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Computational and Mathematical Methods in Medicine
Volume 2013, Article ID 108910, 9 pages
http://dx.doi.org/10.1155/2013/108910
Research Article

Space Constrained Homology Modelling: The Paradigm of the RNA-Dependent RNA Polymerase of Dengue (Type II) Virus

Bioinformatics & Medical Informatics Team, Biomedical Research Foundation, Academy of Athens, Soranou Efessiou 4, 11527 Athens, Greece

Received 3 July 2013; Accepted 8 July 2013

Academic Editor: Carla Sofia Carvalho

Copyright © 2013 Dimitrios Vlachakis et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. A. T. Brünger, “X-ray crystallography and NMR reveal complementary views of structure and dynamics,” Nature Structural Biology, vol. 4, supplement, pp. 862–865, 1997. View at Google Scholar
  2. H. Wieman, K. Tøndel, E. Anderssen, and F. Drabløs, “Homology-based modelling of targets for rational drug design,” Mini-Reviews in Medicinal Chemistry, vol. 4, no. 7, pp. 793–804, 2004. View at Google Scholar
  3. H. Venselaar, R. P. Joosten, B. Vroling et al., “Homology modelling and spectroscopy, a never-ending love story,” European Biophysics Journal, vol. 39, no. 4, pp. 551–563, 2010. View at Publisher · View at Google Scholar · View at Scopus
  4. A. Kubarenko, M. Frank, and A. N. R. Weber, “Structure-function relationships of Toll-like receptor domains through homology modelling and molecular dynamics,” Biochemical Society Transactions, vol. 35, no. 6, pp. 1515–1518, 2007. View at Publisher · View at Google Scholar · View at Scopus
  5. M. Wiltgen and G. P. Tilz, “Homology modelling: a review about the method on hand of the diabetic antigen GAD 65 structure prediction,” Wiener Medizinische Wochenschrift, vol. 159, no. 5-6, pp. 112–125, 2009. View at Publisher · View at Google Scholar · View at Scopus
  6. G. Folkers, F. Alber, I. Amrhein et al., “Integrated homology modelling and X-ray study of herpes simplex virus I thymidine kinase: a case study,” Journal of Receptor and Signal Transduction Research, vol. 17, no. 1–3, pp. 475–494, 1997. View at Google Scholar · View at Scopus
  7. H. Ago, T. Adachi, A. Yoshida et al., “Crystal structure of the RNA-dependent RNA polymerase of hepatitis C virus,” Structure, vol. 7, no. 11, pp. 1417–1426, 1999. View at Publisher · View at Google Scholar · View at Scopus
  8. K. H. Choi, J. M. Groarke, D. C. Young et al., “The structure of the RNA-dependent RNA polymerase from bovine viral diarrhea virus establishes the role of GTP in de novo initiation,” Proceedings of the National Academy of Sciences of the United States of America, vol. 101, no. 13, pp. 4425–4430, 2004. View at Publisher · View at Google Scholar · View at Scopus
  9. P. Gouet, E. Courcelle, D. I. Stuart, and F. Métoz, “ESPript: analysis of multiple sequence alignments in PostScript,” Bioinformatics, vol. 15, no. 4, pp. 305–308, 1999. View at Publisher · View at Google Scholar · View at Scopus
  10. C. H. Calisher and E. A. Gould, “Taxonomy of the virus family Flaviviridae,” Advances in Virus Research, vol. 59, pp. 1–19, 2003. View at Publisher · View at Google Scholar · View at Scopus
  11. S. E. Behrens, C. W. Grassmann, H. J. Thiel, G. Meyers, and N. Tautz, “Characterization of an autonomous subgenomic pestivirus RNA replicon,” Journal of Virology, vol. 72, no. 3, pp. 2364–2372, 1998. View at Google Scholar · View at Scopus
  12. S. E. Behrens, L. Tomei, and R. de Francesco, “Identification and properties of the RNA-dependent RNA polymerase of hepatitis C virus,” The EMBO Journal, vol. 15, no. 1, pp. 12–22, 1996. View at Google Scholar · View at Scopus
  13. Y. Tao, D. L. Farsetta, M. L. Nibert, and S. C. Harrison, “RNA synthesis in a cage—structural studies of reovirus polymerase λ3,” Cell, vol. 111, no. 5, pp. 733–745, 2002. View at Publisher · View at Google Scholar · View at Scopus
  14. K. K. Ng, M. M. Cherney, A. L. Vázquez et al., “Crystal structures of active and inactive conformations of a caliciviral RNA-dependent RNA polymerase,” The Journal of Biological Chemistry, vol. 277, no. 2, pp. 1381–1387, 2002. View at Publisher · View at Google Scholar · View at Scopus
  15. J. L. Hansen, A. M. Long, and S. C. Schultz, “Structure of the RNA-dependent RNA polymerase of poliovirus,” Structure, vol. 5, no. 8, pp. 1109–1122, 1997. View at Google Scholar · View at Scopus
  16. S. J. Butcher, J. M. Grimes, E. V. Makeyev, D. H. Bamford, and D. I. Stuart, “A mechanism for initiating RNA-dependent RNA polymerization,” Nature, vol. 410, no. 6825, pp. 235–240, 2001. View at Publisher · View at Google Scholar · View at Scopus
  17. G. Kamer and P. Argos, “Primary structural comparison of RNA-dependent polymerases from plant, animal and bacterial viruses,” Nucleic Acids Research, vol. 12, no. 18, pp. 7269–7282, 1984. View at Publisher · View at Google Scholar · View at Scopus
