拥挤环境下的高分子扩散动力学

发布时间：2018-06-15 01:25

本文选题：分子拥挤 + 亚扩散　；参考：《中国科学技术大学》2016年博士论文

【摘要】：扩散现象广泛存在于自然界中,并且对一系列物理化学反应的过程起着重要作用。随着高分子科学的发展,研究者们发现在高分子体系中,分子拥挤效应对其中的大分子的扩散有明显的影响,并由此影响到了很多高分子体系中的物理和化学过程,例如蛋白质在DNA链上搜寻目标、大分子配体在搜寻平面上目标等。对分子拥挤环境下的大分子扩散动力学研究有助于我们揭开对高分子体系的化学物理本质的理解。本文从以下二个方面研究了大分子在拥挤环境下通过扩散进行的不同物理过程：1.大分子在拥挤环境下的亚扩散在气体或者小分子液体中,分子扩散的均方位移与扩散时间成正比关系r2(t))～t,而在大分子拥挤体系,如生物细胞中,研究者们观察到了大分子的亚扩散行为,即r2(t)～tα,α1。本文中通过朗之万动力学模拟方法,研究拥挤剂粒子的浓度以及尺寸对体系中示踪粒子亚扩散指数和扩散系数的关系。2.蛋白质在拥挤环境下搜寻DNA上目标位点的动力学蛋白质分子在细胞拥挤环境中寻找DNA上特定位点的过程对DNA的转录、复制等过程中起重要作用。前人在研究此过程中提出促进扩散模型,即蛋白质交替进行溶液本体中的三维扩散和沿DNA链方向的一维扩散。我们在本文中利用朗之万动力学模拟方法,构建了简单的蛋白质在DNA链上通过促进扩散寻找目标位点的模型,研究DNA-蛋白质间的非特异性相互吸引强度和体系中分子拥挤剂浓度对蛋白质搜寻DNA链上目标的速率的影响。3.配体在拥挤环境下搜寻表面上目标位点的动力学在表面上发生化学物理过程,如细胞表面的分子识别中,反应中的配体搜寻表面上受体的过程有着重要作用。前人在研究中提出,配体在搜寻表面上受体的过程中交替进行三维扩散和吸附于表面的二维扩散。在本文中,我们构建了单个配体在分子拥挤环境下搜寻平面上目标位点的粗粒化模型,并通过朗之万动力学模拟,研究配体-表面间的非特异性相互吸引强度ε和体系中分子拥挤剂浓度(?)对搜寻时间ttatol的影响。
[Abstract]:Diffusion exists widely in nature and plays an important role in a series of physicochemical reactions. With the development of polymer science, researchers have found that in polymer systems, molecular crowding has a significant effect on the diffusion of macromolecules, and thus affects the physical and chemical processes in many polymer systems. For example, proteins search for targets on DNA strands, macroligands search targets on the plane, and so on. The study on the diffusion kinetics of macromolecules in the crowded environment is helpful for us to understand the nature of chemistry and physics of polymer systems. In this paper, the different physical processes of diffusion of macromolecules in crowded environment are studied in the following two aspects: 1. Subdiffusion of macromolecules in gas or small molecular liquids, the mean square shift of molecular diffusion is proportional to diffusion time, whereas in macromolecular crowded systems, such as in biological cells, the mean square shift of molecular diffusion is proportional to diffusion time. The researchers observed the subdiffusion behavior of macromolecules, r2(t)~t 伪, 伪 1. By using Langevin kinetic simulation method, the relationship between the concentration and size of the crowding agent particles on the subdiffusion index and diffusion coefficient of tracer particles in the system is studied. Dynamic protein molecules searching for target sites in DNA in crowded environment the process of searching for specific sites on DNA in a crowded environment plays an important role in the process of DNA transcription and replication. In the course of this study, a model of promoting diffusion was proposed, that is, protein alternately carried out three-dimensional diffusion in solution body and one-dimensional diffusion along DNA strand. In this paper, we use Langevin kinetic simulation method to construct a simple model of protein searching for target sites on DNA strand by promoting diffusion. The effects of DNA-protein nonspecific attraction intensity and concentration of molecular crowding agent in the system on the rate of protein searching for targets on DNA strands were studied. The kinetics of ligands searching for target sites on the surface in a crowded environment is characterized by chemical-physical processes on the surface, such as molecular recognition on the cell surface, in which the ligand in the reaction plays an important role in the search for receptors on the surface. In previous studies, it was proposed that the ligands alternately undergo three-dimensional diffusion and two-dimensional diffusion adsorbed on the surface in the process of searching for receptors on the surface. In this paper, we construct a coarse-grained model of a single ligand to search for target sites in a molecular crowded environment, and simulate it by Langevan dynamics. The nonspecific attraction between ligands and surfaces and the concentration of molecular crowding agent in the system are studied. Effect on search time ttatol.
【学位授予单位】：中国科学技术大学
【学位级别】：博士
【学位授予年份】：2016
【分类号】：Q61

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