1.Acupuncture regulates dynamic flux of Ca2+, Na+, and H2O2 in skeletal muscle injury induced by eccentric exercise in rats.
Xue-Lin ZHANG ; Qian ZHAO ; Ai-Shan LIU ; Ming-Liang DUAN ; Jing-Jing DING ; Hua WANG
Acta Physiologica Sinica 2025;77(1):47-61
This study aimed to investigate the effects of acupuncture on dynamic changes in Ca2+, Na+, and H2O2 flux following eccentric exercise-induced muscle injury. The total of 324 healthy male Wistar rats were randomly divided into 6 groups: control group (C), eccentric exercise group (E), eccentric exercise with acupuncture group (EA), EA with TRP channel blocker group (EAT), EA with NOX2 blocker group (EAN) and EA with placebo group (EAP). Gastrocnemius muscles were subject to lengthening contractions with percutaneous electrical stimulation, followed by immediate pretreatment with blocking agents. After 30 min, acupuncture needling was administered to the gastrocnemius muscle, and real-time dynamic changes of Ca2+, Na+ and H2O2 flux were measured with non-invasive micro-test technique during the needle retention period, immediately, 3 h, 6 h, and 24 h post-extraction respectively. Results showed that compared with the E group, acupuncture significantly increased net Ca2+ efflux (P < 0.05), extended the period of net Na+ influx, and significantly decreased net H2O2 efflux (P < 0.05). However, these effects were significantly attenuated in the EAT and EAN groups, where excessive net H2O2 efflux was observed (P < 0.001). These findings indicate that acupuncture regulates the dynamic changes of Ca2+, Na+ and H2O2 flux by activating the TRP channels and interacting with NOX2 activity following eccentric exercise-induced skeletal muscle injury.
Animals
;
Muscle, Skeletal/metabolism*
;
Rats, Wistar
;
Rats
;
Male
;
Calcium/metabolism*
;
Hydrogen Peroxide/metabolism*
;
Physical Conditioning, Animal
;
Sodium/metabolism*
;
Acupuncture Therapy
;
NADPH Oxidase 2
2.Hydrogen sulfide ameliorates hypoxic pulmonary hypertension in rats by inhibiting aerobic glycolysis-pyroptosis.
Yuan CHENG ; Yun-Na TIAN ; Man HUANG ; Jun-Peng XU ; Wen-Jie CAO ; Xu-Guang JIA ; Li-Yi YOU ; Wan-Tie WANG
Acta Physiologica Sinica 2025;77(3):465-471
The present study aimed to explore whether hydrogen sulfide (H2S) improved hypoxic pulmonary hypertension (HPH) in rats by inhibiting aerobic glycolysis-pyroptosis. Male Sprague-Dawley (SD) rats were randomly divided into normal group, normal+NaHS group, hypoxia group, and hypoxia+NaHS group, with 6 rats in each group. The control group rats were placed in a normoxic (21% O2) environment and received daily intraperitoneal injections of an equal volume of normal saline. The normal+NaHS group rats were placed in a normoxic environment and intraperitoneally injected with 14 μmol/kg NaHS daily. The hypoxia group rats were placed in a hypoxia chamber, and the oxygen controller inside the chamber maintained the oxygen concentration at 9% to 10% by controlling the N2 flow rate. An equal volume of normal saline was injected intraperitoneally every day. The hypoxia+NaHS group rats were also placed in an hypoxia chamber and intraperitoneally injected with 14 μmol/kg NaHS daily. After the completion of the four-week modeling, the mean pulmonary artery pressure (mPAP) of each group was measured using right heart catheterization technique, and the right ventricular hypertrophy index (RVHI) was weighed and calculated. HE staining was used to observe pathological changes in lung tissue, Masson staining was used to observe fibrosis of lung tissue, and Western blot was used to detect protein expression levels of hexokinase 2 (HK2), pyruvate dehydrogenase (PDH), pyruvate kinase isozyme type M2 (PKM2), nucleotide-binding oligomerization domain-like receptor protein 3 (NLRP3), GSDMD-N-terminal domain (GSDMD-N), Caspase-1, interleukin-1β (IL-1β) and IL-18 in lung tissue. ELISA was used to detect contents of IL-1β and IL-18 in lung tissue. The results showed that, compared with the normal control group, there were no significant changes in all indexes in the normal+NaHS group, while the hypoxia group exhibited significantly increased mPAP and RVHI, thickened pulmonary vascular wall, narrowed lumen, increased collagen fibers, up-regulated expression levels of aerobic glycolysis-related proteins (HK2 and PKM2), up-regulated expression levels of pyroptosis-related proteins (NLRP3, GSDMD-N, Caspase-1, IL-1β, and IL-18), and increased contents of IL-1β and IL-18. These changes of the above indexes in the hypoxia group were significantly reversed by NaHS. These results suggest that H2S can improve rat HPH by inhibiting aerobic glycolysis-pyroptosis.
