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Cytochrome P450 Enzyme Design by Constraining the Catalytic Pocket in a Diffusion Model

Research 2025年第1期2024卷 618-630页

作者： Qian Wang Xiaonan Liu Hejian Zhang Huanyu Chu Chao Shi Lei Zhang Jie Bai Pi Liu Jing Li Xiaoxi Zhu Yuwan Liu Zhangxin Chen Rong Huang Hong Chang Tian Liu Zhenzhan Chang Jian Cheng Huifeng Jiang Key Laboratory of Engineering Biology for Low-Carbon Manufacturing Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjin 300308China University of Chinese Academy of Sciences Beijing 100049China National Center of Technology Innovation for Synthetic Biology Tianjin 300308China College of Biotechnology Tianjin University of Science and TechnologyTianjin 300457China Department of Biochemistry and Biophysics School of Basic Medical SciencesPeking UniversityBeijing 100191China College of Life Science and Technology Wuhan Polytechnic UniversityWuhanHubei 430023China State Key Laboratory of Elemento-Organic Chemistry College of ChemistryNankai UniversityTianjin 300071China College of Life Science Nankai UniversityTianjin 300071China

Although cytochrome P450 enzymes are the most versatile biocatalysts in nature,there is insufficient comprehension of the molecular mechanism underlying their functional innovation ***,by combining ancestral sequence reconstruction,reverse mutation assay,and progressive forward accumulation,we identified 5 founder residues in the catalytic pocket of flavone 6-hydroxylase(F6H)and proposed a"3-point fixation"model to elucidate the functional innovation mechanisms of P450s in *** to this design principle of catalytic pocket,we further developed a de novo diffusion model(P450Diffusion)to generate artificial ***,among the 17 non-natural P450s we generated,10 designs exhibited significant F6H activity and 6 exhibited a 1.3-to 3.5-fold increase in catalytic capacity compared to the natural *** work not only explores the design principle of catalytic pockets of P450s,but also provides an insight into the artificial design of P450 enzymes with desired functions.

关键词： cytochrome P progressive forward accumulationwe cytochrome p enzymes molecular mechanism ancestral sequence reconstructionreverse mutation assayand de novo design catalytic pocket functional innovation

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Effect of purine diet on prognosis of deep brain stimulation for Parkinson's disease

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Food science and Human Wellness 2025年第3期14卷 1026-1033页

作者： Bowen Chang Yuge Jiang Chuanxing Feng Bowen Li Jiaming Mei Chaoshi Niu Department of Neurosurgery The First Affi liated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefei 230001China Key Laboratory of Xin’an Medicine Ministry of EducationAnhui Provincial Key Laboratory of R&D of Chinese MedicineAnhui University of Chinese MedicineHefei 230038China Center for Food Nutrition and Functional Food Engineering School of Food Science and TechnologyJiangnan UniversityWuxi 214122China

Uric acid(UA)is a naturally antioxidant that is strongly associated with the development and progression of Parkinson's disease(PD).The purine diet is an important exogenous pathway that modulates blood UA *** brain stimulation(DBS)is an important tool for PD *** study aimed to explore the effects of preoperative purine diet on the prognosis of patients with PD after ***-four patients with PD who underwent DBS were included in this study,and their clinical data,blood UA levels,and daily purine *** were followed up for improvement 1 year after *** found that patient higher purine intake was strongly associated with the rate of improvement after DBS and was a protective factor for patient *** purine intake from meat and seafood was significantly higher in the responsive patients than in the lessresponsive *** analysis showed that UA mediated 78%of the effect of purine intake on motor symptom improvement after *** summary,we observed that purine intake is strongly associated with the rate of improvement in motor symptoms after subthalamic nucleus-DBS in patients with *** study provides a reference for preoperative diet planning in patients with PD undergoing DBS.

关键词： Purine diet Nutrition Parkinson’s disease Deep brain stimulation Brain connectivity

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Single‑Neuron Reconstruction of the Macaque Primary Motor Cortex Reveals the Diversity of Neuronal Morphology

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Neuroscience Bulletin 2025年第3期41卷 525-530页

作者： Siyu Li Yan Shen Yefei Chen Zexuan Hong Lewei Zhang Lufeng Ding Chao‑Yu Yang Xiaoyang Qi Quqing Shen Yanyang Xiao Pak‑Ming Lau Zhonghua Lu Fang Xu Guo‑Qiang Bi CAS Key Laboratory of Brain Function and Disease Division of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefei 230026China Interdisciplinary Center for Brain Information Shenzhen-Hong Kong Institute of Brain ScienceShenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhen 518055China Shenzhen Technological Research Center for Primate Translational Medicine Shenzhen Key Laboratory for Molecular Biology of Neural DevelopmentShenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhen 518055China The Key Laboratory of Biomedical Imaging Science and System Chinese Academy of SciencesShenzhen 518055China CAS Key Laboratory of Brain Connectome and Manipulation the Brain Cognition and Brain Disease InstituteShenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhen 518055China Faculty of Life and Health Sciences Shenzhen University of Advanced TechnologyShenzhen 518107China

