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Volumn 23, Issue 3, 2010, Pages 283-300

Homology modeling and molecular dynamics simulations of Dengue virus NS2B/NS3 protease: Insight into molecular interaction

Author keywords

Dengue NS2B NS3 protease; GRID; GROMACS; Molecular dynamics simulation; West Nile NS2B NS3 protease

Indexed keywords

NS3 PROTEASE, DENGUE VIRUS; PROTEINASE INHIBITOR; SERINE PROTEINASE; VIRUS PROTEIN;

EID: 77950675654     PISSN: 09523499     EISSN: 10991352     Source Type: Journal    
DOI: 10.1002/jmr.977     Document Type: Article
Times cited : (48)

References (56)
  • 1
    • 34247625945 scopus 로고    scopus 로고
    • Structural evidence for regulation and specificity of flaviviral protease and evolution of the Flaviviridae fold
    • Aleshin AE, Shiryaev SA, Strongin AY, Liddington RC. 2007. Structural evidence for regulation and specificity of flaviviral protease and evolution of the Flaviviridae fold. Protein Sci. 16(5): 795-806.
    • (2007) Protein Sci , vol.16 , Issue.5 , pp. 795-806
    • Aleshin, A.E.1    Shiryaev, S.A.2    Strongin, A.Y.3    Liddington, R.C.4
  • 2
    • 29444438470 scopus 로고    scopus 로고
    • Recent advances in the molecular biology of West Nile Virus
    • Beasley DW. 2005. Recent advances in the molecular biology of West Nile Virus. Curr. Mol. Med. 5(8): 835-850.
    • (2005) Curr. Mol. Med , vol.5 , Issue.8 , pp. 835-850
    • Beasley, D.W.1
  • 3
    • 0002775934 scopus 로고
    • Interaction models for water in relation to protein hydration
    • Pollman B (ed.), D. Reidel Publishing Company: Dordrecht
    • Berendsen HJC, Postma JPM, van Gunsteren WF, Hermans J. 1981. Interaction models for water in relation to protein hydration. In Intermolecular Forces, Pollman B (ed.), D. Reidel Publishing Company: Dordrecht; 331-342.
    • (1981) Intermolecular Forces , pp. 331-342
    • Berendsen, H.J.C.1    Postma, J.P.M.2    van Gunsteren, W.F.3    Hermans, J.4
  • 5
    • 0033955886 scopus 로고    scopus 로고
    • Phylogeny of the genus Flavivirus using complete coding sequences of arthropod-borne viruses and viruses with no known vector
    • Billoir F, de Chesse R, Tolou H, de Micco P, Gould EA, de Lamballerie X. 2000. Phylogeny of the genus Flavivirus using complete coding sequences of arthropod-borne viruses and viruses with no known vector. J. Gen. Virol. 81(3): 781-790.
    • (2000) J. Gen. Virol , vol.81 , Issue.3 , pp. 781-790
    • Billoir, F.1    de Chesse, R.2    Tolou, H.3    de Micco, P.4    Gould, E.A.5    de Lamballerie, X.6
  • 6
    • 0032930982 scopus 로고    scopus 로고
    • Homology model of the dengue 2 virus NS3 protease: Putative interactions with both substrate and NS2B cofactor
    • Brinkworth RI, Fairlie DP, Leung D, Young PR. 1999. Homology model of the dengue 2 virus NS3 protease: putative interactions with both substrate and NS2B cofactor. J. Gen. Virol. 80: 1167-1177.
    • (1999) J. Gen. Virol , vol.80 , pp. 1167-1177
    • Brinkworth, R.I.1    Fairlie, D.P.2    Leung, D.3    Young, P.R.4
  • 8
    • 77950660832 scopus 로고    scopus 로고
    • Center for Disease Control and Prevention (CDC), Center for Disease Control and Prevention website
    • Center for Disease Control and Prevention (CDC). 2006. Division of Vector-Borne Infectious Disease West Nile Virus, Center for Disease Control and Prevention website, http:///www.cdc.gov/ncidod/dvbid/westnile/index.htm.
