1.The Mechanism of Exercise Regulating Intestinal Flora in The Prevention and Treatment of Depression
Lei-Zi MIN ; Jing-Tong WANG ; Qing-Yuan WANG ; Yi-Cong CUI ; Rui WANG ; Xin-Dong MA
Progress in Biochemistry and Biophysics 2025;52(6):1418-1434
Depression, a prevalent mental disorder with significant socioeconomic burdens, underscores the urgent need for safe and effective non-pharmacological interventions. Recent advances in microbiome research have revealed the pivotal role of gut microbiota dysbiosis in the pathogenesis of depression. Concurrently, exercise, as a cost-effective and accessible intervention, has demonstrated remarkable efficacy in alleviating depressive symptoms. This comprehensive review synthesizes current evidence on the interplay among exercise, gut microbiota modulation, and depression, elucidating the mechanistic pathways through which exercise ameliorates depressive symptoms via the microbiota-gut-brain (MGB) axis. Depression is characterized by gut microbiota alterations, including reduced alpha and beta diversity, depletion of beneficial taxa (e.g., Bifidobacterium, Lactobacillus, and Coprococcus), and overgrowth of pro-inflammatory and pathogenic bacteria (e.g., Morganella, Klebsiella, and Enterobacteriaceae). Metagenomic analyses reveal disrupted metabolic functions in depressive patients, such as diminished synthesis of short-chain fatty acids (SCFAs), impaired tryptophan metabolism, and dysregulated bile acid conversion. For instance, Bifidobacterium longum deficiency correlates with reduced synthesis of neuroactive metabolites like homovanillic acid, while decreased Coprococcus abundance limits butyrate production, exacerbating neuroinflammation. Furthermore, elevated levels of indole derivatives from Clostridium species inhibit serotonin (5-HT) synthesis, contributing to depressive phenotypes. These dysbiotic profiles disrupt the MGB axis, triggering systemic inflammation, neurotransmitter imbalances, and hypothalamic-pituitary-adrenal (HPA) axis hyperactivity. Exercise exerts profound effects on gut microbiota composition, diversity, and metabolic activity. Longitudinal studies demonstrate that sustained aerobic exercise increases alpha diversity, enriches SCFA-producing genera (e.g., Faecalibacterium prausnitzii, Roseburia, and Akkermansia), and suppresses pathobionts (e.g., Desulfovibrio and Streptococcus). For example, a meta-analysis of 25 trials involving 1 044 participants confirmed that exercise enhances microbial richness and restores the Firmicutes/Bacteroidetes ratio, a biomarker of metabolic health. Notably, endurance training promotes Veillonella proliferation, which converts lactate into propionate, enhancing energy metabolism and delaying fatigue. Exercise also strengthens intestinal barrier integrity by upregulating tight junction proteins (e.g., ZO-1, occludin), thereby reducing lipopolysaccharide (LPS) translocation and systemic inflammation. However, excessive exercise may paradoxically diminish microbial diversity and exacerbate intestinal permeability, highlighting the importance of moderate intensity and duration. Exercise ameliorates depressive symptoms through multifaceted interactions with the gut microbiota, primarily via 4 interconnected pathways. First, exercise mitigates neuroinflammation by elevating anti-inflammatory SCFAs such as butyrate, which suppresses NF-κB signaling to attenuate microglial activation and oxidative stress in the hippocampus. Animal studies demonstrate that voluntary wheel running reduces hippocampal TNF‑α and IL-17 levels in stress-induced depression models, while fecal microbiota transplantation (FMT) from exercised mice reverses depressive behaviors by modulating the TLR4/NF‑κB pathway. Second, exercise regulates neurotransmitter dynamics by enriching GABA-producing Lactobacillus and Bifidobacterium, thereby counteracting neuronal hyperexcitability. Aerobic exercise also enhances the abundance of Lactobacillus plantarum and Streptococcus thermophilus, which facilitate 5-HT and dopamine synthesis. Clinical trials reveal that 12 weeks of moderate exercise increases fecal Coprococcus and Blautia abundance, correlating with improved 5-HT bioavailability and reduced depression scores. Third, exercise normalizes HPA axis hyperactivity by reducing cortisol levels and restoring glucocorticoid receptor sensitivity. In rodent models, chronic stress-induced corticosterone elevation is reversed by probiotic supplementation (e.g., Lactobacillus), which enhances endocannabinoid signaling and hippocampal