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Volumn 1834, Issue 1, 2013, Pages 221-230

Stereochemical features of the envelope protein Domain III of dengue virus reveals putative antigenic site in the five-fold symmetry axis

Author keywords

Dengue virus; Domain III; Induced fit; Molecular dynamics; Putative epitope; Surface pore

Indexed keywords

HISTIDINE; VIRUS ENVELOPE PROTEIN;

EID: 84870721058     PISSN: 15709639     EISSN: 18781454     Source Type: Journal    
DOI: 10.1016/j.bbapap.2012.09.007     Document Type: Article
Times cited : (13)

References (63)
  • 1
    • 0030618006 scopus 로고    scopus 로고
    • Sensitivity of malaria, schistosomiasis and dengue to global warming
    • W.J.M. Martens, T.H. Jetten, and D.A. Focks Sensitivity of malaria, schistosomiasis and dengue to global warming Clim. Chang. 35 2 1997 145 156
    • (1997) Clim. Chang. , vol.35 , Issue.2 , pp. 145-156
    • Martens, W.J.M.1    Jetten, T.H.2    Focks, D.A.3
  • 2
    • 50849098592 scopus 로고    scopus 로고
    • Global spread and persistence of dengue
    • J.L. Kyle, and E. Harris Global spread and persistence of dengue Annu. Rev. Microbiol. 62 2008 71 92
    • (2008) Annu. Rev. Microbiol. , vol.62 , pp. 71-92
    • Kyle, J.L.1    Harris, E.2
  • 5
    • 78650538214 scopus 로고    scopus 로고
    • A DNA vaccine candidate encoding the structural PRAM/e proteins elicits a strong immune response and protects mice against dengue-4 virus infection
    • D.M. Lima, S.O. de Paula, F.R.F. de Oliveira, P.V.B. Palma, F.R. Morais, A.C. Gomes-Ruiz, M.T.P. de Aquino, and B.A.L. Fonseca A DNA vaccine candidate encoding the structural PRAM/e proteins elicits a strong immune response and protects mice against dengue-4 virus infection Vaccine 29 4 2011 831 838
    • (2011) Vaccine , vol.29 , Issue.4 , pp. 831-838
    • Lima, D.M.1    De Paula, S.O.2    De Oliveira, F.R.F.3    Palma, P.V.B.4    Morais, F.R.5    Gomes-Ruiz, A.C.6    De Aquino, M.T.P.7    Fonseca, B.A.L.8
  • 8
    • 29144497159 scopus 로고    scopus 로고
    • Class ii virus membrane fusion proteins
    • M. Kielian Class ii virus membrane fusion proteins Virology 344 1 2005 38 47
    • (2005) Virology , vol.344 , Issue.1 , pp. 38-47
    • Kielian, M.1
  • 9
    • 33749266195 scopus 로고    scopus 로고
    • The role of histidine residues in low-pH-mediated viral membrane fusion
    • T. Kampmann, D.S. Mueller, A.E. Mark, P.R. Young, and B. Kobe The role of histidine residues in low-pH-mediated viral membrane fusion Structure 14 10 2006 1481 1487
    • (2006) Structure , vol.14 , Issue.10 , pp. 1481-1487
    • Kampmann, T.1    Mueller, D.S.2    Mark, A.E.3    Young, P.R.4    Kobe, B.5
  • 10
    • 1642499388 scopus 로고    scopus 로고
    • Structure of the dengue virus envelope protein after membrane fusion
    • Y. Modis, S. Ogata, D. Clements, and S.C. Harrison Structure of the dengue virus envelope protein after membrane fusion Nature 427 6972 2004 313 319
    • (2004) Nature , vol.427 , Issue.6972 , pp. 313-319
    • Modis, Y.1    Ogata, S.2    Clements, D.3    Harrison, S.C.4
  • 11
    • 55949125587 scopus 로고    scopus 로고
    • The pH sensor for flavivirus membrane fusion
    • S.C. Harrison The pH sensor for flavivirus membrane fusion J. Cell Biol. 183 2 2008 177 179
    • (2008) J. Cell Biol. , vol.183 , Issue.2 , pp. 177-179
    • Harrison, S.C.1
  • 12
    • 55949108725 scopus 로고    scopus 로고
    • Identification of specific histidines as pH sensors in flavivirus membrane fusion
    • R. Fritz, K. Stiasny, and F.X. Heinz Identification of specific histidines as pH sensors in flavivirus membrane fusion J. Cell Biol. 183 2 2008 353 361
    • (2008) J. Cell Biol. , vol.183 , Issue.2 , pp. 353-361
