JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE
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2025
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IF 3.5
Xiaodan Wang,Yuye Zhang,Shaoping Jiang,Shijie Zhu,Ying Zhu,Ping Chang,Jiaxin Zheng
BACKGROUND Sufu is very popular worldwide, especially among Asians, but sometimes has a slight bitter taste, so the source and mechanism of its bitterness are worth exploring. In this study on the basis of bitter prediction analysis, bitter peptides in sufu were screened via homology modeling and molecular docking. RESULTS Molecular docking selected 14 peptides that bind to the T2R1 bitter receptor modeled by SWISS-MODEL homology. Peptides with a binding energy of −6.7 kcal mol −1 were selected for solid-phase synthesis based on affinity scoring assessment, and the flavor characteristics of the synthesized peptides were verified through sensory evaluation and electronic tongue. Finally, the Q value of the synthesized peptides was computed, and the content of their hydrophobic side chain groups was evaluated. The molecular docking results showed that bitter peptides of sufu form hydrogen bonds with bitter receptors, and the binding is stable. The flavor characteristics of the synthesized peptides were primarily bitter and umami, and the proportion of hydrophobic side-chain groups in the synthesized peptides was significant. CONCLUSION These results provide a theoretical basis for future screening of bitter peptides and improving the bitter taste of fermented bean products. © 2025 Society of Chemical Industry.
研究领域:
食品科学
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分子生物学
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结构生物学
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生物信息学
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风味化学
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DOI
PubMed
高影响因子
PLANT PHYSIOLOGY AND BIOCHEMISTRY
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2023
·
IF 6.5
Minglei Tao,Shengzhi Liu,Yaohan Li,Amin Liu,Jingkui Tian,Yuchang Liu,Hongwei Fu,Wei Zhu
Coumarin is an important secondary metabolite that affects plant physiology. It is a lactone of cis- o -hydroxycinnamic acid and widely exists in medicinal plants . Clematis terniflora DC. is a plant belonging to Ranunculaceae and is rich in variety of coumarins. Feruloyl-CoA 6′-hydroxylase has been reported as a key enzyme in the formation of coumarin basic skeleton only in some common plants, however, its evidence in other species is still lacking especially for the biosynthesis of coumarins in C . terniflora . In the present study, we identified a feruloyl-CoA 6′-hydroxylase CtF6′H in C . terniflora , and functional characterization indicated that CtF6′H could hydroxylate feruloyl-CoA to 6-hydroxyferuloyl-CoA. Furthermore, the expression level of CtF6′H was differed among different tissues in C. terniflora , while under UV-B radiation, the level of CtF6′H was increased in the leaves. Biochemical characteristics and subcellular location showed that CtF6′H was mainly present in the cytosol. The crystal structure of CtF6′H was simulated by homology modeling to predict the potential residues affecting enzyme activity . This study provides the additional evidence of feruloyl-CoA 6′-hydroxylase in different plant species and enriches our understanding of biosynthetic mechanism of coumarin in C . terniflora .
研究领域:
植物生理学
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生物化学
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分子生物学
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植物化学
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DOI
PubMed
高影响因子
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
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2020
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IF 4.192
Yong-Qiang Li,Li-Sha Bai,Cai-Xia Zhao,Jing-Jing Xu,Zhong-Juan Sun,Yan-Ling Dong,De-Xian Li,Xi-Li Liu,Zhi-Qing Ma
Insect carboxylesterases are major enzymes involved in metabolism of xenobiotics including insecticides. Two carboxylesterase genes, CarE001A and CarE001H, were cloned from the destructive agricultural pest Helicoverpa armigera. Quantitative real-time polymerase chain reaction showed that CarE001A and CarE001H were predominantly expressed in fat body and midgut, respectively; developmental expression analyses found that the expression levels of both CarEs were significantly higher in fifth-instar larvae than in other life stages. Recombinant CarE001A and CarE001H expressed in the Escherichia coli exhibited high enzymatic activity toward α-naphthyl acetate. Inhibition assays showed that organophosphates had strong inhibition on CarEs activity compared to pyrethroids. Metabolism assays indicated that CarE001A and CarE001H were able to metabolize β-cypermethrin and λ-cyhalothrin. Homology modeling and molecular docking analyses demonstrated that β-cypermethrin could fit nicely into the active pocket of both carboxylesterases. These results suggested that CarE001A and CarE001H could play important roles in the detoxification of pyrehtroids in H. armigera.
