Bacci Marco, Chinappi Mauro, Casciola Carlo Massimo, Cecconi Fabio
Dipartimento di Ingegneria Civile e Ambientale, Università degli Studi di Firenze, via Santa Marta 3, 50139, Firenze, Italy.
Phys Rev E Stat Nonlin Soft Matter Phys. 2013 Aug;88(2):022712. doi: 10.1103/PhysRevE.88.022712. Epub 2013 Aug 14.
Coarse-grained simulations of protein translocation across narrow pores suggest that the transport is characterized by long stall events. The translocation bottlenecks and the associated free-energy barriers are found to be strictly related to the structural properties of the protein native structure. The ascending ramps of the free-energy profile systematically correspond to regions of the chain denser in long range native contacts formed with the untranslocated portion of the protein. These very regions are responsible for the stalls occurring during the protein transport along the nanopore. The decomposition of the free energy in internal energyand entropic terms shows that the dominant energetic contribution can be estimated on the base of the protein native structure only. Interestingly, the essential features of the dynamics are retained in a reduced phenomenological model of the process describing the evolution of a suitable collective variable in the associated free-energy landscape.
对蛋白质跨窄孔转运的粗粒度模拟表明，这种转运的特征是存在长时间的停滞事件。发现转运瓶颈和相关的自由能障碍与蛋白质天然结构的结构特性密切相关。自由能分布的上升斜坡系统地对应于与蛋白质未转运部分形成长程天然接触的链更密集的区域。正是这些区域导致了蛋白质沿纳米孔转运过程中的停滞。自由能在内能和熵项中的分解表明，主要的能量贡献仅可基于蛋白质天然结构来估计。有趣的是，该过程的基本动力学特征在一个简化的唯象模型中得以保留，该模型描述了相关自由能景观中一个合适的集体变量的演化。
