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，构成了蛋白质界的很大一部分。金属蛋白本身约占基因组的 30%。它们含有作为单个原子或簇的一部分的金属离子，并在微生物、植物和动物界中发挥多种维持生命的作用。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、分子氧结合、储存和活化、底物运输和催化。在许多金属酶中，例如细胞色素 C 氧化酶（通过呼吸需求对哺乳动物的生命至关重要）、固氮酶和亚硝酸还原酶（鉴于它们在氮循环中的中心位置而至关重要）、氢化酶（氢分子的产生者 - 未来替代能源的候选者），催化作用涉及将电子和质子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（一种比二氧化碳强约 300 倍的臭氧消耗和温室气体）对全球变暖做出越来越大的贡献。当前的提案建立在申请人之间的密切合作的基础上，他们共同在反硝化领域做出了重大贡献，并在我们对金属酶生物机制所涉及的复杂过程的理解方面取得了重大进展。我们的综合方法使我们处于非常有利的地位，可以开展综合结构机械计划，该计划旨在解决在全球重要的生物系统中的生物反应中，与瞬时蛋白质复合物相比，大自然是否利用束缚域来增强催化作用的问题。我们专注于含铜亚硝酸还原酶 (CuNiR) - 利用它们的自然相遇（自由扩散）和束缚复合物 - 来学习构建最佳配置和集成氧化还原装置的自然设计规则。我们将阐明定义催化效率并使长程电子运动与活性位点氧化还原化学耦合的设计原理。这需要了解协调的蛋白质运动如何影响（i）长程电子转移机制，（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。将出现一般设计原则，指导合成生物学生物氧化还原装置的预测工程。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阻色谱-小角度 X 射线散射与动态光散射 （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，并使英国在这一重要领域处于全球领先地位。

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