Collaborative Research: Integrative Modeling and Analysis of Animal-Cell Cytokinesis

合作研究：动物细胞胞质分裂的综合建模与分析

• 批准号: 0714864
• 负责人: Jeffrey Morgan
• 金额: $ 60.04万
• 依托单位: University of Houston
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-08-01 至 2012-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0714864&HistoricalAwards=false
• 关键词: Collaborative; Research; Integrative; Modeling; Analysis

A major challenge of molecular cell biology is to elucidate the biochemical mechanisms by which cells grow and divide. Given the complexities involved, there is no doubt that mathematical modeling will play an increasingly important role in meeting this challenge. The assembled team of investigators has recently developed a whole-cell modeling framework in which cellular biochemical dynamics and changes in cell morphology are inter-dependent, and have used it to construct a simple self-replicating cell model in which an established mechanism of eukaryotic cell cycle regulation is incorporated. The resulting system can produce stable self-replicating behavior, with cytoplasm volume and membrane surface area doubling in synchrony with the periodicity in component concentrations. Because the biochemical dynamics of processes that affect changes in cell morphology in vivo can be modeled, exploring in vivo mechanisms by which growing and dividing cells "pinch" during the division process (cytokinesis) is possible. Towards this end, the objective of the proposed project is to model cytokinesis as it occurs in animal cells and to compare such models to the known cytokinetic behavior of real cells. Cytokinesis occurs near the end of mitosis, and involves the rapid assembly and contraction of a membrane-associated actomyosin ring located at the cell equator. Cytokinesis is exquisitely choreographed with other mitotic events, such that the ring assembles as anaphase begins and daughter chromatids begin to separate. The ring contracts as the chromatids separate, and the ring completes contraction soon after separation is complete. The choreography of these terminal events of mitosis will be modeled. Biochemical reactions and kinetic parameters will be assumed based on what is known experimentally. Once developed, cytokinesis models will be installed into the existing whole-cell model in which cell cycle regulation is treated explicitly. In this way, cytokinesis can be modeled within an in vivo setting. Cell morphology changes involved in cell growth and division will also be estimated by minimizing membrane bending energies. In real cells, membrane composition is altered at the cleavage furrow during cytokinesis, and this aspect will be modeled and analyzed for its ability to promote cell division. These aspects will be integrated into a self-replicating whole-cell model to observe "pinching" behavior about its equator as the cell divides. All of this will be driven by an explicit biochemical mechanism and synchronized with other cell cycle events. The complexity of the models will be scaled in proportion to what is known experimentally, such that they will be closely connected to reality, possess predictive ability, and thus be useful to experimentalists. Models will be analyzed to assess the importance of a cytoskeletal contractile ring vs. local changes in membrane composition in effecting cytokinesis. This integrative approach results in a mathematical model which couples a system of ordinary and partial differential equations with a constrained minimization problem (associated with the determination of cell shape). The primary mathematical challenges stem from the need to determine system parameters within physically realistic ranges so that the solution to the mathematical model exhibits physically reasonable, stable self-replicating behavior. The project is significant because of the novelty of modeling animal-cell cytokinetics on the biochemical/mechanistic level and under both in vitro and in vivo settings. In the broadest sense, the project will assess the feasibility of building a comprehensive cell model piecemeal by designing individual cellular "modules" in vitro and installing them into a whole-cell frame once appropriate in vitro behavior is observed. Ultimately a comprehensive molecular-level cell model will be required to explore the pathogenesis of many human diseases, especially cancer, and to test the intended and unintended metabolic effects of new pharmaceuticals.Living cells can be simplistically viewed as tiny sacs filled with water, salts and molecules such as DNA and proteins. One of the most fundamental aspects of such cells is their ability to self-replicate. To do this, a cell must grow to twice its original size, make a second copy of its DNA, move each copy of the DNA to different ends of the cell, and finally divide around its middle to form two cells. During the last part of this process (technically called "cytokinesis"), the cell constructs a little belt around its middle, but on the inside of itself such that the belt cannot be seen from the outside of the cell. This internal belt is constructed of many protein units of the same type, linked end-to-end like a stacked set of sticky blocks. Also, the belt is tied to the surface (called a membrane) of the cell. When the cell sends a signal to this belt, the belt starts to tighten around the belly of the cell (by removing blocks, one at a time) and it pulls the membrane in with it. This squeezing doesn't stop until the belt has constricted to a very small circumference, the membrane has pinched completely and two cells are made. The investigators have recently developed a new mathematical approach to modeling cell growth and division at the level of molecules reacting. In this project, this approach will be used to investigate the fine details (at the molecular level) of how this belt is assembled and how it squeezes. Another factor that appears to help this pinching process occur has to do with the types of molecules in the membrane right at the region where the belt is attached. Experiments have shown that the molecules in this region are different from those in the rest of the membrane, but no one understands why they are different. A second aspect of this project will be to investigate this question. Membranes are generally most stable when they are flat rather then bent. This pinching process during cell division requires that they bend a lot, which suggests that pinching might require a lot of energy. It is suspected that the different molecules found in this region help the membrane bend without requiring so much energy. Again, using a mathematical modeling approach, the researchers will investigate whether this might explain why different types of molecules are found in this region. These processes are not only significant from the perspective of basic cell biology, they are also involved in understanding diseases such as cancer. Cancerous cells grow and divide uncontrollably--something has gone awry with the cell division process described above. Modeling these processes using mathematics and computers is important because these processes are so complicated that it is literally impossible for any person to keep track of all the factors and understand how they interact as time changes. However, using mathematics and computers, these factors and interactions can be tracked, which permits the careful testing of what had previously been simply word-based explanations. By such careful testing, it might be possible to understand better how cells grow and divide, and how to reestablish control of uncontrolled cancerous cell growth.

