MetDIT: Transforming and Analyzing Clinical Metabolomics Data with Convolutional Neural Networks.

Clinical metabolomics is growing as an essential tool for precision medicine. However, classical machine learning algorithms struggle to comprehensively encode and analyze the metabolomics data due to their high dimensionality and complex intercorrelations. This article introduces a new method called MetDIT, designed to analyze intricate metabolomics data effectively using deep convolutional neural networks (CNN). MetDIT comprises two components: TransOmics and NetOmics. Since CNN models have difficulty in processing one-dimensional (1D) sequence data efficiently, we developed TransOmics, a framework that transforms sequence data into two-dimensional (2D) images while maintaining a one-to-one correspondence between the sequences and images. NetOmics, the second component, leverages a CNN architecture to extract more discriminative representations from the transformed samples. To overcome the overfitting due to the small sample size and class imbalance, we introduced a feature augmentation module (FAM) and a loss function to improve the model performance. Furthermore, we systematically optimized the model backbone and image resolution to balance the model parameters and computational costs. To demonstrate the performance of the proposed MetDIT, we conducted extensive experiments using three different clinical metabolomics data sets and achieved better classification performance than classical machine learning methods used in metabolomics, including Random Forest, SVM, XGBoost, and LightGBM. The source code is available at the GitHub repository at https://github.com/Li-OmicsLab/MetDIT, and the WebApp can be found at http://metdit.bioinformatics.vip/.

A method for mining condition-specific co-expressed genes in Camellia sinensis based on k-means clustering.

BACKGROUND: As one of the world's most important beverage crops, tea plants (Camellia sinensis) are renowned for their unique flavors and numerous beneficial secondary metabolites, attracting researchers to investigate the formation of tea quality. With the increasing availability of transcriptome data on tea plants in public databases, conducting large-scale co-expression analyses has become feasible to meet the demand for functional characterization of tea plant genes. However, as the multidimensional noise increases, larger-scale co-expression analyses are not always effective. Analyzing a subset of samples generated by effectively downsampling and reorganizing the global sample set often leads to more accurate results in co-expression analysis. Meanwhile, global-based co-expression analyses are more likely to overlook condition-specific gene interactions, which may be more important and worthy of exploration and research. RESULTS: Here, we employed the k-means clustering method to organize and classify the global samples of tea plants, resulting in clustered samples. Metadata annotations were then performed on these clustered samples to determine the "conditions" represented by each cluster. Subsequently, we conducted gene co-expression network analysis (WGCNA) separately on the global samples and the clustered samples, resulting in global modules and cluster-specific modules. Comparative analyses of global modules and cluster-specific modules have demonstrated that cluster-specific modules exhibit higher accuracy in co-expression analysis. To measure the degree of condition specificity of genes within condition-specific clusters, we introduced the correlation difference value (CDV). By incorporating the CDV into co-expression analyses, we can assess the condition specificity of genes. This approach proved instrumental in identifying a series of high CDV transcription factor encoding genes upregulated during sustained cold treatment in Camellia sinensis leaves and buds, and pinpointing a pair of genes that participate in the antioxidant defense system of tea plants under sustained cold stress. CONCLUSIONS: To summarize, downsampling and reorganizing the sample set improved the accuracy of co-expression analysis. Cluster-specific modules were more accurate in capturing condition-specific gene interactions. The introduction of CDV allowed for the assessment of condition specificity in gene co-expression analyses. Using this approach, we identified a series of high CDV transcription factor encoding genes related to sustained cold stress in Camellia sinensis. This study highlights the importance of considering condition specificity in co-expression analysis and provides insights into the regulation of the cold stress in Camellia sinensis.

Construction of smartphone-integrated nanozyme sensor based on amino acid-modulated gold nanoparticles.

Amino acids are not only the building blocks of proteins but also lead to the development of novel nanomaterials with unique properties. Herein, we proposed a simple strategy to produce gold nanoparticles (Au NPs) with peroxidase-like (POD-like) activities by using a series of amino acids as reducing agents, named Au NPs@M (M represents different amino acids). The Au NPs@His was identified as the nanozyme with the most potent catalytic performance, which was used in combination with smartphones to achieve rapid detection of hydrogen peroxide with a detection limit of 0.966 µM. It also enables rapid detection of glucose with a detection limit of 2.904 µM, highlighting the significant contribution of Au NPs@His in expediting the detection of critical biomolecules. This work not only provides a convenient and highly efficient method to identify glucose but also shows the potential of histidine as a reducing agent in constructing Au nanomaterials exerting enzyme-like catalysis.

