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Volumn 441, Issue 1-2, 2009, Pages 45-52

Estimates of natural selection due to protein tertiary structure inform the ancestry of biallelic loci

Author keywords

Fitness; Molecular evolution; Population genetics; Scaled selection coefficient

Indexed keywords

ALLELE; ARTICLE; GENE FREQUENCY; GENOTYPE; INTRASPECIFIC VARIATION; MOLECULAR EVOLUTION; NATURAL SELECTION; PHENOTYPE; POPULATION GENETICS; PRIORITY JOURNAL; PROBABILITY; PROTEIN TERTIARY STRUCTURE; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 67349264075     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2008.07.020     Document Type: Article
Times cited : (2)

References (52)
  • 1
    • 0030801002 scopus 로고    scopus 로고
    • Gapp ed BLAST and PSI-BLAST: a new generation of protein database search programs
    • Altschul S.F., et al. Gapp ed BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25 (1997) 3389-3402
    • (1997) Nucleic Acids Res. , vol.25 , pp. 3389-3402
    • Altschul, S.F.1
  • 2
    • 33845503073 scopus 로고    scopus 로고
    • Adaptive evolution of transcription factor binding sites
    • Berg J., Willmann S., and Lässig M. Adaptive evolution of transcription factor binding sites. BMC Evol. Biol. 4 (2004) 42
    • (2004) BMC Evol. Biol. , vol.4 , pp. 42
    • Berg, J.1    Willmann, S.2    Lässig, M.3
  • 3
    • 0033954256 scopus 로고    scopus 로고
    • The Protein Data Bank
    • Berman H.M., et al. The Protein Data Bank. Nucleic Acids Res. 28 (2000) 235-242
    • (2000) Nucleic Acids Res. , vol.28 , pp. 235-242
    • Berman, H.M.1
  • 4
    • 0032991552 scopus 로고    scopus 로고
    • Characterization of single-nucleotide polymorphisms in coding regions of human genes
    • Cargill M., et al. Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nat. Genet. 22 (1999) 231-238
    • (1999) Nat. Genet. , vol.22 , pp. 231-238
    • Cargill, M.1
  • 5
    • 0035937259 scopus 로고    scopus 로고
    • Predicting the functional consequences of non-synonymous single nucleotide polymorphisms: structure-based assessment of amino acid variation
    • Chasman D., and Adams R.M. Predicting the functional consequences of non-synonymous single nucleotide polymorphisms: structure-based assessment of amino acid variation. J. Mol. Biol. 307 (2001) 683-706
    • (2001) J. Mol. Biol. , vol.307 , pp. 683-706
    • Chasman, D.1    Adams, R.M.2
  • 6
    • 33751520430 scopus 로고    scopus 로고
    • Natural selection on human microRNA binding sites inferred from SNP data
    • Chen K., and Rajewsky N. Natural selection on human microRNA binding sites inferred from SNP data. Nat. Genet. 38 (2006) 1452-1456
    • (2006) Nat. Genet. , vol.38 , pp. 1452-1456
    • Chen, K.1    Rajewsky, N.2
  • 7
    • 24344500211 scopus 로고    scopus 로고
    • Initial sequence of the chimpanzee genome and comparison with the human genome
    • Chimpanzee Sequencing and Analysis Consortium
    • Chimpanzee Sequencing and Analysis Consortium. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437 (2005) 69-87
    • (2005) Nature , vol.437 , pp. 69-87
  • 8
    • 34547809931 scopus 로고    scopus 로고
    • Quantifying the impact of protein tertiary structure on molecular evolution
    • Choi S.C., Hobolth A., Robinson D.M., Kishino H., and Thorne J.L. Quantifying the impact of protein tertiary structure on molecular evolution. Mol. Biol. Evol. 24 (2007) 1769-1782
