Protein Choreography

蛋白质编排

• 批准号: MR/T02223X/1
• 负责人: Jonathan Phillips
• 金额: $ 153.6万
• 依托单位: UNIVERSITY OF EXETER
• 依托单位国家: 英国
• 项目类别: Fellowship
• 财政年份: 2020
• 资助国家: 英国
• 起止时间: 2020 至 无数据
• 项目状态: 未结题
• 来源: https://gtr.ukri.org/projects?ref=MR%2FT02223X%2F1
• 关键词: Protein; Choreography

The processes of life are dynamic - it is change on a molecular level that enables us to grow and move, but also to become ill and treat disease. Just as the shape and posture of our body can determine our readiness to perform a task, the structure and conformation of a protein molecule can determine its function or activity. It is the ability for proteins to dynamically and rapidly reconfigure that underpins many critical activities in biology, disease and medicine.However, we are currently limited to study proteins, including many important enzymes, at high resolution in space or time - but not both. Static structural models have contributed to major advances, such as in gene editing technology, based on the reprogramming of the enzyme 'CRISPR/Cas9'. This structural information is also crucial for drug discovery, accurately guiding design and optimisation efforts.These are major new applications that rely on precisely controlling dynamic changes in protein structure. These aims - and our understanding of fundamental biology - will be greatly advanced by bridging high resolution information in both time and space.My research will pioneer an integrated experimental and computational approach to determine with unprecedented spatio-temporal resolution how enzymes are dynamically regulated and how they catalyse chemical reactions. We now have a unique opportunity to make measurements of the structural perturbations in large enzymes both with high structural resolution (per amino acid building block) and high temporal resolution (per millisecond). The information that we gain will be used to build high resolution dynamic structural models in which individual features reconfigure according to their individual rates, determined experimentally with millisecond and amino acid precision. This work will focus on two areas of recent high profile success in developing tools for biotechnology and medicine which depend on the exquisite control of enzyme dynamic structural changes. (i) Gene editing: There is a growing effort to engineer CRISPR/Cas9 enzymes to improve their efficiency and to create entirely new tools for targeted mutation of the genome in situ. This has potentially broad application in research, but also to specifically treat genetic diseases. We will study gene editing enzymes to provide mechanistic insight to explain their behaviour and to guide the development of variants with improved activities. (ii) Allosteric drug discovery. There has been major recent investment by both big pharma and by venture capital/biotechnology partnerships to discover 'allosteric' drugs that control enzyme function by controlling the protein conformation. These drugs have potential benefits in selectivity and the ability to modify otherwise intractable targets in disease. We will ascertain whether the new millisecond time-resolved measurements that we will develop can differentiate signatures of allosteric regulation and thus form the basis of a direct screen for allosteric drugs.This research programme brings together expertise in building novel experimental methods, cutting edge data science approaches, development of new software tools and a direct relevance to fundamental biology and applications in biotechnology and drug discovery.

生命的过程是动态的——正是分子水平上的变化使我们能够成长和移动，但也使我们生病和治疗疾病。正如我们身体的形状和姿势可以决定我们是否准备好完成一项任务一样，蛋白质分子的结构和构象可以决定它的功能或活性。它是蛋白质动态和快速重新配置的能力，支撑着生物学、疾病和医学中的许多关键活动。然而，我们目前仅限于研究蛋白质，包括许多重要的酶，在空间或时间上的高分辨率-而不是两者。静态结构模型为重大进步做出了贡献，例如基于“CRISPR/Cas9”酶重编程的基因编辑技术。这种结构信息对于药物发现也至关重要，可以准确地指导设计和优化工作。这些都是依赖于精确控制蛋白质结构动态变化的重要新应用。这些目标——以及我们对基础生物学的理解——将通过连接时间和空间的高分辨率信息而大大推进。我的研究将开创一种综合实验和计算方法，以前所未有的时空分辨率确定酶是如何动态调节的，以及它们是如何催化化学反应的。我们现在有一个独特的机会来测量大型酶的结构扰动，同时具有高结构分辨率（每氨基酸构建块）和高时间分辨率（每毫秒）。我们获得的信息将用于建立高分辨率动态结构模型，其中个体特征根据其个体速率重新配置，以毫秒和氨基酸精度实验确定。这项工作将集中在最近在开发生物技术和医学工具方面取得成功的两个领域，这两个领域依赖于对酶动态结构变化的精细控制。(i)基因编辑：人们越来越努力设计CRISPR/Cas9酶，以提高其效率，并为基因组的原位靶向突变创造全新的工具。这在研究中有潜在的广泛应用，但也专门用于治疗遗传疾病。我们将研究基因编辑酶，以提供解释其行为的机制见解，并指导具有改进活性的变体的开发。（ii）变构药物发现。最近，大型制药公司和风险资本/生物技术合作伙伴都进行了大量投资，以发现通过控制蛋白质构象来控制酶功能的“变构”药物。这些药物在选择性和修饰疾病中其他难治性靶点的能力方面具有潜在的益处。我们将确定我们将开发的新的毫秒时间分辨率测量是否可以区分变构调节的特征，从而形成直接筛选变构药物的基础。该研究项目汇集了建立新颖实验方法、前沿数据科学方法、开发新软件工具以及与基础生物学和生物技术和药物发现应用直接相关的专业知识。

项目成果

Drawing Processes of Life: Molecules, Cells, Organisms

绘制生命过程：分子、细胞、有机体

• 发表时间: 2023
• 作者: Anderson-Tempini Gemma

Allosteric Regulation of Glycogen Phosphorylase by Order/Disorder Transition of the 250' and 280s Loops.

• DOI: 10.1021/acs.biochem.2c00671
• 发表时间: 2023-04-18
• 期刊: BIOCHEMISTRY
• 影响因子: 2.9
• 作者: Kish, Monika;Subramanian, Sivaraman;Smith, Victoria;Lethbridge, Natasha;Cole, Lindsay;Vollmer, Frank;Bond, Nicholas. J.;Phillips, Jonathan J.
• 通讯作者: Phillips, Jonathan J.

Engineering and exploiting synthetic allostery of NanoLuc luciferase.

纳米荧光素酶的工程和利用合成变构。

• DOI: 10.1038/s41467-022-28425-2
• 发表时间: 2022-02-10
• 期刊: Nature communications
• 影响因子: 16.6
• 作者: Guo Z;Parakra RD;Xiong Y;Johnston WA;Walden P;Edwardraja S;Moradi SV;Ungerer JPJ;Ai HW;Phillips JJ;Alexandrov K
• 通讯作者: Alexandrov K

HDfleX: Software for flexible high structural resolution of hydrogen/deuterium-exchange mass spectrometry data

HDfleX：用于氢/氘交换质谱数据的灵活高结构分辨率的软件

• DOI: 10.1101/2021.12.09.471740
• 发表时间: 2021
• 作者: Seetaloo N

HDfleX: Software for Flexible High Structural Resolution of Hydrogen/Deuterium-Exchange Mass Spectrometry Data.

• DOI: 10.1021/acs.analchem.1c05339
• 发表时间: 2022-03-22
• 期刊: ANALYTICAL CHEMISTRY
• 影响因子: 7.4
• 作者: Seetaloo, Neeleema;Kish, Monika;Phillips, Jonathan J.
• 通讯作者: Phillips, Jonathan J.