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Nphos:Database and Predictor of Protein N-phosphorylation

第六届全国磷化学化工学术讨论会

作者： ming sun, xiao-hongliu and yu-fen zhao the key laboratory of bioorganic phosphorous chemistry,ministry of education,china Department of chemistry,School of Life Science and Engineering,Tsinghua University,Beijing 100084,china, School of chemistry and Life Science,Tianjin Normal University,Tianjin 300074,china

Protein kinases play a critical role in cell signaling pathways by catalyzing the transfer of the α-phosphoryl group from ATP to the hydroxyl group of substrate side chain. This process affects essentially every cellular process including metabolism, growth, differentiation, motility, membrane transport, learning and memory. To ensure the signaling fidelity, the kinases must be specific and act only on a defined subset of cellular targets. Understanding the basis for this substrate specificity of different protein kinases is therefore

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Genomics, Proteomics & Bioinformatics 2024年第3期22卷 139-151页

作者： ming-xiao zhao Ruo-Fan Ding Qiang Chen Junhua Meng Fulai Li Songsen Fu Biling Huang Yan Liu Zhi-Liang Ji yufen zhao Institute of Drug Discovery Technology Ningbo UniversityNingbo 315211China Department of Chemical Biology Key Laboratory for Chemical Biology of Fujian ProvinceCollege of Chemistry and Chemical EngineeringXiamen UniversityXiamen 361005China State key laboratory of Cellular Stress Biology School of Life SciencesFaculty of Medicine and Life SciencesXiamen UniversityXiamen 361102China Zhejiang key laboratory of Pathophysiology Department of Biochemistry and Molecular BiologyHealth Science CenterNingbo UniversityNingbo 315211China BGI Genomics BGI-ShenzhenShenzhen 518083China key laboratory of bioorganic Phosphorus chemistry&Chemical Biology Department of ChemistryTsinghua UniversityBeijing 100084China

Protein N-phosphorylation is widely present in nature and participates in various biological ***,current knowledge on N-phosphorylation is extremely limited compared to that on *** this study,we collected 11,710 experimentally verified N-phosphosites of 7344 proteins from 39 species and subsequently constructed the database Nphos to share up-to-date information on protein *** these substantial data,we characterized the sequential and structural features of protein ***,after comparing hundreds of learning models,we chose and optimized gradient boosting decision tree(GBDT)models to predict three types of human N-phosphorylation,achieving mean area under the receiver operating characteristic curve(AUC)values of 90.56%,91.24%,and 92.01%for pHis,pLys,and pArg,***,we discovered 488,825 distinct N-phosphosites in the human *** models were also deployed in Nphos for interactive N-phosphosite *** summary,this work provides new insights and points for both flexible and focused investigations of *** will also facilitate a deeper and more systematic understanding of protein N-phosphorylation modification by providing a data and technical *** is freely available at http://***/Nphos/and http://***/Nphos/.

关键词： N-phosphorylation Post-translational modification Machine learning Database Benchmark dataset

Natural products inspired[3+2]cycloaddition enables efficient construction of hydroxylated tetrahydrofuran acetals and concise syntheses of lignans

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Science china chemistry 2024年第7期67卷 2306-2313页

作者： Dong-yue Cai Weiming Shi zhao-Hui Jin Zhi-Xiang yu Jin-Xin zhao Jian-Min yue State key laboratory of Drug Research Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghai 201203China University of Chinese Academy of Sciences Beijing 100049China Beijing National laboratory for Molecular Sciences(BNLMS) Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of EducationCollege of ChemistryPeking UniversityBeijing 100871China

Mimicking biosynthetic pathways of hongkonoids led to the development of a new Cu(Ⅰ)-catalyzed[3+2]cycloaddition ofα-hydroxyketone andβ-keto enol ethers,affording tetrahydrofuran acetals in a highly diastereoselective manner and 100%atom *** studies on the mechanism disclosed a concerted but asynchronous Michael addition/aldol *** the same importance,this methodology provides a practical biomimetic approach for one-step construction of the dibenzylbutyrolactol lignan backbone starting from two phenyl propane derivatives,opening up a powerful new approach for lignan synthesis,which is showcased by succinct total syntheses of two biologically important aryltetralin-type lignans,β-apopicropodophyllin and *** the mild and operationally simple conditions,the developed chemistry might have a promising prospect in potential industrial applications.

