Table of Contents
Journal of Viruses
Volume 2014, Article ID 752656, 6 pages
http://dx.doi.org/10.1155/2014/752656
Research Article

Recognition of Errors in the Refinement and Validation of Three-Dimensional Structures of AC1 Proteins of Begomovirus Strains by Using ProSA-Web

Department of Science, Faculty of Arts, Science and Commerce, Mody Institute of Technology and Science, Lakshmangarh, Sikar, Rajasthan 332311, India

Received 22 June 2013; Revised 2 October 2013; Accepted 2 October 2013; Published 2 January 2014

Academic Editor: Sílvia Bofill-Mas

Copyright © 2014 Rajneesh Prajapat 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. R. E. Matthews, “Classification and nomenclature of viruses,” Intervirology, vol. 12, no. 3–5, pp. 129–296, 1979. View at Google Scholar · View at Scopus
  2. R. M. Goodman, “Geminiviruses,” Journal of General Virology, vol. 54, pp. 9–21, 1981. View at Google Scholar
  3. J. Stanley, D. M. Bisaro, R. W. Briddon et al., “Family Geminiviridae,” in Virus Taxonomy: Eighth Report of the International Committee on Taxonomy of Viruses, pp. 301–326, Academic Press, 2005. View at Google Scholar
  4. C. M. Fauquet, R. W. Briddon, J. K. Brown et al., “Geminivirus strain demarcation and nomenclature,” Archives of Virology, vol. 153, no. 4, pp. 783–821, 2008. View at Publisher · View at Google Scholar · View at Scopus
  5. M. R. Rojas, C. Hagen, W. J. Lucas, and R. L. Gilbertson, “Exploiting chinks in the plant's armor: evolution and emergence of geminiviruses,” Annual Review of Phytopathology, vol. 43, pp. 361–394, 2005. View at Publisher · View at Google Scholar · View at Scopus
  6. A. Marwal, A. Sahu, R. Prajapat, D. K. Choudhary, and R. K. Gaur, “Molecular and recombinational characterization of begomovirus infecting an ornamental plant Alternanthera sessilis: a new host of Tomato Leaf Curl Kerala Virus reported in India,” Science International, vol. 1, pp. 51–56, 2013. View at Google Scholar
  7. R. Prajapat, A. Marwal, A. Sahu, and R. K. Gaur, “Molecular in silico structure and recombination analysis of betasatellite in Calotropis procera associated with begomovirus,” Archives of Phytopathology and Plant Protection, vol. 45, pp. 1980–1990, 2012. View at Google Scholar
  8. A. Marwal, A. Sahu, R. Prajapat, D. K. Choudhary, and R. K. Gaur, “First report of association of begomovirus with the leaf curl disease of a common weed Datura inoxia,” Indian Journal of Virology, vol. 23, pp. 83–84, 2012. View at Publisher · View at Google Scholar · View at Scopus
  9. R. Prajapat, A. Marwal, A. Sahu, and R. K. Gaur, “First report of Begomovirus infecting Sonchus asper in India,” Science International, vol. 1, pp. 108–110, 2013. View at Google Scholar
  10. J. A. Fox, S. McMillan, and B. F. F. Ouellette, “A compilation of molecular biology web servers: 2006 update on the Bioinformatics links directory,” Nucleic Acids Research, vol. 34, pp. W3–W5, 2006. View at Publisher · View at Google Scholar · View at Scopus
  11. H. M. Berman, S. K. Burley, W. Chiu et al., “Outcome of a workshop on archiving structural models of biological macromolecules,” Structure, vol. 14, no. 8, pp. 1211–1217, 2006. View at Publisher · View at Google Scholar · View at Scopus
  12. M. J. Sippl, “Recognition of errors in three-dimensional structures of proteins,” Proteins, vol. 17, no. 4, pp. 355–362, 1993. View at Publisher · View at Google Scholar · View at Scopus
  13. L. Banci, I. Bertini, F. Cantini et al., “Solution structure and intermolecular interactions of the third metal-binding domain of ATP7A, the Menkes disease protein,” The Journal of Biological Chemistry, vol. 281, no. 39, pp. 29141–29147, 2006. View at Publisher · View at Google Scholar · View at Scopus