研究领域:
昆虫学
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分子生物学
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农药毒理学
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DOI
PubMed
高影响因子
JOURNAL OF BIOSCIENCE AND BIOENGINEERING
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2019
·
IF 2.032
Xiaohong Lu,Juhua Chen,Linshu Jiao,Lei Zhong,Zhaoxin Lu,Chong Zhang,Fengxia Lu
Directed evolution methodologies have been used as promising strategies for improving the catalytic properties of many existing enzymes . In the presented work, this approach was applied to improve the enzyme activity of l -asparaginase I obtained from Bacillus megaterium H-1. After two rounds of error-prone polymerase chain reaction (epPCR) and two generations of sequential DNA shuffling , all of 5 different mutants showed a significant increase in the enzyme activity of l -asparaginase I, ranging from 6.27 to 22.78 IU/mL. Among these mutants, D-9B and DD-12G displayed the relatively high catalytic activity , which were 20.22-fold and 21.33-fold higher than the wild-type enzyme (WT), respectively. Furthermore, the catalytic efficiency ( k cat / K m ) of D-9B and DD-12G were also improved, which were 132.73 min −1 mM −1 and 146.39 min −1 mM −1 , respectively, in comparison to that of WT (3.39 min −1 mM −1 ). In addition, mutant DD-12G showed tolerance toward wider range of pH values and higher temperatures than its WT counterpart. Homology modeling of above two mutants reflected a reduction of hydrogen bonds and an introduction of flexible residues in the loops near the active catalytic site Thr15. These changes contributed to the flexibility of loops, which may lead to further enhancement in catalytic efficiency. Results also showed that approximately 88.5% (0.978 mg/kg) acrylamide could be removed from mutant DD-12G pre-treated fried potato chips. This study clearly shows that directional evolution methods can indeed be utilized to improve the activity of l -asparaginase, which could also provide research basis for future application in food industry.
研究领域:
生物技术
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酶学
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食品科学
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DOI
PubMed
高影响因子
Frontiers in Plant Science
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2016
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IF 4.495
Zhao Yucheng,Wang Nana,Zeng Zhixiong,Xu Sheng,Huang Chuanlong,Wang Wei,Liu Tingting,Luo Jun,Kong Lingyi
Coumarins are main active components of Peucedanum praeruptorum Dunn. Among them, methoxylated coumarin compound, such as bergapten, xanthotoxin, and isopimpinellin, has high officinal value and plays an important role in medicinal field. However, major issues associated with the biosynthesis mechanism of coumarins remain unsolved and no corresponding enzyme has been cloned from P. praeruptorum. In this study, a local BLASTN program was conducted to find the candidate genes from P. praeruptorum transcriptome database using the nucleotide sequence of Ammi majus bergaptol O-methyltransferase (AmBMT, GenBank accession No: AY443006) as a template. As a result, a 1335 bp full-length of cDNA sequence which contains an open reading frame of 1080 bp encoding a BMT polypeptide of 359 amino acids was obtained. The recombinant protein was functionally expressed in Escherichia coli and displayed an observed activity to bergaptol. In vitro experiments show that the protein has narrow substrate specificity for bergaptol. Expression profile indicated that the cloned gene had a higher expression level in roots and can be induced by methyl jasmonate (MeJA). Subcellular localization analysis showed that the BMT protein was located in cytoplasm in planta. Homology modeling and docking based site-directed mutagenesis have been employed to investigate the amino acid residues in BMT required for substrate binding and catalysis. Conservative amino acid substitutions at residue H264 affected BMT catalysis, whereas substitutions at residues F171, M175, D226, and L312 affected substrate binding. The systemic study summarized here will enlarge our knowledge on OMTs and provide useful information in investigating the coumarins biosynthesis mechanism in P. praeruptorum.
