Graduate School of Energy Science, Kyoto University, Uji, Kyoto 611-0011, Japan.
J Chem Phys. 2011 Jul 28;135(4):045103. doi: 10.1063/1.3617247.
The morphometric approach (MA) is a powerful tool for calculating a solvation free energy (SFE) and related quantities of solvation thermodynamics of complex molecules. Here, we extend it to a solvent consisting of m components. In the integral equation theories, the SFE is expressed as the sum of m terms each of which comprises solute-component j correlation functions (j = 1,..., m). The MA is applied to each term in a formally separate manner: The term is expressed as a linear combination of the four geometric measures, excluded volume, solvent-accessible surface area, and integrated mean and Gaussian curvatures of the accessible surface, which are calculated for component j. The total number of the geometric measures or the coefficients in the linear combinations is 4m. The coefficients are determined in simple geometries, i.e., for spherical solutes with various diameters in the same multicomponent solvent. The SFE of the spherical solutes are calculated using the radial-symmetric integral equation theory. The extended version of the MA is illustrated for a protein modeled as a set of fused hard spheres immersed in a binary mixture of hard spheres. Several mixtures of different molecular-diameter ratios and compositions and 30 structures of the protein with a variety of radii of gyration are considered for the illustration purpose. The SFE calculated by the MA is compared with that by the direct application of the three-dimensional integral equation theory (3D-IET) to the protein. The deviations of the MA values from the 3D-IET values are less than 1.5%. The computation time required is over four orders of magnitude shorter than that in the 3D-IET. The MA thus developed is expected to be best suited to analyses concerning the effects of cosolvents such as urea on the structural stability of a protein.
形态计量学方法 (MA) 是计算复杂分子溶剂化自由能 (SFE) 和相关溶剂化热力学量的有力工具。在这里,我们将其扩展到由 m 个组分组成的溶剂中。在积分方程理论中,SFE 表示为 m 项之和,每项都包含溶质-组分 j 相关函数(j = 1,..., m)。MA 以形式上单独的方式应用于每个项:该项表示为四个几何量的线性组合,排除体积、溶剂可及表面积以及可及表面的积分平均和高斯曲率,这些几何量是针对组分 j 计算的。线性组合中的几何量或系数的总数为 4m。在简单的几何形状中确定系数,即对于具有相同多组分溶剂中不同直径的球形溶质。使用径向对称积分方程理论计算球形溶质的 SFE。将 MA 的扩展版本用于浸入硬球二元混合物中的一组融合硬球模型的蛋白质。为了说明目的,考虑了几种不同分子直径比和组成的混合物以及 30 种具有各种旋转半径的蛋白质结构。通过 MA 计算的 SFE 与直接将三维积分方程理论 (3D-IET) 应用于蛋白质的 SFE 进行了比较。MA 值与 3D-IET 值的偏差小于 1.5%。所需的计算时间比 3D-IET 短四个数量级以上。因此,开发的 MA 有望最适合分析诸如脲等共溶剂对蛋白质结构稳定性的影响。