Molecular modeling methods have been applied to the structural characterization of the interaction between chiral metal complexes [Co(phen)2dppz]3+ (where phen = 1, 10-phenanthroline, dppz = dipyrido[3,2-a: 2’, 3’-c...Molecular modeling methods have been applied to the structural characterization of the interaction between chiral metal complexes [Co(phen)2dppz]3+ (where phen = 1, 10-phenanthroline, dppz = dipyrido[3,2-a: 2’, 3’-c]phenazine) and the oligonucleotide (B-DNA fragment). The natures of two kinds of the binding modes, which are currently intense controversy, have been explored. Barton proposed that there is enantio-selective DMA binding by the octahedral complexes and intercalative access by these complexes from the major groove; but Norden suggested that both enantiomers bind extremely strongly to DNA from the minor groove without any noticeable enantio-selectivity. Our results support and extend structural models based upon Norden’s studies, and conflict with Barton’s model.展开更多
Unrestrained molecular dynamics （MD） simulations have been carded out to characterize the stability of DNA conformations and the dynamics of A-DNA^B-DNA conformational transitions in aqueous RbC1 solutions. The PARM...Unrestrained molecular dynamics （MD） simulations have been carded out to characterize the stability of DNA conformations and the dynamics of A-DNA^B-DNA conformational transitions in aqueous RbC1 solutions. The PARM99 force field in the AMBER8 package was used to investigate the effect of RbC1 concentration on the dynamics of the A^B conformational tran- sition in the DNA duplex d（CGCGAATTCGCG）2. Canonical A- and B-form DNA were assumed for the initial conformation and the final conformation had a length per complete turn that matched the canonical B-DNA. The DNA structure was moni- tored for 3.0 ns and the distances between the C5＇ atoms were obtained from the simulations. It was found that all of the double stranded DNA strands of A-DNA converged to the structure of B-form DNA within 1.0 ns during the unrestrained MD simula- tions. In addition, increasing the RbC1 concentration in aqueous solution hindered the A^B conformational transition and the transition in aqueous RbC1 solution was faster than that in aqueous NaC1 solution for the same electrolyte strength. The effects of the types and concentrations of counterions on the dynamics of the A^B conformational transition can be understood in terms of the variation in water activity and the number of accumulated counterions in the major grooves of A-DNA. The ru- bidium ion distributions around both fixed A-DNA and B-DNA were obtained using the restrained MD simulations to help ex- plain the effect of RbC1 concentration on the dynamics of the A^B conformational transition.展开更多
目的探讨乙型肝炎病毒DNA聚合酶反式调节蛋白1(HBV DNA polymerase trans activated protein 1,HBVDNAPTP1)在羧酸酯酶1(carboxylesterase 1,CES1)介导的单核细胞凋亡信号通路中的作用机制。方法利用Phyre2在线工具预测得到CES1三级结构...目的探讨乙型肝炎病毒DNA聚合酶反式调节蛋白1(HBV DNA polymerase trans activated protein 1,HBVDNAPTP1)在羧酸酯酶1(carboxylesterase 1,CES1)介导的单核细胞凋亡信号通路中的作用机制。方法利用Phyre2在线工具预测得到CES1三级结构,分别用pCMV-Myc载体构建HBVDNAPTP1基因、pCMV-HA载体构建CES1基因及其截短体219-264aa和265-303aa的真核细胞表达质粒。分别转染细胞后通过免疫荧光和免疫共沉淀法确定HBVDNAPTP1和CES1互相作用的区段。后通过HBVDNAPTP1和CES1单独转染及共转染,检测其对细胞凋亡率的影响;同时在分离人外周血单个核细胞(Peripheral blood mononuclear cell,PBMC)上转染上述质粒,以确定CES1和HBVDNAPTP1对单核细胞形态的影响。利用qRT-PCR和Western blot检测不同质粒转染后下游Janus激酶-1(Janus kinase,JAK1)和信号传导及转录激活蛋白3(Signal transducer and activator of transcription 3,STAT3)的基因和蛋白的表达情况。结果HBVDNAPTP1与CES1有靶向关系,其中HBVDNAPTP1与CES1全长靶向结合效果最好,故后续实验以CES1全长序列为对象开展。CCK-8和PBMC电镜实验结果表明,与Control组和NC组相比,ov-HBVDNAPTP1组、ov-CES1组和ov-HBVDNAPTP1+ov-CES1组THP-1细胞的凋亡率均升高(P<0.001),细胞受损;与ov-HBVDNAPTP1组和ov-CES1组相比,ov-HBVDNAPTP1+ov-CES1组细胞凋亡率进一步升高(P<0.01),凋亡细胞、坏死细胞的数量增多。qRT-PCR和Western blot结果显示,HBVDNAPTP1和CES1均可以在转录水平和翻译水平上显著上调JAK1和STAT3的表达,且二者同时作用时上调趋势更加明显。结论本研究证实HBVDNAPTP1与CES1二者可协同抑制THP-1细胞增殖并诱导细胞损伤;还可协同上调JAK1/STAT3信号通路在转录和蛋白水平的表达来调控单核细胞凋亡。该发现为深入理解HBV感染相关免疫调控机制提供了新的理论依据。展开更多
文摘Molecular modeling methods have been applied to the structural characterization of the interaction between chiral metal complexes [Co(phen)2dppz]3+ (where phen = 1, 10-phenanthroline, dppz = dipyrido[3,2-a: 2’, 3’-c]phenazine) and the oligonucleotide (B-DNA fragment). The natures of two kinds of the binding modes, which are currently intense controversy, have been explored. Barton proposed that there is enantio-selective DMA binding by the octahedral complexes and intercalative access by these complexes from the major groove; but Norden suggested that both enantiomers bind extremely strongly to DNA from the minor groove without any noticeable enantio-selectivity. Our results support and extend structural models based upon Norden’s studies, and conflict with Barton’s model.
