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Volumn 78, Issue 2, 2010, Pages 236-248

Large-scale analysis of secondary structure changes in proteins suggests a role for disorder-to-order transitions in nucleotide binding proteins

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOTIDE BINDING PROTEIN; PROTEOME; PURINE NUCLEOTIDE; NUCLEOTIDE; PROTEIN;

EID: 77449117443     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22531     Document Type: Article
Times cited : (15)

References (63)
  • 1
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 2
    • 36749081458 scopus 로고    scopus 로고
    • Assessment of disorder predictions in CA.SP7
    • Bordoli L, Kiefer F, Schwede T. Assessment of disorder predictions in CA.SP7. Proteins 2007;69 (Suppl 8):129-136.
    • (2007) Proteins , vol.69 , Issue.SUPPL. 8 , pp. 129-136
    • Bordoli, L.1    Kiefer, F.2    Schwede, T.3
  • 3
    • 14644435825 scopus 로고    scopus 로고
    • Intrinsically unstructured proteins and their functions
    • DOI 10.1038/nrm1589
    • Dyson HJ, Wright PE. Intrinsically unstructured proteins and their functions. Nat Rev Mol Cell Biol 2005;6:197-208. (Pubitemid 40314921)
    • (2005) Nature Reviews Molecular Cell Biology , vol.6 , Issue.3 , pp. 197-208
    • Dyson, H.J.1    Wright, P.E.2
  • 4
    • 0036174712 scopus 로고    scopus 로고
    • Continuum secondary structure captures protein flexibility
    • DOI 10.1016/S0969-2126(02)00700-1, PII S0969212602007001
    • Andersen CA, Palmer AG, Brunak S, Rost B. Continuum secondary structure captures protein flexibility. Structure 2002;10:175-184. (Pubitemid 34164596)
    • (2002) Structure , vol.10 , Issue.2 , pp. 175-184
    • Andersen, C.A.F.1    Palmer, A.G.2    Brunak, S.3    Rost, B.4
  • 5
    • 0042622240 scopus 로고    scopus 로고
    • GlobPlot: Exploring protein sequences for globularity and disorder
    • DOI 10.1093/nar/gkg519
    • Linding R, Russell RB, Neduva V, Gibson TJ. GlobPlot: exploring protein sequences for globularity and disorder. Nucl Acids Res 2003;31:3701-3708. (Pubitemid 37442227)
    • (2003) Nucleic Acids Research , vol.31 , Issue.13 , pp. 3701-3708
    • Linding, R.1    Russell, R.B.2    Neduva, V.3    Gibson, T.J.4
  • 6
    • 13944277320 scopus 로고    scopus 로고
    • Prediction of protein B-factor profiles
    • Yuan Z, Bailey TL, Teasdale RD. Prediction of protein B-factor profiles. Proteins 2005;58:905-912.
    • (2005) Proteins , vol.58 , pp. 905-912
    • Yuan, Z.1    Bailey, T.L.2    Teasdale, R.D.3
  • 8
    • 22744437069 scopus 로고    scopus 로고
    • Natively disordered proteins: Functions and predictions
    • DOI 10.2165/00822942-200403020-00005
    • Romero P, Obradovic Z, Dunker AK. Natively disordered proteins: functions and predictions. Appl Bioinform 2004;3:105-113. (Pubitemid 41032063)
    • (2004) Applied Bioinformatics , vol.3 , Issue.2-3 , pp. 105-113
    • Romero, P.1    Obradovic, Z.2    Dunker, A.K.3
  • 10
    • 34548736602 scopus 로고    scopus 로고
    • Molecular dynamics simulations reveal a disorder-to-order transition on phosphorylation of smooth muscle myosin
    • DOI 10.1529/biophysj.106.095802
    • Espinoza-Fonseca LM, Kast. D, Thomas DD, Molecular dynamics simulations reveal a disorder-to-order transition on phosphorylation of smooth muscle myosin. Biophys J 2007;93:2083-2090. (Pubitemid 47437590)
    • (2007) Biophysical Journal , vol.93 , Issue.6 , pp. 2083-2090
    • Espinoza-Fonseca, L.M.1    Kast, D.2    Thomas, D.D.3
  • 12
    • 0021161723 scopus 로고
    • The reactivity of anti-peptide antibodies is a function of the atomic mobility of sites in a protein
    • DOI 10.1038/312127a0
    • Tainer JA, Getzoff ED, Alexander H, Houghten RA, Olson AJ, Lerner RA, Hendrickson WA. The reactivity of anti-peptide antibodies is a function of the atomic mobility of sites in a protein. Nature 1984;312:127-134. (Pubitemid 14000076)
    • (1984) Nature , vol.312 , Issue.5990 , pp. 127-134
    • Tainer, J.A.1    Getzoff, E.D.2    Alexander, H.3
  • 14
    • 1542358787 scopus 로고    scopus 로고
    • Prediction and functional analysis of native disorder in proteins from the three kingdoms of life
    • Ward JJ, Sodhi JS, Mcguffm 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.
