Effects of the Cellular Environment on Protein Assembly

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。目前关于蛋白质折叠机制的许多知识都是在理想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。细胞内的拥挤、序列突变以及pH和/或温度的变化都可能导致折叠过程偏离正轨。这可能导致不正确折叠实体的形成，这些实体反过来可以自组装形成富含β -片结构的大纤维聚集体。大多数（如果不是全部的话）蛋白质似乎能够聚集，这表明聚集是多肽链的固有特性。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角度探讨控制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，对这些过程的研究使其成为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和肽模型，具有明确的手性和定向氢键。这些模型将应用于研究细胞中存在的环境因素（禁闭、拥挤和表面相互作用）影响下的整体折叠和聚集。粗粒度模拟将辅以原子细节模拟，旨在探索聚集的早期阶段，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）的研究组密切合作进行。对蛋白质折叠和聚集基本原理的深入了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。预计在本项目背景下进行的模拟结果将指导新的实验研究。所有开发的计算程序都将免费向公众开放。PI积极参与对科学领域代表性不足的群体（包括少数民族和妇女）的指导，参与课程开发和推广项目。PI将改编她之前在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（加州州立大学洛杉矶分校）的研究生水平课程。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。该倡议参与了向圣巴巴拉当地小学儿童开展的化学推广活动，并计划在目前的筹资周期内制定一项旨在使年轻女孩参与科学的推广方案。

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.