Theoretical modeling on mechanochemical feedbacks of cellular processes

细胞过程机械化学反馈的理论模型

• 批准号: 8558026
• 负责人: Jian Liu
• 金额: $ 91.57万
• 依托单位: NATIONAL HEART, LUNG, AND BLOOD INSTITUTE
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/8558026
• 关键词: Accounting; Actins; Adhesions; Affinity; Antigens; Area; Bacteria; Behavior; Binding; Biochemical; Biochemical Pathway; Cell Adhesion; Cell division; Cell membrane; Cell physiology; Cell-Cell Adhesion; Cells; Cellular biology; Characteristics; Chemical Dynamics; Chemistry; Chromosome Segregation; Chromosome Structures; Chromosomes; Clathrin; Collaborations; Complex; Couples; Coupling; Cues; Cyclin B; Cytoplasm; Cytoskeleton; Data; Dependence; Distal; Dynein ATPase; Endocytosis; Ensure; Event; Extracellular Matrix; F-Actin; Failure; Feedback; Focal Adhesion Kinase 1; Focal Adhesions; Goals; Integrins; Intracellular Membranes; Ligands; Lipids; Liquid substance; Mechanics; Mediating; Membrane; Membrane Protein Traffic; Microtubules; Mitosis; Mitotic; Mitotic spindle; Modeling; Nature; Organelles; Paper; Pathway interactions; Pattern; Phagocytosis; Phosphatidylinositols; Phosphotransferases; Positioning Attribute; Preparation; Prevention; Process; Proteins; Publications; Regulation; Research; Role; Shapes; Signal Transduction; Singapore; Structure; Surface; System; Theoretical model; Traction; Travel; United States National Institutes of Health; Universities; Vision; Work; Writing; base; cell motility; chemical reaction; coping; genetic regulatory protein; internal control; mast cell; mathematical model; membrane activity; phosphoinositide-3,4,5-triphosphate; polymerization; prevent; protein transport; receptor binding; research study; response; seal; sensor; trafficking; transmission process

1. Membrane Trafficking: a) Membrane wave: In the central dogma of endocytosis, ligand-receptor bindings stimulate upstream signals at PM, which triggers multiple cascades of early responses that finally converge to actin cytoskeleton nucleation and endocytic apparatus assembly. However, exactly what these early responses at the PM look like remains unknown. Our experiments demonstrate that antigen stimulation of mast cells (RBL-2H3) results in cycles of recruitment and shedding of actin regulatory proteins and endocytic proteins (FBP17, endophilin, FCHo, and clathrin) in the form of traveling waves at PM. We establish a theoretical model that underscores the well-known membrane curvature-sensitivities of endocytic proteins and their biochemical pathways in response to upstream stimulations. Our model shows that the traveling waves of the endocytic proteins mirror the local membrane shape changes. While a weaker upstream stimulation leads to traveling wave, a stronger one will result in a stable membrane tubule, upon which endocytosis begins. Our experiments verify such model predictions. These findings reveal a checkpoint control in the initiation of endocytosis. The intrinsic couplings among curvature-sensitive endocytic proteins dictate a threshold upstream stimulation, only above which, endocytosis can proceed. The traveling wave of endocytic proteins at PM, on the other hand, reflects weaker stimulations, and the fact that cell utilizes such internal control to cope with external cue to avoid unnecessary cellular processes. We hypothesize that such a mechanism can be of great implication in many other endomembrane trafficking processes, e.g., phagocytosis. We are currently writing this paper. b) Phagocytosis: During phagocytosis, cell extends its filapodia around the target, forming cup-shaped membrane invagination that subsequently seals at its distal margins to form intracellular, membrane-bounded organelle. In contrast to endocytosis, phagocytosis is strongly modulated by the size, the shape, and even the stiffness of the