메뉴 건너뛰기




Volumn 8, Issue 10, 2013, Pages

β-Propeller Blades as Ancestral Peptides in Protein Evolution

Author keywords

[No Author keywords available]

Indexed keywords

BETA PINWHEEL; BETA PROPELLER BLADE; LUMINAL DOMAIN OF INOSITOL REQUIRING ENZYME 1; PEPTIDE DERIVATIVE; PROTEIN IRE1; TYPE II BETA PRISM; UNCLASSIFIED DRUG; WW DOMAIN PROTEIN;

EID: 84885439160     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0077074     Document Type: Article
Times cited : (68)

References (60)
  • 1
    • 0035783063 scopus 로고    scopus 로고
    • Fold change in evolution of protein structures
    • Grishin NV, (2001) Fold change in evolution of protein structures. J Struct Biol 134: 167-185.
    • (2001) J Struct Biol , vol.134 , pp. 167-185
    • Grishin, N.V.1
  • 2
    • 33744783371 scopus 로고    scopus 로고
    • Evolution of protein fold in the presence of functional constraints
    • Andreeva A, Murzin AG, (2006) Evolution of protein fold in the presence of functional constraints. Curr Opin Struct Biol 16: 399-408.
    • (2006) Curr Opin Struct Biol , vol.16 , pp. 399-408
    • Andreeva, A.1    Murzin, A.G.2
  • 3
    • 33846074754 scopus 로고    scopus 로고
    • SISYPHUS-structural alignments for proteins with non-trivial relationships
    • Andreeva A, Prlic A, Hubbard TJ, Murzin AG, (2007) SISYPHUS-structural alignments for proteins with non-trivial relationships. Nucleic Acids Res 35: D253-259.
    • (2007) Nucleic Acids Res , vol.35
    • Andreeva, A.1    Prlic, A.2    Hubbard, T.J.3    Murzin, A.G.4
  • 4
    • 44949143819 scopus 로고    scopus 로고
    • Cradle-loop barrels and the concept of metafolds in protein classification by natural descent
    • Alva V, Koretke KK, Coles M, Lupas AN, (2008) Cradle-loop barrels and the concept of metafolds in protein classification by natural descent. Curr Opin Struct Biol 18: 358-365.
    • (2008) Curr Opin Struct Biol , vol.18 , pp. 358-365
    • Alva, V.1    Koretke, K.K.2    Coles, M.3    Lupas, A.N.4
  • 6
    • 0035253621 scopus 로고    scopus 로고
    • KH domain: one motif, two folds
    • Grishin NV, (2001) KH domain: one motif, two folds. Nucleic Acids Res 29: 638-643.
    • (2001) Nucleic Acids Res , vol.29 , pp. 638-643
    • Grishin, N.V.1
  • 7
    • 0035106757 scopus 로고    scopus 로고
    • Sialidase-like Asp-boxes: sequence-similar structures within different protein folds
    • Copley RR, Russell RB, Ponting CP, (2001) Sialidase-like Asp-boxes: sequence-similar structures within different protein folds. Protein Sci 10: 285-292.
    • (2001) Protein Sci , vol.10 , pp. 285-292
    • Copley, R.R.1    Russell, R.B.2    Ponting, C.P.3
  • 8
    • 33749262632 scopus 로고    scopus 로고
    • Common evolutionary origin of swapped-hairpin and double-psi beta barrels
    • Coles M, Hulko M, Djuranovic S, Truffault V, Koretke K, et al. (2006) Common evolutionary origin of swapped-hairpin and double-psi beta barrels. Structure 14: 1489-1498.
    • (2006) Structure , vol.14 , pp. 1489-1498
    • Coles, M.1    Hulko, M.2    Djuranovic, S.3    Truffault, V.4    Koretke, K.5
  • 9
    • 0041317258 scopus 로고    scopus 로고
    • More than the sum of their parts: on the evolution of proteins from peptides
    • Soding J, Lupas AN, (2003) More than the sum of their parts: on the evolution of proteins from peptides. Bioessays 25: 837-846.
