CO2还原用甲酸脱氢酶分子改造的研究进展

doi:10.13560/j.cnki.biotech.bull.1985.2024-1038

生物技术通报 ›› 2025, Vol. 41 ›› Issue (3): 14-24.doi: 10.13560/j.cnki.biotech.bull.1985.2024-1038

CO₂还原用甲酸脱氢酶分子改造的研究进展

陆峰¹(), 黄玉红², 林燕娜³, 马富强¹()

^1.中国科学院苏州生物医学工程技术研究所中国科学院生物医学检验技术重点实验室医药酶工程研究中心，苏州 215163
^2.中国科学院过程工程研究所离子液体清洁过程北京市重点实验室，北京 100190
^3.威海先进医用材料与高端医疗器械山东省实验室，威海 264210

收稿日期:2024-10-24 出版日期:2025-03-26 发布日期:2025-03-20
通讯作者: 马富强，男，博士，研究员，研究方向：医药酶工程；E-mail: mafuqiang318@sibet.ac.cn
作者简介:陆峰，男，博士，助理研究员，研究方向：医药酶工程；E-mail: luf@sibet.ac.cn
基金资助:
国家重点研发计划(2021YFC2104200);江苏省自然科学基金青年基金项目(BK20240408);中国博士后科学基金面上资助项目(2024M762324);江苏省卓越博士后计划资助项目(2024ZB492);中国科学院青年创新促进会(2022327);山东省实验室项目(SYS202209)

Advances on Molecular Modifications of Formate Dehydrogenase for CO₂ Reduction

LU Feng¹(), HUANG Yu-hong², LIN Yan-na³, MA Fu-qiang¹()

^1.Medical Enzyme Engineering Center, CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163
^2.Beijing Key Laboratory of Ionic Liquids Clean Process, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190
^3.Shandong Lab of Advanced Biomaterials and Medical Devices in Weihai, Weihai 264210

Received:2024-10-24 Published:2025-03-26 Online:2025-03-20

摘要/Abstract

摘要：

随着全球对可持续能源转型和温室气体减排的迫切需求，CO₂的高效绿色转化成为能源、环境科学以及化学工程等多个领域的研究热点。特别是在应对气候变化的背景下，CO₂的捕集和利用被视为实现碳中和的重要途径之一。甲酸脱氢酶（FDH）作为将CO₂还原为甲酸盐的重要生物催化剂，在绿色化学和生物能源转化中展现出巨大的应用潜力，然而其催化活性、热稳定性和辅酶特异性等方面仍存在一定局限性。近年来，随着蛋白质工程技术和分子生物学的不断发展，研究者们提出了多种改造FDH性能的策略，使得FDH的应用前景得到极大提升。例如通过定向突变、结构优化等酶工程手段提高酶的底物亲和力，增强酶的刚性和构象稳定性以及改变辅酶结合位点，拓宽其在绿色转化过程中的应用前景。本文将对近年来FDH催化CO₂还原的研究进展进行全面总结，着重分析FDH在催化效率、热稳定性、辅酶特异性等方面的改进措施，探讨分子改造过程中所采取的具体策略，并总结这些策略的规律，以期为未来FDH的分子改造提供新的思路和方法，推动其在CO₂还原反应中的应用发展。此外，随着人工智能、机器学习和基因编辑等技术的发展，未来FDH的分子改造将更加高效和精确，这些新兴技术有望在较短的时间内筛选出具有优异性能的FDH突变体，为其在解决全球气候变化和能源危机方面提供可行的绿色解决方案。

关键词: CO₂还原, 甲酸脱氢酶, 分子改造, 催化效率, 热稳定性, 辅因子特异性, 甲酸盐, NAD⁺/NADH

Abstract:

With the urgent global demand for sustainable energy transformation and greenhouse gas emission reduction, the efficient green conversion of CO₂ has become a research hotspot in various fields such as energy, environmental science, and chemical engineering. Especially in the context of combating climate change, CO₂ capture and utilization is seen as one of the key strategies to achieve carbon neutrality. Formate dehydrogenase (FDH) as an important biocatalyst for reducing CO₂ to formate, has shown significant potential in green chemistry and bioenergy conversion. However, it still has certain limitations regarding catalytic activity, thermal stability, and coenzyme specificity. In recent years, with the continuous development of protein engineering technology and molecular biology, researchers have proposed a variety of strategies to modify the performance of FDH, significantly enhancing its application prospects. For example, enzyme engineering means such as directed mutation and structure optimization can improve the substrate affinity of the enzyme, enhance the rigidity and conformational stability of the enzyme, and change the coenzyme binding site to broaden its application prospects in the process of green transformation. In this paper, the research progress of FDH catalytic CO₂ reduction in recent years will be comprehensively summarized, focusing on the improvement measures of FDH in terms of catalytic efficiency, thermal stability, coenzyme specificity, etc., the specific strategies adopted in the molecular transformation process will be discussed, and the rules of these strategies will be summarized, in order to provide new ideas and methods for the molecular transformation of FDH in the future and promote the development of its application in CO₂ reduction reaction. In addition, with the development of artificial intelligence, machine learning, gene editing and other technologies, the molecular modification of FDH will be more efficient and precise in the future, and these emerging technologies are expected to screen out FDH mutants with excellent performance in a short time, providing a feasible green solution in solving the global climate change and energy crisis.

Key words: CO? reduction, formate dehydrogenase, molecular modification, catalytic efficiency, thermal stability, cofactor specificity, formate, NAD?/NADH

陆峰, 黄玉红, 林燕娜, 马富强. CO₂还原用甲酸脱氢酶分子改造的研究进展[J]. 生物技术通报, 2025, 41(3): 14-24.

LU Feng, HUANG Yu-hong, LIN Yan-na, MA Fu-qiang. Advances on Molecular Modifications of Formate Dehydrogenase for CO₂ Reduction[J]. Biotechnology Bulletin, 2025, 41(3): 14-24.

图/表 6

图1 多酶级联催化CO2合成甲醇流程图FDH：甲酸脱氢酶；FaldDH：甲醛脱氢酶；ADH：醇脱氢酶；NADH：还原型烟酰胺腺嘌呤二核苷酸；NAD+：氧化型烟酰胺腺嘌呤二核苷酸；W/Mo：钨/钼

Fig. 1 Flowchart of multi-enzyme cascade catalysis for CO2 to methanol synthesisFDH: Formate dehydrogenase; FaldDH: formaldehyde dehydrogenase; ADH: alcohol dehydrogenase; NADH: reduced nicotinamide adenine dinucleotide; NAD+: oxidized nicotinamide adenine dinucleotide; W/Mo: tungsten/molybdenum

表1 CO2还原用FDH的种类及其动力学参数

Table 1 Types and kinetic parameters of FDH for CO2 reduction

类型 Types	物种 Species	FDH	分子量 Mw /kD	k_cat /（s^-1）	K_M /（mmol·L^-1）	k_cat/K_M / （mmol·L^-1·s^-1）	参考文献 Reference
NAD⁺依赖型FDH	Candida boidinii	CbFDH	41.0	0.015 0	31.3	0.000 400	［20］
	Thiobacillus sp. KNK65MA	TsFDH	45.0	0.318	9.23	0.034 0	［20］
	Thermochaetoides thermophila DSM 1495	CtFDH	45.0	0.023 0	0.320	0.069 0	［21］
	Candida methylica	CmFDH	42.0	0.008 00	0.780	0.010 0	［21］
	Thermothelomyces thermophilus ATCC 42464	MtFDH	42.0	0.100	0.400	0.250	［22］
	Paracoccus sp. MKU1	PsFDH	44.0	0.073 0	0.928	0.079 0	［23］
金属依赖型FDH	Desulfovibrio desulfuricans	DdFDH	135	46.6	0.015 7	2.97×10³	［24］
	Desulfovibrio vulgaris Hildenborough	DvFdhAB	97.4	315	0.420	750	［25］
	Cupriavidus necator	FdsABG	178	11.0	2.70	4.07	［26］
	Acetobacterium woodii	FdhF1/2	169	372	3.80	97.9	［27］
	Escherichia coli	EcFDH-H	79.0	1.00	8.30	0.120	［28］
	Clostridium Ijungdahlii	ClFDH	80.0	0.012 0	7.27	0.001 65	［29］
	Clostridium ljungdahlii	ClFDH	75.0	5.66	66.2	0.085 5	［30］
	Clostridium autoethanogenum	CaFDH	75.0	4.00	23.2	0.170	［31］
	Clostridium coskatii	CcFDH	75.0	5.62	59.7	0.094 0	［31］
	Clostridium ragsdalei	CrFDH	75.0	3.28	31.2	0.110	［31］
	Clostridium carboxidivorans P7T	FDH_H_CloCa	80.7	0.080 0	0.050 0	1.60	［32］
	Pseudomonas oxalaticus	Formate Dehydrogenase	315	3.00	40.0	0.075 0	［33-34］
	Desulfosporosinus acididurans	DaFDH	93.0	4.09	34.9	0.117	［18］
	Paraclostridium bifermentans	PbFDH	93.0	4.45	30.6	0.145	［18］
	Clostridium scatologenes	CsFDH	79.0	1.55	48.9	0.031 7	［18］

