gene Ontology; MCMC; Molecular evolution; Protein structure impact

Indexed keywords

ARTICLE; BAYES THEOREM; DNA SEQUENCE; GENETIC ANALYSIS; MOLECULAR EVOLUTION; PROTEIN INTERACTION; PROTEIN STRUCTURE;

EID: 34547809931     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msm097     Document Type: Article
Times cited : (48)

References (53)
  • 1
    • 0034069495 scopus 로고    scopus 로고
    • Ashburner M, Ball CA, Blake JA, et al. (20 co-authors). 2000. Gene ontology: tool for the unification of biology. Nat Genet. 25:25-29.
    • Ashburner M, Ball CA, Blake JA, et al. (20 co-authors). 2000. Gene ontology: tool for the unification of biology. Nat Genet. 25:25-29.
  • 2
    • 33845503073 scopus 로고    scopus 로고
    • Adaptive evolution of transcription factor binding sites
    • Berg J, Willmann S, Lässig M. 2004. Adaptive evolution of transcription factor binding sites. BMC Evol Biol. 4:42.
    • (2004) BMC Evol Biol , vol.4 , pp. 42
    • Berg, J.1    Willmann, S.2    Lässig, M.3
  • 4
    • 33748143748 scopus 로고    scopus 로고
    • Structural determinants of the rate of protein evolution in yeast
    • Bloom JD, Drummond DA, Arnold FH, Wilkie CO. 2006. Structural determinants of the rate of protein evolution in yeast. Mol Biol Evol. 23:1751-1761.
    • (2006) Mol Biol Evol , vol.23 , pp. 1751-1761
    • Bloom, J.D.1    Drummond, D.A.2    Arnold, F.H.3    Wilkie, C.O.4
  • 5
    • 0037255072 scopus 로고    scopus 로고
    • Boeckmann B, Bairoch A, Apweiler R, et al. (12 co-authors). 2003. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 31:365-370.
    • Boeckmann B, Bairoch A, Apweiler R, et al. (12 co-authors). 2003. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 31:365-370.
  • 7
    • 0028172520 scopus 로고
    • Phylogenetic relationships among eutherian orders estimated from inferred sequences of mitochondrial proteins: Instability of a tree based on a single gene
    • Cao Y, Adachi J, Janke A, Pääbo S, Hasegawa M. 1994. Phylogenetic relationships among eutherian orders estimated from inferred sequences of mitochondrial proteins: instability of a tree based on a single gene. J Mol Evol. 39:519-527.
    • (1994) J Mol Evol , vol.39 , pp. 519-527
    • Cao, Y.1    Adachi, J.2    Janke, A.3    Pääbo, S.4    Hasegawa, M.5
  • 8
    • 0041974049 scopus 로고
    • Marginal likelihood from the Gibbs output
    • Chib S. 1995. Marginal likelihood from the Gibbs output. J Am Stat Assoc. 90:1313-1321.
    • (1995) J Am Stat Assoc , vol.90 , pp. 1313-1321
    • Chib, S.1
  • 9
    • 1842715143 scopus 로고    scopus 로고
    • Marginal likelihood from the Metropolis-Hastings output
    • Chib S, Jeliazkov I. 2001. Marginal likelihood from the Metropolis-Hastings output. J Am Stat Assoc. 96:270-281.
    • (2001) J Am Stat Assoc , vol.96 , pp. 270-281
    • Chib, S.1    Jeliazkov, I.2
  • 10
    • 0022706389 scopus 로고
    • The relation between the divergence of sequence and structure in proteins
    • Chothia C, Lesk AM. 1986. The relation between the divergence of sequence and structure in proteins. EMBO J. 5:823-826.
    • (1986) EMBO J , vol.5 , pp. 823-826
    • Chothia, C.1    Lesk, A.M.2
  • 11
    • 28744439583 scopus 로고    scopus 로고
    • Pseudo-likelihood analysis of codon substitution models with neighbor-dependent rates
    • Christensen O, Hobolth A, Jensen J. 2005. Pseudo-likelihood analysis of codon substitution models with neighbor-dependent rates. J Comput Biol. 12:1166-1182.
    • (2005) J Comput Biol , vol.12 , pp. 1166-1182
    • Christensen, O.1    Hobolth, A.2    Jensen, J.3
  • 12
    • 30744441602 scopus 로고    scopus 로고
    • A single determinant dominates the rate of yeast protein evolution
    • Drummond DA, Raval A, Wilkie CO. 2005. A single determinant dominates the rate of yeast protein evolution. Mol Biol Evol. 23:327-337.
