EAGER: (ST1) Collaborative Research: Exploring the emergence of peptide-based compartments through iterative machine learning, molecular modeling, and cell-free protein synthesis

EAGER：（ST1）协作研究：通过迭代机器学习、分子建模和无细胞蛋白质合成探索基于肽的隔室的出现

• 批准号: 1939463
• 负责人: Andrew Ferguson
• 金额: $ 14.99万
• 依托单位: University of Chicago
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-08-15 至 2022-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1939463&HistoricalAwards=false
• 关键词: EAGER; ST1; Collaborative; Research; Exploring

Non-technical Abstract:The cell is the fundamental building block of all living things. The materials within the cell are separated and protected from the environment by the cell membrane that is composed of molecules derived from fatty acids. These molecules function well under relatively benign natural conditions, such as in water at room temperature and pressure. Under harsh environments, such as extreme temperatures and pressures prevalent in industrial processes, these molecules are unstable therefore making it difficult to deploy cells within such environments. Furthermore, it is difficult to engineer natural membrane molecules with new functions such as the ability to sense their environment or bind particular surfaces or target molecules. It is the primary goal of this work to discover and synthesize a new class of molecules based on proteins as an alternative 'chassis' material for synthetic cell membranes that have improved mechanical and chemical stability and can be engineered to endow the membrane with new functions. Profs. Ferguson and Liu combine fast experimental synthesis and testing with computer simulations and artificial intelligence tools to search for new synthetic membranes with the ability to survive in harsh environments and the capacity to assemble synthetic cells together into synthetic tissues. By combining experiment and computation within a virtuous cycle, wherein computation guides experiment and experiment informs computational modeling, massive savings in labor, time, and resources are realized compared to traditional trial-and-improvement experimentation. In the course of this work, Profs. Ferguson and Liu provide research opportunities for post-doctoral, graduate, undergraduate, and high-school trainees, incorporate the outcomes of the research into classes that they teach, and engage in outreach activities through a Girls in Science and Engineering summer camp, Detroit Area Pre-College Engineering Program, and University of Chicago After School Matters summer internship program.Technical Abstract:The aim of this work is to discover novel peptidic biomaterials as an alternative "chassis" material for synthetic cells. While biology has settled on using lipid bilayer membrane as the material for compartmentalizing cytoplasm and for membrane-bound organelles, polypeptides offer an alternative biomaterial that can establish peptidic microcompartments with improved mechanical and chemical stability and the capacity for additional engineered biological function. Peptidic chassis materials offer unique advantages compared to lipid and polymersome membrane materials in terms of biocompatibility, chemical and mechanical stability, and capacity for additional functionalization that make them extremely desirable for applications in biomedicine, drug delivery, biosensing, and deployment in non-natural environments. The discovery of peptide sequences capable of spontaneous self-assembly into solute-filled microcompartments with desired materials properties is frustrated by the vast size of the protein sequence search space that makes exhaustive exploration intractable and Edisonian trial-and-improvement inefficient. In this work, we establish an integrated data-driven modeling and high-throughput cell-free synthesis platform to rapidly traverse sequence space. In a tightly integrated feedback loop between theory and modeling, we employ an 'active learning' paradigm to extract information from experimental data, guide rational traversal of the vast peptide sequence space, and optimally deploy experimental resources. Completion of this work will lead to the discovery of highly sought-after peptide-based synthetic cell 'chassis materials' that are more robust to harsh environments and which have complementary binding functionality to enable self-organization of the synthetic cells into synthetic tissues. In the course of this work, Profs. Ferguson and Liu offer research opportunities for high-school and undergraduate students to provide exposure to scientific research and improve representation in the STEM pipeline, train graduate and post-doctoral trainees in integrated computational and experimental research, incorporate the scientific outcomes in course materials, and engage in outreach activities through a Girls in Science and Engineering summer camp, Detroit Area Pre-College Engineering Program, and University of Chicago After School Matters summer internship program.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.

