메뉴 건너뛰기




Volumn 3, Issue , 2008, Pages

Comparable contributions of structural-functional constraints and expression level to the rate of protein sequence evolution

Author keywords

[No Author keywords available]

Indexed keywords

ANIMALIA; MAMMALIA;

EID: 54949151498     PISSN: None     EISSN: 17456150     Source Type: Journal    
DOI: 10.1186/1745-6150-3-40     Document Type: Review
Times cited : (31)

References (46)
  • 1
    • 0001895697 scopus 로고
    • Evolutionary divergence and convergence of proteins
    • New York: Academic Press Bryson V, Vogel HJ
    • Zuckerkandl E Pauling L Evolutionary divergence and convergence of proteins Evolving Gene and Proteins New York: Academic Press Bryson V, Vogel HJ 1965, 97-166.
    • (1965) Evolving Gene and Proteins , pp. 97-166
    • Zuckerkandl, E.1    Pauling, L.2
  • 3
    • 24944526640 scopus 로고    scopus 로고
    • Converging on a general model of protein evolution
    • 16054255
    • Herbeck JT Wall DP Converging on a general model of protein evolution Trends Biotechnol 2005, 23(10):485-487. 16054255
    • (2005) Trends Biotechnol , vol.23 , Issue.10 , pp. 485-487
    • Herbeck, J.T.1    Wall, D.P.2
  • 4
    • 33748980210 scopus 로고    scopus 로고
    • Evolutionary systems biology: Links between gene evolution and function
    • 16962765
    • Koonin EV Wolf YI Evolutionary systems biology: Links between gene evolution and function Curr Opin Biotechnol 2006, 17(5):481-487. 16962765
    • (2006) Curr Opin Biotechnol , vol.17 , Issue.5 , pp. 481-487
    • Koonin, E.V.1    Wolf, Y.I.2
  • 5
    • 54949095966 scopus 로고    scopus 로고
    • Evolutionary Systems Biology
    • Sunderland, MA: Sinauer Associates, Inc Pagel M, Pomiankowski A
    • Koonin EV Wolf YI Evolutionary Systems Biology Evolutionary Genomics and Proteomics Sunderland, MA: Sinauer Associates, Inc Pagel M, Pomiankowski A 2008, 11-25.
    • (2008) Evolutionary Genomics and Proteomics , pp. 11-25
    • Koonin, E.V.1    Wolf, Y.I.2
  • 6
    • 33646182934 scopus 로고    scopus 로고
    • An integrated view of protein evolution
    • 16619049
    • Pal C Papp B Lercher MJ An integrated view of protein evolution Nat Rev Genet 2006, 7(5):337-348. 16619049
    • (2006) Nat Rev Genet , vol.7 , Issue.5 , pp. 337-348
    • Pal, C.1    Papp, B.2    Lercher, M.J.3
  • 7
    • 33745107471 scopus 로고    scopus 로고
    • Influence of metabolic network structure and function on enzyme evolution
    • 1779518 16684370
    • Vitkup D Kharchenko P Wagner A Influence of metabolic network structure and function on enzyme evolution Genome Biol 2006, 7(5):R39. 1779518 16684370
    • (2006) Genome Biol , vol.7 , Issue.6
    • Vitkup, D.1    Kharchenko, P.2    Wagner, A.3
  • 8
    • 0033565762 scopus 로고    scopus 로고
    • Do essential genes evolve slowly?
    • 10421576
    • Hurst LD Smith NG Do essential genes evolve slowly? Curr Biol 1999, 9(14):747-750. 10421576
    • (1999) Curr Biol , vol.9 , Issue.14 , pp. 747-750
    • Hurst, L.D.1    Smith, N.G.2
  • 9
    • 0035963414 scopus 로고    scopus 로고
    • Protein dispensability and rate of evolution
    • 1049 11429604
    • Hirsh AE Fraser HB Protein dispensability and rate of evolution Nature 2001, 411:6841-1046. 1049 11429604
    • (2001) Nature , vol.411 , pp. 1046-1049
    • Hirsh, A.E.1    Fraser, H.B.2
  • 10
    • 0036078078 scopus 로고    scopus 로고
    • Essential genes are more evolutionarily conserved than are nonessential genes in bacteria
    • 1383730 12045149
    • Jordan IK Rogozin IB Wolf YI Koonin EV Essential genes are more evolutionarily conserved than are nonessential genes in bacteria Genome Res 2002, 12(6):962-968 1383730 12045149
    • (2002) Genome Res , vol.12 , Issue.6 , pp. 962-968
