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.

项目概要/摘要 我们的长期目标是推进计算蛋白质设计，以设计新的生物功能和 揭示生物调节原理的分子/细胞工程策略。该提案结合了 我们在这些领域提供了两项 NIGMS 资助。 在我们的计算蛋白质设计工作中，我们通过计算设计了能够感知和 对细胞中新的小分子信号做出反应，这是一种在代谢工程中具有重要应用的能力， 诊断、生物修复和探测基本细胞过程。我们还拥有先进的方法 完全从头设计具有精确可调形状的蛋白质。拟议的工作建立在我们的新方法的基础上 为了解决一个尚未解决的核心挑战，同时设计从头蛋白质和用户的几何形状 定义的功能位点以针对功能优化的原子精度放置在其中。这项工作应该大大 扩大可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 可以控制生物行为以响应新信号的模块化系统。 我们对天然蛋白质功能的研究旨在了解中央调节蛋白如何在 互连的细胞网络，以及这些网络如何因突变等扰动而改变。 我们研究了由相反调节器控制的双态开关（GTPase），因为该基序在 生物学。通过 GTPase Gsp1 的系统诱变并整合系统测量 通过生物物理学的尺度（遗传相互作用图谱），我们发现了以前未知的变构位点 GTPase 是其功能的核心。我们的研究结果还提出了一种新模型，即多效性 GTPase Gsp1 差异性地调节不同的细胞功能。在这里，我们将在这些结果的基础上研究其机制 Gsp1 中的变构并评估其在其他 GTPases 中的普遍性，对理解机制有影响 疾病突变和调节剂的开发。我们还计划测试我们的 GTPase 调控模型 通过确定 GTPases 调节剂微调扰动的定量细胞后果。未来 方向包括将这些扰动测量扩展到其他中央生物开关。这 细胞控制的未揭示原理可以指导细胞工程，并与计算相结合 设计的新功能最终可能会带来对抗疾病失调的新方法。