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Volumn 32, Issue 6, 2014, Pages 950-958

A 3D structural model and dynamics of hepatitis C virus NS3/4A protease (genotype 4a, strain ED43) suggest conformational instability of the catalytic triad: Implications in catalysis and drug resistivity

Author keywords

catalysis; dynamics; genotype 4; HCV; structure

Indexed keywords

ASPARTIC ACID; BOCEPREVIR; HISTIDINE; NONSTRUCTURAL PROTEIN 3; NONSTRUCTURAL PROTEIN 4; SERINE; TELAPREVIR; NS3 PROTEIN, HEPATITIS C VIRUS; VIRUS PROTEIN;

EID: 84896691986     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.2013.800001     Document Type: Article
Times cited : (10)

References (55)
  • 1
    • 78649898944 scopus 로고    scopus 로고
    • Conformational stability of hepatitis C virus NS3 protease
    • Abian, O., Vega, S., Neira, J. L., &, Valazquez-Campoy, A. (2010). Conformational stability of hepatitis C virus NS3 protease. Biophysics Journal, 99, 3811-3820.
    • (2010) Biophysics Journal , vol.99 , pp. 3811-3820
    • Abian, O.1    Vega, S.2    Neira, J.L.3    Valazquez-Campoy, A.4
  • 2
    • 77955975126 scopus 로고    scopus 로고
    • Molecular epidemiology of hepatitis C virus genotypes in Khyber Pakhtoonkhaw of Pakistan
    • Ali, A., Ahmed, H., &, Idrees, M. (2010). Molecular epidemiology of hepatitis C virus genotypes in Khyber Pakhtoonkhaw of Pakistan. Virology Journal, 7, 203-1-203-7.
    • (2010) Virology Journal , vol.7 , pp. 2031-2037
    • Ali, A.1    Ahmed, H.2    Idrees, M.3
  • 4
    • 32144432437 scopus 로고    scopus 로고
    • The SWISS-MODEL workspace: A web-based environment for protein structure homology modeling
    • Arnold, K., Bordoli, L., Kopp, J., &, Schwede, T. (2006). The SWISS-MODEL workspace: A web-based environment for protein structure homology modeling. Bioinformatics, 22, 195-201.
    • (2006) Bioinformatics , vol.22 , pp. 195-201
    • Arnold, K.1    Bordoli, L.2    Kopp, J.3    Schwede, T.4
  • 5
    • 0033522886 scopus 로고    scopus 로고
    • The solution structure of the N-terminal proteinase domain of the hepatitis C virus (HCV) NS3 protein provides new insights into its activation and catalytic mechanism
    • Barbato, G., Cicero, D. O., Nardi, M. C., Steinkuhler, C., Cortese, R., De Francesco, R., &, Bazzo, R. (1999). The solution structure of the N-terminal proteinase domain of the hepatitis C virus (HCV) NS3 protein provides new insights into its activation and catalytic mechanism. The Journal of Molecular Biology, 289, 371-384.
    • (1999) The Journal of Molecular Biology , vol.289 , pp. 371-384
    • Barbato, G.1    Cicero, D.O.2    Nardi, M.C.3    Steinkuhler, C.4    Cortese, R.5    De Francesco, R.6    Bazzo, R.7
  • 6
    • 0030928381 scopus 로고    scopus 로고
    • Complete nucleotide sequence of a type 4 hepatitis C virus variant, the predominant genotype in the middle east
    • Chamberlain, R. W., Adams, N., Saeed, A. A., Simmonds, P., &, Elliott, R. M. (1997). Complete nucleotide sequence of a type 4 hepatitis C virus variant, the predominant genotype in the middle east. Journal of Genetic Virology, 1997, 1341-1347.
    • (1997) Journal of Genetic Virology , vol.1997 , pp. 1341-1347
    • Chamberlain, R.W.1    Adams, N.2    Saeed, A.A.3    Simmonds, P.4    Elliott, R.M.5
  • 7
    • 79952170631 scopus 로고    scopus 로고
    • Hepatitis C virus NS3/4A protease inhibitors: A light at the end of the tunnel
    • Chatel-Chaix, L., Baril, M., &, Lamarre, D. (2010). Hepatitis C virus NS3/4A protease inhibitors: A light at the end of the tunnel. Viruses, 2, 1752-1765.