Animals
;
Rats, Sprague-Dawley
;
Male
;
Hypertension, Pulmonary/metabolism*
;
Glycolysis/drug effects*
;
Hydrogen Sulfide/therapeutic use*
;
Hypoxia/complications*
;
Rats
;
Pyroptosis/drug effects*
3.Mechanism analysis of ω-3 polyunsaturated fatty acids in alleviating oxidative stress and promoting osteogenic differentiation of MC3T3-E1 cells through activating Nrf2/NQO1 pathway.
Jiahui HUANG ; Long CHEN ; Chen XU ; Haojie YU ; Shishuai ZHOU ; Jianzhong GUAN
Chinese Journal of Reparative and Reconstructive Surgery 2025;39(11):1459-1467
OBJECTIVE:
To explore the mechanism by which ω-3 polyunsaturated fatty acids (hereinafter referred to as "ω-3") exert antioxidant stress protection and promote osteogenic differentiation in MC3T3-E1 cells, and to reveal the relationship between ω-3 and the key antioxidant stress pathway involving nuclear factor E2-related factor 2 (Nrf2) and NAD (P) H quinone oxidoreductase 1 (NQO1) in MC3T3-E1 cells.
METHODS:
The optimal concentration of H 2O 2 (used to establish the oxidative stress model of MC3T3-E1 cells in vitro) and the optimal intervention concentrations of ω-3 were screened by cell counting kit 8. MC3T3-E1 cells were divided into blank control group, oxidative stress group (H 2O 2), low-dose ω-3 group (H 2O 2+low-dose ω-3), and high-dose ω-3 group (H 2O 2+high-dose ω-3). After osteoblastic differentiation for 7 or 14 days, the intracellular reactive oxygen species (ROS) level was measured by fluorescence staining and flow cytometry, and the mitochondrial morphological changes were observed by biological transmission electron microscope; the expression levels of Nrf2, NQO1, heme oxygenase 1 (HO-1), Mitofusin 1 (Mfn1), and Mfn2 were detected by Western blot to evaluate the cells' antioxidant stress capacity; the expression levels of Runt-related transcription factor 2 (RUNX2) and osteocalcin (OCN) were detected by immunofluorescence staining and Western blot; osteogenic potential of MC3T3-E1 cells was evaluated by alkaline phosphatase (ALP) staining and alizarin red staining.
RESULTS:
Compared with the oxidative stress group, the content of ROS in the low and high dose ω-3 groups significantly decreased, and the protein expressions of Nrf2, NQO1, and HO-1 significantly increased ( P<0.05). At the same time, the mitochondrial morphology of MC3T3-E1 cells improved, and the expressions of mitochondrial morphology-related proteins Mfn1 and Mfn2 significantly increased ( P<0.05). ALP staining and alizarin red staining showed that the low-dose and high-dose ω-3 groups showed stronger osteogenic ability, and the expressions of osteogenesis-related proteins RUNX2 and OCN significantly increased ( P<0.05). And the above results showed a dose-dependence in the two ω-3 treatment groups ( P<0.05).
