JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
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2025
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IF 6.2
Puhong Yi,Yue Xu,Yuhua Hao,Zhiqiang Liu,Yaping Xue,Liqun Jin,Yuguo Zheng
ω-Transaminases (ω-TAs) are attractive biocatalysts in the asymmetric synthesis of chiral amines. Recently, a promising ω-TA from Salmonella enterica (SeTA) has been used to produce the valuable herbicide l-phosphinothricin (l-PPT). To improve the catalytic activity of SeTA, a combination strategy involving structural analysis and mutability landscape construction was conducted. A flexible region (loop1) enhancing the catalytic activity of SeTA was identified, and a distal mutant I22D (M1) was successfully screened. M1 showed a 3.24-fold increase in specific activity, along with greater thermal stability. Its half-life (t1/2) was 30.95-fold (45 °C) and 17.53-fold (55 °C) longer than that of WT, and Tm increased by 7.6 °C. MD simulations revealed that the distal mutation induced long-range effects through allostery, resulting in the substrate tunnel being more spacious, reshaping the active pocket, and stabilizing the local conformation. These findings can provide insights into the distal sites and functional relationships of ω-TAs for improving their performance.
研究领域:
生物化学
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酶工程
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计算生物学
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DOI
PubMed
高影响因子
Foods
·
2025
·Vol. 14
·期 9
·1538
·
IF 5.1
Zepeng Li,Runmin Wang,Xiantai Lai,Wenyi Liao,Runfeng Liao,Zhuohong Wu,Guoyan Zhang,Xianghui Qi
D-tagatose is a functional sweetener with glucose-regulating and prebiotic properties, but its bioproduction from D-galactose faces many limitations, particularly the high production costs. In particular, the current biosynthesis of D-tagatose suffers from thermal instability and the substrate selectivity issues of L-arabinose isomerase (L-AI) required to convert D-galactose into D-tagatose. In this study, recombinantEscherichia coliBW25113/pQE-80L-araAF118M/F279Iexpressing double mutant L-AI was immobilized to enhance its stability and reusability. The optimal conditions for whole-cell catalysis were 60 °C, pH 6.5, 5 mM Mn2+, and 20 h, with a yield of 55.2 g/L of D-tagatose. Immobilization with 3% sodium alginate and 2% CaCl2retained 90% of the production efficiency displayed by free cells. Notably, the immobilized cells exhibited enhanced heat resistance (60–70 °C) and operational stability, retaining 76% activity after five cycles. The D-tagatose production was further increased to 129.43 g/L by increasing the substrate concentration to 250 g/L. Compared to free cells, immobilized cells retained 83.6% of the initial yield up to 10 batches. This study presents a cost-effective and sustainable method for the production of D-tagatose using optimized whole-cell catalysis through immobilization, which paves the way to solve industrial challenges such as thermal instability and low substrate efficiency.
研究领域:
生物化学
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食品科学
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DOI
PubMed
高影响因子
ACS Applied Nano Materials
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2025
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IF 5.5
Ketao Yan,Yidan Chen,Tiantian Feng,Ziwei Xiang,Yuzhu Long,Yuzhu Yuan,Wei Wen,Xiuhua Zhang,Shengfu Wang,Suxiao Wang,Jichao Liang,Huayu Xiong
Diabetic wounds pose an ongoing challenge due to their difficult healing and complex microenvironmental nature, and the presence of bacterial infections significantly exacerbates this issue. Here, leveraging the characteristics of the bacterial infection microenvironment, we developed a nanomedicine based on a hollow covalent organic framework (HCOF) for the synergistic application of chemodynamic therapy (CDT) and photodynamic therapy (PDT) in antimicrobial treatment. With HCOF as the carrier, photosensitizer Chlorin e6 (Ce6) is loaded by electrostatic adsorption, and then a manganese dioxide (MnO2) nanoshell was grown on the Ce6@HCOF surface to obtain Ce6@HCOF@MnO2. The nanomedicine exhibits a glutathione (GSH) stimulus response, thereby releasing Mn2+ and Ce6. Mn2+ engages in a Fenton-like reaction with the naturally occurring hydrogen peroxide (H2O2) at the wound site, resulting in the production of highly reactive hydroxyl radicals, while Ce6 generates singlet oxygen under laser irradiation, thus achieving CDT/PDT dual-mode synergistic therapy. Notably, Ce6@HCOF@MnO2 has not only demonstrated the ability to promote collagen deposition but also accelerated skin regeneration and aided in the repair of diabetic wounds. This pioneering approach possesses significant potential for the multifaceted management of bacterial infections and the diseases they precipitate.
