Modeling the influence of translation-elongation kinetics on protein structure and function

项目摘要 分子生物学中的一个新兴范例是翻译动力学可以影响新生蛋白质的行为。 在mRNA分子中引入同义密码子突变，这改变了密码子突变的速率。 位置由核糖体翻译，但不是它们编码的氨基酸，已被证明会影响 新生蛋白质是否会折叠和发挥功能、错误折叠和功能失常、聚集或有效地移位 到不同的细胞室。不同物种的基因组使用同义密码子， 频率，这表明mRNA分子可能编码额外的信息层，以指导 编码序列中翻译速度的变化，从而影响蛋白质的命运。的确， 可以改变翻译速率的同义突变现在已经与多种疾病联系在一起， 包括血友病和癌症的亚型。这些发现是一个转变，从流行的观点， 蛋白质的氨基酸序列单独编码其结构和功能，其中蛋白质的动力学 合成与体内蛋白质行为有关。由于翻译动力学和新生蛋白质的偶联 行为的研究相对不足，许多关于这种现象的基本生物学问题 仍然没有答案。这些问题包括：密码子翻译速率的分子起源是什么？如何 我们能否模拟翻译延伸动力学对蛋白质结构和功能的影响？怎么 翻译速度的变化导致实验观察到的折叠和功能的变化， 囊性纤维化跨膜传导调节蛋白和时钟蛋白KaiB？本研究 计划，一系列的计算工具将开发和应用，以解决这些问题。这些工具 包括粗粒度分子动力学模拟、化学动力学建模和生物信息学 技术.这种计算工具非常适合解决这些问题，因为它们提供了一种方法， 在分子水平上模拟蛋白质合成，探索改变密码子翻译速率对 新生蛋白质的折叠和功能，并提取与翻译动力学相关的分子信息， 下一代测序数据集。此外，这项研究的一些预期结果将 由我们的实验合作者进行测试。这一建议将推动新生的蛋白质组领域， 检查这些生物分子系统的细节，难以通过实验测量，通过提供 实验观察的分子解释，并通过挑战该领域目前的范式， 激发全新的研究方向。

Project Summary An emerging paradigm in molecular biology is that translation kinetics can influence nascent protein behavior. Introducing synonymous codon mutations into an mRNA molecule, which changes the rate at which codon positions are translated by the ribosome but not the amino acids they encode, has been shown to influence whether a nascent protein will fold and function, misfold and malfunction, aggregate, or efficiently translocate to a different cellular compartment. The genomes of different species use synonymous codons with different frequencies, suggesting that mRNA molecules may encode an additional layer of information to guide the variation in translation speed across a coding sequence and thereby influence the fate of a protein. Indeed, synonymous mutations that can change translation rates have now been linked to a variety of diseases, including subtypes of hemophilia and cancer. These findings are a shift away from the prevailing view that a protein's amino acid sequence alone encodes its structure and function to one in which the kinetics of protein synthesis are relevant to in vivo protein behavior. As the coupling been translation kinetics and nascent protein behavior has been relatively understudied, many fundamental biological questions about this phenomenon remain unanswered. These questions include: what are the molecular origins of codon translation rates? How can we model the influence of translation elongation kinetics on protein structure and function? How do changes in translation speed lead to the experimentally observed changes in the folding and function of the Cystic Fibrosis Transmembrane Conductance Regulator protein and the clock protein KaiB? In this research program, a range of computational tools will be developed and applied to address these questions. These tools include coarse-grained molecular dynamics simulations, chemical kinetic modeling, and bioinformatics techniques. Such computational tools are well-suited to address these questions as they provide a means to simulate protein synthesis at the molecular level, explore the impact of changing codon translation rates on nascent protein folding and function, and extract molecular information relevant to translation kinetics from Next-Generation Sequencing data sets. Additionally, a number of anticipated findings from this research will be tested by our experimental collaborator. This proposal will advance the nascent proteome field by examining details of these biomolecular systems that are difficult to measure experimentally, by providing molecular explanations for experimental observations, and by challenging the field's current paradigms to motivate entirely new research directions.