메뉴 건너뛰기




Volumn 3, Issue 5, 2010, Pages 155-172

Prediction and comparative analysis of MHC binding peptides and epitopes in Nanoviridae nano-organisms

Author keywords

Antidotes; Antigenicity; Epitopes; MHC binders; Nanoviridae family

Indexed keywords

ANIMALIA; BABUVIRUS; BANANA BUNCHY TOP VIRUS; DNA VIRUSES; MILK VETCH DWARF VIRUS; MUSA TEXTILIS; NANOVIRIDAE; NANOVIRUS; SUBTERRANEAN CLOVER STUNT VIRUS; VICIA FABA;

EID: 77952874780     PISSN: None     EISSN: 0974276X     Source Type: Journal    
DOI: 10.4172/jpb.1000135     Document Type: Article
Times cited : (2)

References (53)
  • 1
    • 0000104080 scopus 로고
    • An empirical hydrophobicity scale for alpha-amino-acids and some of its applications
    • Aboderin AA (1971) An empirical hydrophobicity scale for alpha-amino-acids and some of its applications. Int J Biochem 2: 537-544.
    • (1971) Int J Biochem , vol.2 , pp. 537-544
    • Aboderin, A.A.1
  • 2
    • 0023465103 scopus 로고
    • Extension of the fragment method to calculate amino acid zwitterions and side chain partition coefficients
    • Abraham DJ, Leo AJ (1987) Extension of the fragment method to calculate amino acid zwitterions and side chain partition coefficients. Proteins 2: 130-152.
    • (1987) Proteins , vol.2 , pp. 130-152
    • Abraham, D.J.1    Leo, A.J.2
  • 4
    • 23144433033 scopus 로고    scopus 로고
    • Pcleavage: An SVM based method for prediction of constitutive proteasome and immunoproteasome cleavage sites in antigenic sequences
    • Bhasin M, Raghava GP (2005) Pcleavage: an SVM based method for prediction of constitutive proteasome and immunoproteasome cleavage sites in antigenic sequences. Nucleic Acids Res 33: W202-207.
    • (2005) Nucleic Acids Res , vol.33
    • Bhasin, M.1    Raghava, G.P.2
  • 5
    • 0037461027 scopus 로고    scopus 로고
    • MHCBN: A comprehensive database of MHC binding and non-binding peptides
    • Bhasin M, Singh H, Raghava GPS (2003) MHCBN: a comprehensive database of MHC binding and non-binding peptides. Bioinformatics 19: 665-666.
    • (2003) Bioinformatics , vol.19 , pp. 665-666
    • Bhasin, M.1    Singh, H.2    Raghava, G.P.S.3
  • 6
    • 0031825709 scopus 로고    scopus 로고
    • Prediction of MHC class II-binding peptides using an evolutionary algorithm and artificial neural network
    • Brusic V, Rudy G, Honeyman G, Hammer J, Harrison L (1998) Prediction of MHC class II-binding peptides using an evolutionary algorithm and artificial neural network. Bioinformatics 14: 121-130.
    • (1998) Bioinformatics , vol.14 , pp. 121-130
    • Brusic, V.1    Rudy, G.2    Honeyman, G.3    Hammer, J.4    Harrison, L.5
  • 7
    • 0016192651 scopus 로고
    • Surface tension of amino acid solutions: A hydrophobicity scale of the amino acid residues
    • Bull HB, Breese K (1974) Surface tension of amino acid solutions: A hydrophobicity scale of the amino acid residues. Arch Biochem Biophys 161: 665-670.
    • (1974) Arch Biochem Biophys , vol.161 , pp. 665-670
    • Bull, H.B.1    Breese, K.2
  • 8
    • 0017187836 scopus 로고
    • The nature of accessible and buried surfaces in proteins
    • Chothia C (1976) The nature of accessible and buried surfaces in proteins. J Mol Biol 105: 1-12.
    • (1976) J Mol Biol , vol.105 , pp. 1-12
    • Chothia, C.1
  • 9
    • 0025388957 scopus 로고
    • Hydrophobicity indices at ph 3.4 determined by HPLC
    • Cowan R, Whittaker RG (1990) Hydrophobicity indices at ph 3.4 determined by HPLC. Pept Res 3: 75-80.
    • (1990) Pept Res , vol.3 , pp. 75-80
    • Cowan, R.1    Whittaker, R.G.2
  • 10
    • 0023079507 scopus 로고
    • Banana bunchy top: An economically important tropical plant virus disease
    • Dale JL (1987) Banana bunchy top: An economically important tropical plant virus disease. Adv. Virus Res 33: 301-325.
