Aspects of protein-DNA interactions: a review of quantitative thermodynamic theory for modelling synthetic circuits utilising LacI and CI repressors, IPTG and the reporter gene lacZ.
Aspects of protein-DNA interactions: a review of quantitative thermodynamic theory for modelling synthetic circuits utilising LacI and CI repressors, IPTG and the reporter gene lacZ.
复制标题
蛋白质-DNA 相互作用的各个方面：利用 LacI 和 CI 阻遏物、IPTG 和报告基因 lacZ 模拟合成电路的定量热力学理论综述。
DOI：
10.1007/s12551-016-0231-9
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发表时间：
2016
影响因子：
--
通讯作者：
Shearwin,KeithE
中科院分区：
文献类型：
--
作者：
Munro,PeterD;Ackers,GaryK;Shearwin,KeithE
Protein–DNA interactions are central to the control of gene expression across all forms of life. The development of approaches to rigorously model such interactions has often been hindered both by a lack of quantitative binding data and by the difficulty in accounting for parameters relevant to the intracellular situation, such as DNA looping and thermodynamic non-ideality. Here, we review these considerations by developing a thermodynamically based mathematical model that attempts to simulate the functioning of anEscherichia coliexpression system incorporating two of the best characterised prokaryotic DNA binding proteins, Lac repressor and lambda CI repressor. The key aim was to reproduce experimentally observed reporter gene activities arising from the expression of either wild-type CI repressor or one of three positive-control CI mutants. The model considers the role of several potentially important, but sometimes neglected, biochemical features, including DNA looping, macromolecular crowding and non-specific binding, and allowed us to obtain association constants for the binding of CI and its variants to a specific operator sequence.
