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Synthetic and Systems Biotechnology 2017年第3期2卷 208-218页

作者： Chun You Rui Huang Xinlei Wei Zhiguang Zhu Yi-Heng Percival Zhang Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences32 West 7th AvenueTianjin Airport Economic AreaTianjin300308People's Republic of China Biological Systems engineering Department Virginia Tech304 Seitz HallBlacksburgVA 24061USA

Two natural nicotinamide-based coenzymes(NAD and NADP)are indispensably required by the vast majority of oxidoreductases for catabolism and anabolism,*** NAD(P)-dependent oxidoreductases prefer one coenzyme as an electron acceptor or donor to the other depending on their different metabolic *** coenzyme preference associated with coenzyme imbalance presents some challenges for the construction of high-efficiency in vivo and in vitro synthetic biology *** the coenzyme preference of NAD(P)-dependent oxidoreductases is an important area of protein engineering,which is closely related to product-oriented synthetic biology *** review focuses on the methodology of nicotinamide-based coenzyme engineering,with its application in improving product yields and decreasing production *** nicotinamide-containing coenzymes have been proposed to replace natural coenzymes because they are more stable and less costly than natural *** advances in the switching of coenzyme preference from natural to biomimetic coenzymes are also covered in this *** coenzyme preferences from natural to biomimetic coenzymes has become an important direction for coenzyme engineering,especially for in vitro synthetic pathways and in vivo bioorthogonal redox pathways.

关键词： Coenzyme engineering Nicotinamide-based coenzymes NAD NADP protein engineering Synthetic biology Biomimetic coenzymes

Topology: a unique dimension in protein engineering

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Science China Chemistry 2018年第1期61卷 3-16页

作者： Lianjie Xu Wen-Bin Zhang Key Laboratory of Polymer Chemistry & Physics of Ministry of Education Center for Soft Matter Science and EngineeringCollege of Chemistry and Molecular Engineering Peking University

Controlling protein topology has been a long standing challenge to go beyond their linear configuration defined by the translation mechanism of cellular machinery. In this mini-review, we focus on the topological diversity in proteins and review the major categories of protein topologies known to date, including branched/star proteins, circular proteins, lasso proteins, knotted proteins, and protein catenanes. The discovery of these topologically complex natural proteins and their synthetic pathways, the rational design and recombinant synthesis of artificial topological proteins and their biophysical studies, are summarized and discussed with regard to their general features and broad implications. The complexity of protein topology is recognized and the routes to diverse protein topologies are illustrated. We believe that topology engineering is an important way to modify protein properties without altemating their native sequences and shall bring in valuable dynamic features central to the creation of artificial protein machinery.

关键词： protein topology protein engineering catenane rotaxane knot lasso peptide

Applications of protein engineering in the microbial synthesis of plant triterpenoids

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Synthetic and Systems Biotechnology 2023年第1期8卷 20-32页

作者： Yan Luo Yaozhu Jiang Linhao Chen Chun Li Ying Wang Key Laboratory of Medical Molecule Science and Pharmaceutics engineering Institute of Biochemical EngineeringSchool of Chemistry and Chemical EngineeringBeijing Institute of TechnologyBeijingChina Key Laboratory for Industrial Biocatalysis Ministry of EducationDepartment of Chemical EngineeringTsinghua UniversityBeijingChina

Triterpenoids are a class of natural products widely used in fields related to medicine and health due to their biological activities such as hepatoprotection,anti-inflammation,anti-viral,and *** the advancement in biotechnology,microorganisms have been used as cell factories to produce diverse natural *** the significant progress that has been made in the construction of microbial cell factories for the heterogeneous biosynthesis of triterpenoids,the industrial production of triterpenoids employing microorganisms has been stymied due to the shortage of efficient enzymes as well as the low expression and low catalytic activity of heterologous proteins in *** engineering has been demonstrated as an effective way for improving the specificity,catalytic activity,and stability of the enzyme,which can be employed to overcome these *** review summarizes the current progress in the studies of Oxidosqualene cyclases(OSCs),cytochrome P450s(P450s),and UDP-glycosyltransferases(UGTs),the key enzymes in the triterpenoids synthetic *** main obstacles restricting the efficient catalysis of these key enzymes are analyzed,the applications of protein engineering for the three key enzymes in the microbial synthesis of triterpenoids are systematically reviewed,and the challenges and prospects of protein engineering are also discussed.