CONCLUSION
ω-3 can enhance the antioxidant capacity of MC3T3-E1 cells under oxidative stress conditions and upregulate their osteogenic activity, possibly through the Nrf2/NQO1 signaling pathway.
Oxidative Stress/drug effects*
;
NF-E2-Related Factor 2/metabolism*
;
NAD(P)H Dehydrogenase (Quinone)/metabolism*
;
Animals
;
Mice
;
Osteogenesis/drug effects*
;
Cell Differentiation/drug effects*
;
Fatty Acids, Omega-3/pharmacology*
;
Signal Transduction/drug effects*
;
Osteoblasts/drug effects*
;
Reactive Oxygen Species/metabolism*
;
Cell Line
;
Hydrogen Peroxide/pharmacology*
;
Core Binding Factor Alpha 1 Subunit/metabolism*
;
Antioxidants/pharmacology*
;
Heme Oxygenase-1/metabolism*
4.Influences of dihydromyricetin on proliferation and apoptosis of chondrocytes in osteoarthritis induced by H2O2 through ROS/p38-MAPK signal pathway.
Ying CHENG ; Hui-Juan CHEN ; Ting YANG
China Journal of Orthopaedics and Traumatology 2025;38(4):396-402
OBJECTIVE:
To analyze the influences of dihydromyricetin on the proliferation and apoptosis of chondrocytes in osteoarthritis induced by hydrogen peroxide (H2O2) through reactive oxygen species (ROS)/p38 mitogen activated protein kinase (p38-MAPK) pathway.
METHODS:
Five C57BL/6J mice were euthanized by cervical dislocation after anesthesia. Chondrocytes were extracted and cultured.After passage, the chondrocytes were divided into control group, H2O2 group (0.8 μmol·L-1 H2O2), dihydromyricetin low concentration group (0.8 μmol·L-1 H2O2+20 μmol·L-1 dihydromyricetin), dihydromyricetin high concentration group (0.8 μmol·L-1 H2O2+80 μmol·L-1 dihydromyricetin), and ROS inhibitor N-acetylcysteine (NAC) group (0.8 μmol·L-1 H2O2+5 mmol·L-1 NAC). The activity of chondrocytes was measured by methyl thiazolyl tetrazolium (MTT) assay. The apoptosis rate of chondrocytes was measured by Hoechst 33342 method. The level of ROS in chondrocytes was measured by 2, 7-dichlorofluorescein diacetate (DCFH-DA) fluorescence probe.The level of Type II collagen α1 (Col2α1) mRNA was measured by qRT-PCR.And the expression of Col2α1, p-p38-MAPK/p38-MAPK, B cell lymphoma gene-2 (Bcl-2) and Bcl-2 associated X protein (Bax) proteins was detected by Western blot.
RESULTS:
The chondrocytes showed swirling fibrous mass, and the expression of COL2α was positive. Compared with the control group, the chondrocyte viability, apoptosis rate, ROS fluorescence intensity, p-p38-MAPK/p38-MAPK, and the expression of Bax protein in H2O22 group increased, the level of Col2α1 mRNA, and the expression of Col2α1 and Bcl-2 proteins decreased (P<0.05). Compared with H2O2 group, the chondrocyte viability, apoptosis rate, ROS fluorescence intensity, p-p38-MAPK/p38-MAPK, and the expression of Bax protein in dihydromyricetin low concentration group, dihydromyricetin high concentration group, and NAC group decreased, the level of Col2α1 mRNA, and the expression of Col2α1 and Bcl-2 proteins increased (P<0.05).
CONCLUSION
Dihydromyricetin may inhibit chondrocyte apoptosis, inflammatory reaction and oxidative stress by inhibiting ROS/p38-MAPK pathway. Dihydromyricetin may be a potential drug for treating osteoarthritis.
