Main role of fractal-like nature of conformational space in subdiffusion in proteins

IF 2.4 3区 物理与天体物理 Q1 Mathematics
Luca Maggi, Modesto Orozco
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引用次数: 0

Abstract

Protein dynamics involves a myriad of mechanical movements happening at different time and space scales, which make it highly complex. One of the less understood features of protein dynamics is subdiffusivity, defined as sublinear dependence between displacement and time. Here, we use all-atoms molecular dynamics (MD) simulations to directly interrogate an already well-established theory and demonstrate that subdiffusivity arises from the fractal nature of the network of metastable conformations over which the dynamics, thought of as a diffusion process, takes place.

Abstract Image

构象空间的分形性质在蛋白质亚扩散中的主要作用
蛋白质动力学涉及在不同时间和空间尺度上发生的无数机械运动,因此非常复杂。亚扩散性是蛋白质动力学中较少被人了解的特征之一,它被定义为位移与时间之间的亚线性关系。在这里,我们利用全原子分子动力学(MD)模拟直接探究了这一业已成熟的理论,并证明了亚扩散性源于可变构象网络的分形性质,在此网络上发生的动力学过程被认为是一个扩散过程。
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来源期刊
Physical review. E
Physical review. E 物理-物理:流体与等离子体
CiteScore
4.60
自引率
16.70%
发文量
0
审稿时长
3.3 months
期刊介绍: Physical Review E (PRE), broad and interdisciplinary in scope, focuses on collective phenomena of many-body systems, with statistical physics and nonlinear dynamics as the central themes of the journal. Physical Review E publishes recent developments in biological and soft matter physics including granular materials, colloids, complex fluids, liquid crystals, and polymers. The journal covers fluid dynamics and plasma physics and includes sections on computational and interdisciplinary physics, for example, complex networks.
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