Role of ergodicity, aging, and Gaussianity in resolving the origins of biomolecule subdiffusion,Physical Chemistry Chemical Physics

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Role of ergodicity, aging, and Gaussianity in resolving the origins of biomolecule subdiffusion
Physical Chemistry Chemical Physics ( IF 2.9 ) Pub Date : 2022-06-09 , DOI: 10.1039/d2cp01161a
Jun Li ₁

Affiliation

The internal motions of biomolecules are essential to their function. Although biological macromolecules conventionally show subdiffusive dynamics, only recently has subdiffusion been associated with non-ergodicity. These findings have stimulated new questions in biophysics and statistical mechanics. Is non-ergodic subdiffusion a general strategy shared by biomolecules? What underlying mechanisms are responsible for it? Here, we performed extensive molecular dynamics (MD) simulations to characterize the internal dynamics of six different biomolecules, ranging from single or double-stranded DNA, a single domain protein (KRAS), two globular proteins (PGK and SHP2), to an intrinsically disordered protein (SNAP-25). We found that the subdiffusive behavior of these biomolecules falls into two classes. The internal motion of the first three cases is ergodic subdiffusion and can be interpreted by fractional Brownian motion (FBM), while the latter three cases involve non-ergodic subdiffusion and can be modeled by mixed origins of continuous-time random walk (CTRW) and FBM.

中文翻译：

遍历性、老化和高斯性在解析生物分子再扩散起源中的作用

生物分子的内部运动对其功能至关重要。尽管生物大分子通常表现出亚扩散动力学，但直到最近，亚扩散才与非遍历性相关联。这些发现激发了生物物理学和统计力学的新问题。非遍历子扩散是生物分子共享的一般策略吗？什么潜在的机制对此负责？在这里，我们进行了广泛的分子动力学 (MD) 模拟，以表征六种不同生物分子的内部动力学，范围从单链或双链 DNA、单结构域蛋白 (KRAS)、两种球状蛋白 (PGK 和 SHP2) 到固有的无序蛋白（SNAP-25）。我们发现这些生物分子的亚扩散行为分为两类。

更新日期：2022-06-09

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