Department of Physics, University of Prince Edward Island, Charlottetown, PE, C1A 4P3, Canada.
Cell Biochem Biophys. 2013 May;66(1):29-36. doi: 10.1007/s12013-012-9394-6.
In this study, we employ the discontinuous molecular dynamics simulation method to investigate the collapse properties of a single heteropolymer chain in an explicit solvent. Solvent density ρ, fraction of hydrophobic monomers n H (defined as the ratio of the number of hydrophobic monomers to the total number of monomers) and a hydrophobicity parameter λ (which controls the energy mismatch between the monomers and solvent particles) were systematically varied to examine their role in polymer collapse. The average static structure factor of the polymer was used to find the so-called θ-point characterizing the state of an ideal chain. Phase diagrams of ρ versus λ for the coil-globule transition were mapped out for different values of n H. Increasing the fraction of hydrophobic monomers n H, solvent density ρ, and hydrophobicity parameter λ were all shown to aid in stabilizing the globule phase. In an effort to explore scaling behaviour of the coil-globule phase diagram as a function of n H, and to investigate whether the phase boundaries for different n H collapsed on to one universal curve, we rescaled λ by n H (δ) λ; we determined δ = 1.72, in contrast to mean-field predictions of δ = 2.0.
在这项研究中，我们采用不连续分子动力学模拟方法研究了在明溶剂中单个杂聚物链的坍塌性质。系统地改变溶剂密度 ρ、疏水性单体分数 n H（定义为疏水性单体数与单体总数的比值）和疏水性参数 λ（控制单体和溶剂粒子之间的能量失配），以考察它们在聚合物坍塌中的作用。使用聚合物的平均静态结构因子找到描述理想链状态的所谓θ点。针对不同的 n H 值，绘制了 ρ 对 λ 的相图以研究构象转变。增加疏水性单体分数 n H、溶剂密度 ρ 和疏水性参数 λ 都有助于稳定球蛋白相。为了探索作为 n H 函数的线圈-球相图的标度行为，并研究不同 n H 的相界是否会收缩到一个通用曲线上，我们通过 n H（δ）λ 对 λ 进行了标度；我们确定 δ = 1.72，而不是平均场预测的 δ = 2.0。
