Theoretical study of the Usutu virus helicase 3D structure, by means of computer-aided homology modelling

Theor Biol Med Model. 2009 Jun 25;6:9. doi: 10.1186/1742-4682-6-9.


Background: Usutu virus belongs to the Flaviviridae viral family and constitutes an important pathogen. The viral helicase is an ideal target for inhibitor design, since this enzyme is essential for the survival, proliferation and transmission of the virus.

Results: Towards a drug-design approach, the 3D model of the Usutu virus helicase structure has been designed, using conventional homology modelling techniques and the known 3D-structure of the Murray Valley Encephalitis virus helicase, of the same viral family, as template. The model was then subjected to extended molecular dynamics simulations in a periodic box, filled with explicit water molecules for 10 nanoseconds. The reliability of the model was confirmed by obtaining acceptable scores from a variety of in silico scoring tools, including Procheck and Verify3D.

Conclusion: [corrected] The 3D model of the Usutu virus helicase exhibits in silico all known structural characteristics of the Flaviviridae viral family helicase enzymes and could provide the platform for further de novo structure-based design of novel anti-Usutu agents.

Publication types

  • Comparative Study

MeSH terms

  • Adenosine Triphosphate / metabolism
  • Amino Acid Sequence
  • Binding Sites
  • Computer Simulation
  • Encephalitis Virus, Murray Valley / enzymology
  • Encephalitis Virus, Murray Valley / genetics
  • Flaviviridae / enzymology*
  • Flaviviridae / genetics
  • Models, Molecular*
  • Molecular Sequence Data
  • Protein Conformation
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • RNA Helicases / chemistry*
  • RNA Helicases / genetics
  • RNA Helicases / metabolism
  • Sequence Homology, Amino Acid
  • Static Electricity
  • Structural Homology, Protein
  • Thermodynamics


  • Adenosine Triphosphate
  • RNA Helicases