Comprehensive metabolome characterization and comparison between two sources of Dragon's blood by integrating liquid chromatography/mass spectrometry and chemometrics.

Dragon's Blood (DB) serves as a precious Chinese medicine facilitating blood circulation and stasis dispersion. Daemonorops draco (D. draco; Qi-Lin-Jie) and Dracaena cochinchinensis (D. cochinchinenesis; Long-Xue-Jie) are two reputable plant sources for preparing DB. This work was designed to comprehensively characterize and compare the metabolome differences between D. draco and D. cochinchinenesis, by integrating liquid chromatography/mass spectrometry and untargeted metabolomics analysis. Offline two-dimensional liquid chromatography/ion mobility-quadrupole time-of-flight mass spectrometry (2D-LC/IM-QTOF-MS), by utilizing a powerful hybrid scan approach, was elaborated for multicomponent characterization. Configuration of an XBridge Amide column and an HSS T3 column in offline mode exhibited high orthogonality (A0 0.80) in separating the complex components in DB. Particularly, the hybrid high-definition MSE-high definition data-dependent acquisition (HDMSE-HDDDA) in both positive and negative ion modes was applied for data acquisition. Streamlined intelligent data processing facilitated by the UNIFI™ (Waters) bioinformatics platform and searching against an in-house chemical library (recording 223 known compounds) enabled efficient structural elucidation. We could characterize 285 components, including 143 from D. draco and 174 from D. cochinchinensis. Holistic comparison of the metabolomes among 21 batches of DB samples by the untargeted metabolomics workflows unveiled 43 significantly differential components. Separately, four and three components were considered as the marker compounds for identifying D. draco and D. cochinchinenesis, respectively. Conclusively, the chemical composition and metabolomic differences of two DB resources were investigated by a dimension-enhanced analytical approach, with the results being beneficial to quality control and the differentiated clinical application of DB.

Biomimetic mineralization based on self-assembling peptides.

Biomimetic science has attracted great interest in the fields of chemistry, biology, materials science, and energy. Biomimetic mineralization is the process of synthesizing inorganic minerals under the control of organic molecules or biomolecules under mild conditions. Peptides are the motifs that constitute proteins, and can self-assemble into various hierarchical structures and show a high affinity for inorganic substances. Therefore, peptides can be used as building blocks for the synthesis of functional biomimetic materials. With the participation of peptides, the morphology, size, and composition of mineralized materials can be controlled precisely. Peptides not only provide well-defined templates for the nucleation and growth of inorganic nanomaterials but also have the potential to confer inorganic nanomaterials with high catalytic efficiency, selectivity, and biotherapeutic functions. In this review, we systematically summarize research progress in the formation mechanism, nanostructural manipulation, and applications of peptide-templated mineralized materials. These can further inspire researchers to design structurally complex and functionalized biomimetic materials with great promising applications.

Study on Quality Characteristic of Chebulae Fructus and Its Adulterants and Degradation Pathway of Hydrolyzable Tannins.

Chebulae Fructus (CF) is known as one of the richest sources of hydrolyzable tannins (HTs). In this study, ultra-performance liquid chromatography coupled with a photodiode array detector method was established for simultaneous determination of the 12 common phenolcarboxylic and tannic constituents (PTCs). Using this method, quantitative analysis was accomplished in CF and other four adulterants, including Terminaliae Belliricae Fructus, Phyllanthi Fructus, Chebulae Fructus Immaturus, and Canarii Fructus. Based on a quantitative analysis of the focused compounds, discrimination of CF and other four adulterants was successfully accomplished by hierarchical cluster analysis and principal component analysis. Additionally, the total contents of the 12 compounds that we focused on in this study were unveiled as 148.86 mg/g, 96.14 mg/g, and 18.64 mg/g in exocarp, mesocarp, and endocarp and seed of CF, respectively, and PTCs were witnessed to be the most abundant in the exocarp of CF. Noticeably, the HTs (chebulagic acid, chebulanin acid, chebulinic acid, and punicalagin) were observed to be ultimately degraded to chebulic acid, gallic acid, and ellagic acid during sunlight-drying of the fresh fruits. As a result, our study indicated that CF and its adulterants could be distinguished by the observed 12 PTCs, which were mainly distributed in the exocarp of the fruits. The HTs were prone to degrade into the three simple phenolcarboxylic acids during drying or processing, allowing us to obtain a more comprehensive understanding of the PTCs, with great significance in the improved quality of CF and related products.

