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BioMed Research International
Volume 2013 (2013), Article ID 973867, 9 pages
http://dx.doi.org/10.1155/2013/973867
Research Article

Dynamic Folding Pathway Models of the Trp-Cage Protein

1Korea Research Institute of Standards and Science, Daejon 305-600, Republic of Korea
2School of Liberal Arts and Sciences, Korea National University of Transportation, Chungju 380-702, Republic of Korea
3Department of Physics and Astronomy, University of South Carolina, Columbia, SC 29208, USA

Received 5 April 2013; Accepted 10 June 2013

Academic Editor: Themis Lazaridis

Copyright © 2013 In-Ho Lee and Seung-Yeon Kim. 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. W. Neidigh, R. M. Fesinmeyer, and N. H. Andersen, “Designing a 20-residue protein,” Nature Structural Biology, vol. 9, no. 6, pp. 425–430, 2002. View at Publisher · View at Google Scholar · View at Scopus
  2. L. Qiu, S. A. Pabit, A. E. Roitberg, and S. J. Hagen, “Smaller and faster: the 20-residue Trp-cage protein folds in 4 μs,” Journal of the American Chemical Society, vol. 124, no. 44, pp. 12952–12953, 2002. View at Publisher · View at Google Scholar · View at Scopus
  3. Z. Ahmed, I. A. Beta, A. V. Mikhonin, and S. A. Asher, “UV-resonance Raman thermal unfolding study of Trp-cage shows that it is not a simple two-state miniprotein,” Journal of the American Chemical Society, vol. 127, no. 31, pp. 10943–10950, 2005. View at Publisher · View at Google Scholar · View at Scopus
  4. H. Neuweiler, S. Doose, and M. Sauer, “A microscopic view of miniprotein folding: enhanced folding efficiency through formation of an intermediate,” Proceedings of the National Academy of Sciences of the United States of America, vol. 102, no. 46, pp. 16650–16655, 2005. View at Publisher · View at Google Scholar · View at Scopus
  5. K. H. Mok, L. T. Kuhn, M. Goez et al., “A pre-existing hydrophobic collapse in the unfolded state of an ultrafast folding protein,” Nature, vol. 447, no. 7140, pp. 106–109, 2007. View at Publisher · View at Google Scholar · View at Scopus
  6. A. T. Iavarone, A. Patriksson, D. van der Spoel, and J. H. Parks, “Fluorescence probe of Trp-cage protein conformation in solution and in gas phase,” Journal of the American Chemical Society, vol. 129, no. 21, pp. 6726–6735, 2007. View at Publisher · View at Google Scholar · View at Scopus
  7. W. W. Streicher and G. I. Makhatadze, “Unfolding thermodynamics of Trp-cage, a 20 residue miniprotein, studied by differential scanning calorimetry and circular dichroism spectroscopy,” Biochemistry, vol. 46, no. 10, pp. 2876–2880, 2007. View at Publisher · View at Google Scholar · View at Scopus
  8. P. Hudáky, P. Stráner, V. Farkas, G. Váradi, G. Tóth, and A. Perczel, “Cooperation between a salt bridge and the hydrophobic core triggers fold stabilization in a Trp-cage miniprotein,” Biochemistry, vol. 47, no. 3, pp. 1007–1016, 2008. View at Publisher · View at Google Scholar · View at Scopus
  9. B. Barua, J. C. Lin, V. D. Williams, P. Kummler, J. W. Neidigh, and N. H. Andersen, “The Trp-cage: optimizing the stability of a globular miniprotein,” Protein Engineering, Design and Selection, vol. 21, no. 3, pp. 171–185, 2008. View at Publisher · View at Google Scholar · View at Scopus
  10. D. V. Williams, A. Byrne, J. Stewart, and N. H. Andersen, “Optimal salt bridge for Trp-cage stabilization,” Biochemistry, vol. 50, no. 7, pp. 1143–1152, 2011. View at Publisher · View at Google Scholar · View at Scopus
  11. P. Rovo, P. Straner, A. Lang et al., “Structural insights into the Trp-cage folding intermediate formation,” Chemistry, vol. 19, no. 8, pp. 2628–2640, 2013.
  12. C. Simmerling, B. Strockbine, and A. E. Roitberg, “All-atom structure prediction and folding simulations of a stable protein,” Journal of the American Chemical Society, vol. 124, no. 38, pp. 11258–11259, 2002. View at Publisher · View at Google Scholar · View at Scopus
  13. C. D. Snow, B. Zagrovic, and V. S. Pande, “The Trp cage: folding kinetics and unfolded state topology via molecular dynamics simulations,” Journal of the American Chemical Society, vol. 124, no. 49, pp. 14548–14549, 2002. View at Publisher · View at Google Scholar · View at Scopus
  14. R. Zhou, “Trp-cage: folding free energy landscape in explicit water,” Proceedings of the National Academy of Sciences of the United States of America, vol. 100, no. 23, pp. 13280–13285, 2003. View at Publisher · View at Google Scholar · View at Scopus
  15. J. W. Pitera and W. Swope, “Understanding folding and design: replica-exchange simulations of “Trp-cage” miniproteins,” Proceedings of the National Academy of Sciences of the United States of America, vol. 100, no. 13, pp. 7587–7592, 2003. View at Publisher · View at Google Scholar · View at Scopus
  16. S. Chowdhury, M. C. Lee, G. Xiong, and Y. Duan, “Ab initio folding simulation of the Trp-cage mini-protein approaches NMR resolution,” Journal of Molecular Biology, vol. 327, no. 3, pp. 711–717, 2003. View at Publisher · View at Google Scholar · View at Scopus