研究领域:
植物生物化学
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分子生物学
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生药学
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酶学
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DOI
PubMed
高影响因子
BIOCHEMICAL ENGINEERING JOURNAL
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2024
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IF 3.7
Yi Wang,Chuanting Qin,Xiaoxue Wang,Ting Wang,Jian Dong,Yuan Lu
The sense of smell in animals enables them to detect and discriminate among many volatile odor molecules in complex environments. This task is accomplished by the family of G-proteins (olfactory receptor proteins, odorant-binding proteins, and chemosensory proteins). Here, we mechanistically elucidate how odors bind to odorant-binding proteins (OBPs) by studying the binding properties of 50 odorant ligands to six OBPs. We confirmed that OBP7 from Ailuropoda melanoleuca and OBP9 from Anopheles gambiae have binding affinities for 16 odors, and further analyzed the structures and protein-ligand interactions by homology modeling and molecular docking. This study found that OBP7 had an affinity for nonanol and camphor, and the docking results indicated that Glu120 was a residue that played a key role in the binding process of OBP7 to odorant ligands. We also explored the binding properties between OBP9 and ligands as well as the binding mechanism, and found that OBP9 bound well to some odorant molecules with repellent efficacy, such as nonanol, camphor, and citral. These findings not only contributed to our understanding of how OBPs were sensitively bound to odorant ligands but also promoted them as suitable targets for applied research in various industrial fields such as pesticides, cosmetics, and pharmaceuticals.
研究领域:
分子生物学
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生物化学
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神经科学
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化学生物学
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产品关联
DOI
高影响因子
Frontiers in Plant Science
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2017
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IF 4.291
Su Ping,Guan Hongyu,Zhang Yifeng,Wang Xing,Gao Linhui,Zhao Yujun,Hu Tianyuan,Zhou Jiawei,Ma Baowei,Tu Lichan,Tong Yuru,Huang Luqi,Gao Wei
Tripterygium wilfordii produces not only ent-kaurene, which is an intermediate of gibberellin (GA) biosynthesis in flowering plants, but also 16α-hydroxy-ent-kaurane, whose physiological role has not been characterized. The two compounds are biosynthesized from the universal diterpenoid precursor (E,E,E)-geranylgeranyl diphosphate (GGPP) by diterpene synthases, which have been discovered and functionally characterized in T. wilfordii. Here, we described the functional characterization of four cytochrome P450 reductases (TwCPR) and one ent-kaurene oxidase (TwKO). Four TwCPRs were found to have relatively ubiquitous expression in T. wilfordii root, stem, leaf, and flower tissues. Co-expression of both a TwCPR and TwKO in yeast showed that TwCPR3 has a slightly better activity for providing the electrons required for these reactions, indicating that TwCPR3 is more suitable for use in the functional analysis of other cytochrome P450 monooxygenases. TwKO catalyzed the three-step oxidation of the C4α methyl of the tetracyclic diterpene intermediate ent-kaurene to form ent-kaurenoic acid as an early step in GA biosynthesis. Notably, TwKO could also convert 16α-hydroxy-ent-kaurane to 16α-hydroxy-ent-kaurenoic acid, indicating an important function of 16α-hydroxy-ent-kaurane in the anti-HIV principle tripterifordin biosynthetic pathway in planta. Homology modeling and molecular docking were used to investigate the unknown crucial active amino acid residue involved in the catalytic reaction of TwKO, and one key residue (Leu387) contributed to the formation of 16α-hydroxy-ent-kaurenoic acid, most likely by forming hydrogen bonds with the hydroxyl group (-OH) of 16α-hydroxy-ent-kaurane, which laid the basis for further investigation of the multifunctional nature of KO catalysis. Also, our findings paved the way for the complete biosynthesis of the anti-HIV principle tripterifordin.