    • (2006) Division of Vector-Borne Infectious Disease West Nile Virus
  • 9
    • 0025201350 scopus 로고
    • Evidence that the N-terminal domain of nonstructural protein NS3 from yellow fever virus is a serine protease responsible for site-specific cleavages in the viral polyprotein
    • Chambers TJ, Weir RC, Grakoui A, McCourt DW, Bazan JF, Fletterick RJ, Rice CM. 1990a. Evidence that the N-terminal domain of nonstructural protein NS3 from yellow fever virus is a serine protease responsible for site-specific cleavages in the viral polyprotein. Proc. Natl. Acad. Sci. U.S.A. 87(22): 8898-8902.
    • (1990) Proc. Natl. Acad. Sci. U.S.A , vol.87 , Issue.22 , pp. 8898-8902
    • Chambers, T.J.1    Weir, R.C.2    Grakoui, A.3    McCourt, D.W.4    Bazan, J.F.5    Fletterick, R.J.6    Rice, C.M.7
  • 11
    • 13244281716 scopus 로고    scopus 로고
    • Site-directed mutagenesis and kinetic studies of the West Nile Virus NS3 protease identify key enzyme-substrate interactions
    • Chappell KJ, Nall TA, Stoermer MJ, Fang NX, Tyndall JD, Fairlie DP, Young PR. 2005. Site-directed mutagenesis and kinetic studies of the West Nile Virus NS3 protease identify key enzyme-substrate interactions. J. Biol. Chem. 280(4): 2896-2903.
    • (2005) J. Biol. Chem , vol.280 , Issue.4 , pp. 2896-2903
    • Chappell, K.J.1    Nall, T.A.2    Stoermer, M.J.3    Fang, N.X.4    Tyndall, J.D.5    Fairlie, D.P.6    Young, P.R.7
  • 12
    • 33845976698 scopus 로고    scopus 로고
    • Insights to substrate binding and processing by West Nile Virus NS3 protease through combined modeling, protease mutagenesis, and kinetic studies
    • Chappell KJ, Stoermer MJ, Fairlie DP, Young PR. 2006. Insights to substrate binding and processing by West Nile Virus NS3 protease through combined modeling, protease mutagenesis, and kinetic studies. J. Biol. Chem. 281(50): 38448-38458.
    • (2006) J. Biol. Chem , vol.281 , Issue.50 , pp. 38448-38458
    • Chappell, K.J.1    Stoermer, M.J.2    Fairlie, D.P.3    Young, P.R.4
  • 13
    • 45549101510 scopus 로고    scopus 로고
    • Mutagenesis of the West Nile Virus NS2B cofactor domain reveals two regions essential for protease activity
    • Chappell KJ, Stoermer MJ, Fairlie DP, Young PR. 2008. Mutagenesis of the West Nile Virus NS2B cofactor domain reveals two regions essential for protease activity. J. Gen. Virol. 89: 1010-1014.
    • (2008) J. Gen. Virol , vol.89 , pp. 1010-1014
    • Chappell, K.J.1    Stoermer, M.J.2    Fairlie, D.P.3    Young, P.R.4
  • 14
    • 0030667792 scopus 로고    scopus 로고
    • Cotranslational membrane insertion of the serine proteinase precursor NS2B-NS3(Pro) of dengue type 2 is required for efficient in vitro processing and is mediated through the hydrophobic regions of NS2B
    • Clum S, Ebner KE, Padmanabhan R. 1997. Cotranslational membrane insertion of the serine proteinase precursor NS2B-NS3(Pro) of dengue type 2 is required for efficient in vitro processing and is mediated through the hydrophobic regions of NS2B. J. Biol. Chem. 272(49): 30715-30723.
