Table of Contents
ISRN Neurology
Volume 2011 (2011), Article ID 265253, 10 pages
http://dx.doi.org/10.5402/2011/265253
Research Article

Identification of Potential Drug Targets Implicated in Parkinson's Disease from Human Genome: Insights of Using Fused Domains in Hypothetical Proteins as Probes

1Department of Bioinformatics, School of Bioengineering, SRM University, Kattankulathur, Tamil Nadu 603 203, India
2Physics Department, Bangalore University, Jnanabharathi Campus, Bangalore 560 056, India
3Department of Biotechnology, Sir M. Visvesvaraya Institute of Technology, Near Hunasamaranahalli, Via Yelahanka, Bangalore 562 157, India

Received 20 April 2011; Accepted 21 May 2011

Academic Editors: A. Conti, C. Johansson, A. Mamelak, and B. Moreno-López

Copyright © 2011 N. Rathankar 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. N. Lev and E. Melamed, “Heredity in Parkinson's disease: new findings,” Israel Medical Association Journal, vol. 3, no. 6, pp. 435–438, 2001. View at Google Scholar
  2. M. Y. Galperin, “Conserved 'hypothetical' proteins: new hints and new puzzles,” Comparative and Functional Genomics, vol. 2, no. 1, pp. 14–18, 2001. View at Publisher · View at Google Scholar · View at Scopus
  3. I. Iliopoulos, S. Tsoka, M. A. Andrade et al., “Genome sequences and great expectations,” Genome Biology, vol. 2, no. 1, INTERACTIONS0001, 2001. View at Google Scholar
  4. P. Suravajhala, “Hypo, hype and “hyp” human proteins,” Bioinformation, vol. 2, no. 1, pp. 31–33, 2007. View at Google Scholar
  5. S. A. Teichmann, C. Chothia, and M. Gerstein, “Advances in structural genomics,” Current Opinion in Structural Biology, vol. 9, no. 3, pp. 390–399, 1999. View at Publisher · View at Google Scholar
  6. T. C. Terwilliger, G. Waldo, T. S. Peat, J. M. Newman, K. Chu, and J. Berendzen, “Class-directed structure determination: foundation for a protein structure initiative,” Protein Science, vol. 7, no. 9, pp. 1851–1856, 1998. View at Google Scholar
  7. C. Vogel, C. Berzuini, M. Bashton, J. Gough, and S. A. Teichmann, “Supra-domains: evolutionary units larger than single protein domains,” Journal of Molecular Biology, vol. 336, no. 3, pp. 809–823, 2004. View at Publisher · View at Google Scholar · View at Scopus
  8. M. Gerstein and H. Hegyi, “Comparing genomes in terms of protein structure: surveys of a finite parts list,” FEMS Microbiology Reviews, vol. 22, no. 4, pp. 277–304, 1998. View at Publisher · View at Google Scholar · View at Scopus
  9. T. Mebatsion, M. J. Schnell, and K. K. Conzelmann, “Mokola virus glycoprotein and chimeric proteins can replace rabies virus glycoprotein in the rescue of infectious defective rabies virus particles,” Journal of Virology, vol. 69, no. 3, pp. 1444–1451, 1995. View at Google Scholar · View at Scopus
  10. S. D. Lupton, L. L. Brunton, V. A. Kalberg, and R. W. Overell, “Dominant positive and negative selection using a hygromycin phosphotransferase-thymidine kinase fusion gene,” Molecular and Cellular Biology, vol. 11, no. 6, pp. 3374–3378, 1991. View at Google Scholar
  11. A. J. Enright, I. Illopoulos, N. C. Kyrpides, and C. A. Ouzounis, “Protein interaction maps for complete genomes based on gene fusion events,” Nature, vol. 402, no. 6757, pp. 86–90, 1999. View at Publisher · View at Google Scholar · View at Scopus
  12. B. C. Mondal, S. Majumdar, U. B. Dasgupta, U. Chaudhuri, P. Chakrabarti, and S. Bhattacharyya, “e19a2 BCR-ABL fusion transcript in typical chronic myeloid leukaemia: a report of two cases,” Journal of Clinical Pathology, vol. 59, no. 10, pp. 1102–1103, 2006. View at Publisher · View at Google Scholar · View at Scopus