研究领域:
生物材料学
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医学
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药剂学
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产品关联
DOI
高影响因子
MOLECULAR CELL
·
2025
·
IF 16.6
Jianfeng He,Yongyi Zhu,Zichao Tian,Mengqin Liu,Anmin Gao,Wangmi Fu,Fei Lu,Yutong Sun,Yajun Guo,Rongqing Pan,Yuchen Ji,Jianxiang Chen,Huasong Lu,Juan Lin,Xingguo Liang,Chun Kim,Chun Zhou,Huipeng Jiao
Z-DNA-binding protein 1 (ZBP1; also known as DAI or DLM-1) regulates cell death and inflammation by sensing left-handed double-helical nucleic acids, including Z-RNA and Z-DNA. However, the physiological conditions that generate Z-form nucleic acids (Z-NAs) and activate ZBP1-dependent signaling pathways remain largely elusive. In this study, we developed a probe, Zα-mFc, that specifically detected both Z-DNA and Z-RNA. Utilizing this probe, we discovered that inhibiting spliceosome causes nuclear accumulation of Z-RNA:DNA hybrids, which are sensed by ZBP1 via its Zα domains, triggering apoptosis and necroptosis in mammalian cells. Furthermore, we solved crystal structures of the human or mouse Zα1 domain complexed with a 6-bp RNA:DNA hybrid, revealing that the RNA:DNA hybrid adopts a left-handed conformation. Our findings demonstrate that the spliceosome acts as a checkpoint preventing accumulation of Z-RNA:DNA hybrids, which potentially function as endogenous ligands activating ZBP1-dependent cell death pathways.
研究领域:
分子生物学
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免疫学
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细胞生物学
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产品关联
DOI
PubMed
高影响因子
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
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2025
·
IF 6.2
Yun-Fei Zhu,Xing-Yue Zhou,Cai Lan,Yong-Ping Wen,Hai-Jun Fu,Zhi-Chao Li,Ya-Ping Li,Shi-Ying Li,Fei-Hong Huang,Long Wang,Lu Yu,Da-Lian Qin,An-Guo Wu,Jian-Ming Wu,Xiao-Gang Zhou
Aging leads to progressive decline in the functions of cells, tissues, and organs, severely affecting muscle performance and overall health, highlighting the urgent need for effective therapeutic agents. This study investigated the antiaging properties of tricin, a flavonoid abundant in grains, using biological models, including human fibroblasts, Caenorhabditis elegans (C. elegans), and mice. Tricin significantly alleviated the senescent phenotype in human fibroblasts induced by D-galactose (D-gal), doxorubicin, and replicative senescence, as evidenced by reduced SA-β-gal activity, downregulated senescence markers (p16, p21), and decreased SASP factors. Mechanistically, tricin binds to AMPK and activates the AMPK-mTOR-p70S6K signaling pathway, promoting autophagy and delaying cellular aging. In vivo, tricin extended lifespan, enhanced stress resistance, and improved mobility in C. elegans through aak-2/AMPK-mediated autophagy. In D-gal-induced aging mice, tricin improved muscle function, reducing p16, p21, and SASP expression in muscle tissues. These findings underscore tricin’s potential as a promising antiaging therapeutic via AMPK-mediated autophagy activation.