    • (2010) Viruses , vol.2 , pp. 1752-1765
    • Chatel-Chaix, L.1    Baril, M.2    Lamarre, D.3
  • 8
    • 0027180507 scopus 로고
    • Verification of protein structures: Patterns of nonbonded interactions
    • Colovos, C., &, Yeates, T. O. (1993). Verification of protein structures: Patterns of nonbonded interactions. Protein Science, 2, 1511-1519.
    • (1993) Protein Science , vol.2 , pp. 1511-1519
    • Colovos, C.1    Yeates, T.O.2
  • 9
    • 0034629363 scopus 로고    scopus 로고
    • Inhibition of the hepatitis C virus NS3/4A protease. The crystal structures of two protease-inhibitor complexes
    • Di Marco, S., Rizzi, M., Volpari, C., Walsh, M. A., Narjes, F., Colarusso,., Sollazzo, M. (2000). Inhibition of the hepatitis C virus NS3/4A protease. The crystal structures of two protease-inhibitor complexes. Journal of Biological Chemistry, 275, 7152-7157.
    • (2000) Journal of Biological Chemistry , vol.275 , pp. 7152-7157
    • Di Marco, S.1    Rizzi, M.2    Volpari, C.3    Walsh, M.A.4    Narjes, F.5    Colarusso6    Sollazzo, M.7
  • 10
    • 0036900680 scopus 로고    scopus 로고
    • Establishment of a simple assay in vitro for hepatitis C virus NS3 serine protease based on recombinant substrate and single-chain protease
    • Du, G., Hou, L., Guan, R., Tong, Y., &, Wang, H. (2002). Establishment of a simple assay in vitro for hepatitis C virus NS3 serine protease based on recombinant substrate and single-chain protease. World Journal of Gastroenterology, 8, 1088-1093.
    • (2002) World Journal of Gastroenterology , vol.8 , pp. 1088-1093
    • Du, G.1    Hou, L.2    Guan, R.3    Tong, Y.4    Wang, H.5
  • 11
    • 36449007836 scopus 로고
    • Constant pressure molecular dynamics simulation-The Langevin piston method
    • Feller, S. E., Zhang, Y. H., Pastor, R. W., &, Brooks, B. R. (1995). Constant pressure molecular dynamics simulation-the Langevin piston method. Journal of Physical Chemistry, 103, 4613-4621.
    • (1995) Journal of Physical Chemistry , vol.103 , pp. 4613-4621
    • Feller, S.E.1    Zhang, Y.H.2    Pastor, R.W.3    Brooks, B.R.4
  • 12
    • 0015935205 scopus 로고
    • The charge relay system in chymotrypsin and chymotrypsinogen
    • Fersht, A. R., &, Sperling, J. (1973). The charge relay system in chymotrypsin and chymotrypsinogen. Journal of Molecular Biology, 74, 137-149.
    • (1973) Journal of Molecular Biology , vol.74 , pp. 137-149
    • Fersht, A.R.1    Sperling, J.2
  • 13
    • 38649125211 scopus 로고    scopus 로고
    • A Wide range of NS3/4A protease catalytic efficiencies in HCV-infected individuals
    • Franco, S., Clotet, B., &, Martinez, M. A. (2008). A Wide range of NS3/4A protease catalytic efficiencies in HCV-infected individuals. Virus Research, 131, 260-270.
    • (2008) Virus Research , vol.131 , pp. 260-270
    • Franco, S.1    Clotet, B.2    Martinez, M.A.3
  • 14
    • 0031473847 scopus 로고    scopus 로고
    • SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling
    • Guex, N., &, Peitsch, M. C. (1997). SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling. Electrophoresis, 18, 2714-2723.
