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Binding of bacterial secondary messenger molecule c di-GMP is a STING operation

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Protein & Cell 2013年第2期4卷 117-129页

作者： Neil Shaw Songying Ouyang zhi-jie liu Tianjin Key Laboratory of Protein Science School of Life SciencesNankai UniversityTianjin 300071China National Laboratory of Biomacromolecules Institute of BiophysicsChinese Academy of SciencesBeijing 100101China

Initial skirmishes between the host and pathogen result in spillage of the contents of the bacterial *** the spillage,the secondary messenger molecule,cyclic dimeric guanosine monophosphate(c di-GMP),was recently shown to be bound by stimulator of interferon genes(STING).Binding of c di-GMP by STING activates the Tank Binding Kinase(TBK1)mediated signaling cascades that galvanize the body’s defenses for elimi-nation of the *** addition to c di-GMP,STING has also been shown to function in innate immune re-sponses against pathogen associated molecular pat-terns(PAMPs)originating from the DNA or RNA of *** pivotal role of STING in host defense is exemplified by the fact that STING-/-mice die upon infection by ***,STING plays an essential role in innate immune responses against *** opens up an exciting possibility of targeting STING for development of adjuvant therapies to boost the im-mune defenses against invading ***,STING could be targeted for mitigating the inflamma-tory responses augmented by the innate immune *** review summarizes and updates our current understanding of the role of STING in innate immune responses and discusses the future challenges in de-lineating the mechanism of STING-mediated responses.

关键词： innate immune response adaptor protein dimeric assembly crystal structure c di-GMP

The emerging roles of the DDX41 protein in immunity and diseases

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Protein & Cell 2017年第2期8卷 83-89页

作者： Yan Jiang Yanping Zhu zhi-jie liu Songying Ouyang National Laboratory of Biomacromolecules Institute of Biophysics Chinese Academy of Sciences Beijing 100101 China iHuman Institute Shanghai Tech University Shanghai 201210 China Department of Microbiology Immunology and Molecular Genetics University of California Los Angeles Los Angeles CA 90095 USA

RNA helicases are involved in almost every aspect of RNA, from transcription to RNA decay. DExD/H-box hell- cases compdse the largest SF2 helicase superfamily, which are characterized by two conserved RecA-like domains. In recent years, an increasing number of unexpected functions of these proteins have been discovered. They play important roles not only in innate immune response but also in diseases like cancers and chronic hepatitis C. In this review, we summarize the recant literatures on one member of the SF2 superfamily, the DEAD- box protein DDX41. After bacterial or viral infection, DNA or cyclic-di-GMP is released to cells. After phosphorylation of Tyr414 by BTK kinase, DDX41 will act as a sensor to recognize the invaders, followed by induction of type I interferons （IFN）. After the immune response, DDX41 is degraded by the E3 ligase TRIM21, using Lys9 and Lys115 of DDX41 as the ubiquitination sites. Besides the roles in Innate immunity, DDX41 is also related to diseases. An increasing number of both inherited and acquired mutetions in DDX41 gane are identified from myelodysplastic syndrome and/or acute myeloid leukemia （MDS/AML） patients. The review focuses on DDX41, as well as its homolog Abstrakt in Drosophila, which is important for survlval at all stages throughout the life cycle of the fly.

关键词： DDX41 innate immunity RNA helicases myelodysplastic syndrome acute myeloid leukemia

Structural biology study of human TNF receptor associated factor 4 TRAF domain

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Protein & Cell 2013年第9期4卷 687-694页

作者： Fengfeng Niu Heng Ru Wei Ding Songying Ouyang zhi-jie liu National Laboratory of Biomacromolecules Institute of BiophysicsChinese Academy of SciencesBeijing 100101China Institute of Molecular and Clinical Medicine Kunming Medical UniversityKunming 650500China University of Chinese Academy of Sciences Beijing 100049China

TRAF4 is a unique member of TRAF family,which is es-sential for innate immune response,nervous system and other *** addition to being an adaptor protein,TRAF4 was identifi ed as a regulator protein in recent *** have determined the crystal structure of TRAF domain of TRAF4(residues 292-466)at 2.60Åresolution by X-ray crystallography *** trimericly assembled TRAF4 resembles a mushroom shape,containing a super helical“stalk”which is made of three right-handed intertwinedαhelixes and a C-terminal“cap”,which is divided at resi-due L302 as a *** to other TRAFs,both intermolecular hydrophobic interaction in super helical“stalk”and hydrogen bonds in“cap”regions contribute directly to the formation of TRAF4 ***,differ-ing from other TRAFs,there is an additional fl exible loop(residues 421-426),which contains a previously identifi ed phosphorylated site S426 exposing on the *** S426 was reported to be phosphorylated by IKKαwhich is the pre-requisite for TRAF4-NOD2 complex formation and thus to inhibit NOD2-induced NF-κB ***,the crystal structure of TRAF4-TRAF is valuable for under-standing its molecular basis for its special function and provides structural information for further studies.

