Homology modeling and molecular dynamics study of West Nile virus NS3 protease: a molecular basis for the catalytic activity increased by the NS2B cofactor

Proteins. 2006 Nov 15;65(3):692-701. doi: 10.1002/prot.21129.


The West Nile virus (WNV) NS3 serine protease, which plays an important role in assembly of infective virion, is an attractive target for anti-WNV drug development. Cofactors NS2B and NS4A increase the catalytic activity of NS3 in dengue virus and Hepatitis C virus, respectively. Recent studies on the WNV-NS3 characterize the catalytically active form of NS3 by tethering the 40-residue cofactor NS2B. It is suggested that NS2B is essential for the NS3 activity in WNV, while there is no information of the WNV-NS3-related crystal structure. To understand the role of NS2B/substrate in the NS3 catalytic activity, we built a series of models: WNV-NS3 and WNV-NS3-NS2B and WNV-NS3-NS2B-substrate using homology modeling and molecular modeling techniques. Molecular dynamics (MD) simulations were performed for 2.75 ns on each model, to investigate the structural stabilization and catalytic triad motion of the WNV NS3 protease with and without NS2B/substrate. The simulations show that the NS3 rearrangement occurs upon the NS2B binding, resulting in the stable D75-OD1...H51-NH hydrogen bonding. After the substrate binds to the NS3-NS2B active site, the NS3 protease becomes more stable, and the catalytic triad is formed. These results provide a structural basis for the activation and stabilization of the enzyme by its cofactor and substrate.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Binding Sites
  • Catalytic Domain
  • Models, Molecular
  • Molecular Sequence Data
  • Protein Conformation
  • RNA Helicases / chemistry
  • Sequence Alignment
  • Serine Endopeptidases / chemistry*
  • Structural Homology, Protein
  • Substrate Specificity
  • Thermodynamics
  • Viral Nonstructural Proteins / chemistry*
  • West Nile virus / chemistry
  • West Nile virus / enzymology*


  • NS2B protein, flavivirus
  • NS3 protein, flavivirus
  • NS3 protein, hepatitis C virus
  • Viral Nonstructural Proteins
  • Serine Endopeptidases
  • RNA Helicases