Collaborative Research: Tackling Functional Protein States at Atomic Detail by Integrating Weighted Ensemble Simulations with Magnetic Resonance Restraints

这个项目的目的是描述蛋白质的交替结构，蛋白质是生命的主力，其生物学功能是由它们的结构决定的。表征这些所谓的“功能结构”的一个主要挑战是，这些结构往往过于多样化或转瞬即逝，无法用单个原子水平的实验技术捕获。因此，尚未满足的需求是一种能够在原子水平上确定功能性蛋白质结构结构的策略，甚至更重要的是，一种能够洞察功能结构如何相互转换的策略。该项目将开发一种新的软件工具，可以确定蛋白质的功能结构，蛋白质如何从一种结构转变为另一种结构，以及结构相互转化的速率。该工具结合了计算机模拟与实验测量的蛋白质内部距离的使用，并将通过流行的，免费提供的WESTPA模拟软件包提供。这个跨学科的合作项目为参与研究的研究生和本科生提供了宝贵的培训场地，并支持各种教育和推广活动，包括两年一次的WESTPA软件研讨会，为科学界提供使用新工具确定蛋白质功能结构的培训。生物物理学的一个新前沿是蛋白质功能状态的结构表征。蛋白质是生命的主力，其功能由其结构决定。描述蛋白质结构的一个主要挑战是，许多蛋白质不仅采用单一的结构状态，而且采用与蛋白质的生物学功能相关的替代状态。由于这些功能态的多样性和瞬态性，在原子水平上确定它们的结构对实验技术来说是难以捉摸的。因此，一个未被满足的需求是一种能够生成功能状态的原子细节结构的策略，甚至更重要的是，一种能够提供详细了解状态之间相互转换途径和相应动力学的策略。该项目的一个关键进展是开发了一种通用策略，该策略将磁共振实验的稀疏距离限制与严格的模拟相结合，以提供原子水平结构和功能蛋白质状态的动力学。该项目将提供一种新的模拟工具，将通过免费提供的WESTPA软件提供给科学界。为了进一步增强该软件的可访问性，WESTPA软件将与亚马逊网络服务上的Orion云计算平台集成，亚马逊网络服务是世界上最大的按需云计算设施。该项目由分子和细胞生物科学部的分子生物物理集群资助，部分资金来自化学部门的化学测量和成像项目。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。

This project is designed to characterize the alternate structures of proteins—the workhorses of life whose functions in biology are determined by their structures. A major challenge to characterizing these so-called “functional structures” is that these structures are often too diverse or fleeting to be captured by experimental techniques at the level of individual atoms. An unmet need is therefore a strategy that can determine the structures of functional protein structures at the atomic level and even more crucially, a strategy that can provide insights into how the functional structures interconvert. This project will develop a new software tool that can determine the functional structures of proteins, how the proteins move to convert from one structure to another, and the rates at which the structures interconvert. This tool combines the use of computer simulations with distances within proteins that are measured by experiments and will be made available through a popular, freely available WESTPA simulation software package. This interdisciplinary, collaborative project is providing a valuable training ground for graduate and undergraduate students participating in the research, and is supporting diverse educational and outreach activities, including biennial WESTPA software workshops to provide training to the scientific community in using the new tool for determining the functional structures of proteins. A new frontier in biophysics has been the structural characterization of protein functional states. Proteins are the workhorses of life and their functions are determined by their structures. A major challenge to characterizing protein structures is that many proteins adopt not just a single structural state, but alternate states that are relevant to the biological functions of the proteins. Due to the diversity and often transient nature of such functional states, the determination of their structures at the atomic level has been elusive to experimental techniques. An unmet need is therefore a strategy that can generate atomically detailed structures of functional states, and even more crucially, a strategy that can provide detailed insight into the pathways for interconversion between the states and corresponding kinetics. A key advance of the project is the development of a general strategy that integrates sparse distance restraints from magnetic resonance experiments with rigorous simulations to provide atomic level structures and dynamics of functional protein states. This project will provide a new simulation tool that will be made available to the scientific community through the freely available WESTPA software. To further enhance the accessibility of the software, the WESTPA software will be integrated with the Orion cloud-computing platform on Amazon Web Services, the world’s largest on-demand, cloud-computing facility. This project is funded by the Molecular Biophysics Cluster in the Division of Molecular and Cellular Biosciences, with partial co-funding from the Chemical Measurement and Imaging Program in the Division of Chemistry.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.