    • (2007) Mol. Biol. Evol. , vol.24 , pp. 1769-1782
    • Choi, S.C.1    Hobolth, A.2    Robinson, D.M.3    Kishino, H.4    Thorne, J.L.5
  • 9
    • 0022706389 scopus 로고
    • The relation between the divergence of sequence and structure in proteins
    • Chothia C., and Lesk A.M. The relation between the divergence of sequence and structure in proteins. EMBO J. 5 (1986) 823-826
    • (1986) EMBO J. , vol.5 , pp. 823-826
    • Chothia, C.1    Lesk, A.M.2
  • 11
    • 0033274920 scopus 로고    scopus 로고
    • Genealogical processes for Fleming-Viot models with selection and recombination
    • Donnelly P., and Kurtz T. Genealogical processes for Fleming-Viot models with selection and recombination. Ann. Appl. Probab. 9 (1999) 1091-1148
    • (1999) Ann. Appl. Probab. , vol.9 , pp. 1091-1148
    • Donnelly, P.1    Kurtz, T.2
  • 12
    • 0035998637 scopus 로고    scopus 로고
    • The common ancestor at a nonneutral locus
    • Fearnhead P. The common ancestor at a nonneutral locus. J. Appl. Probab. 39 (2002) 38-54
    • (2002) J. Appl. Probab. , vol.39 , pp. 38-54
    • Fearnhead, P.1
  • 14
    • 0027485083 scopus 로고
    • Comparison of conformational characteristics in structurally similar protein pairs
    • Flores T.P., Orengo C.A., Moss D.S., and Thornton J.M. Comparison of conformational characteristics in structurally similar protein pairs. Protein Sci. 2 (1993) 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
  • 15
    • 25844449770 scopus 로고    scopus 로고
    • Galaxy: a platform for interactive large-scale genome analysis
    • Giardine B., et al. Galaxy: a platform for interactive large-scale genome analysis. Genome Res. 15 (2005) 1451-1455
    • (2005) Genome Res. , vol.15 , pp. 1451-1455
    • Giardine, B.1
  • 16
    • 0028168856 scopus 로고
    • A codon-based model of nucleotide substitution for protein-coding DNA sequences
    • Goldman N., and Yang Z. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol. Biol. Evol. 11 (1994) 725-736
    • (1994) Mol. Biol. Evol. , vol.11 , pp. 725-736
    • Goldman, N.1    Yang, Z.2
  • 17
    • 0031875569 scopus 로고    scopus 로고
    • Evolutionary distances for protein-coding sequences: modeling site-specific residue frequencies
    • Halpern A.L., and Bruno W.J. Evolutionary distances for protein-coding sequences: modeling site-specific residue frequencies. Mol. Biol. Evol. 15 (1998) 910-917
    • (1998) Mol. Biol. Evol. , vol.15 , pp. 910-917
    • Halpern, A.L.1    Bruno, W.J.2
  • 18
    • 34547808850 scopus 로고    scopus 로고
    • Context dependence, ancestral misidentification, and spurious signatures of natural selection
    • Hernandez R.D., Williamson S.H., and Bustamante C.D. Context dependence, ancestral misidentification, and spurious signatures of natural selection. Mol. Biol. Evol. 24 (2007) 1792-1800
    • (2007) Mol. Biol. Evol. , vol.24 , pp. 1792-1800
    • Hernandez, R.D.1    Williamson, S.H.2    Bustamante, C.D.3
  • 20
    • 0026690571 scopus 로고
    • A new approach to protein fold recognition
    • Jones D.T., Taylor W.R., and Thornton J.M. A new approach to protein fold recognition. Nature 358 (1992) 86-89
    • (1992) Nature , vol.358 , pp. 86-89
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 21
    • 0023815589 scopus 로고
    • The coalescent process in models with selection
    • Kaplan N.L., Darden T., and Hudson R.R. The coalescent process in models with selection. Genetics 120 (1988) 819-829
