Bulletin of the Korean Chemical Society

Korean Chemical Society (대한화학회)
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A Lattice Model Study of Native Contact Restraints in Protein Folding

  • 발행 : 1996.09.20
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초록

To explore protein folding mechanism, we simulated a folding pathway in a simplified 3×3×3 cubic lattice. In the lattice folding Monte Carlo simulations, each of the 28 possible native packing pairs that exist in the native conformation was used as a conformational restraint. The native packing restraints in the lattice model could be considered as a disulfide linkage restraint in a real protein. The results suggest that proteins denatured with a small disulfide loop can, but not always, fold faster than proteins without any disulfide linkage and than proteins with a larger disulfide loop. The results also suggest that there is a rough correlation between loop size of the native packing restraint and folding time. That is, the order of native residue-residue packing interaction in protein folding is likely dependent on the residue-residue distance in primary sequence. The strength of monomer-monomer pairwise interaction is not important in the determination of the packing order in lattice folding. From the folding simulations of five strong folding lattice sequences, it was also found that the context encoded in the primary sequence, which we do not yet clearly understand, plays more crucial role in the determination of detailed folding kinetics. Our restrained lattice model approach would provide a useful strategy to the future protein folding experiments by suggesting a protein engineering for the fast or slow folding research.

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참고문헌

  1. Science v.181 Anfinsen, C. B.
  2. Biochem. J. v.270 Creighton, T. E.
  3. Biochemistry v.33 Baker, D.;Agard, D. A.
  4. Proteins v.18 Kolinski, A.;Skolnick, J.
  5. Curr. Opin. Struct. Biol. v.5 Karplus, M.;Sali, A.
  6. Protein Science v.4 Dill, K. A.;Bromberg, S.;Yue, K.;Fiebig, K. M.;Yee, D. P.;Thomas, P. D.;Chan, H. S.
  7. Nature v.369 Sali, A.;Shakhnovich, E.;Karplus, M.
  8. J. Mol. Biol. v.235 Sali, A.;Shakhnovich, E.;Karplus, M.
  9. J. Phys. Chem. v.94 Hao, M.-H.;Scheraga, H. A.
  10. Biopolymers v.3 Poland, D. C.;Scheraga, H. A.
  11. J. Biol. Chem. v.263 Pace, C. N.;Grimsley, G. R.;Thomson, J. A.;Barnett, B. J.
  12. Proc. Natl. Acad. Sci. USA v.86 Matsumura, M.;Sognor, G.;Thomson, J. A.;Barnett, B. J.
  13. Nature v.341 Matsumura, M.;Sognor, G.;Thomson, J. A.;Barnett, B. J.
  14. J. Chem. Phys. v.90 Chan, H. S.;Dill, K. A.
  15. J. Chem. Phys. v.92 Chan, H. S.;Dill, K. A.
  16. Proteins v.15 Tidor, B.;Karplus, M.
  17. Methods Enzymol. v.202 Matsumura, M.;Matthews, B. W.
  18. Biochemistry v.32 Clarke, J.;Fersht, A. R.
  19. J. Chem. Phys. v.93 Shakhnovich, E. I.;Gutin, A. M.
  20. J. Chem. Phys. v.21 Metropolis, N.;Rosenbluth, A. W.;Rosenbluth M. N.;Teller, A. H.;Teller, E.
  21. Proteins v.6 Kuwajima, K.
  22. Biochemistry v.33 Abkevich, V. I.;Gutin, A. M.;Shakhnovich, E. I.
  23. Annu. Rev. Biochem. v.51 Kim, P. S.;Baldwin, R.
  24. Annu. Rev. Biochem. v.59 Kim, P. S.;Baldwin, R.
  25. Annu. Rev. Biochem. v.62 Matthews, C. R.
  26. J. Mol. Biol. v.224 Matouschek, A.;Serrano, L.;Fersht, A. R.
  27. J. Mol. Biol. v.224 Matouschek, A.;Serrano, L.;Meiering, E.;Bycroft, M.;Fersht, A. R.
  28. J. Mol. Biol. v.224 Serrano, L.;Matouschek, A.;Fersht, A. R.
  29. J. Mol. Biol. v.224 Serrano, L.;Matouschek, A.;Fersht, A. R.
  30. Nature v.369 Baldwin, R. L.
  31. Nature v.346 Shakhnovich, E. I.;Gutin, A. M.
  32. J. Phys. Chem. v.94 Hao, M.-H.;Scherage, H. A.
  33. Science v.250 Skolnick, J.;Kolinski, A.
  34. J. Mol. Biol. v.221 Skolnick, J.;Kolinski, A.
  35. J. Mol. Biol. v.237 Vieth, M.;Kolinski, A.;Brooks, C. L.;Skolnick, J.
  36. Proc. Natl. Acad. Sci. USA v.89 Leopold, P. E.;Montal, M.;Onuchie