Biophysics Program, Institute for Physical Sciences and Technology, University of Houston, Houston, Texas 77204, United States.
J Phys Chem B. 2012 Jul 26;116(29):8513-22. doi: 10.1021/jp212535n. Epub 2012 Jun 1.
We investigate the structural transitions in a polymer induced by spherical and nonspherical crowding particles over a wide range of conditions. The polymer conformations are specified by the radius of gyration and the quality of the solvent in the absence of crowding particles. In the presence of crowding particles, the structures are altered by the volume fraction, size, shape, and polydispersity of the crowders. We show that crowding induces an array of structural changes, ranging from helix, helical hairpin (HH), and multiple helix bundles (HBs), depending on the interplay of multiple length and energy scales including the solvent quality, length of the polymer, temperature, and the characteristics of the crowding agents. In nearly good solvents, the polymer undergoes coil-helix transition in accord with the predictions based on the entropic stabilization mechanism. Higher-order (HH and HB) structures are obtained in poor or moderately poor solvents. In a binary mixture of spherical crowders, the effect of the two components is largely additive with the polymer undergoing greater compaction at higher volume fraction. In contrast to spherical crowders, spherocylinder-like crowders have a dramatically different effect on the diagram of states of the polymer. In the presence of spherocylinders, the polymer prefers to form a nearly ideal helix, especially at low temperatures and high aspect ratios of the crowders, at volume fractions that are not large enough for nematic order. Surprisingly, there is a complete absence of HH and HB in the range of conditions explored here. The dominant formation of spherocylinder-induced helix formation is due to the tendency of the spherocylinders and the polymer to align along the director formed by an increase in nematic order only in the vicinity of the polymer. Our study, which has produced several testable predictions, shows that only by probing the effects of crowding on a polymer (or a protein and RNA) over a wide range of conditions can the diagram of states be quantitatively described.
我们研究了在广泛的条件下，球形和非球形拥挤粒子对聚合物结构转变的影响。在不存在拥挤粒子的情况下，聚合物构象由转动半径和溶剂质量来确定。在存在拥挤粒子的情况下，结构会因拥挤剂的体积分数、大小、形状和多分散性而发生改变。我们表明，拥挤诱导了一系列结构变化，范围从螺旋、螺旋发夹（HH）和多螺旋束（HB），这取决于多个长度和能量尺度的相互作用，包括溶剂质量、聚合物长度、温度和拥挤剂的特性。在近良溶剂中，聚合物经历了从线圈到螺旋的转变，这与基于熵稳定机制的预测一致。在较差或中等较差的溶剂中，会得到更高阶（HH 和 HB）的结构。在球形拥挤剂的二元混合物中，两种成分的影响在很大程度上是相加的，聚合物在较高的体积分数下经历更大的压缩。与球形拥挤剂相比，类球形拥挤剂对聚合物状态图有显著不同的影响。在类球形拥挤剂的存在下，聚合物更倾向于形成几乎理想的螺旋，特别是在低温和高拥挤剂纵横比下，在体积分数不足以形成向列有序的情况下。令人惊讶的是，在我们所探索的条件范围内，完全没有 HH 和 HB。在这种情况下，聚合物形成类球形拥挤诱导螺旋的主要原因是，类球形拥挤剂和聚合物倾向于沿着仅在聚合物附近形成的向列有序的指向排列。我们的研究产生了一些可测试的预测，表明只有通过在广泛的条件下探测拥挤对聚合物（或蛋白质和 RNA）的影响，才能定量描述状态图。
