SOLVENT ACCESSIBLE SURFACE-AREA AND EXCLUDED VOLUME IN PROTEINS - ANALYTICAL EQUATIONS FOR OVERLAPPING SPHERES AND IMPLICATIONS FOR THE HYDROPHOBIC EFFECT
SOLVENT ACCESSIBLE SURFACE-AREA AND EXCLUDED VOLUME IN PROTEINS - ANALYTICAL EQUATIONS FOR OVERLAPPING SPHERES AND IMPLICATIONS FOR THE HYDROPHOBIC EFFECT
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DOI：
10.1016/0022-2836(84)90231-6
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发表时间：
1984-01-01
影响因子：
5.6
通讯作者：
RICHMOND, TJ
中科院分区：
文献类型：
--
作者：
RICHMOND, TJ
通过计算一个蛋白质分子的溶剂可及表面积，即任意数量的重叠球体外的表面积，推导出一个解析公式。提供了该函数相对于原子坐标的方向导数，以方便与分子对接算法和能量计算一起使用的最小化程序。导出了可达表面内封闭体积的解析公式，即排除体积。虽然面积函数不是特定于蛋白质结构的，但推导的动机是需要计算上可行的蛋白质疏水效应模拟。一个使用面积方程的计算机程序已经过测试，在蛋白质螺旋的对接中应用有限。根据溶液的统计力学推导了溶质分子的疏水相互作用自由能和转移自由能与溶剂排除体积的可能关系。
An analytical formula was derived from the calculation of the solvent accessible surface area of a protein molecule or equivalently the surface area exterior to an arbitrary number of overlapping spheres. The directional derivative of this function with respect to atomic coordinates is provided to facilitate minimization procedures used with molecular docking algorithms and energy calculations. An analytical formula for the calculation of the volume enclosed within the accessible surface, the excluded volume, is also derived. Although the area function is not specific to the structures of proteins, the derivation was motivated by the need for a computationally feasible simulation of the hydrophobic effect in proteins. A computer program using the equations for area has been tested and has had limited application to the docking of protein .alpha.-helices. Possible relationships of the solvent excluded volume to hydrophobic interaction free energy and transfer free energy of solute molecules are derived from the statistical mechanics of solution.