Computational modeling of the mechanisms of microtubule disassembly by biological nanomachines

细胞中含有由蛋白质复合物组成的分子机器，可将化学能转化为机械能。这些机器在重要的细胞过程中帮助组装或拆卸细胞结构。了解这些生物机器的作用机制及其与底物构象变化的关系是现代分子生物学的挑战之一。本项目使用多尺度的计算模型来阐明一类与微管相关的分子机器如何完成细胞骨架中这个最大结构的切断，其动态组织和重排是细胞分裂、运动和发育的重要过程。这项研究将解决我们对微管及其与微管相关蛋白的复合物的动态特性的理解中的一个关键空白，以及它们对机械输入的大小和几何形状的依赖，并将更好地理解分子机器是如何工作的。该项目将为本科生和研究生提供计算生物物理化学方面的教育和培训，让他们参与跨学科的科学项目，并通过在辛辛那提当地公立学校的外展活动，以及通过为参加辛辛那提大学“科学与工程领域的女性”项目的新生提供研究经验机会，增加在科学领域代表性不足的群体的参与。该项目的研究结果将由研究者、博士后和学生通过出版物、会议报告和访问当地学校的方式向公众传播。该项目将阐明微管的主要重塑作用是通过切断与各种细胞活性相关的atp酶（AAA+）家族的酶来完成的。根据所提出的切断机制，多尺度模拟将确定表征微管细丝断裂的分子和热力学参数。由于已知AAA+蛋白的作用涉及对其底物蛋白施加拉力，因此在本项目中，模拟可以达到长时间和长度尺度，以跟踪切断酶的作用，主要是六聚体功能状态的角朊蛋白，将由合作者进行实验，以提取微管上unfolase作用的标记物。此外，这些六聚体酶活性状态之间的变构转变对微管分解的贡献将被确立。粗粒度模拟和实验的结合将最终为切断酶的动力作用提供定量的见解。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

Cells contain molecular machines consisting of protein complexes that convert chemical energy into mechanical work. These machines use the work to help either assemble or disassemble cellular structures during vital cell processes. Understanding the mechanisms of action of these biological machines and their relationship with conformational changes in their substrates are among the challenges of modern molecular biology. This project uses computational modeling at multiple scales to elucidate how a class of molecular machines associated with microtubules accomplishes the severing of this largest structure in the cytoskeleton, whose dynamic organization and rearrangement is an essential process of cell division, motility, and development. This research will address a critical gap in our understanding of the dynamic properties of microtubules and their complexes with microtubule associated proteins undergoing wear and their dependence on the magnitude and geometry of mechanical input and will lead to a better understanding of how molecular machines work. The project will provide education and training of undergraduate and graduate students in computational biophysical chemistry by involving them in interdisciplinary scientific projects and increase the participation of groups underrepresented in science through the outreach at local Cincinnati Public School and through research experience opportunities for freshmen students participating in the "Women in Science and Engineering" program at the University of Cincinnati. The results of the project will be disseminated to the public by the investigator, postdoc, and students through publications, conference presentations, and visits to local schools. This project will elucidate the major remodeling action of microtubules performed by severing enzymes from the ATPases Associated with various cellular Activities (AAA+) family. The multiscale simulations will determine molecular and thermodynamic parameters that characterize the breaking of a microtubule filament according to the proposed severing mechanisms. Because the action of AAA+ proteins is known to involve the application of pulling forces on their substrate proteins, in this project simulations that can reach the long time and length-scales required to follow the action of severing enzymes, primarily katanin in its hexameric functional states, will be complemented by experiments conducted by collaborators to extract markers of the unfoldase action on microtubules. Furthermore, the contribution of allosteric transitions between the active states of these hexameric enzymes to microtubule disassembly will be established. The combination of coarse-grained simulations and experiments will ultimately provide quantitative insight into the power stroke action of severing enzymes.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.