Table of Contents
Computational Biology Journal
Volume 2013 (2013), Article ID 938169, 9 pages
http://dx.doi.org/10.1155/2013/938169
Research Article

Graph-Theoretic Models of Mutations in the Nucleotide Binding Domain 1 of the Cystic Fibrosis Transmembrane Conductance Regulator

1Department of Mathematics and Statistics, East Tennessee State University, Johnson City, TN 37614, USA
2Institute for Quantitative Biology, East Tennessee State University, Johnson City, TN 37614, USA

Received 30 November 2012; Revised 12 March 2013; Accepted 12 March 2013

Academic Editor: Alessandra Lumini

Copyright © 2013 Debra J. Knisley 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. K. Roberts, P. Cushing, P. Boisguerin, D. Madden, and B. Donald, “Computational Design of a PDZ domain peptide inhibitor that rescues CFTR activity,” PLOS Computational Biology, vol. 8, no. 4, Article ID e1002477, 2012. View at Publisher · View at Google Scholar
  2. A. Aleksandrov, P. Kota, L. Cui et al., “Allosteric modulation balances thermodynamic stability and restores function of ΔF508 CFTR,” Journal of Molecular Biology, vol. 419, pp. 41–60, 2012. View at Publisher · View at Google Scholar
  3. A. W. R. Serohijos, T. Hegedus, A. A. Aleksandrov et al., “Phenylalanine-508 mediates a cytoplasmic-membrane domain contact in the CFTR 3D structure crucial to assembly and channel function,” Proceedings of the National Academy of Sciences of the United States of America, vol. 105, no. 9, pp. 3256–3261, 2008. View at Publisher · View at Google Scholar · View at Scopus
  4. L. He, A. A. Aleksandrov, A. W. R. Serohijos et al., “Multiple membrane-cytoplasmic domain contacts in the cystic fibrosis transmembrane conductance regulator (CFTR) mediate regulation of channel gating,” Journal of Biological Chemistry, vol. 283, no. 39, pp. 26383–26390, 2008. View at Publisher · View at Google Scholar · View at Scopus
  5. T. C. Hwang and D. N. Sheppard, “Gating of the CFTR Cl- channel by ATP-driven nucleotide-binding domain dimerisation,” Journal of Physiology, vol. 587, no. 10, pp. 2151–2161, 2009. View at Publisher · View at Google Scholar · View at Scopus
  6. The Cystic Fibrosis Mutation Database, http://www.genet.sickkids.on.ca/.
  7. A. W. R. Serohijos, T. Hegedus, J. R. Riordan, and N. V. Dokholyan, “Diminished self-chaperoning activity of the ΔF508 mutant of CFTR results in protein misfolding,” PLoS Computational Biology, vol. 4, no. 2, Article ID e1000008, 2008. View at Publisher · View at Google Scholar · View at Scopus
  8. A. A. Aleksandrov, P. Kota, L. A. Aleksandrov et al., “Regulatory insertion removal restores maturation, stability and function of ΔF508 CFTR,” Journal of Molecular Biology, vol. 401, no. 2, pp. 194–210, 2010. View at Publisher · View at Google Scholar · View at Scopus
  9. D. B. Luckie, J. H. Wilterding, M. Krha, and M. E. Krouse, “CFTR and MDR: ABC transporters with homologous structure but divergent function,” Current Genomics, vol. 4, no. 3, pp. 109–121, 2003. View at Google Scholar
  10. B. K. Berdiev, Y. J. Qadri, and D. J. Benos, “Assessment of the CFTR and ENaC association,” Molecular BioSystems, vol. 5, no. 2, pp. 123–227, 2009. View at Publisher · View at Google Scholar · View at Scopus
  11. G. Seavilleklein, N. Amer, A. Evagelidis et al., “PKC phosphorylation modulates PKA-dependent binding of the R domain to other domains of CFTR,” American Journal of Physiology—Cell Physiology, vol. 295, no. 5, pp. C1366–C1375, 2008. View at Publisher · View at Google Scholar · View at Scopus
  12. H. A. Lewis, X. Zhao, C. Wang et al., “Impact of the ΔF508 mutation in first nucleotide-binding domain of human cystic fibrosis transmembrane conductance regulator on domain folding and structure,” Journal of Biological Chemistry, vol. 280, no. 2, pp. 1346–1353, 2005. View at Publisher · View at Google Scholar · View at Scopus
