Robert C H
Department of Biochemistry and Biophysics, Oregon State University, Corvallis 97331, USA.
Biophys J. 1995 Sep;69(3):840-8. doi: 10.1016/S0006-3495(95)79957-X.
Existing methods for predicting translational friction properties of complex molecules start by explicitly building up their three-dimensional shape with spherical subunits. This treatment has been used especially for two types of systems: rigid assemblies and flexible chain molecules. However, many protein/DNA complexes such as chromatin consist of a small number of globular, relatively rigid, bound protein interspersed by long stretches of flexible DNA chain. I present a higher level of treatment of such macromolecules that avoids explicit subunit modeling as much as possible. An existing analytical formulation of the hydrodynamics equations is shown to be accurate when used with the present treatment. Thus the approach is fast and can be applied to hydrodynamic studies of highly degenerate multiple equilibria, such as those encountered in problems of the regulation of chromatin structure. I demonstrate the approach by predicting the effect of a hypothetical unwinding process in dinucleosomes and by simulating the distribution of sedimentation coefficients for cooperative and random models for a chromatin saturation process.
现有的预测复杂分子平移摩擦特性的方法，首先是用球形亚基明确构建其三维形状。这种处理方法尤其适用于两种类型的系统：刚性组装体和柔性链分子。然而，许多蛋白质/DNA复合物，如染色质，由少量球状、相对刚性的结合蛋白组成，其间穿插着长段柔性DNA链。我提出了一种对这类大分子的更高级处理方法，尽可能避免明确的亚基建模。当与当前处理方法一起使用时，现有的流体动力学方程解析公式被证明是准确的。因此，该方法速度快，可应用于高度简并的多重平衡的流体动力学研究，比如在染色质结构调控问题中遇到的平衡。我通过预测双核小体中假设的解旋过程的影响，以及模拟染色质饱和过程中协同模型和随机模型的沉降系数分布，来演示该方法。
