Analysis of the proteostasis network and the thermostability of the proteome

蛋白质是我们细胞的核心成分。每种蛋白质通常折叠或采用特定的三维结构，也称为天然状态，这是蛋白质功能和稳定所必需的。在过去的50年里，蛋白质折叠领域取得了巨大的进步。值得注意的是，它首次明确了折叠所需的信息包含在蛋白质序列中。然后发现，折叠通常是由专门的分子机器伴侣协助的。现在的主要挑战是确定这两种作用的结合如何导致一个稳定的蛋白质组，这是细胞中所有蛋白质的集合。虽然伴侣蛋白可以在个体基础上进行评估，但由于无数优雅而复杂的生化分析，将这些知识转化为细胞环境仍然很困难，在细胞环境中，数百万种不同的蛋白质在非常有限的环境中共存。因此，我们需要开发新的系统范围的方法和工具来确定单个伴侣如何对蛋白质组的整体稳定性做出贡献。***在这个研究项目中，我们建议采用几种互补的方法来探测哪些蛋白质由于三维结构的丧失而在应力下不稳定。我们的假设是，不稳定是由使蛋白质更脆弱的内在特征和特定伴侣在压力情况下无法防止其不稳定造成的。为了验证这一想法，我们将采用特征良好的酿酒酵母模型生物，它比人类细胞更不复杂，更具延展性。我们将首先确定蛋白质组中的哪些蛋白质更经常不稳定，并使用计算生物学方法确定这些蛋白质之间的哪些特征是共享的。然后，我们将选择性地从细胞中去除特定的伴侣蛋白，以确定哪些蛋白质在这些条件下进一步不稳定。我们的目标是揭示控制蛋白质组稳定性的一些基本规则。更好地了解蛋白质组如何保持稳定具有广泛的意义，从我们对细胞衰老的理解到依赖于重组蛋白生产的工业应用。**

Proteins are central components of our cells. Each protein typically folds or adopts a specific three-dimensional structure, also called native state, that is required for the protein to be functional and stable. The protein folding field witnessed tremendous advances in the past 50 years. Notably, it first became clear that the information required for folding is contained within the protein sequence. It was then discovered that folding is often assisted by chaperones that are specialized molecular machines. A major challenge is now to determine how the combination of these two actions leads to a stable proteome, which is the ensemble of all proteins in the cell. While chaperone proteins can be assessed on an individual basis, thanks to a myriad of elegant and sophisticated biochemical assays, it remains difficult to translate this knowledge into the cellular context, in which millions of different proteins cohabit in a very confined environment. We therefore need to develop new systems-wide approaches and tools to determine how the individual chaperones contribute to the overall stability of the proteome. ***In this research program, we propose to employ several complementary approaches to probe which proteins are destabilized upon stresses due to the loss of their three-dimensional structures. Our hypothesis is that destabilization is caused by both intrinsic features that make the proteins more vulnerable and the inability of specific chaperones to prevent their destabilization under the stress situations. To test this idea, we will employ the well characterized Saccharomyces cerevisiae yeast model organism that is less complex and more malleable than human cells. We will first determine which proteins in the proteome are more often destabilized and identify which characteristics are shared among those proteins using computational biology approaches. We will then selectively remove specific chaperones from cells to determine which proteins are further destabilized in these conditions. Our goal is to unveil some of the fundamental rules that govern proteome stability. A better knowledge of how the proteome can be maintained stable has wide implications from our understanding of cellular aging to industrial applications that rely on recombinant protein production. **