非技术摘要：细胞是所有生物的基本组成部分。 细胞内的物质被由脂肪酸衍生的分子组成的细胞膜隔离并免受环境影响。 这些分子在相对温和的自然条件下（例如在室温和压力下的水中）可以很好地发挥作用。在恶劣的环境下，例如工业过程中普遍存在的极端温度和压力，这些分子不稳定，因此很难在这种环境中部署电池。 此外，很难设计出具有新功能的天然膜分子，例如感知环境或结合特定表面或目标分子的能力。 这项工作的主要目标是发现和合成一类基于蛋白质的新型分子，作为合成细胞膜的替代“底盘”材料，该材料具有改进的机械和化学稳定性，并且可以被设计为赋予膜新功能。 教授。弗格森和刘将快速实验合成和测试与计算机模拟和人工智能工具结合起来，寻找能够在恶劣环境中生存并能够将合成细胞组装成合成组织的新型合成膜。 通过将实验和计算结合在一个良性循环中，其中计算指导实验，实验为计算建模提供信息，与传统的试验和改进实验相比，可以节省大量的劳动力、时间和资源。 在这项工作的过程中，教授。弗格森和刘为博士后、研究生、本科生和高中学员提供研究机会，将研究成果纳入他们所教授的课程中，并通过底特律地区的科学与工程女孩夏令营参与外展活动大学预科工程项目和芝加哥大学课后事务暑期实习项目。技术摘要：这项工作的目的是发现新型肽生物材料作为合成细胞的替代“底盘”材料。 虽然生物学已决定使用脂质双层膜作为分隔细胞质和膜结合细胞器的材料，但多肽提供了一种替代生物材料，可以建立具有改善的机械和化学稳定性以及额外工程生物功能的能力的肽微区室。 与脂质和聚合物膜材料相比，肽底盘材料在生物相容性、化学和机械稳定性以及额外功能化的能力方面具有独特的优势，这使得它们非常适合生物医学、药物输送、生物传感和非自然环境中的应用。 能够自发自组装成具有所需材料特性的溶质填充微区室的肽序列的发现因蛋白质序列搜索空间的巨大而受挫，这使得详尽的探索变得困难，爱迪生式的试验和改进效率低下。 在这项工作中，我们建立了一个集成的数据驱动建模和高通量无细胞合成平台，以快速遍历序列空间。 在理论和建模之间紧密集成的反馈循环中，我们采用“主动学习”范式从实验数据中提取信息，指导对广阔的肽序列空间的合理遍历，并优化部署实验资源。 这项工作的完成将导致人们发现备受追捧的基于肽的合成细胞“底盘材料”，这种材料对恶劣环境更加坚固，并且具有互补的结合功能，使合成细胞能够自组织成合成组织。 在这项工作的过程中，教授。弗格森和刘为高中生和本科生提供研究机会，让他们接触科学研究并提高 STEM 管道中的代表性，培训研究生和博士后学员进行综合计算和实验研究，将科学成果纳入课程材料，并通过科学与工程女孩夏令营、底特律地区大学预科工程计划和芝加哥大学课后事务暑期实习计划参与外展活动。该奖项反映了 NSF 的法定使命，并通过使用基金会的知识分子优点和更广泛的影响审查标准。

项目成果

In search of a novel chassis material for synthetic cells: emergence of synthetic peptide compartment

寻找新型合成细胞底盘材料：合成肽隔室的出现

• DOI: 10.1039/d0sm01644f
• 发表时间: 2020-12
• 期刊: Soft Matter
• 影响因子: 3.4
• 作者: Sharma, Bineet;Ma, Yutao;Ferguson, Andrew L.;Liu, Allen P.
• 通讯作者: Liu, Allen P.

Computational Design of Self-Assembling Peptide Chassis Materials for Synthetic Cells

合成细胞自组装肽底盘材料的计算设计

• DOI: 10.1039/d2me00169a
• 发表时间: 2022-01
• 期刊: Molecular Systems Design & Engineering
• 影响因子: 3.6
• 作者: Ma, Yutao;Kapoor, Rohan;Sharma, Bineet;Liu, Allen;Ferguson, Andrew L
• 通讯作者: Ferguson, Andrew L

Facile formation of giant elastin-like polypeptide vesicles as synthetic cells

作为合成细胞轻松形成巨型弹性蛋白样多肽囊泡

• DOI: 10.1039/d1cc05579h
• 发表时间: 2021-12
• 期刊: Chemical Communications
• 影响因子: 4.9
• 作者: Sharma, Bineet;Ma, Yutao;Hiraki, Harrison L;Baker, Brendon M;Ferguson, Andrew L;Liu, Allen P
• 通讯作者: Liu, Allen P