Table of Contents Author Guidelines Submit a Manuscript
The Scientific World Journal
Volume 2013, Article ID 580456, 10 pages
http://dx.doi.org/10.1155/2013/580456
Research Article

Molecular Dynamic Simulation to Explore the Molecular Basis of Btk-PH Domain Interaction with Ins(1,3,4,5)P4

1Center for Systems Biology, Soochow University, Suzhou 215006, China
2Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
3Department of Bioinformatics, Medical College, Soochow University, Suzhou 215123, China

Received 28 July 2013; Accepted 7 September 2013

Academic Editors: P. Minkiewicz, Y. Muto, and W. A. Thompson

Copyright © 2013 Dan Lu 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. J. Gomez-Rodriguez, J. A. Readinger, I. C. Viorritto, K. L. Mueller, R. A. Houghtling, and P. L. Schwartzberg, “Tec kinases, actin, and cell adhesion,” Immunological Reviews, vol. 218, no. 1, pp. 45–64, 2007. View at Publisher · View at Google Scholar · View at Scopus
  2. C. I. Smith, T. C. Islam, P. T. Mattsson, A. J. Mohamed, B. F. Nore, and M. Vihinen, “The Tec family of cytoplasmic tyrosine kinases: mammalian Btk, Bmx, Itk, Tec, Txk and homologs in other species,” Bioessays, vol. 23, no. 5, pp. 436–446, 2001. View at Publisher · View at Google Scholar · View at Scopus
  3. A. Maas and R. W. Hendriks, “Role of Bruton's tyrosine kinase in B cell development,” Developmental Immunology, vol. 8, no. 3-4, pp. 171–181, 2001. View at Google Scholar · View at Scopus
  4. G. Matthew and G. K. William, “Role of inositol phospholipid signaling in natural killer cell biology,” Front Immunology, vol. 4, article 47, 2013. View at Publisher · View at Google Scholar
  5. A. J. Mohamed, L. Yu, C. M. Bäckesjö et al., “Bruton's tyrosine kinase (Btk): function, regulation, and transformation with special emphasis on the PH domain,” Immunological Reviews, vol. 228, no. 1, pp. 58–73, 2009. View at Publisher · View at Google Scholar · View at Scopus
  6. T. S. Rans and R. England, “The evolution of gene therapy in X-linked severe combined immunodeficiency,” Annals of Allergy, Asthma and Immunology, vol. 102, no. 5, pp. 357–363, 2009. View at Publisher · View at Google Scholar · View at Scopus
  7. J. D. Thomas, P. Sideras, C. I. Smith, I. Vorechovsky, V. Chapman, and W. E. Paul, “Colocalization of X-linked agammaglobulinemia and X-linked immunodeficiency genes,” Science, vol. 261, no. 5119, pp. 355–358, 1993. View at Google Scholar · View at Scopus
  8. M. Vihinen, B. H. Belohradsky, R. N. Haire et al., “BTKbase, mutation database for X-linked agammaglobulinemia (XLA),” Nucleic Acids Research, vol. 25, no. 9, pp. 166–171, 1997. View at Google Scholar · View at Scopus
  9. T. Kaneko, R. Joshi, S. M. Feller, and S. S. Li, “Phosphotyrosine recognition domains: the typical, the atypical and the versatile,” Cell Communication and Signaling, vol. 10, no. 1, p. 32, 2012. View at Google Scholar
  10. G. Koytiger, A. Kaushansky, A. Gordus, J. Rush, P. K. Sorger, and G. Macbeath, “Phosphotyrosine signaling proteins that drive oncogenesis tend to be highly interconnected,” Molecular & Cellular Proteomics, vol. 12, no. 5, pp. 1204–1213, 2013. View at Google Scholar
  11. K. Chudasama, J. Winnay, S. Johansson et al., “Short syndrome with partial lipodystrophy due to impaired phosphatidylinositol 3 kinase signaling,” The American Journal of Human Genetics, vol. 93, no. 1, pp. 150–157, 2013. View at Google Scholar