    • (2004) J Mol Biol , vol.337 , pp. 635-645
    • Ward, J.J.1    Sodhi, J.S.2    Mcguffm, L.J.3    Buxton, B.F.4    Jones, D.T.5
  • 16
    • 38149063767 scopus 로고    scopus 로고
    • Structural disorder promotes assembly of protein complexes
    • Hegyi H, Schad E, Tompa P. Structural disorder promotes assembly of protein complexes. BMC Struct Biol 2007;7:65.
    • (2007) BMC Struct Biol , vol.7 , pp. 65
    • Hegyi, H.1    Schad, E.2    Tompa, P.3
  • 17
    • 0029058666 scopus 로고
    • Structural analysis of a novel interaction by calmodulin: High-affinity binding of a peptide in the absence of calcium
    • Urbauer JL, Short JH, Dow LK, Wand AJ. Structural analysis of a novel interaction by calmodulin: high-affinity binding of a peptide in the absence of calcium. Biochemistry 1995;34:8099-8109.
    • (1995) Biochemistry , vol.34 , pp. 8099-8109
    • Urbauer, J.L.1    Short, J.H.2    Dow, L.K.3    Wand, A.J.4
  • 19
    • 0035815664 scopus 로고    scopus 로고
    • Evidence for a Partially Folded Intermediate in α-Synuclein Fibril Formation
    • DOI 10.1074/jbc.M010907200
    • Uversky VN, Li J, Fink AL, Evidence for a partially folded intermediate in alpha-synudein fibril formation. J Biol Chem 2001 ;276: 10737-10744. (Pubitemid 38089246)
    • (2001) Journal of Biological Chemistry , vol.276 , Issue.14 , pp. 10737-10744
    • Uversky, V.N.1    Li, J.2    Fink, A.L.3
  • 20
    • 0032829561 scopus 로고    scopus 로고
    • Heme binding and polymerization by Plasmodium falciparum histidine rich protein II: Influence of pH on activity and conformation
    • DOI 10.1016/S0014-5793(99)01260-0, PII S0014579399012600
    • Lynn A, Chandra S, Malhotra P, Chauhan VS. Heme binding and polymerization by Plasmodium falciparum histidine rich protein II: influence of pH on activity and conformation. FEBS Lett 1999;459: 267-271. (Pubitemid 29475045)
    • (1999) FEBS Letters , vol.459 , Issue.2 , pp. 267-271
    • Lynn, A.1    Chandra, S.2    Malhotra, P.3    Chauhan, V.S.4
  • 22
    • 0034610396 scopus 로고    scopus 로고
    • Thermal behavior of proteins: Heat-resistant proteins and their heat-induced secondary structural changes
    • Kim TD, Ryu HJ, Cho HI, Yang CH, Kim J. Thermal behavior of proteins: heat-resistant proteins and their heat-induced secondary structural changes. Biochemistry 2000:39:14839-14846.
    • (2000) Biochemistry , vol.39 , pp. 14839-14846
    • Kim, T.D.1    Ryu, H.J.2    Cho, H.I.3    Yang, C.H.4    Kim, J.5
  • 23
    • 0038148710 scopus 로고    scopus 로고
    • Conformational diversity and protein evolution-a 60-year-old hypothesis revisited
    • James LC, Tawfik DS. Conformational diversity and protein evolution-a 60-year-old hypothesis revisited. Trends Biochem Sci 2003; 28:361-368.
