메뉴 건너뛰기




Volumn 8, Issue 5, 2012, Pages

Structure and age jointly influence rates of protein evolution

Author keywords

[No Author keywords available]

Indexed keywords

KNOWLEDGE BASED SYSTEMS;

EID: 84863663815     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1002542     Document Type: Article
Times cited : (15)

References (58)
  • 2
    • 0035963414 scopus 로고    scopus 로고
    • Protein dispensability and rate of evolution
    • Hirsh AE, Fraser HB, (2001) Protein dispensability and rate of evolution. Nature 411: 1046-1049.
    • (2001) Nature , vol.411 , pp. 1046-1049
    • Hirsh, A.E.1    Fraser, H.B.2
  • 3
    • 0027399170 scopus 로고
    • Ancient conserved regions in new gene sequences and the protein databases
    • Green P, Lipman D, Hillier L, Waterston R, States D, et al. (1993) Ancient conserved regions in new gene sequences and the protein databases. Science 259: 1711-1716.
    • (1993) Science , vol.259 , pp. 1711-1716
    • Green, P.1    Lipman, D.2    Hillier, L.3    Waterston, R.4    States, D.5
  • 4
    • 0034978556 scopus 로고    scopus 로고
    • Highly expressed genes in yeast evolve slowly
    • Pál C, Papp B, Hurst LD, (2001) Highly expressed genes in yeast evolve slowly. Genetics 158: 927-931.
    • (2001) Genetics , vol.158 , pp. 927-931
    • Pál, C.1    Papp, B.2    Hurst, L.D.3
  • 5
    • 30744441602 scopus 로고    scopus 로고
    • A single determinant dominates the rate of yeast protein evolution
    • Drummond DA, Raval A, Wilke CO, (2006) A single determinant dominates the rate of yeast protein evolution. Mol Biol Evol 23: 327-337.
    • (2006) Mol Biol Evol , vol.23 , pp. 327-337
    • Drummond, D.A.1    Raval, A.2    Wilke, C.O.3
  • 8
    • 0035012056 scopus 로고    scopus 로고
    • Synonymous codon usage, accuracy of translation, and gene length in Caenorhabditis elegans
    • Marais G, Duret L, (2001) Synonymous codon usage, accuracy of translation, and gene length in Caenorhabditis elegans. J Mol Evol 52: 275-280.
    • (2001) J Mol Evol , vol.52 , pp. 275-280
    • Marais, G.1    Duret, L.2
  • 10
    • 16344381521 scopus 로고    scopus 로고
    • Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks
    • Hahn MW, Kern AD, (2005) Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks. Mol Biol Evol 22: 803-806.
    • (2005) Mol Biol Evol , vol.22 , pp. 803-806
    • Hahn, M.W.1    Kern, A.D.2
  • 11
    • 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: 1751-1761.
    • (2006) Mol Biol Evol , vol.23 , pp. 1751-1761
    • Bloom, J.D.1    Drummond, D.A.2    Arnold, F.H.3    Wilke, C.O.4
  • 12
    • 70349911882 scopus 로고    scopus 로고
    • Structural determinants of protein evolution are context-sensitive at the residue level
    • Franzosa EA, Xia Y, (2009) Structural determinants of protein evolution are context-sensitive at the residue level. Mol Biol Evol 26: 2387-2395.
    • (2009) Mol Biol Evol , vol.26 , pp. 2387-2395
    • Franzosa, E.A.1    Xia, Y.2
  • 13
    • 77649250720 scopus 로고    scopus 로고
    • Universal distribution of protein evolution rates as a consequence of protein folding physics
    • Lobkovsky AE, Wolf YI, Koonin EV, (2010) Universal distribution of protein evolution rates as a consequence of protein folding physics. Proc Natl Acad Sci U S A 107: 2983-2988.
