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Advances in Bioinformatics
Volume 2011, Article ID 176813, 8 pages
http://dx.doi.org/10.1155/2011/176813
Research Article

Cotranslational Protein Folding and Terminus Hydrophobicity

Department of Statistics, Macquarie University, Sydney, NSW 2109, Australia

Received 27 December 2010; Revised 28 February 2011; Accepted 24 March 2011

Academic Editor: Huixiao Hong

Copyright © 2011 Sheenal Srivastava 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. A. Dill, “Principles of protein folding—a perspective from simple exact models,” Protein Science, vol. 4, no. 4, pp. 561–602, 1995. View at Google Scholar · View at Scopus
  2. D. C. Phillips, “The hen egg-white lysozyme molecule,” Proceedings of the National Academy of Sciences, vol. 57, no. 3, pp. 483–495, 1967. View at Google Scholar
  3. S. H. White and R. E. Jacobs, “Statistical distribution of hydrophobic residues along the length of protein chains,” Biophysical Journal, vol. 57, no. 4, pp. 911–921, 1990. View at Google Scholar · View at Scopus
  4. T. O. Baldwin, “Protein folding in vivo: the importance of ribosomes,” Nature Cell Biology, vol. 1, no. 6, pp. 154–155, 1999. View at Google Scholar · View at Scopus
  5. A. V. Nicola, W. Chen, and A. Helenius, “Co-translational folding of an alphavirus capsid protein in the cytosol of living cells,” Nature Cell Biology, vol. 1, no. 6, pp. 341–345, 1999. View at Google Scholar · View at Scopus
  6. A. N. Fedorov and T. O. Baldwin, “Cotranslational protein folding,” Journal of Biological Chemistry, vol. 272, no. 52, pp. 32715–32718, 1997. View at Publisher · View at Google Scholar · View at Scopus
  7. M. A. Basharov, “Cotranslational folding of proteins,” Biochemistry, vol. 65, no. 12, pp. 1639–1644, 2000. View at Publisher · View at Google Scholar · View at Scopus
  8. M. A. Basharov, “Protein folding,” Journal of Cellular and Molecular Medicine, vol. 7, no. 3, pp. 223–237, 2003. View at Google Scholar · View at Scopus
  9. V. A. Kolb, “Cotranslational protein folding,” Molecular Biology, vol. 35, no. 4, pp. 584–590, 2001. View at Publisher · View at Google Scholar · View at Scopus
  10. C. Giglione, S. Fieulaine, and T. Meinnel, “Cotranslational processing mechanisms: towards a dynamic 3D model,” Trends in Biochemical Sciences, vol. 34, no. 8, pp. 417–426, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  11. H. Kadokura and J. Beckwith, “Detecting folding intermediates of a protein as it passes through the bacterial translocation channel,” Cell, vol. 138, no. 6, pp. 1164–1173, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  12. N. Alexandrov, “Structural argument for N-terminal initiation of protein folding,” Protein Science, vol. 2, no. 11, pp. 1989–1991, 1993. View at Google Scholar · View at Scopus
  13. P. Røgen, “Evaluating protein structure descriptors and tuning Gauss integral based descriptors,” Journal of Physics: Condensed Matter, vol. 17, no. 18, pp. S1523–S1538, 2005. View at Publisher · View at Google Scholar · View at Scopus
  14. C. A. Orengo, A. D. Michie, S. Jones, D. T. Jones, M. B. Swindells, and J. M. Thornton, “CATH—a hierarchic classification of protein domain structures,” Structure, vol. 5, no. 8, pp. 1093–1108, 1997. View at Google Scholar · View at Scopus
  15. T. Norcross and T. Yeates, “A framework for describing topological frustration in models of protein folding,” Journal of Molecular Biology, vol. 362, no. 3, pp. 605–621, 2006. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  16. C. M. Deane, M. Dong, F. P. E. Huard, B. K. Lance, and G. R. Wood, “Cotranslational protein folding—fact or fiction?” Bioinformatics, vol. 23, no. 13, pp. i142–i148, 2007. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  17. J. J. Ellis, F. P. E. Huard, C. M. Deane, S. Srivastava, and G. R. Wood, “Directionality in protein fold prediction,” BMC Bioinformatics, vol. 11, no. 172, 2010. View at Publisher · View at Google Scholar · View at PubMed
  18. K. F. Lau and K. A. Dill, “A lattice statistical mechanics model of the conformational and sequence spaces of proteins,” Macromolecules, vol. 22, no. 10, pp. 3989–3997, 1989. View at Google Scholar · View at Scopus
  19. A. Irback and C. Troein, “Enumerating designing sequences in the HP model,” Journal of Biological Physics, vol. 28, no. 1, pp. 1–15, 2001. View at Publisher · View at Google Scholar · View at Scopus
  20. M. Mitzenmacher, S. Whitesides, and N. Lesh, “A complete and effective move set for simplifed protein folding,” in Proceedings of the 7th Annual International Conference on Research in Computational Molecular Biology, New York, NY, USA, 2003.
  21. H. M. Lu and J. Liang, “A model study of protein nascent chain and cotranslational folding using hydrophobic-polar residues,” Proteins, vol. 70, pp. 442–449, 2008. View at Google Scholar
  22. G. Wang and R. L. Dunbrack, “Pisces: a protein sequence culling server,” Bioinformatics, vol. 19, no. 12, pp. 1589–1591, 2003. View at Google Scholar
  23. J. Kyte and R. F. Doolittle, “A simple method for displaying the hydropathic character of a protein,” Journal of Molecular Biology, vol. 157, pp. 105–132, 1982. View at Google Scholar
  24. J. Janin, “Surface and inside volumes in globular proteins,” Nature, vol. 277, pp. 491–492, 1979. View at Google Scholar
  25. J. L. Cornette, K. B. Cease, H. Margalit, J. L. Spouge, J. A. Berzofsky, and C. DeLisi, “Hydrophobicity scales and computational techniques for detecting amphiphatic structures in proteins,” Journal of Molecular Biology, vol. 195, pp. 659–685, 1987. View at Google Scholar
  26. D. Eisenberg, E. Schwarz, M. Komaromy, and R. Wall, “Analysis of membrane and surface protein sequences with the hydrophobic moment plot,” Journal of Molecular Biology, vol. 179, pp. 125–142, 1984. View at Google Scholar
  27. A. Zemla, “LGA: a method for finding 3D similarities in protein structures,” Nucleic Acids Research, vol. 31, no. 13, pp. 3370–3374, 2003. View at Google Scholar