메뉴 건너뛰기




Volumn 12, Issue 12, 2011, Pages

The relationship between proteome size, structural disorder and organism complexity

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; PROTEOME;

EID: 82655175850     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2011-12-12-r120     Document Type: Article
Times cited : (150)

References (50)
  • 1
    • 2942568227 scopus 로고    scopus 로고
    • A molecular timescale of eukaryote evolution and the rise of complex multicellular life.
    • 10.1186/1471-2148-4-2, 341452, 15005799
    • Hedges SB, Blair JE, Venturi ML, Shoe JL. A molecular timescale of eukaryote evolution and the rise of complex multicellular life. BMC Evol Biol 2004, 4:2. 10.1186/1471-2148-4-2, 341452, 15005799.
    • (2004) BMC Evol Biol , vol.4 , pp. 2
    • Hedges, S.B.1    Blair, J.E.2    Venturi, M.L.3    Shoe, J.L.4
  • 2
    • 33646909100 scopus 로고    scopus 로고
    • Protein family expansions and biological complexity.
    • 10.1371/journal.pcbi.0020048, 1464810, 16733546
    • Vogel C, Chothia C. Protein family expansions and biological complexity. PLoS Comput Biol 2006, 2:e48. 10.1371/journal.pcbi.0020048, 1464810, 16733546.
    • (2006) PLoS Comput Biol , vol.2
    • Vogel, C.1    Chothia, C.2
  • 3
    • 33646566815 scopus 로고    scopus 로고
    • Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Mutation rate and the cost of complexity.
    • 10.1093/molbev/msj104, 16469852
    • Haygood R. Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Mutation rate and the cost of complexity. Mol Biol Evol 2006, 23:957-963. 10.1093/molbev/msj104, 16469852.
    • (2006) Mol Biol Evol , vol.23 , pp. 957-963
    • Haygood, R.1
  • 4
    • 0030874420 scopus 로고    scopus 로고
    • Size and complexity among multicellular organisms.
    • Bell G, Mooers AO. Size and complexity among multicellular organisms. Biol J Linn Soc 1997, 60:345-363.
    • (1997) Biol J Linn Soc , vol.60 , pp. 345-363
    • Bell, G.1    Mooers, A.O.2
  • 5
    • 0035992053 scopus 로고    scopus 로고
    • The g-value paradox.
    • 10.1046/j.1525-142X.2002.01069.x, 12004964
    • Hahn MW, Wray GA. The g-value paradox. Evol Dev 2002, 4:73-75. 10.1046/j.1525-142X.2002.01069.x, 12004964.
    • (2002) Evol Dev , vol.4 , pp. 73-75
    • Hahn, M.W.1    Wray, G.A.2
  • 6
    • 0033048066 scopus 로고    scopus 로고
    • Moonlighting proteins.
    • 10.1016/S0968-0004(98)01335-8, 10087914
    • Jeffery CJ. Moonlighting proteins. Trends Biochem Sci 1999, 24:8-11. 10.1016/S0968-0004(98)01335-8, 10087914.
    • (1999) Trends Biochem Sci , vol.24 , pp. 8-11
    • Jeffery, C.J.1
  • 7
    • 33845608152 scopus 로고    scopus 로고
    • The phylogenetic distribution of metazoan micro-RNAs: insights into evolutionary complexity and constraint.
    • Sempere LF, Cole CN, McPeek MA, Peterson KJ. The phylogenetic distribution of metazoan micro-RNAs: insights into evolutionary complexity and constraint. J Exp Zool B Mol Dev Evol 2006, 306:575-588.
    • (2006) J Exp Zool B Mol Dev Evol , vol.306 , pp. 575-588
    • Sempere, L.F.1    Cole, C.N.2    McPeek, M.A.3    Peterson, K.J.4
  • 8
    • 33847698971 scopus 로고    scopus 로고
    • The relationship between non-protein-coding DNA and eukaryotic complexity.
    • 10.1002/bies.20544, 17295292
    • Taft RJ, Pheasant M, Mattick JS. The relationship between non-protein-coding DNA and eukaryotic complexity. Bioessays 2007, 29:288-299. 10.1002/bies.20544, 17295292.
