Acta Phys. -Chim. Sin. ›› 2003, Vol. 19 ›› Issue (08): 723-726.doi: 10.3866/PKU.WHXB20030810

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Empirical Aqueous Solvation Model for Protein Based on Accessible Surface Areas

Hou Ting-Jun;Zhang Wei;Huang Qin;Qiao Xue-Bin;Xu Xiao-Jie   

  1. College of Chemistry and Molecular Engineering, Peking University, Beijing　100871
  • Received:2003-01-23 Revised:2003-03-25 Published:2003-08-15
  • Contact: Xu Xiao-Jie E-mail:xiaojxu@chem.pku.edu.cn

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Abstract: A simplified aqueous solvation model (SAWSA 2) for protein was developed. The model classified the atoms in protein into 20 basic types; and the aqueous free energies of solvation was calculated by solvent-accessible surface areas of each atom type and corresponding solvation parameters. The solvation parameter for each atom type was obtained by fitted the calculated aqueous free energies of solvation from PB/SA of 110 proteins. The solvation model developed in this work was applied to predict the solvation free energies of 20 proteins. The predicted values from SAWSA 2 model were in good agreement with those from PB/SA model, and were much better than those given by the two models previously reported.

Key words: Aqueous free energy of solvation, Solvation effect, Molecular surface, 　Protein, PB/SA(Possion-Boltzmann/Molecular surface area model)