  12. M. Vihinen, M. D. Cooper, G. de Saint Basile et al., “BTKbase: a database of XLA-causing mutations,” Immunology Today, vol. 16, no. 10, pp. 460–465, 1995. View at Publisher · View at Google Scholar · View at Scopus
  13. T. G. Kutateladze, “Molecular analysis of protein—phosphoinositide interactions,” Current Topics in Microbiology and Immunology, vol. 362, pp. 111–126, 2012. View at Google Scholar
  14. P. Mayinger, “Phosphoinositides and vesicular membrane traffic,” Biochimica et Biophysica Acta, vol. 1821, no. 8, pp. 1104–1113, 2012. View at Google Scholar
  15. L. E. Rameh, A. Arvidsson, K. L. Carraway et al., “A comparative analysis of the phosphoinositide binding specificity of pleckstrin homology domains,” Journal of Biological Chemistry, vol. 272, no. 35, pp. 22059–22066, 1997. View at Publisher · View at Google Scholar · View at Scopus
  16. A. M. Scharenberg, O. El-Hillal, D. A. Fruman et al., “Phosphatidylinositol-3,4,5-trisphosphate (Ptdlns-3,4,5-P3)/Tec kinase-dependent calcium signaling pathway: a target for SHIP-mediated inhibitory signals,” The EMBO Journal, vol. 17, no. 7, pp. 1961–1972, 1998. View at Publisher · View at Google Scholar · View at Scopus
  17. K. Saito, A. M. Scharenberg, and J.-P. Kinet, “Interaction between the Btk PH Domain and Phosphatidylinositol-3,4,5-trisphosphate Directly Regulates Btk,” Journal of Biological Chemistry, vol. 276, no. 19, pp. 16201–16206, 2001. View at Publisher · View at Google Scholar · View at Scopus
  18. K. Murayama, M. Kato-Murayama, C. Mishima et al., “Crystal structure of the Bruton's tyrosine kinase PH domain with phosphatidylinositol,” Biochemical and Biophysical Research Communications, vol. 377, no. 1, pp. 23–28, 2008. View at Publisher · View at Google Scholar · View at Scopus
  19. T. J. Gibson, M. Hyvönen, A. Musacchio, M. Saraste, and E. Birney, “PH domain: the first anniversary,” Trends in Biochemical Sciences, vol. 19, no. 9, pp. 349–353, 1994. View at Publisher · View at Google Scholar · View at Scopus
  20. C. C. Milburn, M. Deak, S. M. Kelly, N. C. Price, D. R. Alessi, and D. M. F. van Aalten, “Binding of phosphatidylinositol 3,4,5-trisphosphate to the pleckstrin homology domain of protein kinase B induces a conformational change,” Biochemical Journal, vol. 375, no. 3, pp. 531–538, 2003. View at Publisher · View at Google Scholar · View at Scopus
  21. T. F. Jenny and S. A. Benner, “A prediction of the secondary structure of the pleckstrin homology domain,” Proteins, vol. 20, no. 1, pp. 1–3, 1994. View at Publisher · View at Google Scholar · View at Scopus
  22. B. J. Mayer, R. Ren, K. L. Clark, and D. Baltimore, “A putative modular domain present in diverse signaling proteins,” Cell, vol. 73, no. 4, pp. 629–630, 1993. View at Publisher · View at Google Scholar · View at Scopus
  23. H. S. Yoon, P. J. Hajduk, A. M. Petros, E. T. Olejniczak, R. P. Meadows, and S. W. Fesik, “Solution structure of a pleckstrin-homology domain,” Nature, vol. 369, no. 6482, pp. 672–675, 1994. View at Publisher · View at Google Scholar · View at Scopus
  24. E. Baraldi, K. D. Carugo, M. Hyvönen et al., “Structure of the PH domain from Bruton's tyrosine kinase in complex with inositol 1,3,4,5-tetrakisphosphate,” Structure, vol. 7, no. 4, pp. 449–460, 1999. View at Publisher · View at Google Scholar · View at Scopus
