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Volumn 6, Issue , 2006, Pages

Tracing the origin of functional and conserved domains in the human proteome: Implications for protein evolution at the modular level

Author keywords

[No Author keywords available]

Indexed keywords

PROTEOME; EPIDERMAL GROWTH FACTOR;

EID: 33751204154     PISSN: 14712148     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-6-91     Document Type: Article
Times cited : (10)

References (59)
  • 1
    • 0034625235 scopus 로고    scopus 로고
    • The impact of comparative genomics on our understanding of evolution
    • Koonin EV, Aravind L, Kondrashov AS: The impact of comparative genomics on our understanding of evolution. Cell 2000, 101:573-576.
    • (2000) Cell , vol.101 , pp. 573-576
    • Koonin, E.V.1    Aravind, L.2    Kondrashov, A.S.3
  • 6
    • 0036180314 scopus 로고    scopus 로고
    • Rosetta Stone proteins: Chance and necessity?
    • Veitia RA: Rosetta Stone proteins: chance and necessity? Genome Biol 2002, 3:1-3.
    • (2002) Genome Biol , vol.3 , pp. 1-3
    • Veitia, R.A.1
  • 7
    • 0034887573 scopus 로고    scopus 로고
    • Scale-free behavior in protein domain networks
    • Wuchty S: Scale-free behavior in protein domain networks. Mol Biol Evol 2001, 18:1694-1702.
    • (2001) Mol Biol Evol , vol.18 , pp. 1694-1702
    • Wuchty, S.1
  • 8
    • 0035816218 scopus 로고    scopus 로고
    • Domain combinations in archaeal, eubacterial and eukaryotic proteomes
    • Apic G, Gough J, Teichmann SA: Domain combinations in archaeal, eubacterial and eukaryotic proteomes. J Mol Biol 2001, 310:311-325.
    • (2001) J Mol Biol , vol.310 , pp. 311-325
    • Apic, G.1    Gough, J.2    Teichmann, S.A.3
  • 9
    • 12344261833 scopus 로고    scopus 로고
    • The relationship between domain duplication and recombination
    • Vogel C, Teichmann SA, Pereira-Leal J: The relationship between domain duplication and recombination. J Mol Biol 2005, 346:355-365.
    • (2005) J Mol Biol , vol.346 , pp. 355-365
    • Vogel, C.1    Teichmann, S.A.2    Pereira-Leal, J.3
  • 10
    • 26244442102 scopus 로고    scopus 로고
    • Modules, multidomain proteins and organismic complexity
    • Tordai H, Nagy A, Farkas K, Bányai L, Patthy L: Modules, multidomain proteins and organismic complexity. FEBS J 2005, 272:5064-5078.
    • (2005) FEBS J , vol.272 , pp. 5064-5078
    • Tordai, H.1    Nagy, A.2    Farkas, K.3    Bányai, L.4    Patthy, L.5
  • 11
    • 33745611416 scopus 로고    scopus 로고
    • Gene fusion/fission is a major contributor to evolution of multi-domain bacterial proteins
    • Pasek S, Risler JL, Brezellec P: Gene fusion/fission is a major contributor to evolution of multi-domain bacterial proteins. Bioinformatics 2006, 22:1418-1423.
    • (2006) Bioinformatics , vol.22 , pp. 1418-1423
    • Pasek, S.1    Risler, J.L.2    Brezellec, P.3
  • 12
    • 33646268799 scopus 로고    scopus 로고
    • Domain deletions and substitutions in the modular protein evolution
    • Weiner J 3rd, Beaussart F, Bornberg-Bauer E: Domain deletions and substitutions in the modular protein evolution. FEBS J 2006, 273:2037-2047.
    • (2006) FEBS J , vol.273 , pp. 2037-2047
    • Weiner III, J.1    Beaussart, F.2    Bornberg-Bauer, E.3
  • 13
    • 33644907773 scopus 로고    scopus 로고
    • Evolution of circular permutations in multidomain proteins
    • Weiner J 3rd, Bornberg-Bauer E: Evolution of circular permutations in multidomain proteins. Mol Biol Evol 2006, 23:734-743.
