很多蛋白质的力学响应决定了其生物功能。单分子操纵技术特别是磁镊可以精确测量蛋白质在生理拉力下的响应。在此拉力下蛋白质去折叠一般发生在从毫秒到小时的时间尺度，而全原子分子动力学模拟一般仅能到纳秒至微秒，从而难以模拟蛋白质去折叠过程。本项目将结合单分子磁镊拉伸试验，使用我们发展的加权系综动力学模拟方法研究蛋白质在不同拉力下的去折叠动力学。加权系综模拟代替产生单个长轨道的传统模拟方法，从许多不同的初始构象出发独立模拟多条短轨道，通过分析这些短轨道在构象空间的重叠关系，拼接重建出系统的长时间动力学行为。这个方法使得我们能在合理计算时间内模拟构建如titin蛋白I27结构域等的长时间去折叠动力学，并直接比较我们进一步的实验结果。通过本项目有望建立可行的蛋白质去折叠全原子模拟方案，揭示拉力下的蛋白质去折叠的分子机制，为利用基因工程改造蛋白质序列实现特定力学特性提供系统的理论实验方法。

Mechanical responses of proteins are critical to biological functions of many proteins. Single molecular manipulation techniques, especially magnetic tweezers, can measure the mechanical response of proteins to physiological relevant forces with high spatial and temporal resolution. Under physiological forces, proteins usually unfold in time scale of milli-seconds to hours. On the other hand, all-atomic molecular dynamics simulations usually can only be done over nano-seconds to micro-seconds time scale. Therefore, it is very difficult to study the proteins unfolding process by traditional molecular dynamic simulation. In this project, inspired by magnetic tweezers experiment of protein stretching, we will apply the reweighted ensemble dynamics simulation method we developed to study the unfolding dynamics of protein at different forces. By using reweighted ensemble dynamics simulation method instead of the traditional simulation method, an ensemble independent short simulation trajectories will be generated from different initial conformations. From analysis of the overlap region of there short trajectories, the long time scale dynamics of the system can be reconstructed. We will use affordable computation time to reproduce the long time scale dynamics of protein unfolding like titin I27 domain, and directly compare with our experimental results. The proposed project will provide an all-atom simulation scheme to study protein unfolding problem, elucidate the molecular mechanism of force-dependent protein unfolding, and provide a theory-experiment combined method to modify the mechanical properties of proteins by gene engineering techniques.