neurogenesis. Furthermore, exercise upregulates brain-derived neurotrophic factor (BDNF) via microbial metabolites like butyrate, promoting histone acetylation and synaptic plasticity. FMT experiments confirm that exercise-induced microbiota elevates prefrontal BDNF expression, reversing stress-induced neuronal atrophy. Fourth, exercise reshapes microbial metabolic crosstalk, diverting tryptophan metabolism toward 5-HT synthesis instead of neurotoxic kynurenine derivatives. Butyrate inhibits indoleamine 2,3-dioxygenase (IDO), a key enzyme in the kynurenine pathway linked to depression. Concurrently, exercise-induced Akkermansia enrichment enhances mucin production, fortifies the gut barrier, and reduces LPS-driven neuroinflammation. Collectively, these mechanisms underscore exercise as a potent modulator of the microbiota-gut-brain axis, offering a holistic approach to alleviating depression through microbial and neurophysiological synergy. Current evidence supports exercise as a potent adjunct therapy for depression, with personalized regimens (e.g., aerobic, resistance, or yoga) tailored to individual microbiota profiles. However, challenges remain in optimizing exercise prescriptions (intensity, duration, and type) and integrating them with probiotics, prebiotics, or FMT for synergistic effects. Future research should prioritize large-scale randomized controlled trials to validate causality, multi-omics approaches to decipher MGB axis dynamics, and mechanistic studies exploring microbial metabolites as therapeutic targets. The authors advocate for a paradigm shift toward microbiota-centric interventions, emphasizing the bidirectional relationship between physical activity and gut ecosystem resilience in mental health management. In conclusion, this review underscores exercise as a multifaceted modulator of the gut-brain axis, offering novel insights into non-pharmacological strategies for depression. By bridging microbial ecology, neuroimmunology, and exercise physiology, this work lays a foundation for precision medicine approaches targeting the gut microbiota to alleviate depressive disorders.
2.Mechanism of salvianolic acid B protecting H9C2 from OGD/R injury based on mitochondrial fission and fusion
Zi-xin LIU ; Gao-jie XIN ; Yue YOU ; Yuan-yuan CHEN ; Jia-ming GAO ; Ling-mei LI ; Hong-xu MENG ; Xiao HAN ; Lei LI ; Ye-hao ZHANG ; Jian-hua FU ; Jian-xun LIU
Acta Pharmaceutica Sinica 2024;59(2):374-381
This study aims to investigate the effect of salvianolic acid B (Sal B), the active ingredient of Salvia miltiorrhiza, on H9C2 cardiomyocytes injured by oxygen and glucose deprivation/reperfusion (OGD/R) through regulating mitochondrial fission and fusion. The process of myocardial ischemia-reperfusion injury was simulated by establishing OGD/R model. The cell proliferation and cytotoxicity detection kit (cell counting kit-8, CCK-8) was used to detect cell viability; the kit method was used to detect intracellular reactive oxygen species (ROS), total glutathione (t-GSH), nitric oxide (NO) content, protein expression levels of mitochondrial fission and fusion, apoptosis-related detection by Western blot. Mitochondrial permeability transition pore (MPTP) detection kit and Hoechst 33342 fluorescence was used to observe the opening level of MPTP, and molecular docking technology was used to determine the molecular target of Sal B. The results showed that relative to control group, OGD/R injury reduced cell viability, increased the content of ROS, decreased the content of t-GSH and NO. Furthermore, OGD/R injury increased the protein expression levels of dynamin-related protein 1 (Drp1), mitofusions 2 (Mfn2), Bcl-2 associated X protein (Bax) and cysteinyl aspartate specific proteinase 3 (caspase 3), and decreased the protein expression levels of Mfn1, increased MPTP opening level. Compared with the OGD/R group, it was observed that Sal B had a protective effect at concentrations ranging from 6.25 to 100 μmol·L-1. Sal B decreased the content of ROS, increased the content of t-GSH and NO, and Western blot showed that Sal B decreased the protein expression levels of Drp1, Mfn2, Bax and caspase 3, increased the protein expression level of Mfn1, and decreased the opening level of MPTP. In summary, Sal B may inhibit the opening of MPTP, reduce cell apoptosis and reduce OGD/R damage in H9C2 cells by regulating the balance of oxidation and anti-oxidation, mitochondrial fission and fusion, thereby providing a scientific basis for the use of Sal B in the treatment of myocardial ischemia reperfusion injury.
