Kierzek A, Zielenkiewicz P
Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw.
Acta Biochim Pol. 1997;44(3):549-56.
The effect of an empirical solvation energy term on energy minimization of ribonuclease T1 was established using different sets of Atomic Solvation Parameters. The results are compared to minimization in vacuo and in a 10 A water shell. The best solvent model as judged from the comparison to the crystal structure was an empirical solvation potential derived from free energies of transfer of amino-acid side-chain analogues from vapour to water. The use of this model causes, however, energy and gradient oscillations, which make it inapplicable with standard protocols of molecular dynamics simulations. The empirical solvation model which was found by other authors (von Freyberg et al., 1993, J. Mol. Biol. 233, 275-292) to give good results in the NMR structure refinement led to distortions of the ribonuclease native structure. The model based on statistical analysis of crystal structures did not perform better than minimization in vacuo.
利用不同组的原子溶剂化参数，确定了经验溶剂化能项对核糖核酸酶T1能量最小化的影响。将结果与在真空中以及在10埃水壳中的能量最小化情况进行了比较。从与晶体结构的比较判断，最佳的溶剂模型是一种基于氨基酸侧链类似物从气相转移到水相的自由能推导出来的经验溶剂化势。然而，使用该模型会导致能量和梯度振荡，这使得它不适用于分子动力学模拟的标准协议。其他作者（冯·弗雷贝格等人，1993年，《分子生物学杂志》233卷，275 - 292页）发现的在核磁共振结构精修中能给出良好结果的经验溶剂化模型，却导致了核糖核酸酶天然结构的扭曲。基于晶体结构统计分析的模型并不比在真空中的能量最小化表现更好。
