Article
Biochemistry & Molecular Biology
Yawen Zhou, Linshu Jiao, Juan Shen, Huibing Chi, Zhaoxin Lu, Huawei Liu, Fengxia Lu, Ping Zhu
Summary: In this study, smart libraries were constructed using semi-rational design to improve the catalytic activity of type II L-asparaginase from Bacillus licheniformis. Mutants with significantly enhanced catalytic efficiency were obtained through saturation mutations and combinatorial mutations. The quintuple mutant ILRAC showed the highest specific activity and k(cat)/K-m, and also exhibited improved pH stability and thermal stability. Structural alignment and molecular dynamic simulation revealed that the stability and substrate binding of ILRAC contributed to its enhanced thermal stability and enzymatic activity. This study presents a novel semi-rational approach to enhance the enzymatic activity of type II L-asparaginase and provides insights for industrial applications.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Licheng Zhou, Qing Meng, Ran Zhang, Bo Jiang, Qun Wu, Jingjing Chen, Tao Zhang
Summary: In this study, a comprehensive strategy was proposed to improve the thermostability of alginate lyase with strict substrate specificity. Through sequence-based and structure-based analysis, as well as computer-aided Delta Delta Gfold value calculation, four point mutations were selected and combined to generate a mutant with increased thermostability and retained enzyme activity.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Agricultural Engineering
Kyoungseon Min, Hoyong Kim, Hyun June Park, Siseon Lee, Ye Jean Jung, Ji Hyun Yoon, Jin-Suk Lee, Kyoungmoon Park, Young Je Yoo, Jeong Chan Joo
Summary: In this study, the catalytic performance of Bacillus circulans xylanase (Bcx) was enhanced through rational design, resulting in the engineered mutant R49N with improved catalytic efficiency, conformational stability, and production of xylose oligomers. This approach can be applied to enhance the catalytic performance of industrially important enzymes by controlling flexibility.
BIORESOURCE TECHNOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Zhangliang Zhu, Lei Li, Wei Zhang, Chao Li, Shuhong Mao, Fuping Lu, Hui-Min Qin
Summary: The study identified a putative D-allulose 3-epimerase from a thermophilic organism and found that mutagenesis improved its catalytic efficiency towards D-fructose, showing potential as an industrial biocatalyst for D-allulose production.
ENZYME AND MICROBIAL TECHNOLOGY
(2021)
Article
Agriculture, Multidisciplinary
Shuping Xu, Pu Zheng, Ping Sun, Pengcheng Chen, Dan Wu
Summary: In this study, the flavin-dependent two-component monooxygenase was used to convert phloretin into 3-hydroxyphloretin. Rational design of the substrate pocket and loop of the enzyme led to the identification of a mutant with improved yield and catalytic efficiency. Molecular docking and dynamics simulations provided insights into the mechanism behind the increased product yield.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Chemistry, Physical
Xiaowen Wu, Yingying Jiang, Zengyu Wang, Xiaobin Yu, Zhoutong Sun, Wei Luo
Summary: This study improved the thermal stability of a formate dehydrogenase from Lodderomyces elongisporus through semi-rational design, resulting in a mutant with enhanced thermal stability and unchanged specific activity. The mutant exhibited good stability in alkaline environment and improved operational stability in catalytic reactions.
MOLECULAR CATALYSIS
(2022)
Article
Biotechnology & Applied Microbiology
Guangqi Li, Xuan Zhou, Zhihong Li, Yunpeng Liu, Dongyang Liu, Youzhi Miao, Qun Wan, Ruifu Zhang
Summary: This study characterized and engineered a thermophilic GH10 family xylanase XynAF1 to improve its thermostability, resulting in a 6-fold increase in stability through rational design and saturation mutagenesis. The high-resolution X-ray crystallographic structure of XynAF1 revealed a rigid skeleton contributing to its hyperthermophilic characteristics. The study provides a promising biocatalyst for high-temperature biotechnological applications.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Krit Charupanit, Varomyalin Tipmanee, Thana Sutthibutpong, Praopim Limsakul
Summary: This study utilized computational methods to construct the protein sequence space of PETase-PET binding energy and identified mutation sites and appropriate side-chain properties that could enhance PETase activity. Molecular dynamics simulations revealed that PETase variants with S238C or Q119F may improve PETase efficiency. The findings have important implications for protein engineering and PETase improvement.