    • (1997) J. Biol. Chem , vol.272 , Issue.49 , pp. 30715-30723
    • Clum, S.1    Ebner, K.E.2    Padmanabhan, R.3
  • 17
    • 0025864149 scopus 로고
    • Both nonstructural proteins NS2B and NS3 are required for the proteolytic processing of dengue virus nonstructural proteins
    • Falgout B, Pethel M, Zhange YM, Lai CJ. 1991. Both nonstructural proteins NS2B and NS3 are required for the proteolytic processing of dengue virus nonstructural proteins. J. Virol. 65(5): 2467-2475.
    • (1991) J. Virol , vol.65 , Issue.5 , pp. 2467-2475
    • Falgout, B.1    Pethel, M.2    Zhange, Y.M.3    Lai, C.J.4
  • 18
    • 0027499688 scopus 로고
    • Deletion analysis of dengue virus type 4 nonstructural protein NS2B: Identification of a domain required for NS2B-NS3 protease activity
    • Falgout B, Miller RH, Lai CJ. 1993. Deletion analysis of dengue virus type 4 nonstructural protein NS2B: identification of a domain required for NS2B-NS3 protease activity. J. Virol. 67(4): 2034-2042.
    • (1993) J. Virol , vol.67 , Issue.4 , pp. 2034-2042
    • Falgout, B.1    Miller, R.H.2    Lai, C.J.3
  • 19
    • 9644272490 scopus 로고    scopus 로고
    • Identification and characterization of nonsubstrate based inhibitors of the essential dengue and West Nile Virus proteases
    • Ganesh VK, Muller N, Judge K, Luan CH, Padmanabhan R, Murthy KH. 2005. Identification and characterization of nonsubstrate based inhibitors of the essential dengue and West Nile Virus proteases. Bioorg. Med. Chem. 13(1): 257-264.
    • (2005) Bioorg. Med. Chem , vol.13 , Issue.1 , pp. 257-264
    • Ganesh, V.K.1    Muller, N.2    Judge, K.3    Luan, C.H.4    Padmanabhan, R.5    Murthy, K.H.6
  • 20
    • 0021871375 scopus 로고
    • A computational procedure for determining energetically favorable binding sites on biologically important macromolecules
    • Goodford PJ. 1985. A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J. Med. Chem. 28(7): 849-857.
    • (1985) J. Med. Chem , vol.28 , Issue.7 , pp. 849-857
    • Goodford, P.J.1
  • 21
    • 77950657896 scopus 로고    scopus 로고
    • GRID22a, Moldiscovery Ltd. 215 Marsh Road, HA5 5NE Pinner, Middlesex, UK, 2004 Pinner, Middlesex, UK
    • GRID22a. 2004. Moldiscovery Ltd. 215 Marsh Road, HA5 5NE Pinner, Middlesex, UK, 2004 Pinner, Middlesex, UK (http://www.moldiscovery.com).
    • (2004)
  • 22
    • 0031823546 scopus 로고    scopus 로고
    • Dengue and dengue hemorrhagic fever
    • Gubler DJ. 1998. Dengue and dengue hemorrhagic fever. Clin. Microbiol. Rev. 11(3): 480-496.
    • (1998) Clin. Microbiol. Rev , vol.11 , Issue.3 , pp. 480-496
    • Gubler, D.J.1
  • 23
    • 0029279259 scopus 로고
    • Dengue/dengue hemorrhagic fever: The emergence of a global health problem
    • Gubler DJ, Clark GG. 1995. Dengue/dengue hemorrhagic fever: the emergence of a global health problem. Emerg. Infect. Dis. 1(2): 55-57.
    • (1995) Emerg. Infect. Dis , vol.1 , Issue.2 , pp. 55-57
    • Gubler, D.J.1    Clark, G.G.2
  • 24
    • 0035683706 scopus 로고    scopus 로고
    • West Nile Virus: Uganda, 1937, to New York City, 1999
    • Hayes CG. 2001. West Nile Virus: Uganda, 1937, to New York City, 1999. Ann. N.Y. Acad. Sci. 951: 25-37.