研究领域:
植物生物化学
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酶学
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分子生物学
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生药学
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产品关联
DOI
PubMed
高影响因子
Scientific Reports
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2021
·Vol. 11
·期 1
·1-11
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IF 4.38
Xue Shu-Wen,Tian Yue-Xin,Pan Jin-Cheng,Liu Ya-Ni,Ma Yan-Ling
Pseudomonas aeruginosa DN1 can efficiently utilize fluoranthene as its sole carbon source, and the initial reaction in the biodegradation process is catalyzed by a ring-hydroxylating dioxygenase (RHD). To clarify the binding interaction of RHD with fluoranthene in the strain DN1, the genes encoding alpha subunit (RS30940) and beta subunit (RS05115) of RHD were functionally characterized through multi-technique combination such as gene knockout and homology modeling as well as molecular docking analysis. The results showed that the mutants lacking the characteristic alpha subunit and/or beta subunit failed to degrade fluoranthene effectively. Based on the translated protein sequence and Ramachandran plot, 96.5% of the primary amino-acid sequences of the alpha subunit in the modeled structure of the RHD were in the permitted region, 2.3% in the allowed region, but 1.2% in the disallowed area. The catalytic mechanism mediated by key residues was proposed by the simulations of molecular docking, wherein the active site of alpha subunit constituted a triangle structure of the mononuclear iron atom and the two oxygen atoms coupled with the predicted catalytic ternary of His 217 -His 222 -Asp 372 for the dihydroxylation reaction with fluoranthene. Those amino acid residues adjacent to fluoranthene were nonpolar groups, and the C 7 -C 8 positions on the fluoranthene ring were estimated to be the best oxidation sites. The distance of C 7 -O and C 8 -O was 3.77 Å and 3.04 Å respectively, and both of them were parallel. The results of synchronous fluorescence and site-directed mutagenesis confirmed the roles of the predicted residues during catalysis. This binding interaction could enhance our understanding of the catalytic mechanism of RHDs and provide a solid foundation for further enzymatic modification.
研究领域:
微生物学
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生物化学
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分子生物学
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环境科学
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DOI
PubMed
高影响因子
INVESTIGATIONAL NEW DRUGS
·
2022
·Vol. 40
·期 5
·977-989
·
IF 3.651
Duan Zelin,Zhou Zhiyun,Lu Feifei,Zhang Yawen,Guo Xvqin,Gui Chunshan,Zhang Hongjian
Targeting tumor metabolic vulnerabilities such as “glutamine addiction” has become an attractive approach for the discovery of novel antitumor agents. Among various mechanisms explored, SLC1A5, a membrane transporter that plays an important role in glutamine cellular uptake, represents a viable target to interfere with tumor’s ability to acquire critical nutrients during proliferation. In the present study, a stably transfected HEK293 cell line with human SLC1A5 (HEK293-SLC1A5) was established for the screening and identification of small molecule SLC1A5 inhibitors. This in vitro system, in conjunction with direct measurement of SLC1A5-mediated L-glutamine-2,3,3,4,4-D 5 (substrate) uptake, was practical and efficient in ensuring the specificity of SLC1A5 inhibition. Among a group of diverse compounds tested, mianserin (a tetracyclic antidepressant) demonstrated a marked inhibition of SLC1A5-mediated glutamine uptake. Subsequent investigations using SW480 cells demonstrated that mianserin was capable of inhibiting SW480 tumor growth both in vitro and in vivo, and the in vivo antitumor efficacy was correlated to the reduction of glutamine concentrations in tumor tissues. Computational analysis revealed that hydrophobic interactions between SLC1A5 and its inhibitors could be a critical factor in drug design. Taken together, the current findings confirmed the feasibility of targeting SLC1A5-mediated glutamine uptake as a novel approach for antitumor intervention. It is anticipated that structural insights obtained based on homology modeling would lead to the discovery of more potent and specific SLC1A5 inhibitors for clinical development.