关键词： [3+2]cycloaddition transition-metal catalysis tetrahydrofuran lignans natural products

Ferricyanide-Promoted Oxidative Activation and Ligation of Protein Thioacids in Neutral Aqueous Media

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CCS chemistry 2024年第8期6卷 2031-2043页

作者： Guo-Chao Chu Lu-Jun Liang Rui zhao Yan-Yan Guo Chun-Tong Li Chong Zuo Huasong Ai xiao Hua Zi-Chen Li Yi-ming Li Lei Liu NewCornerstone Science laboratory Tsinghua-Peking Center for Life SciencesMinistry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical BiologyCenter for Synthetic and Systems BiologyDepartment of ChemistryTsinghua UniversityBeijing 100084 School of Food and Biological Engineering Hefei University of TechnologyHefei 230009 Center for BioAnalytical chemistry Hefei National Laboratory of Physical Science at MicroscaleUniversity of Science and Technology of ChinaHefei 230026 Department of chemistry University of Science and Technology of ChinaHefei 230026

Ferricyanide-promoted oxidative activation of Nacylatedα-aminothioacids for amide bond formation withα-aminonitriles was recently shown to be a plausible pathway for prebiotic peptide *** we describe the finding that by adding sodium azide and thiols,ferricyanide oxidation can elicit highly efficient and clean conversion of fully unprotected peptide or protein thioacids in neutral aqueous media to the corresponding *** transformation enables the development of ferricyanide-promoted thioacid-based native chemical ligation(NCL)as a new redox-based method for chemical protein synthesis,which does not need to change pH and is therefore operationally easy for ligation at small *** effectiveness of the ferricyanide-promoted thioacid-based NCL was illustrated by synthesis of an ISG15-modified MDA5 segment under nondenaturing conditions and synthesis of an acetylated ubiquitin(Ub)-modified histone H2A through an N-to-C sequential *** work broadens the concept of on-demand oxidative activation strategy for protein ligation and provides a new useful supplement to the repertoire of methods for chemical protein synthesis,particularly for studies on proteins carrying Ub family modifications.

关键词： chemical protein synthesis protein thioacid ferricyanide oxidation native chemical ligation ubiquitin family modifications

Nickel phosphorous trisulfide:A ternary 2D material with an ultra-low coefficient of friction

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Friction 2024年第10期12卷 2313-2324,F0004页

作者： Haoyu DENG Tongtong yu Changhe DU Ruilin SHEN Yongkang zhao Xinjian HE Yange fenG Liqiang ZHANG Daoai WANG State key laboratory of Solid Lubrication Lanzhou Institute of Chemical PhysicsChinese Academy of SciencesLanzhou 730000China Center of Materials Science and Optoelectronics Engineering University of Chinese Academy of SciencesBeijing 100049China Qingdao Center of Resource chemistry and New Materials Qingdao 266100China Shandong laboratory of Yantai Advanced Materials and Green Manufacturing Yantai 265503China

Ultra-low friction is crucial for the anti-friction,anti-wear,and long-life operation of ***,very few two-dimensional materials can achieve ultra-low friction,and they have some limitations in their ***,exploring novel materials with ultra-low friction properties is greatly *** emergence of ternary two-dimensional materials has opened new opportunities for nanoscale ultra-low *** study introduced nickel phosphorous trisulfide(NiPS3,referred to as NPS),a novel two-dimensional ternary material capable of achieving ultralow friction in a vacuum,into the large nanotribology ***-size and high-quality NPS crystals with up to 14 mm×6 mm×0.3 mm dimensions were grown using the chemical vapor transport *** NPS nanosheets were obtained using mechanical *** dependence of the NPS nanotribology on layer,velocity,and angle was systematically investigated using lateral force ***,the coefficient of friction(COF)of NPS with multilayers was decreased to about 0.0045 under 0.005 Pa vacuum condition(with load up to 767.8 nN),achieving the ultra-low friction *** analysis of the frictional dissipation energy and adhesive forces showed that NPS with multilayers had minimum frictional dissipation energy and adhesive forces since the interlayer interactions were weak and the meniscus force was excluded under vacuum *** study on the nanoscale friction of a ternary two-dimensional material lays a foundation for exploring the nanoscale friction and friction origin of other two-dimensional materials in the future.