关键词： TRAF4 TRAF domain crystal structure ad-ditional loop phosphorylation site

Rotational Isomeric State Model of Poly(vinylidene chloride) Based Upon ab Initio Electronic Structure Calculations

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Chemical Research in Chinese Universities 2009年第1期25卷 108-111页

作者： ZHANG zhi-jie liu Yu-hua Lü Zhong-yuan LI Ze-sheng Institute of Theoretical Chemistry State Key Laboratory of Theoretical and Computational Chemistry Jilin University Changchun 130021 P. R. China

The rotational isomeric state（RIS） model was constructed for poly（vinylidene chloride）（PVDC） based on quantum chemistry calculations. The statistical weighted parameters were obtained from RIS representations and ab initio energies of conformers for model molecules 2,2,4,4-tetrachloropentane（TCP） and 2,2,4,4,6, 6-hexachloroheptane（HCH）. By employing the RIS method, the characteristic ratio C∞ was calculated for PVDC. The calculated characteristic ratio for PVDC is in good agreement with experiment result. Additionally, we studied the influence of the statistical weighted parameters on C∞ by calculating δC∞/δlnw. According to the values of δC∞/δlnw, the effects of second-order Cl-CH2 pentane type interaction and C1--C1 long range interaction on C∞ were found to be important. In contrast, first-order interaction is unimportant.

关键词： Ab initio calculations Characteristic ratio Poly(vinylidene chloride)

Protein-protein complexation in bioluminescence

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Protein & Cell 2011年第12期2卷 957-972页

作者： Maxim S.Titushin Yingang Feng John Lee Eugene S.Vysotski zhi-jie liu National Laboratory of Biomacromolecules Institute of BiophysicsChinese Academy of SciencesBeijing 100101China Qingdao Institute of Bioenergy and Bioprocess Technology Chinese Academy of SciencesQingdao 266101China Department of Biochemistry and Molecular Biology University of GeorgiaAthensGA 30602USA Laboratory of Photobiology Institute of Biophysics Russian Academy of SciencesSiberian BranchKrasnoyarsk 660036Russia

In this review we summarize the progress made towards understanding the role of protein-protein interactions in the function of various bioluminescence systems of marine organisms,including bacteria,jellyfish and soft corals,with particular focus on methodology used to detect and characterize these *** some bioluminescence systems,protein-protein interactions involve an“accessory protein”whereby a stored substrate is efficiently delivered to the bioluminescent enzyme *** types of complexation mediate energy transfer to an“antenna protein”altering the color and quantum yield of a bioluminescence *** structures of the complexes reveal an important role of electrostatic forces in governing the corresponding weak interactions and define the nature of the interaction *** most reliable structural model is available for the protein-protein complex of the Ca2+-regulated photoprotein clytin and green-fluorescent protein(GFP)from the jellyfish Clytia gregaria,solved by means of Xray crystallography,NMR mapping and molecular *** provides an example of the potential strategies in studying the transient complexes involved in *** is emphasized that structural studies such as these can provide valuable insight into the detailed mechanism of bioluminescence.

关键词： green-fluorescent protein(GFP) photoprotein luciferase lumazine protein Förster resonance energy transfer(FRET) docking

Green synthesis of luminescent La-MOF nanoparticle from waste poly(ethylene terephthalate) for high-performance in Fe(Ⅲ) detection

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Rare Metals 2024年第8期43卷 3833-3843页

作者： zhi Gong zhi-Kui Dai zhi-Yue Dong Qiu-Xuan liu Valentin A.Milichko Hua-Jian liu jie liu Ran Niu Jiang Gong Key Laboratory of Material Chemistry for Energy Conversion and Storage Hubei Key Laboratory of Material Chemistry and Service FailureHubei Engineering Research Center for Biomaterials and Medical Protective MaterialsSemiconductor Chemistry CenterSchool of Chemistry and Chemical EngineeringMinistry of EducationHuazhong University of Science and TechnologyWuhan 430074China School of Chemical Engineering and Pharmacy Wuhan Institute of TechnologyWuhan 430073China Collaborative Innovation Center for Advanced Organic Chemical Materials Co-constructed by the Province and Ministry Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules and College of Chemistry and Chemical EngineeringHubei UniversityWuhan 430062China School of Physics and Engineering ITMO UniversitySt.Petersburg197101Russia School of Materials Science and Engineering Hubei UniversityWuhan430062China Guangdong Provincial Key Laboratory of Technique and Equipment for Macromolecular Advanced Manufacturing School of Mechanical and Automotive EngineeringKey Laboratory of Polymer Processing EngineeringMinistry of EducationSouth China University of TechnologyGuangzhou 510641China

