Solvation free energies of peptides: Comparison of approximate continuum solvation models with accurate solution of the Poisson-Boltzmann equation
Solvation free energies of peptides: Comparison of approximate continuum solvation models with accurate solution of the Poisson-Boltzmann equation
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DOI：
10.1021/jp962156k
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发表时间：
1997-02-13
影响因子：
3.3
通讯作者：
Friesner, RA
中科院分区：
文献类型：
--
作者：
Edinger, SR;Cortis, C;Friesner, RA
我们将从许多近似溶剂化模型获得的溶剂化自由能与泊松-玻尔兹曼方程的精确解进行了比较，该方程适用于肽结构的大数据集，范围从单个氨基酸到长度为九的肽序列。根据泊松-玻尔兹曼结果确定模型预测不同肽构象（相同序列）相对能量的能力。我们发现广泛使用的距离相关介电模型会产生定性错误的结果；相比之下，斯蒂尔和同事的广义玻恩模型（泊松-玻尔兹曼方程的近似）提供了相当好的溶剂化自由能，并且在构象的排序方面表现得相当好。基于表面积的模型产生中等质量的结果。我们的结果表明，如果希望使用快速、近似溶剂化模型进行分子动力学模拟，那么广义 Born 模型目前显然是首选的替代方案。
We have compared solvation free energies obtained from a number of approximate solvation models with an accurate solution of the Poisson-Boltzmann equation for a large data set of peptide structures, ranging from a single amino acid to a peptide sequence of length nine. The models are assessed for their ability to predict relative energetics of different peptide conformations (of the same sequence) as determined from the Poisson-Boltzmann results. We find that the widely used distance dependent dielectric model yields qualitatively erroneous results; in contrast, the generalized Born model of Still and co-workers, an approximation to the Poisson-Boltzmann equation, provides reasonably good solvation free energies and performs rather well in rank ordering of conformations. A surface area based model produces results of intermediate quality. Our results suggest that the generalized Born model is presently the clearly preferred alternative if one wishes to carry out molecular dynamics simulations with a fast, approximate solvation model.