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The zinc-finger protein ZFYVE1 modulates TLR3-mediated signaling by facilitating TLR3 ligand binding

Cellular & Molecular Immunology 2020年第7期17卷 741-752页

作者： Xuan Zhong Lu Feng Wen-Hua Xu Xin Wu Yi-Di Ding Yan Zhou Cao-Qi Lei Hong-Bing Shu College of Life Sciences Wuhan UniversityWuhan 430072China Department of Infectious Diseases Zhongnan Hospital of Wuhan UniversityWuhan UniversityWuhan 430072China Medical Research Institute Wuhan UniversityWuhan 430072China

Recognition of viral dsRNA by Toll-like receptor 3(TLR3)leads to the induction of downstream antiviral effectors and the innate antiviral immune ***,we identified the zinc-finger FYVE domain-containing protein ZFYVE1,a guanylate-binding protein(GBP),as a positive regulator of TLR3-mediated *** of ZFYVE1 promoted the transcription of downstream antiviral genes upon stimulation with the synthetic TLR3 ligand poly(I:C).Conversely,ZFYVE1 deficiency had the opposite ***1^(−/−) mice were less susceptible than wild-type mice to inflammatory death induced by poly(I:C)but not ***1 was associated with TLR3,and the FYVE domain of ZFYVE1 and the ectodomain of TLR3 were shown to be responsible for their ***1 was bound to poly(I:C)and increased the binding affinity of TLR3 to poly(I:C).These findings suggest that ZFYVE1 plays an important role in the TLR3-mediated innate immune and inflammatory responses by promoting the ligand binding of TLR3.

关键词： TLR3 ZFYVE1 ligand binding immune response

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ligand binding mechanism of H-FABP revealed by molecular dynamics simulations

Ligand binding mechanism of H-FABP revealed by molecular dyn...

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2019中国化学会第十五届全国计算（机）化学学术会议

作者：郭玥 Mojie Duan 武汉物理与数学研究所 State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics Wuhan Institute of Physics and Mathematics Chinese Academy of Sciences

As a member of fatty acids transporter family, the heart fatty acid binding proteins（H-FABP） responses for many important biological activities such as energy supply, lipid metabolism, signal transduction and precursor synthesis. The binding mechanism of fatty acid with FABP is critical to the understanding of FABP functions. In this work, by combining with all-atom conventional molecular dynamics（cMD） simulations and enhanced sampling technologies, the association/disassociation processes of fatty acids from FABP were investigated. The free energy landscape as a functions of binding related reaction coordinates was obtained by bias-exchange metadynamics（BE-MetaD）. Our results show that there are two pathways for the ligand binding or unbinding. Moreover, path Metadynamic simulations were used to characterize the intermediates and the kinetic properties of the association/disassociation processes. Our results provide the atomic level description of FA binding/unbinding process and would greatly improve the understanding of the ligand binding mechanism of H-FABP.

关键词： H-FABP ligand binding BE-MetaD path metadynamics binding pathway

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Comparison of ligand migration and binding in heme proteins of the globin family

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Chinese Physics B 2015年第12期24卷 109-118页

作者： Karin Nienhaus G.Ulrich Nienhaus Institute of Applied Physics (APH) Karlsruhe Institute of Technology (KIT) Institute of Nanotechnology (INT) and Institute of Toxicology and Genetics (ITG) Karlsruhe Institute of Technology (KIT) Department of Physics University of Illinois at Urbana-Champaign

The binding of small diatomic ligands such as carbon monoxide or dioxygen to heme proteins is among the simplest biological processes known. Still, it has taken many decades to understand the mechanistic aspects of this process in full detail. Here, we compare ligand binding in three heme proteins of the globin family, myoglobin, a dimeric hemoglobin, and neuroglobin. The combination of structural, spectroscopic, and kinetic experiments over many years by many laboratories has revealed common properties of globins and a clear mechanistic picture of ligand binding at the molecular level. In addition to the ligand binding site at the heme iron, a primary ligand docking site exists that ensures efficient ligand binding to and release from the heme iron. Additional, secondary docking sites can greatly facilitate ligand escape after its dissociation from the heme. Although there is only indirect evidence at present, a preformed histidine gate appears to exist that allows ligand entry to and exit from the active site. The importance of these features can be assessed by studies involving modified proteins（via site-directed mutagenesis） and comparison with heme proteins not belonging to the globin family.

