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Crystal Structure of Cytidine Deaminase Human APOBEC3F Chimeric Catalytic Domain in Complex with DNA

Chinese Journal of Chemistry 2018年第12期36卷 1241-1248页

作者： Chao Cheng Tianlong Zhang Chunxi Wang Wenxian Lan Jianping Ding Chunyang Cao State Key Laboratory of Bioorganic and Natural product Chemistry Center for Excellence in Molecular SynthesisShanghai Institute of Organic ChemistryChinese Academy of Sciences345 Lingling RoadShanghai200032China Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences320 Yueyang RoadShanghai200031China University of Chinese Academy of sciences No.19(A)Yuquan RoadShijingshan DistrictBeijing 100049China

APOBEC3F (A3F) demonstrates antivirus activity through its A3F‐CD2 domain catalyzing deamination of cytidine in target motif 5’‐TC in viral cDNA during reverse transcription. But structural basis is unclear. Previously, chimeric A3F‐CD2 (i.e., A3Fc‐CD2, where residues 195—217 of A3F‐CD2 were replaced with residues 197—221 of A3G‐CD2) was found soluble with deamination activity. Here, we report crystal structures of A3Fc‐CD2 in complexes with single‐stranded DNA (5’‐ATTTT5C6A7A8T9T‐3’ and 5’‐ATTTT5C6A7A8C9T‐3’) at resolutions of 1.98 Å and 2.30 Å, respectively. They demonstrate that one molecular DNA binds two A3Fc‐CD2 molecules (monomers A and B) at two sites, distinct from the reported complex structure of human A3F‐CD2 with a 10‐dT DNA. The first site is formed by residues Tyr333, Lys358 and Tyr359 in monomer A, far away from Zn2+ binding motif, interacting with bases dT5, dC6 and dA7 through π‐π stacking and hydrogen bonds. The second site is composed of Trp277, Y307YFW310 near to Zn2+ binding region in monomer B, interacting with base dA8, mainly through π‐π stacking and hydrophobic interactions, determining deamination preference of DNA sequence. Subsequent biochemical investigations further confirm the contribution of these residues to DNA binding and deamination activities. These studies are helpful to understand the mechanism how A3F‐CD2 catalyzes cytidine deamination.

关键词： APOBEC3F HIV‐1 deamination DNA structure

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Expression Level of a Transcription Factor Gene Mdhd-Zip Up-regulated during Apple fruit Senescence

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Agricultural Science & Technology 2016年第5期17卷 1065-1069页

作者： Xiaoxiao CHANG Shoukun HAN Kun MENG Ting ZHANG Lihong MA Jingping RAO Department of Horticulture Northwest A&F University Yangling 712100 China Institute of Farm product Storage and Processing Xinjiang Academy of Agricultural Sciences Urumqi 830091 China Shaanxi Huasheng fruit Company Xi'an 712100 China

[Objective] This study aimed to explore the role of one apple transcription factor of homeodomain-leucine zipper(MdHD-Zip) during apple fruit senescence.[Method] Postharvest Red Fuji fruits(Malus domestica Borkh ‘Red Fuji') were stored at room temperature(18 ℃-20 ℃) and cold condition(0 ± 1 ℃) *** firmness and ethylene production during storage process were *** level of Md HD-Zip was detected by real-time quantitative PCR during apple fruit storage under room temperature and cold condition.[Result] Expression level of Md HD-Zip was found up-regulated in later stage of apple fruit senescence at room temperature,while it showed a peak level after one month of cold storage.[Conclusion] The results of the present study suggest that Md HD-Zip may play a role in regulating apple fruit senescence.

关键词： Apple fruit Md HD-Zip Storage

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Analysis of Phospholipids in Crucian Carp(Carassius auratus) Muscle by Offline HPLC-MALDI-TOF MS

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Chemical Research in Chinese Universities 2011年第3期27卷 371-374页

作者： LI Guo-chen WANG Yan-hong WU Ren-an WANG Shi-cheng Inspection and Testing Center of Agro-product Safety and Environment Quality Institute of Applied EcologyChinese Academy of SciencesShenyang 110016P.R.China National Chromatographic Research&Analysis Center Dalian Institute of Chemical PhysicsChinese Academy of SciencesDalian 116023P.R.China

The interest in the analysis of phospholipids(PLs), especially phosphatidylcholine(PC), has been increasing due to the importance of them in biochemistry as well as in industry. A method was reported based on the offline combination of MALDI-TOF MS and normal-phase HPLC for analyzing PLs extracted from crucian carp. Total PLs of crucian carp were extracted and then separated by HPLC before the collected subfractions were analyzed by MALDI-TOF MS. The mass spectra obtained show peaks of H+, Na+ and K+ adducts of PC molecules. It is shown that the prior separation of PLs by HPLC is highly necessary to remove the signal suppressing and to avoid the possible overlapping. With this method, 9 possible PC molecules in crucian carp and the corresponding fatty acid compositions were given from the well-resolved mass spectra.

