Why does Nature use modular enzyme architectures for biological catalysis?

为什么 Nature 使用模块化酶结构进行生物催化？

• 批准号: BB/N013972/1
• 负责人: Samar Hasnain
• 金额: $ 52.16万
• 依托单位: University of Liverpool
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2017
• 资助国家: 英国
• 起止时间: 2017 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FN013972%2F1
• 关键词: Why; does; Nature; use; modular

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.

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，既可以作为单个原子，也可以作为簇的一部分，在微生物、植物和动物王国中扮演着各种维持生命的角色。许多酶利用金属的氧化态进行氧化还原循环。金属蛋白参与的基本生物过程包括电子储存和转移、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(通过呼吸需求对哺乳动物的生命至关重要)、固氮酶和亚硝酸盐还原酶(鉴于它们在氮循环中的中心地位而必不可少)、氢酶(产生分子氢--未来替代能源的候选者)，催化涉及到电子和质子被控制地输送到底物被利用的活性部位。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N2O而对全球变暖做出越来越大的贡献，N2O是一种臭氧消耗和温室气体，其效力约为二氧化碳的300倍。目前的提案建立在申请者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，并在我们对涉及金属酶生物学机制的复杂过程的理解方面取得了重大进展。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-机械方案，旨在解决以下问题：与全球重要的生物系统中的生物反应相比，大自然是否利用连接结构域来增强催化作用。我们专注于含铜的亚硝酸还原酶(CuNiRs)--利用它们的自然相遇(自由扩散)和束缚的复合体--来学习大自然的设计规则，以构建优化配置和集成的氧化还原设备。我们将阐明定义催化效率和实现远程电子运动与活性部位氧化还原化学耦合的设计原则。这需要了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中心不同氧化态的形成来改变催化中的限速步骤。将出现指导用于合成生物的生物氧化还原装置的预测工程的一般设计原则。该计划中开发的新方法和途径(例如，(I)结合停流和基于FRET的方法，能够通过分子信标方法报告氧化还原化学，以及(Ii)开发基于实验室的尺寸排除层析-小角X射线散射动态光散射(SEC-SAXS-DLS)以研究蛋白质复合体)将与我们研究蛋白质复合体的能力广泛相关。这些新的能力和科学成果将对结构-机械生物学产生重大影响，并使英国保持在这一重要领域的全球努力的前沿。

项目成果

An unprecedented dioxygen species revealed by serial femtosecond rotation crystallography in copper nitrite reductase.

• DOI: 10.1107/s2052252517016128
• 发表时间: 2018-01-01
• 期刊: IUCrJ
• 影响因子: 3.9
• 作者: Halsted TP;Yamashita K;Hirata K;Ago H;Ueno G;Tosha T;Eady RR;Antonyuk SV;Yamamoto M;Hasnain SS
• 通讯作者: Hasnain SS

Identification of a tyrosine switch in copper-haem nitrite reductases.

• DOI: 10.1107/s2052252518008242
• 发表时间: 2018-07-01
• 期刊: IUCrJ
• 影响因子: 3.9
• 作者: Dong J;Sasaki D;Eady RR;Antonyuk SV;Hasnain SS
• 通讯作者: Hasnain SS

Characterization of the quinol-dependent nitric oxide reductase from the pathogen Neisseria meningitidis, an electrogenic enzyme.

• DOI: 10.1038/s41598-018-21804-0
• 发表时间: 2018-02-26
• 期刊: Scientific reports
• 影响因子: 4.6
• 作者: Gonska N;Young D;Yuki R;Okamoto T;Hisano T;Antonyuk S;Hasnain SS;Muramoto K;Shiro Y;Tosha T;Ädelroth P
• 通讯作者: Ädelroth P