215
Views
12
CrossRef citations to date
0
Altmetric
Articles

NS2B/NS3 protease: allosteric effect of mutations associated with the pathogenicity of tick-borne encephalitis virus

, , , , , & show all
Pages 638-651 | Received 23 Jun 2011, Accepted 24 Mar 2012, Published online: 26 Jun 2012

References

  • Aleshin , E. , Shiryaev , S.A. , Strongin , A.Y. and Liddington , R.C. 2007 . Structural evidence for regulation and specificity of flaviviral proteases and evolution of the Flaviviridae fold . Protein Science , 16 : 795 – 806 .
  • Al-Lazikani , B. , Jung , J. , Xiang , Z. and Honig , B. 2001 . Protein structure prediction . Current Opinion in Chemical Biology , 5 : 51 – 56 .
  • Arai , M. , Mitsuke , H. , Ikeda , M. , Xia , J.X. , Kikuchi , T. , Satake , M. and Shimizu , T. 2004 . ConPred II: A consensus prediction method for obtaining transmembrane topology models with high reliability . Nucleic Acids Research , 32 : 390 – 393 .
  • Belikov , S.I. , Leonova , G.N. , Kondratov , I.G. , Romanova , E.V. and Pavlenko , E.V. 2010 . Coding nucleotide sequences of tick-borne encephalitis virus strains isolated from human blood without clinical symptoms of infection . Russian Journal of Genetics , 46 : 315 – 322 .
  • Berendsen , J.C. , Postma , J.P.M. , Van Gunsteren , W.F. and Hermans , J. 1981 . Interaction models for water in relation to protein hydration . Intermolecular Forces , 11 : 331 – 342 .
  • Berman , H.M. , Westbrook , J. , Feng , Z. , Gilliland , G. , Bhat , T.N. , Weissig , H. , … and Bourne , P.E. 2000 . The protein data bank . Nucleic Acids Research , 28 : 235 – 242 .
  • Biedrzycka , A. , Cauchi , M.R. , Bartholomeusz , A. , Gorman , J.J. and Wright , P.J. 1987 . Characterization of protease cleavage sites involved in the formation of the envelope glycoprotein and three non-structural proteins of dengue virus type 2, new guinea C strain . Journal of General Virology , 68 : 1317 – 1326 .
  • Billoir , F. , de Chesse , R. , Tolou , H. , de Micco , P. , Gould , E.A. and de Lamballerie , X. 2000 . Phylogeny of the genus flavivirus using complete coding sequences of arthropod-borne viruses and viruses with no known vector . Journal of General Virology , 81 : 781 – 790 .
  • Borisevich , V. , Seregin , A. , Nistler , R. , Mutabazi , D. and Yamshchikov , V. 2006 . Biological properties of chimeric West Nile viruses . Virology , 349 : 371 – 381 .
  • Brodsky , L.I. , Drachev , A.L. , Leontovich , A.M. and Feranchuk , S.I. 1993 . A novel method of multiple alignment of biopolymer sequences . Biosystems , 30 : 65 – 79 .
  • Chambers , T.J. , Hahn , C.S. , Galler , R. and Rice , C.M. 1990 . Flavivirus genome organization, expression, and replication . Annual Review of Microbiology , 44 : 649 – 688 .
  • Chambers , T.J. , Weir , R.C. , Grakoui , A. , McCourt , D.W. , Bazan , J.F. , Fletterick , R.J. and Rice , C.M. 1990 . 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 . Proceedings of the National Academy of Sciences of the United States of the America , 87 : 8898 – 8902 .
  • Dentzer , T.G. , Lorenz , I.C. , Evans , M.J. and Rice , C.M. 2009 . Determinants of the hepatitis C virus nonstructural protein 2 protease domain required for production of infectious virus . Journal of Virology , 83 : 12702 – 12713 .
  • Duan , Y. , Wu , C. , Chowdhury , S. , Lee , M.C. , Xiong , G. , … and Kollman , P. 2003 . A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations . Journal of Computational Chemistry , 24 : 1999 – 2012 .
  • Ecker , M. , Allison , S.L. , Meixner , T. and Heinz , F.X. 1999 . Sequence analysis and genetic classification of tick-borne encephalitis viruses from Europe and Asia . Journal of General Virology , 80 : 179 – 185 .
  • Erbel , P. , Schiering , N. , D’Arcy , A. , Renatus , M. , Kroemer , M. , Lim , S.P. , … and Hommel , U. 2006 . Structural basis for the activation of flaviviral NS3 proteases from dengue and West Nile virus . Nature Structural & Molecular Biology , 13 : 372 – 373 .
  • Falgout , B. , Miller , R.H. and Lai , C.J. 1993 . Deletion analysis of dengue virus type 4 nonstructural protein NS2B: Identification of a domain required for NS2B-NS3 protease activity . Journal of Virology , 67 : 2034 – 2042 .