    • (1987) Adv. Virus Res , vol.33 , pp. 301-325
    • Dale, J.L.1
  • 11
    • 0021691817 scopus 로고
    • Analysis of membrane and surface protein sequences with the hydrophobic moment plot
    • Eisenberg D, Schwarz E, Komaromy M, Wall R (1984a) Analysis of membrane and surface protein sequences with the hydrophobic moment plot. J Mol Biol 179: 125-142.
    • (1984) J Mol Biol , vol.179 , pp. 125-142
    • Eisenberg, D.1    Schwarz, E.2    Komaromy, M.3    Wall, R.4
  • 12
    • 0000929505 scopus 로고
    • The hydrophobic moment detects periodicity in protein hydrophobicity
    • Eisenberg D, Weiss RM, Terwilliger TC (1984b) The hydrophobic moment detects periodicity in protein hydrophobicity. Proc Natl Acad Sci USA 81: 140-144.
    • (1984) Proc Natl Acad Sci USA , vol.81 , pp. 140-144
    • Eisenberg, D.1    Weiss, R.M.2    Terwilliger, T.C.3
  • 13
    • 0022249654 scopus 로고
    • Induction of hepatitis A virusneutralizing antibody by a virus-specific synthetic peptide
    • Emani EA, Hughes JV, Perlow DS, Boger J (1985) Induction of hepatitis A virusneutralizing antibody by a virus-specific synthetic peptide. J Virol 55: 836-839.
    • (1985) J Virol , vol.55 , pp. 836-839
    • Emani, E.A.1    Hughes, J.V.2    Perlow, D.S.3    Boger, J.4
  • 15
    • 0000461280 scopus 로고
    • Confidence limits on phylogenies: An approach using the bootstrap
    • Felsenstein J (1985) Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39: 783-791.
    • (1985) Evolution , vol.39 , pp. 783-791
    • Felsenstein, J.1
  • 16
    • 0017873321 scopus 로고
    • Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins
    • Garnier J, Osguthorpe DJ, Robson B (1978) Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. J Mol Biol 120: 97-120.
    • (1978) J Mol Biol , vol.120 , pp. 97-120
    • Garnier, J.1    Osguthorpe, D.J.2    Robson, B.3
  • 17
    • 0029884694 scopus 로고    scopus 로고
    • GOR: Secondary structure prediction method version IV
    • Garnier J, Gibrat JF, Robson B (1996) GOR: secondary structure prediction method version IV. Methods Enzymol 266: 540-553.
    • (1996) Methods Enzymol , vol.266 , pp. 540-553
    • Garnier, J.1    Gibrat, J.F.2    Robson, B.3
  • 20
    • 77952852795 scopus 로고
    • An aphid-transmitted virus affecting subterranean clover
    • Grylls NE, Butler FC (1956) An aphid-transmitted virus affecting subterranean clover. J Aust Znst agric Sci 22: 73-74.
    • (1956) J Aust Znst Agric Sci , vol.22 , pp. 73-74
    • Grylls, N.E.1    Butler, F.C.2
  • 21
    • 0021977590 scopus 로고
    • Amino acid side chain partition energies and distributions of residues in soluble proteins
    • Guy HR (1985) Amino acid side chain partition energies and distributions of residues in soluble proteins. Biophys J 47: 61-70.
    • (1985) Biophys J , vol.47 , pp. 61-70
    • Guy, H.R.1
  • 22
    • 1642310582 scopus 로고    scopus 로고
    • Reprogramming plant gene expression: A prerequisite to geminivirus DNA replication
    • Hanley-Bowdoin L, Settlage SB, Robertson D (2004) Reprogramming plant gene expression: a prerequisite to geminivirus DNA replication. Mol Plant Pathol 5: 149-156.
    • (2004) Mol Plant Pathol , vol.5 , pp. 149-156
    • Hanley-Bowdoin, L.1    Settlage, S.B.2    Robertson, D.3
  • 23
    • 0000448982 scopus 로고
    • Prediction of protein antigenic determinants from amino acid sequences
    • Hopp TP, Woods KR (1981) Prediction of protein antigenic determinants from amino acid sequences. Proc Natl Acad Sci USA 78: 3824-3828.
    • (1981) Proc Natl Acad Sci USA , vol.78 , pp. 3824-3828
    • Hopp, T.P.1    Woods, K.R.2
  • 24
    • 0018784438 scopus 로고
    • Surface and inside volumes in globular proteins
    • Janin J (1979) Surface and inside volumes in globular proteins. Nature 277: 491-492.