3.Exosomal miRNA-222 Alerts shRNA-PCSK9 Induction Brain Tau Hyperphosphorylation
Lei WANG ; Qian JIANG ; Hong WANG ; Ling YUAN ; Nan LYU ; Di HAO ; Xiaoxue CUI ; Zi WANG
Chinese Journal of Modern Applied Pharmacy 2024;41(5):636-643
OBJECTIVE
To investigate whether the microRNA-222(miRNA-222) carried by plasma exosomes can serve as an early warning marker for cognitive impairment induced by shRNA-PCSK9.
METHODS
The high-fat diet(HFD) was used to prepare a hypercholesterolemic mouse model group. The model group mice were divided into HFD-shRNA control group and HFD-shRNA-PCSK9 group. The shRNA-PCSK9 was constructed, injected intravenously into the body, and the expression of PCSK9 mRNA was detected by real-time PCR(RT-PCR). Tau protein and phosphorylation in brain tissue were observed by immunohistochemistry (IHC). Western blotting was used to detect Tau protein and P-Tau protein. Serum amyloid Aβ1-42Ab levels were determined by ELISA. The kits extracted plasma exosomes step by step, identify the exosome morphology by negative staining electron microscopy, and determined the size of exosomes by NTA technology. RT-PCR technique was used to detect the expression level of miRNA-222 carried in plasma exosomes.
RESULTS
The model mouse were prepared by feeding HFD for 13 weeks, whose total cholesterol(TC) and low-density lipoprotein(LDL-C) contents in serum were significantly increased. At the same time, the expression of PCSK9 mRNA in the brain tissue of model group was significantly increased. After shRNA-PCSK9 lentivirus interference, PCSK9 mRNA expression was inhibited, and IHC observed that shRNA-PCSK9 induced abnormal expression and hyperphosphorylation of Tau protein in brain tissue, indicating that the pathological changes of neurofibrillary tangles had occurred. However, at this time, serum Aβ1-42Ab had not been significantly increased, and it had not yet been of significance for the diagnosis of cognitive impairment. The miRNA in plasma exosomes was extracted, and RT-PCR results showed that the expression of miRNA-222 carried in the exosomes of the HFD-shRNA-PCSK9 group was significantly lower than that of the HFD-shRNA control group.
CONCLUSION
Plasma exosomes carried miRNA-222 provides an early warning marker for shRNA-PCSK9- induced cognitive impairment.
4.Influencing factors in scale-up of extraction process for Yunpi Xiaoshi Prescription
Xin-Rong LIN ; Zi-Wei GAO ; Ya-Chun SHU ; Xia ZHAO ; Lei WU
Chinese Traditional Patent Medicine 2024;46(2):391-396
AIM To investigate the influencing factors in scale-up of extraction process for Yunpi Xiaoshi Prescription.METHODS HPLC was adopted in the content determination of catechin,ferulic acid,taxifolin,isovitexin,narirutin,atractylenolideⅡ,naringin,morin,hesperidin,luteolin,hederagenin,atractylenolideⅠ,naringenin and hesperetin,the fingerprints were established,after which the effects of container volume,optimal fire and feeding quantity on the contents of various constituents were evaluated.RESULTS Fifteen batches of samples demonstrated the similarities of more than 0.995.Fourteen constituents showed good linear relationships within their own ranges(r>0.999 0),whose average recoveries were 96.4%-103.3%with the RSDs of 0.5%-2.7%.The influencing degree of optimal fire was greater than that of container volume and feeding quantity.CONCLUSION The combination of multi-component content determination and fingerprints can provide data basis and theoretical reference for the technology of consistency evaluation in scale-up of extraction process for Yunpi Xiaoshi Prescription.