关键词： Phospholipid Phosphatidylcholine Phosphatidylethanolamine Sphingomyelin HPLC MALDI Crucian Carp

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Effects of Exogenousα-Ketoglutaric Acid on 2-Acetyl-1-Pyrroline,Yield Formation and Grain Quality Characters of Aromatic Rice

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Phyton-International Journal of Experimental Botany 2021年第2期90卷 437-447页

作者： Bin Du Qixia Wu Shuochen Jiang Dingyue Zhang Yue Qiao Yimei Xie Jianlong Xu Jianqiang Zhu College of Agriculture Yangtze UniversityJingzhou434023China National Selenium-Rich product Quality Supervision and Inspection Center Enshi434023China Institute of Crop Science Chinese Academy of Agricultural SciencesBeijing100081China

The improvement of grain quality in aromatic rice is very important for farmer to increase their *** study was conducted with a two-year field experiment and three aromatic rice cultivars in order to study the effects of exogenousα-ketoglutaric acid on yield formation,grain quality characters and the biosynthesis of 2-acetyl-1-pyrroline(2-AP,key component of aromatic rice’s fragrance)in aromatic *** heading stage,0.50 mmol L^(-1)(T1)and 1.00 mmol L^(-1)(T2)α-ketoglutaric acid solutions were overhead sprinkle to aromatic rice plants,respectively while the treatment which was overhead sprinkled with distilled water was set as control(CK).The results showed that 17.34%-33.04%and 21.39%-34.74%higher grain 2-AP contents were recorded in T1 and T2 treatments,*** with CK,T1 and T2 treatments significantly reduced the transcript level of gene BADH2 which is related to the 2-AP biosynthesis in aromatic rice.3.86%-7.51%higher grain protein contents and 1.15%-3.37%higher head rice rates were also recorded inα-ketoglutaric acid treatments than ***,T1 and T2 treatments remarkably decreased the chalky rice rate,chalkiness and grain amylose ***,there was no remarkable difference in grain yield and related trails(effective panicle number,grain number per panicle,seed-setting rate and 1000-grain weight)among CK,T1 and T2 *** conclusion,application of exogenousα-ketoglutaric acid enhanced 2-AP biosynthesis and improved grain quality of aromatic rice.

关键词： α-ketoglutaric acid aromatic rice chalkiness protein 2-acetyl-1-pyrroline

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Dracomolphesin A-E,five 3,4-seco-phenylpropanoids with Nrf2 inducing activity from Dracocephalum moldavica

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Chinese Chemical Letters 2020年第5期31卷 1259-1262页

作者： Huaran Zhang Lintao Xu Xiaoqing Liu Jiangjiang Fan Xiaoning Wang Tao Shen Shuqi Wang Dongmei Ren Department of Natural product Chemistry Key Laboratory of Chemical Biology(Ministry of Education)School of Pharmaceutical SciencesShandong UniversityJi'nan 250012China Department of Thoracic Surgery Qilu Hospital of Shandong UniversityJi'nan 250012China

Dracomolphesin A-E(1-5),five 3,4-seco-phenylpropanoids featuring an aromatic ring opened framework,were isolated from the aerial parts of Dracocephalum *** structures with absolute configurations were determined by spectroscopic methods coupled with Mosher ***,these compounds represented an example of aromatic ring cleavage products of *** possible biosynthetic pathway of these compounds was *** 1,2,4 and 5 were demonstrated to be Nrf2 pathway activators.