Exploration of the Dynamic Variations of the Characteristic Constituents and the Degradation Products of Catalpol during the Process of Radix Rehmanniae.

Radix Rehmanniae (RR), a famous traditional Chinese medicine (TCM) widely employed in nourishing Yin and invigorating the kidney, has three common processing forms in clinical practice, including fresh Radix Rehmanniae (FRR), raw Radix Rehmanniae (RRR), and processed Radix Rehmanniae (PRR). However, until now, there has been less exploration of the dynamic variations in the characteristic constituents and degradation products of catalpol as a representative iridoid glycoside with the highest content in RR during the process from FRR to PRR. In this study, an ultra-performance liquid chromatography coupled with photodiode array detector (UPLC-PDA) method was successfully established for the simultaneous determination of ten characteristic components to explore their dynamic variations in different processed products of RR. Among them, iridoid glycosides, especially catalpol, exhibited a sharp decrease from RRR to PRR. Then, three degradation products of catalpol were detected under simulated processing conditions (100 °C, pH 4.8 acetate buffer solution), which were isolated and identified as jiofuraldehyde, cataldehyde, and norviburtinal, respectively. Cataldehyde was first reported as a new compound. Moreover, the specificity of norviburtinal in self-made PRR samples was discovered and validated, which was further confirmed by testing in commercially available PRR samples. In conclusion, our study revealed the decrease in iridoid glycosides and the production of new degradation substances during the process from FRR to PRR, which is critical for unveiling the processing mechanism of RR.

Crude Tieguanyin oolong tea polysaccharides regulate intestinal immune and gut microflora in dextran sulfate sodium-induced mice colitis.

BACKGROUND: The global incidence and prevalence of inflammatory bowel diseases (IBDs) have been increasing. Epidemiological studies, clinical trials, and animal experiments have indicated a negative association between the consumption of tea and IBD. This study aims to investigate the protective effects of crude Tieguanyin oolong tea polysaccharides (CTPS) on experimental colitis, while also exploring the underlying mechanisms. RESULTS: The administration of CTPS significantly alleviated IBD in the mouse model, and was found to regulate T-cell mediated immune responses in the colon by modulating cytokine production associated with T cells. Furthermore, CTPS demonstrated a positive impact on the gut microbiota, reversing the increase in pathogenic Helicobacter and enhancing the relative abundances of beneficial bacteria such as Akkermansia, Lachnospiraceae, and Odoribacter. Oral administration of CTPS also led to an improvement in intestinal metabolism, specifically by increasing the levels of short-chain fatty acids. CONCLUSION: This study provides the first in vivo evidence of the protective effects of CTPS on colitis in mice. The effects are likely facilitated through the regulation of T cell-mediated responses and modulation of the gut microbiota, suggesting that CTPS may be a potential preventive and therapeutic approach for IBD. © 2023 Society of Chemical Industry.

Quantitative Ratiometric Biosensors Based on Fluorescent Ferrocene-Modified Histidine Dipeptide Nanoassemblies.

Fluorescent proteins (FPs) provide a ratiometric readout for quantitative assessment of the destination of internalized biomolecules. FP-inspired peptide nanostructures that can compete with FPs in their capacity are the most preferred building blocks for the synthesis of fluorescent soft matter. However, realizing a ratiometric emission from a single peptide fluorophore remains exclusive since multicolor emission is a rare property in peptide nanostructures. Here, we describe a bioinspired peptidyl platform for ratiometric intracellular quantitation by employing a single ferrocene-modified histidine dipeptide. The intensiometric ratio of green to blue fluorescence correlates linearly with the concentration of the peptide by three orders of magnitude. The ratiometric fluorescence of the peptide is an assembly-induced emission originating from hydrogen bonds and aromatic interactions. Additionally, modular design enables ferrocene-modified histidine dipeptides to use as a general platform for the construction of intricate peptides that retain the ratiometric fluorescent properties. The ratiometric peptide technique promises flexibility in the design of a wide spectrum of stoichiometric biosensors for quantitatively understanding the trafficking and subcellular fate of biomolecules.

Rethreading Design of Ratiometric roGFP2 Mimetic Peptide for Hydrogen Peroxide Sensing.