    • (1997) Electrophoresis , vol.18 , pp. 2714-2723
    • Guex, N.1    Peitsch, M.C.2
  • 15
    • 0036882394 scopus 로고    scopus 로고
    • Serine protease mechanism and specificity
    • Hedstrom, L. (2002). Serine protease mechanism and specificity. Chemical Reviews, 102, 4501-4523.
    • (2002) Chemical Reviews , vol.102 , pp. 4501-4523
    • Hedstrom, L.1
  • 16
    • 0035214935 scopus 로고    scopus 로고
    • Inhibition of hepatitis C virus NS3 function by antisense oligodeoxynucleotides and protease inhibitor
    • Heintges, T., Enche, J., Putlitz, J., &, Wands, J. R. (2001). Inhibition of hepatitis C virus NS3 function by antisense oligodeoxynucleotides and protease inhibitor. Journal of Medical Virology, 65, 671-680.
    • (2001) Journal of Medical Virology , vol.65 , pp. 671-680
    • Heintges, T.1    Enche, J.2    Putlitz, J.3    Wands, J.R.4
  • 21
    • 42249110672 scopus 로고    scopus 로고
    • Hepatitis C genotype 4: What we know and what we dont yet know
    • Kamal, S. M., &, Nasser, I. A. (2008). Hepatitis C genotype 4: What we know and what we dont yet know. Hepatology, 47, 1371-1383.
    • (2008) Hepatology , vol.47 , pp. 1371-1383
    • Kamal, S.M.1    Nasser, I.A.2
  • 24
    • 81855220325 scopus 로고    scopus 로고
    • The therapeutic approaches for hepatitis C virus: Protease inhibitors and polymerase inhibitors
    • Kwo, P. Y., &, Vinayek, R. (2011). The therapeutic approaches for hepatitis C virus: Protease inhibitors and polymerase inhibitors. Gut and Liver, 4, 406-417.
    • (2011) Gut and Liver , vol.4 , pp. 406-417
    • Kwo, P.Y.1    Vinayek, R.2
  • 26
    • 59149085501 scopus 로고    scopus 로고
    • The global burden of hepatitis C
    • Levanchy, D. (2009). The global burden of hepatitis C. Liver International, 29, 74-81.
    • (2009) Liver International , vol.29 , pp. 74-81
    • Levanchy, D.1
  • 28
    • 0032566351 scopus 로고    scopus 로고
    • Correlations of the basicity of His 57 with transition state analogue binding, substrate reactivity, and the strength of the low-barrier hydrogen bond in chymotrypsin
    • Lin, J., Cassidy, C. S., &, Frey, P. A. (1998). Correlations of the basicity of His 57 with transition state analogue binding, substrate reactivity, and the strength of the low-barrier hydrogen bond in chymotrypsin. Biochemistry, 37, 11940-11948.
    • (1998) Biochemistry , vol.37 , pp. 11940-11948
    • Lin, J.1    Cassidy, C.S.2    Frey, P.A.3
  • 29
    • 0026610767 scopus 로고
    • Assessment of protein models with three-dimensional profiles
    • Luthy, R., Bowie, J. U., &, Eisenberg, D. (1992). Assessment of protein models with three-dimensional profiles. Nature, 356, 83-85.
    • (1992) Nature , vol.356 , pp. 83-85
    • Luthy, R.1    Bowie, J.U.2    Eisenberg, D.3
  • 31
    • 3142714765 scopus 로고    scopus 로고
    • Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations
    • MacKerell, A. D., Feig, M., &, Brooks, C. L. (2004). Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. Journal of Computational Chemistry, 25, 1400-1415.
    • (2004) Journal of Computational Chemistry , vol.25 , pp. 1400-1415
    • Mackerell, A.D.1    Feig, M.2    Brooks, C.L.3
  • 33
    • 0035793211 scopus 로고    scopus 로고
    • Solution structure and dynamics of the single-chain hepatitis C virus NS3 protease NS4A cofactor complex
    • McCoy, M. A., Senior, M. M., Gesell, J. J., Ramanathan, L., &, Wyss, D. F. (2001). Solution structure and dynamics of the single-chain hepatitis C virus NS3 protease NS4A cofactor complex. Journal of Molecular Biology, 305, 1099-1110.