关键词： 3,4-seco-phenylpropanoids Dracocephalum moldavica Nrf2 pathway Dioxygenase Antioxidant

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In vitro Antioxidant Effects of Porphyra haitanensis Peptides on H_2O_2-Induced Damage in HepG2 Cells

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Journal of Ocean University of China 2021年第2期20卷 421-428页

作者： CHEN Shengjun YU Jiao HU Xiao YANG Xianqing LI Laihao QI Bo DENG Jianchao Key Laboratory of Aquatic product Processing Ministry of Agriculture and Rural AffairsNational Research and Development Center for Aquatic Product ProcessingSouth China Sea Fisheries Research InstituteChinese Academy of Fishery SciencesGuangzhou 510300China Co-Innovation Center of Jiangsu Marine Bio-Industry Technology Jiangsu Ocean UniversityLianyungang 222005China College of Food Science&Technology Shanghai Ocean UniversityShanghai 201306China

In this study,protein from Porphyra haitanensis was used as raw material to prepare an antioxidant peptide,and its antioxidant activity was evaluated in vitro.A model of H_2O_2-induced oxidative damage in Hep G2 cells was established,and the effects of Porphyra haitanensis hydrolysates (PHHs) on superoxide dismutase (SOD) activity and malondialdehyde (MDA) content were ***,the structure of PHHs was identified by ESI-MS/*** results showed that the 1,1-diphenyl-2-pyridylhydrazine(DPPH)-free radical-scavenging ability of PHHs was the strongest (59.28%at 1.0 mg m L~(-1)) when hydrolyzed with an acidic protease for 4 *** with different concentrations had protective effects on H_2O_2-induced damage to Hep G2 cells,and the protective effect was enhanced with increasing *** the level was 400μg m L~(-1),the cell survival rate was as high as 88.62%.Moreover,PHHs can significantly reduce oxidative damage to Hep G2 cells by H_2O_2,improve SOD activity,and reduce MDA *** tetrapeptide Asp-Lys-Ser-Thr,with a molecular weight of 448 Da,was identified as an important fraction of PHHs by high-resolution mass spectrometry.

关键词： Porphyra haitanensis hydrolysates(PHHs) antioxidant peptides radical-scavenging activity cell antioxidant capacity electrospray ionization-mass spectrometry

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Second-generation DNA-encoded multiple display on a constant macrocyclic scaffold enabled by an orthogonal protecting group strategy

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Chinese Chemical Letters 2022年第5期33卷 2559-2563页

作者： Qigui Nie Shuting Zhong Yangfeng Li Gong Zhang Yizhou Li Chongqing Key Laboratory of Natural product Synthesis and Drug Research School of Pharmaceutical SciencesChongqing UniversityChongqing 401331China Key Laboratory of Biorheological Science and Technology Ministry of EducationCollege of BioengineeringChongqing UniversityChongqing 401331China

DNA-encoded chemical library(DEL)represents an emerging drug discovery technology to construct com-pound libraries with abundant chemical *** drug-like small molecule DELs facilitate the discovery of binders against targets with defined pockets,macrocyclic DELs harboring extended scaffolds enable targeting of the protein–protein interaction(PPI)*** previously demonstrated the design of the first-generation DNA-encoded multiple display based on a constant macrocyclic scaffold,which harvested binders against difficult targets such as tumor necrosis factor-α(TNF-α).Here,we developed a novel strategy which utilized four orthogonal amine-protecting groups on DNA,to explore larger chem-ical combinations on the same constant macrocyclic scaffold,following the parallel paradigm to mimic the versatile antibody-like multivalent epitope recognition *** successfully integrated these or-thogonal protecting groups with acylation and made a mock second-generation DNA-encoded display *** work illustrates a strategy to produce larger encoded multiple display on a constant macrocyclic scaffold,which could facilitate potential binder discovery with enhanced affinity to clinically significant PPI targets.

关键词： DNA-encoded library Macrocyclic scaffold DNA-compatible Protein–protein interaction Chemical probe

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Nondestructive determination of the freshness change in bighead carp heads under variable temperatures by using excitation-emission matrix fl uorescence and back-propagation neural networks

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Journal of Future Foods 2022年第2期2卷 160-166页

作者： Ce Shi Zengtao Ji Xinting Yang Zhixin Jia Ruize Dong Ge Shi Information Technology Research Center Beijing Academy of Agriculture and Forestry SciencesBeijing 100097China National Engineering Research Center for Information Technology in Agriculture Beijing Academy of Agricultural and Forestry SciencesBeijing 100097China National Engineering Laboratory for Agri-product Quality Traceability Beijing Academy of Agricultural and Forestry SciencesBeijing 100097China Key Laboratory of Cold Chain Logistics Technology for Agro-product Ministry of Agriculture and Rural AffairsBeijing 100097China