Animals
;
Chondrocytes/metabolism*
;
Apoptosis/drug effects*
;
Hydrogen Peroxide/toxicity*
;
Osteoarthritis/physiopathology*
;
Mice, Inbred C57BL
;
Reactive Oxygen Species/metabolism*
;
Mice
;
Flavonols/pharmacology*
;
p38 Mitogen-Activated Protein Kinases/genetics*
;
Cell Proliferation/drug effects*
;
Male
;
Signal Transduction/drug effects*
;
MAP Kinase Signaling System/drug effects*
;
Cells, Cultured
5.Neuroprotective and antidiabetic lanostane-type triterpenoids from the fruiting bodies of Ganoderma theaecolum.
Jiaocen GUO ; Li YANG ; Luting DAI ; Qingyun MA ; Jiaoyang YAN ; Qingyi XIE ; Yougen WU ; Haofu DAI ; Youxing ZHAO
Chinese Journal of Natural Medicines (English Ed.) 2025;23(2):245-256
Eight previously undescribed lanostane triterpenoids, including five nortriterpenoids with 26 carbons, ganothenoids A-E (1-5), and three lanostanoids, ganothenoids F-H (6-8), along with 24 known ones (9-32), were isolated from the fruiting bodies of Ganodrma theaecolum. The structures of the novel compounds were elucidated using comprehensive spectroscopic methods, including electronic circular dichroism (ECD) and nuclear magnetic resonance (NMR) calculations. Compounds 1-32 were assessed for their neuroprotective effects against H2O2-induced damage in human neuroblastoma SH-SY5Y cells, as well as their inhibitory activities against protein tyrosine phosphatase 1B (PTP1B) and α-glucosidase. Compound 4 demonstrated the most potent neuroprotective activity against H2O2-induced oxidative stress by suppressing G0/G1 phase cell cycle arrest, reducing reactive oxygen species (ROS) levels, and inhibiting cell apoptosis through modulation of B-cell lymphoma 2 protein (Bcl-2) and Bcl-2 associated X-protein (Bax) protein expression. Compounds 26, 12, and 28 exhibited PTP1B inhibitory activities with IC50 values ranging from 13.92 to 56.94 μmol·L-1, while compound 12 alone displayed significant inhibitory effects on α-glucosidase with an IC50 value of 43.56 μmol·L-1. Additionally, enzyme kinetic analyses and molecular docking simulations were conducted for compounds 26 and 12 with PTP1B and α-glucosidase, respectively.
Humans
;
Fruiting Bodies, Fungal/chemistry*
;
Triterpenes/isolation & purification*
;
Neuroprotective Agents/isolation & purification*
;
Protein Tyrosine Phosphatase, Non-Receptor Type 1/metabolism*
;
Ganoderma/chemistry*
;
Apoptosis/drug effects*
;
Hypoglycemic Agents/isolation & purification*
;
Molecular Structure
;
alpha-Glucosidases/metabolism*
;
Cell Line, Tumor
;
Reactive Oxygen Species/metabolism*
;
Oxidative Stress/drug effects*
;
Hydrogen Peroxide/toxicity*
;
Molecular Docking Simulation
6.Hydrogen Sulfide Alleviates Lipid Peroxidation-Mediated Carbonyl Stress in Uranium-Intoxicated Kidney Cells via Nrf2/ARE Signaling.
Jia Lin LIU ; Min WANG ; Rui ZHANG ; Ji Fang ZHENG ; Xi Xiu JIANG ; Qiao Ni HU
Biomedical and Environmental Sciences 2025;38(4):484-500
OBJECTIVE:
To explore the protective effects and underlying mechanisms of H 2S against lipid peroxidation-mediated carbonyl stress in the uranium-treated NRK-52E cells.
METHODS:
Cell viability was evaluated using CCK-8 assay. Apoptosis was measured using flow cytometry. Reagent kits were used to detect carbonyl stress markers malondialdehyde, 4-hydroxynonenal, thiobarbituric acid reactive substances, and protein carbonylation. Aldehyde-protein adduct formation and alcohol dehydrogenase, aldehyde dehydrogenase 2, aldo-keto reductase, nuclear factor E2-related factor 2 (Nrf2), and cystathionine β-synthase (CBS) expression were determined using western blotting or real-time PCR. Sulforaphane (SFP) was used to activate Nrf2. RNA interference was used to inhibit CBS expression.