  13. K. Truong and M. Ikura, “Domain fusion analysis by applying relational algebra to protein sequence and domain databases,” BMC Bioinformatics, vol. 4, article 16, 2003. View at Publisher · View at Google Scholar · View at Scopus
  14. J. M. Chia and P. R. Kolatkar, “Implications for domain fusion protein-protein interactions based on structural information,” BMC Bioinformatics, vol. 5, article 161, 2004. View at Publisher · View at Google Scholar · View at Scopus
  15. F. J. Giles, J. E. Cortes, and H. M. Kantarjian, “Targeting the kinase activity of the BCR-ABL fusion protein in patients with chronic myeloid-leukemia,” Current Molecular Medicine, vol. 5, no. 7, pp. 615–623, 2005. View at Publisher · View at Google Scholar · View at Scopus
  16. A. R. Mushegian, D. E. Bassett, M. S. Boguski, P. Bork, and E. V. Koonin, “Positionally cloned human disease genes: patterns of evolutionary conservation and functional motifs,” Proceedings of the National Academy of Sciences of the United States of America, vol. 94, no. 11, pp. 5831–5836, 1997. View at Publisher · View at Google Scholar · View at Scopus
  17. J. Schultz, F. Milpetz, P. Bork, and C. P. Ponting, “SMART, a simple modular architecture research tool: identification of signaling domains,” Proceedings of the National Academy of Sciences of the United States of America, vol. 95, no. 11, pp. 5857–5864, 1998. View at Publisher · View at Google Scholar · View at Scopus
  18. A. G. Murzin, S. E. Brenner, T. Hubbard, and C. Chothia, “SCOP: a structural classification of proteins database for the investigation of sequences and structures,” Journal of Molecular Biology, vol. 247, no. 4, pp. 536–540, 1995. View at Publisher · View at Google Scholar · View at Scopus
  19. M. Wang and G. Caetano-Anollés, “Global phylogeny determined by the combination of protein domains in proteomes,” Molecular Biology and Evolution, vol. 23, no. 12, pp. 2444–2454, 2006. View at Publisher · View at Google Scholar · View at Scopus
  20. A. Marchler-Bauer, J. B. Anderson, P. F. Cherukuri et al., “CDD: a Conserved Domain Database for protein classification,” Nucleic Acids Research, vol. 33, pp. D192–D196, 2005. View at Publisher · View at Google Scholar · View at Scopus
  21. D. Brown and K. Sjölander, “Functional classification using phylogenomic inference,” PLoS Computational Biology, vol. 2, no. 6, article e77, pp. 479–483, 2006. View at Publisher · View at Google Scholar · View at Scopus
  22. S. R. Eddy, “Hidden markov models,” Current Opinion in Structural Biology, vol. 6, pp. 361–365, 1996. View at Google Scholar
  23. P. Shannon, A. Markiel, O. Ozier et al., “Cytoscape: a software environment for integrated models of biomolecular interaction networks,” Genome Research, vol. 13, no. 11, pp. 2498–2504, 2003. View at Publisher · View at Google Scholar
  24. L. Madsen, A. Schulze, M. Seeger, and R. Hartmann-Petersen, “Ubiquitin domain proteins in disease,” BMC Biochemistry, vol. 8, supplement 1, article S1, 2007. View at Google Scholar
  25. A. Samii, A. DePold Hohler, and R. Goodkin, “Functional neurosurgery for movement disorders,” in Neurosurgery, Springer Specialist Surgery Series-XI, pp. 607–616, 2005. View at Google Scholar
  26. M. Kanehisa and S. Goto, “KEGG: kyoto encyclopedia of genes and genomes,” Nucleic Acids Research, vol. 28, no. 1, pp. 27–30, 2000. View at Google Scholar
  27. N. Hulo, A. Bairoch, V. Bulliard et al., “The 20 years of PROSITE,” Nucleic Acids Research, vol. 36, supplement 1, pp. D245–D249, 2008. View at Publisher · View at Google Scholar
  28. T. Kawabata, M. Ota, and K. Nishikawa, “The protein mutant database,” Nucleic Acids Research, vol. 27, no. 1, pp. 355–357, 1999. View at Publisher · View at Google Scholar