Computational Modeling of Protein Degradation by Biological Nanomachines

细胞存活严重依赖于严格调控的蛋白质降解机制。介导蛋白质降解的生物纳米机器使用重复的机械力来展开、转移（移动）和破坏多余或有缺陷的蛋白质。了解这些机制对于破译基本细胞过程的细节至关重要。该项目将在多个尺度上使用计算机模拟来阐明1)蛋白质展开和易位动作对力方向性的依赖；2)降解过程中涉及的生物机器组件之间协作的性质。通过该项目获得的知识将促进对这些生物纳米机器结构和功能之间关系的理解，并将揭示蛋白质展开和易位的基本原理。本项目通过解决先进的科学问题，将计算生物物理化学的本科生和研究生的培养结合起来。将通过教育和指导工作促进代表性不足的少数民族更多地参与计算科学。这一目标将通过辛辛那提大学和中央州立大学（CSU）（一所历史悠久的黑人学院和大学）之间的合作来实现，并将把CSU的外展活动与PI实验室中代表性不足的少数民族的研究经验机会结合起来。该项目的研究成果将由项目负责人、研究生和本科生通过出版物、会议报告、网络和科罗拉多州立大学的研讨会向公众广泛传播。该项目将阐明机械各向异性对细菌Clp atp酶多结构域底物蛋白展开和易位的影响，Clp atp酶是生物纳米机器的AAA+超家族成员。将开发多尺度模型，以探测具有不同拓扑结构和沿特定方向机械稳定性的底物蛋白质的多结构域结构的纳米机器介导的线程。使用这些模型的计算机模拟将由合作者进行实验来补充，以确定限制和不限制几何形状的重塑途径。该项目还将阐明Clp atp酶和肽酶组分在蛋白质穿线中的协同作用。将进行原子和粗粒度模型的计算机模拟，以详细了解肽酶的变构构象转变及其在底物易位中的作用。这些模拟与合作者进行的实验研究相结合，将建立残留物水平的相互作用，这是这些生物机器中组件专业化的基础。

Cell survival is critically dependent on tightly regulated protein degradation mechanisms. Biological nanomachines that mediate protein degradation use repetitive mechanical forces to unfold, translocate (move), and destroy excess or defective proteins. Understanding these mechanisms is of central importance for deciphering the details of essential cellular processes. This project will use computer simulations at multiple scales to elucidate 1) the dependence of protein unfolding and translocation actions on force directionality and 2) the nature of collaboration between components of the biological machines involved in the degradation process. The knowledge gained through this project will advance understanding of the relationship between structure and function in these biological nanomachines and will reveal fundamental principles of protein unfolding and translocation. This project integrates the training of undergraduate and graduate students in computational biophysical chemistry through addressing advanced scientific problems. Increased participation of underrepresented minorities in computational sciences will be promoted through educational and mentoring efforts. This goal will be achieved through the collaboration between the University of Cincinnati and Central State University (CSU), a Historically Black College and University, and will combine outreach activities at CSU with research experience opportunities for underrepresented minorities in the PI's laboratory. The results of this project will be disseminated widely to the general public by the PI, graduate and undergraduate students through publications, conference presentations, the web, and seminars at CSU.This project will elucidate the effect of mechanical anisotropy on unfolding and translocation of multidomain substrate proteins by bacterial Clp ATPases, which are members of the AAA+ superfamily of biological nanomachines. Multiscale models will be developed to probe nanomachine-mediated threading of multidomain constructs of substrate proteins with diverse topology and mechanical stability along specific directions. Computer simulations using these models will be complemented by experiments conducted by collaborators to pinpoint remodeling pathways in restricted and unrestricted geometries. The project will also elucidate the collaboration between Clp ATPase and peptidase components for protein threading. Computer simulations of atomistic and coarse-grained models will be performed to obtain a detailed understanding of allosteric conformational transitions of the peptidase and their role in substrate translocation. These simulations, in conjunction with experimental studies conducted by collaborators, will establish the residue-level interactions that underlie component specialization in these biological machines.