图2 CbFDH的结构及催化机制A：CbFDH三维结构（PDB：6D4C），红色和绿色分别为同源二聚体，橙色为NAD+；B：CbFDH的活性中心及与NAD+相近的氨基酸残基；C：NAD+依赖型FDH甲酸氧化（绿色）或CO2还原（粉色）的作用机制

Fig. 2 Structure and catalytic mechanism of CbFDHA: Three-dimensional structure of CbFDH (PDB: 6D4C). The two dimers are colored in red and green, while the NAD+ cofactor is colored in orange. B: Active center of CbFDH and amino acid residues closed to NAD+. C: Mechanism of action of NAD+-dependent FDH for formate oxidation (green arrows) or CO2 reduction (inverse sense, pink arrows)

图3 大肠杆菌FDH N的三维结构及辅因子示意图A：大肠杆菌FDH N的三维结构（PDB：1KQF）；3个多肽链分别用蓝色（链A）、粉色（链B）和绿色（链C）表示；钼喋呤（A链）、5个［4Fe-4S］簇（A链和B链）和2个血红素（C链）分别显示为粉色、绿色和红色； B：大肠杆菌FDH N中钼辅因子的图示及其化学式结构

Fig. 3 Three-dimensional structure and cofactor diagram of E. coli FDH NA: Three-dimensional structure of Escherichia coli FDH N (PDB: 1KQF). The three polypeptide chains are indicated by blue (chain A), pink (chain B) and green (chain C). The molybdopterin (in chain A), the five [4Fe-4S] clusters (in chain A and chain B) and the two heme (chain C) are displayed in pink, green and red, respectively. B: Graphic of the molybdenum cofactor and its chemical formula structure in E. coli FDH N

图4 金属依赖型FDH还原CO2成甲酸的可能机理A：FDH带正电的精氨酸残基静电捕获CO2； B：与金属Mo/W结合的硫醇氢攻击被精氨酸残基捕获的CO2，价态由四价氧化为六价；C：金属Mo/W在接受质子电子和释放甲酸的作用下，价态由六价又还原为四价，恢复初始状态

Fig. 4 Feasible mechanism of CO2 reduction to formic acid with metal-dependent FDHA: CO2 is electrostatically captured by positively charged arginine residues of FDH. B: Hydrogen mercaptan bound to metal Mo/W attacks CO2 captured by arginine residues, and the valence state is oxidized from four to six. C: Under the action of accepting proton electrons and releasing formic acid, the valence state of metal Mo/W is reduced from six to four, and the initial state is restored

图5 分子改造提升FDH的催化活性、热稳定性以及辅酶偏好性示意图

Fig. 5 Schematic diagram of catalytic activity, thermal stability and coenzyme preference of FDH enhanced by molecular modification

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CO₂还原用甲酸脱氢酶分子改造的研究进展

Advances on Molecular Modifications of Formate Dehydrogenase for CO₂ Reduction

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