Article
Agricultural Engineering
Juanjuan Ding, Shengping You, Jiaxing Zhang, Hongtao Zhang, Hui Wang, Wei Zhang, Wei Qi, Rongxin Su, Zhimin He
Summary: The study focused on the structural characteristics and catalytic mechanism of 17β-hydroxysteroid dehydrogenase type 3 (17β-HSD3), aiming to improve its catalytic activity for the production of testosterone (TS) through rational design strategy. By regulating the hydrophobicity and polarity of key residues, a new variant G186R/Y195W was created, increasing its binding affinity with the substrate and leading to a significant enhancement in testosterone production. The combination of structural and mechanism analysis enabled the successful implementation of rational design strategy for enhancing TS bioproduction catalyzed by 17β-HSD3.
BIORESOURCE TECHNOLOGY
(2021)
Article
Agriculture, Multidisciplinary
Jing Guo, Yi Wang, Xuan Zhang, Wenjun Gao, Zhiqiang Cai, Tingting Hong, Zaiwei Man, Qing Qing
Summary: Saturation mutagenesis on BsCsn46A revealed the importance of Pro121 in chitosanase activity, showing that replacing proline in the helix structure can significantly improve enzyme specific activity and affinity.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2021)
Article
Biochemical Research Methods
Ekin Kestevur Dogru, Gulce Guralp, Arzu Uyar, Nur Basak Surmeli
Summary: Steroid-based chemicals have widespread application in the pharmaceutical industry due to their effects on metabolism, immune functions, and sexual characteristics. This study focused on CYP119 mutants and found that the L69G mutant showed significantly increased affinity for progesterone and also catalyzed progesterone hydroxylation. The designed enzyme L69G CYP119 has the potential to be a versatile biocatalyst for progesterone hydroxylation under industrial production conditions.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2023)
Article
Engineering, Multidisciplinary
Xue Cai, Jiang-Wei Shen, Yu Qiang, Jing Hua, Zhang-Qi Ma, Zhi-Qiang Liu, Yu-Guo Zheng
Summary: Through design and engineering of the lipase from Sporisorium reilianum (SRL), an enhanced variant V13 was obtained, which showed high activity towards cis-(+/−)-dimethyl 1-acetylpiperidine-2,3-dicarboxylate. This study provides a general strategy for enhancing enzyme activity in other lipases and enzymes with a lid moiety.
Article
Chemistry, Medicinal
Veronica A. Jimenez, Karen R. Navarrete, Mario Duque-Norena, Kelly P. Marrugo, Maria A. Contreras, Cristian H. Campos, Joel B. Alderete
Summary: In this study, two novel glycomimetic peptides targeting E-selectin were discovered through mutations of a reference selectin-binding peptide, and their binding potential was evaluated using molecular dynamics simulations. By modifying the peptides with cysteine residues, improved E-selectin binding capabilities were achieved. Experimental validation confirmed the E-selectin binding capacity of CIEELQAR and CIELFQAR as peptides with high recognition capacity.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Biochemistry & Molecular Biology
Agnieszka M. Wojtkiewicz, Michal Glanowski, Piotr Waligorski, Tomasz Janeczko, Maciej Szaleniec
Summary: Bacteria and fungi possess enzymes called 3-ketosteroid-Delta(1)-dehydrogenases (KstDs) that are able to metabolize steroids. In this study, we focused on the KstD enzyme AcmB from Sterolibacterium denitrificans Chol-1 and compared its pH optima for hydrogenation and dehydrogenation to that of KstD from Nocardia corallina. We also investigated the enantiospecificity of AcmB and observed the introduction of a third deuteron into the steroid core.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Yihao Li, Dan Meng, Jiali Xie, Ruoyu Li, Zifan Wang, Jinlong Li, Lin Mou, Xinhao Deng, Ping Deng
Summary: JAK3 is a promising target for autoimmune disease treatment, but its selective targeting is challenging due to high homology with other JAK family members. This study designed a series of 1,7-dihydro-dipyrrolo [2,3-b:3 ',2 '-e] pyridine derivatives using the backbone growth method and identified 14 JAK3 inhibitors. Molecular dynamics simulations confirmed the structural stability of these inhibitors. Analysis showed that binding efficiency was achieved mainly through electrostatic and VDW interactions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