    • Fritz, R.1    Stiasny, K.2    Heinz, F.X.3
  • 16
    • 77955210055 scopus 로고    scopus 로고
    • Probing the mechanism of pH-induced large-scale conformational changes in dengue virus envelope protein using atomistic simulations
    • M.K. Prakash, A. Barducci, and M. Parrinello Probing the mechanism of pH-induced large-scale conformational changes in dengue virus envelope protein using atomistic simulations Biophys. J. 99 2 2010 588 594
    • (2010) Biophys. J. , vol.99 , Issue.2 , pp. 588-594
    • Prakash, M.K.1    Barducci, A.2    Parrinello, M.3
  • 17
    • 0032486594 scopus 로고    scopus 로고
    • Monoclonal antibody mapping of the envelope glycoprotein of the dengue 2 virus, Jamaica
    • J.T. Roehrig, R.A. Bolin, and R.G. Kelly Monoclonal antibody mapping of the envelope glycoprotein of the dengue 2 virus, Jamaica Virology 246 2 1998 317 328
    • (1998) Virology , vol.246 , Issue.2 , pp. 317-328
    • Roehrig, J.T.1    Bolin, R.A.2    Kelly, R.G.3
  • 18
    • 0034899311 scopus 로고    scopus 로고
    • Monoclonal antibodies that bind to domain III of dengue virus e glycoprotein are the most efficient blockers of virus adsorption to vero cells
    • W.D. Crill, and J.T. Roehrig Monoclonal antibodies that bind to domain III of dengue virus e glycoprotein are the most efficient blockers of virus adsorption to vero cells J. Virol. 75 16 2001 7769 7773
    • (2001) J. Virol. , vol.75 , Issue.16 , pp. 7769-7773
    • Crill, W.D.1    Roehrig, J.T.2
  • 19
    • 33644973069 scopus 로고    scopus 로고
    • Quantifying the specific binding between West Nile virus envelope domain III protein and the cellular receptor alphaVbeta3 integrin
    • J.W. Lee, J.J. Chu, and M.L. Ng Quantifying the specific binding between West Nile virus envelope domain III protein and the cellular receptor alphaVbeta3 integrin J. Biol. Chem. 281 3 2006 1352 1360
    • (2006) J. Biol. Chem. , vol.281 , Issue.3 , pp. 1352-1360
    • Lee, J.W.1    Chu, J.J.2    Ng, M.L.3
  • 20
    • 34548627957 scopus 로고    scopus 로고
    • Characterization of an antigenic site that contains a dominant, type-specific neutralization determinant on the envelope protein domain III (ed3) of dengue 2 virus
    • G.D. Gromowski, and A.D.T. Barrett Characterization of an antigenic site that contains a dominant, type-specific neutralization determinant on the envelope protein domain III (ed3) of dengue 2 virus Virology 366 2 2007 349 360
    • (2007) Virology , vol.366 , Issue.2 , pp. 349-360
    • Gromowski, G.D.1    Barrett, A.D.T.2
  • 21
    • 79960997906 scopus 로고    scopus 로고
    • Molecular complexity and fragment-based drug discovery: Ten years on
    • A.R. Leach, and M.M. Hann Molecular complexity and fragment-based drug discovery: ten years on Curr. Opin. Chem. Biol. 15 4 2011 489 496
    • (2011) Curr. Opin. Chem. Biol. , vol.15 , Issue.4 , pp. 489-496
    • Leach, A.R.1    Hann, M.M.2
  • 23
    • 80054850498 scopus 로고    scopus 로고
    • Effect of local thermal fluctuations on folding kinetics: A study from the perspective of nonextensive statistical mechanics
    • J.P. Dal Molin, M.A.A. da Silva, and A. Caliri Effect of local thermal fluctuations on folding kinetics: a study from the perspective of nonextensive statistical mechanics Phys. Rev. E. 84 4 2011 041903
    • (2011) Phys. Rev. E. , vol.84 , Issue.4 , pp. 041903
    • Dal Molin, J.P.1    Da Silva, M.A.A.2    Caliri, A.3
  • 24
    • 79954480854 scopus 로고    scopus 로고
    • Toward prediction of functional protein pockets using blind docking and pocket search algorithms
    • C. Hetenyi, and D. van der Spoel Toward prediction of functional protein pockets using blind docking and pocket search algorithms Prot. Sci. 20 5 2011 880 893
