合成偶极矩在生物复合物机械解离中的作用
Role of Resultant Dipole Moment in Mechanical Dissociation of Biological Complexes
摘要：
蛋白质-肽相互作用在许多细胞过程中起着重要作用，其结构表征是当前实验和理论研究的主要焦点。20年前，有人提出采用受控分子动力学来评估蛋白质-肽相互作用的强度。使用导向分子动力学模拟背后的想法是，机械稳定性可以用作计算上要求很高的结合亲和力估计的有希望和有效的替代方案。然而，机械稳定性定义为力-延伸曲线的峰值，取决于牵拉方向的选择。在这里，我们提出了一个不寻常的选择的方向上的合力偶极矩矢量，这还没有在模拟中探索到目前为止。采用显式溶剂全原子分子动力学模拟方法，利用操纵分子动力学技术研究了蛋白质-肽体系沿两种不同矢量运动时的机械阻力。与常用的沿着质心矢量的肽解结合相比，沿着合成偶极矩矢量的新的拉动方向导致更强的力。我们的研究结果表明，合成偶极矩是影响蛋白质-肽复合物的机械稳定性的因素之一。
英文摘要：
Protein-peptide interactions play essential roles in many cellular processes and their structural characterization is the major focus of current experimental and theoretical research. Two decades ago, it was proposed to employ the steered molecular dynamics to assess the strength of protein-peptide interactions. The idea behind using steered molecular dynamics simulations is that the mechanical stability can be used as a promising and an efficient alternative to computationally highly demanding estimation of binding affinity. However, mechanical stability defined as a peak in force-extension profile depends on the choice of the pulling direction. Here we propose an uncommon choice of the pulling direction along resultant dipole moment vector, which has not been explored in simulations so far. Using explicit solvent all-atom MD simulations, we apply steered molecular dynamics technique to probe mechanical resistance of protein-peptide system pulled along two different vectors. A novel pulling direction, along the resultant dipole moment vector, results in stronger forces compared to commonly used peptide unbinding along center of masses vector. Our results demonstrate that resultant dipole moment is one of the factors influencing the mechanical stability of protein-peptide complex.
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