Department of Physics, Applied Physics and Astronomy and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, USA.
J Chem Phys. 2011 Jun 14;134(22):225101. doi: 10.1063/1.3592712.
We describe the effects of confinement on the structure, hydration, and the internal dynamics of ubiquitin encapsulated in reverse micelles (RM). We performed molecular dynamics simulations of the encapsulation of ubiquitin into self-assembled protein/surfactant reverse micelles to study the positioning and interactions of the protein with the RM and found that ubiquitin binds to the RM interface at low salt concentrations. The same hydrophobic patch that is recognized by ubiquitin binding domains in vivo is found to make direct contact with the surfactant head groups, hydrophobic tails, and the iso-octane solvent. The fast backbone N-H relaxation dynamics show that the fluctuations of the protein encapsulated in the RM are reduced when compared to the protein in bulk. This reduction in fluctuations can be explained by the direct interactions of ubiquitin with the surfactant and by the reduced hydration environment within the RM. At high concentrations of excess salt, the protein does not bind strongly to the RM interface and the fast backbone dynamics are similar to that of the protein in bulk. Our simulations demonstrate that the confinement of protein can result in altered protein dynamics due to the interactions between the protein and the surfactant.
我们描述了限制对包埋在反胶束（RM）中的泛素的结构、水合作用和内部动力学的影响。我们进行了将泛素封装到自组装的蛋白质/表面活性剂反胶束中的分子动力学模拟，以研究蛋白质与 RM 的定位和相互作用，发现泛素在低盐浓度下与 RM 界面结合。在体内与泛素结合结构域识别的相同疏水区被发现与表面活性剂头基、疏水尾部和异辛烷溶剂直接接触。快速的骨架 N-H 弛豫动力学表明，与在本体中的蛋白质相比，包埋在 RM 中的蛋白质的波动减小。这种波动的减小可以通过泛素与表面活性剂的直接相互作用以及 RM 内的水合环境的减少来解释。在过量盐的高浓度下，蛋白质不会与 RM 界面强烈结合，并且快速的骨架动力学与本体中的蛋白质相似。我们的模拟表明，由于蛋白质与表面活性剂之间的相互作用，蛋白质的限制可以导致蛋白质动力学的改变。
