Integrative modeling of JCVI-Syn3A nucleoids with a modular approach.
Integrative modeling of JCVI-Syn3A nucleoids with a modular approach.
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DOI：
10.1016/j.crstbi.2023.100121
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发表时间：
2024
影响因子：
2.8
通讯作者：
Autin, Ludovic
中科院分区：
文献类型：
--
作者：
Goodsell, David S;Autin, Ludovic
提出了一种基于网格的方法，用于创建整个细菌类核的3D模型，集成超微结构信息冷冻电子断层扫描，基因组和蛋白质组数据，以及生物分子和组件的实验原子结构。该方法用于生成最小基因组细菌JCVI-Syn 3A的模型，产生一系列模型来测试关于基因组的转录、浓缩和总体分布的假设。晶格模型还用于生成整个JCVI-Syn 3A单元的原子模型。采用新的模块化构建方法构建细菌类核模型。最小细胞JCVI-syn 3A的类核模型整合了现有的实验数据。假设放置的RNA聚合酶和黏结蛋白进行了探讨。
A lattice-based method is presented for creating 3D models of entire bacterial nucleoids integrating ultrastructural information cryoelectron tomography, genomic and proteomic data, and experimental atomic structures of biomolecules and assemblies. The method is used to generate models of the minimal genome bacterium JCVI-Syn3A, producing a series of models that test hypotheses about transcription, condensation, and overall distribution of the genome. Lattice models are also used to generate atomic models of an entire JCVI-Syn3A cell. Models of bacterial nucleoids are built with a new modular construction approach. Nucleoid models of minimal cell JCVI-syn3A integrate available experimental data. Hypotheses for placement of RNA polymerases and cohesins are explored.
DOI：
10.1021/acs.jpcb.7b11770
发表时间：
2018-05-31
期刊：
The journal of physical chemistry. B
影响因子：
--
作者：
Goodsell DS;Autin L;Olson AJ
通讯作者：
Olson AJ