Computational modeling of the mechanisms of microtubule disassembly by biological nanomachines

细胞包含由蛋白质复合体组成的分子机器，蛋白质复合体将化学能转化为机械功。在至关重要的细胞过程中，这些机器利用这项工作来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。该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是如何完成细胞骨架中这一最大结构的切割的，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质的复合体在磨损过程中的动力学性质以及它们对机械输入的大小和几何形状的依赖方面的一个关键空白，并将有助于更好地理解分子机器的工作原理。该项目将通过让本科生和研究生参与跨学科科学项目，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，并通过在当地辛辛那提公立学校的外联活动和通过为参加辛辛那提大学“科学和工程领域的女性”方案的新生提供研究经验机会，增加科学界代表性不足的群体的参与。该项目的结果将由研究人员、博士后和学生通过出版物、会议报告和对当地学校的访问向公众传播。这个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动相关的ATPase(AAA+)家族的酶来实现的。多尺度模拟将根据所提出的切断机制确定表征微管细丝断裂的分子和热力学参数。由于AAA+蛋白质的作用已知涉及对其底物蛋白质施加拉力，在这个项目中，模拟可以达到跟踪断裂酶(主要是处于六聚体功能状态的katanin)的行动所需的长时间和长度尺度，将由合作者进行的实验来补充，以提取微管上展开酶作用的标记。此外，还将确定这些六聚体酶活性状态之间的变构转换对微管分解的贡献。粗粒度模拟和实验的结合最终将为切断酶的力量中风行为提供定量的洞察。这一奖项反映了NSF的法定使命，并通过使用基金会的智力优势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.