    • (2006) Mol Biol Evol , vol.23 , pp. 734-743
    • Weiner III, J.1    Bornberg-Bauer, E.2
  • 14
    • 16244423379 scopus 로고    scopus 로고
    • Multi-domain proteins in the three kingdoms of life: Orphan domains and other unassigned regions
    • Ekman D, Bjorklund AK, Frey-Skott J, Elofsson A: Multi-domain proteins in the three kingdoms of life: orphan domains and other unassigned regions. J Mol Biol 2005, 348:231-243.
    • (2005) J Mol Biol , vol.348 , pp. 231-243
    • Ekman, D.1    Bjorklund, A.K.2    Frey-Skott, J.3    Elofsson, A.4
  • 15
    • 4444242626 scopus 로고    scopus 로고
    • cis-Regulatory and protein evolution in orthologous and duplicate genes
    • Castillo-Davis CI, Hartl DL, Achaz G: cis-Regulatory and protein evolution in orthologous and duplicate genes. Genome Res 2004, 14:1530-1536.
    • (2004) Genome Res , vol.14 , pp. 1530-1536
    • Castillo-Davis, C.I.1    Hartl, D.L.2    Achaz, G.3
  • 16
    • 25444525409 scopus 로고    scopus 로고
    • Comparative mapping of sequence-based and structure-based protein domains
    • Zhang Y, Chandonia JM, Ding C, Holbrook SR: Comparative mapping of sequence-based and structure-based protein domains. BMC Bioinformatics 2005, 6:77.
    • (2005) BMC Bioinformatics , vol.6 , pp. 77
    • Zhang, Y.1    Chandonia, J.M.2    Ding, C.3    Holbrook, S.R.4
  • 17
    • 0028961335 scopus 로고
    • SCOP: A structural classification of protein database for the investigation of sequences and structures
    • Murzin AG, Brenner SE, Hubbard T, Chothia C: SCOP: a structural classification of protein database for the investigation of sequences and structures. J Mol Biol 1995, 247:536-540.
    • (1995) J Mol Biol , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 18
    • 13444272079 scopus 로고    scopus 로고
    • The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis
    • Pearl F, Todd A, Sillitoe I, Dibley M, Redfern O, Lewis T, Bennett C, Marsden R, Grant A, Lee D, et al.: The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis. Nucleic Acids Res 2005, 33:D247-D251.
    • (2005) Nucleic Acids Res , vol.33
    • Pearl, F.1    Todd, A.2    Sillitoe, I.3    Dibley, M.4    Redfern, O.5    Lewis, T.6    Bennett, C.7    Marsden, R.8    Grant, A.9    Lee, D.10
  • 19
    • 0027991446 scopus 로고
    • The FSSP database of structurally aligned protein fold families
    • Holm L, Sander C: The FSSP database of structurally aligned protein fold families. Nucleic Acids Res 1994, 22:3600-3609.
    • (1994) Nucleic Acids Res , vol.22 , pp. 3600-3609
    • Holm, L.1    Sander, C.2
  • 22
    • 0032568655 scopus 로고    scopus 로고
    • SMART, a simple modular architecture research tool: Identification of signaling domains
    • Schultz J, Milpetz F, Bork P, Ponting CP: SMART, a simple modular architecture research tool: identification of signaling domains. Proc Natl Acad Sci U S A 1998, 95:5857-5864.
    • (1998) Proc Natl Acad Sci U S A , vol.95 , pp. 5857-5864
    • Schultz, J.1    Milpetz, F.2    Bork, P.3    Ponting, C.P.4
  • 23
    • 0036853192 scopus 로고    scopus 로고
    • Structural characterization of the human proteome
    • Muller A, MacCallum RM, Sternberg MJ: Structural characterization of the human proteome. Genome Res 2002, 12:1625-1641.
