Domain motion coupled to radical catalysis in ornithine aminomutase

原子和分子含有被称为电子的带负电荷的小粒子。通常，一个原子或分子上的两个电子相互配对，从而降低它们的总能量，提高它们的稳定性。分子或原子上未成对或孤立的电子称为自由基。与自由基相关的能量增加会导致它们不稳定，并对其他分子起反应，例如氧气或水。在活的有机体内，这些异常自由基反应的目标可能会破坏DNA或蛋白质等细胞成分，导致癌症、衰老甚至死亡。像所有生物一样，人类有专门的分子来执行特定的生物功能。其中一些功能是由专门设计的酶执行的。有趣的是，研究发现了越来越多的酶，它们使用自由基来进行不寻常的、非常困难的化学反应。这些酶中的某一类使用维生素B12，它是自由基的储存库。当底物与B12-酶结合时，B12-分子分裂为两个自由基。这使得自由基继电器系统随之而来；在催化反应过程中，孤立的电子将在酶的空腔中从一个分子跳到下一个分子。与所有使用自由基的酶一样，B12酶面临的两个重要挑战是(I)控制自由基产生的时间和(Ii)控制酶腔内自由基的反应性和轨迹。在催化循环的过程中，酶必须在一系列高度同步的事件中将反应自由基引向预期的目标，同时最小化或防止自由基因与错误的分子或原子(即水、氧或酶本身)碰撞而自行熄灭。为了更好地了解酶一般如何控制自由基的穿透，我们将重点介绍一种特殊的酶，称为鸟氨酸氨基变位酶。这种酶的独特之处在于它不仅含有维生素B12，还含有维生素B6。B6和B12都是监测催化循环中自由基扩散的灵敏探针，使鸟氨酸氨基变位酶成为详细研究酶介导的自由基化学的理想体系。我们最近确定了酶的分子结构(即酶的每个原子在三维空间中的位置)。根据这些信息，我们可以检查酶的独特结构特征，使其能够将自由基定向到预期的目标。作为本计划的一部分，我们还将通过将酶置于大磁场中的技术来研究自由基对的距离和相对取向。在这种特殊的物理状态下，自由基将充当微型磁铁，我们将能够获得关于它们的直接环境(即邻近原子)以及与第二个自由基的距离和方向的信息。我们还将在催化循环的不同阶段捕获酶，并使用上述技术来确定酶如何以及在多大程度上改变其构象，以使有效的自由基繁殖。通过这项研究，我们将更好地了解酶如何控制和利用与能量相关的自由基，使化学上困难和具有能量挑战的反应得以进行。

Atoms and molecules contain small negatively charged particles called electrons. Typically, two electrons on an atom or molecule pair with one another, thereby lowering their overall energy and increasing their stability. An unpaired or lone electron on a molecule or atom is referred to as a radical. The increased energy associated with radicals cause them to be unstable and reactive towards other molecules, for example oxygen or water. Within a living organism, the targets for these aberrant radical reactions can damage cellular components like DNA or protein, leading to cancers, aging or even death. Humans, like all living things, have specialised molecules for carrying out specific biological functions. Some of these functions are executed by specifically designed enzymes. Interestingly, research is uncovering an ever increasing list of enzymes which use radicals to carry out unusual and very difficult chemical reactions. A certain class of these enzymes uses vitamin B12, which serves as a reservoir for radicals. The B12-molecule splits into two radicals when the substrate binds to the B12-enzyme. This permits a radical relay system to ensue; the lone electron will hop from one molecule to the next in the enzyme cavity during the course of the catalytic reaction. Two important challenges faced by B12-enzymes, as with all enzymes which use radicals, are (i) controlling the timing of radical production and (ii) controlling the reactivity and trajectory of radicals within the enzyme cavity. During the course of the catalytic cycle, the enzyme must direct the reactive radicals toward their intended targets in a series of highly synchronized events, whilst at the same time minimize or prevent the radical from extinguishing itself by collision with the wrong molecule or atom (i.e. water, oxygen, or the enzyme itself). To better understand how enzymes in general control the peregrination of radicals, we will focus on a particular enzyme, termed ornithine aminomutase. This enzyme is unique in that it not only contains vitamin B12, but also vitamin B6. Both B6 and B12 serve as sensitive probes for monitoring radical propagation during the catalytic cycle, making ornithine aminomutase an ideal system for detailed investigation of enzyme-mediate radical chemistry. We have recently determined the molecular architecture of the enzyme, (i.e. where each atom of the enzyme is located in a three dimensional space). From this information, we can examine the unique structural features of the enzyme that enables it to direct radicals towards their intended target. As part of this programme we will also investigate the distance and relative orientation of the radical pair, by a technique whereby we place the enzyme in a large magnetic field. Under this particular physical state, the radicals will act as miniature magnets, and we will be able to derive information on their immediate environment, (i.e. neighbouring atoms) as well as the distance and orientation to a second radical. We will also trap the enzyme at different stages of the catalytic cycle, and use the above techniques to determine how and to what extent the enzyme changes its conformation to enable productive radical propagation. From this research, we will better understand how enzymes control and harness the energy associated radicals, enabling chemically difficult and energetically challenging reactions to be performed.