target. Such dependence has been utilized both by bacteria and host cells for entry and its prevention, respectively. In addition, lipids (e.g., PI(4,5)P2, DAG, and PI(3,4,5)P3) and actin regulatory proteins (e.g., Cdc42, WASP, and PKCs) form distinct gradients along the surface of phagocytic cup. And such spatial patterns evolve as the phagocytic cup seals its distal end. Despite intensive studies, underlying physical mechanism of phagocytosis is largely unknown. We establish a coherent theoretical model of phagocytosis. The key model ingredient is the coupling between the membrane curvature-sensitivity of phosphoinositide lipid enzymatic activities and membrane protrusion mediated by actin polymerizations. This model not only quantitatively accounts for the aforementioned peculiar nature of phagocytosis, but also unravels their commonality. Thus, our model suggests an evolutionary path along which endocytosis, phagocytosis, and other endomembrane trafficking events diverge. This paper is submitted to PNAS. 2. Cell Division: a) Spatial-temporal regulation of spindle assembly checkpoint: We establish a theoretical model that describes the mitotic spindle structure (chromosomes, mitotic spindles, and the spindle poles) as a coherent transport system. Depending on whether the chromosome is properly attached, SAC and cyclin B circulate within transport system by dynein, and exchange with cytoplasm in accordance to their well-known biochemical regulations. The basis of such coherent transport is the compartmentalization underscored by direct and indirect protein affinities with these mitotic structures. Our model results show that such transport system recapitulates the observed spatial-temporal pattern of SAC and cyclin B. Moreover, the transport system dictates a stepwise SP accumulation of these proteins, which tightly couples with each proper chromosome attachment event. Furthermore, the jump in SP accumulation increases as the number of unattached chromosomes decreases: the last chromosome attachment results in a jump in SP accumulation > two folds of that from the second-to-last attachment. Finally, our model predicts that cyclin B degradation starts at SP, which is consistent with experiment observation. Such degradation always couples with the last chromosome attachment event, and remains robust against typical fluctuations due to the large boost in SP accumulation. Our model thus provides a robust mechanism for silencing SAC activity in accordance to the last chromosome attachment. This paper is currently being drafted. 3. Cell Motility: a) Mechanochemistry of focal adhesion formation: Focal adhesions are essential to mediate cell extracellular matrix (ECM) adhesion and force transmission during cell motilities, which involve the crosstalk between physical signals such as contractile forces or membrane dynamics, and chemical signaling events such as focal adhesion kinase related regulation pathways. However, the underline mechanism of the biophysical regulations of force transmission among actin cytoskeleton, cell membrane, focal complex and ECM remains poorly understood. We collaborated with Dr. Clare Waterman, and constructed a mathematical model to understand the behavior of focal adhesion complex under different experimental conditions. By integrating the cell membrane dynamics, actin network fluid dynamics, and the mechanochemistry of focal complex, the model reveals itself the capability to capture the essential characteristics of focal adhesions in cell motility. In particular, the model explains the oscillation of traction force both in terms of position and magnitude within focal adhesions at different ECM stiffness. The model thus provides a comprehensive vision of the focal adhesion dynamics. This paper is currently in preparation for publication.

