DOI QR코드

DOI QR Code

Understanding β-Hairpin Formation: Computational Studies for Three Different Hairpins

  • 발행 : 2008.04.20

초록

We have studied the folding mechanism of $\beta$ -hairpins in the proteins 1GB1, 3AIT and 1A2P by conducting unfolding simulations at moderately high temperatures. The analysis of trajectories obtained from molecular dynamics simulations in explicit aqueous solution suggests that the positions of the hydrophobic core residues lead to subtle differences in the details of folding dynamics. However, the folding of three different hairpins can be explained by a unified mechanism that is a blend of the hydrogen-bond-centric and the hydrophobiccentric models. The initial stage of $\beta$-hairpin folding involves various partially folded intermediate structures which are stabilized by both the van der Waals interactions of hydrophobic core residues and the electrostatic interactions of non-native hydrogen bonds. The native structure is obtained by forming native contacts in the final tune-up process. Depending on the relative positions of the hydrophobic residues, the actual mechanism of hairpi n folding may or may not exhibit well-defined intermediates.

키워드

참고문헌

  1. Munoz, V.; Serrano, L. Curr. Opin. Biotechnol. 1995, 6, 382 https://doi.org/10.1016/0958-1669(95)80066-2
  2. Williams, S.; Causgrove, T. P.; Gilmanshin, R.; Fang, K. S.; Callender, R. H.; Woodruff, W. H.; Dyer, R. B. Biochemistry 1996, 35, 691 https://doi.org/10.1021/bi952217p
  3. Thompson, P. A.; Eaton, W. A.; Hofrichter, J. Biochemistry 1997, 36, 9200 https://doi.org/10.1021/bi9704764
  4. Blanco, F.; Ramírez-Alvarado, M.; Serrano, L. Curr. Opin. Struct. Biol. 1998, 8, 107 https://doi.org/10.1016/S0959-440X(98)80017-1
  5. Galzitskaya, O. V.; Higo, J.; Finkelstein, A. V. Curr. Proein Pept. Sci. 2002, 3, 191 https://doi.org/10.2174/1389203024605340
  6. Munoz, V.; Serrano, L. Curr. Opin. Biotechnol. 1995, 6, 382 https://doi.org/10.1016/0958-1669(95)80066-2
  7. Bonvin, A. M.; van Gunsteren, W. F. J. Mol. Biol. 2000, 296, 255 https://doi.org/10.1006/jmbi.1999.3446
  8. 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
  9. Pande, V. S.; Rokhsar, D. S. Proc. Natl. Acad. Sci. USA 1999, 96, 9062 https://doi.org/10.1073/pnas.96.16.9062
  10. Dinner, A. R.; Lazaridis, T.; Karplus, M. Proc. Natl. Acad. Sci. USA 1999, 96, 9068 https://doi.org/10.1073/pnas.96.16.9068
  11. Ma, B.; Nussinov, R. J. Mol. Biol. 2000, 296, 1091 https://doi.org/10.1006/jmbi.2000.3518
  12. Zhou, Y.; Linhananta, A. Proteins 2002, 47, 154 https://doi.org/10.1002/prot.10065
  13. Zagrovic, B.; Sorin, E. J.; Pande, V. J. Mol. Biol. 2001, 313, 151 https://doi.org/10.1006/jmbi.2001.5033
  14. Garcia, A. E.; Sanbonmatsu, K. Y. Proteins 2001, 42, 345 https://doi.org/10.1002/1097-0134(20010215)42:3<345::AID-PROT50>3.0.CO;2-H
  15. Zhou, Y.; Berne, B. J.; Germain, R. Proc. Natl. Acad. Sci. USA 2001, 98, 14931 https://doi.org/10.1073/pnas.201543998
  16. Klimov, D. K.; Thirumalai, D. Proc. Natl. Acad. Sci. USA 2000, 97, 2544 https://doi.org/10.1073/pnas.97.6.2544
  17. Ma, B.; Nussinov, R. Protein Sci. 2003, 12, 1882 https://doi.org/10.1110/ps.0306103
  18. Lee, J.; Jang, S.; Pak, Y.; Shin, S. Bull. Korean Chem. Soc. 2003, 24, 785 https://doi.org/10.5012/bkcs.2003.24.6.785
  19. Lee, J.; Lee, K.; Shin, S. J. Phys. Chem. B 2002, 106, 8796 https://doi.org/10.1021/jp0141732
  20. 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
  21. Ryckaert, J.-P.; Ciccotti, G.; Berendsen, H. J. C. J. Comp. Phys. 1977, 23, 327 https://doi.org/10.1016/0021-9991(77)90098-5
  22. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684 https://doi.org/10.1063/1.448118
  23. Vriend, G. J. Mol. Graph. 1990, 8, 52 https://doi.org/10.1016/0263-7855(90)80070-V
  24. Lee, J.; Shin, S. Biophys. J. 2001, 81, 2507 https://doi.org/10.1016/S0006-3495(01)75896-1
  25. Jang, S.; Shin, S.; Pak, Y. J. Am. Chem. Soc. 2002, 124, 4976 https://doi.org/10.1021/ja025675b
  26. Jang, S.; Kim, E.; Shin, S.; Pak, Y. J. Am. Chem. Soc. 2003, 125, 14841 https://doi.org/10.1021/ja034701i
  27. Boczko, E. M.; Brooks III, C. L. Science 1995, 269, 393 https://doi.org/10.1126/science.7618103
  28. Kim, M. G.; Kim, M.-S.; Park, H.; Lee, S.; Suh, J. Bull. Korean Chem. Soc. 2007, 28, 1151 https://doi.org/10.5012/bkcs.2007.28.7.1151

피인용 문헌

  1. Calculations of Free Energy Surfaces for Small Proteins and a Protein-RNA Complex Using a Lattice Model Approach vol.32, pp.spc8, 2011, https://doi.org/10.5012/bkcs.2011.32.8.3051
  2. 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, 2008, https://doi.org/10.1016/j.comptc.2011.06.013