Discovery and characterisation of new enzymes for hydrogen production and green chemistry

使用氢作为可持续燃料和能源载体需要解决几个技术挑战，包括实施可再生资源的清洁和高效生产技术。在自然界中，H2是由几种微生物通过氢化酶产生的，氢化酶是一组复杂的金属酶，催化H2代谢中的关键反应。在三种不同的氢化酶中，[FeFe]-氢化酶在生理H2产生中至关重要。因此，它们因可能的生物技术应用而受到广泛关注。例如，[FeFe]-氢化酶已经被工程化并在合适的细胞底盘中过表达，分别用于从废生物质或水的黑暗和光驱动的H2生产。此外，纯化的[FeFe]-氢化酶已被固定在半导体纳米颗粒上，并用于将太阳能直接储存为H2。限制[FeFe]-氢化酶更广泛开发的主要因素之一是它们对大气氧的敏感性：O2是一种强有力的抑制剂，并且抑制作用通常是不可逆的，但最近报道了一些O2稳定的[FeFe]-氢化酶的例子。鉴定具有改进性能的新型[FeFe]-氢化酶（例如，更快的周转率和/或更高的稳定性）对于在工业过程中利用它们将是至关重要的。目前，实际开发受到阻碍的事实，只有少数这些酶已经详细的实验特征，这限制了“目录”的酶可用于任何给定的应用。2）显著扩大可用于H2生产技术的酶的工具箱; 3）探索[FeFe]-氢化酶在绿色化学过程中的任何非常规反应性。在项目的初始阶段，学生将利用生物资讯学工具，透过序列研究及建立结构模型，以电脑模拟方式鉴定新型[FeFe]-氢化酶。这一阶段的目标是鉴定具有非常规特征的基因，这些特征可能对酶的性能产生积极影响，例如存在额外的酶亚基或可能影响催化作用的特定残基。随后，在轮换项目期间获得的专业知识的基础上，学生将进入湿实验室并选择最佳靶标（通过选择的基因的克隆、重组过表达和纯化）。将使用已建立的体内（通过天然/异源HydEFG成熟系统）或体外（通过预制的合成辅因子2FeMIM）掺入催化簇的方法。新酶将表征其比活性（H2产生和H2氧化的反应速率）和稳定性（特别是对温度、溶剂和O2）。还将与外部合作伙伴Stephen卡尔博士合作进行生物物理表征，包括光谱学、晶体学和X射线衍射还将测试新酶还原/氧化有用辅因子的能力，如NAD（P）+/NAD（P）H，或非天然底物，其可以突出这些酶在绿色化学过程中的工业开发的新视野。蛋白质工程方法将被认为是改善性能和/或重新定向对人工底物的反应。

Using hydrogen as a sustainable fuel and energy carrier requires tackling several technical challenges, including the implementation of clean and efficient production technologies from renewable resources. H2 is produced in nature by several microorganisms that rely on hydrogenases, a vast group of complex metallo-enzymes that catalyse the key reaction in H2 metabolism.Between the three phylogenetically distinct classes of hydrogenases, [FeFe]-hydrogenases are crucial in physiological H2 production. Consequently, they received extensive attention for possible biotechnological applications. For example, [FeFe]-hydrogenases have been engineered and overexpressed in suitable cellular chassis for both dark and light-driven H2 production from waste biomass or water, respectively. Moreover, purified [FeFe]-hydrogenases have been immobilised on semiconductor nanoparticles and utilised to direct storage of solar energy into H2.One of the main factors limiting a broader exploitation of [FeFe]-hydrogenases is their sensitivity to atmospheric oxygen: O2 is a powerful inhibitor and inhibition is usually irreversible, but some examples of O2-stable [FeFe]-hydrogenases have recently been reported.Identifying novel [FeFe]-hydrogenases with improved performances (for example, faster turnover rates and/or higher stability) will be crucial to exploit them in industrial processes. Currently, practical exploitation is hindered by the fact that only a small number of these enzymes have been experimentally characterised in detail, and this limits the "catalogue" of enzymes available for any given application.The core aims of this PhD project are: 1) to provide a more comprehensive view of the diversity of [FeFe]-hydrogenases; 2) to significantly expand the toolbox of available enzymes to be exploited for H2 production technologies; 3) to explore any unconventional reactivity of [FeFe]-hydrogenases to be exploited in green chemistry processes.In the initial phase of the project, the student will use bioinformatics tools to identify novel [FeFe]-hydrogenases in silico, by performing sequence studies and building structural models. This phase will aim at identifying genes with unconventional features that could positively influence the enzyme performances, such as the presence of additional enzyme subunits or specific residues that may allegedly influence catalysis.Subsequently, building on the expertise acquired during the rotation project, the student will move to the wet lab and produce a selection of the best targets (via cloning of the selected genes, recombinant overexpression and purification). Established methods to incorporate the catalytic cluster in vivo (via the native/heterologous HydEFG maturation system) or in vitro (via the pre-made synthetic cofactor 2FeMIM) will be used.The new enzymes will be characterised for their specific activity (reaction rate for H2 production and H2 oxidation) and for their stability (particularly towards temperature, solvents and O2). Biophysical characterisation will also be performed including spectroscopy, crystallography, and X-ray diffraction in collaboration with an external partner, Dr Stephen Carr (Research Complex at Harwell).The new enzyme(s) will also be tested for the ability to reduce/oxidise useful cofactors, such as NAD(P)+/NAD(P)H, or unnatural substrates that can highlight new horizons in the industrial exploitation of these enzymes within green chemistry processes. Protein engineering approaches will be considered to improve the performances and/or to redirect the reactivity towards artificial substrates.