RESULTS:
GYY4137 (an H 2S donor) pretreatment significantly reversed the uranium-induced increase in carbonyl stress markers and aldehyde-protein adducts. GYY4137 effectively restored the uranium-decreased Nrf2 expression, nuclear translocation, and ratio of nuclear to cytoplasmic Nrf2, accompanied by a reversal of the uranium-decreased expression of CBS and aldehyde-metabolizing enzymes. The application of CBS siRNA efficiently abrogated the SFP-enhanced effects on the expression of CBS, Nrf2 activation, nuclear translocation, and ratio of nuclear to cytoplasmic Nrf2 and concomitantly reversed the SFP-enhanced effects of the uranium-induced mRNA expression of aldehyde-metabolizing enzymes. Simultaneously, CBS siRNA reversed the SFP-mediated alleviation of the uranium-induced increase in reactive aldehyde levels, apoptosis rates, and uranium-induced cell viability.
CONCLUSION
H 2S induces Nrf2 activation and nuclear translocation, which modulates the expression of aldehyde-metabolizing enzymes and the CBS/H 2S axis. Simultaneously, the Nrf2-controlled CBS/H 2S axis may at least partially promote Nrf2 activation and nuclear translocation. These events form a cycle-regulating mode through which H 2S attenuates the carbonyl stress-mediated NRK-52E cytotoxicity triggered by uranium.
NF-E2-Related Factor 2/genetics*
;
Animals
;
Hydrogen Sulfide/pharmacology*
;
Rats
;
Signal Transduction/drug effects*
;
Lipid Peroxidation/drug effects*
;
Cell Line
;
Uranium/toxicity*
;
Antioxidant Response Elements
;
Kidney/metabolism*
;
Oxidative Stress/drug effects*
;
Cell Survival/drug effects*
;
Apoptosis/drug effects*
7.Investigating the protective effect of naringenin on hydrogen peroxide induced oxidative damage of human periodontal ligament stem cells by regulating the forkhead box protein O-1/β-catenin pathway.
Li ZHANG ; Shiyuan PENG ; Feiyang TANG ; Jingwei JIAN ; Shuosheng YUAN ; Xiaomei XU
West China Journal of Stomatology 2025;43(4):559-569
OBJECTIVES:
Investigating the protective effect of naringenin (NAR) on the osteogenic potential of human periodontal ligament stem cells (hPDLSCs) under oxidative stress and its related mechanisms.
METHODS:
The oxidative damage model of hPDLSCs was established using hydrogen peroxide (H2O2) andthe hPDLSCs were treated with different concentrations of NAR and 0.5 μmol/L forkhead box protein O-1 (FOXO1) inhibitor AS1842856. After that, the cell counting kit-8 (CCK8) was used to determine the optimal concentrations of H2O2 and NAR. The alkaline phosphatase (ALP) staining and real time fluorescent quantitative reverse transcription polymerase chain reaction (qRT-PCR) were employed to assess the expression of ALP, runt-related transcription factor 2 (RUNX2) and osteocalcin (OCN) in hPDLSCs of each group. The enzyme-linked immunosorbent assay (ELISA) and 2',7'-dichlorofluorescin diacetate (DCFH-DA) staining were utilized to evaluate the expression of reactive oxygen species (ROS), malondialdehyde (MDA) and lactate dehydrogenase (LDH) in hPDLSCs. Meanwhile, qRT-PCR and western blot were used to detect the expression levels of FOXO1 and β-catenin, both are pathway related genes and proteins.
