拥挤环境下的促进扩散动力学研究

发布时间：2019-05-24 07:40

【摘要】：DNA结合蛋白,例如转入因子和DNA修复蛋白,搜寻其坐落在DNA大量非特异性结合位点中的特异性结合靶点位置的过程在许多生物反应过程中起到了至关重要的作用,这些生物反应过程包括了基因的表达和管理等。在二十世纪七十年代,Riggs等人在体外实验中发现特异性结合蛋白对其DNA上特异性靶点的搜寻过程是非常迅速并且高效率的,其速率比三维极限扩散速率(three dimensional diffusion limit)大约100倍。为了解释异常大的蛋白质与DNA特异性结合速率与三维极限扩散速率之间的矛盾,Berg等人在一系列开创性文章中提出并发展了如今被广泛接受和应用的促进扩散机理。促进扩散机理的基本思想是蛋白质搜寻特异性靶点的过程采用了在溶液中三维扩散与在DNA链上一维滑移相结合的方式。随后,许多关于促进扩散的理论方面、实验方面、数值模拟方面的研究被进行和发展。在第一章中,我们给出一个关于促进扩散研究进展的综述。近十年以来,学者们更加关注在体内环境下的促进扩散机理的研究。在生物细胞内存在着10%-40%细胞体积分数的大分子,例如蛋白质,核糖体等。这些在细胞内的大分子导致了一个拥挤的细胞内环境。分子拥挤效应对靶点搜寻动力学有着非常重要的影响。在第二章中,我们采用了理论分析和二维朗之万模拟的方法,研究了分子拥挤效应在靶点搜寻动力学中的作用。我们发现搜寻时间τ随着拥挤剂粒子浓度φ的增加单调增加,并且通过对搜寻过程中的动力学细节的深入研究,我们发现造成这种单调增加行为的主要原因是平均循环数和平均一维扩散时间的单调增加,同时平均二维扩散时间随着拥挤剂粒子浓度的变化基本保持不变。另外,对于二维扩散,拥挤分子带来的牢笼效应减小了二维跳跃长度并且收窄了二维跳跃长度的分布。在细胞内,接近30%的DNA链位点被拥挤大分子覆盖,形成路障,从而阻碍特异性结合蛋白的一维搜寻。在第三章中,我们利用三维朗之万动力学模拟方法研究了路障粒子对促进扩散动力学的影响。对于一对以靶点粒子为中心对称摆放的路障粒子的情况来说,我们发现随着路障粒子与靶点粒子的摆放距离的增加,平均搜寻时间τ先是快速下降然后趋于平缓。对于多个路障粒子任意摆放的情况,随着任意摆放的路障粒子浓度φ的增加,搜寻时间可能起初增加并逐级达到最大值,然后令人惊奇的减小。搜寻时间也可能总是随着路障粒子的浓度增加而增加,这取决于非特异性结合能的大小和DNA链占总空间的体积分数。我们的研究结果协调了之前研究文献中对路障粒子在靶点搜寻过程中的角色的结论分歧。尤其,上述的τ随着φ变化的非单调行为表明,在φ到达某一临界值后路障粒子可能有利于靶点搜寻。在第四章中,蛋白质在溶液中的亚扩散和其隐含的分子拥挤条件是我们所关注的。在三维溶液中,我们使用分数布朗运动的方法去模拟蛋白质粒子的非正常布朗运动和亚扩散运动。我们展示了对于非特异性结合能ε的变化平均搜寻时间τ有明显的最小值,无论是在正常扩散还是亚扩散的情况。我们发现对于更小的亚扩散指数α这个随ε变化的最佳的靶点搜寻时间就越长,并且这样的趋势非常明显。我们将对于更小α的情况平均搜寻时间的增加归结为平均三维扩散时间的增加和分数布朗运动的运动特性造成的更多重复位点搜寻所造成的。我们相信我们的工作为细胞内环境下的促进扩散动力学的研究提供了更深入的认识和新的视野。
[Abstract]:DNA-binding proteins, such as transfer-in factors and DNA repair proteins, are critical to the process of searching for their specific binding target sites located in a large number of non-specific binding sites of DNA, These bioreaction processes include the expression and management of genes, and the like. In the 1970s, Riggs et al., in vitro, found that the search for specific binding proteins to their DNA-specific targets was very rapid and efficient, with a rate of about 100-fold higher than the three-dimensional limit diffusion limit. In order to explain the contradiction between the abnormally large protein and the DNA-specific binding rate and the three-dimensional limit diffusion rate, Berg et al. proposed and developed a diffusion mechanism that is now widely accepted and applied in a series of groundbreaking articles. The basic idea of promoting the diffusion mechanism is that the process of protein search specific target uses three-dimensional diffusion in solution and one-dimensional slip on the DNA chain. Subsequently, a number of theoretical aspects of the promotion of diffusion, experimental aspects, and numerical simulation have been developed and developed. In the first chapter, we present a review of the progress in the study of the diffusion of diffusion. For nearly a decade, scholars have paid more attention to the study of the mechanism of promoting the diffusion in the in-vivo environment. Macromolecules, such as proteins, ribosomes, and the like, are present in the biological cells of 10% to 40% of the cell volume fraction. These macromolecules in the cells result in a crowded intracellular environment. The molecular crowding effect has a very important effect on the target search dynamics. In the second chapter, we used the theoretical analysis and the two-dimensional Langevan's method to study the role of the molecular crowding