5.Experimental study on anti-fatigue effect of Polysaccharides of Panax notoginseng
Pan-Pan WEI ; Zi-Jun YAN ; Meng-Yue DENG ; Die XIA ; Yu-Zhen DING ; Lei ZHANG ; Tong CHEN
The Chinese Journal of Clinical Pharmacology 2024;40(1):87-91
Objective To explore the effect of Polysaccharides of Panax notoginseng(PPN)on anti-exercise fatigue in mice.Methods One hundred male KM mice were randomly divided into negative control group,positive control group and experimental-L,-M,-H groups,with 20 cases per group.Experimental-L,-M,-H groups was given 100,200,400 mg·kg-1 PPN,respectively;positive control group was given 200 mg·kg-1 vitamin C;negative control group was given 0.1 mL·10 g-1 0.9%NaCl.Five groups were gavaged once a day for 28 days.After the last administration,the loaded swimming time was measured;after 90 minutes of the unloaded swimming test,the mice were allowed to rest for 30 minutes,the levels of lactic acid(LD),blood urea nitrogen(BUN),glycogen,and malondialdehyde(MDA)were measured,the safety of PPN with organ indices and histopathology.Results LD levels in negative control group,positive control group and experimental-L,-M,-Hgroupswere(4.76±0.84),(2.86±0.34),(3.00±0.69),(2.35±0.65)and(1.39±0.48)mg·kg-1;BUN contents were(13.65±1.25),(12.55±0.91),(12.12±1.24),(11.06±1.30)and(9.85±1.05)mmol·L-1;liver glycogen contents were(3.24±0.56),(11.11±2.16),(5.61±1.41),(6.60±1.49)and(12.05±2.25)mg·g-1;MDA levels were(2.36±0.21),(1.23±0.41),(1.93±0.23),(1.73±0.21)and(1.04±0.18)mg prot·mL-1.Compared with negative control group,the differences of above indexes in the positive control group and experimental-L,-M,-H groups were statistically significant(P<0.05,P<0.01,P<0.001).Conclusion PPN can increase exercise endurance in mice and has an anti-fatigue effect.This study provides a theoretical basis for the application of PPN in the field of anti-fatigue research.
6.Antioxidant activity and organ protection of Panax notoginseng polysaccharide on oxidative damage and aging model mice
Meng-Yue DENG ; Pan-Pan WEI ; Ming LI ; Zi-Jun YAN ; Die XIA ; Yu-Zhen DING ; Lei ZHANG ; Tong CHEN
The Chinese Journal of Clinical Pharmacology 2024;40(6):889-893
Objective To study the antioxidant activity and organ protection of different components of Panax notoginseng polysaccharide(PNPS)in D-galactose-induced oxidative damage aging model mice.Methods KM mice were randomly divided into normal group,model group,vitamin C(VC)group(given 200 mg·kg-1 VC),crude polysaccharide from Panax notoginseng(CPPN)group,neutral polysaccharide from Panax notoginseng(NPPN)group and acidic polysaccharide from Panax notoginseng(APPN-Ⅰ,APPN-Ⅱ,APPN-Ⅲ)group(given 400 mg·kg-1 CPPN,NPPN,APPN-Ⅰ,APPN-Ⅱ,APPN-Ⅲ,respectively).Except for the normal group,oxidative injury aging mouse models were established by intraperitoneal injection of 1 g·kg-1 D-galactose.The mice were sacrificed after continuous administration for 42 days,and serum and liver homogenate were prepared.Malondialdehyde(MDA)was determined by thiobarbituric acid method;superoxide dismutase(SOD)was determined by tetrazole salt method;glutathione peroxidase(GSH-Px)was determined by double antibody sandwich method.Results Serum SOD in the normal group,model group,VC group,CPPN group,NPPN group and APPN-Ⅰ,APPN-Ⅱ,APPN-Ⅲ groups were(15.07±0.69),(12.79±1.51),(15.56±1.01),(13.69±0.96),(14.27±0.64),(14.31±0.99),(14.18±0.79)and(15.85±0.89)U·mL-1;serum GSH-Px were(105.35±4.97),(90.36±4.31),(111.51±7.00),(113.03±8.06),(118.77±5.19),(123.60±8.08),(131.65±3.60)and(149.22±13.32)ng·L-1;serum MDA were(1.72±0.26),(4.16±0.92),(2.26±0.59),(2.82±0.47),(2.46±0.50),(1.98±0.41),(2.39±0.39)and(2.07±0.24)nmol·mL-1;the liver SOD were(234.22±3.84),(205.04±7.28),(234.63±6.37),(214.99±17.66),(234.13±3.63),(234.63±3.44),(233.87±5.63)and(235.42±2.33)U·mgprot-1;liver GSH-Px