Bulletin of the Korean Chemical Society

Korean Chemical Society (대한화학회)
권호 표지
DOI QR코드

DOI QR Code

Folding Dynamics of β-Hairpins: Molecular Dynamics Simulations

  • Published : 2003.06.20
Download PDF
⟨ Previous Next ⟩

Abstract

We have studied the folding mechanism of β-hairpins from proteins of 1GB1, 3AIT and 1A2P by unfolding simulations at high temperatures. The analysis of trajectories obtained from molecular dynamics simulations in explicit aqueous solution suggests that the three β-hairpin structures follow different mechanism of folding. The results of unfolding simulations showed that the positions of the hydrophobic core residues influence the folding dynamics. We discussed the characteristics of different mechanisms of β-hairpin folding based on the hydrogen-bond-centric and the hydrophobic-centric models.

Keywords

References

  1. Fersht, A. Structure and Mechanism in Protein Science; Freeman:New York, 1999.
  2. Winkler, J. R.; Gray, H. B. Acc. Chem. Res. 1998, 31, 697. https://doi.org/10.1021/ar980087h
  3. Onuchic, J. N.; Luthey-Schulten, Z.; Wolynes, P. G. Ann. Rev. Phys. Chem. 1997, 48, 545. https://doi.org/10.1146/annurev.physchem.48.1.545
  4. Shakhnovich, E. I. Curr. Opin. Struct. Biol. 1997, 7, 29. https://doi.org/10.1016/S0959-440X(97)80005-X
  5. Dobson, C. M.; Sali, A.; Karplus, M. Angew. Chem. Int. Ed. 1998,37, 868. https://doi.org/10.1002/(SICI)1521-3773(19980420)37:7<868::AID-ANIE868>3.0.CO;2-H
  6. Dill, K. A. Protein Sci. 1999, 8, 1166. https://doi.org/10.1110/ps.8.6.1166
  7. Duan, Y.; Kollman, P. A. Science 1998, 282, 740. https://doi.org/10.1126/science.282.5389.740
  8. Munoz, V.; Serrano, L. Curr. Opin. Biotechnol. 1995, 6, 382. https://doi.org/10.1016/0958-1669(95)80066-2
  9. Thompson, P. A.; Eaton, W. A.; Hofrichter, J. Biochemistry 1997,36, 9200. https://doi.org/10.1021/bi9704764
  10. Blanco, F.; Ramirez-Alvarado, M.; Serrano, L. Curr. Opin. Struct.Biol. 1998, 8, 107. https://doi.org/10.1016/S0959-440X(98)80017-1
  11. Chang, S.-G.; Choi, K.-D.; Kim, D.-Y.; Kang, H.-T.; Song, M.-C.;Shin, H.-C. Bull. Korean Chem. Soc. 2002, 23, 1369. https://doi.org/10.5012/bkcs.2002.23.10.1369
  12. Munoz, V.; Thompson, P. A.; Hofrichter, J.; Eaton, W. A. Nature1997, 390, 196. https://doi.org/10.1038/36626
  13. Bonvin, A. M.; van Gunsteren, W. F. J. Mol. Biol. 2000, 296, 255. https://doi.org/10.1006/jmbi.1999.3446
  14. Prevost, M.; Ortmans, I. Proteins Struct. Funct. Genet. 1997, 29,212. https://doi.org/10.1002/(SICI)1097-0134(199710)29:2<212::AID-PROT9>3.0.CO;2-E
  15. Pande, V. S.; Rokhsar, D. S. Proc. Natl. Acad. Sci. USA 1999, 96,9062. https://doi.org/10.1073/pnas.96.16.9062
  16. Dinner, A. R.; Lazaridis, T.; Karplus, M. Proc. Natl. Acad. Sci.USA 1999, 96, 9068. https://doi.org/10.1073/pnas.96.16.9068
  17. Ma, B.; Nussinov, R. J. Mol. Biol. 2000, 296, 1091. https://doi.org/10.1006/jmbi.2000.3518
  18. Karplus, M.; Sali, A. Curr. Opin. Struct. Biol. 1995, 5, 58. https://doi.org/10.1016/0959-440X(95)80010-X
  19. Lazaridis, T.; Karplus, M. Science 1997, 278, 1928. https://doi.org/10.1126/science.278.5345.1928