    • (1988) Genetics , vol.120 , pp. 819-829
    • Kaplan, N.L.1    Darden, T.2    Hudson, R.R.3
  • 22
    • 0000800333 scopus 로고
    • On the probability of fixation of mutant genes in a population
    • Kimura M. On the probability of fixation of mutant genes in a population. Genetics 47 (1962) 713-719
    • (1962) Genetics , vol.47 , pp. 713-719
    • Kimura, M.1
  • 24
    • 0344033683 scopus 로고    scopus 로고
    • A comparative study of machine-learning methods to predict the effects of single nucleotide polymorphisms on protein function
    • Krishnan V.G., and Westhead D.R. A comparative study of machine-learning methods to predict the effects of single nucleotide polymorphisms on protein function. Bioinformatics 19 (2003) 2199-2209
    • (2003) Bioinformatics , vol.19 , pp. 2199-2209
    • Krishnan, V.G.1    Westhead, D.R.2
  • 25
    • 0030877679 scopus 로고    scopus 로고
    • Ancestral processes with selection
    • Krone S., and Neuhauser C. Ancestral processes with selection. Theor. Popul. Biol. 51 (1997) 210-237
    • (1997) Theor. Popul. Biol. , vol.51 , pp. 210-237
    • Krone, S.1    Neuhauser, C.2
  • 26
    • 6344267228 scopus 로고    scopus 로고
    • Pattern of sequence variation across 213 environmental response genes
    • Livingston R.J., et al. Pattern of sequence variation across 213 environmental response genes. Genome Res. 14 (2004) 1821-1831
    • (2004) Genome Res. , vol.14 , pp. 1821-1831
    • Livingston, R.J.1
  • 27
    • 0028024626 scopus 로고
    • A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates with application to the chloroplast genome
    • Muse S.V., and Gaut B.S. A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates with application to the chloroplast genome. Mol. Biol. Evol. 11 (1994) 715-724
    • (1994) Mol. Biol. Evol. , vol.11 , pp. 715-724
    • Muse, S.V.1    Gaut, B.S.2
  • 28
    • 27644482258 scopus 로고    scopus 로고
    • Evolutionary population genetics of promoters: predicting binding sites and functional phylogenies
    • Mustonen V., and Lässig M. Evolutionary population genetics of promoters: predicting binding sites and functional phylogenies. Proc. Natl. Acad. Sci. U. S. A. 102 (2005) 15936-15941
    • (2005) Proc. Natl. Acad. Sci. U. S. A. , vol.102 , pp. 15936-15941
    • Mustonen, V.1    Lässig, M.2
  • 29
    • 0042991419 scopus 로고    scopus 로고
    • Correcting for ascertainment biases when analyzing SNP data: applications to the estimation of linkage disequilibrium
    • Nielsen R., and Signorovitch J. Correcting for ascertainment biases when analyzing SNP data: applications to the estimation of linkage disequilibrium. Theor. Popul. Biol. 63 (2003) 245-255
    • (2003) Theor. Popul. Biol. , vol.63 , pp. 245-255
    • Nielsen, R.1    Signorovitch, J.2
  • 30
    • 0042354654 scopus 로고    scopus 로고
    • Estimating the distribution of selection coefficients from phylogenetic data with applications to mitochondrial and viral DNA
    • Nielsen R., and Yang Z. Estimating the distribution of selection coefficients from phylogenetic data with applications to mitochondrial and viral DNA. Mol. Biol. Evol. 20 (2003) 1231-1239
    • (2003) Mol. Biol. Evol. , vol.20 , pp. 1231-1239
    • Nielsen, R.1    Yang, Z.2
  • 31
    • 0036713510 scopus 로고    scopus 로고
    • Human non-synonymous SNPs: server and survey