1.膜运输： a）膜波： 在内吞作用的中心法则中，配体-受体结合刺激PM处的上游信号，其触发最终会聚到肌动蛋白细胞骨架成核和内吞装置组装的早期反应的多个级联。然而，总理的这些早期反应究竟是什么样子仍然未知。我们的实验表明，肥大细胞（RBL-2 H3）的抗原刺激的结果在募集和脱落的肌动蛋白调节蛋白和内吞蛋白（FBP 17，内亲蛋白，FCHo，网格蛋白）在PM的行波形式的循环。我们建立了一个理论模型，强调了众所周知的膜曲率敏感性的内吞蛋白及其生化途径，以响应上游刺激。我们的模型表明，内吞蛋白的行波反映了局部膜形状的变化。当较弱的上游刺激导致行波时，较强的上游刺激将导致稳定的膜小管，在其上开始内吞作用。我们的实验验证了这样的模型预测。这些发现揭示了在胞吞作用的起始中的检查点控制。曲率敏感的内吞蛋白质之间的内在耦合决定了上游刺激的阈值，只有高于该阈值，内吞作用才能进行。另一方面，PM时内吞蛋白的行波反映了较弱的刺激，以及细胞利用这种内部控制来科普外部提示以避免不必要的细胞过程的事实。我们假设这样的机制可能在许多其他内膜运输过程中具有重要意义，例如，吞噬作用我们目前正在撰写这篇论文。 B）吞噬作用： 在吞噬过程中，细胞将其丝状伪足延伸到目标周围，形成杯状膜内陷，随后在其远端边缘密封，形成细胞内的膜结合细胞器。与内吞作用相反，吞噬作用强烈地受到靶的大小、形状甚至硬度的调节。这种依赖性已被细菌和宿主细胞分别用于进入和预防。此外，脂质（例如，PI（4，5）P2、DAG和PI（3，4，5）P3）和肌动蛋白调节蛋白（例如，Cdc 42、WASP和PKCs）沿着吞噬杯表面形成明显的梯度。当吞噬杯封闭其末端时，这种空间模式就进化了。尽管进行了深入的研究，但吞噬作用的基本物理机制在很大程度上是未知的。我们建立了一个连贯的理论模型吞噬。模型的关键成分是磷脂酰肌醇脂质酶活性的膜曲率敏感性和肌动蛋白聚合介导的膜突起之间的耦合。这个模型不仅定量地解释了上述吞噬作用的特殊性质，而且揭示了它们的共同性。因此，我们的模型提出了一个进化的路径沿着的内吞作用，吞噬作用，和其他内膜运输事件分歧。 本文已提交给PNAS。 2.细胞分裂： a）纺锤体组装检查点的时空调节： 我们建立了一个理论模型，将有丝分裂纺锤体结构（染色体、有丝分裂纺锤体和纺锤体极）描述为一个连贯的运输系统。SAC和细胞周期蛋白B通过动力蛋白在转运系统内循环，并根据它们众所周知的生化调节与细胞质交换，这取决于染色体是否正确附着。这种连贯运输的基础是由蛋白质与这些有丝分裂结构的直接和间接亲和力所强调的区室化。我们的模型结果表明，这样的运输系统概括了所观察到的时空格局的SAC和细胞周期蛋白B。此外，运输系统决定了这些蛋白质的逐步SP积累，其与每个适当的染色体附着事件紧密耦合。此外，SP积累的跳跃随着未附着染色体数目的减少而增加：最后一个染色体附着导致SP积累的跳跃>倒数第二个染色体附着的两倍。最后，我们的模型预测细胞周期蛋白B降解开始于SP，这与实验观察一致。 这种降解总是与最后的染色体附着事件相结合，并且由于SP积累的大幅增加而对典型波动保持稳健。因此，我们的模型提供了一个强大的机制，沉默SAC活动根据最后的染色体附着。目前正在起草这份文件。 3.细胞运动： a）粘着斑形成的机械化学： 粘着斑是细胞运动过程中细胞与细胞外基质（ECM）粘附和力传递的重要机制，涉及细胞收缩力或膜动力学等物理信号与粘着斑激酶相关调控通路等化学信号之间的相互作用。然而，肌动蛋白细胞骨架，细胞膜，焦点复合物和ECM之间的力传递的生物物理调节机制仍然知之甚少。我们与克莱尔沃特曼博士合作，构建了一个数学模型，以了解不同实验条件下粘着斑复合物的行为。通过整合细胞膜动力学、肌动蛋白网络流体动力学和焦点复合物的机械化学，该模型揭示了其自身捕获细胞运动中焦点粘附的基本特征的能力。特别是，该模型解释了在不同ECM刚度下，焦点粘连内的位置和幅度的牵引力振荡。因此，该模型提供了一个全面的视野的焦点粘附动力学。 该文件目前正在准备出版。