    • (2011) Prot. Sci. , vol.20 , Issue.5 , pp. 880-893
    • Hetenyi, C.1    Van Der Spoel, D.2
  • 26
    • 58149487623 scopus 로고    scopus 로고
    • Mechanism of ns2b-mediated activation of ns3pro in dengue virus: Molecular dynamics simulations and bioassays
    • Z. Zuo, O.W. Liew, G. Chen, P.C.J. Chong, S.H. Lee, K. Chen, H. Jiang, C.M. Puah, and W. Zhu Mechanism of ns2b-mediated activation of ns3pro in dengue virus: molecular dynamics simulations and bioassays J. Virol. 83 2 2009 1060 1070
    • (2009) J. Virol. , vol.83 , Issue.2 , pp. 1060-1070
    • Zuo, Z.1    Liew, O.W.2    Chen, G.3    Chong, P.C.J.4    Lee, S.H.5    Chen, K.6    Jiang, H.7    Puah, C.M.8    Zhu, W.9
  • 27
    • 77950675654 scopus 로고    scopus 로고
    • Homology modeling and molecular dynamics simulations of dengue virus ns2b/ns3 protease: Insight into molecular interaction
    • K. Wichapong, S. Pianwanit, W. Sippl, and S. Kokpol Homology modeling and molecular dynamics simulations of dengue virus ns2b/ns3 protease: insight into molecular interaction J. Mol. Recognit. 23 3 2010 283 300
    • (2010) J. Mol. Recognit. , vol.23 , Issue.3 , pp. 283-300
    • Wichapong, K.1    Pianwanit, S.2    Sippl, W.3    Kokpol, S.4
  • 28
    • 80054984233 scopus 로고    scopus 로고
    • Role of pH on dimeric interactions for DENV envelope protein: An insight from molecular dynamics study
    • K.D. Dubey, A.K. Chaubey, and R.P. Ojha Role of pH on dimeric interactions for DENV envelope protein: an insight from molecular dynamics study Biochim. Biophys. Acta Protein Proteomics 1814 12 2011 1796 1801
    • (2011) Biochim. Biophys. Acta Protein Proteomics , vol.1814 , Issue.12 , pp. 1796-1801
    • Dubey, K.D.1    Chaubey, A.K.2    Ojha, R.P.3
  • 30
    • 11144244755 scopus 로고    scopus 로고
    • Variable surface epitopes in the crystal structure of dengue virus type 3 envelope glycoprotein
    • Y. Modis, S. Ogata, D. Clements, and S.C. Harrison Variable surface epitopes in the crystal structure of dengue virus type 3 envelope glycoprotein J. Virol. 79 2 2005 1223 1231
    • (2005) J. Virol. , vol.79 , Issue.2 , pp. 1223-1231
    • Modis, Y.1    Ogata, S.2    Clements, D.3    Harrison, S.C.4
  • 32
    • 38549181654 scopus 로고    scopus 로고
    • Solution structure and neutralizing antibody binding studies of domain III of the dengue-2 virus envelope protein
    • K.C. Huang, M.C. Lee, C.W. Wu, K.J. Huang, H.Y. Lei, and J.W. Cheng Solution structure and neutralizing antibody binding studies of domain III of the dengue-2 virus envelope protein Proteins 70 3 2008 1116 1119
    • (2008) Proteins , vol.70 , Issue.3 , pp. 1116-1119
    • Huang, K.C.1    Lee, M.C.2    Wu, C.W.3    Huang, K.J.4    Lei, H.Y.5    Cheng, J.W.6
  • 33
    • 66149103151 scopus 로고    scopus 로고
    • Crystal structure of dengue virus type 1 envelope protein in the postfusion conformation and its implications for membrane fusion
    • V. Nayak, M. Dessau, K. Kucera, K. Anthony, M. Ledizet, and Y. Modis Crystal structure of dengue virus type 1 envelope protein in the postfusion conformation and its implications for membrane fusion J. Virol. 83 9 2009 4338 4344
    • (2009) J. Virol. , vol.83 , Issue.9 , pp. 4338-4344
    • Nayak, V.1    Dessau, M.2    Kucera, K.3    Anthony, K.4    Ledizet, M.5    Modis, Y.6
  • 35
    • 46249092554 scopus 로고    scopus 로고
    • Gromacs 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
    • B. Hess, C. Kutzner, D. van der Spoel, and E. Lindahl Gromacs 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation J. Chem. Theory Comput. 4 3 2008 435 447
    • (2008) J. Chem. Theory Comput. , vol.4 , Issue.3 , pp. 435-447