    • Ramensky V., Bork P., and Sunyaev S. Human non-synonymous SNPs: server and survey. Nucleic Acids Res. 30 (2002) 3894-3900
    • (2002) Nucleic Acids Res. , vol.30 , pp. 3894-3900
    • Ramensky, V.1    Bork, P.2    Sunyaev, S.3
  • 32
  • 33
    • 15544374861 scopus 로고    scopus 로고
    • Site interdependence attributed to tertiary structure in amino acid sequence evolution
    • Rodrigue N., Lartillot N., Bryant D., and Philippe H. Site interdependence attributed to tertiary structure in amino acid sequence evolution. Gene 347 (2005) 207-217
    • (2005) Gene , vol.347 , pp. 207-217
    • Rodrigue, N.1    Lartillot, N.2    Bryant, D.3    Philippe, H.4
  • 34
    • 33748126145 scopus 로고    scopus 로고
    • Assessing site-interdependent phylogenetic models of sequence evolution
    • Rodrigue N., Philippe H., and Lartillot N. Assessing site-interdependent phylogenetic models of sequence evolution. Mol. Biol. Evol. 23 (2006) 1762-1775
    • (2006) Mol. Biol. Evol. , vol.23 , pp. 1762-1775
    • Rodrigue, N.1    Philippe, H.2    Lartillot, N.3
  • 35
    • 0031566432 scopus 로고    scopus 로고
    • Recognition of analogous and homologous protein folds: analysis of sequence and structure conservation
    • Russell R.B., Saqi M.A., Sayle R.A., Bates P.A., and Sternberg M.J. Recognition of analogous and homologous protein folds: analysis of sequence and structure conservation. J. Mol. Biol. 269 (1997) 423-439
    • (1997) J. Mol. Biol. , vol.269 , pp. 423-439
    • Russell, R.B.1    Saqi, M.A.2    Sayle, R.A.3    Bates, P.A.4    Sternberg, M.J.5
  • 36
    • 22144437325 scopus 로고    scopus 로고
    • The application of statistical physics to evolutionary biology
    • Sella G., and Hirsh A.E. The application of statistical physics to evolutionary biology. Proc. Natl. Acad. Sci. U. S. A. 102 (2005) 9541-9546
    • (2005) Proc. Natl. Acad. Sci. U. S. A. , vol.102 , pp. 9541-9546
    • Sella, G.1    Hirsh, A.E.2
  • 37
    • 0035173378 scopus 로고    scopus 로고
    • dbSNP: the NCBI database of genetic variation
    • Sherry S.T., et al. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 29 (2001) 308-311
    • (2001) Nucleic Acids Res. , vol.29 , pp. 308-311
    • Sherry, S.T.1
  • 38
    • 0034494235 scopus 로고    scopus 로고
    • Most recent common ancestor probability distributions in gene genealogies under selection
    • Slade P.F. Most recent common ancestor probability distributions in gene genealogies under selection. Theor. Popul. Biol. 58 (2000) 291-305
    • (2000) Theor. Popul. Biol. , vol.58 , pp. 291-305
    • Slade, P.F.1
  • 39
    • 33749247600 scopus 로고    scopus 로고
    • Potential regulatory SNPs in promoters of human genes: a systematic approach
    • Stepanova M., Tiazhelova T., Skoblov M., and Baranova A. Potential regulatory SNPs in promoters of human genes: a systematic approach. Mol. Cell Probes. 20 (2006) 348-358
    • (2006) Mol. Cell Probes. , vol.20 , pp. 348-358
    • Stepanova, M.1    Tiazhelova, T.2    Skoblov, M.3    Baranova, A.4
  • 40
    • 22244437614 scopus 로고    scopus 로고
    • Physicochemical constraint violation by missense substitutions mediates impairment of protein function and disease severity
    • Stone E.A., and Sidow A. Physicochemical constraint violation by missense substitutions mediates impairment of protein function and disease severity. Genome Res. 15 (2005) 978-986
    • (2005) Genome Res. , vol.15 , pp. 978-986