关键词： flash photolysis ligand binding time-resolved spectroscopy heme protein

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Identification and Characterization of GH Receptor and Serum GH-binding Protein in Chinese Sturgeon (Acipenser sinensis)

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Acta Biochimica et Biophysica Sinica 2004年第12期36卷 811-816页

作者： Zhi-Yong LIAO1,2 and Shang-Quan ZHU2* 1College of Life Sciences, Jiangxi Normal University, Nanchang 330027, China 2Key Laboratory of Proteomics Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Graduate School of the Chinese Academy of Sciences, Shanghai 200031, China College of Life Sciences Jiangxi Normal UniversityNanchang 330027 China Key Laboratory of Proteomics Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Graduate School of the Chinese Academy of SciencesShanghai 200031 China

Chinese sturgeon, a kind of cartilage ganoid, has a history of over one billion years and it is called the living fossil of aquatic biology since it keeps some evolutionary trace. Here, we characterized the growth hormone receptor (GHR) and serum growth hormone binding protein (GHBP) of Chinese sturgeon. It was shown that GHR was expressed in various tissues, mainly in hepatic, kidney and intestine tissues. GHR on the hepatic membrane has high and specific affinity for bream GH (brGH) and Scatchard analysis of the binding data showed a single class of high affinity binding site with an association constant Ka of 3.1×109 M–1. A specific band around 94 kD was detected by SDS-PAGE in cross-linking studies of membrane receptors. After incubation of Chinese sturgeon serum with 125I-brGH, a 125I-brGH-GHBP complex was identified by Sephadex G-75, indicating that in the serum exists GHBP specially binding to brGH.

关键词： Chinese sturgeon growth hormone receptor growth hormone binding protein ligand binding

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A computational study of the chemokine receptor CXCR1 bound with interleukin-8

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Chinese Physics B 2018年第3期27卷 534-543页

作者：王洋 Cecylia Severin Lupala 王亭李选选 Ji-Hye Yun Jae-hyun Park 金泽宇 Weontae Lee 汤雷翰刘海广 Complex Systems Division Beijing Computational Science Research CenterBeijing 100193China Genome Center University of CaliforniaDavis451 East Health Science DriveDavisCA95616USA Department of Engineering physics Tsinghua UniversityBeijing 100086China Department of Biochemistry College of Life Science&BiotechnologyYonsei UniversitySeou103722South Korea Department of Physics and Institute of Computational and Theoretical Studies Hong Kong Baptist UniversityHong KongChina

CXCR1 is a G-protein coupled receptor, transducing signals from chemokines, in particular the interleukin-8 （1L8） molecules. This study combines homology modeling and molecular dynamics simulation methods to study the structure of CXCRI-IL8 complex. By using CXCR4-vMIP-II crystallography structure as the homologous template, CXCRI-IL8 complex structure was constructed, and then refined using all-atom molecular dynamics simulations. Through extensive simulations, CXCRI-IL8 binding poses were investigated in detail. Furthermore, the role of the N-terminal of CXCR1 receptor was studied by comparing four complex models differing in the N-terminal sequences. The results indicate that the receptor N-terminal affects the binding of IL8 significantly. With a shorter N-terminal domain, the binding of IL8 to CXCR1 becomes unstable. The homology modeling and simulations also reveal the key receptor-ligand residues involved in the electrostatic interactions known to be vital for complex formation.

关键词： CXCRI-IL8 complex homology modeling ligand binding molecular dynamics

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