    • (2010) Proc Natl Acad Sci U S A , vol.107 , pp. 2983-2988
    • Lobkovsky, A.E.1    Wolf, Y.I.2    Koonin, E.V.3
  • 14
    • 34548357121 scopus 로고    scopus 로고
    • Assessing the determinants of evolutionary rates in the presence of noise
    • Plotkin JB, Fraser HB, (2007) Assessing the determinants of evolutionary rates in the presence of noise. Mol Biol Evol 24: 1113-1121.
    • (2007) Mol Biol Evol , vol.24 , pp. 1113-1121
    • Plotkin, J.B.1    Fraser, H.B.2
  • 15
    • 47549097539 scopus 로고    scopus 로고
    • Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution
    • Drummond DA, Wilke CO, (2008) Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell 134: 341-352.
    • (2008) Cell , vol.134 , pp. 341-352
    • Drummond, D.A.1    Wilke, C.O.2
  • 16
    • 54849410447 scopus 로고    scopus 로고
    • Structural perspectives on protein evolution
    • Franzosa E, Xia Y, (2008) Structural perspectives on protein evolution. Annu Rep Comput Chem 4: 3-21.
    • (2008) Annu Rep Comput Chem , vol.4 , pp. 3-21
    • Franzosa, E.1    Xia, Y.2
  • 17
    • 33646182934 scopus 로고    scopus 로고
    • An integrated view of protein evolution
    • Pál C, Papp B, Lercher MJ, (2006) An integrated view of protein evolution. Nat Rev Genet 7: 337-348.
    • (2006) Nat Rev Genet , vol.7 , pp. 337-348
    • Pál, C.1    Papp, B.2    Lercher, M.J.3
  • 18
    • 0031805465 scopus 로고    scopus 로고
    • Assessing the impact of secondary structure and solvent accessibility on protein evolution
    • Goldman N, Thorne JL, Jones DT, (1998) Assessing the impact of secondary structure and solvent accessibility on protein evolution. Genetics 149: 445-458.
    • (1998) Genetics , vol.149 , pp. 445-458
    • Goldman, N.1    Thorne, J.L.2    Jones, D.T.3
  • 19
    • 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: 177-196.
    • (1999) J Mol Biol , vol.291 , pp. 177-196
    • Mirny, L.A.1    Shakhnovich, E.I.2
  • 20
    • 0033969946 scopus 로고    scopus 로고
    • Solvent accessibility and purifying selection within proteins of Escherichia coli and Salmonella enterica
    • Bustamante CD, Townsend JP, Hartl DL, (2000) Solvent accessibility and purifying selection within proteins of Escherichia coli and Salmonella enterica. Mol Biol Evol 17: 301-308.
    • (2000) Mol Biol Evol , vol.17 , pp. 301-308
    • Bustamante, C.D.1    Townsend, J.P.2    Hartl, D.L.3
  • 21
    • 65349140199 scopus 로고    scopus 로고
    • Solvent exposure imparts similar selective pressures across a range of yeast proteins
    • Conant GC, Stadler PF, (2009) Solvent exposure imparts similar selective pressures across a range of yeast proteins. Mol Biol Evol 26: 1155-1161.
    • (2009) Mol Biol Evol , vol.26 , pp. 1155-1161
    • Conant, G.C.1    Stadler, P.F.2
  • 22
    • 0041673352 scopus 로고    scopus 로고
    • Structural determinant of protein designability
    • England JL, Shakhnovich EI, (2003) Structural determinant of protein designability. Phys Rev Lett 90: 218101.
    • (2003) Phys Rev Lett , vol.90 , pp. 218101
    • England, J.L.1    Shakhnovich, E.I.2
  • 23
    • 43149112799 scopus 로고    scopus 로고
    • Contact density affects protein evolutionary rate from bacteria to animals
    • Zhou T, Drummond DA, Wilke CO, (2008) Contact density affects protein evolutionary rate from bacteria to animals. J Mol Biol 66: 395-404.
    • (2008) J Mol Biol , vol.66 , pp. 395-404
    • Zhou, T.1    Drummond, D.A.2    Wilke, C.O.3
  • 24
    • 44949206468 scopus 로고    scopus 로고
    • Protein robustness promotes evolutionary innovations on large evolutionary time-scales
    • Ferrada E, Wagner A, (2008) Protein robustness promotes evolutionary innovations on large evolutionary time-scales. Proc Biol Sci 275: 1595-1602.