This study established back-propagation neural networks(BPNNs)for evaluating the freshness of bighead carp(Hypophthalmichthys nobilis)heads during chilled storage via fluorescence spectroscopy using an excitation-emission matrix(EEM).The total volatile basic nitrogen(TVB-N)and total aerobic count(TAC)of fish increased obviously during storage at 0,4,8,12,and 16°C,while sensory scores decreased with increasing storage *** EEM fluorescence intensity was measured,and its change was correlated with the freshness indicators of the *** characteristic components of EEM data were extracted by parallel factor analysis,and two freshness indicators were used to construct the EEM-BPNNs *** results demonstrated that the relative errors of the EEM-BPNNs model for TVB-N and TAC were less than 14%.This result indicated that the EEM-BPNNs model could determine the freshness of fish in cold chains in a rapid and nondestructive way.

关键词： Excitation-emission matrix Freshness Back-propagation neural networks Parallel factor analysis Chilled storage

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Insights into microbiota community dynamics and flavor development mechanism during golden pomfret(Trachinotus ovatus)fermentation based on single-molecule real-time sequencing and molecular networking analysis

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Food Science and Human Wellness 2024年第1期13卷 101-114页

作者： Yueqi Wang Qian Chen Huan Xiang Dongxiao Sun-Waterhouse Shengjun Chen Yongqiang Zhao Laihao Li Yanyan Wu Key Laboratory of Aquatic product Processing Ministry of Agriculture and Rural Affairs of The People’s Republic of ChinaNational R&D Center for Aquatic Product ProcessingSouth China Fisheries Research InstituteChinese Academy of Fishery SciencesGuangzhou 510300China Co-Innovation Center of Jiangsu Marine Bio-industry Technology Jiangsu Ocean UniversityLianyungang 222005China School of Chemical sciences The University of AucklandAuckland 92019New Zealand Collaborative Innovation Center of Seafood Deep Processing Dalian Polytechnic UniversityDalian 116034China

Popular fermented golden pomfret(Trachinotus ovatus)is prepared via spontaneous fermentation;however,the mechanisms underlying the regulation of its flavor development remain *** study shows the roles of the complex microbiota and the dynamic changes in microbial community and flavor compounds during fish ***-molecule real-time sequencing and molecular networking analysis revealed the correlations among different microbial genera and the relationships between microbial taxa and volatile *** underlying flavor development were also elucidated via KEGG based functional ***,Shewanella,and Staphylococcus were the dominant microbial ***-nine volatile compounds were detected in the fermented fish samples,with thirteen identified as characteristic volatile compounds(ROAV>1).Volatile profiles resulted from the interactions among the microorganisms and derived enzymes,with the main metabolic pathways being amino acid biosynthesis/metabolism,carbon metabolism,and glycolysis/*** study demonstrated the approaches for distinguishing key microbiota associated with volatile compounds and monitoring the industrial production of high-quality fermented fish products.

关键词： Fermented golden pomfret Microbiota community Volatile compound Co-occurrence network Metabolic pathway

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Natural products:potential therapeutic agents for atherosclerosis

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Chinese Journal of Natural Medicines 2022年第11期20卷 830-845页

作者： CHENG Xiaobei ZHAO Caili JIN Zhiwei HU Jianping ZHANG Zhenzhen ZHANG Chao State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Bioactive Natural product Research School of Traditional Chinese PharmacyChina Pharmaceutical UniversityNanjing 210009China Institute of Veterinary Medicine Jiangsu Academy of Agricultural SciencesNanjing 210014China

Atherosclerosis(AS)is an invisible killer among cardiovascular diseases(CVD),which has seriously threatened the life of *** complex pathogenesis of AS involves multiple interrelated events and cell types,such as macrophages,endothelial cells,vascular smooth muscle cells and immune ***,the efficacy of recommended statin treatment is not *** products(NPs)have attracted increasing attention with regard to their broad structural diversity and biodiversity,which makes them a promising library in the demand for lead compounds with cardiovascular protective *** can preclude the development of AS by regulating lipid metabolism,ameliorating inflammation,stabilizing plaques,and remodeling the gut microbiota,which lays a foundation for the application of NPs in clinical therapeutics.

关键词： Atherosclerosis Cardiovascular diseases Pathogenesis Target Natural products

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