    • (2003) Trends Biochem Sci , vol.28 , pp. 361-368
    • James, L.C.1    Tawfik, D.S.2
  • 24
    • 0030587932 scopus 로고    scopus 로고
    • An α to β conformational switch in EF-Tu
    • AbelK,YoderMD,HilgenfeldR,JuruakF.Analpha-betaconformationalswitchinEF- Tu.Structure1996;4:1153-1159.(Pubitemid27005383)
    • (1996) Structure , vol.4 , Issue.10 , pp. 1153-1159
    • Abel, K.1    Yoder, M.D.2    Hilgenfeld, R.3    Jurnak, F.4
  • 25
    • 0034703718 scopus 로고    scopus 로고
    • X-ray structures of the universal translation initiation factor IF2/eIF5B: Conformational changes on GDP and GTP binding
    • Roll-Mecak A, Cao C, Dever TE, Burley SK. X-ray structures of the universal translation initiation factor IF2/eIF5B: conformational changes on GDP and GTP binding. Cell 2000;103:781-792.
    • (2000) Cell , vol.103 , pp. 781-792
    • Roll-Mecak, A.1    Cao, C.2    Dever, T.E.3    Burley, S.K.4
  • 26
    • 33747816204 scopus 로고    scopus 로고
    • Identifying sequence regions undergoing conformational change via predicted continuum secondary structure
    • DOI 10.1093/bioinformatics/btl198
    • Boden M, Bailey TL. Identifying sequence regions undergoing conformational change via predicted continuum secondary structure. Bioinformatics 2006;22:1809-1814. (Pubitemid 44283024)
    • (2006) Bioinformatics , vol.22 , Issue.15 , pp. 1809-1814
    • Boden, M.1    Bailey, T.L.2
  • 27
    • 0028980362 scopus 로고
    • The alpha-helical to beta-strand transition in the amino-terminal fragment of the amyloid, beta-peptide modulates amyloid formation
    • Soto C, Castaoo EM, Frangione B, Inestrosa NC. The alpha-helical to beta-strand transition in the amino-terminal fragment of the amyloid, beta-peptide modulates amyloid formation. J Biol Chem 1995;270:3063-3067.
    • (1995) J Biol Chem , vol.270 , pp. 3063-3067
    • Soto, C.1    Castaoo, E.M.2    Frangione, B.3    Inestrosa, N.C.4
  • 28
    • 0026631361 scopus 로고
    • NMR studies of amyloid, beta.-peptides; proton assignments, secondary structure, and mechanism of an. alpha.-helix. fwdarw. beta.-sheet conversion for a homologous, 28-residue, N-terminal fragment
    • Zagorski MG, Barrow CJ. NMR studies of amyloid, beta.-peptides; proton assignments, secondary structure, and mechanism of an. alpha.-helix. fwdarw. beta.-sheet conversion for a homologous, 28-residue, N-terminal fragment. Biochemistry 1992;31:5621-5631.
    • (1992) Biochemistry , vol.31 , pp. 5621-5631
    • Zagorski, M.G.1    Barrow, C.J.2
  • 29
    • 0028925377 scopus 로고
    • Prion protein, peptides induce alpha-helix to beta-sheet conformational transitions
    • Nguyen. J, Baldwin MA, Cohen FE, Prusiner SB. Prion protein, peptides induce alpha-helix to beta-sheet conformational transitions. Biochemistry 1995;34:4186-4192.
    • (1995) Biochemistry , vol.34 , pp. 4186-4192
    • Nguyen, J.1    Baldwin, M.A.2    Cohen, F.E.3    Prusiner, S.B.4
  • 31
    • 0025297936 scopus 로고
    • The maturation-dependent conformational change of the major capsid protein of bacteriophage T4 involves a substantial change in secondary structure
    • DOI 10.1021/bi00475a020
    • Steven AC, Greenstone H, Bauer AC, Williams RW. The maturation-dependent conformational change of the major capsid protein of bacteriophage T4 involves a substantial change in secondary structure. Biochemistry 1990;29:5556-5561. (Pubitemid 20202281)
    • (1990) Biochemistry , vol.29 , Issue.23 , pp. 5556-5561
    • Steven, A.C.1    Greenstone, H.2    Bauer, A.C.3    Williams, R.W.4
  • 32
    • 0025779596 scopus 로고
    • A conformational switch is associated with receptor affinity in peptides derived from the CD4-binding domain of gpl.20 from HIV i
    • Reed J, Kinzel V. A conformational switch is associated with receptor affinity in peptides derived from the CD4-binding domain of gpl.20 from HIV I. Biochemistry 1991;30:4521-4528.