    • (2001) Journal of Molecular Biology , vol.305 , pp. 1099-1110
    • McCoy, M.A.1    Senior, M.M.2    Gesell, J.J.3    Ramanathan, L.4    Wyss, D.F.5
  • 34
    • 0035889689 scopus 로고    scopus 로고
    • Linear programming optimization and a double statistical filter for protein threading protocols
    • Meller, J., &, Elber, R. (2001). Linear programming optimization and a double statistical filter for protein threading protocols. Proteins, 45, 241-261.
    • (2001) Proteins , vol.45 , pp. 241-261
    • Meller, J.1    Elber, R.2
  • 36
    • 22044440709 scopus 로고    scopus 로고
    • Chronic hepatitis C: Genotypes 4 to 9
    • Nguyen, M. H., &, Keefe, E. B. (2005). Chronic hepatitis C: Genotypes 4 to 9. Clinics in Liver Disease, 9, 411-426.
    • (2005) Clinics in Liver Disease , vol.9 , pp. 411-426
    • Nguyen, M.H.1    Keefe, E.B.2
  • 37
    • 38949191974 scopus 로고    scopus 로고
    • Challenges in modern drug discovery: A case study of Boceprevir, an HCV protease inhibitor for the treatment of hepatitis C virus infection
    • Njoroge, F., Chen, K. X., Shih, N., &, Piwinski, J. J. (2008). Challenges in modern drug discovery: A case study of Boceprevir, an HCV protease inhibitor for the treatment of hepatitis C virus infection. Accounts of Chemical Research, 41, 50-59.
    • (2008) Accounts of Chemical Research , vol.41 , pp. 50-59
    • Njoroge, F.1    Chen, K.X.2    Shih, N.3    Piwinski, J.J.4
  • 38
    • 84863438978 scopus 로고    scopus 로고
    • Understanding the drug resistance mechanism of hepatitis C virus NS3/4A to ITMN-191 due to R155K, A156V, D168A/E mutations: A computational study
    • Pan, D., Xue, W., Zhang, W., Liu, H., &, Yao, X. (2012). Understanding the drug resistance mechanism of hepatitis C virus NS3/4A to ITMN-191 due to R155K, A156V, D168A/E mutations: A computational study. Biochemica and Biophysica Acta, 1820, 1526-1534.
    • (2012) Biochemica and Biophysica Acta , vol.1820 , pp. 1526-1534
    • Pan, D.1    Xue, W.2    Zhang, W.3    Liu, H.4    Yao, X.5
  • 39
    • 0029004590 scopus 로고
    • Protein modeling by E-mail
    • Peitsch, M. C. (1995). Protein modeling by E-mail. Biotechnology, 13, 658-660.
    • (1995) Biotechnology , vol.13 , pp. 658-660
    • Peitsch, M.C.1
  • 41
    • 0030598343 scopus 로고    scopus 로고
    • Deviations from standard atomic volumes as a quality measure for protein crystal structures
    • Pontius, J., Richelle, J., &, Wodak, S. J. (1996). Deviations from standard atomic volumes as a quality measure for protein crystal structures. Journal of Molecular Biology, 264, 121-136.
    • (1996) Journal of Molecular Biology , vol.264 , pp. 121-136
    • Pontius, J.1    Richelle, J.2    Wodak, S.J.3
  • 44
    • 77954931489 scopus 로고    scopus 로고
    • Hepatitis C virus non-structural protein 3 (HCV NS3): A multifunctional antiviral target
    • Raney, K. D., Sharma, S. D., Moustafa, I. M., &, Cameron, C. E. (2010). Hepatitis C virus non-structural protein 3 (HCV NS3): A multifunctional antiviral target. The Journal of Biological Chemistry, 285, 22725-22731.