基金support from the National Natural Science Foundation of China (21176132)the Specialized Research Fund for the Doctoral Program of Higher Education (2010000211024)
文摘Unrestrained molecular dynamics （MD） simulations have been carded out to characterize the stability of DNA conformations and the dynamics of A-DNA^B-DNA conformational transitions in aqueous RbC1 solutions. The PARM99 force field in the AMBER8 package was used to investigate the effect of RbC1 concentration on the dynamics of the A^B conformational tran- sition in the DNA duplex d（CGCGAATTCGCG）2. Canonical A- and B-form DNA were assumed for the initial conformation and the final conformation had a length per complete turn that matched the canonical B-DNA. The DNA structure was moni- tored for 3.0 ns and the distances between the C5＇ atoms were obtained from the simulations. It was found that all of the double stranded DNA strands of A-DNA converged to the structure of B-form DNA within 1.0 ns during the unrestrained MD simula- tions. In addition, increasing the RbC1 concentration in aqueous solution hindered the A^B conformational transition and the transition in aqueous RbC1 solution was faster than that in aqueous NaC1 solution for the same electrolyte strength. The effects of the types and concentrations of counterions on the dynamics of the A^B conformational transition can be understood in terms of the variation in water activity and the number of accumulated counterions in the major grooves of A-DNA. The ru- bidium ion distributions around both fixed A-DNA and B-DNA were obtained using the restrained MD simulations to help ex- plain the effect of RbC1 concentration on the dynamics of the A^B conformational transition.
文摘目的探讨乙型肝炎病毒DNA聚合酶反式调节蛋白1(HBV DNA polymerase trans activated protein 1,HBVDNAPTP1)在羧酸酯酶1(carboxylesterase 1,CES1)介导的单核细胞凋亡信号通路中的作用机制。方法利用Phyre2在线工具预测得到CES1三级结构,分别用pCMV-Myc载体构建HBVDNAPTP1基因、pCMV-HA载体构建CES1基因及其截短体219-264aa和265-303aa的真核细胞表达质粒。分别转染细胞后通过免疫荧光和免疫共沉淀法确定HBVDNAPTP1和CES1互相作用的区段。后通过HBVDNAPTP1和CES1单独转染及共转染,检测其对细胞凋亡率的影响;同时在分离人外周血单个核细胞(Peripheral blood mononuclear cell,PBMC)上转染上述质粒,以确定CES1和HBVDNAPTP1对单核细胞形态的影响。利用qRT-PCR和Western blot检测不同质粒转染后下游Janus激酶-1(Janus kinase,JAK1)和信号传导及转录激活蛋白3(Signal transducer and activator of transcription 3,STAT3)的基因和蛋白的表达情况。结果HBVDNAPTP1与CES1有靶向关系,其中HBVDNAPTP1与CES1全长靶向结合效果最好,故后续实验以CES1全长序列为对象开展。CCK-8和PBMC电镜实验结果表明,与Control组和NC组相比,ov-HBVDNAPTP1组、ov-CES1组和ov-HBVDNAPTP1+ov-CES1组THP-1细胞的凋亡率均升高(P<0.001),细胞受损;与ov-HBVDNAPTP1组和ov-CES1组相比,ov-HBVDNAPTP1+ov-CES1组细胞凋亡率进一步升高(P<0.01),凋亡细胞、坏死细胞的数量增多。qRT-PCR和Western blot结果显示,HBVDNAPTP1和CES1均可以在转录水平和翻译水平上显著上调JAK1和STAT3的表达,且二者同时作用时上调趋势更加明显。结论本研究证实HBVDNAPTP1与CES1二者可协同抑制THP-1细胞增殖并诱导细胞损伤;还可协同上调JAK1/STAT3信号通路在转录和蛋白水平的表达来调控单核细胞凋亡。该发现为深入理解HBV感染相关免疫调控机制提供了新的理论依据。