Dear Editor,The primary motor cortex,also known as MOp in rodents,F1,or M1 in primates[1],plays a crucial role in autonomous motor *** is interconnected with other motor control structures such as the basal ganglia,thalamus,and *** these connections,the corticostriatal system plays a significant role in functions including action selection,motor control,sequence learning,and habit formation[2].

关键词： habit formation autonomous motor controlit morphology action selectionmotor corticostriatal system neuron basal gangliathalamusand primary motor cortexalso

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Proteomic analysis of B cells in peripheral lymphatic system reveals the dynamics during the systemic lupus erythematosus progression

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Biophysics Reports 2025年第2期11卷 129-142页

作者： Liming Sun Yuanyuan Yin Yuqing Cao Chunlei Chen Yutong Guo Zeming Cai Jiarui Wu Qingrun Li Key Laboratory of Systems Health Science of Zhejiang Province School of Life Science Hangzhou Institute for Advanced Study University of Chinese Academy of Sciences School of Life Science and Technology ShanghaiTech university CAS Key Laboratory of Systems Biology Shanghai Institute of Biochemistry and Cell Biology Center for Excellence in Molecular Cell Science Chinese Academy of Sciences University of Chinese Academy of Sciences

In this study, we conducted a comprehensive proteomic analysis of B cells from the spleen, mesenteric lymph nodes(mLN), and peripheral blood mononuclear cells(PBMC) in a time-course model of systemic lupus erythematosus(SLE) using female MRL/lpr mice. By combining fluorescence-activated cell sorting(FACS) and 4D-Data-Independent Acquisition(4D-DIA) mass spectrometry, we quantified nearly 8000 proteins, identifying significant temporal and tissue-specific proteomic changes during SLE progression. PBMC-derived B cells exhibited early proteomic alterations by Week 9, while spleen-derived B cells showed similar changes by Week 12. We identified key regulatory proteins, including BAFF, BAFFR, and NFKB2, involved in B cell survival and activation, as well as novel markers such as CD11c and CD117, which have previously been associated with other immune cells. The study high-lights the dynamic reprogramming of B cell proteomes across different tissues, with distinct contributions to SLE pathogenesis, providing valuable insights into the molecular mechanisms underlying B cell dysregulation in lupus. These findings offer potential therapeutic targets and biomarkers for SLE.

关键词： Proteomics B cells Beripheral lymphatic system SLE

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SnS/WSe van der Waals Single-Detector Spectrometer With a Dynamically Selecting Spectral Reconstruction Strategy

IEEE Electron Device Letters

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IEEE Electron Device Letters 2025年第5期46卷 801-804页

作者： Zhou, Yang Mu, Haoran Zhang, Congwen Xu, Renjing Zhang, Guangyu Lin, Shenghuang Songshan Lake Materials Laboratory Dongguan523808 China South China Normal University Moe Key Laboratory of Laser Life Science Guangdong Provincial Key Laboratory of Laser Life Science Guangzhou Key Laboratory of Spectral Analysis and Functional Probes College of Biophotonics Guangzhou510631 China The Hong Kong University of Science and Technology Microelectronics Thrust Guangzhou511442 China Institute of Physics Chinese Academy of Science Beijing100190 China

The single-detector spectrometers based on 2D layer van der Waals (vdW) heterojunctions offer advantages in spectral reconstruction due to their high sensitivity, tunable optical properties, and the ability to cover a broad spectral range. There exist two principal algorithms dominating spectrum reconstruction for this kind spectrometer: the Tikhonov regularization method combined with the Least Squares Method (LSM) and neural network-based approaches, particularly Deep Learning (DL). However, both of the algorithms exhibit inherent limitations in spectral reconstruction, which constrain the versatility of computational spectrometers that rely solely on a single algorithm for reconstructing diverse spectral profiles. To overcome this limitation, we introduce an artificial neural network (ANN)-based classification model capable of dynamically selecting the optimal algorithm throughout the reconstruction process. This enables highly accurate spectral reconstruction within the 440-700 nm wavelength range, achieving a spectral resolution of 6 nm. By harnessing the complementary strengths of multiple algorithms, our approach proposes a novel strategy for combining techniques to enhance the precision of spectral reconstructions, laying the groundwork for more sophisticated methods in the future. © 1980-2012 IEEE.

