Evolution of Translation: From molecules to cells

翻译机制是蛋白质合成的中心，在每个细胞中都有成百上千个拷贝。翻译途径需要大量的大分子RNA：蛋白复合物来保证其正常的功能。虽然这条通路中涉及的单个成分和反应已经得到了很好的研究，但从分子到整个细胞，从空间和时间上都解决了一个完整的图景，仍然缺乏。本研究项目旨在将我们对翻译的功能和演化的认识扩展到更高层次的组织和规模。在分子水平上，该研究的具体目标是研究RNA中的通信途径：设置遗传密码的蛋白质复合物。通过分子动力学模拟获得的网络特性和自由能面，将研究核糖体内的相互作用途径，这些途径导致氨基酰基trna合成和核糖体内通信的特异性和编辑进化。核糖体小亚基的折叠/组装景观将使用全原子和基于知识的氧化石墨烯电势进行计算检查。这些模拟将与同一系统上的折叠实验同时进行。为了研究DNA在细胞拥挤环境中的翻译和折叠动力学，将使用基于gpu的Lattice Microbe程序进行转录/翻译过程的随机模拟。三维晶格模型是基于从完整细胞的单分子，蛋白质组学和低温电子断层扫描数据获得的时空信息。关于翻译过程如何在细胞尺度上发生的假设将使用系统生物学方法进行测试和扩展。所有用于研究大分子RNA：蛋白质组装的可视化、模拟和分析工具将通过流行的VMD生物分子分析软件的MultiSeq和Network View扩展公开提供和更新。对混合MD-Go和元动力学自由能模块的更新将被实施到分子动力学程序NAMD中，该程序可在所有NSF超级计算机设施上使用。此外，任何新的分析工具和结果都将纳入在线提供的一系列计算生物学教学教程。PI的研究小组将继续参与国家科学基金会资助的研究生教学研究员计划，帮助高中教师为他们的课堂准备最先进的科学课程。晶格微生物方法允许随机模拟复杂的细胞过程和反应。所有细胞模拟软件都将公开提供。与首席研究员开发的其他计算生物物理学技术一样，将开发教程和用户指南，以帮助其他研究人员在自己的研究中使用该方法。本项目由分子与细胞生物科学部的分子生物物理集群、物理部的生命系统物理学项目和化学部的化学理论、模型和计算方法项目共同支持。

The translation machinery is the center of protein synthesis and is present in hundreds to thousands of copies in every cell. The translational pathway requires a large number of macromolecular RNA:protein complexes to ensure its proper function. While the individual components and reactions involved in the pathway have been well studied, an integrated picture resolved both spatially and temporally, progressing from molecules to an entire cell is still missing. This research project is designed to extend our knowledge of the function and evolution of translation to higher levels of organization and scale. On the molecular level, the specific goals of the research are to study communication pathways in the RNA:protein complexes that set the genetic code. Interaction pathways that lead to evolution of specificity and editing in the aminoacyl-tRNA syntheses and communication within the ribosome will be studied using network properties and free energy surfaces obtained from molecular dynamics simulations. The folding/assembly landscape of the ribosomal small subunit will be computationally examined using all-atom and knowledge-based GO potentials. These simulations will be carried out simultaneously with folding experiments on the same systems. To study the kinetics of translation and the folding of DNA in the crowded environment of the cell, stochastic simulations of transcription/translation processes will be carried out using the GPU-based Lattice Microbe program. The 3D lattice models are based upon spatial and temporal information obtained from single molecule, proteomics, and cryo-electron tomography data from intact cells. Hypotheses about how the process of translation occurs at a cellular scale will be tested and extended using systems biology approaches. All of the visualization, simulation, and analysis tools to enable the study of macromolecular RNA:protein assemblies will be made publicly available and updated through the MultiSeq and Network View extensions to the popular VMD biomolecular analysis software. Updates to the hybrid MD-Go and metadynamics free energy modules will be implemented into the molecular dynamics program NAMD that is available on all the NSF Supercomputer facilities. In addition any new analysis tools and results will be incorporated into a series of tutorials for teaching computational biology that will be available online. The PI's research group will continue to participate in the NSF sponsored Graduate Teaching Fellows program to help high school teachers prepare state-of-the-art scientific curriculum for their classrooms. The Lattice Microbe method allows stochastic simulations of complex cellular processes and reactions. All cell simulations software will be made publicly available. As with the other computational biophysics techniques developed by the principal investigator, tutorials and users guides will be developed to assist other researchers in using the methodology in their own studies. This project is jointly supported by the Molecular Biophysics Cluster in the Division of Molecular and Cellular Biosciences, the Physics of Living Systems Program in the Physics Division and by the Chemical Theory, Models and Computational Methods Program in the Chemistry Division.