Heterogeneity of biological samples is usually considered a major obstacle for three-dimensional (3D) structure determination of macromolecular complexes. Heterogeneity may occur at the level of composition or conform...Heterogeneity of biological samples is usually considered a major obstacle for three-dimensional (3D) structure determination of macromolecular complexes. Heterogeneity may occur at the level of composition or conformational variability of complexes and affects most 3D structure determination methods that rely on signal averaging. Here, an approach is described that allows sorting structural states based on a 3D statistical approach, the 3D sampling and classification (3D-SC) of 3D structures derived from single particles imaged by cryo electron microscopy (cryo-EM). The method is based on jackknifing & bootstrapping of 3D sub-ensembles and 3D multivariate statistical analysis followed by 3D classification. The robustness of the statistical sorting procedure is corroborated using model data from an RNA polymerase structure and experimental data from a ribosome complex. It allows resolving multiple states within heterogeneous complexes that thus become amendable for a structural analysis despite of their highly flexible nature. The method has important implications for high-resolution structural studies and allows describing structure ensembles to provide insights into the dynamics of multi-component macromolecular assemblies.展开更多
探讨驴油提升皮肤屏障功能的作用及其可能的作用机制。将十二烷基硫酸钠作用于体外重组三维表皮模型(EpiKutis)构建皮肤屏障损伤模型,采用四唑盐比色法(MTT)检测组织活力,利用酶联免疫吸附检测方法(ELISA)检测IL-1α的水平,考察驴油对...探讨驴油提升皮肤屏障功能的作用及其可能的作用机制。将十二烷基硫酸钠作用于体外重组三维表皮模型(EpiKutis)构建皮肤屏障损伤模型,采用四唑盐比色法(MTT)检测组织活力,利用酶联免疫吸附检测方法(ELISA)检测IL-1α的水平,考察驴油对人3D皮肤屏障损伤模型的屏障指数和IL-1α水平的影响。采用转录组高通量测序(RNAseq)技术揭示驴油对皮肤生理的机制,并揭示驴油提升皮肤屏障功能的可能机制。结果表明,驴油可显著提升人3D皮肤屏障损伤模型的屏障指数和降低IL-1α水平,效果与地塞米松类似。驴油作用于人3D皮肤模型后,筛选出1649个差异表达基因,其中619个基因上调,1030个基因下调。基因本体论(Gene Ontology,GO)功能富集分析表明差异表达基因与表皮发育、表皮细胞分化及皮肤发育有关;京都基因与基因组百科全书(kyoto encyclopedia of genes and genomes,KEGG)通路富集分析结果表明差异基因参与TGF-β信号通路、IL-17信号通路、HIF-1信号通路、细胞因子-细胞因子受体相互作用、NF-κB信号通路等重要生物学通路,其中与驴油提升皮肤屏障功能有关的通路可能是TGF-β信号通路、HIF-1信号通路和NF-κB信号通路。展开更多
Many recent exciting discoveries have revealed the versatility of RNAs and their importance in a variety of cellular functions which are strongly coupled to RNA structures. To understand the functions of RNAs, some st...Many recent exciting discoveries have revealed the versatility of RNAs and their importance in a variety of cellular functions which are strongly coupled to RNA structures. To understand the functions of RNAs, some structure prediction models have been developed in recent years. In this review, the progress in computational models for RNA structure prediction is introduced and the distinguishing features of many outstanding algorithms are discussed, emphasizing three- dimensional （3D） structure prediction. A promising coarse-grained model for predicting RNA 3D structure, stability and salt effect is also introduced briefly. Finally, we discuss the major challenges in the RNA 3D structure modeling.展开更多
Generation of three dimensional structures of macromolecules using in silico structural modeling technologies such as homology and de novo modeling has improved dramatically and increased the speed by which tertiary s...Generation of three dimensional structures of macromolecules using in silico structural modeling technologies such as homology and de novo modeling has improved dramatically and increased the speed by which tertiary structures of organisms can be generated. This is especially the case if a homologous crystal structure is already available. High-resolution structures can be rapidly created using only their sequence information as input, a process that has the potential to increase the speed of scientific discovery. In this study, homology modeling and structure prediction tools such as RNA123 and SWISS–MODEL were used to generate the 40 S ribosomal subunit from Plasmodium falciparum. This structure was modeled using the published crystal structure from Tetrahymena thermophila, a homologous eukaryote. In the absence of the Plasmodium falciparum 40 S ribosomal crystal structure, the model accurately depicts a global topology, secondary and tertiary connections, and gives an overall root mean square deviation(RMSD) value of 3.9 ? relative to the template's crystal structure. Deviations are somewhat larger in areas with no homology between the templates. These results demonstrate that this approach has the power to identify motifs of interest in RNA and identify potential drug targets for macromolecules whose crystal structures are unknown. The results also show the utility of RNA homology modeling software for structure determination and lay the groundwork for applying thisapproach to larger and more complex eukaryotic ribosomes and other RNA-protein complexes. Structures generated from this study can be used in in silico screening experiments and lead to the determination of structures for targets/hit complexes.展开更多
文摘Heterogeneity of biological samples is usually considered a major obstacle for three-dimensional (3D) structure determination of macromolecular complexes. Heterogeneity may occur at the level of composition or conformational variability of complexes and affects most 3D structure determination methods that rely on signal averaging. Here, an approach is described that allows sorting structural states based on a 3D statistical approach, the 3D sampling and classification (3D-SC) of 3D structures derived from single particles imaged by cryo electron microscopy (cryo-EM). The method is based on jackknifing & bootstrapping of 3D sub-ensembles and 3D multivariate statistical analysis followed by 3D classification. The robustness of the statistical sorting procedure is corroborated using model data from an RNA polymerase structure and experimental data from a ribosome complex. It allows resolving multiple states within heterogeneous complexes that thus become amendable for a structural analysis despite of their highly flexible nature. The method has important implications for high-resolution structural studies and allows describing structure ensembles to provide insights into the dynamics of multi-component macromolecular assemblies.