    • (2003) Bioessays , vol.25 , pp. 837-846
    • Soding, J.1    Lupas, A.N.2
  • 11
    • 0031626899 scopus 로고    scopus 로고
    • Function driven protein evolution. A possible proto-protein for the RNA-binding proteins
    • Fetrow JS, Godzik A (1998) Function driven protein evolution. A possible proto-protein for the RNA-binding proteins. Pac Symp Biocomput: 485-496.
    • (1998) Pac Symp Biocomput , pp. 485-496
    • Fetrow, J.S.1    Godzik, A.2
  • 12
    • 0035783055 scopus 로고    scopus 로고
    • On the evolution of protein folds: are similar motifs in different protein folds the result of convergence, insertion, or relics of an ancient peptide world?
    • Lupas AN, Ponting CP, Russell RB, (2001) On the evolution of protein folds: are similar motifs in different protein folds the result of convergence, insertion, or relics of an ancient peptide world? J Struct Biol 134: 191-203.
    • (2001) J Struct Biol , vol.134 , pp. 191-203
    • Lupas, A.N.1    Ponting, C.P.2    Russell, R.B.3
  • 13
    • 3042709433 scopus 로고    scopus 로고
    • Prebiotic chemistry and the origin of the RNA world
    • Orgel LE, (2004) Prebiotic chemistry and the origin of the RNA world. Crit Rev Biochem Mol Biol 39: 99-123.
    • (2004) Crit Rev Biochem Mol Biol , vol.39 , pp. 99-123
    • Orgel, L.E.1
  • 14
    • 77952793285 scopus 로고    scopus 로고
    • Evolution of outer membrane beta-barrels from an ancestral beta beta hairpin
    • Remmert M, Biegert A, Linke D, Lupas AN, Soding J, (2010) Evolution of outer membrane beta-barrels from an ancestral beta beta hairpin. Mol Biol Evol 27: 1348-1358.
    • (2010) Mol Biol Evol , vol.27 , pp. 1348-1358
    • Remmert, M.1    Biegert, A.2    Linke, D.3    Lupas, A.N.4    Soding, J.5
  • 15
    • 41149106300 scopus 로고    scopus 로고
    • Evolution of the beta-propeller fold
    • Chaudhuri I, Soding J, Lupas AN, (2008) Evolution of the beta-propeller fold. Proteins 71: 795-803.
    • (2008) Proteins , vol.71 , pp. 795-803
    • Chaudhuri, I.1    Soding, J.2    Lupas, A.N.3
  • 16
    • 16344373015 scopus 로고    scopus 로고
    • Protein homology detection by HMM-HMM comparison
    • Soding J, (2005) Protein homology detection by HMM-HMM comparison. Bioinformatics 21: 951-960.
    • (2005) Bioinformatics , vol.21 , pp. 951-960
    • Soding, J.1
  • 17
    • 23144452044 scopus 로고    scopus 로고
    • The HHpred interactive server for protein homology detection and structure prediction
    • Soding J, Biegert A, Lupas AN, (2005) The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res 33: W244-248.
    • (2005) Nucleic Acids Res , vol.33
    • Soding, J.1    Biegert, A.2    Lupas, A.N.3
  • 18
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    • Altschul SF, Madden TL, Schaffer 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    Schaffer, A.A.3    Zhang, J.4    Zhang, Z.5
  • 19
    • 10044222704 scopus 로고    scopus 로고
    • CLANS: a Java application for visualizing protein families based on pairwise similarity
    • Frickey T, Lupas A, (2004) CLANS: a Java application for visualizing protein families based on pairwise similarity. Bioinformatics 20: 3702-3704.
    • (2004) Bioinformatics , vol.20 , pp. 3702-3704
    • Frickey, T.1    Lupas, A.2
  • 22
    • 17644392830 scopus 로고    scopus 로고
    • TM-align: a protein structure alignment algorithm based on the TM-score
    • Zhang Y, Skolnick J, (2005) TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res 33: 2302-2309.
