Luccioli Stefano, Imparato Alberto, Torcini Alessandro
Istituto dei Sistemi Complessi, CNR, via Madonna del Piano 10, I-50019 Sesto Fiorentino, Italy.
Phys Rev E Stat Nonlin Soft Matter Phys. 2008 Sep;78(3 Pt 1):031907. doi: 10.1103/PhysRevE.78.031907. Epub 2008 Sep 8.
The equilibrium free-energy landscape of off-lattice model heteropolymers as a function of an internal coordinate, namely the end-to-end distance, is reconstructed from out-of-equilibrium steered molecular dynamics data. This task is accomplished via two independent methods: By employing an extended version of the Jarzynski equality and the inherent structure formalism. A comparison of the free energies estimated with these two schemes with equilibrium results obtained via the umbrella sampling technique reveals a good quantitative agreement among all the approaches in a range of temperatures around the "folding transition" for the two examined sequences. In particular, for the sequence with good foldability properties, the mechanically induced structural transitions can be related to thermodynamical aspects of folding. Moreover, for the same sequence the knowledge of the landscape profile allows for a good estimation of the lifetimes of the native configuration for temperatures ranging from the folding to the collapse temperature. For the random sequence, mechanical and thermal unfolding appear to follow different paths along the landscape.
通过非平衡定向分子动力学数据重建了非晶格模型杂聚物的平衡自由能景观，该景观是作为内部坐标（即端到端距离）的函数。这项任务通过两种独立的方法完成：采用Jarzynski等式的扩展版本和固有结构形式。将用这两种方案估计的自由能与通过伞形采样技术获得的平衡结果进行比较，结果表明，在两个被研究序列的“折叠转变”附近的一系列温度范围内，所有方法之间都有良好的定量一致性。特别是，对于具有良好折叠性的序列，机械诱导的结构转变可能与折叠的热力学方面有关。此外，对于同一序列，景观轮廓的知识有助于很好地估计从折叠温度到坍塌温度范围内天然构象的寿命。对于随机序列，机械展开和热展开似乎沿着景观遵循不同的路径。