Reconstruction of the miniaturized peptide to mimic the tailored functions of protein has been attractive but challenging. Herein, initialized from the crystal structure of redox-sensitive green fluorescent protein-2 (roGFP2), we propose a practical approach to construct the roGFP2 mimetic peptide by rethreading the aromatic residues adjacent to the chromophore fragment. By fine-tuning the residues of peptides, a mini tetrapeptide (Cys-Phe-Phe-His) was designed, which can act as a hydrogen peroxide sensor using its ratiometric fluorescence. The roGFP2 mimetic tetrapeptide is biocompatible and photostable and has competitive fluorescent properties with roGFP2 by the virtue of its assembly induced emissions. We expand the ratiometric tetrapeptide for sensing hydrogen peroxide in acidic chambers. The results provide a promising approach for the artificial design of miniaturized peptides with the desired function.

Ultrahigh Detectivity Broad Spectrum UV Photodetector with Rapid Response Speed Based on p-ß Ga2 O3 /n-GaN Heterojunction Fabricated by a Reversed Substitution Doping Method.

An excellent broad-spectrum (220-380 nm) UV photodetector, covering the UVA-UVC wavelength range, with an ultrahigh detectivity of ≈1015  cm Hz1/2 W-1 , is reported. It is based on a p-ß Ga2 O3 /n-GaN heterojunction, in which p-ß Ga2 O3 is synthesized by thermal oxidation of GaN and a heterostructure is constructed with the bottom n-GaN. XRD shows the oxide layer is (-201) preferred oriented ß-phase Ga2 O3 films. SIMS and XPS indicate that the residual N atoms as dopants remain in ß Ga2 O3 . XPS also demonstrates that the Fermi level is 0.2 eV lower than the central level of the band gap, indicating that the dominant carriers are holes and the ß Ga2 O3 is p-type conductive. Under a bias of -5 V, the photoresponsivity is 56 and 22 A W-1 for 255 and 360 nm, respectively. Correspondingly, the detectivities reach an ultrahigh value of 2.7 × 1015  cm Hz1/2 W-1 (255 nm) and 1.1 × 1015  cm Hz1/2 W-1 (360 nm). The high performance of this UV photodetector is attributed mainly to the continuous conduction band of the p-ß Ga2 O3 /n-GaN heterojunction without a potential energy barrier, which is more helpful for photogenerated electron transport from the space charge region to the n-type GaN layer.

Peptidyl Virus-Like Nanovesicles as Reconfigurable "Trojan Horse" for Targeted siRNA Delivery and Synergistic Inhibition of Cancer Cells.

The self-assembly of peptidyl virus-like nanovesicles (pVLNs) composed of highly ordered peptide bilayer membranes that encapsulate the small interfering RNA (siRNA) is reported. The targeting and enzyme-responsive sequences on the bilayer's surface allow the pVLNs to enter cancer cells with high efficiency and control the release of genetic drugs in response to the subcellular environment. By transforming its structure in response to the highly expressed enzyme matrix metalloproteinase 7 (MMP-7) in cancer cells, it helps the siRNA escape from the lysosomes, resulting in a final silencing efficiency of 92%. Moreover, the pVLNs can serve as reconfigurable "Trojan horse" by transforming into membranes triggered by the MMP-7 and disrupting the cytoplasmic structure, thereby achieving synergistic anticancer effects and 96% cancer cell mortality with little damage to normal cells. The pVLNs benefit from their biocompatibility, targeting, and enzyme responsiveness, making them a promising platform for gene therapy and anticancer therapy.

Peroxidase-Mimicking Hierarchically Organized Gold Particles for Glucose Detection.

In this work, we synthesize a series of hierarchically organized gold nanoparticles (Au HOPs-X) with peroxidase (POD)-like catalytic activity by the in situ reduction of Au-thiolate hierarchically organized particles (Au HOPs). The initial Au HOPs show little POD-like catalytic activity. However, after the reduction of the particles, the Au HOPs-X showed enhanced POD-like catalytic activity, where X represents the reduction degree of Au HOPs. The reasons are as follows: (1) the Au-thiolate complexes on the surface of the Au HOPs-X were reduced into Au nanoparticles, and the active Au0 content increases with the increase of the reduction degree; (2) the specific surface area of Au HOPs-X becomes larger. Based on this, the Au HOPs-10 with the highest catalytic activity were combined with glucose oxidase to obtain a standard curve as a function of glucose concentrations. The color of the solutions was captured by mobile phone photos to determine their saturation, and the rapid detection of glucose was achieved through the standard curve of glucose concentration and saturation determined in this study.

Gold Nanoparticles Mineralized by Peptide Liquid Crystals with Dual-Functional Enzyme-like Activities: An Automatic Membrane Reactor for Glucose Detection.

