Single molecule dynamics of enzyme catalysis for thermoadaptation and design

本项目结合单分子实验和模拟来研究酶催化和动力学。它还将测试进化如何使酶适应不同温度的新理论，并利用这些知识来设计它们的特性。该项目具有从开发新的生物催化剂到了解生物体如何应对气候变化的潜在影响。该项目将提供最先进的生物物理方法和分子动力学模拟方面的优秀培训，这是一个与新西兰紧密联系的合作项目。这个项目是计算和实验之间的紧密合作：模拟将为实验提供信息，反之亦然，揭示酶催化的原子细节动力学，并利用这些信息来设计和工程生物催化剂。光等离子纳米级传感器，使用“耳语廊模式”，可以以高灵敏度检测单个蛋白质及其运动。在本项目中，该技术将应用于研究催化转化过程中单个酶分子的构象变化。模拟将提供必要的原子水平分析来解释单分子测量，以揭示酶催化和热适应的动力学。该项目还将研究酶是如何适应不同温度下的工作的。酶有一个最适宜的温度，在这个温度下酶的催化活性最高。高于这个温度，它们就不那么活跃了。教科书上关于酶在高温下展开的解释并不能解释这一点，最明显的是对冷适应酶的解释，这些酶稳定且折叠，但在最佳温度以上活性较低。与简单的“化学”催化剂相比，它们在较高的温度下变得不那么活跃，即使它们保持其功能形状。相反，一种基本的物理性质——热容——解释并预测了酶对温度的依赖性。热容量在反应过程中发生变化，并通过酶的动力学“调整”以获得最佳温度。描述这种情况的理论——大分子速率理论（MMRT）——适用于所有的酶，因此在预测代谢活动作为温度的函数方面起着关键作用。实验正在揭示MMRT在细胞、整个生物体甚至生态系统水平上的特点。这意味着理解生物系统对温度变化的反应是很重要的，例如，生态系统将如何对气候变化作出反应。该项目将使用模拟和实验来揭示酶动力学是如何调整的，以确定催化的最佳温度。它将分析和预测突变的影响，并确定酶工程的新原理。

This project combines single molecule experiments with simulations to investigate enzyme catalysis and dynamics. Itwill also test new theories of how evolution adapts enzymes to different temperatures, and use this knowledge todesign their properties. This project has potential impact ranging from developing new biocatalysts to understandinghow organisms respond to climate change. The project will provide excellent training in state-of-the-art biophysicalmethods and molecular dynamics simulations, in a collaborative project, with strong links in New Zealand.This project is a close collaboration between computation and experiment: simulations will inform experiment andvice versa, to reveal the dynamics of enzyme catalysis in atomic detail, and use that information to design and engineerbiocatalysts. Optoplasmonic nanoscale sensors, using 'Whispering-gallery modes,' can detect single proteins and theirmovements with high sensitivity. In this project, this technique will be applied to investigate the conformationalchanges of individual enzyme molecules during catalytic turnover. Simulations will provide the essential atomic-levelanalysis to interpret single-molecule measurements to reveal the dynamics of enzyme catalysis and thermoadaptation.The project will also investigate how enzymes are adapted to work at different temperatures. Enzymes have anoptimum temperature at which they are most catalytically active. Above that temperature, they become less active.The textbook explanation that enzymes unfold at higher temperatures does not explain this, most obviously for cold-adapted enzymes which are stable and folded, but less active, above their optimum temperature. In contrast to simple'chemical' catalysts, they become less active at higher temperatures even though they maintain their functional shape.Instead, a basic physical property - the heat capacity - explains and predicts the temperature dependence of enzymes.The heat capacity changes during the reaction and is 'tuned' by the enzyme's dynamics to give the optimaltemperature. The theory that describes this - macromolecular rate theory, (MMRT) - applies to all enzymes, and sohas a critical role in predicting metabolic activity as a function of temperature. Experiments are revealingcharacteristics of MMRT at the level of cells, whole organisms and even ecosystems. This means that it is important inunderstanding the response of biological systems to temperature changes, for example, how ecosystems will respondto climate change.This project will use simulations and experiments toreveal how enzyme dynamics are tuned todetermine optimum temperatures of catalysis. Itwill analyse and predict effects of mutations andidentify novel principles of enzyme engineering.