    • (2001) Ann. N.Y. Acad. Sci , vol.951 , pp. 25-37
    • Hayes, C.G.1
  • 25
    • 0026458378 scopus 로고
    • Amino acid substitution matrices from protein blocks
    • Henikoff S, Henikoff JG. 1992. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. U.S.A. 89(22): 10915-10919.
    • (1992) Proc. Natl. Acad. Sci. U.S.A , vol.89 , Issue.22 , pp. 10915-10919
    • Henikoff, S.1    Henikoff, J.G.2
  • 27
    • 0024603620 scopus 로고
    • Sequence analysis of cloned dengue virus type 2 genome (New Guinea-C strain)
    • Irie K, Mohan PM, Sasaguri Y, Putnak R, Padmanabhan R. 1989. Sequence analysis of cloned dengue virus type 2 genome (New Guinea-C strain). Gene 75(2): 197-211.
    • (1989) Gene , vol.75 , Issue.2 , pp. 197-211
    • Irie, K.1    Mohan, P.M.2    Sasaguri, Y.3    Putnak, R.4    Padmanabhan, R.5
  • 30
    • 0000243829 scopus 로고
    • PROCHECK: A program to check the stereochemical quality of protein structures
    • Laskowski RA, MacArthur MW, Moss DS, Thornton JM. 1993. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Cryst. 26: 283-291.
    • (1993) J. Appl. Cryst , vol.26 , pp. 283-291
    • Laskowski, R.A.1    Macarthur, M.W.2    Moss, D.S.3    Thornton, J.M.4
  • 31
    • 0035824539 scopus 로고    scopus 로고
    • Activity of recombinant Dengue 2 virus NS3 protease in the presence of a truncated NS2B co-factor, small peptide substrates, and inhibitors
    • Leung D, Schroder K, White H, Fang NX, Stoermer MJ, Abbenante G, Martin JL, Young PR, Fairlie DP. 2001. Activity of recombinant Dengue 2 virus NS3 protease in the presence of a truncated NS2B co-factor, small peptide substrates, and inhibitors. J. Biol. Chem. 276(49): 45762-45771.
    • (2001) J. Biol. Chem , vol.276 , Issue.49 , pp. 45762-45771
    • Leung, D.1    Schroder, K.2    White, H.3    Fang, N.X.4    Stoermer, M.J.5    Abbenante, G.6    Martin, J.L.7    Young, P.R.8    Fairlie, D.P.9
  • 33
    • 0027475018 scopus 로고
    • Cleavage at a novel site in the NS4A region by the yellow fever virus NS2B-3 proteinase is a prerequisite for processing at the downstream 4A/4B signalase site
    • Lin C, Amberg SM, Chambers TJ, Rice RM. 1993. Cleavage at a novel site in the NS4A region by the yellow fever virus NS2B-3 proteinase is a prerequisite for processing at the downstream 4A/4B signalase site. J. Virol. 67: 2327-2335.
    • (1993) J. Virol , vol.67 , pp. 2327-2335
    • Lin, C.1    Amberg, S.M.2    Chambers, T.J.3    Rice, R.M.4
  • 34
    • 0035789518 scopus 로고    scopus 로고
    • Gromacs 3.0: A package for molecular simulationand trajectory analysis
    • Lindahl E, Hess B, van der Spoel D. 2001. Gromacs 3.0: a package for molecular simulationand trajectory analysis. J. Mol. Model.7(8): 306-317.
    • (2001) J. Mol. Model , vol.7 , Issue.8 , pp. 306-317
    • Lindahl, E.1    Hess, B.2    van der Spoel, D.3
  • 35
    • 0027264853 scopus 로고
    • Flavivirus premembrane protein cleavage and spike heterodimer secretion require the function of the viral proteinase NS3
    • Lobigs M. 1993. Flavivirus premembrane protein cleavage and spike heterodimer secretion require the function of the viral proteinase NS3. Proc. Natl. Acad. Sci. U.S.A. 90(13): 6218-6222.
