About this Journal Submit a Manuscript Table of Contents
BioMed Research International
Volume 2013 (2013), Article ID 170586, 14 pages
http://dx.doi.org/10.1155/2013/170586
Research Article

Computational Analysis of the Soluble Form of the Intracellular Chloride Ion Channel Protein CLIC1

1School of Medical and Molecular Biosciences, University of Technology Sydney, P.O. Box 123, Broadway, NSW 2007, Australia
2School of Physics, University of New South Wales, Sydney, NSW 2052, Australia
3St Vincent’s Centre for Applied Medical Research, St Vincent’s Hospital, Darlinghurst, NSW 2010, Australia

Received 10 April 2013; Revised 26 June 2013; Accepted 27 June 2013

Academic Editor: Serdar Kuyucak

Copyright © 2013 Peter M. Jones 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. M. Berryman and A. Bretscher, “Identification of a novel member of the chloride intracellular channel gene family (CLIC5) that associates with the actin cytoskeleton of placental microvilli,” Molecular Biology of the Cell, vol. 11, no. 5, pp. 1509–1521, 2000. View at Scopus
  2. M. Berryman, J. Bruno, J. Price, and J. C. Edwards, “CLIC-5A functions as a chloride channel in vitro and associates with the cortical actin cytoskeleton in vitro and in vivo,” Journal of Biological Chemistry, vol. 279, no. 33, pp. 34794–34801, 2004. View at Publisher · View at Google Scholar · View at Scopus
  3. M. A. Berryman and J. R. Goldenring, “CLIC4 is enriched at cell-cell junctions and colocalizes with AKAP350 at the centrosome and midbody of cultured mammalian cells,” Cell Motility and the Cytoskeleton, vol. 56, no. 3, pp. 159–172, 2003. View at Publisher · View at Google Scholar · View at Scopus
  4. Z. Qian, D. Okuhara, M. K. Abe, and M. R. Rosner, “Molecular cloning and characterization of a mitogen-activated protein kinase-associated intracellular chloride channel,” Journal of Biological Chemistry, vol. 274, no. 3, pp. 1621–1627, 1999. View at Publisher · View at Google Scholar · View at Scopus
  5. R. A. Shanks, M. C. Larocca, M. Berryman et al., “AKAP350 at the golgi apparatus: II. Association of AKAP350 with a novel chloride intracellular channel (CLIC) family member,” Journal of Biological Chemistry, vol. 277, no. 43, pp. 40973–40980, 2002. View at Publisher · View at Google Scholar · View at Scopus
  6. S. J. Harrop, M. Z. DeMaere, W. D. Fairlie et al., “Crystal structure of a soluble form of the intracellular chloride ion channel CLIC1 (NCC27) at 1.4-Å resolution,” Journal of Biological Chemistry, vol. 276, no. 48, pp. 44993–45000, 2001. View at Publisher · View at Google Scholar · View at Scopus
  7. B. M. Tulk, S. Kapadia, and J. C. Edwards, “CLIC1 inserts from the aqueous phase into phospholipid membranes, where it functions as an anion channel,” The American Journal of Physiology, vol. 282, no. 5, pp. C1103–C1112, 2002. View at Scopus
  8. J. C. Edwards, B. Tulk, and P. H. Schlesinger, “Functional expression of p64, an intracellular chloride channel protein,” Journal of Membrane Biology, vol. 163, no. 2, pp. 119–127, 1998. View at Publisher · View at Google Scholar · View at Scopus
  9. J. C. Edwards, C. Cohen, W. Xu, and P. H. Schlesinger, “C-Src control of chloride channel support for osteoclast HCl transport and bone resorption,” Journal of Biological Chemistry, vol. 281, no. 38, pp. 28011–28022, 2006. View at Publisher · View at Google Scholar · View at Scopus
  10. J. C. Edwards and S. Kapadia, “Regulation of the bovine kidney microsomal chloride channel p64 by p59(fyn), a Src family tyrosine kinase,” Journal of Biological Chemistry, vol. 275, no. 41, pp. 31826–31832, 2000. View at Scopus
  11. E. Fernández-Salas, K. S. Suh, V. V. Speransky et al., “mtCLIC/CLIC4, an organellular chloride channel protein, is increased by DNA damage and participates in the apoptotic response to p53,” Molecular and Cellular Biology, vol. 22, no. 11, pp. 3610–3620, 2002. View at Publisher · View at Google Scholar · View at Scopus
  12. P. H. Schlesinger, H. C. Blair, S. L. Teitelbaum, and J. C. Edwards, “Characterization of the osteoclast ruffled border chloride channel and its role in bone resorption,” Journal of Biological Chemistry, vol. 272, no. 30, pp. 18636–18643, 1997. View at Publisher · View at Google Scholar · View at Scopus