  13. S. Y. Huang, D. Bolser, H. Y. Liu, T. C. Hwang, and X. Zou, “Molecular modeling of the heterodimer of human CFTR's nucleotide-binding domains using a protein-protein docking approach,” Journal of Molecular Graphics and Modelling, vol. 27, no. 7, pp. 822–828, 2009. View at Publisher · View at Google Scholar · View at Scopus
  14. T. Hegedus, A. W. R. Serohijos, N. V. Dokholyan, L. He, and J. R. Riordan, “Computational studies reveal phosphorylation-dependent changes in the unstructured R domain of CFTR,” Journal of Molecular Biology, vol. 378, no. 5, pp. 1052–1063, 2008. View at Publisher · View at Google Scholar · View at Scopus
  15. X. Wang, J. Matteson, Y. An et al., “COPII-dependent export of cystic fibrosis transmembrane conductance regulator from the ER uses di-acidic exit code,” Journal of Cell Biology, vol. 167, no. 1, pp. 65–74, 2004. View at Publisher · View at Google Scholar · View at Scopus
  16. M. F. N. Rosser, D. E. Grove, and D. M. Cyr, “The use of small molecules to correct defects in CFTR folding, maturation, and channel activity,” Current Chemical Biology, vol. 3, no. 1, pp. 100–111, 2009. View at Google Scholar · View at Scopus
  17. N. Pedemonte, G. L. Lukacs, K. Du et al., “Small-molecule correctors of defective ΔF508-CFTR cellular processing identified by high-throughput screening,” Journal of Clinical Investigation, vol. 115, no. 9, pp. 2564–2571, 2005. View at Publisher · View at Google Scholar · View at Scopus
  18. A. del Sol, H. Fujihashi, D. Amoros, and R. Nussinov, “Residues crucial for maintaining short paths in network communication mediate signaling in proteins,” Molecular Systems Biology, vol. 2, Article ID 2006.0019, 2006. View at Publisher · View at Google Scholar · View at Scopus
  19. M. Habibi, C. Eslahchi, M. Sadeghi, and H. Pezashk, “The interpretation of protein structures based on graph theory and contact map,” Open Access Bioinformatics, vol. 2, pp. 127–137, 2010. View at Google Scholar
  20. T. Haynes, D. Knisley, E. Seier, and Y. Zou, “A quantitative analysis of secondary RNA structure using domination based parameters on trees,” BMC Bioinformatics, vol. 7, article 108, 2006. View at Publisher · View at Google Scholar · View at Scopus
  21. RAG: RNA-As-Graphs, http://www.biomath.nyu.edu/.
  22. D. Knisley and J. Knisley, “Predicting protein-protein interactions using graph invariants and a neural network,” Computational Biology and Chemistry, vol. 35, no. 2, pp. 108–113, 2011. View at Publisher · View at Google Scholar · View at Scopus
  23. D. West, Introduction to Graph Theory, Prentice Hall, New York, NY, USA, 1996.
  24. J. Bondy and U. S. R. Murty, Graph Theory, Springer, New York, NY, USA, 2010.
  25. M. Charton and B. I. Charton, “The structural dependence of amino acid hydrophobicity parameters,” Journal of Theoretical Biology, vol. 99, no. 4, pp. 629–644, 1982. View at Google Scholar · View at Scopus
  26. J. Kyte and R. F. Doolittle, “A simple method for displaying the hydropathic character of a protein,” Journal of Molecular Biology, vol. 157, no. 1, pp. 105–132, 1982. View at Publisher · View at Google Scholar
  27. H. A. Lewis, C. Wang, X. Zhao et al., “Structure and dynamics of NBD1 from CFTR characterized using crystallography and hydrogen/deuterium exchange mass spectrometry,” Journal of Molecular Biology, vol. 396, no. 2, pp. 406–430, 2010. View at Publisher · View at Google Scholar · View at Scopus
  28. The Protein Databank, http://www.pdb.org/.
  29. I-TASSER, http://zhanglab.ccmb.med.umich.edu/I-TASSER/.
  30. MATLAB, http://www.mathworks.com/products/matlab/index.html.
  31. D. Bonchev and D. H. Rouvray, Chemical Graph Theory: Theory and Fundamentals, Gordon and Breach, New York, NY, USA, 1991.
  32. N. Trinajstic, Chemical Graph Theory, CRC Press, Boca Raton, Fla, USA, 2nd edition, 1992.
  33. H. Yu, B. Burton, C. Huang et al., “Ivacaftor potentiation of multiple CFTR channels with gating mutations,” Journal of Cystic Fibrosis, vol. 11, no. 3, pp. 237–245, 2012. View at Publisher · View at Google Scholar