Single molecule dynamics of enzyme catalysis for thermoadaptation and design

该项目将单分子实验与模拟相结合，研究酶的催化和动力学。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。该项目具有潜在的影响，从开发新的生物催化剂到了解生物体如何应对气候变化。该项目将在新西兰的一个合作项目中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。该项目是计算和实验之间的密切合作：模拟将为实验提供信息，反之亦然，以原子细节揭示酶催化的动力学，并利用这些信息设计和设计生物催化剂。光致等离激元奈米感应器，使用“耳语画廊模式”，可以高灵敏度侦测单一蛋白质及其运动。在这个项目中，这项技术将被应用于研究单个酶分子在催化周转过程中的构象变化。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。该项目还将研究酶如何适应不同的温度。酶有一个最适温度，在这个温度下它们的催化活性最高。教科书上的解释是，酶在更高的温度下展开，但并不能解释这一点，最明显的是对冷适应的酶来说，这种酶在最适温度以上是稳定和折叠的，但活性较低。与简单的“化学”催化剂不同，它们在较高的温度下变得不那么活性，尽管它们保持其功能形状。相反，一个基本的物理属性--热容--解释和预测酶的温度依赖性。热容在反应过程中变化，并由酶的动力学“调整”，以提供最佳温度。描述这一点的理论--大分子速率理论(MMRT)--适用于所有的酶，因此在预测代谢活性作为温度的函数方面具有关键作用。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征。这意味着了解生物系统对温度变化的反应是重要的，例如，生态系统将如何对气候变化做出反应。这个项目将使用模拟和实验来揭示酶动力学是如何被调节以确定催化的最佳温度的。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.