  13. S. M. Valenzuela, M. Mazzanti, R. Tonini et al., “The nuclear chloride ion channel NCC27 is involved in regulation of the cell cycle,” Journal of Physiology, vol. 529, no. 3, pp. 541–552, 2000. View at Publisher · View at Google Scholar · View at Scopus
  14. D. R. Littler, S. J. Harrop, S. C. Goodchild et al., “The enigma of the CLIC proteins: ion channels, redox proteins, enzymes, scaffolding proteins?” FEBS Letters, vol. 584, no. 10, pp. 2093–2101, 2010. View at Publisher · View at Google Scholar · View at Scopus
  15. R. Tonini, A. Ferroni, S. M. Valenzuela et al., “Functional characterization of the NCC27 nuclear protein in stable transfected CHO-K1 cells,” FASEB Journal, vol. 14, no. 9, pp. 1171–1178, 2000. View at Scopus
  16. B. M. Tulk and J. C. Edwards, “NCC27, a homolog of intracellular Cl-channel p64, is expressed in brush border of renal proximal tubule,” The American Journal of Physiology, vol. 274, no. 6, pp. F1140–F1149, 1998. View at Scopus
  17. B. M. Tulk, P. H. Schlesinger, S. A. Kapadia, and J. C. Edwards, “CLIC-1 functions as a chloride channel when expressed and purified from bacteria,” Journal of Biological Chemistry, vol. 275, no. 35, pp. 26986–26993, 2000. View at Publisher · View at Google Scholar · View at Scopus
  18. P. G. Board, M. Coggan, G. Chelvanayagam et al., “Identification, characterization, and crystal structure of the omega class glutathione transferases,” Journal of Biological Chemistry, vol. 275, no. 32, pp. 24798–24806, 2000. View at Publisher · View at Google Scholar · View at Scopus
  19. A. Dulhunty, P. Gage, S. Curtis, G. Chelvanayagam, and P. Board, “The glutathione transferase structural family includes a nuclear chloride channel and a ryanodine receptor calcium release channel modulator,” Journal of Biological Chemistry, vol. 276, no. 5, pp. 3319–3323, 2001. View at Publisher · View at Google Scholar · View at Scopus
  20. L. Kalé, R. Skeel, M. Bhandarkar et al., “NAMD2: greater scalability for parallel molecular dynamics,” Journal of Computational Physics, vol. 151, no. 1, pp. 283–312, 1999. View at Publisher · View at Google Scholar · View at Scopus
  21. 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 Scopus
  22. 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
  23. 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 Scopus
  24. J.-P. Ryckaert, G. Ciccotti, and H. J. C. Berendsen, “Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes,” Journal of Computational Physics, vol. 23, no. 3, pp. 327–341, 1977. View at Scopus
  25. 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 Scopus
  26. N. Guex and M. C. Peitsch, “SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling,” Electrophoresis, vol. 18, no. 15, pp. 2714–2723, 1997. View at Publisher · View at Google Scholar · View at Scopus
  27. E. Lindahl, B. Hess, and D. van der Spoel, “GROMACS 3.0: a package for molecular simulation and trajectory analysis,” Journal of Molecular Modeling, vol. 7, no. 8, pp. 306–317, 2001. View at Publisher · View at Google Scholar · View at Scopus
  28. W. Kabsch and C. Sander, “Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features,” Biopolymers, vol. 22, no. 12, pp. 2577–2637, 1983. View at Scopus
  29. E. G. Alexov and M. R. Gunner, “Incorporating protein conformational flexibility into the calculation of pH-dependent protein properties,” Biophysical Journal, vol. 72, no. 5, pp. 2075–2093, 1997. View at Scopus
  30. R. E. Georgescu, E. G. Alexov, and M. R. Gunner, “Combining conformational flexibility and continuum electrostatics for calculating pKas in proteins,” Biophysical Journal, vol. 83, no. 4, pp. 1731–1748, 2002. View at Scopus
  31. L.-W. Yang, X. Liu, C. J. Jursa et al., “iGNM: a database of protein functional motions based on Gaussian Network Model,” Bioinformatics, vol. 21, no. 13, pp. 2978–2987, 2005. View at Publisher · View at Google Scholar · View at Scopus
  32. A. Nicholls and B. Honig, “A rapid finite difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation,” Journal of Computational Chemistry, vol. 12, no. 4, pp. 435–445, 1991.
  33. C. E. Shannon, “A mathematical theory of communication,” Bell System Technical Journal, vol. 27, no. 3, pp. 379–423, 1948.