研究领域:
肿瘤学
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药理学
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分子生物学
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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
·
2024
·
IF 5.7
Yongmei Chang,Weihuan Xu,Shan Wang,Mengyao Zhu,Yanan Ru,Zhiheng Xu,Guangyou Chen,Yongqiang Li
Helicoverpa armigera Hübner (Lepidoptera: Noctuidae) is a globally devastating pest and has evolved with varying levels of resistance to a broader spectrum of insecticides. CarEs are major enzymes involved in insecticide detoxification and metabolic resistance. Four CarE genes were identified and cloned from H. armigera, and the expression pattern analyses indicated that they were predominantly expressed in the detoxifying tissues and larval feeding periods. The insecticide inductive assays further suggested that these CarE genes with expressions were significantly upregulated after beta-cypermethrin, lambda-cyhalothrin, malathion, and chlorpyrifos exposures. The purified recombinant proteins of both CarE016B and CarE016C by bacterial expression exhibited significantly higher catalytic efficiency toward α-naphthyl acetate and also showed relatively stronger binding with both β-cypermethrin and λ-cyhalothrin compared to the CarE006C and CarE015A. In vitro metabolism assay with HPLC suggests that CarE016B and CarE016C have the ability to metabolize β-cypermethrin, λ-cyhalothrin, and malathion with varying hydrolase activities. GC-MS/MS analysis identified 3-phenoxybenzaldehyde (3-PBAld) as the metabolite of both β-cypermethrin and λ-cyhalothrin. Homology modeling and molecular docking analyses further indicate that these three types of insecticides could be anchored into the active pocket of both CarEs. Collectively, these results demonstrate that both CarE016B and CarE016C play a critical role in the detoxification of pyrethroid and organophosphate insecticides in H. armigera. This study provides the foundations for a comprehensive understanding of the role of the CarEs family in insecticide detoxification and resistance in H. armigera.
研究领域:
昆虫学
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毒理学
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分子生物学
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生物化学
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DOI
PubMed
高影响因子
PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY
·
2025
·
IF 4
Zhengyi Mao,Wen Zhao,Dongping Chen,Zhiyan Jiang,Qiang Liu,Jiayun Li,Yunxuan Wu,Nannan Lv,Jianting Fan
The pine-forest guardian Dastarcus helophoroides mainly rely on olfaction to locate its host accurately and interact socially. Odorant binding proteins of D. helophoroides play an important role in olfactory recognition and transporting odors to olfactory receptors to trigger signal transduction. However, some compounds affect olfactory recognition of D. helophoroides by binding to odorant binding proteins. In this study, DhelOBP4 and DhelOBP21, which are involved in the recognition of plant volatiles, were expressed to explore compounds that affect olfactory recognition. The affinity of 24 compounds with DhelOBP4 and DhelOBP21 was investigated by vitro fluorescence competitive binding assays. It was found that cyetpyrafen, chlorfenapyr and spirodiclofen had high affinity with DhelOBP4 and DhelOBP21. At the same time, we found that these three pesticides had a good evasive effect on the D. helophoroides and elicited EAG response in a dose-dependent manner. Besides, it was found that silencing DhelOBP4 and DhelOBP21 would affect D. helophoroides identifying these three pesticides. Through homology modeling and molecular docking, we identified key amino acid sites involved in the binding of DhelOBP4 and DhelOBP21 to these three pesticides, which might revealed their specific binding molecular interactions. This study is helpful to provide a valuable addition of OBP-pesticide interactions of D. helophoroides .
研究领域:
昆虫学
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农药科学
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分子生物学
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生物化学
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生态学
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神经生物学
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产品关联
DOI
PubMed
高影响因子
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
·
2016
·
IF 2.857
Chun Liu,Fenfen Cheng,Yingen Sun,Hongyu Ma,Xiaoquan Yang
An alkaline isoform of the PR-5 protein (designated GmOLPc) has been purified from soybean hulls and identified by MALDI-TOF/TOF-MS. GmOLPc effectively inhibited in vitro the growth of Phytophthora soja spore and Pseudomonas syringae pv glycinea. The antimicrobial activity of GmOLPc should be mainly ascribed to its high binding affinity with vesicles composed of DPPG, (1,3)-β-d-glucans, and weak endo-(1,3)-β-d-glucanase activity. From the 3D models, predicted by the homology modeling, GmOLPc contains an extended negatively charged cleft. The cleft was proved to be a prerequisite for endo-(1,3)-β-d-glucanase activity. Molecular docking revealed that the positioning of linear (1,3)-β-d-glucans in the cleft of GmOLPc allowed an interaction with Glu83 and Asp101 that were responsible for the hydrolytic cleavage of glucans. Interactions of GmOLPc with model membranes indicated that GmOLPc possesses good surface activity which could contribute to its antimicrobial activity, as proved by the behavior of perturbing the integrity of membranes through surface hydrophobic amino acid residues (Phe89 and Phe94).
研究领域:
植物病理学
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分子生物学
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生物化学
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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）