    • (2008) Proc Biol Sci , vol.275 , pp. 1595-1602
    • Ferrada, E.1    Wagner, A.2
  • 25
    • 77957226070 scopus 로고    scopus 로고
    • Structural Calibration of the Rates of Amino Acid Evolution in a Search for Darwin in Drifting Biological Systems
    • Toft C, Fares MA, (2010) Structural Calibration of the Rates of Amino Acid Evolution in a Search for Darwin in Drifting Biological Systems. Mol Biol Evol 27: 2375-2385.
    • (2010) Mol Biol Evol , vol.27 , pp. 2375-2385
    • Toft, C.1    Fares, M.A.2
  • 26
    • 14544279484 scopus 로고    scopus 로고
    • Inverse relationship between evolutionary rate and age of mammalian genes
    • Albà MM, Castresana J, (2005) Inverse relationship between evolutionary rate and age of mammalian genes. Mol Biol Evol 22: 598-606.
    • (2005) Mol Biol Evol , vol.22 , pp. 598-606
    • Albà, M.M.1    Castresana, J.2
  • 27
    • 66149123308 scopus 로고    scopus 로고
    • The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages
    • Wolf YI, Novichkov PS, Karev GP, Koonin EV, Lipman DJ, (2009) The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages. Proc Natl Acad Sci U S A 106: 7273-7280.
    • (2009) Proc Natl Acad Sci U S A , vol.106 , pp. 7273-7280
    • Wolf, Y.I.1    Novichkov, P.S.2    Karev, G.P.3    Koonin, E.V.4    Lipman, D.J.5
  • 28
  • 29
    • 0142028990 scopus 로고    scopus 로고
    • An evolutionary analysis of orphan genes in Drosophila
    • Domazet-Loso T, Tautz D, (2003) An evolutionary analysis of orphan genes in Drosophila. Genome Res 13: 2213-2219.
    • (2003) Genome Res , vol.13 , pp. 2213-2219
    • Domazet-Loso, T.1    Tautz, D.2
  • 31
    • 42549143433 scopus 로고    scopus 로고
    • Consistent and contrasting properties of lineage-specific genes in the apicomplexan parasites Plasmodium and Theileria
    • Kuo C-H, Kissinger JC, (2008) Consistent and contrasting properties of lineage-specific genes in the apicomplexan parasites Plasmodium and Theileria. BMC Evol Biol 8: 108.
    • (2008) BMC Evol Biol , vol.8 , pp. 108
    • Kuo, C.-H.1    Kissinger, J.C.2
  • 32
    • 33745616793 scopus 로고    scopus 로고
    • Accelerated evolutionary rate may be responsible for the emergence of lineage-specific genes in ascomycota
    • Cai JJ, Woo PCY, Lau SKP, Smith DK, Yuen K-Y, (2006) Accelerated evolutionary rate may be responsible for the emergence of lineage-specific genes in ascomycota. J Mol Biol 63: 1-11.
    • (2006) J Mol Biol , vol.63 , pp. 1-11
    • Cai, J.J.1    Woo, P.C.Y.2    Lau, S.K.P.3    Smith, D.K.4    Yuen, K.-Y.5
  • 33
    • 3042569657 scopus 로고    scopus 로고
    • Bacterial genomes as new gene homes: the genealogy of ORFans in E. coli
    • Daubin V, Ochman H, (2004) Bacterial genomes as new gene homes: the genealogy of ORFans in E. coli. Genome Res 14: 1036-1042.
    • (2004) Genome Res , vol.14 , pp. 1036-1042
    • Daubin, V.1    Ochman, H.2
  • 34
    • 33646938731 scopus 로고    scopus 로고
    • Fold designability, distribution, and disease
    • Wong P, Frishman D, (2006) Fold designability, distribution, and disease. PLoS Comput Biol 2: e40.