    • Stone, E.A.1    Sidow, A.2
  • 41
    • 0035253005 scopus 로고    scopus 로고
    • Integration of genome data and protein structures: prediction of protein folds, protein interactions and "molecular phenotypes" of single nucleotide polymorphisms
    • Sunyaev S., Lathe W., and Bork P. Integration of genome data and protein structures: prediction of protein folds, protein interactions and "molecular phenotypes" of single nucleotide polymorphisms. Curr. Opin. Struct. Biol. 11 (2001) 125-130
    • (2001) Curr. Opin. Struct. Biol. , vol.11 , pp. 125-130
    • Sunyaev, S.1    Lathe, W.2    Bork, P.3
  • 43
    • 34249891061 scopus 로고    scopus 로고
    • The common ancestor process for a Wright-Fisher diffusion
    • Taylor J.E. The common ancestor process for a Wright-Fisher diffusion. Electron. J. Probab. 12 (2007) 808-847
    • (2007) Electron. J. Probab. , vol.12 , pp. 808-847
    • Taylor, J.E.1
  • 44
    • 79959524146 scopus 로고    scopus 로고
    • A haplotype map of the human genome
    • The International HapMap Consortium
    • The International HapMap Consortium. A haplotype map of the human genome. Nature 437 (2005) 1299-1320
    • (2005) Nature , vol.437 , pp. 1299-1320
  • 45
    • 33846101990 scopus 로고    scopus 로고
    • Variation resources at UC Santa Cruz
    • Thomas D.J., et al. Variation resources at UC Santa Cruz. Nucleic Acids Res. 35 (2007) D716-D720
    • (2007) Nucleic Acids Res. , vol.35
    • Thomas, D.J.1
  • 47
    • 0035065485 scopus 로고    scopus 로고
    • SNPs, protein structure, and disease
    • Wang Z., and Moult J. SNPs, protein structure, and disease. Hum. Mutat. 17 (2001) 263-270
    • (2001) Hum. Mutat. , vol.17 , pp. 263-270
    • Wang, Z.1    Moult, J.2
  • 48
    • 0017481191 scopus 로고
    • Is the most frequent allele the oldest?
    • Watterson G.A., and Guess H.A. Is the most frequent allele the oldest?. Theor. Popul. Biol. 11 (1977) 141-160
    • (1977) Theor. Popul. Biol. , vol.11 , pp. 141-160
    • Watterson, G.A.1    Guess, H.A.2
  • 49
    • 0028820333 scopus 로고
    • A new method of inference of ancestral nucleotide and amino acid sequences
    • Yang Z., Kumar S., and Nei M. A new method of inference of ancestral nucleotide and amino acid sequences. Genetics 141 (1995) 1641-1650
    • (1995) Genetics , vol.141 , pp. 1641-1650
    • Yang, Z.1    Kumar, S.2    Nei, M.3
  • 50
    • 33748080427 scopus 로고    scopus 로고
    • Dependence among sites in RNA evolution
    • Yu J., and Thorne J.L. Dependence among sites in RNA evolution. Mol. Biol. Evol. 23 (2006) 1525-1537
    • (2006) Mol. Biol. Evol. , vol.23 , pp. 1525-1537
    • Yu, J.1    Thorne, J.L.2
  • 51
    • 32044453591 scopus 로고    scopus 로고
    • Identification and analysis of deleterious human SNPs
    • Yue P., and Moult J. Identification and analysis of deleterious human SNPs. J. Mol. Biol. 356 (2006) 1263-1274
    • (2006) J. Mol. Biol. , vol.356 , pp. 1263-1274
    • Yue, P.1    Moult, J.2
  • 52
    • 25144523127 scopus 로고    scopus 로고
    • Loss of protein structure stability as a major causative factor in monogenic disease
    • Yue P., Li Z., and Moult J. Loss of protein structure stability as a major causative factor in monogenic disease. J. Mol. Biol. 353 (2005) 459-473
    • (2005) J. Mol. Biol. , vol.353 , pp. 459-473
    • Yue, P.1    Li, Z.2    Moult, J.3


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