    • (2002) Genome Res , vol.12 , pp. 1625-1641
    • Muller, A.1    MacCallum, R.M.2    Sternberg, M.J.3
  • 24
    • 22244450719 scopus 로고    scopus 로고
    • Protein families and their evolutiona structural perspective
    • Orengo CA, Thornton JM: Protein families and their evolutiona structural perspective. Annu Rev Biochem 2005, 74:867-900.
    • (2005) Annu Rev Biochem , vol.74 , pp. 867-900
    • Orengo, C.A.1    Thornton, J.M.2
  • 25
    • 0037138386 scopus 로고    scopus 로고
    • Protein domain analysis in the era of complete genomes
    • Copley RR, Doerks T, Letunic I, Bork P: Protein domain analysis in the era of complete genomes. FEBS Lett 2002, 513:129-134.
    • (2002) FEBS Lett , vol.513 , pp. 129-134
    • Copley, R.R.1    Doerks, T.2    Letunic, I.3    Bork, P.4
  • 26
    • 0028290005 scopus 로고
    • Parser for protein folding units
    • Holm L, Sander C: Parser for protein folding units. Proteins 1994, 19:256-268.
    • (1994) Proteins , vol.19 , pp. 256-268
    • Holm, L.1    Sander, C.2
  • 27
    • 0032804892 scopus 로고    scopus 로고
    • Origin of multicellular eukaryotes - Insights from proteome comparisons
    • Aravind L, Subramanian G: Origin of multicellular eukaryotes - insights from proteome comparisons. Curr Opin Genet Dev 1999, 9:688-694.
    • (1999) Curr Opin Genet Dev , vol.9 , pp. 688-694
    • Aravind, L.1    Subramanian, G.2
  • 30
    • 23144452044 scopus 로고    scopus 로고
    • The HHpred interactive server for protein homology detection and structure prediction
    • Söding J, Biegert A, Lupas AN: The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res 2005, 33:W244-W248.
    • (2005) Nucleic Acids Res , vol.33
    • Söding, J.1    Biegert, A.2    Lupas, A.N.3
  • 31
    • 0031743421 scopus 로고    scopus 로고
    • Profile hidden Markov models
    • Eddy SR: Profile hidden Markov models. Bioinformatics 1998, 14:755-763.
    • (1998) Bioinformatics , vol.14 , pp. 755-763
    • Eddy, S.R.1
  • 32
    • 0037460953 scopus 로고    scopus 로고
    • DomCut: Prediction of inter-domain linker regions in amino acid sequences
    • Suyama M, Ohara O: DomCut: prediction of inter-domain linker regions in amino acid sequences. Bioinformatics 2003, 19:673-674.
    • (2003) Bioinformatics , vol.19 , pp. 673-674
    • Suyama, M.1    Ohara, O.2
  • 34
    • 4844230621 scopus 로고    scopus 로고
    • The Frizzled family: Receptors for multiple signal transduction pathways
    • Huang HC, Klein PS: The Frizzled family: receptors for multiple signal transduction pathways. Genome Biol 2004, 5:234.
    • (2004) Genome Biol , vol.5 , pp. 234
    • Huang, H.C.1    Klein, P.S.2
  • 35
    • 0037076432 scopus 로고    scopus 로고
    • BORIS, a novel male germ-line-specific protein associated with epigenetic reprogramming events, shares the same 11-zinc-finger domain with CTCF, the insulator protein involved in reading imprinting marks in the soma
    • Loukinov DI, Pugacheva E, Vatolin S, Pack SD, Moon H, Chernukhin I, Mannan P, Larsson E, Kanduri C, Vostrov AA, et al.: BORIS, a novel male germ-line-specific protein associated with epigenetic reprogramming events, shares the same 11-zinc-finger domain with CTCF, the insulator protein involved in reading imprinting marks in the soma. Proc Natl Acad Sci U S A 2002, 99:6806-6811.