    • (2006) PLoS Comput Biol , vol.2
    • Wong, P.1    Frishman, D.2
  • 35
    • 0035342441 scopus 로고    scopus 로고
    • Lattice protein folding with two and four-body statistical potentials
    • Gan HH, Tropsha A, Schlick T, (2001) Lattice protein folding with two and four-body statistical potentials. Proteins 43: 161-174.
    • (2001) Proteins , vol.43 , pp. 161-174
    • Gan, H.H.1    Tropsha, A.2    Schlick, T.3
  • 36
    • 0042889108 scopus 로고    scopus 로고
    • Development of a four-body statistical pseudo-potential to discriminate native from non-native protein conformations
    • Krishnamoorthy B, Tropsha A, (2003) Development of a four-body statistical pseudo-potential to discriminate native from non-native protein conformations. Bioinformatics 19: 1540-1548.
    • (2003) Bioinformatics , vol.19 , pp. 1540-1548
    • Krishnamoorthy, B.1    Tropsha, A.2
  • 37
    • 36448967447 scopus 로고    scopus 로고
    • Four-body scoring function for mutagenesis
    • Deutsch C, Krishnamoorthy B, (2007) Four-body scoring function for mutagenesis. Bioinformatics 23: 3009-3015.
    • (2007) Bioinformatics , vol.23 , pp. 3009-3015
    • Deutsch, C.1    Krishnamoorthy, B.2
  • 38
    • 0035943455 scopus 로고    scopus 로고
    • Four-body potentials reveal protein-specific correlations to stability changes caused by hydrophobic core mutations
    • Carter CW, LeFebvre BC, Cammer SA, Tropsha A, Edgell MH, (2001) Four-body potentials reveal protein-specific correlations to stability changes caused by hydrophobic core mutations. J Mol Biol 311: 625-638.
    • (2001) J Mol Biol , vol.311 , pp. 625-638
    • Carter, C.W.1    LeFebvre, B.C.2    Cammer, S.A.3    Tropsha, A.4    Edgell, M.H.5
  • 39
    • 0033853177 scopus 로고    scopus 로고
    • Decoys "R" Us: a database of incorrect conformations to improve protein structure prediction
    • Samudrala R, Levitt M, (2000) Decoys "R" Us: a database of incorrect conformations to improve protein structure prediction. Protein Sci 9: 1399-1401.
    • (2000) Protein Sci , vol.9 , pp. 1399-1401
    • Samudrala, R.1    Levitt, M.2
  • 40
    • 0346492908 scopus 로고    scopus 로고
    • Designability and Thermal Stability of Protein Structures
    • Wingreen N, Li H, Tang C, (2003) Designability and Thermal Stability of Protein Structures. Polymer 45: 12.
    • (2003) Polymer , vol.45 , pp. 12
    • Wingreen, N.1    Li, H.2    Tang, C.3
  • 43
    • 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
  • 44
    • 84857224836 scopus 로고    scopus 로고
    • Role of Low-Complexity Sequences in the Formation of Novel Protein Coding Sequences
    • Toll-Riera M, Radó-Trilla N, Martys F, Albà MM, (2011) Role of Low-Complexity Sequences in the Formation of Novel Protein Coding Sequences. Mol Biol Evol 29: 883-6.
    • (2011) Mol Biol Evol , vol.29 , pp. 883-886
    • Toll-Riera, M.1    Radó-Trilla, N.2    Martys, F.3    Albà, M.M.4
  • 45
    • 67650868984 scopus 로고    scopus 로고
    • Tandem and cryptic amino acid repeats accumulate in disordered regions of proteins
    • Simon M, Hancock JM, (2009) Tandem and cryptic amino acid repeats accumulate in disordered regions of proteins. Genome Biol 10: R59.
    • (2009) Genome Biol , vol.10
    • Simon, M.1    Hancock, J.M.2
  • 46
    • 33749014910 scopus 로고    scopus 로고
    • Evolution of protein structural classes and protein sequence families
    • Choi I-G, Kim S-H, (2006) Evolution of protein structural classes and protein sequence families. Proc Natl Acad Sci U S A 103: 14056-14061.