    • (2005) Nucleic Acids Res , vol.33 , pp. 2302-2309
    • Zhang, Y.1    Skolnick, J.2
  • 23
    • 77951961719 scopus 로고    scopus 로고
    • How significant is a protein structure similarity with TM-score = 0.5?
    • Xu J, Zhang Y, (2010) How significant is a protein structure similarity with TM-score = 0.5? Bioinformatics 26: 889-895.
    • (2010) Bioinformatics , vol.26 , pp. 889-895
    • Xu, J.1    Zhang, Y.2
  • 24
    • 10344232638 scopus 로고    scopus 로고
    • Scoring function for automated assessment of protein structure template quality
    • Zhang Y, Skolnick J, (2004) Scoring function for automated assessment of protein structure template quality. Proteins 57: 702-710.
    • (2004) Proteins , vol.57 , pp. 702-710
    • Zhang, Y.1    Skolnick, J.2
  • 26
    • 0029643953 scopus 로고
    • The refined structure of the quinoprotein methanol dehydrogenase from Methylobacterium extorquens at 1.94 A
    • Ghosh M, Anthony C, Harlos K, Goodwin MG, Blake C, (1995) The refined structure of the quinoprotein methanol dehydrogenase from Methylobacterium extorquens at 1.94 A. Structure. 3: 177-187.
    • (1995) Structure , vol.3 , pp. 177-187
    • Ghosh, M.1    Anthony, C.2    Harlos, K.3    Goodwin, M.G.4    Blake, C.5
  • 27
    • 0032514995 scopus 로고    scopus 로고
    • Atomic structure of clathrin: a beta propeller terminal domain joins an alpha zigzag linker
    • ter Haar E, Musacchio A, Harrison SC, Kirchhausen T, (1998) Atomic structure of clathrin: a beta propeller terminal domain joins an alpha zigzag linker. Cell 95: 563-573.
    • (1998) Cell , vol.95 , pp. 563-573
    • ter Haar, E.1    Musacchio, A.2    Harrison, S.C.3    Kirchhausen, T.4
  • 29
    • 34250899722 scopus 로고    scopus 로고
    • Signal integration in the endoplasmic reticulum unfolded protein response
    • Ron D, Walter P, (2007) Signal integration in the endoplasmic reticulum unfolded protein response. Nat Rev Mol Cell Biol 8: 519-529.
    • (2007) Nat Rev Mol Cell Biol , vol.8 , pp. 519-529
    • Ron, D.1    Walter, P.2
  • 30
    • 0034667598 scopus 로고    scopus 로고
    • Proteins of the endoplasmic-reticulum-associated degradation pathway: domain detection and function prediction
    • Ponting CP, (2000) Proteins of the endoplasmic-reticulum-associated degradation pathway: domain detection and function prediction. Biochem J 351 Pt 2: 527-535.
    • (2000) Biochem J 351 Pt , vol.2 , pp. 527-535
    • Ponting, C.P.1
  • 32
    • 33749233991 scopus 로고    scopus 로고
    • The crystal structure of human IRE1 luminal domain reveals a conserved dimerization interface required for activation of the unfolded protein response
    • Zhou J, Liu CY, Back SH, Clark RL, Peisach D, et al. (2006) The crystal structure of human IRE1 luminal domain reveals a conserved dimerization interface required for activation of the unfolded protein response. Proc Natl Acad Sci U S A 103: 14343-14348.
    • (2006) Proc Natl Acad Sci U S A , vol.103 , pp. 14343-14348
    • Zhou, J.1    Liu, C.Y.2    Back, S.H.3    Clark, R.L.4    Peisach, D.5
  • 33
    • 40749144066 scopus 로고    scopus 로고
    • De novo identification of highly diverged protein repeats by probabilistic consistency
    • Biegert A, Soding J, (2008) De novo identification of highly diverged protein repeats by probabilistic consistency. Bioinformatics 24: 807-814.
