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Protein & Cell 2014年第2期5卷 151-159页

作者： Kelei Bi Yueting Zheng Feng G"ao Jianshu Dong Jiangyun Wang Yi Wang Weimin Gong laboratory of non-coding rna Institute of Biophysics Chinese Academy of Sciences

The arginyl-trna synthetase(ArgRS) catalyzes the esterification reaction between L-arginine and its cognate trnaArg. Previously reported structures of ArgRS shed considerable light on the trna recognition mechanism, while the aspect of amino acid binding in ArgRS remains largely unexplored. Here we report the first crystal structure of E. coli ArgRS(eArgRS) complexed with L-arginine, and a series of mutational studies using isothermal titration calorimetry(ITC). Combined with previously reported work on ArgRS, our results elucidated the structural and functional roles of a series of important residues in the active site, which furthered our understanding of this unique enzyme.

关键词： arginyl-trna synthetase amino acyl-trna synthetase isothermal titration calorimetry site-directed mutation X-ray crystal structure E. coli

A genetically encoded sulfotyrosine for VHR function research

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Protein & Cell 2013年第10期4卷 731-734页

作者： Yueting Zheng Xiaoxuan Lv Jiangyun Wang laboratory of non-coding rna Institute of BiophysicsChinese Academy of SciencesBeijing 100101China

Dear Editor,Protein tyrosine phosphorylation is one of the most prevalent forms of post-translational modification and plays a signifi cant role in the control of a variety of cellular processes,including signal transduction,and is implicated in many human diseases(Eckhart et al.,1979;Karisch et al.,2011).The human vac-cinia H1-related phosphatase(VHR),the fi rst human dual specifi city protein phos-phatase(DSP),hydrolyzes phosphate monoesters from phosphotyrosine,phosphothreonine,or phosphoserine residues(Aroca et al.,1995).DSPs func-tion in signal transduction and in control of the cell cycle;more than 20 mamma-lian DSPs have so far been identifi *** VHR can dephosphorylate both Erk and Jnk in vivo(Schumacher et al.,2002),it differs from other‘typi-cal’mitogen activated protein(MAP)kinase phosphatases(MKPs).With only 185 amino acids,VHR consists of only a catalytic domain with no recogniz-ing or docking domain.

关键词： al. diseases ed.

Large-scale study of long non-coding rna functions based on structure and expression features

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Science China(Life Sciences) 2013年第10期56卷 953-959页

作者： ZHAO Yi WANG Jian CHEN XiaoWei LUO HaiTao ZHAO YunJie XIAO Yi CHEN RenSheng bioinformatics Research Group Advanced Computing Research LaboratoryInstitute of Computing TechnologyChinese Academy ofSciences Department of Physics Huazhong University of Science and Technology laboratory of bioinformatics and non-coding rna Institute of BiophysicsChinese Academy of Sciences

Mammals and other complex organisms can transcribe an abundance of long non-coding rnas(lncrnas)that fulfill a wide variety of regulatory roles in many biological *** roles,including as scaffolds and as guides for protein-coding genes,mainly depend on the structure and expression level of *** this review,we focus on the current methods for analyzing lncrna structure and expression,which is basic but necessary information for in-depth,large-scale analysis of lncrna functions.

关键词： non-coding rna structure expression function

Biosynthetic approach to modeling and understanding metalloproteins using unnatural amino acids

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Science China Chemistry 2017年第2期60卷 188-200页

作者： Yang Yu Chang Cui Jiangyun Wang Yi Lu Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences Department of Chemistry University of Illinois at Urb ana-Champaign laboratory of non-coding rna Institute of BiophysicsChinese Academy of Sciences

