Optimized parameters for continuum solvation calculations with carbohydrates
Optimized parameters for continuum solvation calculations with carbohydrates
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DOI：
10.1021/jp709725b
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发表时间：
2008-04-24
影响因子：
3.3
通讯作者：
Green, David F.
中科院分区：
文献类型：
--
作者：
Green, David F.
连续介质溶剂模型是计算生物分子在溶液中能量学的有效方法。然而，为了使这些方法产生准确的结果，需要一组适当的原子半径或体积。虽然这些已经被开发用于蛋白质和核酸，但碳水化合物却不是如此。在这里，一组优化的参数结合碳水化合物溶液力场的碳水化合物连续溶剂化计算。显式溶剂自由能微扰模拟进行了一组六吡喃糖和用于拟合原子半径的泊松-玻尔兹曼和广义玻恩计算，并配合原子体积与分析连续静电模型。优化半径和Poisson-Boltzmann模型计算的溶剂化能量显着的协议与明确的溶剂模拟，在许多构象的糖在一个大的测试集的均方根误差为1.19千卡/摩尔。广义玻恩模型给出的一致性稍差，但仍有很强的相关性，误差为1.69千卡/摩尔。解析连续静电模型与显式溶剂有很好的相关性。结果，但给出了4.71千卡/摩尔的较大误差。显式和隐式溶剂中计算的溶剂化自由能之间的显着协议提供了强大的动机使用隐式溶剂模型在模拟含碳水化合物的系统。
Continuum solvent models have been shown to be an efficient method for the calculation of the energetics of biomolecules in solution. However, for these methods to produce accurate results, an appropriate set of atomic radii or volumes is needed. While these have been developed for proteins and nucleic acids, the same is not true of carbohydrates. Here, a set of optimized parameters for continuum solvation calculations of carbohydrates in conjunction with the Carbohydrate Solution Force Field are presented. Explicit solvent free-energy perturbation simulations were performed on a set of hexapyranose sugars and used to fit atomic radii for Poisson-Boltzmann and generalized-Born calculations, and to fit atomic volumes for use with the analytical continuum electrostatics model. The solvation energetics computed with the optimized radii and a Poisson-Boltzmann model show remarkable agreement with explicit solvent simulation, with a root-mean-square error of 1.19 kcal/mol over a large test set of sugars in many conformations. The generalized-Born model gives slightly poorer agreement, but still correlates very strongly, with an error of 1.69 kcal/mol. The analytical continuum electrostatics model correlates well with the explicit solvent. results, but gives a larger error of 4.71 kcal/mol. The remarkable agreement between the solvation free energies computed in explicit and implicit solvent provides strong motivation for the use of implicit solvent models in the simulation of carbohydrate-containing systems.