    • (2008) Bioinformatics , vol.24 , pp. 807-814
    • Biegert, A.1    Soding, J.2
  • 34
    • 0029008975 scopus 로고
    • Structure of mannose-specific snowdrop (Galanthus nivalis) lectin is representative of a new plant lectin family
    • Hester G, Kaku H, Goldstein IJ, Wright CS, (1995) Structure of mannose-specific snowdrop (Galanthus nivalis) lectin is representative of a new plant lectin family. Nat Struct Biol 2: 472-479.
    • (1995) Nat Struct Biol , vol.2 , pp. 472-479
    • Hester, G.1    Kaku, H.2    Goldstein, I.J.3    Wright, C.S.4
  • 35
    • 0033593246 scopus 로고    scopus 로고
    • Crystal structure of a dimeric mannose-specific agglutinin from garlic: quaternary association and carbohydrate specificity
    • Chandra NR, Ramachandraiah G, Bachhawat K, Dam TK, Surolia A, et al. (1999) Crystal structure of a dimeric mannose-specific agglutinin from garlic: quaternary association and carbohydrate specificity. J Mol Biol 285: 1157-1168.
    • (1999) J Mol Biol , vol.285 , pp. 1157-1168
    • Chandra, N.R.1    Ramachandraiah, G.2    Bachhawat, K.3    Dam, T.K.4    Surolia, A.5
  • 36
    • 0034214439 scopus 로고    scopus 로고
    • Sequence and structural determinants of mannose recognition
    • Ramachandraiah G, Chandra NR, (2000) Sequence and structural determinants of mannose recognition. Proteins 39: 358-364.
    • (2000) Proteins , vol.39 , pp. 358-364
    • Ramachandraiah, G.1    Chandra, N.R.2
  • 38
    • 32144434430 scopus 로고    scopus 로고
    • Lectins as bioactive plant proteins: a potential in cancer treatment
    • De Mejia EG, Prisecaru VI, (2005) Lectins as bioactive plant proteins: a potential in cancer treatment. Crit Rev Food Sci Nutr 45: 425-445.
    • (2005) Crit Rev Food Sci Nutr , vol.45 , pp. 425-445
    • De Mejia, E.G.1    Prisecaru, V.I.2
  • 39
    • 58149463890 scopus 로고    scopus 로고
    • Impact of snowdrop lectin (Galanthus nivalis agglutinin; GNA) on adults of the green lacewing, Chrysoperla carnea
    • Li Y, Romeis J, (2009) Impact of snowdrop lectin (Galanthus nivalis agglutinin; GNA) on adults of the green lacewing, Chrysoperla carnea. J Insect Physiol 55: 135-142.
    • (2009) J Insect Physiol , vol.55 , pp. 135-142
    • Li, Y.1    Romeis, J.2
  • 40
    • 79751524978 scopus 로고    scopus 로고
    • Differences in the mannose oligomer specificities of the closely related lectins from Galanthus nivalis and Zea mays strongly determine their eventual anti-HIV activity
    • Hoorelbeke B, Van Damme EJ, Rouge P, Schols D, Van Laethem K, et al. (2011) Differences in the mannose oligomer specificities of the closely related lectins from Galanthus nivalis and Zea mays strongly determine their eventual anti-HIV activity. Retrovirology 8: 10.
    • (2011) Retrovirology , vol.8 , pp. 10
    • Hoorelbeke, B.1    Van Damme, E.J.2    Rouge, P.3    Schols, D.4    Van Laethem, K.5
  • 41
    • 36348956861 scopus 로고    scopus 로고
    • Curculin exhibits sweet-tasting and taste-modifying activities through its distinct molecular surfaces
    • Kurimoto E, Suzuki M, Amemiya E, Yamaguchi Y, Nirasawa S, et al. (2007) Curculin exhibits sweet-tasting and taste-modifying activities through its distinct molecular surfaces. J Biol Chem 282: 33252-33256.