were(274.27±23.72),(207.00±15.22),(257.68±16.39),(249.79±18.78),(252.62±10.92),(256.25±21.83),(261.20±17.52)and(263.16±17.98)ng·L-1;liver MDA were(35.70±3.52),(49.65±6.32),(36.15±2.48),(39.17±4.29),(37.40±6.19),(35.34±4.06)and(35.90±5.36),(33.31±7.64)nmol·mgprot-1.Compared with the normal group,SOD,GSH-Px in serum and liver of mice in the model group were significantly reduced,and the content of MDA was significantly increased(all P<0.01).After treatment with different components of Panax notoginseng polysaccharide,the oxidative indicators in mice were significantly improved,among which APPN-Ⅲ have the best antioxidant activity,which could significantly increase the activities of SOD,GSH-Px in serum and liver,and reduce the content of MDA(all P<0.01).Conclusion Different components of Panax notoginseng polysaccharide have antioxidant activity and organ protection in vivo,among which APPN-Ⅲ has the best antioxidant activity and has a good organ protection effect.
7.Clinical trial of tiotropium bromide combined with salmeterol fluticasone in the treatment of lung cancer patients with COPD in stable stage
Zi-Lei XUAN ; Rui-Yang DING ; Wen-Zhu YANG
The Chinese Journal of Clinical Pharmacology 2024;40(8):1096-1100
Objective To investigate the effects of tiotropium bromide combined with salmeterol fluticasone on postoperative lung function,blood gas index,and inflammatory response in patients with lung cancer complicated with stable chronic obstructive pulmonary disease(COPD).Methods Patients with lung cancer complicated with stable COPD after surgery were selected as research subjects and divided into control group and treatment group according to different treatment methods.The control group received 18 μg of tiotropium bromide powder for inhalation therapy,bid,for 3 days before surgery,while the treatment group received additional salmeterol inhalation powder treatment on basis of the control group's treatment,1 inhalation each time,bid,for 3 months.Lung function[forced vital capacity(FVC),forced expiratory volume in one second(FEV1),peak expiratory flow(PEF),FEV1/FVC],modified British Medical Research Council(mMRC)dyspnea scale,chronic obstructive pulmonary disease assessment test(CAT)score,quality of life questionnaire-C30(QLQ-C30)score,blood gas index[arterial oxygen pressure(PaO2),arterial blood oxygen saturation(SaO2),arterial carbon dioxide pressure(PaCO2)],inflammatory response indicators[interleukin-6(IL-6),interleukin-8(IL-8),tumor necrosis factor-α(TNF-α)],and occurrence of adverse drug reactions in the two groups with compared before and after treatment.Results Forty-seven and forty-five cases were included in the treatment and control groups,respectively.After treatment,the total effective rates of the treatment and control groups were 91.49%(43 cases/47 cases)and 75.56%(34 cases/45 cases)respectively,and the differences were statistically significant(P<0.05).After treatment,the FEV1/FVC of the treatment and control groups were(0.62±0.10)%and(0.48±0.05)%;PEF were(1.94±0.20)and(1.02±0.11)L·s-1;mMRC scores were 2.01±0.25 and 2.26±0.23;CAT scores were 16.03±1.74 and 20.03±2.17;QLQ-C30 physical functioning scores were 79.31±8.92 and 75.04±7.86;PaO2 were(70.34±6.98)and(62.02±6.31)mmHg;IL-6 expression levels were(16.43±1.65)and(21.55±2.27)pg·mL-1.The above indexes in the treatment group compared with the control group were all statistically significant(all P<0.05).The main adverse drug reactions in the treatment and control groups were skin allergies and nausea/vomiting,and the total incidence of adverse drug reactions in the treatment and control groups were 34.04%and 23.40%,with no statistically significant difference(P>0.05).Conclusion Tiotropium bromide combined with salmeterol fluticasone is effective for patients with lung cancer complicated with stable COPD after surgery,which significantly improves their lung function,prognosis,and arterial blood gas levels.