    • (2005) Mol Biol Evol , vol.23 , pp. 327-337
    • Drummond, D.A.1    Raval, A.2    Wilkie, C.O.3
  • 13
    • 0019797407 scopus 로고
    • Evolutionary trees from DNA sequences: A maximum likelihood approach
    • Felsenstein J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol. 17:368-376.
    • (1981) J Mol Evol , vol.17 , pp. 368-376
    • Felsenstein, J.1
  • 14
    • 0027485083 scopus 로고
    • Comparison of conformational characteristics in structurally similar protein pairs
    • Flores TP, Orengo CA, Moss DS, Thornton JM. 1993. Comparison of conformational characteristics in structurally similar protein pairs. Protein Sci. 2:1811-1826.
    • (1993) Protein Sci , vol.2 , pp. 1811-1826
    • Flores, T.P.1    Orengo, C.A.2    Moss, D.S.3    Thornton, J.M.4
  • 17
    • 0036856275 scopus 로고    scopus 로고
    • A novel use of equilibrium frequencies in models of sequence evolution
    • Goldman N, Whelan S. 2002. A novel use of equilibrium frequencies in models of sequence evolution. Mol Biol Evol. 19:1821-1831.
    • (2002) Mol Biol Evol , vol.19 , pp. 1821-1831
    • Goldman, N.1    Whelan, S.2
  • 18
    • 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. 11:725-736.
    • (1994) Mol Biol Evol , vol.11 , pp. 725-736
    • Goldman, N.1    Yang, Z.2
  • 19
    • 77956890234 scopus 로고
    • Monte Carlo sampling methods using Markov chains and their applications
    • Hastings WK. 1970. Monte Carlo sampling methods using Markov chains and their applications. Biometrika. 57:97-109.
    • (1970) Biometrika , vol.57 , pp. 97-109
    • Hastings, W.K.1
  • 20
    • 0027092678 scopus 로고
    • Selection of a representative set of structures from the Brookhaven Protein Data Bank
    • Hobohm U, Scharf M, Schneider R, Sander C. 1992. Selection of a representative set of structures from the Brookhaven Protein Data Bank. Protein Sci. 1:409-417.
    • (1992) Protein Sci , vol.1 , pp. 409-417
    • Hobohm, U.1    Scharf, M.2    Schneider, R.3    Sander, C.4
  • 21
    • 4644300141 scopus 로고    scopus 로고
    • Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution
    • Hwang DG, Green P. 2004. Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution. Proc Natl Acad Sci USA. 101:13994-14001.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 13994-14001
    • Hwang, D.G.1    Green, P.2
  • 22
    • 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
  • 23
    • 0026690571 scopus 로고
    • A new approach to protein fold recognition
    • Jones DT, Taylor WR, Thornton JM. 1992. A new approach to protein fold recognition. Nature. 358:86-89.
    • (1992) Nature , vol.358 , pp. 86-89
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 24
    • 0029964055 scopus 로고    scopus 로고
    • Potential energy functions for threading
    • Jones DT, Thornton JM. 1996. Potential energy functions for threading. Curr Opin Struc Biol. 6:210-216.
    • (1996) Curr Opin Struc Biol , vol.6 , pp. 210-216
    • Jones, D.T.1    Thornton, J.M.2
  • 25
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch W, Sander C. 1983. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 22:2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 26
    • 13444292428 scopus 로고    scopus 로고
    • Kanz C, Aldebert P, Althorpe N, et al. (32 co-authors). 2005. The EMBL Nucleotide Sequence Database. Nucleic Acids Res. 33:D29-D33.
    • Kanz C, Aldebert P, Althorpe N, et al. (32 co-authors). 2005. The EMBL Nucleotide Sequence Database. Nucleic Acids Res. 33:D29-D33.
  • 27
    • 0031453963 scopus 로고    scopus 로고
    • OLDERADO: On-line database of ensemble representatives and domains
    • Kelley LA, Sutcliffe MJ. 1997. OLDERADO: On-line database of ensemble representatives and domains. Protein Sci. 6:2628-2630.
    • (1997) Protein Sci , vol.6 , pp. 2628-2630
    • Kelley, L.A.1    Sutcliffe, M.J.2
  • 28
    • 33644826560 scopus 로고    scopus 로고
    • Computing Bayes factors using thermodynamic integration
    • Lartillot N, Philippe H. 2006. Computing Bayes factors using thermodynamic integration. Syst Biol. 55:195-207.