分子细胞生物学的一个主要挑战是阐明细胞生长和分裂的生化机制。鉴于所涉及的复杂性，毫无疑问数学建模将在应对这一挑战中发挥越来越重要的作用。研究人员组成的团队最近开发了一个全细胞建模框架，其中细胞生化动力学和细胞形态的变化是相互依赖的，并用它构建了一个简单的自我复制细胞模型，其中纳入了已建立的真核细胞周期调节机制。由此产生的系统可以产生稳定的自我复制行为，细胞质体积和膜表面积与成分浓度的周期性同步加倍。由于可以对影响体内细胞形态变化的过程的生化动力学进行建模，因此可以探索生长和分裂细胞在分裂过程（细胞分裂）过程中“挤压”的体内机制。为此，拟议项目的目标是模拟动物细胞中发生的胞质分裂，并将此类模型与真实细胞已知的细胞分裂行为进行比较。细胞分裂发生在有丝分裂末期附近，涉及位于细胞赤道处的膜相关肌动球蛋白环的快速组装和收缩。细胞分裂与其他有丝分裂事件精心设计，使得环在后期开始时聚集，子代染色单体开始分离。当染色单体分离时，环收缩，分离完成后环很快完成收缩。这些有丝分裂终末事件的编排将被建模。生化反应和动力学参数将根据实验已知的情况进行假设。一旦开发出来，胞质分裂模型将被安装到现有的全细胞模型中，在该模型中明确处理细胞周期调节。通过这种方式，可以在体内环境中模拟胞质分裂。细胞生长和分裂中涉及的细胞形态变化也将通过最小化膜弯曲能量来估计。在真实细胞中，胞质分裂过程中，卵裂沟的膜组成发生了改变，并且将对这一方面进行建模并分析其促进细胞分裂的能力。这些方面将被整合到自我复制的全细胞模型中，以观察细胞分裂时其赤道的“收缩”行为。所有这一切都将由明确的生化机制驱动，并与其他细胞周期事件同步。模型的复杂性将与实验已知的内容成比例地缩放，这样它们将与现实紧密联系，具有预测能力，从而对实验者有用。将分析模型以评估细胞骨架收缩环与膜组成的局部变化在影响胞质分裂中的重要性。这种综合方法产生了一个数学模型，该模型将常微分方程组和偏微分方程组与约束最小化问题（与单元形状的确定相关）耦合起来。主要的数学挑战源于需要确定物理现实范围内的系统参数，以便数学模型的解决方案表现出物理合理、稳定的自我复制行为。该项目意义重大，因为在生化/机械水平以及体外和体内环境下对动物细胞细胞因子进行建模的新颖性。从最广泛的意义上讲，该项目将通过在体外设计单个细胞“模块”并在观察到适当的体外行为后将它们安装到全细胞框架中来评估零碎构建综合细胞模型的可行性。最终，将需要一个全面的分子水平细胞模型来探索许多人类疾病，特别是癌症的发病机制，并测试新药物的有意和无意的代谢效应。活细胞可以简单地视为充满水、盐和分子（如 DNA 和蛋白质）的微小囊。此类细胞最基本的方面之一是它们的自我复制能力。为此，细胞必须生长到原来大小的两倍，制作第二个 DNA 副本，将每个 DNA 副本移动到细胞的不同末端，最后在中间分裂形成两个细胞。在这个过程的最后部分（技术上称为“细胞分裂”），细胞在其中部周围构建一个小带，但在其自身内部，这样从细胞外部就看不到该带。这条内部带由许多相同类型的蛋白质单元构成，像一组堆叠的粘性块一样首尾相连。此外，带子还绑在电池的表面（称为膜）上。当细胞向这条带子发送信号时，带子开始收紧细胞腹部（通过一次移除一个块），并将膜拉入其中。这种挤压直到带子收缩到非常小的周长、膜完全收缩并形成两个细胞时才会停止。研究人员最近开发了一种新的数学方法，可以在分子反应水平上模拟细胞生长和分裂。在这个项目中，这种方法将用于研究该皮带如何组装以及如何挤压的细节（在分子水平）。似乎有助于发生这种挤压过程的另一个因素与带所连接区域的膜中的分子类型有关。实验表明，该区域的分子与膜其他部分的分子不同，但没有人理解它们为何不同。该项目的第二个方面将是调查这个问题。膜在平坦时（而不是弯曲时）通常最稳定。细胞分裂过程中的这种挤压过程需要它们大量弯曲，这表明挤压可能需要大量能量。 人们怀疑在这个区域发现的不同分子有助于膜弯曲而不需要太多的能量。再次，研究人员将使用数学建模方法来研究这是否可以解释为什么在该区域发现不同类型的分子。这些过程不仅从基础细胞生物学的角度来看具有重要意义，而且还涉及了解癌症等疾病。癌细胞不受控制地生长和分裂——上述细胞分裂过程出现了问题。使用数学和计算机对这些过程进行建模非常重要，因为这些过程非常复杂，任何人几乎不可能跟踪所有因素并了解它们如何随着时间的变化相互作用。然而，使用数学和计算机，可以跟踪这些因素和相互作用，从而可以仔细测试以前仅基于单词的解释。通过如此仔细的测试，也许可以更好地了解细胞如何生长和分裂，以及如何重新控制不受控制的癌细胞生长。