    • Hess, B.1    Kutzner, C.2    Van Der Spoel, D.3    Lindahl, E.4
  • 36
    • 33645941402 scopus 로고
    • The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin
    • W.L. Jorgensen, and J. Tirado-Rives The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin J. Am. Chem. Soc. 110 6 1988 1657 1666
    • (1988) J. Am. Chem. Soc. , vol.110 , Issue.6 , pp. 1657-1666
    • Jorgensen, W.L.1    Tirado-Rives, J.2
  • 38
    • 0000020246 scopus 로고    scopus 로고
    • A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions
    • M.W. Mahoney, and W.L. Jorgensen A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions J. Chem. Phys. 112 20 2000 8910 8922
    • (2000) J. Chem. Phys. , vol.112 , Issue.20 , pp. 8910-8922
    • Mahoney, M.W.1    Jorgensen, W.L.2
  • 39
    • 0001461682 scopus 로고
    • Examination of titration behavior
    • (cited By (since 1996) 102)
    • C. Nozaki, and Y. Tanford Examination of titration behavior Methods Enzymol. 11 C 1967 715 734 (cited By (since 1996) 102)
    • (1967) Methods Enzymol. , vol.11 C , pp. 715-734
    • Nozaki, C.1    Tanford, Y.2
  • 40
    • 84986440341 scopus 로고
    • Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models
    • S. Miyamoto, and P.A. Kollman Settle: an analytical version of the SHAKE and RATTLE algorithm for rigid water models J. Comput. Chem. 13 8 1992 952 962
    • (1992) J. Comput. Chem. , vol.13 , Issue.8 , pp. 952-962
    • Miyamoto, S.1    Kollman, P.A.2
  • 42
    • 0000388705 scopus 로고    scopus 로고
    • LINCS: A linear constraint solver for molecular simulations
    • B. Hess, H. Bekker, H.J.C. Berendsen, and J.G.E.M. Fraaije LINCS: a linear constraint solver for molecular simulations J. Comput. Chem. 18 12 1997 1463 1472
    • (1997) J. Comput. Chem. , vol.18 , Issue.12 , pp. 1463-1472
    • Hess, B.1    Bekker, H.2    Berendsen, H.J.C.3    Fraaije, J.G.E.M.4
  • 43
    • 26144434487 scopus 로고
    • Crystal structure and pair potentials: A molecular-dynamics study
    • M. Parrinello, and A. Rahman Crystal structure and pair potentials: a molecular-dynamics study Phys. Rev. Lett. 45 14 1980 1196 1199
    • (1980) Phys. Rev. Lett. , vol.45 , Issue.14 , pp. 1196-1199
    • Parrinello, M.1    Rahman, A.2
  • 44
    • 33846086933 scopus 로고    scopus 로고
    • Canonical sampling through velocity rescaling
    • G. Bussi, D. Donadio, and M. Parrinello Canonical sampling through velocity rescaling J. Phys. 126 1 2007 (014101 +)
    • (2007) J. Phys. , vol.126 , Issue.1
    • Bussi, G.1    Donadio, D.2    Parrinello, M.3
  • 48
    • 33751223215 scopus 로고    scopus 로고
    • Crystal structure of the west nile virus envelope glycoprotein
    • G.E. Nybakken, C.A. Nelson, B.R. Chen, M.S. Diamond, and D.H. Fremont Crystal structure of the west nile virus envelope glycoprotein J. Virol. 80 23 2006 11467 11474
    • (2006) J. Virol. , vol.80 , Issue.23 , pp. 11467-11474
    • Nybakken, G.E.1    Nelson, C.A.2    Chen, B.R.3    Diamond, M.S.4    Fremont, D.H.5
  • 52
    • 84862884578 scopus 로고    scopus 로고
    • Cytochrome p450 3a4 inhibition by ketoconazole: Tackling the problem of ligand cooperativity using molecular dynamics simulations and free-energy calculations
    • U. Bren, and C. Oostenbrink Cytochrome p450 3a4 inhibition by ketoconazole: tackling the problem of ligand cooperativity using molecular dynamics simulations and free-energy calculations J. Chem. Inf. Model. 52 6 2012 1573 1582
    • (2012) J. Chem. Inf. Model. , vol.52 , Issue.6 , pp. 1573-1582
    • Bren, U.1    Oostenbrink, C.2
  • 53
    • 44649116524 scopus 로고    scopus 로고
    • Dynameomics: Mass annotation of protein dynamics and unfolding in water by high-throughput atomistic molecular dynamics simulations
