Evolution of Translation: Structure, Function, and Folding of RNA/Protein Complexes

进化产生了所有的生物过程。 虽然它的痕迹可以在整个细胞结构中瞥见，但它的一些最清晰的标记可以在控制蛋白质合成关键过程的翻译机制（核糖体及其相关大分子）中看到。这种机制存在于每个细胞中的数千个拷贝中，由许多RNA/蛋白质复合物组成，确保从DNA正确生产蛋白质。虽然已经识别和表征了各个组件，但仍然缺少整个细胞在空间和时间上解析的过程的整体集成图。发展这样一幅图景是理解这一复杂过程进化历史的关键。为了将翻译的功能和演变知识扩展到更高的组织和规模水平，本项目将重点关注三个项目。 首先，蛋白质和RNA分子在蛋白质合成过程中形成许多瞬时复合物，我们将研究这些复合物结合和解结合的物理性质。具体来说，不知道每个结合/解结合事件是独立的还是整个事件链是耦合的。为了研究这个问题，我们将模拟tRNA分子从携带氨基酸的酶到将其带到核糖体的延伸因子的直接迁移或传递。模拟结果将与实验组合作进行的研究进行比较。其次，核糖体的折叠和核糖体蛋白质和RNA的结合中的核糖体签名的作用将通过各种方法计算检查。 了解生命领域特有的特征如何影响核糖体组装，将有助于深入了解自三种主要生物谱系分化以来组装过程是如何演变的。 第三，将开发一种新的计算方法来研究细胞拥挤环境中的翻译过程的动力学。这些3D晶格模拟利用GPU计算的最新进展，能够在细胞周期的时间尺度上在体内条件下模拟粗粒度细菌细胞中的翻译过程。 关于翻译过程如何在细胞尺度上发生的假设将被测试。所有为研究参与翻译的大分子RNA/蛋白质组装而开发的可视化、模拟和分析工具都将通过MultiSeq扩展到免费分发的流行可视化程序VMD。这些技术也将被纳入现有的计算生物学教学中使用的一系列教程。这些教程可在网上，通过定期在全国各地举行的研讨会，并在伊利诺伊大学教授的CHEM/BIOP 470计算化学生物学课程。PI的研究小组将继续参与NSF赞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。 该项目由分子和细胞生物科学部的分子生物物理学和化学部的理论和计算化学计划共同支持。

Evolution has given rise to all the biological processes. While its traces can be glimpsed throughout the fabric of the cell, some of its clearest markings are seen in the translation machinery (the ribosome and its associated macromolecules) that controls the critical process of protein synthesis. This machinery is present in thousands of copies in every cell and is composed of a number of RNA/protein complexes that ensure the proper production of proteins from DNA. While the individual components have been identified and characterized, an integrated picture of the process as a whole, resolved both spatially and temporally over an entire cell, is still missing. Developing such a picture is key to understanding the evolutionary history of this complex process. To extend knowledge of the function and evolution of translation to higher levels of organization and scale, this project will focus on three projects. Firstly, protein and RNA molecules form many transient complexes during the process of protein synthesis which will be studied to examine the physical nature of the binding and unbinding of these complexes. Specifically, it is not known if each binding/unbinding event is independent or if the entire chain of events is coupled. To investigate this issue, the direct migration or handoff of a tRNA molecule from the enzyme that charges it with an amino acid to the elongation factor that takes it to the ribosome will be modeled. The simulation results will be compared to studies carried out in collaboration with experimental groups. Secondly, the role of ribosomal signatures in the folding and binding of ribosomal proteins and RNA will be examined computationally with a variety of methods. An understanding of how signatures unique to a domain of life affect ribosome assembly will provide insight into how the assembly process has evolved since the divergence of the three primary organismal lineages. Thirdly, a new computational approach will be developed to study the kinetics of the translation process in the crowded environment of the cell. These 3D lattice simulations take advantage of recent advances in GPU computing to enable simulations of the translation process in a coarse grained bacterial cell under in vivo conditions on the time scale of the cell cycle. Hypotheses about how the process of translation occurs at a cellular scale will be tested. All of the visualization, simulation, and analysis tools developed to study macromolecular RNA/protein assemblies involved in translation will be made available through the MultiSeq extension to the popular visualization program VMD that is freely distributed. These techniques will also be incorporated into an existing series of tutorials used in teaching computational biology. The tutorials are available online, through workshops periodically given across the country, and in the CHEM/BIOP470 Computational Chemical Biology course taught at the University of Illinois. The PI's research group will continue to participate in the NSF sponsored Graduate Teaching Fellows program that helps high school teachers prepare state-of-the-art scientific curricula for their classrooms. This project is jointly supported by Molecular Biophysics in the Division of Molecular and Cellular Biosciences and the Theoretical and Computational Chemistry Program in the Chemistry Division.