    • (2007) Bioessays , vol.29 , pp. 288-299
    • Taft, R.J.1    Pheasant, M.2    Mattick, J.S.3
  • 9
    • 33846036722 scopus 로고    scopus 로고
    • The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species.
    • 10.1093/nar/gkl884, 1669709, 17108355
    • Kim N, Alekseyenko AV, Roy M, Lee C. The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species. Nucleic Acids Res 2007, 35:D93-98. 10.1093/nar/gkl884, 1669709, 17108355.
    • (2007) Nucleic Acids Res , vol.35
    • Kim, N.1    Alekseyenko, A.V.2    Roy, M.3    Lee, C.4
  • 10
    • 14644435825 scopus 로고    scopus 로고
    • Intrinsically unstructured proteins and their functions.
    • 10.1038/nrm1589, 15738986
    • Dyson HJ, Wright PE. Intrinsically unstructured proteins and their functions. Nat Rev Mol Cell Biol 2005, 6:197-208. 10.1038/nrm1589, 15738986.
    • (2005) Nat Rev Mol Cell Biol , vol.6 , pp. 197-208
    • Dyson, H.J.1    Wright, P.E.2
  • 12
    • 33750999318 scopus 로고    scopus 로고
    • Disorder and sequence repeats in hub proteins and their implications for network evolution.
    • 10.1021/pr060171o, 17081050
    • Dosztanyi Z, Chen J, Dunker AK, Simon I, Tompa P. Disorder and sequence repeats in hub proteins and their implications for network evolution. J Proteome Res 2006, 5:2985-2995. 10.1021/pr060171o, 17081050.
    • (2006) J Proteome Res , vol.5 , pp. 2985-2995
    • Dosztanyi, Z.1    Chen, J.2    Dunker, A.K.3    Simon, I.4    Tompa, P.5
  • 14
    • 33847081239 scopus 로고    scopus 로고
    • Role of intrinsic disorder in transient interactions of hub proteins.
    • Singh GP, Ganapathi M, Dash D. Role of intrinsic disorder in transient interactions of hub proteins. Proteins 2006, 66:761-765.
    • (2006) Proteins , vol.66 , pp. 761-765
    • Singh, G.P.1    Ganapathi, M.2    Dash, D.3
  • 15
    • 38149063767 scopus 로고    scopus 로고
    • Structural disorder promotes assembly of protein complexes.
    • 10.1186/1472-6807-7-65, 2194777, 17922903
    • Hegyi H, Schad E, Tompa P. Structural disorder promotes assembly of protein complexes. BMC Struct Biol 2007, 7:65. 10.1186/1472-6807-7-65, 2194777, 17922903.
    • (2007) BMC Struct Biol , vol.7 , pp. 65
    • Hegyi, H.1    Schad, E.2    Tompa, P.3
  • 16
    • 23944514504 scopus 로고    scopus 로고
    • Structural disorder throws new light on moonlighting.
    • 10.1016/j.tibs.2005.07.008, 16054818
    • Tompa P, Szasz C, Buday L. Structural disorder throws new light on moonlighting. Trends Biochem Sci 2005, 30:484-489. 10.1016/j.tibs.2005.07.008, 16054818.
    • (2005) Trends Biochem Sci , vol.30 , pp. 484-489
    • Tompa, P.1    Szasz, C.2    Buday, L.3
  • 17
    • 1542358787 scopus 로고    scopus 로고
    • Prediction and functional analysis of native disorder in proteins from the three kingdoms of life.
    • 10.1016/j.jmb.2004.02.002, 15019783
    • Ward JJ, Sodhi JS, McGuffin LJ, Buxton BF, Jones DT. Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. J Mol Biol 2004, 337:635-645. 10.1016/j.jmb.2004.02.002, 15019783.
    • (2004) J Mol Biol , vol.337 , pp. 635-645
    • Ward, J.J.1    Sodhi, J.S.2    McGuffin, L.J.3    Buxton, B.F.4    Jones, D.T.5
  • 20
    • 67049119327 scopus 로고    scopus 로고
    • Prediction of protein binding regions in disordered proteins.