    • (1979) Nature , vol.277 , pp. 491-492
    • Janin, J.1
  • 25
    • 0021918946 scopus 로고
    • Prediction of Chain Flexibility in Proteins - A tool for the Selection of Peptide Antigens
    • Karplus PA, Schulz GE (1985) Prediction of Chain Flexibility in Proteins - A tool for the Selection of Peptide Antigens. Naturwissenschafren 72: 212-213.
    • (1985) Naturwissenschafren , vol.72 , pp. 212-213
    • Karplus, P.A.1    Schulz, G.E.2
  • 26
    • 0028861765 scopus 로고
    • Sequence-Analysis of A Faba Bean Necrotic Yellows Virus-Dna Component Containing A Putative Replicase Gene
    • Katul L, Maiss E, Vetten HJ (1995) Sequence-Analysis of A Faba Bean Necrotic Yellows Virus-Dna Component Containing A Putative Replicase Gene. J Gen Virol 76: 475-479.
    • (1995) J Gen Virol , vol.76 , pp. 475-479
    • Katul, L.1    Maiss, E.2    Vetten, H.J.3
  • 27
    • 0033562572 scopus 로고    scopus 로고
    • Application of Computer-assisted Interviews to Sexual Behavior Research
    • Kissinger P, Rice J, Farley T, Trim S, Jewitt K, et al. (1999) Application of Computer-assisted Interviews to Sexual Behavior Research. Am J Epidemiol 149: 950-954.
    • (1999) Am J Epidemiol , vol.149 , pp. 950-954
    • Kissinger, P.1    Rice, J.2    Farley, T.3    Trim, S.4    Jewitt, K.5
  • 28
    • 0027500866 scopus 로고
    • Self-peptides from four HLA-DR alleles share hydrophobic anchor residues near the NH2- terminal including proline as a stop signal for trimming
    • Kropshofer H, Max H, Halder T, Kalbus M, Muller CA, et al. (1993) Self-peptides from four HLA-DR alleles share hydrophobic anchor residues near the NH2- terminal including proline as a stop signal for trimming. J Immunol 151: 4732-4742.
    • (1993) J Immunol , vol.151 , pp. 4732-4742
    • Kropshofer, H.1    Max, H.2    Halder, T.3    Kalbus, M.4    Muller, C.A.5
  • 29
    • 0020475449 scopus 로고
    • A Simple Method for Displaying the Hydropathic Character of a Protein
    • Kyte J, Doolittle RF (1982) A Simple Method for Displaying the Hydropathic Character of a Protein. J Mol Biol 157: 105-132.
    • (1982) J Mol Biol , vol.157 , pp. 105-132
    • Kyte, J.1    Doolittle, R.F.2
  • 30
    • 34247093872 scopus 로고    scopus 로고
    • The nanovirus-encoded Clink protein affects plant cell cycle regulation through interaction with the retinoblastoma-related protein
    • Lageix S, Catrice O, Deragon JM, Gronenborn B, Pelissier T, et al. (2007) The nanovirus-encoded Clink protein affects plant cell cycle regulation through interaction with the retinoblastoma-related protein. J Virol 81: 4177-4185.
    • (2007) J Virol , vol.81 , pp. 4177-4185
    • Lageix, S.1    Catrice, O.2    Deragon, J.M.3    Gronenborn, B.4    Pelissier, T.5
  • 31
    • 75449118921 scopus 로고    scopus 로고
    • Multiple diverse circoviruses infect farm animals and are commonly found in human and chimpanzee feces
    • Li L, Kapoor A, Slikas B, Bamidele OS, Wang C, et al. (2010) Multiple diverse circoviruses infect farm animals and are commonly found in human and chimpanzee feces. J Virol 84: 1674-1682.
    • (2010) J Virol , vol.84 , pp. 1674-1682
    • Li, L.1    Kapoor, A.2    Slikas, B.3    Bamidele, O.S.4    Wang, C.5
  • 32
    • 0042622240 scopus 로고    scopus 로고
    • GlobPlot: Exploring protein sequences for globularity and disorder
    • Linding R, Russell RB, Neduva V, Gibson TJ (2003) GlobPlot: exploring protein sequences for globularity and disorder. Nucleic Acids Res 31: 3701-3708.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3701-3708
    • Linding, R.1    Russell, R.B.2    Neduva, V.3    Gibson, T.J.4
  • 33
    • 0027525106 scopus 로고
    • The antigenic identity of peptide- MHC complexes: A comparison of the conformations of five viral peptides presented by HLA-A2
    • Madden DR, Garboczi DN, Wiley DC (1993) The antigenic identity of peptide- MHC complexes: a comparison of the conformations of five viral peptides presented by HLA-A2. Cell 75: 693-708.