研究领域:
细胞生物学
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分子生物学
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药理学
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产品关联
DOI
PubMed
高影响因子
Molecular Catalysis
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2025
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IF 4.9
Meichen Zhu,Qinzhe Lin,Mengning Zhong,Jian Dong,Leyi Zhao,Qiyun Wu,Huilin Ren,Wenting Du,Jun Li
Chiral amines serve as vital building blocks in pharmaceutical synthesis, yet their stereoselective production remains a significant challenge. Biocatalytic approaches harness the inherent stereospecificity of enzymes to enable precise, sustainable, and highly selective construction of stereocenters. Here, we engineer an imine reductase (IRED) to catalyze the asymmetric synthesis of (3 S )-3-{[(1 R )-1-(naphthalen-1-yl)ethyl]amino}-1-[(2-methylpropan-2-yl)oxycarbonyl]pyrrolidine, the key chiral intermediate of Evocalcet . Computational enzyme design of PcIRED-M3 identified the W219L variant, which enhanced catalytic efficiency 8.9-fold and achieved >99 % diastereomeric excess ( d.e. ) versus 63.15 % in wild-type. The W219L substitution presumably reduces steric hindrance by extending the residue-substrate naphthyl distance from 2.1 Å to 4.7 Å while concurrently improving hydride transfer efficiency. This improvement is also owing to the optimized π-σ orbital alignment with the decreased spacing (from 6.2 Å to 4.9 Å) between the imine carbon and the C-4 position of NADPH’s nicotinamide ring. Reaction parameters optimization (30 % DMSO, K 2 HPO 4 -KH 2 PO 4 buffer pH 7.5, 35 °C) achieved 62.7 % conversion in 48 h. This work establishes the first enzymatic route to Evocalcet intermediates and identifies W219 as a stereochemical gatekeeper residue that allosterically coordinates substrate-cofactor geometry.
研究领域:
生物催化
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酶工程
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有机合成
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药物化学
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计算酶设计
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产品关联
DOI
高影响因子
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
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2025
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IF 6.2
Yuvaraj Ravikumar,Abdullah Arsalan,Xinrui Tang,Guoyan Zhang,Xianghui Qi
l-Arabinose isomerase (l-AI) catalyzes d-galactose to produce the rare, industrially important sugar d-tagatose. Enzyme stability is vital for its application in industrial processes, and rational design-based protein engineering methods have been employed to improve its stability. This study employed molecular dynamics simulations (MDS)-guided rational redesign of flexible regions to improve the thermostability of mesophilic Bifidobacterium adolescentis l-AI (Ba-l-AI). Comparative MDS (200 ns, 340–360 K) of thermophilic l-AIs (Geobacillus kaustophilus Gk-l-AI and Thermotoga maritima Tm-l-AI) and mesophilic Ba-l-AI identified flexible regions in Ba-l-AI via RMSF and ionic interaction. Five stabilizing mutations (G78C, K46R, N187R, K112R, and N190R) were introduced to provide rigidness. MDS of the mutant revealed reduced RMSF/RMSD, improved compactness, and enhanced conformational stability across temperatures, supported by free-energy landscape analysis resembling thermophilic profiles. Experimentally, the mutant exhibited superior thermal stability (72 °C), broader pH/temperature tolerance, and efficient d-tagatose production. The redesigned Ba-l-AI’s rigid backbone and stability highlight its potential for industrial d-tagatose biosynthesis.