  17. S. Chowdhury, M. C. Lee, and Y. Duan, “Characterizing the rate-limiting step of Trp-cage folding by all-atom molecular dynamics simulations,” Journal of Physical Chemistry B, vol. 108, no. 36, pp. 13855–13865, 2004. View at Publisher · View at Google Scholar · View at Scopus
  18. M. Ota, M. Ikeguchi, and A. Kidera, “Phylogeny of protein-folding trajectories reveals a unique pathway to native structure,” Proceedings of the National Academy of Sciences of the United States of America, vol. 101, no. 51, pp. 17658–17663, 2004. View at Publisher · View at Google Scholar · View at Scopus
  19. J. Juraszek and P. G. Bolhuis, “Sampling the multiple folding mechanisms of Trp-cage in explicit solvent,” Proceedings of the National Academy of Sciences of the United States of America, vol. 103, no. 43, pp. 15859–15864, 2006. View at Publisher · View at Google Scholar · View at Scopus
  20. D. Paschek, H. Nymeyer, and A. E. García, “Replica exchange simulation of reversible folding/unfolding of the Trp-cage miniprotein in explicit solvent: on the structure and possible role of internal water,” Journal of Structural Biology, vol. 157, no. 3, pp. 524–533, 2007. View at Publisher · View at Google Scholar · View at Scopus
  21. E. Kim, S. Jang, and Y. Pak, “Consistent free energy landscapes and thermodynamic properties of small proteins based on a single all-atom force field employing an implicit solvation,” Journal of Chemical Physics, vol. 127, no. 14, Article ID 145104, 9 pages, 2007. View at Publisher · View at Google Scholar · View at Scopus
  22. D. Paschek, S. Hempel, and A. E. García, “Computing the stability diagram of the Trp-cage miniprotein,” Proceedings of the National Academy of Sciences of the United States of America, vol. 105, no. 46, pp. 17754–17759, 2008. View at Publisher · View at Google Scholar · View at Scopus
  23. W. Xu and Y. Mu, “Ab initio folding simulation of Trpcage by replica exchange with hybrid Hamiltonian,” Biophysical Chemistry, vol. 137, no. 2-3, pp. 116–125, 2008. View at Publisher · View at Google Scholar · View at Scopus
  24. R. Day, D. Paschek, and A. E. Garcia, “Microsecond simulations of the folding/ unfolding thermodynamics of the Trp-cage miniprotein,” Proteins, vol. 78, no. 8, pp. 1889–1899, 2010. View at Publisher · View at Google Scholar · View at Scopus
  25. D. Passerone and M. Parrinello, “Action-derived molecular dynamics in the study of rare events,” Physical Review Letters, vol. 87, no. 10, Article ID 108302, 4 pages, 2001. View at Scopus
  26. I.-H. Lee, J. Lee, and S. Lee, “Kinetic energy control in action-derived molecular dynamics simulations,” Physical Review B, vol. 68, no. 6, Article ID 064303, 8 pages, 2003.
  27. I.-H. Lee and S.-Y. Kim, “Searching protein folding pathways by optimization of actions,” Journal of Computational and Theoretical Nanoscience, vol. 6, no. 11, pp. 2388–2392, 2009. View at Publisher · View at Google Scholar · View at Scopus
  28. I.-H. Lee, S.-Y. Kim, and J. Lee, “Dynamic folding pathway models of α-helix and β-hairpin structures,” Chemical Physics Letters, vol. 412, no. 4–6, pp. 307–312, 2005. View at Publisher · View at Google Scholar · View at Scopus
  29. I.-H. Lee, S.-Y. Kim, and J. Lee, “Dynamic folding pathway models of the villin headpiece subdomain (HP-36) structure,” Journal of Computational Chemistry, vol. 31, no. 1, pp. 57–65, 2010. View at Publisher · View at Google Scholar · View at Scopus
  30. I. H. Lee, S. Y. Kim, and J. Lee, “Folding models of mini-protein FSD-1,” Journal of Physical Chemistry B, vol. 116, no. 23, pp. 6916–6922, 2012.
  31. W. D. Cornell, P. Cieplak, C. I. Bayly et al., “A second generation force field for the simulation of proteins, nucleic acids, and organic molecules,” Journal of the American Chemical Society, vol. 117, no. 19, pp. 5179–5197, 1995. View at Publisher · View at Google Scholar · View at Scopus
  32. D. Qiu, P. S. Shenkin, F. P. Hollinger, and W. C. Still, “The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate Born radii,” Journal of Physical Chemistry A, vol. 101, no. 16, pp. 3005–3014, 1997. View at Scopus
  33. J. W. Ponder and F. M. Richard, “An efficient Newton-like method for molecular mechanics energy minimization of large molecules,” Journal of Computational Chemistry, vol. 8, no. 7, pp. 1016–1024, 1987.
  34. I.-H. Lee, Y.-H. Kim, and R. M. Martin, “One-way multigrid method in electronic-structure calculations,” Physical Review B, vol. 61, no. 7, pp. 4397–4400, 2000. View at Scopus
  35. D. C. Liu and J. Nocedal, “On the limited memory BFGS method for large scale optimization,” Mathematical Programming B, vol. 45, no. 3, pp. 503–528, 1989. View at Scopus
  36. A. E. García, “Large-amplitude nonlinear motions in proteins,” Physical Review Letters, vol. 68, no. 17, pp. 2696–2699, 1992. View at Scopus