Shuhong Mao, Qianqian Guo, Panpan Xu, Dengke Gao, Xiaotao Cheng, Menglu Zhu, Dengyue Sun, Zhangliang Zhu, Fuping Lu, Hui-Min Qin
JOURNAL OF CHEMICAL TECHNOLOGY AND BIOTECHNOLOGY
(2019)
Article
Biotechnology & Applied Microbiology
Zhangliang Zhu, Dengke Gao, Chao Li, Ying Chen, Menglu Zhu, Xin Liu, Masaru Tanokura, Hui-Min Qin, Fuping Lu
MICROBIAL CELL FACTORIES
(2019)
Article
Biochemistry & Molecular Biology
Hui-Min Qin, Dengke Gao, Menglu Zhu, Chao Li, Zhangliang Zhu, Hongbin Wang, Weidong Liu, Masaru Tanokura, Fuping Lu
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2020)
Article
Agriculture, Multidisciplinary
Dengyue Sun, Xin Liu, Menglu Zhu, Ying Chen, Chao Li, Xiaotao Cheng, Zhangliang Zhu, Fuping Lu, Hui-Min Qin
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2019)
Article
Biotechnology & Applied Microbiology
Shuhong Mao, Xiaotao Cheng, Zhangliang Zhu, Ying Chen, Chao Li, Menglu Zhu, Xin Liu, Fuping Lu, Hui-Min Qin
ENZYME AND MICROBIAL TECHNOLOGY
(2020)
Article
Agriculture, Multidisciplinary
Chao Li, Mian Wu, Xin Gao, Zhangliang Zhu, Yu Li, Fuping Lu, Hui-Min Qin
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2020)
Article
Agricultural Engineering
Shuhong Mao, Xin Liu, Xin Gao, Zhangliang Zhu, Dengyue Sun, Fuping Lu, Hui-Min Qin
BIORESOURCE TECHNOLOGY
(2020)
Article
Chemistry, Physical
Fenghua Wang, Menglu Zhu, Zhan Song, Chao Li, Yuying Wang, Zhangliang Zhu, Dengyue Sun, Fuping Lu, Hui-Min Qin
Article
Biotechnology & Applied Microbiology
Zhangliang Zhu, Lei Li, Wei Zhang, Chao Li, Shuhong Mao, Fuping Lu, Hui-Min Qin
Summary: The study identified a putative D-allulose 3-epimerase from a thermophilic organism and found that mutagenesis improved its catalytic efficiency towards D-fructose, showing potential as an industrial biocatalyst for D-allulose production.
ENZYME AND MICROBIAL TECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Yingyu Zhou, Wanyi Qiu, Yimei Wang, Rong Wang, Tomohiro Takano, Xuyang Li, Zhangliang Zhu, Haruyo Nakajima-Adachi, Masaru Tanokura, Satoshi Hachimura, Takuya Miyakawa
Summary: This study demonstrated that beta-elemene has effects on recovering metabolic changes in the brains of obese mice induced by a high-fat diet, as well as partially reversing the changes in gut bacteria composition and content. Predictions revealed potential interactions between different brain regions' metabolites and gut microbiota.
Article
Biology
Yingyu Zhou, Tomohiro Takano, Xuyang Li, Yimei Wang, Rong Wang, Zhangliang Zhu, Masaru Tanokura, Takuya Miyakawa, Satoshi Hachimura
Summary: Beta-elemene regulates the balance of proinflammatory cytokines in mouse white adipose tissue through MAPK signaling, affecting the imbalance of M1-M2 macrophages and inhibiting the phosphorylation of MAPK pathways. These results suggest that beta-elemene may be a potential therapeutic medicine for macrophage-mediated chronic diseases.
COMMUNICATIONS BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Chao Li, Xin Gao, Hongbin Qi, Wei Zhang, Lei Li, Cancan Wei, Meijing Wei, Xiaoxuan Sun, Shusen Wang, Liyan Wang, Yingbin Ji, Shuhong Mao, Zhangliang Zhu, Masaru Tanokura, Fuping Lu, Hui-Min Qin
Summary: In this study, a genetically encoded biosensor based on a D-allulose-responsive transcriptional regulator was redesigned for real-time monitoring of D-allulose. Furthermore, an ultrahigh-throughput droplet-based microfluidic screening platform was constructed for the directed evolution of ketose 3-epimerases (KEases). Structural analysis revealed a lid conformation in Sinorhizobium fredii D-allulose 3-epimerase (SfDAE) that regulates substrate recognition, and through rational design and directed evolution, a mutant M3-2 with 17-fold enhanced catalytic efficiency was identified. This research provides a paradigm for the design and optimization of biosensor-based microdroplet screening platforms.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Multidisciplinary
Zhangliang Zhu, Xin Gao, Zhan Song, Chao Li, Fuping Lu, Masaru Tanokura, Hui-Min Qin
ACS SUSTAINABLE CHEMISTRY & ENGINEERING
(2020)
Article
Chemistry, Physical
Dengyue Sun, Dengke Gao, Xin Liu, Menglu Zhu, Chao Li, Ying Chen, Zhangliang Zhu, Fuping Lu, Hui-Min Qin
CATALYSIS SCIENCE & TECHNOLOGY
(2019)
Article
Chemistry, Multidisciplinary
Zhangliang Zhu, Chao Li, Xin Liu, Dengke Gao, Xueyu Wang, Masaru Tanokura, Hui-Min Qin, Fuping Lu