  20. Wang, L.; Duan, Y.; Shortle, R.; Imperiali, B.; Kollman, P. A.Protein Sci. 1999, 8, 1292. https://doi.org/10.1110/ps.8.6.1292
  21. Finkelstein, A. V. Protein Eng. 1997, 10, 843. https://doi.org/10.1093/protein/10.8.843
  22. Dinner, A. R.; Karplus, M. J. Mol. Biol. 1999, 292, 403. https://doi.org/10.1006/jmbi.1999.3051
  23. Daggett, V. Acc. Chem. Res. 2002, 35, 422. https://doi.org/10.1021/ar0100834
  24. Lee, J.; Shin, S. Biophy. J. 2001, 81, 2507. https://doi.org/10.1016/S0006-3495(01)75896-1
  25. Lee, J.; Shin, S. J. Phys. Chem. B 2002, 106, 8796. https://doi.org/10.1021/jp0141732
  26. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.;Swaminathan, S.; Karplus, M. J. Comp. Chem. 1983, 4, 187. https://doi.org/10.1002/jcc.540040211
  27. Kruger, P.; Luke, M.; Szameit, A. Comp. Phys. Comm. 1991, 62, 371. https://doi.org/10.1016/0010-4655(91)90108-W
  28. Wriggers, W.; Milligan, R. A.; McCammon, J. A. J. StructuralBiology 1999, 125, 185. https://doi.org/10.1006/jsbi.1998.4080
  29. Laskowski, R. A.; MacArthur, M. W.; Thornton, J. M. J. Appl.Crystallog. 1993, 26, 283. https://doi.org/10.1107/S0021889892009944
  30. Lee, J.; Lee, K.; Shin, S. Biophy. J. 2000, 78, 1665.
  31. van Aalten, D. M. F.; Amadei, A.; Linssen, A. B. M.; Eijsink, V.G. H.; Vriend, G. Proteins Struct. Funct. Genet. 1995, 22, 45. https://doi.org/10.1002/prot.340220107
  32. Vriend, G. J. Mol. Graph. 1990, 8, 52. https://doi.org/10.1016/0263-7855(90)80070-V
  33. Noda, I. Appl. Spectrosc. 1993, 47, 1329. https://doi.org/10.1366/0003702934067694
  34. Noda, I.; Dowrey, A. I.; Marcott, C.; Story, G. M.; Ozaki, Y. Appl. Spectrosc. 2000, 54, 236A. https://doi.org/10.1366/0003702001950454
  35. Lee, J.; Suh, S. W.; Shin, S. J. Biomol. Struct. Dyn. 2000, 18, 297. https://doi.org/10.1080/07391102.2000.10506667
  36. Klimov, D. K.; Thirumalai, D. Proc. Natl. Acad. Sci. USA 2000,97, 2544. https://doi.org/10.1073/pnas.97.6.2544
  37. Zagrovic, B.; Sorin, E. J.; Pande, V. J. Mol. Biol. 2001, 313, 151. https://doi.org/10.1006/jmbi.2001.5033
  38. Zhou, R.; Berne, B. J.; Germain, R. Proc. Natl. Acad. Sci. USA2001, 98, 14931. https://doi.org/10.1073/pnas.201543998

Cited by

  1. Molecular dynamics simulations of folding processes of a β-hairpin in an implicit solvent vol.3, pp.3, 2006, https://doi.org/10.1088/1478-3975/3/3/001
  2. Accurate free energy calculation along optimized paths pp.1096987X, 2009, https://doi.org/10.1002/jcc.21420
  3. Prediction of Chiral Discrimination by β-Cyclodextrins Using Grid-based Monte Carlo Docking Simulations vol.26, pp.5, 2003, https://doi.org/10.5012/bkcs.2005.26.5.769
  4. Understanding β-Hairpin Formation: Computational Studies for Three Different Hairpins vol.29, pp.4, 2008, https://doi.org/10.5012/bkcs.2008.29.4.741
  5. Time-dependent density functional theory study on the hydrogen bonding in electronic excited states of 6-amino-3-((thiophen-2-yl) methylene)-phthalide in methanol solution vol.972, pp.1, 2003, https://doi.org/10.1016/j.comptc.2011.06.013