    • (1993) Cell , vol.75 , pp. 693-708
    • Madden, D.R.1    Garboczi, D.N.2    Wiley, D.C.3
  • 34
    • 0013668380 scopus 로고
    • Some aspects of the bunchy top disease of banana and other Musa spp
    • Magee CJP (1953) Some aspects of the bunchy top disease of banana and other Musa spp. Proc Royal Society of New South Wales 87: 3-18.
    • (1953) Proc Royal Society of New South Wales , vol.87 , pp. 3-18
    • Magee, C.J.P.1
  • 35
    • 0003257588 scopus 로고    scopus 로고
    • Epidemiology and control of faba bean necrotic yellows virus
    • A. Hadidi, R.K. Khetarpal and H. Koganezawa (eds.). APS Press, The American Phytopathological Society, St. Paul, Minnesota, USA
    • Makkouk KM, Vetten HJ, Katul L, Franz A, Madkour MA (1998) Epidemiology and control of faba bean necrotic yellows virus. In: Plant Virus Disease Control. A. Hadidi, R.K. Khetarpal and H. Koganezawa (eds.). APS Press, The American Phytopathological Society, St. Paul, Minnesota, USA pp 534-540.
    • (1998) Plant Virus Disease Control , pp. 534-540
    • Makkouk, K.M.1    Vetten, H.J.2    Katul, L.3    Franz, A.4    Madkour, M.A.5
  • 37
    • 38349128597 scopus 로고
    • Progress report on bunchy-top of abaca or manila hemp
    • Ocfemia GO (1926) Progress report on bunchy-top of abaca or manila hemp. Phytopathology 16: 894.
    • (1926) Phytopathology , vol.16 , pp. 894
    • Ocfemia, G.O.1
  • 38
    • 0007273635 scopus 로고
    • Bunchy-top of abaca or manila hemp I. A study of the cause of the disease and its method of transmission
    • Ocfemia GO (1930) Bunchy-top of abaca or manila hemp I. A study of the cause of the disease and its method of transmission. Am J Bot 17: 1-18.
    • (1930) Am J Bot , vol.17 , pp. 1-18
    • Ocfemia, G.O.1
  • 39
    • 38349189285 scopus 로고
    • Bunchy top of abaca or Manila hemp-2. Further studies on the transmission of the disease and a trial planting of abaca seedlings in a bunchy top devasted field
    • Ocfemia GO, Buhay GG (1934) Bunchy top of abaca or Manila hemp-2. Further studies on the transmission of the disease and a trial planting of abaca seedlings in a bunchy top devasted field. Philippine Agriculturists 22: 267-80.
    • (1934) Philippine Agriculturists , vol.22 , pp. 267-280
    • Ocfemia, G.O.1    Buhay, G.G.2
  • 40
    • 20044383396 scopus 로고
    • Small spherical partials found in broad been plants infected with Milk- Vetch Dwarf Virus
    • Ohki ST, Doi Y, Yora K (1975) Small spherical partials found in broad been plants infected with Milk- Vetch Dwarf Virus. Phytopathological note 41: 508-510.
    • (1975) Phytopathological Note , vol.41 , pp. 508-510
    • Ohki, S.T.1    Doi, Y.2    Yora, K.3
  • 42
    • 0007263471 scopus 로고    scopus 로고
    • Epidemiology and integrated management of Abaca Bunchy Top in Philippines
    • In: Molina A, Roa V, Bay-Petersen J, Carpio A, Joven J, Philippines
    • Raymundo AD, Bajet NB (2000) Epidemiology and integrated management of Abaca Bunchy Top in Philippines, In: Molina A, Roa V, Bay-Petersen J, Carpio A, Joven J (Eds) Proceedings in Davao City. Philippines 89-97.
    • (2000) Proceedings In Davao City , pp. 89-97
    • Raymundo, A.D.1    Bajet, N.B.2
  • 43
    • 0033301936 scopus 로고    scopus 로고
    • Genetics and molecular genetics of the MHC
    • Rhodes DA, Trowsdale J (1999) Genetics and molecular genetics of the MHC. Rev in immunogenetics 1: 21-31.
    • (1999) Rev In Immunogenetics , vol.1 , pp. 21-31
    • Rhodes, D.A.1    Trowsdale, J.2
  • 45
    • 0024278357 scopus 로고
    • Hydrophilicity of polar amino acid side-chains is markedly reduced by flanking peptide bonds
    • Roseman MA (1988) Hydrophilicity of polar amino acid side-chains is markedly reduced by flanking peptide bonds. J Mol Biol 200: 513-522.