Developing luminescent metal-organic frameworks(MOFs) capable of high-efficiency Fe^(3+)sensing has aroused great attraction in the fields of biology,chemistry,***,previous solvothermal methods are limited by organic solvent usage,time consuming,high pressure,and high-energy ***,we propose the waste-toMOF strategy towards the scale-up production of La-MOF nanoparticles through the ball milling of recycled poly(-ethylene terephthalate)(PET) bottles and La(NO_(3))_(3)·_(6)H_(2)*** goes on alkaline hydrolysis to form 1,4-benzenedicarboxylic acid sodium salt(Na_(2)BDC) and ethylene glycol by ball ***,BDC reacts with La^(3+)to form *** as-prepared La-MOF crystal nanoparticles possess a rod-like morphology with the size of few hundred ***,La-MOF nanoparticles display high selectivity and sensitivity for Fe^(3+)*** quenching constant and limit of detection are 5.29×10^(3)(mol·L^(-1))^(-1) and 0.147 μmol·L^(-1),respectively,thus surpassing many advanced Fe^(3+) *** to the result of density functional theory,the high Fe^(3+) detection performance of La-MOF is related to the complexing of Fe^(3+)with La-MOF,which leads to the gradual dissociation of the coordination bond between terephthalic acid and La^(3+).It is anticipated that the mechanochemistry milling-based wasteto-MOF strategy provides a new platform for the massive production of functional MOFs in a green manner.

关键词： Metal-organic framework Waste polyester Mechanochemistry milling Fluorescence sensor

Structural and functional analyses of human DDX41 DEAD domain

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Protein & Cell 2017年第1期8卷 72-76页

作者： Yan Jiang Yanping Zhu Weicheng Qiu Yong-Jun liu Genhong Cheng zhi-jie liu Songying Ouyang National Laboratory of Biomacromolecules Institute of BiophysicsChinese Academy of Sciences Beijing 100101 China Baylor Research Institute Baylor Scott and White Health DallasTX 75246 USA Department of Microbiology Immunology and Molecular GeneticsUniversity of California Los Angeles Los Angeles CA 90095 USA Institute of Molecular and Clinical Medicine Kunming MedicalUniversity Kunming 650500 China

Dear Editor, DEAD-box proteins, which are named after the strictly con- served amino acid sequence Asp-Glu-Ala-Asp, were first identified as a distinct family in the late 1980s when alignments based on eight homologue... 详细信息

关键词： Acute Myeloid Leukemia Isothermal Titration Calorimetry Mutate Amino Acid Helicase Domain Thermal Shift Assay

Prediction for permeability index of blast furnace based on VMD-PSO-BP model

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Journal of Iron and Steel Research International 2024年第3期31卷 573-583页

作者： Xiao-jie liu Yu-jie Zhang Xin Li zhi-feng Zhang Hong-yang Li Ran liu Shu-jun Chen School of Metallurgy and Energy North China University of Science and TechnologyTangshan 063210HebeiChina Chengde Branch HBIS Group Co.Ltd.Chengde 067000HebeiChina

The permeability index is one of the important production indicators to monitor the operation of blast *** is crucial to grasp the trends of changes in the new permeability index in *** the complex vibration spectrum of the permeability index,a prediction model of the permeability index based on the VMD-PSO-BP(variational mode decomposition-particle swarm optimization-back propagation)method was ***,the key factors that affect the permeability index of blast furnace were studied from multiple ***,the permeability index was divided into multiple sub-modes based on the difference of frequency bands by the VMD algorithm,and a PSO-BP prediction model was established for each ***,the prediction results of each sub-mode were summed to obtain the final *** results show that the composite prediction accuracy by using the VMD algorithm is 3%higher than that of the traditional prediction method,which has better applicability.

关键词： Big data-Blast furnace Air permeability Variational mode decomposition Particle swarm optimization Back propagation Model prediction

Crystal structure of a novel non-Pfam protein PF2046 solved using low resolution B-factor sharpening and multi-crystal averaging methods

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Protein & Cell 2010年第5期1卷 453-458页

作者： Jing Su Yang Li Neil Shaw Weihong Zhou Min Zhang Hao Xu Bi-Cheng Wang zhi-jie liu National Laboratory of Biomacromolecules Institute of BiophysicsChinese Academy of SciencesBeijing 100101China College of Life Sciences Nankai UniversityTianjin 300071China School of Life Sciences Anhui UniversityHefei 230039China Department of Biochemistry and Molecular Biology University of GeorgiaAtlantaGA 30605USA

Sometimes crystals cannot diffract X-rays beyond 3.0Åresolution due to the intrinsic flexibility associated with the *** resolution diffraction data not only pose a challenge to structure determination,but also hamper interpretation of mechanistic *** of a 25.6 kDa non-Pfam,hypothetical protein,PF2046,diffracted X-rays to 3.38Åresolution.A combination of SeMet derived heavy atom positions with multiple cycles of B-factor sharpening,multi-crystal averaging,restrained refinement followed by manual inspection of electron density and model building resulted in a final model with a R value of 23.5(R_(free)=24.7).The asymmetric unit was large and consisted of six molecules arranged as a homodimer of *** of the structure revealed the presence of a RNA binding domain suggesting a role for PF2046 in the processing of nucleic acids.

关键词： low resolution diffraction PF2046 Bfactor sharpening a homodimer of trimers