DOI QR코드

DOI QR Code

Computational Prediction of Solvation Free Energies of Amino Acids with Genetic Algorithm

  • Park, Jung-Hum (Department of Bioscience and Biotechnology, Sejong University) ;
  • Lee, Jin-Won (Department of Life Science, Hanyang University) ;
  • Park, Hwang-Seo (Department of Bioscience and Biotechnology, Sejong University)
  • 투고 : 2010.02.17
  • 심사 : 2010.03.05
  • 발행 : 2010.05.20

초록

We propose an improved solvent contact model to estimate the solvation free energies of amino acids from individual atomic contributions. The modification of the solvation model involves the optimization of three kinds of parameters in the solvation free energy function: atomic fragmental volume, maximum atomic occupancy, and atomic solvation parameters. All of these atomic parameters for 17 atom types are developed by the operation of a standard genetic algorithm in such a way to minimize the difference between experimental and calculated solvation free energies. The present solvation model is able to predict the experimental solvation free energies of amino acids with the squared correlation coefficients of 0.94 and 0.93 for the parameterization with Gaussian and screened Coulomb potential as the envelope functions, respectively. This result indicates that the improved solvent contact model with the newly developed atomic parameters would be a useful tool for the estimation of the molecular solvation free energy of a protein in aqueous solution.

키워드

참고문헌

  1. Rost, B.; Sander, C. J. Mol. Biol. 1993, 232, 584. https://doi.org/10.1006/jmbi.1993.1413
  2. Parsegian, V. A.; Rand, R. P.; Fuller, N. L.; Rau, D. C. Methods Enzymol. 1986, 127, 400. https://doi.org/10.1016/0076-6879(86)27032-9
  3. Liu, K.; Cruzan, J.; Saykally, R. Science 1996, 271, 929. https://doi.org/10.1126/science.271.5251.929
  4. Makarov, V.; Pettitt, B. M.; Feig, M. Acc. Chem. Res. 2002, 35, 376. https://doi.org/10.1021/ar0100273
  5. Gu, C.; Lustig, S.; Trout, B. L. J. Phys. Chem. B 2006, 110, 1476. https://doi.org/10.1021/jp054602m
  6. Vorobjev, Y. N.; Vila, J. A.; Scheraga, H. A. J. Phys. Chem. B 2008, 112, 11122. https://doi.org/10.1021/jp709969n
  7. Jorgensen, W. L.; Duffy, E. M. Adv. Drug Delivery Rev. 2002, 54, 355. https://doi.org/10.1016/S0169-409X(02)00008-X
  8. Wesson, L.; Eisenberg, D. Protein Sci. 1992, 1, 227.
  9. Eisenberg, D.; Mclachlan, A. D. Nature 1986, 319, 199. https://doi.org/10.1038/319199a0
  10. Ooi, T.; Oobatake, M. Proc. Natl. Acad. Sci. U. S. A. 1991, 88, 2859. https://doi.org/10.1073/pnas.88.7.2859
  11. Schiffer, C. A.; Caldwell, J. W.; Stroud, R. M.; Kollman, P. A. Protein Sci. 1992, 1, 396.
  12. Kang, Y. K.; Nemethy, G.; Scheraga, H. A. J. Phys. Chem. 1987, 91, 4105. https://doi.org/10.1021/j100299a032
  13. Colonnacesari, F.; Sander, C. Biophys. J. 1990, 57, 1103. https://doi.org/10.1016/S0006-3495(90)82630-8
  14. Born, M. Z. Physics 1920, 1, 45. https://doi.org/10.1007/BF01881023
  15. Kirkwood, J. G. J. Chem. Phys. 1934, 2, 351. https://doi.org/10.1063/1.1749489
  16. Tanford, C.; Kirkwood, J. G. J. Am. Chem. Soc. 1957, 79, 5333. https://doi.org/10.1021/ja01577a001
  17. Klapper, I.; Hagstrom, R.; Fine, R.; Sharp, K. Proteins 1986, 1, 47. https://doi.org/10.1002/prot.340010109
  18. Garde, S.; Hummer, G.; Garcia, A.; Pratt, L.; Paulaitis, M. Phys. Rev. E 1996, 53, R4310. https://doi.org/10.1103/PhysRevE.53.R4310
  19. Hummer, G.; Soumpasis, D. Phys. Rev. E 1994, 50, 5085. https://doi.org/10.1103/PhysRevE.50.5085
  20. Colonna-Cesari, F.; Sander, C. Biophys. J. 1990, 57, 1103. https://doi.org/10.1016/S0006-3495(90)82630-8
  21. Stouten, P. F. W.; Frommel, C.; Nakamura, H.; Sander, C. Mol. Simul. 1993, 10, 97. https://doi.org/10.1080/08927029308022161
  22. Park, J.-H.; Ko, S.; Park, H. Bull. Korean Chem. Soc. 2008, 29, 921. https://doi.org/10.5012/bkcs.2008.29.5.921
  23. Park, H.; Jung, S.-K.; Bahn, Y. J.; Jeong, D. G.; Ryu, S. E.; Kim, S. J. Bull. Korean Chem. Soc. 2009, 30, 1313. https://doi.org/10.5012/bkcs.2009.30.6.1313
  24. Dixit, S. B.; Bhasin, R.; Rajasekaran, E.; Jayaram, B. J. Chem. Soc. Faraday Trans. 1997, 93, 1105. https://doi.org/10.1039/a603913h
  25. Chang, J.; Lenhoff, A. M.; Sandler, S. I. J. Phys. Chem. B 2007, 111, 2098. https://doi.org/10.1021/jp0620163
  26. Sadowski, J.; Gasteiger, J.; Klebe, G. J. Chem. Inf. Comput. Sci. 1994, 34, 1000. https://doi.org/10.1021/ci00020a039
  27. Goller, A. H.; Hennemann, M.; Keldenich, J.; Clark, T. J. Chem. Inf. Model 2006, 46, 648. https://doi.org/10.1021/ci0503210
  28. Cheng, A.; Merz, K. M., Jr. J. Med. Chem. 2003, 46, 3572. https://doi.org/10.1021/jm020266b
  29. Liu, R.; So, S.-S. J. Chem. Inf. Comput. Sci. 2001, 41, 1633. https://doi.org/10.1021/ci010289j

피인용 문헌

  1. Comprehensive Studies on the Free Energies of Solvation and Conformers of Glycine: A Theoretical Study vol.32, pp.6, 2011, https://doi.org/10.5012/bkcs.2011.32.6.1985
  2. Structural and vibrational study on zwitterions of l-threonine in aqueous phase using the FT-Raman and SCRF calculations vol.1045, pp.None, 2010, https://doi.org/10.1016/j.molstruc.2013.04.016