    • (1991) Biochemistry , vol.30 , pp. 4521-4528
    • Reed, J.1    Kinzel, V.2
  • 33
    • 0027253445 scopus 로고
    • A spring-loaded mechanism for the conformational change of influenza hemagglutinin
    • DOI 10.1016/0092-8674(93)90260-W
    • Carr CM, Kim PS. A spring-loaded mechanism for the conformational change of influenza hemagglutinin. Cell 1993;73:823-832. (Pubitemid 23159019)
    • (1993) Cell , vol.73 , Issue.4 , pp. 823-832
    • Carr, C.M.1    Kim, P.S.2
  • 34
    • 14844355848 scopus 로고    scopus 로고
    • The essential role of the flexible termini in the temperature- Responsiveness of the oligomeric state and chaperone-like activity for the polydisperse small heat shock protein IbpB from Escherichia coli
    • DOI 10.1016/j.jmb.2005.01.029
    • Jiao W, Qian M, Li P, Zhao L, Chang Z. The essential role of the flexible termini in the temperature-responsiveness of the oligomeric state and chaperone-like activity for the polydisperse small heat shock protein IbpB from Escherichia coli. J Mol Biol 2005;347:871-884. (Pubitemid 40357925)
    • (2005) Journal of Molecular Biology , vol.347 , Issue.4 , pp. 871-884
    • Jiao, W.1    Qian, M.2    Li, P.3    Zhao, L.4    Chang, Z.5
  • 35
    • 0028074902 scopus 로고
    • FT-IR and near-infared FT-Raman studies of the secondary structure of insulinotropin in the solid state: α-helix to β-sheet conversion induced by phenol and/or by high shear force
    • DOI 10.1002/jps.2600830819
    • Kim Y, Rose CA, Liu Y, Ozaki Y, Datta G, Tu AT. FT-IR and nearinfrared FT-Raman studies of the secondary structure of insulinotropin. in the solid state: alpha-helix to beta-sheet conversion induced by phenol and/or by high shear force. J Pharm. Sci 1994;83: 1175-1180. (Pubitemid 24247357)
    • (1994) Journal of Pharmaceutical Sciences , vol.83 , Issue.8 , pp. 1175-1180
    • Kim, Y.1    Rose, C.A.2    Liu, Y.3    Ozaki, Y.4    Datta, G.5    Tu, A.T.6
  • 39
    • 34548418045 scopus 로고    scopus 로고
    • Between order and disorder in protein structures: Analysis of dual personality fragments in proteins
    • Zhang Y, Stec B, Godzik A. Between order and disorder in protein structures: analysis of " dual personality" fragments in proteins. Structure 2007;15:1141-1147.
    • (2007) Structure , vol.15 , pp. 1141-1147
    • Zhang, Y.1    Stec, B.2    Godzik, A.3
  • 43
    • 3242887525 scopus 로고    scopus 로고
    • STRIDE: A web server for secondary structure assignment from known atomic coordinates of proteins
    • Heinig M, Frishman D. STRIDE: a web server for secondary structure assignment from known atomic coordinates of proteins. Nuci Acids Res 2004;32:W500-W502.
    • (2004) Nuci Acids Res , vol.32
    • Heinig, M.1    Frishman, D.2
  • 44
    • 0032169688 scopus 로고    scopus 로고
    • PQS: A protein quaternary structure file server
    • Henrick K, Thornton JM. PQS: a protein quaternary structure file server. Trends Biochem Sci 1998;23:358-361.
    • (1998) Trends Biochem Sci , vol.23 , pp. 358-361
    • Henrick, K.1    Thornton, J.M.2
  • 48
    • 47049099111 scopus 로고    scopus 로고
    • Ontologizer 2.0-a multifunctional tool for GO term enrichment analysis and data exploration
    • Bauer S, Grossmann S, Vingron M, Robinson PN. Ontologizer 2.0-a multifunctional tool for GO term enrichment analysis and data exploration. Bioinformatics 2008:24:1650-1651.
    • (2008) Bioinformatics , vol.24 , pp. 1650-1651
    • Bauer, S.1    Grossmann, S.2    Vingron, M.3    Robinson, P.N.4
  • 49
    • 3242891318 scopus 로고    scopus 로고
    • The DISOPRED server for the prediction of protein disorder
    • Oxford University Press
    • Ward JJ, Meguffin LJ, Bryson K, Buxton BF, Jones DT. The DISOPRED server for the prediction of protein disorder. Bioinformatics. Vol.20. Oxford University Press; 2004. pp 2138-2139.