    • (2007) J Biol Chem , vol.282 , pp. 33252-33256
    • Kurimoto, E.1    Suzuki, M.2    Amemiya, E.3    Yamaguchi, Y.4    Nirasawa, S.5
  • 42
    • 35348914415 scopus 로고    scopus 로고
    • Multiplicity of carbohydrate-binding sites in beta-prism fold lectins: occurrence and possible evolutionary implications
    • Sharma A, Chandran D, Singh DD, Vijayan M, (2007) Multiplicity of carbohydrate-binding sites in beta-prism fold lectins: occurrence and possible evolutionary implications. J Biosci 32: 1089-1110.
    • (2007) J Biosci , vol.32 , pp. 1089-1110
    • Sharma, A.1    Chandran, D.2    Singh, D.D.3    Vijayan, M.4
  • 43
    • 17644408452 scopus 로고    scopus 로고
    • Structural mechanism governing the quaternary organization of monocot mannose-binding lectin revealed by the novel monomeric structure of an orchid lectin
    • Liu W, Yang N, Ding J, Huang RH, Hu Z, et al. (2005) Structural mechanism governing the quaternary organization of monocot mannose-binding lectin revealed by the novel monomeric structure of an orchid lectin. J Biol Chem 280: 14865-14876.
    • (2005) J Biol Chem , vol.280 , pp. 14865-14876
    • Liu, W.1    Yang, N.2    Ding, J.3    Huang, R.H.4    Hu, Z.5
  • 44
    • 50649101663 scopus 로고    scopus 로고
    • DNA topoisomerases: harnessing and constraining energy to govern chromosome topology
    • Schoeffler AJ, Berger JM, (2008) DNA topoisomerases: harnessing and constraining energy to govern chromosome topology. Q Rev Biophys 41: 41-101.
    • (2008) Q Rev Biophys , vol.41 , pp. 41-101
    • Schoeffler, A.J.1    Berger, J.M.2
  • 45
    • 33645652225 scopus 로고    scopus 로고
    • The "GyrA-box" is required for the ability of DNA gyrase to wrap DNA and catalyze the supercoiling reaction
    • Kramlinger VM, Hiasa H, (2006) The "GyrA-box" is required for the ability of DNA gyrase to wrap DNA and catalyze the supercoiling reaction. J Biol Chem 281: 3738-3742.
    • (2006) J Biol Chem , vol.281 , pp. 3738-3742
    • Kramlinger, V.M.1    Hiasa, H.2
  • 46
    • 0029955899 scopus 로고    scopus 로고
    • Conversion of DNA gyrase into a conventional type II topoisomerase
    • Kampranis SC, Maxwell A, (1996) Conversion of DNA gyrase into a conventional type II topoisomerase. Proc Natl Acad Sci U S A 93: 14416-14421.
    • (1996) Proc Natl Acad Sci U S A , vol.93 , pp. 14416-14421
    • Kampranis, S.C.1    Maxwell, A.2
  • 47
    • 11244308067 scopus 로고    scopus 로고
    • Structure of the topoisomerase IV C-terminal domain: a broken beta-propeller implies a role as geometry facilitator in catalysis
    • Hsieh TJ, Farh L, Huang WM, Chan NL, (2004) Structure of the topoisomerase IV C-terminal domain: a broken beta-propeller implies a role as geometry facilitator in catalysis. J Biol Chem 279: 55587-55593.
    • (2004) J Biol Chem , vol.279 , pp. 55587-55593
    • Hsieh, T.J.1    Farh, L.2    Huang, W.M.3    Chan, N.L.4
  • 48
    • 22544467771 scopus 로고    scopus 로고
    • The structural basis for substrate specificity in DNA topoisomerase IV
    • Corbett KD, Schoeffler AJ, Thomsen ND, Berger JM, (2005) The structural basis for substrate specificity in DNA topoisomerase IV. J Mol Biol 351: 545-561.
    • (2005) J Mol Biol , vol.351 , pp. 545-561
    • Corbett, K.D.1    Schoeffler, A.J.2    Thomsen, N.D.3    Berger, J.M.4
  • 49
    • 77954288774 scopus 로고    scopus 로고
    • Dali server: conservation mapping in 3D
    • Holm L, Rosenstrom P, (2010) Dali server: conservation mapping in 3D. Nucleic Acids Res 38: W545-549.