关键词： Oxidosqualene cyclase Cytochrome P450 UDP-Glycosyltransferase Triterpenoids protein engineering

Enhanced chemoselectivity of a plant cytochrome P450 through protein engineering of surface and catalytic residues

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aBIOTECH 2021年第3期2卷 215-225页

作者： Xiaopeng Zhang Wei Luo Yinying Yao Xuming Luo Chao Han Yang Zhong Bo Zhang Dawei Li Lida Han Sanwen Huang Per Greisen Yi Shang Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518116China Yunnan Key Laboratory of Potato Biology The CAAS-YNNU-YINMORE Joint Academy of Potato SciencesYunnan Normal UniversityKunming 650500China National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research Huazhong Agricultural UniversityWuhan 430070China Biotechnology Research Institute Chinese Academy of Agricultural SciencesBeijing 100081China Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture Sino-Dutch Joint Lab of Horticultural GenomicsInstitute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijing 100081China Novo Nordisk Research Center Seattle Inc SeattleWA 98109USA

Cytochrome P450s(P450s)are the most versatile catalysts utilized by plants to produce structurally and functionally diverse *** the high degree of gene redundancy and challenge to functionally characterize plant P450s,protein engineering is used as a complementarystrategy to study the mechanisms of P450-mediated reactions,or to alter their *** previously proposed an approach of engineering plant P450s based on combining high accuracy homology models generated by Rosetta combined with data-driven design using evoluti onary information of these *** this strategy,we repurposed a multi-functional P450(CYP87D20)into a monooxygenase after red esigning its active *** most plant P450s are membrane-anchored proteins that are adapted to the micro-environments of plant cells,expressing them in heterologous hosts usually results in problems of expression or ***,we applied compu-tational design to tackle these issues by simultaneous optimization of the protein surface and active *** screening 17 variants,effective su bstitutions of surface residues were observed to improve both expression and activity of *** addition,the identified substitutions were additive and by com-bining them a highly eficient C11 hydroxylase of cucurbitadienol was created to participate in the mogrol *** study shows the importance of considering the interplay between surface and active site residues for P450 *** integrated strategy also opens an avenue to create more tai loring enzymes with desired functions for the metabolic engineering of high-valued compounds like mogrol,the precursor of natural sweetener mogrosides.

关键词： Plant cytochrome P450 protein engineering Rosetta Amino acid co-evolution Surface residue

Divergent protein engineering of Transaminase for the Synthesis of Chiral Rivastigmine and Apremilast Precursors

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Chinese Journal of Chemistry 2024年第19期42卷 2335-2340页

作者： Langyu Tang Xinjie Yang Ningning Sun Guojiao Wu Yuzhou Wu Fangrui Zhong Hubei engineering Research Center for Biomaterials and Medical Protective Materials Hubei Key Laboratory of Bioinorganic Chemistry&Materia MedicaSchool of Chemistry and Chemical EngineeringHuazhong University of Science and Technology1037 Luoyu RoadWuhanHubei 430074China Longgang Institute of Zhejiang Sci-Tech University WenzhouZhejiang 325802China Shenzhen Huazhong University of Science and Technology Research Institute ShenzhenGuangdong 518000China

Comprehensive Summary The implementation of divergent protein engineering on the natural transaminase Vf-ω-TA led to the development of two effective mutants(M2 and M8),enabling the enzymatic synthesis of chiral amine precursors of Rivastigmine and Apremilast,*** evolution of the enzymes was guided by crystal structures and a focused mutagenesis strategy,allowing them to effectively address the challenging ketone substrates with significant steric *** the optimized reaction parameters,transamination proceeded smoothly in good conversions and with perfect stereochemical control(>99%ee).These processes utilize inexpensiveα-methylbenzylamine as an amine donor and avoid the continuous acetone removal and costly LDH/GDH/NADH systems.