RESULTS:
H2O2 exposure led to an increase in oxidative damage in hPDLSCs, characterized by a rise in intracellular ROS levels and increased expression of MDA and LDH (P<0.05). At the same time, the osteogenic differentiation ability of hPDLSCs decreased, as evidenced by lighter ALP staining and reduced expression levels of osteogenic differentiation-related genes ALP, RUNX2 and OCN (P<0.05). Co-treatment with NAR alleviated the oxidative damage in hPDLSCs, enhanced their antioxidant capacity, and restored their osteogenic ability. The FOXO1 inhibitor AS1842856 downregulated the expression of β-catenin (P<0.05) and significantly diminished both the antioxidant effect of NAR and its ability to restore osteogenesis (P<0.05).
CONCLUSIONS
NAR can enhance the antioxidant capacity of hPDLSCs by activating the FOXO1/β-catenin signaling pathway within hPDLSCs, thereby mitigating oxidative stress damage and alleviating the loss of osteogenic capacity.
Humans
;
Oxidative Stress/drug effects*
;
Periodontal Ligament/cytology*
;
Hydrogen Peroxide
;
Forkhead Box Protein O1/metabolism*
;
Stem Cells/cytology*
;
Flavanones/pharmacology*
;
beta Catenin/metabolism*
;
Osteogenesis/drug effects*
;
Signal Transduction
;
Core Binding Factor Alpha 1 Subunit/metabolism*
;
Alkaline Phosphatase/metabolism*
;
Osteocalcin/metabolism*
;
Cells, Cultured
;
Cell Differentiation/drug effects*
8.Expression and enzymatic characterization of a chitosanase with tolerance to a wide range of pH from Bacillus atrophaeus.
Wenjuan DU ; Awagul TURSUN ; Zhiqin DONG ; Huijuan MA ; Zhenghai MA
Chinese Journal of Biotechnology 2025;41(1):352-362
To screen and identify a chitosanase with high stability, we cloned the chitosanase gene from Bacillus atrophaeus with a high protease yield from the barren saline-alkali soil and expressed this gene in Escherichia coli. The expressed chitosanase of B. atrophaeus (BA-CSN) was purified by nickel-affinity column chromatography. The properties including optimal temperature, optimal pH, substrate specificity, and kinetic parameters of BA-CSN were characterized. The results showed that BA-CSN had the molecular weight of 31.13 kDa, the optimal temperature of 55 ℃, the optimal pH 5.5, and good stability at temperatures below 45 ℃ and pH 4.0-9.0. BA-CSN also had good stability within 4 h of pH 3.0 and 10.0, be activated by K+, Na+, Mn2+, Ca2+, Mg2+, and Co2+, (especially by Mn2+), and be inhibited by Fe3+, Cu2+, and Ag+. BA-CSN showcased the highest relative activity in the hydrolysis of colloidal chitosan, and it had good hydrolysis ability for colloidal chitin. Under the optimal catalytic conditions, BA-CSN demonstrated the Michaelis constant Km and maximum reaction rate Vmax of 9.94 mg/mL and 26.624 μmoL/(mL·min), respectively, for colloidal chitosan. In short, BA-CSN has strong tolerance to acids and alkali, possessing broad industrial application prospects.
Bacillus/genetics*
;
Hydrogen-Ion Concentration
;
Escherichia coli/metabolism*
;
Glycoside Hydrolases/biosynthesis*
;
Substrate Specificity
;
Enzyme Stability
;
Chitosan/metabolism*
;
Temperature
;
Kinetics
;
Cloning, Molecular
;
Bacterial Proteins/biosynthesis*
;
Recombinant Proteins/genetics*
9.Construction of novel transmembrane fusion antioxidant enzymes and their protective effect against hydrogen peroxide-mediated cellular oxidative damage.
