Development of a generalized born model parametrization for proteins and nucleic acids
Development of a generalized born model parametrization for proteins and nucleic acids
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DOI：
10.1021/jp984440c
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发表时间：
1999-05-06
影响因子：
3.3
通讯作者：
Brooks, CL
中科院分区：
文献类型：
--
作者：
Dominy, BN;Brooks, CL
Still及其同事提出的广义Born模型（Qui，D.; Shenkin，P. S.; Hollinger，F. P的;尽管如此，W。C. J.Phys.Chem.A1997，101，3005-3014）在CHARMM全氢和极性氢力场内被具体参数化用于蛋白质、肽和核酸。建立了包括氨基酸残基、核酸碱基、二肽、二核苷酸、蛋白质和DNA链的原子静电环境和分子静电溶剂化自由能的数据库，并且使用来自相应力场参数的原子半径和电荷来求解数值有限差分泊松计算。这些数据提供了必要的输入参数化广义玻恩模型为一个特定的力场。这些模型在再现整体分子溶剂化趋势的性能进行了检查，发现是相当不错的。此外，静电溶剂化自由能差异的计算表明，构象自由能的变化很好地再现。最后，利用这种广义玻恩模型在分子动力学模拟（有和没有截止）显示出良好的协议与明确的溶剂模拟一个小的56残基蛋白质在水中。
The generalized Born model proposed by Still and co-workers (Qui, D.; Shenkin, P. S.; Hollinger, F. P.; Still, W. C. J. Phys. Chem. A 1997, 101, 3005-3014) is parametrized specifically for proteins, peptides, and nucleic acids within the CHARMM all hydrogen and polar hydrogen force fields. A database of atomic electrostatic environments and molecular electrostatic solvation free energies comprising amino acid residues, nucleic acid bases, dipeptides, dinucleotides, proteins, and DNA strands is established, and numerical finite difference Poisson calculations are solved using atomic radii and charges from the corresponding force field parameters. These data provide the necessary input to parametrize generalized Born models for a particular force field. The performance of these models in reproducing overall molecular solvation trends is examined and found to be quite good. Furthermore, calculations of electrostatic solvation free energy differences suggest that conformational free energy changes are well reproduced. Finally, the utilization of this generalized Born model in molecular dynamics simulations (both with and without cutoffs) is shown to give excellent agreement with explicit solvent simulations of a small 56-residue protein in water.