文摘探讨驴油提升皮肤屏障功能的作用及其可能的作用机制。将十二烷基硫酸钠作用于体外重组三维表皮模型(EpiKutis)构建皮肤屏障损伤模型,采用四唑盐比色法(MTT)检测组织活力,利用酶联免疫吸附检测方法(ELISA)检测IL-1α的水平,考察驴油对人3D皮肤屏障损伤模型的屏障指数和IL-1α水平的影响。采用转录组高通量测序(RNAseq)技术揭示驴油对皮肤生理的机制,并揭示驴油提升皮肤屏障功能的可能机制。结果表明,驴油可显著提升人3D皮肤屏障损伤模型的屏障指数和降低IL-1α水平,效果与地塞米松类似。驴油作用于人3D皮肤模型后,筛选出1649个差异表达基因,其中619个基因上调,1030个基因下调。基因本体论(Gene Ontology,GO)功能富集分析表明差异表达基因与表皮发育、表皮细胞分化及皮肤发育有关;京都基因与基因组百科全书(kyoto encyclopedia of genes and genomes,KEGG)通路富集分析结果表明差异基因参与TGF-β信号通路、IL-17信号通路、HIF-1信号通路、细胞因子-细胞因子受体相互作用、NF-κB信号通路等重要生物学通路,其中与驴油提升皮肤屏障功能有关的通路可能是TGF-β信号通路、HIF-1信号通路和NF-κB信号通路。
基金supported by the National Natural Science Foundation of China(Grant Nos.11074191,11175132,and 11374234)the National Basic Research Programof China(Grant No.2011CB933600)the Program for New Century Excellent Talents of China(Grant No.NCET 08-0408)
文摘Many recent exciting discoveries have revealed the versatility of RNAs and their importance in a variety of cellular functions which are strongly coupled to RNA structures. To understand the functions of RNAs, some structure prediction models have been developed in recent years. In this review, the progress in computational models for RNA structure prediction is introduced and the distinguishing features of many outstanding algorithms are discussed, emphasizing three- dimensional （3D） structure prediction. A promising coarse-grained model for predicting RNA 3D structure, stability and salt effect is also introduced briefly. Finally, we discuss the major challenges in the RNA 3D structure modeling.
基金supported by European Union Grant Contract No. 018834Development of New Drugs for the Treatment of Malaria “ANTIMAL, ISP-KEN-02 PROJECT: Drug Discovery from Kenya's Biodiversity and the Chinese Government for travel fellowships to the Institute of Materia Medica Symposium on Drug Discovery of Infectious Diseas,May 2015
文摘Generation of three dimensional structures of macromolecules using in silico structural modeling technologies such as homology and de novo modeling has improved dramatically and increased the speed by which tertiary structures of organisms can be generated. This is especially the case if a homologous crystal structure is already available. High-resolution structures can be rapidly created using only their sequence information as input, a process that has the potential to increase the speed of scientific discovery. In this study, homology modeling and structure prediction tools such as RNA123 and SWISS–MODEL were used to generate the 40 S ribosomal subunit from Plasmodium falciparum. This structure was modeled using the published crystal structure from Tetrahymena thermophila, a homologous eukaryote. In the absence of the Plasmodium falciparum 40 S ribosomal crystal structure, the model accurately depicts a global topology, secondary and tertiary connections, and gives an overall root mean square deviation(RMSD) value of 3.9 ? relative to the template's crystal structure. Deviations are somewhat larger in areas with no homology between the templates. These results demonstrate that this approach has the power to identify motifs of interest in RNA and identify potential drug targets for macromolecules whose crystal structures are unknown. The results also show the utility of RNA homology modeling software for structure determination and lay the groundwork for applying thisapproach to larger and more complex eukaryotic ribosomes and other RNA-protein complexes. Structures generated from this study can be used in in silico screening experiments and lead to the determination of structures for targets/hit complexes.
