Computational design of proteins and protein functions

蛋白质和蛋白质功能的计算设计

• 批准号: 10406129
• 负责人: Tanja Kortemme
• 金额: $ 33.62万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-07-01 至 2027-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10406129
• 关键词: Address; Allosteric Site; Area; Behavior; Biological; Biological Process; Biology; Biomedical Engineering; Biomedical Research; Biophysics; Bioremediations; Cell physiology; Cells; Data; Development; Diagnostic; Disease; Engineering; Future; Genetic; Geometry; Goals; Grant; Guanosine Triphosphate Phosphohydrolases; Lead; Measurement; Methods; Modeling; Molecular; Mutagenesis; Mutation; National Institute of General Medical Sciences; Protein Engineering; Proteins; Regulation; Research; Shapes; Signal Transduction; Signaling Molecule; Site; System; Technology; Testing; Work; cell growth regulation; cellular engineering; design; genetic regulatory protein; genome-wide; metabolic engineering; practical application; protein function; response; small molecule

PROJECT SUMMARY/ABSTRACT Our long-term goals are to advance computational protein design to engineer new biological functions and molecular/cellular engineering strategies to uncover principles of biological regulation. This proposal combines our two NIGMS grants in these areas. In our work on computational protein design, we have computationally engineered proteins that sense and respond to new small molecule signals in cells, a capability with important applications in metabolic engineering, diagnostics, bioremediation, and probing fundamental cellular processes. We have also advanced methods to design proteins with precisely tunable shapes entirely de novo. The proposed work builds on our new methods to address a central unsolved challenge, to simultaneously design the geometries of de novo proteins and user- defined functional sites placed into them with atomic accuracy optimized for function. This work should greatly expand the space of new functions that can be designed. We plan to integrate de novo designed proteins into modular systems that can control biological behavior in response to new signals. Our work on natural protein functions seeks to understand how central regulatory proteins operate in interconnected cellular networks, and how these networks are altered upon perturbations such as mutations. We studied a two-state switch (a GTPase) controlled by opposing regulators because this motif is prevalent in biology. Through systematic mutagenesis of the GTPase Gsp1 and integrating measurements at the systems scale (genetic interaction mapping) with biophysics, we uncovered previously unknown allosteric sites on the GTPase central to its function. Our findings moreover suggest a new model how the pleiotropic GTPase Gsp1 differentially regulates distinct cellular functions. Here we will build on these results to investigate the mechanism of allostery in Gsp1 and assess its generality in other GTPases, with implications for understanding mechanisms of disease mutations and for development of modulators. We also plan to test our model of GTPase regulation by determining quantitative cellular consequences of fine-tuned perturbations to GTPases regulators. Future directions include expansion of these perturbation measurements to other central biological switches. The uncovered principles of cellular control can guide cellular engineering, and in conjunction with computationally designed new functions may ultimately lead to new ways to counteract misregulation in disease.

项目摘要/摘要 我们的长期目标是将计算蛋白设计推进到设计新的生物学功能和 分子/细胞工程策略，以揭示生物调节原则。该建议结合了 我们在这些领域的两个纽约人赠款。 在我们在计算蛋白设计方面的工作中，我们具有计算工程的蛋白质， 响应细胞中新的小分子信号，这是具有代谢工程中重要应用的能力， 诊断，生物修复和探测基本的细胞过程。我们也有先进的方法 设计具有从头开始的精确调谐形状的蛋白质。拟议的工作以我们的新方法为基础 要应对中心未解决的挑战，同时设计从头蛋白质和用户的几何形状 - 定义的功能位点将其放置在其功能的原子精度中。这项工作应该很大 扩展可以设计的新功能的空间。我们计划将从头设计的蛋白质整合到 可以控制生物学行为的模块化系统，以响应新信号。 我们在天然蛋白质功能方面的工作旨在了解中心调节蛋白如何在 互连的蜂窝网络，以及在扰动（例如突变）时如何改变这些网络。 我们研究了一个由相对调节器控制的两态开关（GTPase），因为此主题很普遍 生物学。通过GTPase GSP1的系统诱变并在系统上集成测量 与生物物理学的比例尺（遗传相互作用映射），我们发现了先前未知的变构位点 GTPase的功能中心。此外，我们的发现提出了一个新模型，多效性GTPase GSP1如何 差异调节不同的细胞功能。在这里，我们将基于这些结果来研究机制 GSP1中的变构和在其他GTPases中评估其普遍性，对理解机制的影响 疾病突变和调节剂的发展。我们还计划测试我们的GTPase调节模型 通过确定对GTPases调节剂的微调扰动的定量细胞后果。未来 方向包括将这些扰动测量结果扩展到其他中央生物学开关。这 未发现的细胞控制原理可以指导细胞工程，并结合计算 设计的新功能最终可能会导致应对疾病中的正常调节的新方法。