Why does Nature use modular enzyme architectures for biological catalysis?

氧化还原蛋白，包括金属蛋白，构成了蛋白质王国的很大一部分。金属蛋白本身约占基因组的30%。它们含有金属离子，或作为单个原子，或作为簇的一部分，在微生物、植物和动物王国中起着各种维持生命的作用。许多酶利用金属的氧化态来进行氧化还原循环。金属蛋白参与的基本生物过程包括电子储存和转移、二氧结合、储存和激活、底物运输和催化。在许多金属酶中，如细胞色素c氧化酶（哺乳动物生命通过呼吸需求必不可少），氮酶和亚硝酸盐还原酶（鉴于它们在氮循环中的中心位置而必不可少），氢化酶（分子氢的生产者-未来替代能源的候选物），催化包括电子和质子的受控传递到利用底物的活性位点。亚硝酸盐还原酶是反硝化过程的核心，反硝化过程是微生物生物能量学的一个重要分支，对陆地和海洋氮循环至关重要，因为它通过释放一氧化二氮对全球变暖的贡献越来越大，一氧化二氮是一种消耗臭氧的温室气体，其效力比二氧化碳强300倍。目前的提案建立在申请人之间的密切合作基础上，他们共同在反硝化领域做出了重大贡献，并为我们对涉及金属酶生物机制的复杂过程的理解提供了重大进展。我们的联合方法使我们处于非常有利的地位，可以开展一个综合的结构机制计划，旨在解决在全球重要的生物系统中，与瞬态蛋白质复合物相比，大自然是否利用拴链结构域来增强生物反应中的催化作用。我们专注于含cu亚硝酸盐还原酶(CuNiRs) -利用它们的自然相遇（自由扩散）和系留复合物-学习自然的设计规则，以构建最佳配置和集成的氧化还原装置。我们将阐明定义催化效率的设计原则，并使远程电子运动耦合到活性位点氧化还原化学。这需要理解协调的蛋白质运动如何影响(i)远程电子转移机制，（ii）局部化学变化（键形成/断裂）以及（iii）这些如何通过驱动活性位点不同氧化态的形成来改变催化中的限速步骤。一般设计原则将出现，将指导合成生物学生物氧化还原装置的预测工程。在这个项目中开发的新方法和方法(例如（i)结合了停止流动和基于fret的方法，通过“分子信标”方法报告氧化还原化学，（ii）开发基于实验室的尺寸排除色谱-动态光散射小角度x射线散射（SEC-SAXS-DLS）用于研究蛋白质复合物）将与我们研究蛋白质复合物的能力具有广泛的相关性。这些新的能力和科学成果将对结构机制生物学产生重大影响，并使英国在这一重要领域保持全球领先地位。

Redox proteins, including metalloproteins, form a large portion of the protein kingdom. Metalloproteins themselves form ~ 30% of a genome. These contain metal ions either as a single atom or as part of a cluster and play a variety of life sustaining roles in the microbial, plant and animal kingdoms. Many enzymes exploit the oxidation states of metals to perform redox cycling. Fundamental biological processes in which metalloproteins participate include electron storage and transfer, dioxygen binding, storage and activation, and substrate transport, and catalysis. In many metalloenzymes such as cytochrome c oxidase (essential for mammalian life through respiratory requirements), nitrogenases and nitrite reductases (essential in view of their central position in the nitrogen cycle), hydrogenases (producers of molecular hydrogen - a candidate for a future alternative energy source), catalysis involves the controlled delivery of electrons and protons to the active site where substrate is utilised. Nitrite reductases are central to the denitrification process, an important branch of microbial bioenergetics and crucial to terrestrial and oceanic nitrogen cycling, since it makes an increasing contribution to global warming by release of N2O, an ozone-depleting and greenhouse gas some 300-fold more potent than CO2. The current proposal builds on close collaboration between the applicants where they collectively have made major contributions in the field of denitrification and have provided significant advances in our understanding of complex processes that are involved in biological mechanisms of metalloenzymes. Our combined approaches puts us in a very strong position to undertake an integrated structural-mechanistic programme that is aimed at addressing the question of whether Nature exploits tethered domains to enhance catalysis compared to transient protein complexes in biological reactions in globally important biological systems. We focus on Cu-containing nitrite reductases (CuNiRs) - exploiting their natural encounter (freely diffusing) and tethered complexes - to learn Nature's design rules for construction of optimally configured and integrated redox devices. We will elucidate design principles that define catalytic efficiencies and enable coupling of long-range electron movements to active site redox chemistry. This requires understanding of how coordinated protein movements impact on (i) mechanisms of long-range electron transfers, (ii) localised chemical change (bond formation / breakage) and (iii) how these can change the rate-limiting step in catalysis by driving the formation of different oxidation states of the active site. General design principles will emerge that will guide predictive engineering of biological redox devices for synthetic biology.New methods and approaches developed in this programme (e.g. (i) combined stopped-flow and FRET-based approach enabling the reporting on redox chemistry via a 'molecular beacon' approach and (ii) development of laboratory-based size-exclusion chromatography-small angle X-ray scattering with dynamic light scattering (SEC-SAXS-DLS) for studying protein complexes) will have broad relevance to our capabilities for studying protein complexes. These new capabilities and the scientific outcome will have significant impact on structural-mechanistic biology and keep the UK at the forefront of global effort in this important field.