    • Jordan, I.K.1    Rogozin, I.B.2    Wolf, Y.I.3    Koonin, E.V.4
  • 11
    • 0142124263 scopus 로고    scopus 로고
    • Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution
    • 403683 14525925
    • Krylov DM Wolf YI Rogozin IB Koonin EV Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution Genome Res 2003, 13(10);2229-2235. 403683 14525925
    • (2003) Genome Res , vol.13 , Issue.10 , pp. 2229-2235
    • Krylov, D.M.1    Wolf, Y.I.2    Rogozin, I.B.3    Koonin, E.V.4
  • 13
    • 33745744354 scopus 로고    scopus 로고
    • Coping with the quantitative genomics 'elephant': The correlation between the gene dispensability and evolution rate
    • 16697070
    • Wolf YI Coping with the quantitative genomics 'elephant': The correlation between the gene dispensability and evolution rate Trends Genet 2006, 16697070.
    • (2006) Trends Genet
    • Wolf, Y.I.1
  • 14
    • 0034978556 scopus 로고    scopus 로고
    • Highly expressed genes in yeast evolve slowly
    • 1461684 11430355
    • Pal C Papp B Hurst LD Highly expressed genes in yeast evolve slowly Genetics 2001, 158(2):927-931. 1461684 11430355
    • (2001) Genetics , vol.158 , Issue.2 , pp. 927-931
    • Pal, C.1    Papp, B.2    Hurst, L.D.3
  • 16
    • 17744376961 scopus 로고    scopus 로고
    • Evolution of proteins and gene expression levels are coupled in Drosophila and are independently associated with mRNA abundance, protein length, and number of protein-protein interactions
    • 15746013
    • Lemos B Bettencourt BR Meiklejohn CD Hartl DL Evolution of proteins and gene expression levels are coupled in Drosophila and are independently associated with mRNA abundance, protein length, and number of protein-protein interactions Mol Biol Evol 2005, 22(5):1345-1354. 15746013
    • (2005) Mol Biol Evol , vol.22 , Issue.5 , pp. 1345-1354
    • Lemos, B.1    Bettencourt, B.R.2    Meiklejohn, C.D.3    Hartl, D.L.4
  • 17
    • 0035799707 scopus 로고    scopus 로고
    • Lethality and centrality in protein networks
    • 11333967
    • Jeong H Mason SP Barabasi AL Oltvai ZN Lethality and centrality in protein networks Nature 2001, 411(6833):41-42. 11333967
    • (2001) Nature , vol.411 , Issue.6833 , pp. 41-42
    • Jeong, H.1    Mason, S.P.2    Barabasi, A.L.3    Oltvai, Z.N.4
  • 18
    • 2942678187 scopus 로고    scopus 로고
    • Evolutionary rate depends on number of protein-protein interactions independently of gene expression level
    • 420460 15165289
    • Fraser HB Hirsh AE Evolutionary rate depends on number of protein-protein interactions independently of gene expression level BMC Evol Biol 2004, 4(1):13. 420460 15165289
    • (2004) BMC Evol Biol , vol.4 , Issue.1 , pp. 13
    • Fraser, H.B.1    Hirsh, A.E.2
  • 20
    • 0242284421 scopus 로고    scopus 로고
    • A simple dependence between protein evolution rate and the number of protein-protein interactions
    • 166126 12769820
    • Fraser HB Wall DP Hirsh AE A simple dependence between protein evolution rate and the number of protein-protein interactions BMC Evol Biol 2003, 3(1):11. 166126 12769820
    • (2003) BMC Evol Biol , vol.3 , Issue.1 , pp. 11
    • Fraser, H.B.1    Wall, D.P.2    Hirsh, A.E.3
  • 21
    • 6344241652 scopus 로고    scopus 로고
    • Conservation and coevolution in the scale-free human gene coexpression network
    • 15282333
    • Jordan IK Marino-Ramirez L Wolf YI Koonin EV Conservation and coevolution in the scale-free human gene coexpression network Mol Biol Evol 2004, 21(11):2058-2070. 15282333
    • (2004) Mol Biol Evol , vol.21 , Issue.11 , pp. 2058-2070
    • Jordan, I.K.1    Marino-Ramirez, L.2    Wolf, Y.I.3    Koonin, E.V.4
  • 22
    • 16844363315 scopus 로고    scopus 로고