Metalloproteins have inspired chemists for many years to synthesize artificial catalysts that mimic native *** a complementary approach to studying native enzymes or making synthetic models,biosynthetic approach using small and stable proteins to model native enzymes has offered advantages of incorporating non-covalent secondary sphere interactions under physiological ***,most biosynthetic models are restricted to natural amino *** overcome this limitation,incorporating unnatural amino acids into the biosynthetic models has shown *** this review,we summarize first synthetic,semisynthetic and biological methods of incorporates unnatural amino acids(UAAs)into proteins,followed by progress made in incorporating UAAs into both native metalloproteins and their biosynthetic models to fine-tune functional properties beyond native enzymes or their variants containing natural amino acids,such as reduction potentials of azurin,O_2 reduction rates and percentages of product formation of HCO models in Mb,the rate of radical transport in ribonucleotide reductase(RNR)and the proton and electron transfer pathways in photosystemⅡ(PSⅡ).We also discuss how this endeavour has allowed systematic investigations of precise roles of conserved residues in metalloproteins,such as Metl21 in azurin,Tyr244 that is cross-linked to one of the three His ligands to CuB in HCO,Tyr122,356,730 and 731 in RNR and TyrZ in PSⅡ.These examples have demonstrated that incorporating UAAs has provided a new dimension in our efforts to mimic native enzymes and in providing deeper insights into structural features responsible high enzymatic activity and reaction mechanisms,making it possible to design highly efficient artificial catalysts with similar or even higher activity than native enzymes.

关键词： metalloenzymes heme proteins copper proteins ribonucleotide reductase protein design

Crystal structure of E. synthetase and ligand revealed key residues coil arglnyl-trna binding studies in arginine recognition

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Protein & Cell 2014年第2期5卷 151-159页

作者： Kelei Bi Yueting Zheng Feng Gao Jianshu Dong Jiangyun Wang Yi Wang Weimin Gong laboratory of non-coding rna Institute of Biophysics Chinese Academy of Sciences Beijing 100101 China

The arginyl-trna synthetase （ArgRS） catalyzes the esterification reaction between L-arginine and its cog- nate trnaArg. Previously reported structures of ArgRS shed considerable light on the trna recognition mech- anism, while the aspect of amino acid binding in ArgRS remains largely unexplored. Here we report the first crystal structure of E. coli ArgRS （eArgRS） complexed with L-arginine, and a series of mutational studies using isothermal titration calorimetry （ITC）. Combined with previously reported work on ArgRS, our results eluci- dated the structural and functional roles of a series of important residues in the active site, which furthered our understanding of this unique enzyme.

关键词： arginyl-trna synthetase amino acyl-trnasynthetase isothermal titration calorimetry site-directedmutation X-ray crystal structure E. coil

Vitamin B2 functionalized iron oxide nanozymes for mouth ulcer healing

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Science China(Life Sciences) 2020年第1期63卷 68-79页

作者： Yunhao Gu Yixin Huang Zhiyue Qiu Zhuobin Xu Dandan Li Lei Chen Jing Jiang Lizeng Gao Institute of Translational Medicine Department of PharmacologySchool of MedicineYangzhou UniversityYangzhou 225001China Jiangsu Key laboratory of Experimental and Translational non-coding rna Research Yangzhou UniversityYangzhou 225001China

Mouth ulcer is associated with inflammation and high risk of bacterial infection, which aggravates the patient's ***, there is no effective treatment for mouth ulcer. Herein, we report that vitamin-modified iron oxide nanoparticles improve the healing of mouth ulcer through anti-inflammation and antibacterial activities. We discovered that vitamin B2(VB2)modified iron oxide nanoparticles performed enhanced peroxidase-like, catalase-like, and superoxide dismutase(SOD)-like activities, acting as typical iron oxide nanozymes(IONzymes) with triad activities. In particular, VB2 modification significantly improved the SOD-like activity, thus providing a reactive oxygen species(ROS)-scavenging ability. Cellular antioxidant experiments showed that vitamin B2 modified IONzymes(VB2-IONzymes) protect human oral keratinocytes(HOK) and BALB/3 T3 cells from hydrogen peroxide(H2O2), and these cells have high biocompatibility to eukaryotic cells. In addition, VB2-IONzymes exerted an antibacterial activity against Streptococcus mutans, Staphylococcus aureus, and Escherichia coli. Importantly, VB2-IONzymes accelerated the recovery of mouth ulcer and reduced the local secretion of inflammatory factors in mouse ulcer model via ROS scavenging and antibacterial activity. Taken together, our work demonstrates that vitamin B2 modification endows iron oxide nanoparticles with enhanced enzyme-like activities and VB2-IONzymes may be a promising reagent in the treatment of mouth ulcer because of their intrinsic anti-inflammation and antibacterial capabilities.