  • Falgout , B. , Pethel , M. , Zhang , Y.M. and Lai , C.J. 1991 . Both nonstructural proteins NS2B and NS3 are required for the proteolytic processing of dengue virus nonstructural proteins . Journal of Virology , 65 : 2467 – 2475 .
  • Fogolari , F. , Brigo , A. and Molinari , H. 2002 . The Poisson-Boltzmann equation for biomolecular electrostatics: A tool for structural biology . Journal of Molecular Recognition , 15 : 377 – 392 .
  • Garoff , H. , Hewson , R. and Opstelten , D.J. 1998 . Virus maturation by budding . Microbiology and Molecular Biology Reviews , 62 : 1171 – 1190 .
  • Gorbalenya , E. , Donchenko , A.P. , Koonin , E.V. and Blinov , V.M. 1989 . N-terminal domains of putative helicases of flavi- and pestiviruses may be serine proteases . Nucleic Acids Research , 17 : 3889 – 3897 .
  • Heinz , F.X. and Mandl , C.W. 1993 . The molecular biology of tick-borne encephalitis virus . Review Article. APMIS , 101 : 735 – 745 .
  • Heyman , P. , Cochez , C. , Hofhuis , A. , van der Giessen , J. , Sprong , H. , Porter , S.R. , … and Papa , A. 2010 . A clear and present danger: Tick-borne diseases in Europe . Expert Review of Anti-Infective Therapy , 8 : 33 – 50 .
  • Jaskierny , J. , Panahi , A. and Feig , M. 2011 . Effect of flanking residues on the conformational sampling of the internal fusion peptide from Ebola virus . Proteins , 79 : 1109 – 1117 .
  • Kabsch , W.A. 1978 . A method is discussed for obtaining the best proper rotation to relate two sets of vectors . Acta Crystallographica , 34 : 827 – 828 .
  • Kabsch , W. and Sander , C. 1983 . Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features . Biopolymers , 22 : 2577 – 2637 .
  • Kiermayr , S. , Kofler , R.M. , Mandl , C.W. , Messner , P. and Heinz , F.X. 2004 . Isolation of capsid protein dimers from the tick-borne encephalitis flavivirus and in vitro assembly of capsid-like particles . Journal of Virology , 78 : 8078 – 8084 .
  • Kyte , J. and Doolittle , R.F. 1982 . A simple method for displaying the hydropathic character of a protein . Journal of Molecular Biology , 157 : 105 – 132 .
  • Leonova , G.N. 1997 . The antigenic, biological and molecular genetic characteristics of the tick-borne encephalitis virus population in the Far East . Zhurnal Mikrobiologii, Epidemiologii i Immunobiologii , 5 : 94 – 97 .
  • Leonova , G.N. , Belikov , S.I. , Kulakova , N.V. , Pavlenko , E.V. and Borisevich , V.G. 2004 . Molecular typing of the tick-borne encephalitis virus isolated from patients with different-infection severities in the south of Russia’s Far East . Molekuliarnaia Genetika, Mikrobiologia, i Virusologa , 2 : 32 – 37 .
  • Lescar , J. , Luo , D. , Xu , T. , Sampath , A. , Lim , S.P. , Canard , B. and Vasudevan , S.G. 2008 . Towards the design of antiviral inhibitors against flaviviruses: The case for the multifunctional NS3 protein from dengue virus as a target . Antiviral Research , 80 : 94 – 101 .
  • Lindenbach , B.D. and Rice , C.M. 2001 . “ Flaviviridae: The viruses and their replication ” . In Fields virology , Edited by: Knipe , D.M. and Howley , P.M. 991 – 1041 . Philadelphia , PA : Lippincott-Raven Publishers .
  • Lobigs , M. 1993 . Flavivirus premembrane protein cleavage and spike heterodimer secretion require the function of the viral proteinase NS3 . Proceedings of the National Academy of Sciences of the United States of the America , 90 : 6218 – 6222 .
  • Luo , D. , Xu , T. , Watson , R.P. , Scherer-Becker , D. , Sampath , A. , Jahnke , W. , … and Lescar , J. 2008 . Insights into RNA unwinding and ATP hydrolysis by the flavivirus NS3 protein . EMBO Journal , 23 : 3209 – 3219 .
  • Mackenzie , J.M. , Jones , M.K. and Young , P.R. 1996 . Immunolocalization of the dengue virus nonstructural glycoprotein NS1 suggests a role in viral RNA replication . Virology , 220 : 232 – 240 .
  • Mackow , E. , Makino , Y. , Zhao , B.T. , Zhang , Y.M. , Markoff , L. , Buckler-White , A. , … and Lai , C.J. 1987 . The nucleotide sequence of dengue type 4 virus: Analysis of genes coding for nonstructural proteins . Virology , 159 : 217 – 228 .