effect in the target search dynamics. We find that the search time is increasing monotonously with the increasing of the concentration of the congestion agent, and by further study of the dynamics detail in the search process, we find that the main reason for this monotonic increase is that the average number of cycles and the average one-dimensional diffusion time increase monotonically, While the average two-dimensional diffusion time is substantially unchanged as the change in the concentration of the congestion agent particles. In addition, for the two-dimensional diffusion, the cage effect brought by the congested molecules reduces the two-dimensional jump length and narrows the distribution of the two-dimensional jump length. Within the cell, nearly 30% of the DNA strand sites are covered by the congested macromolecules to form a barrier that blocks the one-dimensional search of specific binding proteins. In the third chapter, we study the effect of the barrier particles on the promotion of the diffusion kinetics by using the three-dimensional dynamic simulation method. In the case of a pair of barrier particles that are placed symmetrically about the target particle, we find that, as the distance between the barrier particles and the target particles increases, the average search time is then rapidly reduced and then tends to be gentle. The search time may initially increase and reach the maximum with any placement of the plurality of barrier particles, and then a surprising reduction as the concentration of the barrier particles in any place increases. The search time may also always increase as the concentration of the barrier particles increases, depending on the size of the non-specific binding energy and the volume fraction of the DNA strand in the total space. Our findings have coordinated the conclusions of the previous study on the role of the barrier particles in the target search process. In particular, the above-described non-monotonic behavior of the roadblock as the threshold value changes indicates that the barrier particles may be in favor of the target search after reaching a certain critical value. In the fourth chapter, the subdiffusion of the protein in the solution and its implied molecular crowding conditions are of concern to us. In the three-dimensional solution, we use fractional Brownian motion to simulate the abnormal Brownian motion and the sub-diffusion motion of the protein particles. We have shown that the mean search time for changes in non-specific binding energy levels has a significant minimum value, whether in normal or sub-proliferation. We have found that for a smaller sub-diffusion index, the longer the best target search time with time changes, and such a trend is very clear. The increase in the average search time for smaller cases is attributed to the increase in the average three-dimensional diffusion time and the more repeated site search resulting from the motion characteristics of the fractional Brownian motion. We believe that our work provides a more in-depth understanding and a new field of view for the study of the promotion of diffusion kinetics in the intracellular environment.
【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】：2017
【分类号】：Q61

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