关键词： two-dimensional(2D)materials NiPS3 ultra-low friction nanotribology

Vaccariside A, Novel Saponin from Vaccaria segetalis (Neck.) Garcke

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Chinese Chemical Letters 1999年第11期10卷 921-924页

作者： Ji MA Wen Cat YE Hou ming WU Fa Hu HE Jing Zhen DENG Shou Xun zhao( Department of Phytochemistry, china Pharmaceutical University, Naming 210009)(State key laboratory of bioorganic and Natural Products chemistry.Shanghai institute of organic chemistry china Pharmaceut Univ Dept Phytochem Nanjing 210009 Peoples R China Chinese Acad Sci Shanghai Inst Organ Chem State Key Lab Bioorgan & Nat Prod Chem Shanghai 200032 Peoples R China

A new triterpenoid saponin, vaccariside A 1 was isolated from the seeds of l'accaria segetalis using various chromatographic methods. The structure of compound 1 was elucidated by comprehensive spectroscopic analysis as 3-O-beta-D-galactopyranosyl-(1-2)-[beta-D-quinovpyranosyl-(1-4)-beta-D-xylopyranosyl-(1-3)]-beta-D-glucuronopyranosyl quillaic acid 28-O-beta-D-glucopyranosyl-(1-3)-[beta-D-xylopyranosyl-(1-4)]-alpha-L-rhamnopyranosyl-(1-2)-3-O-acetyl-beta-D-fucopyranoside.

关键词： vaccariside A. saponin Vaccaria segetalis

Distance-basedα-amylase biosensor fabricated with amylopectin-coated mesoporous membrane

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Chinese Chemical Letters 2024年第1期35卷 446-450页

作者： Binglu zhao Mashooq Khan yulin Liu Wenjun Tai Chongyang Mu Wenli Wu Mei zhao Yaohong Ma Li yu Jin-ming Lin Qiongzheng Hu Qilu University of Technology(Shandong Academy of Sciences) Shandong Analysis and Test CenterJi’nan 250014China School of Pharmaceutical Sciences Qilu University of Technology(Shandong Academy of Sciences)Ji’nan 250014China key laboratory of Colloid and Interface chemistry Shandong UniversityMinistry of EducationJi’nan 250100China key laboratory for Biosensors of Shandong Province Biology InstituteQilu University of Technology(Shandong Academy of Sciences)Ji’nan 250353China Beijing key laboratory of Microanalytical Methods and Instrumentation MOE Key Laboratory of Bioorganic Phosphorus Chemistry&Chemical BiologyDepartment of ChemistryTsinghua UniversityBeijing 100084China

Paper-based biosensors are widely employed in point-of-care testing(POCT)due to their convenience,portability,low cost,and ease of *** study reports an integrated distance-based paper biosensor fabricated with a mesoporous membrane coated with stimuli-responsive *** detection ofα-amylase(AMY)using amylopectin-coated mesoporous membrane is demonstrated as an *** introducing the AMY solution,it is observed that the aqueous solution flows along the paper strip due to AMY-catalyzed hydrolysis of *** flow distance is proportional to the concentration of AMY with a detection limit as low as 4 mU/*** addition,the detection of AMY is demonstrated in human ***,the inhibitory effect of acarbose on AMY is *** reagent-free and disposable biosensor allows single-step rapid detection of the *** approach is very promising for the development of user-friendly,equipment-free,and cost-effective biosensors with remarkable sensitivity and excellent selectivity for disease diagnosis and hypoglycemic drug screening.

关键词： Paper biosensor α-Amylase Stimuli-responsive polymer Mesoporous membrane Distance Point-of-care testing

Convenient and Efficient Synthesis of L-Rhamnopyranosyl Phosphoramidates via H-Phosphonate

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Chinese Chemical Letters 2003年第7期14卷 685-688页

作者： Qi sun Qiang xiao Yong JU yu fen zhao The key laboratory of bioorganic Phosphorus chemistry of education ministry Department of ChemistrySchool of Life Sciences and EngineeringTsinghua UniversityBeijing 100084

The a-L-rhamnopyranosyl phosphomonoesters conjugated with L-amino acid methyl esters were stereoselectively synthesized in a convenient route by utilizing H-phosphonate intermediate.

关键词： H-Phosphonate L-rhamnose phosphoramidate.

EFFECTS OF PHOSPHORYLATION ON THE CONFORMATION OF PEPTIDE AND PROTEIN

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EFFECTS OF PHOSPHORYLATION ON THE CONFORMATION OF PEPTIDE AN...

Repeating Unit of O-deacetylated GXM of C. neoformans Serotype

第17届国际磷化学大会

作者： Yan-Mei Li yu-fen zhao key laboratory of bioorganic Phosphorus chemistry and Chemical Biology (ministry of education) Department of chemistry Tsinghua University Beijing 100084

＜正＞The regulation of biochemical activity by protein post-translational modifications is a pervasive cellular control mechanism. Protein phosphorylation is a key posttranslational modification

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Repeating Unit of O-deacetylated GXM of C. neoformans Seroty...