8.Simultaneous determination of 6 aconitum-type alkaloids in Xiaozhong ointment by ultra-high performance liquid chromatography triple quadrupole mass spectrometry
Tian-Li XIA ; De-Ping ZHAO ; Ao XUE ; Mei-Ling JIN ; Zi-Yue ZHU ; Qing LI ; Ning ZHANG ; Xia LEI
The Chinese Journal of Clinical Pharmacology 2024;40(9):1341-1344
Objective To establish a method for the simultaneous determination of aconitine,neoaconitine,hypaconitine,benzoyl aconitine,benzoyl mesaconine and benzoylhypacoitine in Xiaozhong ointment by UPLC-TQD-MS.Methods ACQUITY UPLC BEH C18 column(50 mm ×2.1 mm,1.7 μm),mobile phase 0.1%formic acid water(A)-acetonitrile(B),gradient elution,column temperature 40 ℃,flow rate 0.3 mL·min-1,injection volume 5 μL;electrospray ionization source(ESI+)and multiple reaction monitoring(MRM)were used for mass spectrometry analysis.Results The concentration of aconitine,new aconitine,hypaconitine,benzoyl aconitine,benzoyl new aconitine and benzoyl hypaconitine were 1.0-100.0 ng·mL-1,respectively,the average recovery were 98.62%-101.24%.The mass fractions of the six components were 0.18,0.33,0.38,0.43,0.28,0.06μg·g-1.Conclusion The method can be used to determine the content of 6 aconitine-type alkaloids in Xiaozhong ointment,and provide reference for the quality evaluation and clinical safe use of Xiaozhong ointment.
9.Association of Cytokines with Clinical Indicators in Patients with Drug-Induced Liver Injury
Hua Wei CAO ; Ting Ting JIANG ; Ge SHEN ; Wen DENG ; Yu Shi WANG ; Yu Zi ZHANG ; Xin Xin LI ; Yao LU ; Lu ZHANG ; Yu Ru LIU ; Min CHANG ; Ling Shu WU ; Jiao Yuan GAO ; Xiao Hong HAO ; Xue Xiao CHEN ; Ping Lei HU ; Jiao Meng XU ; Wei YI ; Yao XIE ; Hui Ming LI
Biomedical and Environmental Sciences 2024;37(5):494-502
Objective To explore characteristics of clinical parameters and cytokines in patients with drug-induced liver injury(DILI)caused by different drugs and their correlation with clinical indicators. Method The study was conducted on patients who were up to Review of Uncertainties in Confidence Assessment for Medical Tests(RUCAM)scoring criteria and clinically diagnosed with DILI.Based on Chinese herbal medicine,cardiovascular drugs,non-steroidal anti-inflammatory drugs(NSAIDs),anti-infective drugs,and other drugs,patients were divided into five groups.Cytokines were measured by Luminex technology.Baseline characteristics of clinical biochemical indicators and cytokines in DILI patients and their correlation were analyzed. Results 73 patients were enrolled.Age among five groups was statistically different(P=0.032).Alanine aminotransferase(ALT)(P=0.033)and aspartate aminotransferase(AST)(P=0.007)in NSAIDs group were higher than those in chinese herbal medicine group.Interleukin-6(IL-6)and tumor necrosis factor alpha(TNF-α)in patients with Chinese herbal medicine(IL-6:P<0.001;TNF-α:P<0.001)and cardiovascular medicine(IL-6:P=0.020;TNF-α:P=0.001)were lower than those in NSAIDs group.There was a positive correlation between ALT(r=0.697,P=0.025),AST(r=0.721,P=0.019),and IL-6 in NSAIDs group. Conclusion Older age may be more prone to DILI.Patients with NSAIDs have more severe liver damage in early stages of DILI,TNF-α and IL-6 may partake the inflammatory process of DILI.
