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Computational and Mathematical Methods in Medicine
Volume 2015, Article ID 746157, 9 pages
http://dx.doi.org/10.1155/2015/746157
Research Article

Structural, Dynamical, and Energetical Consequences of Rett Syndrome Mutation R133C in MeCP2

Computational Biophysics and Bioinformatics, Department of Physics, Clemson University, Clemson, SC 29634, USA

Received 15 December 2014; Accepted 11 March 2015

Academic Editor: Volkhard Helms

Copyright © 2015 Tugba G. Kucukkal and Emil Alexov. 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. D. D. Armstrong, “The neuropathology of Rett syndrome—overview 1994,” Neuropediatrics, vol. 26, no. 2, pp. 100–104, 1995. View at Publisher · View at Google Scholar · View at Scopus
  2. B. Hagberg, “Clinical manifestations and stages of Rett syndrome,” Mental Retardation and Developmental Disabilities Research Reviews, vol. 8, no. 2, pp. 61–65, 2002. View at Publisher · View at Google Scholar · View at Scopus
  3. S. B. Naidu, “Rett Syndrome,” Indian Journal of Pediatrics, vol. 64, no. 5, pp. 651–659, 1997. View at Publisher · View at Google Scholar · View at Scopus
  4. B. A. Hagberg, “Rett syndrome: clinical peculiarities, diagnostic approach, and possible cause,” Pediatric Neurology, vol. 5, no. 2, pp. 75–83, 1989. View at Publisher · View at Google Scholar · View at Scopus
  5. B. Hendrich and W. Bickmore, “Human diseases with underlying defects in chromatin structure and modification,” Human Molecular Genetics, vol. 10, no. 20, pp. 2233–2242, 2001. View at Publisher · View at Google Scholar · View at Scopus
  6. H. G. Dunn and P. M. MacLeod, “Rett syndrome: review of biological abnormalities,” Canadian Journal of Neurological Sciences, vol. 28, no. 1, pp. 16–29, 2001. View at Google Scholar · View at Scopus
  7. H. G. Dunn, “Importance of Rett syndrome in child neurology,” Brain and Development, vol. 23, supplement 1, pp. S38–S43, 2001. View at Publisher · View at Google Scholar · View at Scopus
  8. R. E. Amir and H. Y. Zoghbi, “Rett syndrome: methyl-CpG-binding protein 2 mutations and phenotype-genotype correlations,” The American Journal of Medical Genetics, vol. 97, no. 2, pp. 147–152, 2000. View at Publisher · View at Google Scholar
  9. S. Akbarian, “The neurobiology of Rett syndrome,” Neuroscientist, vol. 9, no. 1, pp. 57–63, 2003. View at Publisher · View at Google Scholar · View at Scopus
  10. D. D. Armstrong, “Review of Rett syndrome,” Journal of Neuropathology and Experimental Neurology, vol. 56, no. 8, pp. 843–849, 1997. View at Publisher · View at Google Scholar · View at Scopus
  11. R. M. Zachariah and M. Rastegar, “Linking epigenetics to human disease and rett syndrome: the emerging novel and challenging concepts in MeCP2 research,” Neural Plasticity, vol. 2012, Article ID 415825, 10 pages, 2012. View at Publisher · View at Google Scholar · View at Scopus
  12. J. L. Neul and H. Y. Zoghbi, “Rett syndrome: a prototypical neurodevelopmental disorder,” Neuroscientist, vol. 10, no. 2, pp. 118–128, 2004. View at Publisher · View at Google Scholar · View at Scopus
  13. R. J. Klose, S. A. Sarraf, L. Schmiedeberg, S. M. McDermott, I. Stancheva, and A. P. Bird, “DNA binding selectivity of MeCP2 due to a requirement for A/T sequences adjacent to methyl-CpG,” Molecular Cell, vol. 19, no. 5, pp. 667–678, 2005. View at Publisher · View at Google Scholar · View at Scopus
  14. V. H. Adams, S. J. McBryant, P. A. Wade, C. L. Woodcock, and J. C. Hansen, “Intrinsic disorder and autonomous domain function in the multifunctional nuclear protein, MeCP2,” The Journal of Biological Chemistry, vol. 282, no. 20, pp. 15057–15064, 2007. View at Publisher · View at Google Scholar · View at Scopus
  15. R. P. Ghosh, R. A. Horowitz-Scherer, T. Nikitina, L. M. Gierasch, and C. L. Woodcock, “Rett syndrome-causing mutations in human MeCP2 result in diverse structural changes that impact folding and DNA interactions,” The Journal of Biological Chemistry, vol. 283, no. 29, pp. 20523–20534, 2008. View at Publisher · View at Google Scholar · View at Scopus
  16. J. Christodoulou, A. Grimm, T. Maher, and B. Bennetts, “RettBASE: the IRSA MECP2 variation database—a new mutation database in evolution,” Human mutation, vol. 21, no. 5, pp. 466–472, 2003. View at Publisher · View at Google Scholar · View at Scopus