Jianru PAN ; Ziyi ZHANG ; Jinnan CHU ; Yanan HAN ; Xueying ZHENG ; Shirong CAI ; Huocong HE
Chinese Journal of Biotechnology 2025;41(4):1547-1558
Reactive oxygen species (ROS) are major contributors to radiation therapy-induced side effects in cancer patients. A fusion antioxidant enzyme comprising glutathione S-transferase (GST), superoxide dismutase 1 (SOD1), and a transmembrane peptide has been shown to effectively mitigate ROS-induced damage. To enhance its targeting capability, the fusion protein was further modified by incorporating a matrix metalloproteinase-2/9 substrate peptide (X) and the transmembrane peptide R9, yielding the antioxidant enzyme GST-SOD1-X-R9 (GS1XR). This modification reduced its transmembrane ability in tumor cells, thereby selectively protecting normal cells from oxidative stress. However, the use of non-human GST poses potential immunogenicity risks. In this study, we employed seamless cloning technology to construct an expression vector containing the human GST gene to replace the non-human GST gene, and then expressed and purified novel fusion antioxidant enzymes GS1R and GS1XR. The protective effects of newly constructed GS1R and GS1XR against hydrogen peroxide (H2O2)-induced oxidative damage in L-02 cells were then evaluated using GS1 as a control. Enzymatic activity assays revealed that the specific activity of GST in GS1XR remained unchanged compared to the unmodified protein, while SOD activity was enhanced. Exposure to 200 μmol/L H₂O₂ transiently activated the nuclear factor-erythroid 2-related factor 2 (Nrf2) pathway; however, this activation diminished after 24 h, reducing cell viability to 48.4%. Both GS1R and GS1XR effectively scavenged intracellular ROS, directly counteracting oxidative stress and promoting Nrf2 nuclear translocation, thereby activating antioxidant pathways and restoring cell viability to normal levels. The two enzymes showed comparable efficacy. In contrast, GS1, lacking transmembrane capability, was restricted to scavenging extracellular ROS and provided only limited protection. In conclusion, both novel fusion antioxidant enzymes demonstrated significant potential in safeguarding normal cells from ROS-mediated oxidative damage. The findings provide a foundation for further investigation in related field.
Humans
;
Oxidative Stress/drug effects*
;
Hydrogen Peroxide
;
Antioxidants/metabolism*
;
Glutathione Transferase/metabolism*
;
Recombinant Fusion Proteins/pharmacology*
;
Superoxide Dismutase-1
;
Reactive Oxygen Species/metabolism*
;
Superoxide Dismutase/biosynthesis*
10.AcidBasePred: a protein acid-base tolerance prediction platform based on deep learning.
Rong HUANG ; Hejian ZHANG ; Min WU ; Zhiyue MEN ; Huanyu CHU ; Jie BAI ; Hong CHANG ; Jian CHENG ; Xiaoping LIAO ; Yuwan LIU ; Yajian SONG ; Huifeng JIANG
Chinese Journal of Biotechnology 2024;40(12):4670-4681
The structures and activities of enzymes are influenced by pH of the environment. Understanding and distinguishing the adaptation mechanisms of enzymes to extreme pH values is of great significance for elucidating the molecular mechanisms and promoting the industrial applications of enzymes. In this study, the ESM-2 protein language model was used to encode the secreted microbial proteins with the optimal performance above pH 9 and below pH 5, which yielded 47 725 high-pH protein sequences and 66 079 low-pH protein sequences, respectively. A deep learning model was constructed to identify protein acid-base tolerance based on amino acid sequences. The model showcased significantly higher accuracy than other methods, with the overall accuracy of 94.8%, precision of 91.8%, and a recall rate of 93.4% on the test set. Furthermore, we built a website (https://enzymepred.biodesign.ac.cn), which enabled users to predict the acid-base tolerance by submitting the protein sequences of enzymes. This study has accelerated the application of enzymes in various fields, including biotechnology, pharmaceuticals, and chemicals. It provides a powerful tool for the rapid screening and optimization of industrial enzymes.
Deep Learning
;
Hydrogen-Ion Concentration
;
Amino Acid Sequence
;
Enzymes/metabolism*
;
Sequence Analysis, Protein
;
Proteins/metabolism*
;
Bacterial Proteins/metabolism*

Result Analysis
Print
Save
E-mail