Examination and Reconstruction of Alternate Allosteric Networks in Engineered LacI/GalR Transcription Factors

该项目旨在了解和预测蛋白质（即，转录因子），打开和关闭基因发展的手段，处理信息和与周围环境的相互作用。蛋白质处理信号信息的机制称为变构通讯。虽然对变构通讯的研究已经进行了四十多年，但这些基本过程的关键细节仍然知之甚少。这种知识上的差距阻碍了科学家和工程师设计具有定制通信能力的新蛋白质。因此，当前项目的重点是阐明规则，使科学家能够在处理广泛信号的转录因子家族中建立变构通信。这项研究将扩大科学界对变构通信的理解，并能够开发可用于造福社会的新工具（例如，用于生物工业应用的新的和更便宜的过程控制，以及用于个性化医疗的系统）。此外，该项目将涉及下一代科学家的培训和教育，特别是博士。研究生水平。 蛋白质变构是一种非常重要的蛋白质功能，已被证明是一个棘手的问题，以了解在分子水平上。变构通讯是许多用于控制基因表达的转录因子的标志，并使合成生物学家能够重新编程细胞。本研究的具体目标是利用乳糖阻遏物（LacI）的基本结构和功能关系，在几个LacI/GalR同源物中系统地映射和工程化交替变构通信。在更广泛的LacI/GalR家族变构是否已演变为由一组保守残基控制的基本问题，或蛋白质是否是塑料的，并倾向于在不同的残基序列变构，最终将提供洞察变构的结构-功能的关系，并在新的转录因子的工程援助。绘制变构图并确定LacI/GalR家族中赋予变构的进化起源、联系和机制，将为其他蛋白质如何被设计为表现出变构以及如何在现有系统中控制和调节变构提供关键知识。完成后，这项研究将使科学家能够通过开发特定变构操作的设计规则来测试关于替代变构通信的起源和分子力学的断言。反过来，这种算法将产生新的基于LacI/GalR的转录因子，用于广泛的生物技术应用。 该项目由分子和细胞生物科学部的分子生物物理学和系统与合成生物学项目共同资助。该奖项反映了NSF的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

This project aims to understand and predict how proteins (i.e., transcription factors) that turn genes on-and-off develop the means to process information and interact with nearby surroundings. The mechanism in which proteins process signal information is called allosteric communication. While the study of allosteric communication has been underway for more than four decades, critical details of these fundamental processes are still poorly understood. This gap in knowledge prevents scientists and engineers from designing new proteins with custom-built communication abilities. Accordingly, the focus of the current project is to elucidate the rules that will enable scientists to build allosteric communication in a family of transcription factors that process a broad range of signals. This research will expand the scientific communities understanding of allosteric communication and enable the development of new tools that can be used to benefit society (e.g., new and less expensive process controls for bio-industrial applications, and systems for use in personalized medicine). Moreover, this project will involve the training and education of the next generation of scientists, specifically Ph.D. level graduate students. Protein allostery is a vitally important protein function that has proven to be a vexing problem to understand at the molecular level. Allosteric communication is a hallmark of many transcription factors used to control gene expression and have enabled synthetic biologist to reprogram cells. The specific goal of this research is to leverage the basic structure and function relationship of the lactose repressor (LacI) to systematically map and engineer alternate allosteric communication, in several LacI/GalR homologues. Answering the fundamental question of whether allostery in the broader LacI/GalR family has been evolved to be controlled by a set of conserved residues or whether the protein is plastic and predisposed to allostery across different residue sequences will ultimately give insights into allosteric structure-function relationships and aid in the engineering of novel transcription factors. Mapping allostery and determining the evolutionary origin, links, and mechanism by which allostery is conferred in the LacI/GalR family will provide crucial knowledge into how other proteins may be designed to exhibit allostery and how to control and modulate allostery in existing systems. Upon completion, this study will enable scientist to test assertions with regard to the origin and molecular mechanics of alternate allosteric communication via the development of design rules for specific allosteric operations. In turn this algorithm will produce novel LacI/GalR-based transcription factors for use in a broad range of biotechnological applications. This project is co-funded by the Molecular Biophysics and the Systems and Synthetic Biology programs of the Division of Molecular and Cellular Biosciences.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.