研究领域:
生物催化
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蛋白质工程
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结构生物学
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工业生物技术
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计算生物学
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酶学
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产品关联
DOI
PubMed
高影响因子
Nature Communications
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2025
·Vol. 16
·期 1
·1-16
·
IF 15.7
Kang Wei,Wu Zhiyue,Huang Xinzhi,Qi Hongbin,Wu Jiaxuan,Wang Jiahui,Li Jing,Wu Sijin,Kang Byung-Ho,Li Bo,Ma Juncai,Xue Chuang
Biomolecular condensates are dynamic cellular compartments that concentrate proteins and enzymes to regulate biochemical reactions in time and space. While these condensates can enhance enzyme activity, how this function changes as condensates age remains poorly understood. Here, we design synthetic catalytic condensates that selectively recruit enzymes to investigate this temporal evolution. We show that catalytic condensates exhibit time-dependent activity: they initially accelerate enzymatic reactions but gradually lose efficiency due to the transition from liquid-like to solid-like states. This aging process, characterized by protein aggregation and loss of selective barriers, impairs enzyme function both in vitro and living cells. We further demonstrate that small molecules which influence aging dynamics can modulate catalytic efficiency of condensates. Our findings show that condensate aging as a key regulator of enzymatic activity and provide crucial insights for designing functional synthetic condensates.
研究领域:
分子生物学
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生物化学
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细胞生物学
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合成生物学
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产品关联
DOI
PubMed
高影响因子
Synthetic and Systems Biotechnology
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2025
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IF 4.4
Yuke Qin,Shuting Hu,Yibin Yang,Xiaoqiang Jia
The research on whole-cell biosensors tailored for trace and ultra-trace detection remains limited and the biosensors based on natural bacterial heavy metal resistance mechanisms have common issues of low sensitivity. In this study, we designed a promoter P T7-cadO using the Cadmium ions (Cd 2+ )-binding protein binding site cadO with the T7 promoter at first and constructed a single-input whole-cell biosensor, which was named CP100, whose detection limit for Cd 2+ met the WHO requirement, yet its response and sensitivity were quite low. We further introduced the lacI and lac operator ( lacO ) as the signal amplifier to construct a dual-input promoter P T7-cadO-lacO-cadO and developed a biosensor named LC100, whose response and sensitivity were significantly improved, but background leakage became a new problem. Then we redesigned the gene circuit based on the regulatory circuit LCPM-2, which has the structure of “CadR-P J23100 -P T7-cadO-lacO-cadO -mRFP1-LacI”, with the LacI protein as the autoregulatory negative feedback model and finally obtained the biosensor named LC100-2, which achieved the detection of ultra-trace Cd 2+ (0.00001-0.02 nM), with the sensitivity of 3748.22 times that of CP100. Moreover, LC100-2 demonstrated excellent specificity to Cd 2+ among four other divalent metal ions and good anti-interference capability in the mixed divalent metal ions system. The results of the real water sample tests demonstrated that precise quantitative detection of Cd 2+ with a final concentration of 0.001-0.02 nM could be achieved by adding only a small volume of the sample (1 μL). This finding showed promising application potential in the field of trace detection. Additionally, the regulatory circuit LCPM-2 based on the unique dual-input promoter enhanced responses and reduced background leakage simultaneously, thereby providing an innovative strategy for the design and simplification of biosensors’ circuits.
研究领域:
生物传感器
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合成生物学
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环境监测
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分子生物学
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基因工程
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产品关联
DOI
PubMed
高影响因子
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
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2025
·
IF 6.2
Qiang Wang,Hossain M. Zabed,Mei Zhao,Xianghui Qi
Laccases, as multicopper oxidases, play a pivotal role in lignin degradation and hold broad industrial promise in biorefineries, bioremediation, textiles, and pulp and paper processing. However, their use is limited by poor stability under harsh operational conditions. Here, we designed a novel thermostable laccase (WCotA) from Bacillus amyloliquefaciens by combining data-driven mining with rational engineering. WCotA displayed remarkable thermostability and pH tolerance, with an optimal activity at 85 °C and a half-life of 1.0 h. To further improve thermostability, a combinatorial mutation library was constructed and screened, yielding mutant M2. M2 exhibited a prolonged half-life of 2.25 h at 85 °C and enhanced activity of 101.05 U/mg, outperforming the wild type. Structural and molecular dynamics analyses elucidated the mechanisms underlying its improved thermostability. This work provides a robust strategy for laccase discovery and engineering, advancing their sustainable application in industrial processes.