    • (2010) Nucleic Acids Res , vol.38
    • Holm, L.1    Rosenstrom, P.2
  • 50
    • 0037093648 scopus 로고    scopus 로고
    • C-terminal domain of gyrase A is predicted to have a beta-propeller structure
    • Qi Y, Pei J, Grishin NV, (2002) C-terminal domain of gyrase A is predicted to have a beta-propeller structure. Proteins 47: 258-264.
    • (2002) Proteins , vol.47 , pp. 258-264
    • Qi, Y.1    Pei, J.2    Grishin, N.V.3
  • 51
    • 37849008677 scopus 로고    scopus 로고
    • RCC1-like repeat proteins: a pangenomic, structurally diverse new superfamily of beta-propeller domains
    • Stevens TJ, Paoli M, (2008) RCC1-like repeat proteins: a pangenomic, structurally diverse new superfamily of beta-propeller domains. Proteins 70: 378-387.
    • (2008) Proteins , vol.70 , pp. 378-387
    • Stevens, T.J.1    Paoli, M.2
  • 52
    • 2442611949 scopus 로고    scopus 로고
    • The C-terminal domain of DNA gyrase A adopts a DNA-bending beta-pinwheel fold
    • Corbett KD, Shultzaberger RK, Berger JM, (2004) The C-terminal domain of DNA gyrase A adopts a DNA-bending beta-pinwheel fold. Proc Natl Acad Sci U S A 101: 7293-7298.
    • (2004) Proc Natl Acad Sci U S A , vol.101 , pp. 7293-7298
    • Corbett, K.D.1    Shultzaberger, R.K.2    Berger, J.M.3
  • 53
    • 0027988814 scopus 로고
    • The WW domain: a signalling site in dystrophin?
    • Bork P, Sudol M, (1994) The WW domain: a signalling site in dystrophin? Trends Biochem Sci 19: 531-533.
    • (1994) Trends Biochem Sci , vol.19 , pp. 531-533
    • Bork, P.1    Sudol, M.2
  • 55
    • 0028831959 scopus 로고
    • The rsp5-domain is shared by proteins of diverse functions
    • Hofmann K, Bucher P, (1995) The rsp5-domain is shared by proteins of diverse functions. FEBS Lett 358: 153-157.
    • (1995) FEBS Lett , vol.358 , pp. 153-157
    • Hofmann, K.1    Bucher, P.2
  • 56
    • 79955101793 scopus 로고    scopus 로고
    • Structural features and ligand binding properties of tandem WW domains from YAP and TAZ, nuclear effectors of the Hippo pathway
    • Webb C, Upadhyay A, Giuntini F, Eggleston I, Furutani-Seiki M, et al. (2011) Structural features and ligand binding properties of tandem WW domains from YAP and TAZ, nuclear effectors of the Hippo pathway. Biochemistry 50: 3300-3309.
    • (2011) Biochemistry , vol.50 , pp. 3300-3309
    • Webb, C.1    Upadhyay, A.2    Giuntini, F.3    Eggleston, I.4    Furutani-Seiki, M.5
  • 57
    • 0014800108 scopus 로고
    • Distinguishing homologous from analogous proteins
    • Fitch WM, (1970) Distinguishing homologous from analogous proteins. Syst Zool 19: 99-113.
    • (1970) Syst Zool , vol.19 , pp. 99-113
    • Fitch, W.M.1
  • 58
    • 0031566432 scopus 로고    scopus 로고
    • Recognition of analogous and homologous protein folds: analysis of sequence and structure conservation
    • Russell RB, Saqi MA, Sayle RA, Bates PA, Sternberg MJ, (1997) Recognition of analogous and homologous protein folds: analysis of sequence and structure conservation. J Mol Biol 269: 423-439.
    • (1997) J Mol Biol , vol.269 , pp. 423-439
    • Russell, R.B.1    Saqi, M.A.2    Sayle, R.A.3    Bates, P.A.4    Sternberg, M.J.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.