关键词： Asymmetric catalysis Chiral amine protein engineering Directed evolution Biocatalysis Transaminase Enantioselectivity Syntheticmethods Amination Enzymes

Recent advances in keratinase production via protein engineering,breeding,and fermentation

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Advanced Agrochem

Advanced Agrochem 2024年第3期3卷 188-196页

作者： Ali Raza Ishaq Zheng Zhang Penghui He Min Xiong Shouwen Chen State Key Laboratory of Biocatalysis and Enzyme engineering Environmental Microbial Technology Center of Hubei ProvinceCollege of Life SciencesHubei UniversityWuhan430062China

The gene editing and synthetic biological tools have led to the implementation of diverse metabolic engineering approaches to enhance the production of specific *** keratinases can convert keratin wastes into valuable compounds for *** the market for keratinases cannot be satisfied by production from wild hosts,it is obligatory to develop hosts with high keratinase *** intention of this review is to evaluate microbial keratinase advancement through protein engineering,breeding techniques,and fermentation *** main aim of protein engineering is to improve the heat resistance ability and catalytic activity of keratinases by employing mutagenesis ***,modifying the expression elements and host engineering are also two unique ways to augment the keratinase *** to accelerate the production of modified keratinase,this review attempts to highlight the optimization of expression elements,such as promoter engineering,UTR,signal peptide,and codon ***,the approaches of host engineering including strengthening precursor supply,membrane surface engineering,and optimization of secretion pathways were also explained ***,it is also essential to optimize the medium composition and fermentation condition for high keratinase *** review also addressed the present advancements,difficulties,and tendencies in the field of microbial keratinase production,along with its potential.

关键词： Keratinase protein engineering Expression elements Breeding Fermentation

protein engineering for natural product biosynthesis:expanding diversity for therapeutic applications

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Journal of Bio-X Research 2023年第2期6卷 49-60页

作者： Sarah Oluwatobi Otun Jordy Alexis Lerma-Escalera Khayalethu Ntushelo Ikechukwu Achilonu protein Structure-Function and Research Unit School of Molecular and Cell BiologyFaculty of ScienceUniversity of the WitwatersrandBraamfontein 2050JohannesburgSouth Africa Facultad de Ciencias Químicas Universidad Autónoma de Nuevo LeónSan Nicolás de los GarzaMexico Centro de Investigación en Biotecnología y Nanotecnología Facultad de Ciencias QuímicasParque de Investigación e Innovación TecnológicaUniversidad Autónoma de Nuevo LeónApodacaMexico Department of Agriculture and Animal Health University of South AfricaFlorida 1710South Africa

In this dispensation of the fourth industrial revolution,protein engineering has become a popular approach for increasing enzymatic activity,stability,and titer in the biosynthesis of natural *** is attributed to its numerous advantages(over direct isolation from plants or via chemical synthesis),including decreasing or eliminating reaction byproducts,high precision,moderate handling of intricate and chemically unstable chemicals,overall reusability,and cost ***,protein engineering tools have advanced to redesign and enhance natural product *** methods include direct evolution,substrate engineering,medium engineering,enzyme engineering and immobilization,structure-assisted protein engineering,and advanced *** successes in implementing these emerging protein engineering technologies were critically discussed in this ***,the advantages,limitations,and applications in industrial and medical biotechnology were ***,future research directions and potential were also highlighted.

关键词： antibodies engineering industrial enzymes natural product biosynthesis protein engineering polyketides synthetic biology

protein engineering of arginine deiminase for anti-tumor application

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Protein engineering of arginine deiminase for anti-tumor app...

Switch of substrate specificity of hyperthermophilic acylaminoacyl peptidase by combination of protein and solvent engineering

第十一届中国酶工程学术研讨会

作者：朱蕾蕾 Tianjin Institute of Industrial Biotechnology

Arginine deiminase(ADI) catalyzes the hydrolysis of L-arginine to form citrulline and *** an anti-tumor enzyme,ADI is being used to treat arginine auxotrophic tumors by depleting the arginine in blood ***,ADI’s application as anti-cancer drug is hampered by its low activity towards arginine under physiological conditions,mainly due to its low activity at physiologic concentration of arginine(0.10-0.12 mM).protein engineering was performed to boost activity of PpADI(ADI from Pseudomonas plecoglossicida) at physiological conditions(pH 7.4,120 μM Arg and37℃).Two screening systems in microtiter plate format(based on citrulline detectionand ammonia detection) for improving the overall activity and flow cytometer format based on a ligand-mediated eGFP-expression system for improving activity at physiological arginine concentration were successfully *** several rounds of protein engineering,we successful shifted pH optimum(by 0.5 unit) ,improved thermostability(by 7℃ in T value) and reduced K value(by 7-fold).The final PpADI variant M31 showed a 7-fold reduced S value(0.17 mM compared to 1.23 mM(WT)) and dramatically increased activity at physiological arginine concentration(M31:6.14 s;WT:not detectable).Moreover,M31 showed a significant reduced IC value(by 224-fold) and effective inhibitory effect against melanoma cell lines(IC = 0.02 μg/mL for SK-MEL-28 and G361).Furthermore,structure-function relationship of the improved variants were also ***,our work showed that protein engineering is a powerful tool for reengineering therapeutic enzymes and can benefit the development of therapeutic enzymes significantly.