    • D. Beck, A. Jonsson, D. Schaeffer, K. Scott, R. Day, R. Toofanny, D. Alonso, and V. Daggett Dynameomics: mass annotation of protein dynamics and unfolding in water by high-throughput atomistic molecular dynamics simulations Protein Eng. Des. Sel. 21 6 2008 353 368
    • (2008) Protein Eng. Des. Sel. , vol.21 , Issue.6 , pp. 353-368
    • Beck, D.1    Jonsson, A.2    Schaeffer, D.3    Scott, K.4    Day, R.5    Toofanny, R.6    Alonso, D.7    Daggett, V.8
  • 56
    • 0001858251 scopus 로고
    • Application of a theory of enzyme specificity to protein synthesis
    • D.E. Koshland Application of a theory of enzyme specificity to protein synthesis Proc. Natl. Acad. Sci. U. S. A. 44 2 1958 98 104
    • (1958) Proc. Natl. Acad. Sci. U. S. A. , vol.44 , Issue.2 , pp. 98-104
    • Koshland, D.E.1
  • 57
    • 69549120472 scopus 로고    scopus 로고
    • Conformational selection or induced fit: A flux description of reaction mechanism
    • G.G. Hammes, Y.C. Chang, and T.G. Oas Conformational selection or induced fit: a flux description of reaction mechanism Proc. Natl. Acad. Sci. U. S. A. 106 33 2009 13737 13741
    • (2009) Proc. Natl. Acad. Sci. U. S. A. , vol.106 , Issue.33 , pp. 13737-13741
    • Hammes, G.G.1    Chang, Y.C.2    Oas, T.G.3
  • 58
    • 84860833500 scopus 로고    scopus 로고
    • Reorganizing the protein space at the universal protein resource (UniProt)
    • U. Consortium Reorganizing the protein space at the universal protein resource (UniProt) Nucleic Acids Res. 40 D1 2012 D71 D75
    • (2012) Nucleic Acids Res. , vol.40 D1
    • Consortium, U.1
  • 59
    • 34447637159 scopus 로고    scopus 로고
    • Computational analysis and identification of amino acid sites in dengue e proteins relevant to development of diagnostics and vaccines
    • R. Mazumder, Z.Z. Hu, C.R. Vinayaka, J.L. Sagripanti, S.D.W. Frost, S.L.K. Pond, and C.H. Wu Computational analysis and identification of amino acid sites in dengue e proteins relevant to development of diagnostics and vaccines Virus Genes 35 2 2007 175 186
    • (2007) Virus Genes , vol.35 , Issue.2 , pp. 175-186
    • Mazumder, R.1    Hu, Z.Z.2    Vinayaka, C.R.3    Sagripanti, J.L.4    Frost, S.D.W.5    Pond, S.L.K.6    Wu, C.H.7
  • 60
    • 33846807511 scopus 로고    scopus 로고
    • Dna polymerase beta catalytic efficiency mirrors the Asn279-dCTP H-bonding strength
    • V. Martinek, U. Bren, M.F. Goodman, A. Warshel, and J. Florian Dna polymerase beta catalytic efficiency mirrors the Asn279-dCTP H-bonding strength FEBS Lett. 581 4 2007 775 780
    • (2007) FEBS Lett. , vol.581 , Issue.4 , pp. 775-780
    • Martinek, V.1    Bren, U.2    Goodman, M.F.3    Warshel, A.4    Florian, J.5
  • 61
    • 70350510084 scopus 로고    scopus 로고
    • Dynamic behavior of avian influenza a virus neuraminidase subtype h5n1 in complex with oseltamivir, zanamivir, peramivir, and their phosphonate analogues
    • T. Udommaneethanakit, T. Rungrotmongkol, U. Bren, V. Frecer, and M. Stanislav Dynamic behavior of avian influenza a virus neuraminidase subtype h5n1 in complex with oseltamivir, zanamivir, peramivir, and their phosphonate analogues J. Chem. Inf. Model. 49 10 2009 2323 2332
    • (2009) J. Chem. Inf. Model. , vol.49 , Issue.10 , pp. 2323-2332
    • Udommaneethanakit, T.1    Rungrotmongkol, T.2    Bren, U.3    Frecer, V.4    Stanislav, M.5
  • 63
    • 1542676372 scopus 로고    scopus 로고
    • Microevolution and virulence of dengue viruses
    • R. Rico-Hesse Microevolution and virulence of dengue viruses Adv. Virus Res. 59 2003 315 341
    • (2003) Adv. Virus Res. , vol.59 , pp. 315-341
    • Rico-Hesse, R.1


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