关键词： iron oxide nanozymes vitamin B2 ROS scavenging mouth ulcer anti-inflammation

PTMD: A Database of Human Disease-associated Post-translational Modifications

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Genomics, Proteomics & bioinformatics 2018年第4期16卷 244-251页

作者： Haodong Xu Yongbo Wang Shaofeng Lin Wankun Deng Di Peng Qinghua Cui Yu Xue Department of bioinformatics & Systems Biology MOE Key Laboratory of Molecular Biophysics College of Life Science and Technology and the Collaborative Innovation Center for Biomedical Engineering Huazhong University of Science and Technology Department of Biomedical Informatics School of Basic Medical Sciences MOE Key Laboratory of Molecular Cardiovascular Sciences Center for Non-coding RNA Medicine Peking University

Various posttranslational modifications （PTMs） participate in nearly all aspects of biological processes by regulating protein functions, and aberrant states of PTMs are frequently implicated in human diseases. Therefore, an integral resource of PTM–disease associations （PDAs）would be a great help for both academic research and clinical use. In this work, we reported PTMD,a well-curated database containing PTMs that are associated with human diseases. We manually collected 1950 known PDAs in 749 proteins for 23 types of PTMs and 275 types of diseases from the literature. Database analyses show that phosphorylation has the largest number of disease associations, whereas neurologic diseases have the largest number of PTM associations. We classified all known PDAs into six classes according to the PTM status in diseases and demonstrated that the upregulation and presence of PTM events account for a predominant proportion of diseaseassociated PTM events. By reconstructing a disease–gene network, we observed that breast cancers have the largest number of associated PTMs and AKT1 has the largest number of PTMs connected to diseases. Finally, the PTMD database was developed with detailed annotations and can be a useful resource for further analyzing the relations between PTMs and human diseases. PTMD is freely accessible at http：//***.

关键词： Posttranslational modification Phosphorylation PTM-disease association Disease-gene network AKT1

Bayesian localization microscopy based on intensity distribution of fluorophores

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Protein & Cell 2015年第3期6卷 211-220页

作者： Fan Xu Mingshu Zhang Zhiyong Liu Pingyong Xu Fa Zhang Key Lab of Intelligent Information Processing Institute of Computing Technology Chinese Academy of Sciences Beijing 100190 China University of Chinese Academy of Sciences Beijing 100049 China laboratory of non coding rna Institute of Biophysics Chinese Academy of Sciences Beijing 100101 China

Super-resolution microscopy techniques have overcome the limit of optical diffraction. Recently, the Bayesian analysis of Bleaching and Blinking data （3B） method has emerged as an important tool to obtain super-resolution fluorescence images. 3B uses the change in information caused by adding or removing fiuorophores in the cell to fit the date. When adding a new fluorophore, 3B selects a random initial position, optimizes this position and then determines its reliability. However, the fluorophores are not evenly distributed in the entire image region, and the fluorescence intensilty at a given position positively correlates with the probability of observing a fluorophore at this position. In this paper, we present a Bayesian analysis of Bleaching and Blinking microscopy method based on fluorescence intensity distribution （FID3B）. We utilize the intensity distribution to select more reliable positions as the initial positions of fluorophores. This approach can improve the reconstruction results and significantly reduce the computational time. We validate the perfor. mance of our method using both simulated date and experimental date from cellular structures. The results confirm the effectiveness of our method.

