Mechanism and Structural Dynamics of Translation

理解和描述大分子机器设计背后的动态特性是生物物理研究和生物分子工程的当前前沿。拟议的研究重点是细胞组成部分，这些细胞组成部分是细胞机器的一部分，用于解码遗传信息并在称为翻译的过程中合成功能蛋白质。翻译在核糖体中进行，核糖体是一种对所有活细胞都至关重要的大分子复合物。核糖体由蛋白质和RNA组成，这是两种主要的功能生物分子。结构研究表明，核糖体是一个高度动态的生物分子装配线，其中两个关键功能（肽键形成和解码）似乎完全由RNA完成。然而，为了在活细胞中观察到快速和准确的翻译，需要额外的蛋白质因子。起始因子（IF）和释放因子（RF）参与蛋白质合成的起始和终止，而延伸因子（EF）是肽链延伸的循环过程所必需的。这些翻译因子中的许多是核苷酸水解酶，其充当分子开关，以特定的输出响应特定的输入信号。这些信息处理和决策事件的动力学对于我们理解翻译和生物分子机器性能的设计原理具有极大的意义。我们才刚刚开始了解在分子尺度上传递信息的高度动态网络的设计是如何参与分子过程（如翻译）的。因此，拟议的研究将针对这些通信网络，并提供分子工具，使其能够进行详细分析。拟议的研究计划通过研究细菌EF-Tu和结构相关的翻译GTPases的结构动力学和生化特性来解决这一挑战。翻译GTP酶构成了不同种类的调节酶，虽然共享共同的结构设计，但在核糖体依赖性蛋白质合成期间具有非常不同的酶性质和功能。为了确定特定的酶性质和机制作用如何植根于特定的翻译GTdR的动态性质以及潜在的设计策略是什么，拟议的研究计划将使用最先进的生物物理技术，如荧光光谱，单分子荧光共振能量转移（sm-FRET），快速动力学和分子动力学（MD）模拟的组合。* 了解大分子组装过程的动力学性质，如核糖体，对于蛋白质/ RNA折叠和功能以及新型生物分子纳米机器的合理工程具有重要意义。

Understanding and describing the dynamic properties underlying the design of macromolecular machines is a current frontier in biophysical research and biomolecular engineering. The proposed research focuses on the cellular components that are part of the cells machinery to decode genetic information and to synthesize functional proteins during a process called translation. Translation takes part at the ribosome, a large macromolecular complex that is essential to all living cells. The ribosome is composed of proteins and RNAs, the two major classes of functional biomolecules. Structural studies have revealed that the ribosome is a highly dynamic biomolecular assembly line in which the two key functions (peptide-bond formation and decoding) seem to be carried out solely by RNA. However, for the rapid and accurate translation observed in living cells, additional protein factors are required. Initiation (IF) and release factors (RF) are involved in initiation and termination of protein synthesis, whereas elongation factors (EF) are required for the cyclic process of peptide chain elongation. Many of these translation factors are nucleotide hydrolases that function as molecular switches, responding to a particular input signal with a specific output. The dynamics of these information processing and decision-making events is of great interest for our understanding of translation and the design principles underlying the performance of biomolecular machines. We are just beginning to understand how the design of highly dynamic networks relaying information at the molecular scale is involved in molecular process such as translation. The proposed research will therefore target these communication networks and provide molecular tools enabling their detailed analysis.***The proposed research program addresses this challenge by studying the structural dynamics and biochemical properties of bacterial EF-Tu and structurally related translational GTPases. Translational GTPases constitute a diverse class of regulatory enzymes that although sharing a common structural design, have vastly different enzymatic properties and functions during ribosome-depend protein synthesis. In order to identify how the particular enzymatic properties and mechanistic roles are rooted in the dynamic properties of the particular translational GTPase and what the underlying design strategies are, the proposed research program will use a combination of state-of-the-art biophysical techniques such as fluorescence spectroscopy, single molecule Fluorescence Resonance Energy Transfer (sm-FRET), rapid kinetics and molecular dynamics (MD) simulations. ***Understanding the dynamical properties of processes in macromolecular assemblies like the ribosome will be of great importance for protein / RNA folding and function as well as rational engineering of novel biomolecular nano-machines.**