Computational and Experimental Studies of Microtubule Dynamics and Regulation by Binding Proteins

知识价值。微管（MTs）是关键亚细胞结构的主要组成部分，包括细胞内运输网络和细胞分裂过程中分离染色体的有丝分裂纺锤体。细胞生物学的一个中心问题是理解这些基于mt的结构是如何形成的，是如何动态维持的，以及如何驱动细胞其余部分的组织。传统上，这些问题已经通过鉴定和表征调节MT动力学的蛋白质来解决。虽然这种方法很强大，但还不够：MT细胞骨架是一个复杂的系统，其表现出的行为（“涌现特性”）不能从单个成分的分析中直接预测。这样的系统级问题需要系统级方法：数学和计算建模。本项目的目标是开发、利用和实验测试两个MT动力学计算模型，并利用这些模型来研究MT结合蛋白的功能和机制。这些模型将在两个尺度上建立：一个介观（中等尺度）模型将用于研究细胞样环境中动态MT系统的内在特性，一个分子尺度模型将用于提出关于动态不稳定性机制及其被MT结合蛋白改变的假设。这项工作的长期目标是发展对MT细胞骨架及其由MT结合蛋白调控的预测和定量理解，这将影响从系统生物学到纳米技术等领域。更广泛的影响。该项目的一个重要部分是开发一个免费传播的软件套件“MT工具箱”（MTT），其中将包括分析工具和教学电子教程。MTT将有两个实现：1)一个基于web的界面，允许远程站点的科学家和学生提交作业，以便在我们的服务器上运行模型和他们的分析工具；2)一个自由传播的软件套件，包含所有程序，并提供在线教程、用户和程序员指南。通过这个项目产生的灵活的模型和教程将允许研究人员开发和测试关于机器翻译动力学机制的特定假设，这反过来将有助于设计和指导未来的实验。更广泛地说，它将帮助各级学生和研究人员获得对动态MT系统的直观理解。该项目将培养三名研究生和两名本科生，他们将受益于生物学和计算建模的跨学科培训。与拟议研究相关的项目将被纳入圣母大学教师的研究经验（RET@ND）计划以及圣母大学麦克奈尔计划，该计划旨在促进少数民族学生的研究生和博士研究。

Intellectual merit. Microtubules (MTs) are the primary components of crucial subcellular structures including the intracellular transport network and the mitotic spindle that separates the chromosomes during cell division. A central problem in cell biology is to understand how these MT-based structures form, are dynamically maintained, and drive the organization of the rest of the cell. Classically, these questions have been addressed by identifying and characterizing the proteins that regulate MT dynamics. While this approach has been powerful, it is not sufficient: the MT cytoskeleton is a complex system that exhibits behaviors ("emergent properties") not straightforwardly predictable from analysis of the individual components. Such a system level problem requires system level approaches: mathematical and computational modeling. The goals of this project are to develop, utilize, and experimentally test two computational models of MT dynamics, and to use these models to investigate the function and mechanism of MT binding proteins. These models will be built at two scales: a mesoscopic (medium scale) model that will be used to investigate the intrinsic properties of a system of dynamic MTs in a cell-like environment, and a molecular scale model that will be used to develop hypotheses about the mechanisms of dynamic instability and its alteration by MT binding proteins. The long-term goal of this work is to develop a predictive and quantitative understanding of the MT cytoskeleton and its regulation by MT binding proteins, which will impact fields ranging from systems biology to nanotechnology. Broader impacts. An important part of this project is to develop a freely disseminated software suite "MT Toolbox" (MTT), which will include analysis tools and instructional electronic tutorials. MTT will have two implementations: 1) a web-based interface that will allow scientists and students at remote sites to submit jobs for running the models and their analysis tools on our server; 2) a freely disseminated software suite containing all programs with online tutorials, user, and programmer's guides. The flexible models and tutorials produced through this project will allow researchers to develop and test specific hypotheses about the mechanisms of MT dynamics, which will in turn help design and direct future experiments. More broadly, it will help students and researchers at all levels gain an intuitive understanding of dynamic MT systems. The project will educate three graduate students and two undergraduates who will benefit from interdisciplinary training in biology and computational modeling. Projects related to the proposed research will be incorporated in The Research Experience for Teachers at Notre Dame (RET@ND) program as well as the Notre Dame McNair Program, which promotes graduate and doctoral studies for minority students.