    • (2010) The Journal of Biological Chemistry , vol.285 , pp. 22725-22731
    • Raney, K.D.1    Sharma, S.D.2    Moustafa, I.M.3    Cameron, C.E.4
  • 46
    • 0033180510 scopus 로고    scopus 로고
    • An uniquely purified HCV NS3 protease and NS4A 21 ± 34 peptide form a highly active serine protease complex in peptide hydrolysis
    • Sardana, V. V., Blue, J. T., Zugay-Murphy, J., Sardana, M. K., &, Kuo, L. C. (1999). An uniquely purified HCV NS3 protease and NS4A 21 ± 34 peptide form a highly active serine protease complex in peptide hydrolysis. Protein Expression and Purification, 16, 440-447.
    • (1999) Protein Expression and Purification , vol.16 , pp. 440-447
    • Sardana, V.V.1    Blue, J.T.2    Zugay-Murphy, J.3    Sardana, M.K.4    Kuo, L.C.5
  • 47
    • 0042622380 scopus 로고    scopus 로고
    • SWISS-MODEL: An automated protein homology-modeling server
    • Schwede, T., Kopp, J., Guex, N., &, Peitsch, M. C. (2003). SWISS-MODEL: An automated protein homology-modeling server. Nucleic Acids Research, 31, 3381-3385.
    • (2003) Nucleic Acids Research , vol.31 , pp. 3381-3385
    • Schwede, T.1    Kopp, J.2    Guex, N.3    Peitsch, M.C.4
  • 48
    • 0036882392 scopus 로고    scopus 로고
    • Viral proteases
    • Tong, L. (2002). Viral proteases. Chemical Review, 102, 4609-4626.
    • (2002) Chemical Review , vol.102 , pp. 4609-4626
    • Tong, L.1
  • 50
    • 46249102168 scopus 로고    scopus 로고
    • Molecular basis of Telaprevir resistance due to V36 and T54 mutations in the NS3-4A protease of the hepatitis C virus
    • Welsch, C., Domingues, F. S., Susser, S., Antes, I., Hartmann, C., Mayr, G.,., Lengauer, T. (2008). Molecular basis of Telaprevir resistance due to V36 and T54 mutations in the NS3-4A protease of the hepatitis C virus. Genome Biology, 9, R16-1-R16-18.
    • (2008) Genome Biology , vol.9
    • Welsch, C.1    Domingues, F.S.2    Susser, S.3    Antes, I.4    Hartmann, C.5    Mayr, G.6    Lengauer, T.7
  • 53
    • 84355166397 scopus 로고    scopus 로고
    • Molecular modeling study on the resistance mechanism of HCV NS3/4A serine protease mutants R155K, A156V, and D168A to TMC435
    • Xue, W., Pan, D., Yang, Y., Liu, H., &, Yao, X. (2012). Molecular modeling study on the resistance mechanism of HCV NS3/4A serine protease mutants R155K, A156V, and D168A to TMC435. Antiviral Research, 93, 126-137.
    • (2012) Antiviral Research , vol.93 , pp. 126-137
    • Xue, W.1    Pan, D.2    Yang, Y.3    Liu, H.4    Yao, X.5
  • 54
    • 2642590958 scopus 로고    scopus 로고
    • Complex of NS3 protease and NS4A peptide of BK strain hepatitis C virus: A 2.2 Å resolution structure in a hexagonal crystal form
    • Yan, Y., Li, Y., Munshi, S., Sardana, V., Cole, J. L., Sardana, M.,., Chen, Z. (1998). Complex of NS3 protease and NS4A peptide of BK strain hepatitis C virus: A 2.2 Å resolution structure in a hexagonal crystal form. Protein Science, 7, 837-847.
    • (1998) Protein Science , vol.7 , pp. 837-847
    • Yan, Y.1    Li, Y.2    Munshi, S.3    Sardana, V.4    Cole, J.L.5    Sardana, M.6    Chen, Z.7
  • 55
    • 79960094589 scopus 로고    scopus 로고
    • Mechanistic role of NS4A and substrate in the activation of HCV NS3 protease
    • Zhu, H., &, Briggs, J. M. (2011). Mechanistic role of NS4A and substrate in the activation of HCV NS3 protease. Proteins, 79, 2428-2443.
    • (2011) Proteins , vol.79 , pp. 2428-2443
    • Zhu, H.1    Briggs, J.M.2


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