    • 10.1371/journal.pcbi.1000376, 2671142, 19412530
    • Meszaros B, Simon I, Dosztanyi Z. Prediction of protein binding regions in disordered proteins. PLoS Comput Biol 2009, 5:e1000376. 10.1371/journal.pcbi.1000376, 2671142, 19412530.
    • (2009) PLoS Comput Biol , vol.5
    • Meszaros, B.1    Simon, I.2    Dosztanyi, Z.3
  • 21
    • 79952351014 scopus 로고    scopus 로고
    • Verification of alternative splicing variants based on domain integrity, truncation length and intrinsic protein disorder.
    • 10.1093/nar/gkq843, 3045584, 20972208
    • Hegyi H, Kalmar L, Horvath T, Tompa P. Verification of alternative splicing variants based on domain integrity, truncation length and intrinsic protein disorder. Nucleic Acids Res 2011, 39:1208-1219. 10.1093/nar/gkq843, 3045584, 20972208.
    • (2011) Nucleic Acids Res , vol.39 , pp. 1208-1219
    • Hegyi, H.1    Kalmar, L.2    Horvath, T.3    Tompa, P.4
  • 22
    • 0022203256 scopus 로고
    • Phylogenies and the Comparative Method.
    • Felsenstein J. Phylogenies and the Comparative Method. Am Nat 1985, 125:1-15.
    • (1985) Am Nat , vol.125 , pp. 1-15
    • Felsenstein, J.1
  • 23
    • 33747191719 scopus 로고    scopus 로고
    • Prevalent structural disorder in E. coli and S. cerevisiae proteomes.
    • 10.1021/pr0600881, 16889422
    • Tompa P, Dosztanyi Z, Simon I. Prevalent structural disorder in E. coli and S. cerevisiae proteomes. J Proteome Res 2006, 5:1996-2000. 10.1021/pr0600881, 16889422.
    • (2006) J Proteome Res , vol.5 , pp. 1996-2000
    • Tompa, P.1    Dosztanyi, Z.2    Simon, I.3
  • 25
    • 24044538903 scopus 로고    scopus 로고
    • IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content.
    • 10.1093/bioinformatics/bti541, 15955779
    • Dosztanyi Z, Csizmok V, Tompa P, Simon I. IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content. Bioinformatics 2005, 21:3433-3434. 10.1093/bioinformatics/bti541, 15955779.
    • (2005) Bioinformatics , vol.21 , pp. 3433-3434
    • Dosztanyi, Z.1    Csizmok, V.2    Tompa, P.3    Simon, I.4
  • 26
    • 77957766242 scopus 로고    scopus 로고
    • Reduction in structural disorder and functional complexity in the thermal adaptation of prokaryotes.
    • 10.1371/journal.pone.0012069, 2920320, 20711457
    • Burra PV, Kalmar L, Tompa P. Reduction in structural disorder and functional complexity in the thermal adaptation of prokaryotes. PLoS One 2010, 5:e12069. 10.1371/journal.pone.0012069, 2920320, 20711457.
    • (2010) PLoS One , vol.5
    • Burra, P.V.1    Kalmar, L.2    Tompa, P.3
  • 27
    • 60349101875 scopus 로고    scopus 로고
    • Linking folding and binding.
    • 10.1016/j.sbi.2009.01.006, 19217770
    • Wright PE, Dyson HJ. Linking folding and binding. Curr Opin Struct Biol 2009, 19:1-8. 10.1016/j.sbi.2009.01.006, 19217770.
    • (2009) Curr Opin Struct Biol , vol.19 , pp. 1-8
    • Wright, P.E.1    Dyson, H.J.2
  • 28
    • 0034716987 scopus 로고    scopus 로고
    • EST comparison indicates 38% of human mRNAs contain possible alternative splice forms.
    • 10.1016/S0014-5793(00)01581-7, 10828456
    • Brett D, Hanke J, Lehmann G, Haase S, Delbruck S, Krueger S, Reich J, Bork P. EST comparison indicates 38% of human mRNAs contain possible alternative splice forms. FEBS Lett 2000, 474:83-86. 10.1016/S0014-5793(00)01581-7, 10828456.