    • (2006) Syst Biol , vol.55 , pp. 195-207
    • Lartillot, N.1    Philippe, H.2
  • 29
    • 28444469788 scopus 로고    scopus 로고
    • Mapping PDB chains to UniProtKB entries
    • Martin AC. 2005. Mapping PDB chains to UniProtKB entries. Bioinformatics. 21:4297-4301.
    • (2005) Bioinformatics , vol.21 , pp. 4297-4301
    • Martin, A.C.1
  • 30
    • 0036145846 scopus 로고    scopus 로고
    • Statistical potentials for fold assessment
    • Melo F, Sánchez R, Sali A. 2002. Statistical potentials for fold assessment. Protein Sci. 11:430-448.
    • (2002) Protein Sci , vol.11 , pp. 430-448
    • Melo, F.1    Sánchez, R.2    Sali, A.3
  • 32
    • 0028024626 scopus 로고
    • A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates with application to the chloroplast genome
    • Muse SV, Gaut BS. 1994. A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates with application to the chloroplast genome. Mol Biol Evol. 11:715-724.
    • (1994) Mol Biol Evol , vol.11 , pp. 715-724
    • Muse, S.V.1    Gaut, B.S.2
  • 33
    • 27644482258 scopus 로고    scopus 로고
    • Evolutionary population genetics of promoters: Predicting binding sites and functional phylogenies
    • Mustonen V, Lässig M. 2005. Evolutionary population genetics of promoters: predicting binding sites and functional phylogenies. Proc Natl Acad Sci USA. 102:15936-15941.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 15936-15941
    • Mustonen, V.1    Lässig, M.2
  • 34
    • 0000238336 scopus 로고
    • A simplex method for function minimization
    • Nelder JA, Mead R. 1965. A simplex method for function minimization. Comput J. 7:308-313.
    • (1965) Comput J , vol.7 , pp. 308-313
    • Nelder, J.A.1    Mead, R.2
  • 35
    • 0031972161 scopus 로고    scopus 로고
    • Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene
    • Nielsen R, Yang Z. 1998. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics. 148:929-936.
    • (1998) Genetics , vol.148 , pp. 929-936
    • Nielsen, R.1    Yang, Z.2
  • 36
    • 0035035443 scopus 로고    scopus 로고
    • A dependent-rates model and an MCMC-based methodology for the maximum-likelihood analysis of sequences with overlapping reading frames
    • Pedersen AMK, Jensen JL. 2001. A dependent-rates model and an MCMC-based methodology for the maximum-likelihood analysis of sequences with overlapping reading frames. Mol Biol Evol. 18:763-776.
    • (2001) Mol Biol Evol , vol.18 , pp. 763-776
    • Pedersen, A.M.K.1    Jensen, J.L.2
  • 37
    • 4944234045 scopus 로고    scopus 로고
    • An evolutionary model for protein-coding regions with conserved RNA structure
    • Pedersen JS, Forsberg R, Meyer IM, Hein J. 2004. An evolutionary model for protein-coding regions with conserved RNA structure. Mol Biol Evol. 21:1913-1922.
    • (2004) Mol Biol Evol , vol.21 , pp. 1913-1922
    • Pedersen, J.S.1    Forsberg, R.2    Meyer, I.M.3    Hein, J.4
  • 38
    • 34547801186 scopus 로고    scopus 로고
    • Rambaut A, Drummond A. 2003. Tracer v1.3 URL http://evolve.zoo.ox.ac.uk.
    • Rambaut A, Drummond A. 2003. Tracer v1.3 URL http://evolve.zoo.ox.ac.uk.
  • 39
    • 34547789805 scopus 로고    scopus 로고
    • Robinson DM. 2003. D.R. EVOL: Three Dimensional Realistic Evolution. Ph.D. thesis, Bioinformatics. North Carolina State University.
    • Robinson DM. 2003. D.R. EVOL: Three Dimensional Realistic Evolution. Ph.D. thesis, Bioinformatics. North Carolina State University.
  • 41
    • 15544374861 scopus 로고    scopus 로고
    • Site interdependence attributed to tertiary structure in amino acid sequence evolution
    • Rodrigue N, Lartillot N, Bryant D, Philippe H. 2005. Site interdependence attributed to tertiary structure in amino acid sequence evolution. Gene. 347:207-217.
    • (2005) Gene , vol.347 , pp. 207-217
    • Rodrigue, N.1    Lartillot, N.2    Bryant, D.3    Philippe, H.4
  • 42
    • 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. 23:1762-1775.