  17. N. C. Schanen, “Molecular approaches to the Rett syndrome gene,” Journal of Child Neurology, vol. 14, no. 12, pp. 806–814, 1999. View at Publisher · View at Google Scholar · View at Scopus
  18. S. P. Chandler, D. Guschin, N. Landsberger, and A. P. Wolffe, “The methyl-CpG binding transcriptional repressor MeCP2 stably associates with nucleosomal DNA,” Biochemistry, vol. 38, no. 22, pp. 7008–7018, 1999. View at Publisher · View at Google Scholar · View at Scopus
  19. K. L. Ho, I. W. McNae, L. Schmiedeberg, R. J. Klose, A. P. Bird, and M. D. Walkinshaw, “MeCP2 binding to DNA depends upon hydration at methyl-CpG,” Molecular Cell, vol. 29, no. 4, pp. 525–531, 2008. View at Publisher · View at Google Scholar · View at Scopus
  20. W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein, “Comparison of simple potential functions for simulating liquid water,” The Journal of Chemical Physics, vol. 79, no. 2, pp. 926–935, 1983. View at Publisher · View at Google Scholar · View at Scopus
  21. W. Humphrey, A. Dalke, and K. Schulten, “VMD: visual molecular dynamics,” Journal of Molecular Graphics, vol. 14, no. 1, pp. 33–38, 1996. View at Publisher · View at Google Scholar · View at Scopus
  22. A. D. MacKerell Jr., D. Bashford, M. Bellott et al., “All-atom empirical potential for molecular modeling and dynamics studies of proteins,” Journal of Physical Chemistry B, vol. 102, no. 18, pp. 3586–3616, 1998. View at Publisher · View at Google Scholar · View at Scopus
  23. A. D. MacKerell Jr., M. Feig, and C. L. Brooks III, “Improved treatment of the protein backbone in empirical force fields,” Journal of the American Chemical Society, vol. 126, no. 3, pp. 698–699, 2004. View at Publisher · View at Google Scholar · View at Scopus
  24. A. D. Mackerell Jr., M. Feig, and C. L. Brooks III, “Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulation,” Journal of Computational Chemistry, vol. 25, no. 11, pp. 1400–1415, 2004. View at Publisher · View at Google Scholar · View at Scopus
  25. N. Foloppe and A. D. MacKerell, “All-atom empirical force field for nucleic acids. I. Parameter optimization based on small molecule and condensed phase macromolecular target data,” Journal of Computational Chemistry, vol. 21, no. 2, pp. 86–104, 2000. View at Google Scholar · View at Scopus
  26. A. D. MacKerell Jr. and N. K. Banavali, “All-atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution,” Journal of Computational Chemistry, vol. 21, no. 2, pp. 105–120, 2000. View at Publisher · View at Google Scholar · View at Scopus
  27. T. Darden, D. York, and L. Pedersen, “Particle mesh ewald: an N·log(N) method for ewald sums in large systems,” The Journal of Chemical Physics, vol. 98, no. 12, pp. 10089–10092, 1993. View at Publisher · View at Google Scholar · View at Scopus
  28. G. J. Martyna, D. J. Tobias, and M. L. Klein, “Constant pressure molecular dynamics algorithms,” The Journal of Chemical Physics, vol. 101, no. 5, pp. 4177–4189, 1994. View at Publisher · View at Google Scholar · View at Scopus
  29. S. E. Feller, Y. Zhang, R. W. Pastor, and B. R. Brooks, “Constant pressure molecular dynamics simulation: the Langevin piston method,” The Journal of Chemical Physics, vol. 103, no. 11, pp. 4613–4621, 1995. View at Publisher · View at Google Scholar · View at Scopus
  30. H. C. Andersen, “Rattle: a ‘velocity’ version of the shake algorithm for molecular dynamics calculations,” Journal of Computational Physics, vol. 52, no. 1, pp. 24–34, 1983. View at Publisher · View at Google Scholar · View at Scopus
  31. J. C. Phillips, R. Braun, W. Wang et al., “Scalable molecular dynamics with NAMD,” Journal of Computational Chemistry, vol. 26, no. 16, pp. 1781–1802, 2005. View at Publisher · View at Google Scholar · View at Scopus
  32. W. Kabsch and C. Sander, “Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features,” Biopolymers—Peptide Science Section, vol. 22, no. 12, pp. 2577–2637, 1983. View at Publisher · View at Google Scholar · View at Scopus
  33. G. Vriend, “WHAT IF: a molecular modeling and drug design program,” Journal of Molecular Graphics, vol. 8, no. 1, pp. 52–56, 1990. View at Publisher · View at Google Scholar · View at Scopus
  34. T. M. Yusufzai and A. P. Wolffe, “Functional consequences of Rett syndrome mutations on human MeCP2,” Nucleic Acids Research, vol. 28, no. 21, pp. 4172–4179, 2000. View at Publisher · View at Google Scholar · View at Scopus