    • (2000) FEBS Lett , vol.474 , pp. 83-86
    • Brett, D.1    Hanke, J.2    Lehmann, G.3    Haase, S.4    Delbruck, S.5    Krueger, S.6    Reich, J.7    Bork, P.8
  • 31
    • 56749098074 scopus 로고    scopus 로고
    • Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing.
    • 10.1038/ng.259, 18978789
    • Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 2008, 40:1413-1415. 10.1038/ng.259, 18978789.
    • (2008) Nat Genet , vol.40 , pp. 1413-1415
    • Pan, Q.1    Shai, O.2    Lee, L.J.3    Frey, B.J.4    Blencowe, B.J.5
  • 34
    • 10944229314 scopus 로고    scopus 로고
    • Variation in alternative splicing across human tissues.
    • 10.1186/gb-2004-5-10-r74, 545594, 15461793
    • Yeo G, Holste D, Kreiman G, Burge CB. Variation in alternative splicing across human tissues. Genome Biol 2004, 5:R74. 10.1186/gb-2004-5-10-r74, 545594, 15461793.
    • (2004) Genome Biol , vol.5
    • Yeo, G.1    Holste, D.2    Kreiman, G.3    Burge, C.B.4
  • 35
    • 82655179703 scopus 로고    scopus 로고
    • Increased structural disorder of proteins encoded on human sex chromosomes.
    • 10.1039/c1mb05285c, 22105808
    • Hegyi H, Tompa P. Increased structural disorder of proteins encoded on human sex chromosomes. Mol Biosyst 2012, 8:229-236. 10.1039/c1mb05285c, 22105808.
    • (2012) Mol Biosyst , vol.8 , pp. 229-236
    • Hegyi, H.1    Tompa, P.2
  • 37
    • 79961145412 scopus 로고    scopus 로고
    • Development of a classification scheme for disease-related enzyme information.
    • Sohngen C, Chang A, Schomburg D. Development of a classification scheme for disease-related enzyme information. BMC Bioinformatics 12:329.
    • BMC Bioinformatics , vol.12 , pp. 329
    • Sohngen, C.1    Chang, A.2    Schomburg, D.3
  • 38
    • 84872009437 scopus 로고    scopus 로고
    • Genomes Online Database.
    • Genomes Online Database. , http://www.genomesonline.org/cgi-bin/GOLD
  • 39
    • 84857444429 scopus 로고    scopus 로고
    • ExPASy Bioinformatics Resource Portal: HAMAP.
    • ExPASy Bioinformatics Resource Portal: HAMAP. , http://www.expasy.ch/sprot/hamap/
  • 40
    • 84857441297 scopus 로고    scopus 로고
    • E! Ensembl.
    • e! Ensembl. , http://www.ensembl.org/pub/release-50/
  • 41
    • 84870490179 scopus 로고    scopus 로고
    • National Center for Biotechnology Information.
    • National Center for Biotechnology Information. , http://www.ncbi.nlm.nih.gov/
  • 42
    • 84857445157 scopus 로고    scopus 로고
    • Prediction of Intrinsically Unstructured Proteins.
    • Prediction of Intrinsically Unstructured Proteins. , http://iupred.enzim.hu/
  • 43
    • 84893298266 scopus 로고    scopus 로고
    • Structural Classification of Proteins.
    • Structural Classification of Proteins. , http://scop.mrc-lmb.cam.ac.uk/scop/
  • 44
    • 0028961335 scopus 로고
    • SCOP: a structural classification of proteins database for the investigation of sequences and structures.
    • 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, 247:536-540.
    • (1995) J Mol Biol , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 45
    • 84857442638 scopus 로고    scopus 로고
    • The ASTRAL Compendium for Sequence and Structure Analysis.
    • The ASTRAL Compendium for Sequence and Structure Analysis. , http://astral.berkeley.edu
  • 48
    • 79956337120 scopus 로고    scopus 로고
    • Search Tool for the Retrieval of Interacting Genes/Proteins (STRING).
    • Search Tool for the Retrieval of Interacting Genes/Proteins (STRING). , http://string-db.org/
  • 49
    • 84857445156 scopus 로고    scopus 로고
    • ASAP II.
    • ASAP II. , http://bioinformatics.ucla.edu/ASAP2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.