  14. O. Llorca, M. Betti, J. M. González, A. Valencia, A. J. Márquez, and J. M. Valpuesta, “The three-dimensional structure of an eukaryotic glutamine synthetase: functional implications of its oligomeric structure,” Journal of Structural Biology, vol. 156, no. 3, pp. 469–479, 2006. View at Publisher · View at Google Scholar · View at Scopus
  15. K. Teilum, J. C. Hoch, V. Goffin, S. Kinet, J. A. Martial, and B. B. Kragelund, “Solution structure of human prolactin,” Journal of Molecular Biology, vol. 351, no. 4, pp. 810–823, 2005. View at Publisher · View at Google Scholar · View at Scopus
  16. D. Petrey and B. Honig, “Protein structure prediction: inroads to biology,” Molecular Cell, vol. 20, no. 6, pp. 811–819, 2005. View at Publisher · View at Google Scholar · View at Scopus
  17. K. Ginalski, “Comparative modeling for protein structure prediction,” Current Opinion in Structural Biology, vol. 16, no. 2, pp. 172–177, 2006. View at Publisher · View at Google Scholar · View at Scopus
  18. R. Panteri, A. Paiardini, and F. Keller, “A 3D model of Reelin subrepeat regions predicts Reelin binding to carbohydrates,” Brain Research, vol. 1116, no. 1, pp. 222–230, 2006. View at Publisher · View at Google Scholar · View at Scopus
  19. J. Mansfeld, S. Gebauer, K. Dathe, and R. Ulbrich-Hofmann, “Secretory phospholipase A2 from Arabidopsis thaliana: insights into the three-dimensional structure and the amino acids involved in catalysis,” Biochemistry, vol. 45, no. 18, pp. 5687–5694, 2006. View at Publisher · View at Google Scholar · View at Scopus
  20. M. K. Beissenhirtz, F. W. Scheller, M. S. Viezzoli, and F. Lisdat, “Engineered superoxide dismutase monomers for superoxide biosensor applications,” Analytical Chemistry, vol. 78, no. 3, pp. 928–935, 2006. View at Publisher · View at Google Scholar · View at Scopus
  21. M. Wiederstein and M. J. Sippl, “Protein sequence randomization: efficient estimation of protein stability using knowledge-based potentials,” Journal of Molecular Biology, vol. 345, no. 5, pp. 1199–1212, 2005. View at Publisher · View at Google Scholar · View at Scopus
  22. M. Wiederstein and M. J. Sippl, “ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins,” Nucleic Acids Research, vol. 35, pp. W407–W410, 2007. View at Publisher · View at Google Scholar · View at Scopus
  23. R. A. Laskowski, M. W. MacArthur, D. S. Moss, and J. M. Thornton, “PROCHECK: a program to check the stereochemical quality of protein structures,” Journal of Applied Crystallography, vol. 26, pp. 283–291, 1993. View at Google Scholar
  24. K. M. Goh, N. M. Mahadi, O. Hassan, R. N. Zaliha, R. A. Rahman, and R. M. Illias, “Molecular modeling of a predominant β-CGTase G1 and analysis of ionic interaction in CGTase,” Biotechnology, vol. 7, no. 3, pp. 418–429, 2008. View at Publisher · View at Google Scholar · View at Scopus
  25. S. C. Lovell, I. W. Davis, W. B. Arendall et al., “Structure validation by Cα geometry: φ,ψ and Cβ deviation,” Proteins, vol. 50, no. 3, pp. 437–450, 2003. View at Publisher · View at Google Scholar · View at Scopus
  26. J. Xiao, Z. Li, M. Sun, Y. Zhang, and C. Sun, “Homology modeling and molecular dynamics study of GSK3/SHAGGY-like kinase,” Computational Biology and Chemistry, vol. 28, no. 3, pp. 179–188, 2004. View at Publisher · View at Google Scholar · View at Scopus
  27. G. Chang and C. B. Roth, “Structure of MsbA from E. coli: a homolog of the multidrug resistance ATP binding cassette (ABC) transporters,” Science, vol. 293, no. 5536, pp. 1793–1800, 2001. View at Publisher · View at Google Scholar · View at Scopus