The development of stable multifunctional enzyme mimics with tandem catalytic effects provides a great opportunity to construct economical and convenient bioassays. Inspired by biomineralization, in this work self-assembled N-(9-fluorenylmethoxycarbonyl)-protected tripeptide (Fmoc-FWK-NH2) liquid crystals were used as templates to in situ mineralize Au nanoparticles (AuNPs), and then a dual-functional enzyme-mimicking membrane reactor based on AuNPs and peptide-based hybrids was constructed. AuNPs with a uniform particle size and good dispersion were in situ reduced on the surface of the peptide liquid crystal due to the reduction of the indole group on the tryptophan residue, which exhibited excellent peroxidase-like and glucose oxidase-like activities simultaneously. Meanwhile, the oriented nanofibers aggregated into a three-dimensional network, which was further immobilized on the mixed cellulose membrane to form a membrane reactor. A biosensor was made to realize fast, low-cost, and automatic detection for glucose. This work represents a promising platform for the design and construction of novel multifunctional materials based on the biomineralization strategy.

Self-Assembly of Peptide-Lipid Nanoparticles for the Efficient Delivery of Nucleic Acids.

A transfection formulation is successfully developed to deliver nucleic acids by adding an auxiliary lipid (DOTAP) to the peptide, and the transfection efficiency of pDNA reaches 72.6%, which is close to Lipofectamine 2000. In addition, the designed KHL peptide-DOTAP complex exhibits good biocompatibility by cytotoxicity and hemolysis analysis. The mRNA delivery experiment indicates that the complex had a 9- or 10-fold increase compared with KHL or DOTAP alone. Intracellular localization shows that KHL/DOTAP can achieve good endolysosomal escape. Our design provides a new platform for improving the transfection efficiency of peptide vectors.

Regulation of biosynthesis of the main flavor-contributing metabolites in tea plant (Camellia sinensis): A review.

In the process of adapting to the environment, tea plants (Camellia sinensis) endow tea with unique flavor and health functions, which should be attributed to secondary metabolites, including catechins, L-theanine, caffeine and terpene volatiles. Since the content of these flavor-contributing metabolites are mainly determined by the growth of tea plant, it is very important to understand their alteration and regulation mechanisms. In the present work, we first summarize the distribution, change characteristics of the main flavor-contributing metabolites in different cultivars, organs and under environmental stresses of tea plant. Subsequently, we discuss the regulating mechanisms involved in the biosynthesis of these metabolites based on the existing evidence. Finally, we propose the remarks and perspectives on the future study relating flavor-contributing metabolites. This review would contribute to the acceleration of research on the characteristic secondary metabolites and the breeding programs in tea plants.

The association of female reproductive factors with risk of metabolic syndrome in women from NHANES 1999-2018.

BACKGROUND: Female reproductive factors such as age at first birth (AFB), age at last birth (ALB), number of pregnancies and live births play an essential role in women's health. However, few epidemiological studies have evaluated the association between female reproductive factors and metabolic syndrome (MetS). We therefore conducted a cross-sectional study to investigate the association between MetS risk and female reproductive factors. METHODS: We investigated the relationship between AFB, ALB, number of pregnancies and live births and the incidence of MetS using publicly available data from the National Health and Nutrition Examination Survey (NHANES) from 1999 to 2018. Weighted multivariable logistic regression analysis, restricted cubic spline (RCS) model, and subgroup analysis were used to evaluate the association between AFB and ALB and the risk of MetS in women. In addition, the relationship between the number of pregnancies, live births and MetS risk was also explored. RESULTS: A total of 15,404 women were included in the study, and 5,983 (38.8%) had MetS. RCS models showed an N-shaped relationship between AFB and MetS risk, whereas ALB, number of pregnancies, and live births were linearly associated with MetS. Weighted multivariable logistic regression analysis showed that the number of live births was associated with MetS risk, with ORs of 1.18 (95% CI: 1.04, 1.35) for women with ≥ 5 deliveries compared to women with ≤ 2 births. CONCLUSIONS: AFB was associated with the risk of MetS in an N-shaped curve in women. In addition, women with high live births have a higher incidence of MetS.

Circular RNA circ_0000741/miR-379-5p/TRIM14 signaling axis promotes HDAC inhibitor (SAHA) tolerance in glioblastoma.

