Effects of the Cellular Environment on Protein Assembly

细胞环境对蛋白质组装的影响

• 批准号: 0642086
• 负责人: Joan-Emma Shea
• 金额: $ 80.4万
• 依托单位: University of California-Santa Barbara
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-01-01 至 2012-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0642086&HistoricalAwards=false
• 关键词: Effects; Cellular; Environment; Protein; Assembly

In order to perform its biological function, a protein must fold from a linear chain of amino acids to its three dimensional native structure. Much of the current knowledge of the mechanisms involved in protein folding is the result of experimental and theoretical investigations in idealized dilute environments. Proteins however fold in the more complex cellular environment. Crowding in the cell, sequence mutations, and changes in pH and/or temperature can cause the folding process to go astray. This can lead to the formation of improperly folded entities that can in turn self-assemble to form large fibrillar aggregates enriched in beta-sheet structure. Most, if not all proteins, appear capable of aggregating, intimating that aggregation is an inherent property of polypeptide chains. A comprehensive understanding of protein folding cannot be limited to the study of a single protein, but must include an investigation of interactions between proteins. The aim of this project is to probe from a theoretical perspective the physico-chemical principles governing the assembly of both proteins and peptides into a variety of supramolecular structures. Because of the length and time scales associated with folding and aggregation, the study of these processes lends itself to a hierarchy of computational models. The PI will develop new mid-resolution coarse-grained off-lattice backbone-sidechain protein and peptide models, with explicit chirality and directional hydrogen bonding. These models will be applied to the study of folding and aggregation in the bulk and under the influence of environmental factors present in the cell (confinement, crowding and surface interactions). The coarse-grained simulations will be complemented by atomically detailed simulations geared at probing the early stages of aggregation, the structural nature of protofilaments, and the interaction of aggregation inhibiting peptides with protofilaments. The fully atomic simulations will be performed in close collaboration with the experimental groups of Professor Stephen Meredith (U of Chicago) and Professor Aphroditi Kapurniotu (U of Aachen).A deeper understanding of the fundamental principles governing protein folding and aggregation will have impacts in a number of disciplines including the emerging field of biomaterials. The proposed research is inherently interdisciplinary, and the PI has established collaborations with two leading experimental groups. It is anticipated that results from simulations performed in the context of this project will guide new experimental studies. All computational programs developed will be made freely available to the public. The PI is actively involved in the mentoring of under-represented groups in science (both minority and women), in curricular developments and in outreach programs. The PI will adapt computational modules that she previously developed in a Computational Biochemistry course at UCSB for use in a graduate level class at a minority serving institution (Cal State LA). The PI is also co-chairing a committee for designing a physical chemistry sequence for biochemistry majors. The PI is involved in chemistry outreach activities to local Santa Barbara elementary school children and is planning on developing an outreach program in the present funding cycle targeting the involvement of young girls in science.

为了发挥其生物学功能，蛋白质必须从线性氨基酸链折叠成其三维天然结构。目前对蛋白质折叠机制的认识大多是在理想化的稀释环境中进行实验和理论研究的结果。然而，蛋白质在更复杂的细胞环境中折叠。细胞中的拥挤、序列突变以及pH和/或温度的变化都可能导致折叠过程误入歧途。这可能导致形成不适当折叠的实体，这些实体又可以自组装形成富含β-折叠结构的大纤维状聚集体。大多数（如果不是全部）蛋白质似乎能够聚集，暗示聚集是多肽链的固有性质。对蛋白质折叠的全面理解不能局限于对单个蛋白质的研究，而必须包括对蛋白质之间相互作用的研究。该项目的目的是从理论的角度探讨蛋白质和肽组装成各种超分子结构的物理化学原理。由于与折叠和聚合相关的长度和时间尺度，对这些过程的研究适合于计算模型的层次结构。PI将开发新的中分辨率粗粒度非晶格骨架-侧链蛋白质和肽模型，具有明确的手性和定向氢键。这些模型将被应用到折叠和聚集在散装的影响下，目前在细胞（禁闭，拥挤和表面相互作用）的研究。粗粒度的模拟将补充原子详细的模拟，面向探测聚集的早期阶段，原丝的结构性质，以及聚集抑制肽与原丝的相互作用。全原子模拟将与Stephen Meredith教授（芝加哥大学）和Aphroditi Kapurniotu教授（亚琛大学）的实验组密切合作进行。对蛋白质折叠和聚集的基本原理的更深入理解将对包括新兴生物材料领域在内的许多学科产生影响。拟议的研究本质上是跨学科的，PI已经与两个领先的实验小组建立了合作关系。预计在该项目范围内进行的模拟结果将指导新的实验研究。开发的所有计算程序将免费向公众提供。PI积极参与指导科学领域代表性不足的群体（包括少数民族和妇女），课程开发和推广计划。PI将调整她以前在UCSB的计算生物化学课程中开发的计算模块，用于少数民族服务机构（Cal State LA）的研究生课程。PI还共同主持了一个为生物化学专业设计物理化学序列的委员会。PI参与了针对当地圣巴巴拉小学生的化学外联活动，并计划在本供资周期内制定一项外联方案，目标是让年轻女孩参与科学。