Using self-templating proteins to spatiotemporally organize biochemistry

项目摘要/摘要 蛋白质在空间和时间上的组织在自然过程中无处不在。工程蛋白质系统， 另一方面，通常缺乏这种组织。组织生物合成和监管系统有望改善 生物分子的产量难以产生，并提供了对组织相关病理机制的洞察。 这些疾病包括许多神经退行性疾病；时空调节也涉及信号传递过程， 新陈代谢和衰老。自组装的、可遗传的蛋白质，即普恩，提供了一种很有前途的组织方法 酵母菌和其他生物的生化过程，进而揭示与组织相关的潜在原理 功能障碍。 拟议研究的目的有三个：(I)开发一个用于组织正交普鲁恩结构域的工具包 生物化学；(2)利用蛋白结构域促进生物合成和组织信息流；(3)利用系统一级 识别基于普里恩的组织的候选途径的模型。最近发现的一套类Pron蛋白将 系统地挖掘具有生物合成和调控所需表型的自组装结构域 组织。经过充分研究和新发现的Pron结构域将被用来组织模型酶途径和 转录因子，并了解基于Prion的组织的影响。阿片类药物合成也将在#年组织 这种方式是为了提高效价和产量。最后，将实现一个空间分辨的反应扩散模型。 详细检查基于Prion的组织的功能并预测将从组织中受益的途径 细胞内的Pron阶段。这个模型将对实验中无法达到的量进行定量预测，例如 基于蛋白的无膜细胞器内的详细浓度梯度。 设计生物合成过程的时空组织有可能极大地提高我们的 产生有用数量的顽固生物分子的能力。这些分子可能从阿片分子和他们的 复杂的大环抗菌化合物的前体，所有这些化合物都抵抗化学合成，缺乏高产率 生物合成路线。了解基于Pron的组织的机制和功能也有望揭示 对抗人类病理的策略，其中越来越多的疾病被发现与异常的蛋白质组织有关。

Project Summary/Abstract The organization of proteins, both in space and time, is ubiquitous in natural processes. Engineered protein systems, on the other hand, typically lack this organization. Organizing biosynthetic and regulatory systems promises to improve yields of difficult-to-produce biomolecules and provide insight into the mechanisms of organization-related pathologies. These include many neurodegenerative diseases; spatiotemporal regulation is also implicated in processes of signaling, metabolism, and aging. Self-assembling, heritable proteins, known as prions, offer a promising method to organize biochemical processes in yeast and other organisms, and in turn to reveal principles underlying organization-related dysfunction. The aims of the proposed research are three-fold: (I) Develop a toolkit of orthogonal prion domains to organize biochemistry; (II) Use prion domains to enhance biosynthesis and organize information flow; and (III) Use systems-level models to identify candidate pathways for prion-based organization. A recently discovered suite of prion-like proteins will be mined systematically for self-assembling domains conferring desirable phenotypes for biosynthetic and regulatory organization. Well-studied and newly discovered prion domains will be used to organize model enzymatic pathways and transcription factors, and to understand the effects of prion-based organization. Opioid synthesis will also be organized in this manner in order to improve titers and yields. Finally, a spatially resolved reaction-diffusion model will be implemented to examine the function of prion-based organization in detail and predict pathways that will benefit from organization in an intracellular prion phase. This model will make quantitative predictions of experimentally inaccessible quantities, such as the detailed concentration gradients within prion-based membraneless organelles. Engineering the spatiotemporal organization of biosynthetic processes has the potential to greatly increase our ability to generate useful quantities of recalcitrant biomolecules. These could range from opioid molecules and their precursors to complex macrocyclic antimicrobial compounds, all of which resist chemical synthesis and lack high-yielding biosynthetic routes. Understanding the mechanisms and function of prion-based organization also promises to reveal strategies to combat human pathologies, a growing number of which are found to be related to aberrant protein organization.