研究领域:
酶工程
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分子生物学
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生物催化
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工业微生物学
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蛋白质工程
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产品关联
DOI
PubMed
高影响因子
Journal of Environmental Chemical Engineering
·
2025
·
IF 7.2
Wenwei Tang,Meihuan Tong,Hui Liao,Peiqi Zhang,Xinping Zeng
Aureomycin (CTC) is a commonly used tetracycline antibiotic that causes water and soil pollution and greatly endangers the environment and human health. Microbial degradation to remove residual antibiotics in wastewater is of growing interest. Due to its unique structure and excellent oxidative properties, biogenic manganese oxides (BMO) has been widely studied in the field of water pollutant removal. However, the current preparation of BMO generally suffers from low yield and insufficient production efficiency. In this paper, an efficient manganese-oxidizing bacterium Bacillus sp. D-1 was isolated. Manganese-oxidizing engineering bacteria were constructed to achieve rapid and sufficient BMO production, and the structure and function of the BMO was characterized. SEM was used to characterize the layered structure of the nanoparticles. XPS and XRD were used to determine that the mixture was composed of manganese species with three valence states. BMO was used to degrade 10 mg·L −1 CTC, and the CTC removal rate reached 93.2 % in 24 h, with an optimal reaction pH of 7.6. Finally, LCMS and ECOSAR were used to analyze the oxidative degradation products of CTC and their biological toxicity. Therefore, this paper successfully constructed a high-performance manganese-oxidizing engineering bacterium, revealed the efficient degradation mechanism of CTC by BMO, provided a new strategy for the green treatment of combined pollution of manganese and antibiotics in water bodies, and realized the continuous removal of manganese and water pollutants.
研究领域:
环境微生物学
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环境工程
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分子生物学
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污染物生物修复
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水处理技术
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产品关联
DOI
高影响因子
ACS Applied Materials & Interfaces
·
2025
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IF 8.2
Ziyu Kuai,Yibing Huang,Fengjie Hao,Wantong Jiang,Mengmeng Niu,Yu qin,Ao Song,Yuran Deng,Youzhong Wan,Quan Luo
Atomic precision synthesis and modulation of nanozymes are critical for evaluating their performance and developing functional applications. Herein, we developed an in situ strategy for the controlled synthesis of gold clusterzymes (AuCEs) within the confined cavities of the protein scaffolds. Using a stable dodecameric protein (SP1) as a ligand, we fused a short peptide containing the CCY sequence (SP1-CCY) to the N-terminus of SP1, which is located within its cyclic structure. In this design, cysteine and tyrosine synergistically chelate and reduce Au ions, while the confined protein structure restricts cluster growth, leading to the formation of a 25-gold atom (Au25) nanocluster with strong fluorescence and peroxidase-like activity. Unlike chemical ligands, protein scaffolds offer atomic-level precision and allow for site-specific modulation of the local environment through rational mutations, such as L9D, L9I, and E73I/L9I. This allows precise control of both fluorescence and enzymatic activity via protein engineering. Additionally, heteroatom doping of the Au core with copper endows the AuCEs with significant superoxide dismutase-like activity. Antioxidant assays demonstrate that the optimized AuCEs exhibit potent reactive oxygen species scavenging activity, providing significant protection to Caenorhabditis elegans from oxidative stress and highlighting their potential as therapeutic candidates for aging-related diseases.
研究领域:
纳米医学
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生物材料学
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分子生物学
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老年病学
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抗氧化治疗
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纳米酶
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转化医学
✓ 已验证
产品关联
DOI
PubMed
高影响因子
危险品化学品经营许可证（带存储）