    • (2004) Bioinformatics. Vol. , vol.20 , pp. 2138-2139
    • Ward, J.J.1    Meguffin, L.J.2    Bryson, K.3    Buxton, B.F.4    Jones, D.T.5
  • 51
    • 0001142723 scopus 로고
    • The Helix a Hydrogen bonded configuration of the polypeptide chain
    • Low BW, Baybutt RB. The Helix a hydrogen bonded configuration of the polypeptide chain. J Am. Chem Soc 1952;74:5806-5807.
    • (1952) J Am. Chem Soc , vol.74 , pp. 5806-5807
    • Low, B.W.1    Baybutt, R.B.2
  • 52
    • 0029658119 scopus 로고    scopus 로고
    • Models for die 310-helix/coil, Ir-helix/coil, and in isolated peptides
    • Rohl CA, Doig J. Models for die 310-helix/coil, Ir-helix/coil, and in isolated peptides. Protein Sci 1996;5:1687-1696.
    • (1996) Protein Sci , vol.5 , pp. 1687-1696
    • Rohl, C.A.1    Doig, J.2
  • 53
    • 0029865623 scopus 로고    scopus 로고
    • Context-dependent secondary structure formation of a designed protein sequence
    • Minor DL, Kim PS. Context-dependent secondary structure formation of a designed protein sequence. Nature 1996;380:730-734.
    • (1996) Nature , vol.380 , pp. 730-734
    • Minor, D.L.1    Kim, P.S.2
  • 54
    • 34247223063 scopus 로고    scopus 로고
    • Analysis of chameleon sequences and their implications in biological processes
    • Guo JT, Jaromczyk JW, Xu Y. Analysis of chameleon sequences and their implications in biological processes. Proteins 2007;67:548-558.
    • (2007) Proteins , vol.67 , pp. 548-558
    • Guo, J.T.1    Jaromczyk, J.W.2    Xu, Y.3
  • 55
    • 33749681874 scopus 로고    scopus 로고
    • Analysis of chameleon sequences by energy decomposition on a pairwise per-residue basis
    • Yoon S, Jung H. Analysis of chameleon sequences by energy decomposition on a pairwise per-residue basis. Protein J 2006;25:361-368.
    • (2006) Protein J , vol.25 , pp. 361-368
    • Yoon, S.1    Jung, H.2
  • 56
    • 0031871068 scopus 로고    scopus 로고
    • Chameleon sequences in the PDB
    • Mezei M. Chameleon sequences in the PDB. Protein Eng 1998;11: 411-414.
    • (1998) Protein Eng , vol.11 , pp. 411-414
    • Mezei, M.1
  • 57
    • 41149134509 scopus 로고    scopus 로고
    • Sequence-similar, structure-dissimilar protein pairs in the PDB
    • Kosloff M, Kolodny R. Sequence-similar, structure-dissimilar protein pairs in the PDB. Proteins 2008;71:891-902.
    • (2008) Proteins , vol.71 , pp. 891-902
    • Kosloff, M.1    Kolodny, R.2
  • 59
    • 0036803243 scopus 로고    scopus 로고
    • Intrinsically unstructured proteins
    • Tompa P. Intrinsically unstructured proteins. Trends Biochem Sci 2002;27:527-533.
    • (2002) Trends Biochem Sci , vol.27 , pp. 527-533
    • Tompa, P.1
  • 62
    • 84885949386 scopus 로고    scopus 로고
    • Improved disorder prediction by combination of orthogonal approaches
    • e4433. Epub 2009 Feb 11.
    • Schlessinger A, Punta M, Yachdav G, Kajan L, Rost B. Improved disorder prediction by combination of orthogonal approaches. PLoS ONE 2009;4:e4433. Epub 2009 Feb 11. pp 1-1.0.
    • (2009) PLoS ONE , vol.4 , pp. 1-10
    • Schlessinger, A.1    Punta, M.2    Yachdav, G.3    Kajan, L.4    Rost, B.5
  • 63
    • 34547599318 scopus 로고    scopus 로고
    • Natively unstructured loops differ from other loops
    • el40.
    • Schlessinger A, Liu J, Rost B. Natively unstructured loops differ from other loops. PLoS Comput Biol 2007;3:el40. pp 1335-1346.
    • (2007) PLoS Comput Biol , vol.3 , pp. 1335-1346
    • Schlessinger, A.1    Liu, J.2    Rost, B.3


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