Rethinking biocatalysis and enzymology

酶是大自然使用的催化剂。它们是一种可再生资源，无毒，是大多数药物的靶标。由于酶具有复杂的三维结构，它表现出化学催化剂中很少发现的有趣特征。从可持续性的角度和获得新的反应性来看，使用酶来生产工业产品都是有利的。我们对酶催化的理解往往是肤浅的，在过去的几十年里，酶在合成中的应用几乎没有发展。提高我们对酶催化的认识对药物发现、农业和商品化学品的生产有直接的影响。本研究旨在通过建立新的、意想不到的方法来研究酶和设计生物催化过程，重新思考我们研究酶机制的方式以及我们如何将它们应用于生物催化。未来5年的目标是：1)探索生物催化剂使用的新条件；2)结合各种技术来研究酶。虽然酶通常在稀水条件下使用，但在自然界中它们很少浸入散装水中。例如，微生物在环境中分泌的酶在暴露于空气湿度的表面上起作用。最近，我们证明了一些酶在湿固反应混合物中比在标准稀水条件下更有效，并且机械力（又名机械酶学）可以积极影响酶的过程。我们认为这样的条件更好地模拟酶的自然环境，同时最大限度地减少浪费和避免溶解度问题。我们建议进一步探索这一策略的范围，例如来自其他类别的酶，整个微生物，其他底物和不同类型的反应。酶为了实现其功能，往往依赖于复杂的结构和动力学效应。例如，在变构中，小分子（称为效应器）在远离活性位点的地方结合酶，并增加或降低酶的活性，其机制尚不清楚。我们报道了几种研究变构学的新策略。我们结合了不同的生物物理和合成技术。例如，我们将效应物永久地附着在酶上，以促进机理研究，但也永久地激活酶并创造优质催化剂。我们建议结合几种技术来进行酶变构的研究，并研究酶在湿固反应混合物和机械酶学中的反应性和行为。这项研究具有很高的训练价值，因为它迫使受训者跳出固有的思维模式。由于我们研究的是非传统的酶反应混合物，并创造了应用和研究酶的新方法，我们必须创新。该项目还提供多学科培训的机会，涵盖生物催化、酶学、微生物学、结构生物学、生物物理化学、生物化学、有机合成和材料科学。

Enzymes are the catalysts used by Nature. They are a renewable resource, non-toxic, and the target of most drugs. Thanks to their complex 3D structure, enzymes show interesting characteristics rarely found in chemical catalysts. The use of enzymes to generate industrial products is advantageous both from a sustainability perspective and to access new reactivity. Our understanding of enzyme catalysis is often superficial, and how enzymes are used in synthesis has barely evolved over the past decades. Improving our knowledge of enzyme catalysis has direct implications in drug discovery, agriculture, and the production of commodity chemicals. This research aims at rethinking the way that we investigate enzyme mechanisms and how we employ them in biocatalysis, by establishing novel, unexpected approaches to study enzymes and design biocatalytic processes. The goals for the next 5 years are to: 1) explore new conditions for the use of biocatalysts and 2) combine various techniques to study enzymes. Although enzymes are typically used in dilute aqueous conditions, in nature they are rarely immersed in bulk water. For example, enzymes secreted in the environment by microorganisms operate on surfaces exposed to air moisture. Recently, we demonstrated that some enzymes are more efficient in moist-solid reaction mixtures than under standard dilute aqueous conditions, and that mechanical forces (a.k.a. mechanoenzymology) can positively affect enzymatic processes. We believe that such conditions better mimic the enzyme's natural environment, while minimizing waste and avoiding solubility issues. We propose to further explore the scope of this strategy, for example with enzymes from other classes, whole microorganisms, other substrates, and diverse types of reactions. To achieve their function, enzymes often rely on complex structural and dynamical effects. For example, in allostery, small molecules (called effectors) bind the enzyme away from the active site and increase or decrease their activity, the mechanism of which remains poorly understood. We have reported several new strategies to study allostery. We combine different biophysical and synthetic techniques. For example, we permanently attach the effectors to the enzymes to facilitate mechanistic studies, but also permanently activate the enzyme and create superior catalysts. We propose to combine several techniques to pursue our study of enzyme allostery and examine the reactivity and behavior of enzymes in moist-solid reaction mixtures and in mechanoenzymology. This research has high training value as it forces trainees to think outside the box. Since we work with non-traditional enzymatic reaction mixtures and create new methods to employ and study enzymes, we must innovate. This program also offers opportunities for a multidisciplinary training that spans biocatalysis, enzymology, microbiology, structural biology, biophysical chemistry, biochemistry, organic synthesis and material sciences.