关键词： Key-words arginine deiminase protein engineering directed evolution high-throughput screening

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protein & Cell 2011年第6期2卷 497-506页

作者： Chang Liu Guangyu Yang Lie Wu Guohe Tian Zuoming Zhang Yan Feng State Key Laboratory of Microbial Metabolism School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai 200240China Key Laboratory for Molecular Enzymology and engineering of Ministry of Education Jilin UniversityChangchun 130023China Changchun Institute of Biological Products China National Biotec GroupChangchun 130061China

The inherent evolvability of promiscuous enzymes endows them with great potential to be artificially evolved for novel ***,we succeeded in transforming a promiscuous acylaminoacyl peptidase(apAAP)from the hyperthermophilic archaeon Aeropyrum pernix K1 into a specific carboxylesterase by making a single *** order to fulfill the urgent requirement of thermostable lipolytic enzymes,in this paper we describe how the substrate preference of apAAP can be further changed from p-nitrophenyl caprylate(pNP-C8)to p-nitrophenyl laurate(pNP-C12)by protein and solvent *** one round of directed evolution and subsequent saturation mutagenesis at selected residues in the active site,three variants with enhanced activity towards pNP-C12 were ***,a combined mutant W474V/F488G/R526V/T560W was generated,which had the highest catalytic efficiency(kcat/Km)for pNP-C12,about 71-fold higher than the wild *** activity was further increased by solvent engineering,resulting in an activity enhancement of 280-fold compared with the wild type in the presence of 30%*** structural basis for the improved activity was studied by substrate docking and molecular dynamics *** was revealed that W474V and F488G mutations caused a significant change in the geometry of the active center,which may facilitate binding and subsequent hydrolysis of bulky *** conclusion,the combination of protein and solvent engineering may be an effective approach to improve the activities of promiscuous enzymes and could be used to create naturally rare hyperthermophilic enzymes.

关键词： acylaminoacyl peptidase esterase substrate specificity protein engineering solvent engineering

engineering and finetuning expression of SerC for balanced metabolic flux in vitamin B6 production

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Synthetic and Systems Biotechnology 2024年第2期9卷 388-398页

作者： Kai Chen Linxia Liu Jinlong Li Zhizhong Tian Hongxing Jin Dawei Zhang School of Chemical engineering and Technology Hebei University of TechnologyTianjinChina Tianjin Institute of Industrial Biotechnology Chinese Academy of SciencesTianjinChina National Center of Technology Innovation for Synthetic Biology TianjinChina Key Laboratory of engineering Biology for Low-Carbon Manufacturing Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjinChina University of Chinese Academy of Sciences BeijingChina

Vitamin B6 plays a crucial role in cellular metabolism and stress response,making it an essential component for growth in all known ***,achieving efficient biosynthesis of vitamin B6 faces the challenge of maintaining a balanced distribution of metabolic flux between growth and *** this study,our focus is on addressing this challenge through the engineering of phosphoserine aminotransferase(SerC)to resolve its redundancy and *** enzyme SerC was semi-designed and screened based on sequences and predicted kcat values,*** and heterologous proteins showing potential were then fine-tuned to optimize the production of vitamin *** resulting strain enhances the production of vitamin B6,indicating that different fluxes are distributed to the biosynthesis pathway of serine and vitamin *** study presents a promising strategy to address the challenge posed by multifunctional enzymes,with significant implications for enhancing biochemical production through engineering processes.

关键词： Vitamin B6 Phosphoserine aminotransferase SerC protein engineering Multifunctional enzymes Metabolic flux distribution