10.Nanopore Protein Sequencing
Zi-Yi LI ; Ya-Kun YI ; Lei LIU ; Hai-Chen WU
Progress in Biochemistry and Biophysics 2024;51(10):2498-2518
The success of the Human Genome Project has significantly deepened our understanding of genomics and catalyzed a growing focus on proteomics, as researchers aim to decipher the complex relationship between genes and proteins. Given the central role of proteins in regulating physiological processes—including DNA replication, metabolic reactions, signal transduction, pH balance, and cellular structure—developing advanced protein sequencing technologies is critical. Proteins are fundamental to nearly all biological activities, making their detailed study essential for understanding cellular functions and disease mechanisms. The Edman degradation method, developed in the 1950s, was a breakthrough in sequencing short peptides. However, its limitations in read length (fewer than 50 amino acids) and slow cycle time fall short of modern demands. Mass spectrometry has since emerged as the gold standard in protein sequencing due to its high accuracy, throughput, and reproducibility. The method is enhanced by a robust sample preparation workflow and advances in mass spectrometry technology. Despite these strengths, mass spectrometry faces limitations in dynamic range, sensitivity, read length, and sequence coverage, hindering complete de novo protein sequencing. These technological gaps underscore the need for innovative methods to provide more detailed and accurate protein sequence data. In the past decade, new protein sequencing methods, including tunneling current, fluorescence fingerprinting, and real-time dynamic fluorescence, have shown significant developmental potential. However, these methods are not yet ready for widespread application, as each still faces technical hurdles. Meanwhile, advances in nanopore DNA sequencing have sparked interest in applying nanopore technology to protein sequencing, particularly owing to its speed, convenience, and cost-effectiveness. Unlike DNA sequencing, protein sequencing presents greater challenges due to proteins’ complex three-dimensional structures, heterogeneous electrical charges, difficulties in directional movement, and diverse amino acid compositions, further complicated by post-translational modifications. Researchers have made significant strides in addressing these challenges, such as using unfolding enzymes, high temperatures, high voltage, and deformers to unravel protein structures, and employing charged sequences and electroosmotic flow to control peptide translocation. The latest strategies for nanopore protein sequencing can be broadly categorized into three approaches: strand sequencing, enzyme-assisted nanopore sequencing, and nanopore fingerprinting. In strand sequencing, dragging a protein-oligonucleotide conjugate through a nanopore with the aid of protein motors generates stepped current signals produced by the peptide strand. In enzyme-assisted nanopore sequencing, 20 proteinogenic amino acids and various post-translational modifications have been distinguished using nanopores, and sequencing of short peptides has also been demonstrated. In nanopore fingerprinting, polypeptide fragments resulting from protease digestion of a protein can be identified through nanopore sensing. Despite these advances, further improvements in protein engineering, data processing, identification accuracy, and read length are needed to make these strategies practically useful. This review provides an overview of the current major approaches to nanopore protein sequencing, emphasizing the strategies, recent advances, breakthroughs and challenges in nanopore protein sequencing. As nanopore technology continues to evolve, it is expected to offer more efficient and accurate sequencing solutions in proteomics, potentially leading to new technological breakthroughs in biochemistry and biomedicine.


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