Molecular Simulations of Cotranslational Folding

共翻译折叠的分子模拟

基本信息

批准号：
8769152
负责人：
ADRIAN Hamilton ELCOCK
金额：
$ 25.68万
依托单位：
UNIVERSITY OF IOWA
依托单位国家：
美国
项目类别：
财政年份：
2012
资助国家：
美国
起止时间：
2012-01-15 至 2016-12-31
项目状态：
已结题

项目摘要

DESCRIPTION (provided by applicant): An important current goal in molecular biology is to understand how the synthesis and folding of proteins are coupled to each other. Although the understanding of events that occur as a protein is synthesized by the ribosome has been aided by high-resolution structures of many of the macromolecular components, only low-resolution views of the structure and dynamics of ribosome nascent-chain complexes (RNCs) are currently available. More importantly, essentially all studies of RNCs have been performed under conditions in which the RNC is stalled, i.e. under conditions in which its conformational dynamics are effectively at thermodynamic equilibrium. There is increasing evidence, however, that the fates of nascent proteins can depend significantly on the rate at which translation occurs, which implies that the partitioning of a newly synthesized protein between misfolded and native conformations is at least partly under kinetic control. There is, therefore, an urgent need for methods that can structurally characterize RNCs during active translation. Since experimental characterization is likely to remain an intractable problem it is proposed here to use molecular simulation methods instead. A plan of work is therefore outlined for developing a simulation framework that can accurately model coupled synthesis-folding events in the bacterial ribosome and that can fully define the role of its attached chaperone, trigger factor (TF), both in isolated monosomes and in models of complete polysomes. Three Specific Aims will be pursued. First, explicit-solvent molecular dynamics simulations will be used to determine the extent of trigger factor's conformational flexibility alone and in complex with the ribosome. These studies will establish the limits of TF's conformational adaptability in its functionally relevant states and will provide the basis for developing a realistic simulation model of TF-RNCs. Second, an accurate coarse-grained (CG) simulation model will be developed that allows the conformational behavior of stalled TF-RNC complexes to be directly modeled; properly parameterized, this model will enable a wide range of experimental observations on TF-RNCs to be rationalized at a truly structural level. Finally, the CG simulation model will be used to simulate cotranslational folding events in actively translating RNC complexes (with and without TF) in monosomes and polysomes. These latter studies will provide structural and dynamic pictures of nascent protein chains from the moment that they emerge from the ribosome's exit tunnel to the moment that they complete folding or misfolding in a way that is not achievable by conventional experimental methods. As such, the proposed studies are expected to greatly improve understanding of the factors that affect a nascent protein's propensity to fold or misfold during the course of its translation.

描述（由申请人提供）：分子生物学的重要目前目标是了解蛋白质的合成和折叠如何相互耦合。尽管对许多大分子成分的高分辨率结构对蛋白质发生的事件的理解得到了核糖体的合成，但目前仅可用核糖体新生链复合物（RNC）的结构和动力学的低分辨率视图。更重要的是，本质上，在RNC停滞不前的条件下，即在其构象动力学有效地处于热力学平衡处的条件下，所有RNC的研究均已进行。但是，有越来越多的证据表明，新生蛋白的命运可以显着取决于翻译的发生率，这意味着在错误折叠和天然构象之间将新合成蛋白的分配至少部分在动力学控制之下。因此，迫切需要在主动翻译过程中结构表征RNC的方法。由于实验表征可能仍然是一个棘手的问题，因此在这里提出使用分子模拟方法。因此，概述了一个工作计划，用于开发一个模拟框架，该框架可以准确地对细菌核糖体中的耦合合成折叠事件进行建模，并可以在孤立的单子体和完整多核体模型中充分定义其附着的伴侣触发因子（TF）的作用。将追求三个具体目标。首先，将使用显式溶剂分子动力学模拟来确定触发因子的构象柔韧性的程度，并与核糖体复杂化。这些研究将在其功能相关的状态中建立TF构象适应性的局限性，并为开发TF-RNC的现实模拟模型提供基础。其次，将开发出精确的粗粒（CG）模拟模型，该模型允许直接建模停滞的TF-RNC复合物的构象行为；正确的参数化，该模型将使对TF-RNC的广泛实验观察能够在真正的结构层面上合理化。最后，CG仿真模型将用于模拟单体和多个多膜体中主动翻译RNC复合物（有或不带TF）的共透明折叠事件。这些后一项研究将提供从核糖体的出口隧道到完成的那一刻，到它们以常规实验方法无法实现的方式完成折叠或错误折叠的那一刻。因此，预计拟议的研究将大大提高对影响新生蛋白在翻译过程中折叠或折叠折叠式折叠或错误折叠的因素的理解。