  18. K. H. Choi, A. Gallei, P. Becher, and M. G. Rossmann, “The structure of bovine viral diarrhea virus RNA-dependent RNA polymerase and its amino-terminal domain,” Structure, vol. 14, no. 7, pp. 1107–1113, 2006. View at Publisher · View at Google Scholar · View at Scopus
  19. D. J. Gubler and G. G. Clark, “Dengue/dengue hemorrhagic fever: the emergence of a global health problem,” Emerging Infectious Diseases, vol. 1, no. 2, pp. 55–57, 1995. View at Google Scholar · View at Scopus
  20. T. L. Yap, T. Xu, Y. L. Chen et al., “Crystal structure of the dengue virus RNA-dependent RNA polymerase catalytic domain at 1.85-angstrom resolution,” Journal of Virology, vol. 81, no. 9, pp. 4753–4765, 2007. View at Publisher · View at Google Scholar · View at Scopus
  21. MOE (The Molecular Operating Environment) Version 2005. 06, software available from Chemical Computing Group Inc., 1010 Sherbrooke Street West, Suite 910, Montreal, Canada H3A 2R7, http://www.chemcomp.com.
  22. D. A. Benson, I. Karsch-Mizrachi, D. J. Lipman, J. Ostell, and D. L. Wheeler, “GenBank,” Nucleic Acids Research, vol. 35, supplement 1, pp. D21–D25, 2007. View at Publisher · View at Google Scholar · View at Scopus
  23. C. Combet, C. Blanchet, C. Geourjon, and G. Deléage, “NPS@: network protein sequence analysis,” Trends in Biochemical Sciences, vol. 25, no. 3, pp. 147–150, 2000. View at Publisher · View at Google Scholar · View at Scopus
  24. S. F. Altschul, T. L. Madden, A. A. Schäffer et al., “Gapped BLAST and PSI-BLAST: a new generation of protein database search programs,” Nucleic Acids Research, vol. 25, no. 17, pp. 3389–3402, 1997. View at Publisher · View at Google Scholar · View at Scopus
  25. S. T. Sherry, M. H. Ward, M. Kholodov et al., “DbSNP: the NCBI database of genetic variation,” Nucleic Acids Research, vol. 29, no. 1, pp. 308–311, 2001. View at Google Scholar · View at Scopus
  26. H. Berman, K. Henrick, H. Nakamura, and J. L. Markley, “The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data,” Nucleic Acids Research, vol. 35, supplement 1, pp. D301–D303, 2007. View at Publisher · View at Google Scholar · View at Scopus
  27. D. O'Farrell, R. Trowbridge, D. Rowlands, and J. Jäger, “Substrate complexes of hepatitis C virus RNA polymerase (HC-J4): structural evidence for nucleotide import and de-novo initiation,” Journal of Molecular Biology, vol. 326, no. 4, pp. 1025–1035, 2003. View at Publisher · View at Google Scholar · View at Scopus
  28. M. Levitt, “Accurate modeling of protein conformation by automatic segment matching,” Journal of Molecular Biology, vol. 226, no. 2, pp. 507–533, 1992. View at Publisher · View at Google Scholar · View at Scopus
  29. T. Fechteler, U. Dengler, and D. Schomburg, “Prediction of protein three-dimensional structures in insertion and deletion regions: a procedure for searching data bases of representative protein fragments using geometric scoring criteria,” Journal of Molecular Biology, vol. 253, no. 1, pp. 114–131, 1995. View at Publisher · View at Google Scholar · View at Scopus
  30. A. D. MacKerell Jr., N. Banavali, and N. Foloppe, “Development and current status of the CHARMM force field for nucleic acids,” Biopolymers, vol. 56, no. 4, pp. 257–265, 2000. View at Google Scholar
  31. R. A. Laskowski, J. A. C. Rullmann, M. W. MacArthur, R. Kaptein, and J. M. Thornton, “AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR,” Journal of Biomolecular NMR, vol. 8, no. 4, pp. 477–486, 1996. View at Google Scholar · View at Scopus
  32. W. L. DeLano, “The PyMOL Molecular Graphics System,” DeLano Scientific, San Carlos, CA, USA, 2002, http://www.pymol.org.
  33. S. J. Weiner, P. A. Kollman, D. A. Case et al., “A new force field for molecular mechanical simulation of nucleic acids and proteins,” Journal of the American Chemical Society, vol. 106, no. 3, pp. 765–784, 1984. View at Publisher · View at Google Scholar · View at Scopus
  34. L. A. Kelley, R. M. MacCallum, and M. J. E. Sternberg, “Enhanced genome annotation using structural profiles in the program 3D-PSSM,” Journal of Molecular Biology, vol. 299, no. 2, pp. 499–520, 2000. View at Google Scholar · View at Scopus
  35. F. Ferron, C. Bussetta, H. Dutartre, and B. Canard, “The modeled structure of the RNA dependent RNA polymerase of GBV-C virus suggests a role for motif E in Flaviviridae RNA polymerases,” BMC Bioinformatics, vol. 6, article 255, 2005. View at Publisher · View at Google Scholar · View at Scopus
  36. D. G. Vassylyev and I. Artsimovitch, “Tracking RNA polymerase, one step at a time,” Cell, vol. 123, no. 6, pp. 977–979, 2005. View at Publisher · View at Google Scholar · View at Scopus