Department of Physics and Astronomy, University of Southern Mississippi, Hattiesburg, Mississippi 39406, USA.
Department of Physics and Optical Science, University of North Carolina, Charlotte, North Carolina 28223, USA.
J Chem Phys. 2017 May 21;146(19):195101. doi: 10.1063/1.4983222.
The effect of preferential binding of solute molecules within an aqueous solution on the structure and dynamics of the histone H3.1 protein is examined by a coarse-grained Monte Carlo simulation. The knowledge-based residue-residue and hydropathy-index-based residue-solvent interactions are used as input to analyze a number of local and global physical quantities as a function of the residue-solvent interaction strength (f). Results from simulations that treat the aqueous solution as a homogeneous effective solvent medium are compared to when positional fluctuations of the solute molecules are explicitly considered. While the radius of gyration (R) of the protein exhibits a non-monotonic dependence on solvent interaction over a wide range of f within an effective medium, an abrupt collapse in R occurs in a narrow range of f when solute molecules rapidly bind to a preferential set of sites on the protein. The structure factor S(q) of the protein with wave vector (q) becomes oscillatory in the collapsed state, which reflects segmental correlations caused by spatial fluctuations in solute-protein binding. Spatial fluctuations in solute binding also modify the effective dimension (D) of the protein in fibrous (D ∼ 1.3), random-coil (D ∼ 1.75), and globular (D ∼ 3) conformational ensembles as the interaction strength increases, which differ from an effective medium with respect to the magnitude of D and the length scale.
通过粗粒化蒙特卡罗模拟研究了溶质分子在水溶液中优先结合对组蛋白 H3.1 蛋白质结构和动力学的影响。基于知识的残基-残基和基于疏水性指数的残基-溶剂相互作用被用作输入，以分析许多局部和全局物理量作为残基-溶剂相互作用强度（f）的函数。将水溶液视为均匀有效溶剂介质的模拟结果与明确考虑溶质分子位置波动时的结果进行了比较。虽然蛋白质的回转半径（R）在有效介质中 f 的广泛范围内对溶剂相互作用表现出非单调依赖性，但当溶质分子迅速结合到蛋白质上的优先位置时，R 会在很窄的 f 范围内突然坍塌。具有波矢（q）的蛋白质的结构因子 S（q）在坍塌状态下呈现出振荡，这反映了由溶质-蛋白质结合的空间波动引起的片段相关性。溶质结合的空间波动也会随着相互作用强度的增加，改变纤维状（D∼1.3）、无规卷曲（D∼1.75）和球状（D∼3）构象集合中蛋白质的有效维度（D），与有效介质相比，D 的大小和长度尺度不同。