  34. C. E. Shannon, “A mathematical theory of communication,” Bell System Technical Journal, vol. 27, no. 3, pp. 623–656, 1948.
  35. 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
  36. W. Humphrey, A. Dalke, and K. Schulten, “VMD: visual molecular dynamics,” Journal of Molecular Graphics, vol. 14, no. 1, pp. 27–38, 1996. View at Publisher · View at Google Scholar · View at Scopus
  37. W. L. DeLano, “Unraveling hot spots in binding interfaces: progress and challenges,” Current Opinion in Structural Biology, vol. 12, no. 1, pp. 14–20, 2002.
  38. I. Bahar, A. R. Atilgan, and B. Erman, “Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential,” Folding and Design, vol. 2, no. 3, pp. 173–181, 1997. View at Scopus
  39. P. Doruker, A. R. Atilgan, and I. Bahar, “Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: application to a-amylase inhibitor,” Proteins, vol. 40, pp. 512–524, 2000.
  40. T. Haliloglu, I. Bahar, and B. Erman, “Gaussian dynamics of folded proteins,” Physical Review Letters, vol. 79, no. 16, pp. 3090–3093, 1997. View at Scopus
  41. A. R. Atilgan, S. R. Durell, R. L. Jernigan, M. C. Demirel, O. Keskin, and I. Bahar, “Anisotropy of fluctuation dynamics of proteins with an elastic network model,” Biophysical Journal, vol. 80, no. 1, pp. 505–515, 2001. View at Scopus
  42. T. Kortemme and T. E. Creighton, “Ionisation of cysteine residues at the termini of model α-helical peptides. Relevance to unusual thiol pK(a) values in proteins of the thioredoxin family,” Journal of Molecular Biology, vol. 253, no. 5, pp. 799–812, 1995. View at Publisher · View at Google Scholar · View at Scopus
  43. W. W. Wells, Y. Yang, T. L. Deits, and Z. R. Gan, “Thioltransferases,” Advances in Enzymology and Related Areas of Molecular Biology, vol. 66, pp. 149–201, 1993. View at Scopus
  44. N. Blom, S. Gammeltoft, and S. Brunak, “Sequence and structure-based prediction of eukaryotic protein phosphorylation sites,” Journal of Molecular Biology, vol. 294, no. 5, pp. 1351–1362, 1999. View at Publisher · View at Google Scholar · View at Scopus
  45. N. Blom, T. Sicheritz-Pontén, R. Gupta, S. Gammeltoft, and S. Brunak, “Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence,” Proteomics, vol. 4, no. 6, pp. 1633–1649, 2004. View at Publisher · View at Google Scholar · View at Scopus
  46. D. R. Littler, S. J. Harrop, W. D. Fairlie et al., “The intracellular chloride ion channel protein CLIC1 undergoes a redox-controlled structural transition,” Journal of Biological Chemistry, vol. 279, no. 10, pp. 9298–9305, 2004. View at Publisher · View at Google Scholar · View at Scopus
  47. D. R. Littler, L. J. Brown, S. N. Breit, A. Perrakis, and P. M. G. Curmi, “Structure of human CLIC3 at Åresolution,” Proteins, vol. 78, no. 6, pp. 1594–1600, 2010. View at Publisher · View at Google Scholar · View at Scopus
  48. S. C. Goodchild, M. W. Howell, D. R. Littler et al., “Metamorphic response of the CLIC1 chloride intracellular ion channel protein upon membrane interaction,” Biochemistry, vol. 49, no. 25, pp. 5278–5289, 2010. View at Publisher · View at Google Scholar · View at Scopus
  49. K. S. Suh, M. Mutoh, K. Nagashima et al., “The organellular chloride channel protein CLIC4/mtCLIC translocates to the nucleus in response to cellular stress and accelerates apoptosis,” Journal of Biological Chemistry, vol. 279, no. 6, pp. 4632–4641, 2004. View at Publisher · View at Google Scholar · View at Scopus
  50. M. C. Wilce and M. W. Parker, “Structure and function of glutathione S-transferases,” Biochimica Et Biophysica Acta, vol. 1205, no. 1, pp. 1–18, 1994.
  51. L. M. Espinoza-Fonseca, “Reconciling binding mechanisms of intrinsically disordered proteins,” Biochemical and Biophysical Research Communications, vol. 382, no. 3, pp. 479–482, 2009. View at Publisher · View at Google Scholar · View at Scopus
  52. B. A. Shoemaker, J. J. Portman, and P. G. Wolynes, “Speeding molecular recognition by using the folding funnel: the fly-casting mechanism,” Proceedings of the National Academy of Sciences of the United States of America, vol. 97, no. 16, pp. 8868–8873, 2000. View at Publisher · View at Google Scholar · View at Scopus