    • (2002) Proc Natl Acad Sci U S A , vol.99 , pp. 6806-6811
    • Loukinov, D.I.1    Pugacheva, E.2    Vatolin, S.3    Pack, S.D.4    Moon, H.5    Chernukhin, I.6    Mannan, P.7    Larsson, E.8    Kanduri, C.9    Vostrov, A.A.10
  • 36
    • 12144289308 scopus 로고    scopus 로고
    • Characterization of two novel KRAB-domain-containing zinc finger genes, ZNF460 and ZNF461, on human chromosome 19q13.1. q13.4
    • Dai J, Li Y, Ji C, Jin F, Zheng Z, Wang X, Sun X, Xu X, Gu S, Xie Y, Mao Y: Characterization of two novel KRAB-domain-containing zinc finger genes, ZNF460 and ZNF461, on human chromosome 19q13.1 . q13.4. Cytogenet Genome Res 2003, 103:74-78.
    • (2003) Cytogenet Genome Res , vol.103 , pp. 74-78
    • Dai, J.1    Li, Y.2    Ji, C.3    Jin, F.4    Zheng, Z.5    Wang, X.6    Sun, X.7    Xu, X.8    Gu, S.9    Xie, Y.10    Mao, Y.11
  • 37
    • 0024042080 scopus 로고
    • Structure and complete nucleotide sequence of the Marek's disease herpesvirus gp57-65 gene
    • Coussens PM, Velicer LF: Structure and complete nucleotide sequence of the Marek's disease herpesvirus gp57-65 gene. J Virol 1988, 62:2373-2379.
    • (1988) J Virol , vol.62 , pp. 2373-2379
    • Coussens, P.M.1    Velicer, L.F.2
  • 40
    • 0033961690 scopus 로고    scopus 로고
    • The kelch repeat superfamily of proteins: Propellers of cell function
    • Adams J, Kelso R, Cooley L: The kelch repeat superfamily of proteins: propellers of cell function. Trends Cell Biol 2000, 10:17-24.
    • (2000) Trends Cell Biol , vol.10 , pp. 17-24
    • Adams, J.1    Kelso, R.2    Cooley, L.3
  • 41
    • 0031970010 scopus 로고    scopus 로고
    • The catalytic domain of the P-type ATPase has the haloacid dehalogenase fold
    • Aravind L, Galperin MY, Koonin EV: The catalytic domain of the P-type ATPase has the haloacid dehalogenase fold. Trends Biochem Sci 1998, 23:127-129.
    • (1998) Trends Biochem Sci , vol.23 , pp. 127-129
    • Aravind, L.1    Galperin, M.Y.2    Koonin, E.V.3
  • 42
    • 33644509247 scopus 로고    scopus 로고
    • A general model of G protein-coupled receptor sequences and its application to detect remote homologs
    • Wistrand M, Kall L, Sonnhammer EL: A general model of G protein-coupled receptor sequences and its application to detect remote homologs. Protein Sci 2006, 15:509-521.
    • (2006) Protein Sci , vol.15 , pp. 509-521
    • Wistrand, M.1    Kall, L.2    Sonnhammer, E.L.3
  • 44
    • 0031656460 scopus 로고    scopus 로고
    • Matrix metalloproteinases: Structures, evolution, and diversification
    • Massova I, Kotra LP, Fridman R, Mobashery S: Matrix metalloproteinases: structures, evolution, and diversification. FASEB J 1998, 12:1075-1095.
    • (1998) FASEB J , vol.12 , pp. 1075-1095
    • Massova, I.1    Kotra, L.P.2    Fridman, R.3    Mobashery, S.4
  • 45
    • 18444397733 scopus 로고    scopus 로고
    • Crystal structure of human MMP9 in complex with a reverse hydroxamate inhibitor
    • Rowsell S, Hawtin P, Minshull CA, Jepson H: Crystal structure of human MMP9 in complex with a reverse hydroxamate inhibitor. J Mol Biol 2002, 319:173-181.