  25. T. Kojima, M. Fukuda, Y. Watanabe, F. Hamazato, and K. Mikoshiba, “Characterization of the pleckstrin homology domain of Btk as an inositol polyphosphate and phosphoinositide binding domain,” Biochemical and Biophysical Research Communications, vol. 236, no. 2, pp. 333–339, 1997. View at Publisher · View at Google Scholar · View at Scopus
  26. B. Shen and M. Vihinen, “Conservation and covariance in PH domain sequences: physicochemical profile and information theoretical analysis of XLA-causing mutations in the Btk PH domain,” Protein Engineering, Design and Selection, vol. 17, no. 3, pp. 267–276, 2004. View at Publisher · View at Google Scholar · View at Scopus
  27. M. Hyvönen and M. Saraste, “Stucture of the PH domain and Btk motif from Bruton's tyrosine kinase: molecular explanations for X-linked agammaglobulinaemia,” The EMBO Journal, vol. 16, no. 12, pp. 3396–3404, 1997. View at Publisher · View at Google Scholar · View at Scopus
  28. S. Fujiwara and T. Amisaki, “Identification of high affinity fatty acid binding sites on human serum albumin by MM-PBSA method,” Biophysical Journal, vol. 94, no. 1, pp. 95–103, 2008. View at Publisher · View at Google Scholar · View at Scopus
  29. T. Hou and R. Yu, “Molecular dynamics and free energy studies on the wild-type and double mutant HIV-1 protease complexed with amprenavir and two amprenavir-related inhibitors: mechanism for binding and drug resistance,” Journal of Medicinal Chemistry, vol. 50, no. 6, pp. 1177–1188, 2007. View at Publisher · View at Google Scholar · View at Scopus
  30. P. A. Kollman, I. Massova, C. Reyes et al., “Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models,” Accounts of Chemical Research, vol. 33, no. 12, pp. 889–897, 2000. View at Publisher · View at Google Scholar · View at Scopus
  31. J. Wang, P. Morin, W. Wang, and P. A. Kollman, “Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA,” Journal of the American Chemical Society, vol. 123, no. 22, pp. 5221–5230, 2001. View at Publisher · View at Google Scholar · View at Scopus
  32. T. Hou, J. Wang, Y. Li, and W. Wang, “Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations,” Journal of Chemical Information and Modeling, vol. 51, no. 1, pp. 69–82, 2011. View at Publisher · View at Google Scholar · View at Scopus
  33. C. I. Bayly, P. Cieplak, W. Cornell, and P. A. Kollman, “A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model,” Journal of Physical Chemistry, vol. 97, no. 40, pp. 10269–10280, 1993. View at Google Scholar · View at Scopus
  34. J. Wang, W. Wang, P. A. Kollman, and D. A. Case, “Automatic atom type and bond type perception in molecular mechanical calculations,” Journal of Molecular Graphics and Modelling, vol. 25, no. 2, pp. 247–260, 2006. View at Publisher · View at Google Scholar · View at Scopus
  35. Y. Duan, C. Wu, S. Chowdhury et al., “A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations,” Journal of Computational Chemistry, vol. 24, no. 16, pp. 1999–2012, 2003. View at Publisher · View at Google Scholar · View at Scopus
  36. J. Wang, R. M. Wolf, J. W. Caldwell, P. A. Kollman, and D. A. Case, “Development and testing of a general Amber force field,” Journal of Computational Chemistry, vol. 25, no. 9, pp. 1157–1174, 2004. View at Publisher · View at Google Scholar · View at Scopus
  37. T. Darden, L. Perera, L. Li, and L. Pedersen, “New tricks for modelers from the crystallography toolkit: the particle mesh Ewald algorithm and its use in nucleic acid simulations,” Structure, vol. 7, no. 3, pp. R55–R60, 1999. View at Publisher · View at Google Scholar · View at Scopus