    • (1993) Proc. Natl. Acad. Sci. U.S.A , vol.90 , Issue.13 , pp. 6218-6222
    • Lobigs, M.1
  • 37
    • 77950670976 scopus 로고    scopus 로고
    • MOE, 2006.08. Chemical Computing Group Inc., 1010 Sherbrooke St. W, Suite 910, Montreal, Quebec, Canada H3A 2R7
    • MOE. 2006. 2006.08. Chemical Computing Group Inc., 1010 Sherbrooke St. W, Suite 910, Montreal, Quebec, Canada H3A 2R7, (http://www.chemcomp.com).
    • (2006)
  • 38
  • 39
    • 0033605260 scopus 로고    scopus 로고
    • Dengue Virus NS3 serine protease. Crystal structure and insights into interaction of the active site with substrates by molecular modeling and structural analysis of mutational effects
    • Murthy HM, Clum S, Padmanabhan R. 1999. Dengue Virus NS3 serine protease. Crystal structure and insights into interaction of the active site with substrates by molecular modeling and structural analysis of mutational effects. J. Biol. Chem. 274(9): 5573-5580.
    • (1999) J. Biol. Chem , vol.274 , Issue.9 , pp. 5573-5580
    • Murthy, H.M.1    Clum, S.2    Padmanabhan, R.3
  • 40
    • 0034714111 scopus 로고    scopus 로고
    • Crystal structure of Dengue virus NS3 protease in complex with a Bowman-Birk inhibitor: Implications for flaviviral polyprotein processing and drug design
    • Murthy HM, Judge K, DeLucas L, Padmanabhan R. 2000. Crystal structure of Dengue virus NS3 protease in complex with a Bowman-Birk inhibitor: implications for flaviviral polyprotein processing and drug design. J. Biol. Chem. 301(4): 759-767.
    • (2000) J. Biol. Chem , vol.301 , Issue.4 , pp. 759-767
    • Murthy, H.M.1    Judge, K.2    Delucas, L.3    Padmanabhan, R.4
  • 41
    • 10344248922 scopus 로고    scopus 로고
    • Enzymatic characterization and homology model of a catalytically active recombinant West Nile Virus NS3 protease
    • Nall TA, Chappell KJ, Stoermer MJ, Fang NX, Tyndall JD, Young PR, Fairlie DP. 2004. Enzymatic characterization and homology model of a catalytically active recombinant West Nile Virus NS3 protease. J. Biol. Chem. 279(47): 48535-48542.
    • (2004) J. Biol. Chem , vol.279 , Issue.47 , pp. 48535-48542
    • Nall, T.A.1    Chappell, K.J.2    Stoermer, M.J.3    Fang, N.X.4    Tyndall, J.D.5    Young, P.R.6    Fairlie, D.P.7
  • 42
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino acid sequence of two proteins
    • Needleman SB, Wunsch CD. 1970. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48(3): 443-453.
    • (1970) J. Mol. Biol , vol.48 , Issue.3 , pp. 443-453
    • Needleman, S.B.1    Wunsch, C.D.2
  • 43
  • 44
    • 0026322815 scopus 로고
    • Processing of nonstructural proteins NS4A and NS4B of dengue 2 virus in vitro and in vivo
    • Preugschat F, Strauss JH. 1991. Processing of nonstructural proteins NS4A and NS4B of dengue 2 virus in vitro and in vivo. Virology 185(2): 689-697.
    • (1991) Virology , vol.185 , Issue.2 , pp. 689-697
    • Preugschat, F.1    Strauss, J.H.2
  • 45
    • 42449111776 scopus 로고    scopus 로고
    • Structure-based mutagenesis identifies important novel determinants of the NS2B cofactor of the West Nile Virus two-component NS2B-NS3 proteinase
    • Radichev I, Shiryaev SA, Aleshin AE, Ratnikov BI, Smith JW, Liddington RC, Strongin AY. 2008. Structure-based mutagenesis identifies important novel determinants of the NS2B cofactor of the West Nile Virus two-component NS2B-NS3 proteinase. J. Gen. Virol. 89: 636-641.
