类核及细胞内纳米粒子动力学的多尺度模拟研究与细胞质的微观流变学

In bacterial cells, genome DNA can be compacted and organized by nucleoid-associated proteins (NAPs) to form a highly dynamic structure, that is, nucleoid. Both loci and cytoplasmic particles exhibit subdiffusion, which might be due to the viscoelasticity of bacterial cytoplasm. As both nucleoid dynamics as well as cytoplasm diffusion highly affect many critical biological reactions, such as DNA replication, transcription and segregation, it is important to investigate the mechanical properties of bacterial chromosome and cytoplasm. Recent fluorescence imaging experiments of loci and cytoplasmic nanoparticles in compressed E. coli cells revealed that the diffusion coefficient of cytoplasmic nanoparticles decreased more than 10-fold in compressed cells while the diffusion coefficient of loci remained almost unaffected, which indicated that the subdiffusion of loci and cytoplasm cannot be solely attributed to viscoelasticity of cytoplasm. Therefore, we propose a new mesoscale coarse-grained model of biological macromolecules which combines three different mesoscale models to simulate the interactions between nucleic acids, proteins, and lipid bilayers. To obtain the correct dynamic properties of nucleoid and cytoplasm, our proposed mesoscale model should be mapped to Martini coarse-grained force field by comparing the PMF obtained by our newly developed model to the PMF computed in Martini FF. Then, we employ our new model to investigate the nucleoid and cytoplasm dynamics, from which the rheological properties of bacterial cytoplasm can be extracted. By varying the cytoplasmic proteins concentration and compressive force exerted on the lipid bilayers in our model, we can study how the macromolecules crowding as well as compression affect the mechanical properties of cytoplasm. Note that the heterogeneity of nucleoid and cytoplasm dynamics can be investigated using this model, as the DNA-protein specific interaction is already included in this mesoscale model. Besides, the structural and dynamics information of nucleoid obtained by this mesoscale model can be used as an input for a specific bead-spring model of DNA-“feather-boa model” to simulate the whole bacterial chromosome confined in a reflecting cell wall. We propose to use both Brownian dynamics simulation and fractional Brownian motion (fBm) method for this model to study how the rheological properties of cytoplasm affect the nucleoid dynamics. In addition, by introducing non-equilibrium fluctuations to this simple model, we can investigate how the metabolic reactions of bacterial affects the non-Gaussian behavior of loci and cytoplasmic particles which have been confirmed by recent imaging experiments.

细菌DNA能被NAP蛋白质折叠形成类核。DNA链段与细胞内纳米粒子均呈现反常扩散。类核动力学与细胞质流变特性因都能极大地影响细胞中关键的生化反应而具有重大的研究价值。近期的荧光显微实验揭示在被压缩的大肠杆菌细胞中，类核中DNA链段的反常扩散未受到明显影响，同时细胞内纳米粒子的扩散系数降低超过10倍，表明不能将类核与细胞质中的反常扩散完全归因于细胞质的粘弹性。.本项目中，我们提出建立一个中尺度的粗粒化模型对核酸、蛋白质和脂质双分子层进行模拟研究。通过合理选取力场参数使得该模型所预测的核酸、蛋白质和脂质双分子层之间相互作用的平均力势（PMF）与Martini力场的预测结果一致。我们将使用该模型研究细胞质浓度、外加压力对类核及纳米粒子动力学的影响，并为更粗糙的“feather-boa”模型的参数化提供依据。最后，我们将在两个尺度上研究类核动力学与细胞质微观流变学受细胞质非均一性与代谢作用的影响。

细菌DNA能被NAP蛋白质折叠形成类核，其动力学因能极大地影响细菌细胞中关键的生化反应而具有很大的研究价值。本项目中，我们构建了基于“Feather-Boa”模型的简单的类核模型，通过郎之万动力学模拟，观察到该类核模型中基因座或DNA链段与细胞质纳米颗粒均呈现反常扩散，且呈现非高斯扩散行为，与过往的荧光光学显微实验结果相吻合。其中，细胞质纳米颗粒的粒径，基因座位置，细胞膜形变，以及类核浓度等对细胞质颗粒与基因座运动的影响均被系统性地探究。此研究显示细胞质中的反常扩散在很大程度上可以被归因于细菌类核本身的力学特性而非细胞质的黏弹性。因细菌类核中DNA链段的随机分布，细胞质纳米颗粒与基因座周围的环境是高度非均匀的。故细胞质颗粒与基因座的反常扩散指数及其一定时间间隔的符合拉普拉斯分布的位移分布均能被此项目中提出的简单高分子模型所重现。然而，过往荧光显微镜实验所观察到的细胞质颗粒与基因座扩散行为对细胞外加压力的不同响应则无法被此模型预测，显示出非平衡反应（如代谢反应）对细胞质内扩散的重要影响。为探究在类似模型中引入化学反应的可行性，不同尺度、且均可用于描述化学反应的第一性分子动力学模拟CPMD与反应力场分子动力学ReaxFF-MD被用于模拟同一体系下有机小分子与水分子的相互作用。此外，可以用于描述脂质双分子层与DNA相互作用的中尺度粗粒化模型被构建，并用于研究吸附在脂质双分子层上的DNA链段的反常扩散现象。该中尺度粗粒化模型亦可用于模拟更大尺度上细胞的力学特性及动力学行为。

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