    • (2002) J Mol Biol , vol.319 , pp. 173-181
    • Rowsell, S.1    Hawtin, P.2    Minshull, C.A.3    Jepson, H.4
  • 46
    • 0030068937 scopus 로고    scopus 로고
    • The structural basis for the elastolytic activity of the 92-kDa and 72-kDa gelatinases. Role of the fibronectin type II-like repeats
    • Shipley JM, Doyle GA, Fliszar CJ, Ye QZ, Johnson LL, Shapiro SD, Welgus HG, Senior RM: The structural basis for the elastolytic activity of the 92-kDa and 72-kDa gelatinases. Role of the fibronectin type II-like repeats. J Biol Chem 1996, 271:4335-4341.
    • (1996) J Biol Chem , vol.271 , pp. 4335-4341
    • Shipley, J.M.1    Doyle, G.A.2    Fliszar, C.J.3    Ye, Q.Z.4    Johnson, L.L.5    Shapiro, S.D.6    Welgus, H.G.7    Senior, R.M.8
  • 47
    • 0036601151 scopus 로고    scopus 로고
    • Did evolution leap to create the protein universe?
    • Rost B: Did evolution leap to create the protein universe? Curr Opin Struct Biol 2002, 12:409-416.
    • (2002) Curr Opin Struct Biol , vol.12 , pp. 409-416
    • Rost, B.1
  • 48
    • 19944393249 scopus 로고    scopus 로고
    • Universal sharing patterns in proteomes and evolution of protein fold architecture and life
    • Caetano-Anolles G, Caetano-Anolles D: Universal sharing patterns in proteomes and evolution of protein fold architecture and life. J Mol Evol 2005, 60:484-498.
    • (2005) J Mol Evol , vol.60 , pp. 484-498
    • Caetano-Anolles, G.1    Caetano-Anolles, D.2
  • 49
    • 0036600834 scopus 로고    scopus 로고
    • Evolution of protein structures and functions
    • Kinch LN, Grishin NV: Evolution of protein structures and functions. Curr Opin Struct Biol 2002, 12:400-408.
    • (2002) Curr Opin Struct Biol , vol.12 , pp. 400-408
    • Kinch, L.N.1    Grishin, N.V.2
  • 50
    • 29244447181 scopus 로고    scopus 로고
    • Kalign - An accurate and fast multiple sequence alignment algorithm
    • Lassman T, Sonnhammer EL: Kalign - an accurate and fast multiple sequence alignment algorithm. BMC Bioinformatics 2005, 6:298.
    • (2005) BMC Bioinformatics , vol.6 , pp. 298
    • Lassman, T.1    Sonnhammer, E.L.2
  • 54
    • 0036169928 scopus 로고    scopus 로고
    • Tolerating some redundancy significantly speeds up clustering of large protein databases
    • Li W, Jaroszewski L, Godzik A: Tolerating some redundancy significantly speeds up clustering of large protein databases. Bioinformatics 2002, 18:77-82.
    • (2002) Bioinformatics , vol.18 , pp. 77-82
    • Li, W.1    Jaroszewski, L.2    Godzik, A.3
  • 55
    • 16344373015 scopus 로고    scopus 로고
    • Protein homology detection by HMM-HMM comparison
    • Söding J: Protein homology detection by HMM-HMM comparison. Bioinformatics 2005, 21:951-960.
    • (2005) Bioinformatics , vol.21 , pp. 951-960
    • Söding, J.1
  • 57
    • 0033578684 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on position-specific scoring matrices
    • Jones DT: Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 1999, 292:195-202.
    • (1999) J Mol Biol , vol.292 , pp. 195-202
    • Jones, D.T.1
  • 58
    • 3242891670 scopus 로고    scopus 로고
    • SledgeHMMER: A web server for batch searching Pfam database
    • Chukkapalli G, Guda C, Subramaniam S: SledgeHMMER: A web server for batch searching Pfam database. Nucleic Acids Res 2004, 32:W542-544.
    • (2004) Nucleic Acids Res , vol.32
    • Chukkapalli, G.1    Guda, C.2    Subramaniam, S.3
  • 59
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino acid sequence of two proteins
    • Needleman SB, Wunsch CD: A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 1970, 48:443-453.
    • (1970) J Mol Biol , vol.48 , pp. 443-453
    • Needleman, S.B.1    Wunsch, C.D.2


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