BACKGROUND: Histone deacetylase (HDAC) inhibitor-based therapeutic drug tolerance is a major obstacle to glioblastoma (GBM) treatment. Meanwhile, non-coding RNAs have been reported to be involved in the regulation of HDAC inhibitor (SAHA) tolerance in some human tumors. However, the relationship between circular RNAs (circRNAs) and SAHA tolerance is still unknown. Herein, we explored the role and mechanism of circ_0000741 on SAHA tolerance in GBM. METHODS: Circ_0000741, microRNA-379-5p (miR-379-5p), and tripartite motif-containing 14 (TRIM14) level were detected by real-time quantitative polymerase chain reaction (RT-qPCR). (4-5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT), 5-ethynyl-2'-deoxyuridine (EdU), Colony formation, flow cytometry, and transwell assays were used to detect SAHA tolerance, proliferation, apoptosis, and invasion in SAHA-tolerant GBM cells. Western blot analysis of protein levels of E-cadherin, N-cadherin, and TRIM14. After Starbase2.0 analysis, the binding between miR-379-5p and circ_0000741 or TRIM14 was proved using a dual-luciferase reporter. The role of circ_0000741 on drug tolerance was assessed using a xenograft tumor model in vivo. RESULTS: Circ_0000741 and TRIM14 were upregulated, and miR-379-5p was reduced in SAHA-tolerant GBM cells. Furthermore, circ_0000741 absence reduced SAHA tolerance, suppressed proliferation, invasion, and induced apoptosis in SAHA-tolerant GBM cells. Mechanistically, circ_0000741 might affect TRIM14 content via sponging miR-379-5p. Besides, circ_0000741 silencing enhanced the drug sensitivity of GBM in vivo. CONCLUSION: Circ_0000741 might accelerate SAHA tolerance by regulating the miR-379-5p/TRIM14 axis, which provided a promising therapeutic target for GBM treatment.

[Variations of glucose content in Massa Medicata Fermentata during processing based on quantitative proton nuclear magnetic resonance].

A quantitative proton nuclear magnetic resonance(qHNMR) method was established to determine the glucose content in commercially available Massa Medicata Fermentata(MMF) products and explore the variations of glucose content in MMF products during processing. The qHNMR spectrum of MMF in deuterium oxide was obtained with 2,2,3,3-d_4-3-(trimethylsilyl) propionate sodium salt as the internal standard substance. With the doublet peaks of terminal hydrogen of glucose with chemical shift at δ 4.65 and δ 5.24 as quantitative peaks, the content of glucose in MMF samples was determined. The glucose content showed a good linear relationship within the range of 0.10-6.44 mg·mL~(-1). The relative standard deviations(RSDs) of precision, stability, repeatability, and recovery for determination were all less than 2.3%. The glucose content varied in different commercially available MMF samples, which were associated with the different fermentation days, wheat bran-to-flour ratios, and processing methods. The glucose content in MMF first increased and then decreased over the fermentation time. Compared with the MMF products fermented with wheat bran or flour alone, the products fermented with both wheat bran and flour had increased glucose. The glucose content of bran-fried MMF was slightly lower than that of raw MMF, while the glucose content in charred MMF was extremely low. In conclusion, the qHNMR method established in this study is simple, fast, and accurate, serving as a new method for determining the glucose content in MMF. Furthermore, this study clarifies the variations of glucose content in MMF during processing, which can not only indicate the processing degree but also provide a scientific basis for revealing the fermentation mechanism and improving the quality control of MMF.

Enzyme-Driven, Switchable Catalysis Based on Dynamic Self-Assembly of Peptides.

Covalent regulatory systems of enzymes are widely used to modulate biological enzyme activities. Inspired by the regulation of reactive-site phosphorylation in organisms, we developed peptide-based catecholase mimetics with switchable catalytic activity and high selectivity through the co-assembly of nanofibers comprising peptides and copper ions (Cu2+ ). Through careful design and modification of the peptide backbone structure based on the change in the free energy of the system, we identified the peptide with the most effective reversible catalytic activity. Kinase/phosphatase switches were used to control the reversible transition of nanofiber formation and depolymerization, as well as to modulate the active-site microenvironment. Notably, the self-assembly and disassembly processes of nanofibers were simulated using coarse-grained molecular dynamics. Furthermore, theoretical calculations confirmed the coordination of the peptide and Cu2+ , forming a zipper-like four-ligand structure at the catalytically active center of the nanofibers. Additionally, we conducted a comprehensive analysis of the catalytic mechanism. This study opens novel avenues for designing biomimetic enzymes with ordered structures and dynamic catalytic activities.