    • (2006) Mol Biol Evol , vol.23 , pp. 1762-1775
    • Rodrigue, N.1    Philippe, H.2    Lartillot, N.3
  • 43
    • 0031566432 scopus 로고    scopus 로고
    • Recognition of analogous and homologous protein folds: Analysis of sequence and structure conservation
    • Russell RB, Saqi MAS, Sayle RA, Bates PA, Sternberg MJE. 1997. Recognition of analogous and homologous protein folds: analysis of sequence and structure conservation. J Mol Biol. 269:423-439.
    • (1997) J Mol Biol , vol.269 , pp. 423-439
    • Russell, R.B.1    Saqi, M.A.S.2    Sayle, R.A.3    Bates, P.A.4    Sternberg, M.J.E.5
  • 44
    • 1542510106 scopus 로고    scopus 로고
    • Phylogenetic estimation of context-dependent substitution rates by maximum likelihood
    • Siepel A, Haussler D. 2004. Phylogenetic estimation of context-dependent substitution rates by maximum likelihood. Mol Biol Evol. 21:468-488.
    • (2004) Mol Biol Evol , vol.21 , pp. 468-488
    • Siepel, A.1    Haussler, D.2
  • 45
    • 0000813561 scopus 로고
    • Inadmissibility of the usual estimator for the mean of a multivariate distribution
    • Stein C. 1956. Inadmissibility of the usual estimator for the mean of a multivariate distribution. Proc Third Berkeley Symp Math Statist Prob. 1:197-206.
    • (1956) Proc Third Berkeley Symp Math Statist Prob , vol.1 , pp. 197-206
    • Stein, C.1
  • 46
    • 0028064845 scopus 로고
    • Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
    • Yang Z. 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J Mol Evol. 39:306-314.
    • (1994) J Mol Evol , vol.39 , pp. 306-314
    • Yang, Z.1
  • 47
    • 0031960185 scopus 로고    scopus 로고
    • Synonymous and nonsynonymous rate variation in nuclear genes of mammals
    • Yang Z, Nielsen R. 1998. Synonymous and nonsynonymous rate variation in nuclear genes of mammals. J Mol Evol. 46:409-418.
    • (1998) J Mol Evol , vol.46 , pp. 409-418
    • Yang, Z.1    Nielsen, R.2
  • 48
    • 0036270185 scopus 로고    scopus 로고
    • Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages
    • Yang Z, Nielsen R. 2002. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol Biol Evol. 19:908-917.
    • (2002) Mol Biol Evol , vol.19 , pp. 908-917
    • Yang, Z.1    Nielsen, R.2
  • 49
    • 0034097381 scopus 로고    scopus 로고
    • Codon-substitution models for heterogeneous selection pressure at amino acid sites
    • Yang Z, Nielsen R, Goldman N, Pedersen AMK. 2000. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics. 155:431-449.
    • (2000) Genetics , vol.155 , pp. 431-449
    • Yang, Z.1    Nielsen, R.2    Goldman, N.3    Pedersen, A.M.K.4
  • 50
    • 0031792828 scopus 로고    scopus 로고
    • Models of amino acid substitution and applications to mitochondrial protein evolution
    • Yang Z, Nielsen R, Hasegawa M. 1998. Models of amino acid substitution and applications to mitochondrial protein evolution. Mol Biol Evol. 15:1600-1611.
    • (1998) Mol Biol Evol , vol.15 , pp. 1600-1611
    • Yang, Z.1    Nielsen, R.2    Hasegawa, M.3
  • 51
    • 0036134765 scopus 로고    scopus 로고
    • Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes
    • Yang Z, Swanson WJ. 2002. Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes. Mol Biol Evol. 19:49-57.
    • (2002) Mol Biol Evol , vol.19 , pp. 49-57
    • Yang, Z.1    Swanson, W.J.2
  • 52
    • 33748080427 scopus 로고    scopus 로고
    • Dependence among sites in RNA evolution
    • Yu J, Thorne JL. 2006a. Dependence among sites in RNA evolution. Mol Biol Evol. 23:1525-1537.
    • (2006) Mol Biol Evol , vol.23 , pp. 1525-1537
    • Yu, J.1    Thorne, J.L.2
  • 53
    • 33744903386 scopus 로고    scopus 로고
    • Testing for spatial clustering of amino acid replacements within protein tertiary structure
    • Yu J, Thorne JL. 2006b. Testing for spatial clustering of amino acid replacements within protein tertiary structure. J Mol Evol. 62:682-692.
    • (2006) J Mol Evol , vol.62 , pp. 682-692
    • Yu, J.1    Thorne, J.L.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.