Complete atomistic model of a bacterial cytoplasm for integrating physics, biochemistry, and systems biology.
Complete atomistic model of a bacterial cytoplasm for integrating physics, biochemistry, and systems biology.
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DOI：
10.1016/j.jmgm.2015.02.004
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发表时间：
2015-05
影响因子：
2.9
通讯作者：
Sugita, Yuji
中科院分区：
文献类型：
--
作者：
Feig, Michael;Harada, Ryuhei;Mori, Takaharu;Yu, Isseki;Takahashi, Koichi;Sugita, Yuji
提出了一种生殖支原体细胞质的模型，该模型将来自各种来源的数据集成到一个物理和生物化学一致的模型中。根据基因注释，确定了预期存在于细胞质中的核心基因，并重建了代谢反应网络。来自预测反应的细胞质基因和代谢物被组装成一个综合的原子模型，该模型由具有预测结构的蛋白质、RNA、蛋白质/RNA复合体、代谢物、离子和溶剂组成。由此产生的模型在原子和细胞尺度之间、物理和生化方面之间以及细胞系统的结构和系统视图之间架起了桥梁，并意味着作为各种模拟研究的起点。
A model for the cytoplasm of Mycoplasma genitalium is presented that integrates data from a variety of sources into a physically and biochemically consistent model. Based on gene annotations, core genes expected to be present in the cytoplasm were determined and a metabolic reaction network was reconstructed. The set of cytoplasmic genes and metabolites from the predicted reactions were assembled into a comprehensive atomistic model consisting of proteins with predicted structures, RNA, protein/RNA complexes, metabolites, ions, and solvent. The resulting model bridges between atomistic and cellular scales, between physical and biochemical aspects, and between structural and systems views of cellular systems and is meant as a starting point for a variety of simulation studies.
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影响因子：
2.9
作者：
Huang, Yuanpeng J.;Mao, Binchen;Aramini, James M.;Montelione, Gaetano T.
通讯作者：
Montelione, Gaetano T.
影响因子：
--
作者：
Li Y;Rata I;Chiu SW;Jakobsson E
通讯作者：
Jakobsson E
影响因子：
7.7
作者：
Macklin, Derek N.;Ruggero, Nicholas A.;Covert, Markus W.
通讯作者：
Covert, Markus W.
影响因子：
56.9
作者：
FRASER, CM;GOCAYNE, JD;VENTER, JC
通讯作者：
VENTER, JC
影响因子：
5.6
作者：
Huynen, M;Doerks, T;Bork, P
通讯作者：
Bork, P