    • (2006) Proc Natl Acad Sci U S A , vol.103 , pp. 14056-14061
    • Choi, I.-G.1    Kim, S.-H.2
  • 47
    • 77958497573 scopus 로고    scopus 로고
    • Relaxed purifying selection and possibly high rate of adaptation in primate lineage-specific genes
    • Cai JJ, Petrov DA, (2010) Relaxed purifying selection and possibly high rate of adaptation in primate lineage-specific genes. Genome Biol Evol 2: 393-409.
    • (2010) Genome Biol Evol , vol.2 , pp. 393-409
    • Cai, J.J.1    Petrov, D.A.2
  • 49
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    • Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schäffer, A.A.3    Zhang, J.4    Zhang, Z.5
  • 51
    • 0023645203 scopus 로고
    • Interior and surface of monomeric proteins
    • Miller S, Janin J, Lesk AM, Chothia C, (1987) Interior and surface of monomeric proteins. J Mol Biol 196: 641-656.
    • (1987) J Mol Biol , vol.196 , pp. 641-656
    • Miller, S.1    Janin, J.2    Lesk, A.M.3    Chothia, C.4
  • 52
    • 79958187925 scopus 로고    scopus 로고
    • The relationship between relative solvent accessibility and evolutionary rate in protein evolution
    • Ramsey DC, Scherrer MP, Zhou T, Wilke CO, (2011) The relationship between relative solvent accessibility and evolutionary rate in protein evolution. Genetics 188: 479-488.
    • (2011) Genetics , vol.188 , pp. 479-488
    • Ramsey, D.C.1    Scherrer, M.P.2    Zhou, T.3    Wilke, C.O.4
  • 53
    • 0034623005 scopus 로고    scopus 로고
    • T-Coffee: A novel method for fast and accurate multiple sequence alignment
    • Notredame C, Higgins DG, Heringa J, (2000) T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol 302: 205-217.
    • (2000) J Mol Biol , vol.302 , pp. 205-217
    • Notredame, C.1    Higgins, D.G.2    Heringa, J.3
  • 54
    • 0037100671 scopus 로고    scopus 로고
    • MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
    • Katoh K, Misawa K, Kuma K, Miyata T, (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30: 3059-3066.
    • (2002) Nucleic Acids Res , vol.30 , pp. 3059-3066
    • Katoh, K.1    Misawa, K.2    Kuma, K.3    Miyata, T.4
  • 55
    • 34547803197 scopus 로고    scopus 로고
    • PAML 4: phylogenetic analysis by maximum likelihood
    • Yang Z, (2007) PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 24: 1586-1591.
    • (2007) Mol Biol Evol , vol.24 , pp. 1586-1591
    • Yang, Z.1
  • 56
    • 0043180474 scopus 로고    scopus 로고
    • PISCES: a protein sequence culling server
    • Wang G, Dunbrack RL, (2003) PISCES: a protein sequence culling server. Bioinformatics 19: 1589-1591.
    • (2003) Bioinformatics , vol.19 , pp. 1589-1591
    • Wang, G.1    Dunbrack, R.L.2
  • 57
    • 33744801422 scopus 로고    scopus 로고
    • Computational mutagenesis studies of protein structure-function correlations
    • Masso M, Lu Z, Vaisman II, (2006) Computational mutagenesis studies of protein structure-function correlations. Proteins 64: 234-245.
    • (2006) Proteins , vol.64 , pp. 234-245
    • Masso, M.1    Lu, Z.2    Vaisman, I.I.3
  • 58
    • 34249938371 scopus 로고    scopus 로고
    • Four-body contact potentials derived from two protein datasets to discriminate native structures from decoys
    • Feng Y, Kloczkowski A, Jernigan RL, (2007) Four-body contact potentials derived from two protein datasets to discriminate native structures from decoys. Proteins 68: 57-66.
    • (2007) Proteins , vol.68 , pp. 57-66
    • Feng, Y.1    Kloczkowski, A.2    Jernigan, R.L.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.