关键词： Van der Waals forces

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The role of PilU in the surface behaviors of Pseudomonas aeruginosa

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mlife 2025年第1期4卷 83-95页

作者： Jingchao Zhang Yan Luo Yiwu Zong Shangping Lu Yi Shi Fan Jin Kun Zhao Center for Medical Genetics Sichuan Provincial People's HospitalUniversity of Electronic Science and Technology of ChinaChengduChina Key Laboratory of SystemsBioengineering(Ministry of Education) School of Chemical Engineering and TechnologyFrontiers Science Center for Synthetic BiologyTianjin UniversityTianjinChina Guangzhou General Institute of Medical Research GuangzhouChina School of Life Science and Technology University of Electronic Science and Technology of ChinaChengduChina The Sichuan Provincial Key Laboratory for Human Disease Gene Study The Institute of Laboratory MedicineSichuan Provincial People's HospitalUniversityof Electronic Science and Technology of ChinaChengduChina CAS Key Laboratory of Quantitative Engineering Biology Shenzhen Institute of Synthetic BiologyShenzhenInstitutes of Advanced TechnologyChinese Academy of SciencesShenzhenChina Institute of Fundamental and Frontier Sciences University of Electronic Science andTechnology of ChinaChengduChina

In Pseudomonas aeruginosa,the dynamic activity of type IV pilus(TFP)is essential for various bacterial *** PilU isconsidered a homolog of the TFP disassembling motor PilT,its speciﬁc roles remain *** pilus visualization andsingle-cell tracking techniques,we characterized TFP dynamics and surface behaviors in wild-type andΔpilU *** thatΔpilU cells displayed increased TFP numbers but reduced cell movement and delayed microcolony ***,beyond affecting the twitching motility,ΔpilU cells formed a thick multilayered colony edge on semi-solid sur-faces,slowing colony ***-cell collision responses changed from touch-turn dominance in wild type to touch-upright dominance inΔpilU,affecting colony morphology and ***ﬁndings expand our understanding of PilU'sphysiological roles and provide potential targets for developing strategies to control *** bioﬁlm formation andvirulence.

关键词： colony expansion pilU Pseudomonas aeruginosa twitching type IV pili

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An automatic annotation tool and reference database for T cell subtypes and states at single-cell resolution

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science Bulletin 2025年第10期70卷 1659-1672页

作者： Shen, Wen-Kang Zhang, Chu-Yu Gu, Yi-Min Luo, Tao Chen, Si-Yi Yue, Tao Xie, Gui-Yan Liao, Yu Yuan, Yong Lei, Qian Guo, An-Yuan Department of Thoracic Surgery West China Biomedical Big Data Center West China Hospital Sichuan University Chengdu610041 China Hubei Bioinformatics & Molecular Imaging Key Laboratory College of Life Science and Technology Huazhong University of Science and Technology Wuhan430074 China College of Life Sciences University of Chinese Academy of Sciences Beijing101408 China Department of Rheumatology & Immunology Union Hospital Tongji Medical College Huazhong University of Science and Technology Wuhan430074 China

T cells have various subtypes and states with different functions. However, a reference list and automated annotation tool for T cell subtypes and states are lacking, which is critical for analyzing and comparing T cells under various conditions. We constructed the largest human T cell reference, containing 1,348,268 T cells from 35 conditions and 16 tissues. We classified T cells into 33 subtypes and further stratified them into 68 categories according to subtype and state. Based on this reference, we developed a tool named STCAT to automatically annotate T cells from scRNA-seq data by hierarchical models and marker correction. The accuracy of STCAT was 28% higher than that of existing tools validated on six independent datasets, including cancer and healthy samples. Using STCAT, we consistently discovered that CD4+ Th17 cells were enriched in late-stage lung cancer patients in multiple datasets, whereas MAIT cells were prevalent in milder-stage COVID-19 patients. We also confirmed a decrease in Treg cytotoxicity in post-treatment ovarian cancer. Systematic landscape analyses of CD4+ and CD8+ T cell references revealed that CD4+ Treg cells were enriched in tumor samples and that CD8+ naive-related cells were abundant in healthy individuals. Finally, we deposited all the T cell references and annotations into a TCellAtlas (https://***/TCellAtlas) database, which allows users to browse T cell expression profiles and analyze customized scRNA-seq data by STCAT. In conclusion, comprehensive human T cell subtypes and states reference, automated annotation tool, and database will greatly facilitate research on T cell immunity and tumor immunology. © 2025 science China Press

关键词： T-cells

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Aloin ameliorates cecal ligation and puncture-induced sepsis in mice by attenuating inflammation and modulating gut microbiota

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Food science and Human Wellness 2025年第2期14卷 550-568页

