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Studies of the Monodipole-macrodipole Interactions within α-Helices Using the Point-charge Systems for Alanine

  • Park, Chang-Moon (Department of Chemistry, College of Natural Sciences, Chungnam National University)
  • Published : 2003.06.20
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Abstract

Our previous quantum mechanical calculations using polyalanine model systems showed that the monodipolemacrodipoleinteractions selectively stabilize α-helices and make it possible for α-helices to be formed inhydrophobic environment where the solvent effect is not available. The monodipole-macrodipole interactionsin α-helices were studied molecular mechanically using various point-charge systems available. The resultsshow that all the point-charge systems used in the calculations produce the monodipole-macrodipoleinteractions up to about 60% compared to the results of the quantum mechanical calculations. The results ofmolecular mechanical calculations are explained and discussed compared to the results of the quantummechanical calculations.

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References

  1. Shea, J. E.; Brooks, C. L. Annu. Rev. Phys. Chem. 2001, 52, 499. https://doi.org/10.1146/annurev.physchem.52.1.499
  2. Dauber-Osguthorpe, P.; Roberts, V. A.; Osguthorpe, D. J.; Wolff,J.; Genest, M.; Hagler, A. T. Proteins: Structure, Function andGenetics 1988, 4, 31. https://doi.org/10.1002/prot.340040106
  3. Weiner, S. J.; Kollman, P. A.; Singh, U. C.; Ghio, C.; Alagona, G.;Profeta, S., Jr.; Weiner, P. J. Am. Chem. Soc. 1984, 106, 765. https://doi.org/10.1021/ja00315a051
  4. Weiner, S. J.; Kollman, P. A.; Nguyen, D. T.; Case, D. A. J. Comp.Chem. 1986, 7, 230. https://doi.org/10.1002/jcc.540070216
  5. Maple, J.; Dinur, U.; Hagler, A. T. Proc. Nat. Acad. Sci. USA1988, 85, 5350. https://doi.org/10.1073/pnas.85.15.5350
  6. Dinur, U.; Hagler, A. T. Approaches to empirical force fields in Review of Computational Chemistry; Lipkwowitz, K. B.; Boyd, D. B., Eds.; VCH: New York; 1991; Vol. 2, Chapter 4.
  7. Bellido, M. N.; Rullmann, J. A. C. J. Comp. Chem. 1989, 10, 479. https://doi.org/10.1002/jcc.540100405
  8. 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
  9. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, Jr., K.M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.;Kollman, P. A. J. Am. Chem. Soc. 1995, 117, 5179. https://doi.org/10.1021/ja00124a002
  10. Jorgenson, W. L.; Tirado-Rives, J. J. Am. Chem. Soc. 1988, 110, 1657. https://doi.org/10.1021/ja00214a001
  11. Mayo, S. L.; Olafson, B. D.; Goddard III, W. A. J. Phys. Chem.1990, 94, 8897. https://doi.org/10.1021/j100389a010
  12. Park, C.; Goddard III, W. A. J. Phys. Chem. B 2000, 104, 7784. https://doi.org/10.1021/jp0001743
  13. Sung, S.; Wu, X. W. Proteins 1996, 25, 202. https://doi.org/10.1002/(SICI)1097-0134(199606)25:2<202::AID-PROT6>3.0.CO;2-J
  14. Hirst, J. D.; Brooks, C. L. III. Biochemistry 1995, 34, 7614. https://doi.org/10.1021/bi00023a007
  15. Young, W. S.; Brooks III, C. L. J. Mol. Biol. 1996, 259, 558.
  16. Daura, X.; Jaun, B.; Seebach, D.; van Gunstern, W. F.; Mark, A. E.J. Mol. Biol. 1998, 280, 925. https://doi.org/10.1006/jmbi.1998.1885
  17. Duan, Y.; Kollman, P. A. Science 1998, 282, 740. https://doi.org/10.1126/science.282.5389.740
  18. Park, C.; Carlson, M. J.; Goddard III, W. A. J. Phys. Chem. A2000, 104, 2498. https://doi.org/10.1021/jp9911189
  19. Wada, A. Adv. Biophys. 1976, 9, 1.
  20. Hol, W. G. J.; Van Duijnen, P. T.; Berendsen, H. J. C. Nature 1978,273, 443. https://doi.org/10.1038/273443a0
  21. Wu, X.; Wang, S. J. Phys. Chem. B 2001, 105, 2227. https://doi.org/10.1021/jp004048a
  22. Haynie, D. T.; Freire, E. Proteins 1993, 16, 115. https://doi.org/10.1002/prot.340160202
  23. Kuwajima, K. FASEB J. 1996, 10, 102.
  24. Ptitsyn, O. B. Adv. Protein Chem. 1995, 47, 83. https://doi.org/10.1016/S0065-3233(08)60546-X
  25. Kim, P. S.; Baldwin, R. L. Annu. Rev. Biochem. 1982, 21, 459.
  26. Margulis, C. J.; Stern, H. A.; Berne, B. J. J. Phys. Chem. B 2002,106, 10748. https://doi.org/10.1021/jp0205158

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