    • (2008) J. Gen. Virol , vol.89 , pp. 636-641
    • Radichev, I.1    Shiryaev, S.A.2    Aleshin, A.E.3    Ratnikov, B.I.4    Smith, J.W.5    Liddington, R.C.6    Strongin, A.Y.7
  • 46
    • 0037015076 scopus 로고    scopus 로고
    • Host genetic variability and West Nile Virus susceptibility
    • Samuel CE. 2002. Host genetic variability and West Nile Virus susceptibility. Proc. Natl. Acad. Sci. U.S.A. 99(18): 11555-11557.
    • (2002) Proc. Natl. Acad. Sci. U.S.A , vol.99 , Issue.18 , pp. 11555-11557
    • Samuel, C.E.1
  • 47
    • 33846411423 scopus 로고    scopus 로고
    • Expression and purification of a two-component flaviviral ptoteinase resistant to autocleavage at the NS2B-NS3 junction region
    • Shiryaev SA, Aleshin AE, Ratnikov BI, Smith JW, Liddington RC, Strongin AY. 2007. Expression and purification of a two-component flaviviral ptoteinase resistant to autocleavage at the NS2B-NS3 junction region. Protein Expr. Purif. 52(2): 334-339.
    • (2007) Protein Expr. Purif , vol.52 , Issue.2 , pp. 334-339
    • Shiryaev, S.A.1    Aleshin, A.E.2    Ratnikov, B.I.3    Smith, J.W.4    Liddington, R.C.5    Strongin, A.Y.6
  • 48
    • 0036791359 scopus 로고    scopus 로고
    • Furin at the cutting edge: From protein traffic to embryogenesis and disease
    • Thomas G. 2002. Furin at the cutting edge: from protein traffic to embryogenesis and disease. Nat. Rev. Mol. Cell. Biol. 3(10): 753-766.
    • (2002) Nat. Rev. Mol. Cell. Biol , vol.3 , Issue.10 , pp. 753-766
    • Thomas, G.1
  • 53
    • 0028146784 scopus 로고
    • Processing of the intracellular form of the West Nile Virus capsid protein by the NS2B-NS3 protease: An in vitro study
    • Yamshchikov VF, Compans RW. 1994. Processing of the intracellular form of the West Nile Virus capsid protein by the NS2B-NS3 protease: an in vitro study. J. Virol. 68(9): 5765-5771.
    • (1994) J. Virol , vol.68 , Issue.9 , pp. 5765-5771
    • Yamshchikov, V.F.1    Compans, R.W.2
  • 55
    • 0034616194 scopus 로고    scopus 로고
    • Purified NS2B/NS3 serine protease of Dengue virus type 2 exhibits cofactor NS2B dependence for cleavage for substrates with dibasic amino acids in vitro
    • Yusof R, Clum S, Wetzel M, Murthy HM, Padmanabhan R. 2000. Purified NS2B/NS3 serine protease of Dengue virus type 2 exhibits cofactor NS2B dependence for cleavage for substrates with dibasic amino acids in vitro. J. Biol. Chem. 275(14): 9963-9969.
    • (2000) J. Biol. Chem , vol.275 , Issue.14 , pp. 9963-9969
    • Yusof, R.1    Clum, S.2    Wetzel, M.3    Murthy, H.M.4    Padmanabhan, R.5
  • 56
    • 58149487623 scopus 로고    scopus 로고
    • Mechanism of NS2B-mediated activation of NS3pro in dengue virus: Molecular dynamics simulations and bioassays
    • Zuo Z, Liew OW, Chen G, Chong PC, Lee SH, Chen K, Jiang H, Puah CM, Zhu W. 2009. Mechanism of NS2B-mediated activation of NS3pro in dengue virus: molecular dynamics simulations and bioassays. J. Virol. 83(2): 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.4    Lee, S.H.5    Chen, K.6    Jiang, H.7    Puah, C.M.8    Zhu, W.9


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