物理化学学报 >> 2003, Vol. 19 >> Issue (08): 723-726.doi: 10.3866/PKU.WHXB20030810

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基于原子表面的蛋白质水合自由能预测模型

侯廷军;章威;黄钦;乔学斌;徐筱杰   

  1. 北京大学化学与分子工程学院,北京　100871
  • 收稿日期:2003-01-23 修回日期:2003-03-25 发布日期:2003-08-15
  • 通讯作者: 徐筱杰 E-mail:xiaojxu@chem.pku.edu.cn

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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摘要： 提出了一种计算蛋白质水合自由能的简化模型（SAWSA 2）.模型把蛋白质分子中的原子分为20种不同的原子类型,通过每类原子的溶剂可及化表面以及相应的溶剂化参数,就可以得到分子的水合自由能.不同原子类型的溶剂化参数通过110个蛋白质分子水合自由能拟合得到,水合自由能的标准值采用了基于求解Possion-Boltzmann方程（PB）以及分子表面计算（SA） 相结合的方法.采用得到的模型,预测了20个蛋白质分子的水合自由能,预测值的相对值和绝对值都能和PB/SA的计算值很好地吻合,大大优于两种已报导的水合自由能模型.

关键词: 水合自由能, 溶剂效应, 分子表面, 蛋白质, PB/SA(Possion-Boltzmann/分子表面模型)

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)