  • Muylaert , R. , Chambers , T.J. , Galler , R. and Rice , C.M. 1996 . Mutagenesis of the N-linked glycosylation sites of the yellow fever virus NS1 protein: Effects on virus replication and mouse neurovirulence . Virology , 222 : 159 – 168 .
  • Muylaert , R. , Galler , R. and Rice , C.M. 1997 . Genetic analysis of the yellow fever virus NS1 protein: Identification of a temperature-sensitive mutation which blocks RNA accumulation . Journal of Virology , 71 : 291 – 298 .
  • Petrey , D. , Xiang , Z. , Tang , C.L. , Xie , L. , Gimpelev , M. , Mitros , T. , … and Honig , B. 2003 . Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling . Proteins , 53 : 430 – 435 .
  • Pettersen , E.F. , Goddard , T.D. , Huang , C.C. , Couch , G.S. , Greenblatt , D.M. , Meng , E.C. and Ferrin , T.E. 2004 . UCSF Chimera – a visualization system for exploratory research and analysis . Journal of Computational Chemistry , 25 : 1605 – 1612 .
  • Robin , G. , Chappell , K. , Stoermer , M.J. , Hu , S.H. , Young , P.R. , Fairlie , D.P. and Martin , J.L. 2009 . Structure of West Nile virus NS3 protease: Ligand stabilization of the catalytic conformation . Journal of Molecular Biology , 385 : 1568 – 1577 .
  • Sampath , A. and Padmanabhan , R. 2009 . Molecular targets for flavivirus drug discovery . Antiviral Research , 81 : 6 – 15 .
  • Schnell , J.R. and Chou , J.J. 2008 . Structure and mechanism of the M2 proton channel of influenza A virus . Nature , 7178 : 591 – 595 .
  • Stocks , C.E. and Lobigs , M. 1998 . Signal peptidase cleavage at the flavivirus C-prM junction: Dependence on the viral NS2B-3 protease for efficient processing requires determinants in C, the signal peptide, and prM.Signal peptidase cleavage at the flavivirus C-prM junction: Dependence on the viral NS2B-3 protease for efficient processing requires determinants in C, the signal peptide, and prM . Journal of Virology , 72 : 2141 – 2149 .
  • Suss , J. 2008 . Tick-borne encephalitis in Europe and beyond–the epidemiological situation as of 2007 . Eurosurveillance Weekly , 13 : 1 – 8 .
  • Wang , C.C. , Huang , Z.S. , Chiang , P.L. , Chen , C.T. and Wu , H.N. 2009 . Analysis of the nucleoside triphosphatase, RNA triphosphatase, and unwinding activities of the helicase domain of dengue virus NS3 protein . FEBS Letters , 583 : 691 – 696 .
  • Wheeler , D.L. , Barrett , T. , Benson , D.A. , Bryant , S.H. , Canese , K. , Chetvernin , V. , … and Yaschenko , E. 2008 . Database resources of the national center for biotechnology information . Nucleic Acids Research , 36 : 13 – 21 .
  • Winkler , G. , Maxwell , S.E. , Ruemmler , C. and Stollarl , V. 1989 . Newly synthesized dengue-2 virus nonstructural protein NS1 is a soluble protein but becomes partially hydrophobic and membrane-associated after dimerization . Virology , 171 : 302 – 305 .
  • Yamshchikov , V.F. and Compans , R.W. 1994 . Processing of the intracellular form of the West Nile virus capsid protein by the viral NS2B-NS3 protease: An in vitro study . Journal of Virology , 68 : 5765 – 5771 .
  • Yamshchikov , V.F. and Compans , R.W. 1995 . Formation of the flavivirus envelope: Role of the viral NS2B-NS3 protease . Journal of Virology , 69 : 1995 – 2003 .
  • Yang , S. and Honig , B. 2000 . An integrated approach to the analysis and modeling of protein sequences and structures . Journal of Molecular Biology , 301 : 665 – 711 .
  • Yu , X. , Wang , Q. , Yang , J.C. , Buch , I. , Tsai , C.J. , Ma , B. , … and Zheng , J. 2009 . Mutational analysis and allosteric effects in the HIV-1 capsid protein carboxyl-terminal dimerization domain . Biomacromolecules , 10 : 390 – 399 .
  • Yusof , R. , Clum , S. , Wetzel , M. , Murthy , H.M. and Padmanabhan , R. 2000 . Purified NS2B/NS3 serine protease of dengue virus type 2 exhibits cofactor NS2B dependence for cleavage of substrates with dibasic amino acids in vitro . Journal of Biological Chemistry , 275 : 9963 – 9969 .
  • Zilber , L.A. and Soloviev , V.D. 1946 . Far Eastern tick-borne spring-summer (spring) encephalitis . American Review of Soviet Medicine , 5 : 1 – 80 .

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.