    • (1988) J Mol Biol , vol.200 , pp. 513-522
    • Roseman, M.A.1
  • 46
    • 0028348369 scopus 로고
    • Crystal structure of the human class II MHC protein HLA-DR1 complexed with an influenza virus peptide
    • Stern LJ, Brown JH, Jardetzky TS, Gorga JC, Urban RG, et al. (1994) Crystal structure of the human class II MHC protein HLA-DR1 complexed with an influenza virus peptide. Nature 368: 215-221.
    • (1994) Nature , vol.368 , pp. 215-221
    • Stern, L.J.1    Brown, J.H.2    Jardetzky, T.S.3    Gorga, J.C.4    Urban, R.G.5
  • 47
    • 34547781750 scopus 로고    scopus 로고
    • MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0
    • Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24: 1596-1599.
    • (2007) Mol Biol Evol , vol.24 , pp. 1596-1599
    • Tamura, K.1    Dudley, J.2    Nei, M.3    Kumar, S.4
  • 48
    • 33744807710 scopus 로고    scopus 로고
    • Infectivity of Nanovirus DNAs: Induction of disease by cloned genome components of Faba bean necrotic yellows virus
    • Timchenko T, Katul L, Aronson M, Vega-Arreguin JC, Ramirez BC, et al. (2006) Infectivity of Nanovirus DNAs: Induction of disease by cloned genome components of Faba bean necrotic yellows virus. J Gen Virol 87: 1735-1743.
    • (2006) J Gen Virol , vol.87 , pp. 1735-1743
    • Timchenko, T.1    Katul, L.2    Aronson, M.3    Vega-Arreguin, J.C.4    Ramirez, B.C.5
  • 49
    • 33646876222 scopus 로고    scopus 로고
    • Prediction of HLA-DQ3.2beta ligands: Evidence of multiple registers in class II binding peptides
    • Tong JC, Zhang GL, Tan TW, August JT, Brusic V, et al. (2006) Prediction of HLA-DQ3.2beta ligands: evidence of multiple registers in class II binding peptides. Bioinformatics 22: 1232-1238.
    • (2006) Bioinformatics , vol.22 , pp. 1232-1238
    • Tong, J.C.1    Zhang, G.L.2    Tan, T.W.3    August, J.T.4    Brusic, V.5
  • 50
    • 0019631920 scopus 로고
    • The behaviour of peptides on reverse-phase supports during high-pressure liquid chromatography
    • Wilson KJ, Honegger A, Stotzel RP, Hughes GJ (1981) The behaviour of peptides on reverse-phase supports during high-pressure liquid chromatography. Biochem J 199: 31-41.
    • (1981) Biochem J , vol.199 , pp. 31-41
    • Wilson, K.J.1    Honegger, A.2    Stotzel, R.P.3    Hughes, G.J.4
  • 51
    • 0033046472 scopus 로고    scopus 로고
    • Immunodominance in major histocompatibility complex class I-restricted T lymphocyte responses
    • Yewdell JW, Bennink JR (1999) Immunodominance in major histocompatibility complex class I-restricted T lymphocyte responses. Annu Rev Immunol 17: 51-88.
    • (1999) Annu Rev Immunol , vol.17 , pp. 51-88
    • Yewdell, J.W.1    Bennink, J.R.2
  • 52
    • 0037135676 scopus 로고    scopus 로고
    • Expression in plants and immunogenicity of plant virus-based experimental rabies vaccine
    • Yusibov V, Hooper DC, Spitsin SV, Fleysh N, Kean RB (2002) Expression in plants and immunogenicity of plant virus-based experimental rabies vaccine. Vaccine 20: 3155-3164.
    • (2002) Vaccine , vol.20 , pp. 3155-3164
    • Yusibov, V.1    Hooper, D.C.2    Spitsin, S.V.3    Fleysh, N.4    Kean, R.B.5
  • 53
    • 31144459030 scopus 로고    scopus 로고
    • RNA viral community in human feces: Prevalence of plant pathogenic viruses
    • Zhang T, Breitbart M, Lee WH, Run J, Wei CL (2006) RNA viral community in human feces: Prevalence of plant pathogenic viruses. PLoS Biol 4: e3.
    • (2006) PLoS Biol , vol.4
    • Zhang, T.1    Breitbart, M.2    Lee, W.H.3    Run, J.4    Wei, C.L.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.