作者： Jingqian Su Jianbin Xiao Siyuan Chen Heng Zhao Xiaoni Zhang Zhihua Feng Kunsen Chen Biyun Guan Wenzhi Chen Youqiang Chen Duo Chen Qi Chen Fujian Key Laboratory of Innate Immune Biology Biomedical Research Center of South ChinaCollege of Life ScienceFujian Normal UniversityFuzhou 350117China The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration Fujian Key Laboratory of Special Marine Bioresource Sustainable UtilizationSouthern Institute of OceanographyCollege of Life ScienceFujian Normal UniversityFuzhou 350117China

Most Aloe species are used as new food or functional food *** though widely known for its health benefits,the anti-inflammatory effects and underlying mechanisms of Aloin(Alo),an anthraquinone compound isolated from plant species of the genus Aloe,remain ***,we investigated the protective effects of Alo against cecal ligation and puncture(CLP)-induced sepsis and microflora in *** significantly improved CLP-induced sepsis and the survival rate of septic mice,downregulated the expression of proinflammatory factors,and decreased the infiltration of inflammatory cells in *** upregulated the proportion of peritoneal macrophages,reduced the number of peritoneal bacteria,decreased the content of short-chain fatty acids and bile acids in the abdominal cavity,and suppressed Toll-like receptor(TLR)-2/4/nuclear factor kappa-B(NF-κB)/NOD-like receptor thermal protein domain associated protein 3(NLRP3)/Caspase-1/3/8 ***,Alo altered the composition of the microbiome and promoted the growth of Lactobacillus,which showed a stronger anti-inflammatory ***-genome analysis identified the genes Saa3,Il10,Fpr1,and Eif4a1 associated with the protective effects of Alo in mice with CLP-induced ***,our results provide novel insights into the therapeutic potential and mechanism of action of Alo in the treatment of sepsis.

关键词： Aloin Gut microbiome Sepsis Inflammation Cecal ligation and puncture

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Mobilization of heavy metals from floodplain sediments of the Yellow River during redox fluctuations

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Journal of Environmental sciences 2025年第4期150卷 432-439页

作者： Fuyu Xie Xiaoqing Li Qingxiang Yang Ying Meng Fubo Luan Key Laboratory of Drinking Water Science and Technology Research Center for Eco-Environmental SciencesChinese Academy of SciencesBeijing 100085China University of Chinese Academy of Sciences Beijing 100049China College of Life Sciences Henan Normal UniversityXinxiang 453007China

The floodplain of the Yellow River is a typical area characterized by redox fluctuations and heavy metal ***,the mobilization behavior of heavy metals in floodplain sediments during redox fluctuations remains poorly *** this study,reductive mobilization of Fe and Mn was observed under reducing environments through reduction and dissolution,leading to the subsequent release of adsorbed *** contrast,the mobilization of U occurred under oxic conditions,as the oxidative state of U(VI)has higher ***,insignificant effects on the mobilization of Cd,Cu,Pb,and Hg were noticed during redox fluctuations,indicating higher stability of these ***,we demonstrated that carbon sources can play a key role in the mobilization of heavy metals in floodplain sediments,amplifying the reductive mobilization of Fe,Mn,As and the oxidative mobilization of *** findings contribute to the understanding of the biogeochemical cycling of heavy metal in floodplain sediments of the Yellow River and the factors that control this cycling.

关键词： Biogeochemical cycling Redox fluctuation Heavy metal Carbon supplementation The Yellow River

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Scheme Design and Challenges of DNA Sequencing Terminal Equipment Based on Solid-State Nanopore Sequencing 4th

Scheme Design and Challenges of DNA Sequencing Terminal Equi...

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4th International Conference on Mechanical Design and Simulation, MDS 2024

作者： Zhao, Yuanzhe Zhang, Jie Sun, Zepeng Cao, Zheqi Xu, Liqun Li, Jian Key Laboratory of DGHD MOE School of Life Science and Technology Southeast University Nanjing China Industrial Research Institute Chengdu China

ISBN: (纸本)9789819778867

Nanopore sequencing has become the primary technology for modern DNA sequencing. Solid nanopores are favored for their cost-effectiveness, stability, and scalability, particularly for portable applications. This paper presents a new design for a portable solid-state nanopore sequencing device based on the Linux platform. It employs a cutting-edge biological sequencing chip with a nanopore channel to capture through-hole data. Electrical signals from the chip are processed to create DNA sequence data files. The Linux-based Raspbian OS serves as the control terminal, facilitating seamless communication between components. Data is then transmitted to a cloud platform via a 5G unit for further analysis. This study integrates software and hardware for instrument validation. © The Author(s) 2025.

关键词： Nanopores

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