Journal of the Korean Magnetic Resonance Society (한국자기공명학회논문지)

Korean Magnetic Resonance Society (한국자기공명학회)
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Effects of generalized-Born implicit solvent models in NMR structure refinement

  • Jee, Jun-Goo (Research Institute of Pharmaceutical Sciences, College of Pharmacy, Kyungpook National University)
  • Received : 2013.05.13
  • Accepted : 2013.06.10
  • Published : 2013.06.20
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Abstract

Rapid advances of computational power and method have made it practical to apply the time-consuming calculations with all-atom force fields and sophisticated potential energies into refining NMR structure. Added to the all-atom force field, generalized-Born implicit solvent model (GBIS) contributes substantially to improving the qualities of the resulting NMR structures. GBIS approximates the effects that explicit solvents bring about even with fairly reduced computational times. Although GBIS is employed in the final stage of NMR structure calculation with experimental restraints, the effects by GBIS on structures have been reported notable. However, the detailed effect is little studied in a quantitative way. In this study, we report GBIS refinements of ubiquitin and GB1 structures by six GBIS models of AMBER package with experimental distance and backbone torsion angle restraints. Of GBIS models tested, the calculations with igb=7 option generated the closest structures to those determined by X-ray both in ubiquitin and GB1 from the viewpoints of root-mean-square deviations. Those with igb=5 yielded the second best results. Our data suggest that the degrees of improvements vary under different GBIS models and the proper selection of GBIS model can lead to better results.

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References

  1. Wuthrich, K. NMR of Proteins and Nucleic Acids; Wiley: New York, (1986).
  2. Herrmann, T.; Guntert, P.; Wuthrich, K. Journal of molecular biology. 319, 209. (2002). https://doi.org/10.1016/S0022-2836(02)00241-3
  3. Schmidt, E.; Guntert, P. Journal of the American Chemical Society. 134, 12817. (2012). https://doi.org/10.1021/ja305091n
  4. Lopez-Mendez, B.; Guntert, P. Journal of the American Chemical Society. 128, 13112. (2006). https://doi.org/10.1021/ja061136l
  5. Xia, B.; Tsui, V.; Case, D. A.; Dyson, H. J.; Wright, P. E. Journal of biomolecular NMR. 22, 317. (2002). https://doi.org/10.1023/A:1014929925008
  6. Jee, J. Bull Korean Chem Soc. 31, 2717. (2010). https://doi.org/10.5012/bkcs.2010.31.9.2717
  7. Fujiwara, K.; Tenno, T.; Sugasawa, K.; Jee, J. G.; Ohki, I.; Kojima, C.; Tochio, H.; Hiroaki, H.; Hanaoka, F.; Shirakawa, M. The Journal of biological chemistry. 279, 4760. (2004). https://doi.org/10.1074/jbc.M309448200
  8. Jee, J.; Byeon, I. J.; Louis, J. M.; Gronenborn, A. M. Proteins .71, 1420. (2008).
  9. Ohno, A.; Jee, J.; Fujiwara, K.; Tenno, T.; Goda, N.; Tochio, H.; Kobayashi, H.; Hiroaki, H.; Shirakawa, M. Structure 13, 521. (2005). https://doi.org/10.1016/j.str.2005.01.011
  10. Sekiyama, N.; Jee, J.; Isogai, S.; Akagi, K.; Huang, T. H.; Ariyoshi, M.; Tochio, H.; Shirakawa, M. Journal of biomolecular NMR. 52, 339. (2012). https://doi.org/10.1007/s10858-012-9614-9
  11. Furuita, K.; Jee, J.; Fukada, H.; Mishima, M.; Kojima, C. The Journal of biological chemistry. 285, 12961. (2010). https://doi.org/10.1074/jbc.M109.082602
  12. Jee, J.; Ahn, H. C. Bull Korean Chem Soc. 30, 1139. (2009). https://doi.org/10.5012/bkcs.2009.30.5.1139
  13. Case, D. A.; Cheatham, T. E., 3rd; Darden, T.; Gohlke, H.; Luo, R.; Merz, K. M., Jr.; Onufriev, A.; Simmerling, C.; Wang, B.; Woods, R. J. J Comput Chem. 26, 1668. (2005). https://doi.org/10.1002/jcc.20290
  14. Guntert, P.; Mumenthaler, C.; Wuthrich, K. Journal of molecular biology. 273, 283. (1997). https://doi.org/10.1006/jmbi.1997.1284
  15. Laskowski, R. A.; Rullmannn, J. A.; MacArthur, M. W.; Kaptein, R.; Thornton, J. M. Journal of biomolecular NMR. 8, 477. (1996).
  16. Davis, I. W.; Leaver-Fay, A.; Chen, V. B.; Block, J. N.; Kapral, G. J.; Wang, X.; Murray, L. W.; Arendall, W. B., 3rd; Snoeyink, J.; Richardson, J. S.; Richardson, D. C. Nucleic acids research. 35, W375. https://doi.org/10.1093/nar/gkm216
  17. Koradi, R.; Billeter, M.; Wuthrich, K. J Mol Graph. 14, 51. (1996). https://doi.org/10.1016/0263-7855(96)00009-4
  18. Jee, J. G.; Ikegami, T.; Hashimoto, M.; Kawabata, T.; Ikeguchi, M.; Watanabe, T.; Shirakawa, M. The Journal of biological chemistry. 277, 1388. (2002). https://doi.org/10.1074/jbc.M109726200
  19. Mongan, J.; Simmerling, C.; McCammon, J. A.; Case, D. A.; Onufriev, A. Journal of chemical theory and computation. 3, 156. (2007). https://doi.org/10.1021/ct600085e
  20. Lim, J.; Ahn, H.-C. J Kor Mag Res Soc. 16, 46. (2012).
  21. Sim, D.-W.; Jo, K.-S.; Ryu, K.-S.; Kim, E.-H.; Won, H.-S. J Kor Mag Res Soc. 16, 21. (2012).

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