    • Modularity and evolutionary constraint on proteins
    • 15750592
    • Fraser HB Modularity and evolutionary constraint on proteins Nat Genet 2005, 37(4):351-352. 15750592
    • (2005) Nat Genet , vol.37 , Issue.4 , pp. 351-352
    • Fraser, H.B.1
  • 23
    • 33746192317 scopus 로고    scopus 로고
    • Unifying measures of gene function and evolution
    • 1560323 16777745
    • Wolf YI Carmel L Koonin EV Unifying measures of gene function and evolution Proc Biol Sci 2006, 273:1507-1515. 1560323 16777745
    • (2006) Proc Biol Sci , vol.273 , pp. 1507-1515
    • Wolf, Y.I.1    Carmel, L.2    Koonin, E.V.3
  • 24
    • 30744441602 scopus 로고    scopus 로고
    • A single determinant dominates the rate of yeast protein evolution
    • 16237209
    • Drummond DA Raval A Wilke CO A single determinant dominates the rate of yeast protein evolution Mol Biol Evol 2006, 23(2):327-337. 16237209
    • (2006) Mol Biol Evol , vol.23 , Issue.2 , pp. 327-337
    • Drummond, D.A.1    Raval, A.2    Wilke, C.O.3
  • 25
    • 47549097539 scopus 로고    scopus 로고
    • Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution
    • 186625481
    • Drummond DA Wilke CO Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution Cell 2008, 134(2):341-352. 18662548
    • (2008) Cell , vol.134 , Issue.1 , pp. 341-352
    • Drummond, D.A.1    Wilke, C.O.2
  • 26
    • 33646904645 scopus 로고    scopus 로고
    • Population genetics of translational robustness
    • 1461446 16489231
    • Wilke CO Drummond DA Population genetics of translational robustness Genetics 2006, 173(1):473-481. 1461446 16489231
    • (2006) Genetics , vol.173 , Issue.1 , pp. 473-481
    • Wilke, C.O.1    Drummond, D.A.2
  • 27
    • 31044448435 scopus 로고    scopus 로고
    • A simple physical model for scaling in protein-protein interaction networks
    • 1326177 16384916
    • Deeds EJ Ashenberg O Shakhnovich EI A simple physical model for scaling in protein-protein interaction networks Proc Natl Acad Sci USA 2006, 103(2):311-316. 1326177 16384916
    • (2006) Proc Natl Acad Sci USA , vol.103 , Issue.2 , pp. 311-316
    • Deeds, E.J.1    Ashenberg, O.2    Shakhnovich, E.I.3
  • 28
    • 26244442102 scopus 로고    scopus 로고
    • Modules, multidomain proteins and organismic complexity
    • 16176277
    • Tordai H Nagy A Farkas K Banyai L Patthy L Modules, multidomain proteins and organismic complexity Febs J 2005, 272(19):50645078. 16176277
    • (2005) Febs J , vol.272 , Issue.19 , pp. 5064-5078
    • Tordai, H.1    Nagy, A.2    Farkas, K.3    Banyai, L.4    Patthy, L.5
  • 29
    • 40449095056 scopus 로고    scopus 로고
    • Evolution of protein domain promiscuity in eukaryotes
    • 2259109 18230802
    • Basu MK Carmel L Rogozin IB Koonin EV Evolution of protein domain promiscuity in eukaryotes Genome Res 2008, 18(3):449-461. 2259109 18230802
    • (2008) Genome Res , vol.18 , Issue.3 , pp. 449-461
    • Basu, M.K.1    Carmel, L.2    Rogozin, I.B.3    Koonin, E.V.4
  • 31
    • 34250813107 scopus 로고    scopus 로고
    • Alternative splicing of pre-messenger RNAs in plants in the genomic era
    • 17222076
    • Reddy AS Alternative splicing of pre-messenger RNAs in plants in the genomic era Annu Rev Plant Biol 2007, 58:267-294. 17222076
    • (2007) Annu Rev Plant Biol , vol.58 , pp. 267-294
    • Reddy, A.S.1
  • 32
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • 7723011
    • Murzin AG Brenner SE Hubbard T Chothia C SCOP: A structural classification of proteins database for the investigation of sequences and structures J Mol Biol, 1995, 247(4):536-540. 7723011
    • (1995) J Mol Biol , vol.247 , Issue.4 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 33
