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分子动力学方法是基于分子力场,通过数值求解牛顿动力学方程来模拟原子与分子运动的计算机模拟方法。利用分子动力学能模拟分子系统与时间相关演化轨迹,研究分子系统的热力学与动力学性质。随着计算机技术的高速发展,分子动力学模拟被广泛的应用于生物分子与纳米材料研究。本文以单壁碳纳米管与WW蛋白结构域为例,介绍如何使用分子动力学模拟研究蛋白质与纳米颗粒之间的相互作用。研究发现,单壁碳纳米管能够插入到蛋白质的核心中,且正好阻挡了YAP65WW蛋白结构域的功能位点,从而可能导致YAP65WW蛋白结构域功能的丧失。结果表明,分子动力学模拟提供了一种全新的从分子层次上研究纳米颗粒毒性机制的方法。
Molecular dynamics method is based on the molecular force field, numerical simulation of Newton’s equation of motion to simulate atomic and molecular motion simulation method. Molecular dynamics can be used to simulate the evolution of molecular systems and time-related trajectories to study the thermodynamic and kinetic properties of molecular systems. With the rapid development of computer technology, molecular dynamics simulation is widely used in the research of biomolecules and nanomaterials. In this paper, single-walled carbon nanotubes and the WW protein domain as an example, how to use molecular dynamics simulation study of protein and nanoparticle interaction. The study found that single-walled carbon nanotubes can be inserted into the core of the protein, and just blocks the YAP65WW protein domain function sites, which may lead to YAP65WW protein domain function loss. The results show that molecular dynamics simulation provides a new method to study the mechanism of nanoparticle toxicity at the molecular level.