关键词： super-resolution fluorescence image 3B,intensity distribution

Potential treatment with Chinese and Western medicine targeting NSP14 of SARS-CoV-2

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Journal of Pharmaceutical Analysis 2021年第3期11卷 272-277页

作者： Chao Liu Xiaoxiao Zhu Yiyao Lu Xianqin Zhang Xu Jia Tai Yang non-coding rna and Drug Discovery Key laboratory of Sichuan Province Chengdu Medical CollegeChengduSichuan610500China Basic Medical School Chengdu Medical CollegeChengduSichuan610500China School of Pharmacy Chengdu Medical CollegeChengduSichuan610500China

The outbreak of coronavirus disease 2019(COVID-19)caused by severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)is a serious global health *** raises an urgent need for the development of effective drugs against the deadly ***-CoV-2 non-structural protein 14(NSP14)carrying rna cap guanine N7-methyltransferase and 30-50 exoribonuclease activities could be a potential drug target for ***14 of SARS-CoV-2 shares 98.7%of similarity with the one(PDB 5NFY)of acute respiratory syndrome(SARS)by ***,the SARS-CoV-2 NSP14 structures were modelled by Modeller 9.18 using SARS NSP14(PDB 5NFY)as template for virtual *** on the docking score from AutoDock Vina1.1.2,18 small molecule drugs were selected for further *** on the 5 ns MD simulation trajectory,binding free energy(DG)was calculated by MM/GBSA *** calculated binding free energies of Saquinavir,Hypericin,Baicalein and Bromocriptine for the N-terminus of the homology model wereà37.2711±3.2160,à30.1746±3.1914,à23.8953±4.4800,andà34.1350±4.3683 kcal/mol,respectively,while the calculated binding free energies wereà60.2757±4.7708,à30.9955±2.9975,à46.3099±3.5689,andà59.8104±3.5389 kcal/mol,respectively,when binding to the ***,the compounds including Saquinavir,Hypericin,Baicalein and Bromocriptine could bind to the N-terminus and C-terminus of the homology model of the SARS-CoV-2 NSP14,providing a candidate drug against SARS-CoV-2 for further study.

关键词： SARS-CoV-2 nonstructural protein 14(NSP14) ZINC database Drug docking

Analysis of the p53/CEP-1 regulated non-coding transcriptome in C. elegans by an NSR-seq strategy

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Protein & Cell 2014年第10期5卷 770-782页

作者： Derong Xu Guifeng Wei Ping Lu Jianjun Luo Xiaomin Chen Geir Skogerbo Runsheng Chen laboratory of non-coding rna Institute of Biophysics University of Chinese Academy of Sciences Beijing 100101 China Graduate University of Chinese Academy of Sciences Beijing 100080 China Key laboratory of Forest Protection State Forestry Administration/Research Institute of Forest Ecology Environment andProtection Chinese Academy of Forestry Beijing 100091 China

In recent years, large numbers of non-coding rnas （ncR- NAs） have been identified in C. elegans but their functions are still not well studied. In C. elegans, CEP-1 is the sole homolog of the p53 family of genes. In order to obtain transcription profiles of ncrnas regulated by CEP-1 under normal and UV stressed conditions, we applied the ＇not-so- random＇ hexamers priming strategy to rna sequencing in C. elegans, This NSR-seq strategy efficiently depleted rrna transcripts from the samples and showed high technical replicability. We identified more than 1,000 ncR- NAs whose apparent expression was repressed by CEP-1, while around 200 were activated. Around 40% of the CEP-1 activated ncrnas promoters contain a putative CEP-1- binding site. CEP-1 regulated ncrnas were frequently clustered and concentrated on the X chromosome. These results indicate that numerous ncrnas are involved in CEP-1 transcriptional network and that these are espe- cially enriched on the X chromosome in C. elegans.

关键词： p53/CEP-1 C. elegans ncrna removalrrna NSR-seq high technical replicability