    • 0033858110 scopus 로고    scopus 로고
    • From complete genomes to measures of substitution rate variability within and between proteins
    • 310923 10899148
    • Grishin NV Wolf YI Koonin EV From complete genomes to measures of substitution rate variability within and between proteins Genome Res 2000, 10(7):991-1000. 310923 10899148
    • (2000) Genome Res , vol.10 , Issue.7 , pp. 991-1000
    • Grishin, N.V.1    Wolf, Y.I.2    Koonin, E.V.3
  • 35
    • 0041673352 scopus 로고    scopus 로고
    • Structural determinant of protein designability
    • 12786593
    • England JL Shakhnovich EI Structural determinant of protein designability Phys Rev Lett 2003, 90(21):218101. 12786593
    • (2003) Phys Rev Lett , vol.90 , Issue.21 , pp. 218101
    • England, J.L.1    Shakhnovich, E.I.2
  • 36
    • 33748143748 scopus 로고    scopus 로고
    • Structural determinants of the rate of protein evolution in yeast
    • 16782762
    • Bloom JD Drummond DA Arnold FH Wilke CO Structural determinants of the rate of protein evolution in yeast Mol Biol Evol 2006, 23(9):1751-1761. 16782762
    • (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
  • 37
    • 43149112799 scopus 로고    scopus 로고
    • Contact density affects protein evolutionary rate from bacteria to animals
    • 18379715
    • Zhou T Drummond DA Wilke CO Contact density affects protein evolutionary rate from bacteria to animals J Mol Evol 2008, 66(4):395-404. 18379715
    • (2008) J Mol Evol , vol.66 , Issue.4 , pp. 395-404
    • Zhou, T.1    Drummond, D.A.2    Wilke, C.O.3
  • 38
    • 33845895536 scopus 로고    scopus 로고
    • The frequency of translational misreading errors in E. coli is largely determined by tRNA competition
    • 1705757 17095544
    • Kramer EB Farabaugh PJ The frequency of translational misreading errors in E. coli is largely determined by tRNA competition Rna 2007, 13(1):87-96. 1705757 17095544
    • (2007) Rna , vol.13 , Issue.1 , pp. 87-96
    • Kramer, E.B.1    Farabaugh, P.J.2
  • 39
    • 0346727127 scopus 로고    scopus 로고
    • Protein degradation and protection against misfolded or damaged proteins
    • 14685250
    • Goldberg AL Protein degradation and protection against misfolded or damaged proteins Nature 2003, 426(6968):895-899. 14685250
    • (2003) Nature , vol.426 , Issue.6968 , pp. 895-899
    • Goldberg, A.L.1
  • 43
    • 0030660581 scopus 로고    scopus 로고
    • A genomic perspective on protein families
    • 9381173
    • Tatusov RL Koonin EV Lipman DJ A genomic perspective on protein families Science 1997, 278(5338):631-637. 9381173
    • (1997) Science , vol.278 , Issue.5338 , pp. 631-637
    • Tatusov, R.L.1    Koonin, E.V.2    Lipman, D.J.3
  • 44
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • 390337 15034147
    • Edgar RC MUSCLE: Multiple sequence alignment with high accuracy and high throughput Nucleic Acids Res 2004, 32(5):1792-1797. 390337 15034147
    • (2004) Nucleic Acids Res , vol.32 , Issue.5 , pp. 1792-1797
    • Edgar, R.C.1
  • 45
    • 0029901637 scopus 로고    scopus 로고
    • Inferring phylogenies from protein sequences by parsimony, distance, and likelihood methods
    • 8743697
    • Felsenstein J Inferring phylogenies from protein sequences by parsimony, distance, and likelihood methods Methods Enzymol 1996, 266:418-427. 8743697
    • (1996) Methods Enzymol , vol.266 , pp. 418-427
    • Felsenstein, J.1
  • 46
    • 0001473437 scopus 로고
    • On estimation of a probability density function and mode
    • Parzen E On estimation of a probability density function and mode Ann Math Stat 1962, 33:1065-1076.
    • (1962) Ann Math Stat , vol.33 , pp. 1065-1076
    • Parzen, E.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.