Kinetics of nucleotide entry into RNA polymerase active site provides mechanism for efficiency and fidelity.
Kinetics of nucleotide entry into RNA polymerase active site provides mechanism for efficiency and fidelity.
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DOI：
10.1016/j.bbagrm.2017.02.008
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发表时间：
2017-04
期刊：
影响因子：
--
通讯作者：
Feig M
中科院分区：
文献类型：
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作者：
Wang B;Sexton RE;Feig M
在转录过程中，RNA聚合酶II通过添加与DNA模板互补的核苷酸三磷酸（NTP）来延长RNA。结构研究表明，NTPs通过狭窄的次生孔进入和离开活性位点，但细节仍不清楚。动力学模型，结合分子动力学模拟与实验数据。触发环动力学和匹配和不匹配的NTP的动力学和附近的活性位点的先前模拟与新的模拟描述NTP退出活性位点通过二级孔相结合。马尔可夫状态分析，以确定主要的国家和估计这些国家之间的过渡的动力学速率。动力学模型预测的延伸率和错误掺入率与实验密切一致，并提供了NTP如何通过二级孔进入和退出的机制假设是可行的，以及在RNA延伸过程中实现高延伸率和低错误掺入率的关键特征。
During transcription, RNA polymerase II elongates RNA by adding nucleotide triphosphates (NTPs) complementary to a DNA template. Structural studies have suggested that NTPs enter and exit the active site via the narrow secondary pore but details have remained unclear. A kinetic model is presented that integrates molecular dynamics simulations with experimental data. Previous simulations of trigger loop dynamics and the dynamics of matched and mismatched NTPs in and near the active site were combined with new simulations describing NTP exit from the active site via the secondary pore. Markov state analysis was applied to identify major states and estimate kinetic rates for transitions between those states. The kinetic model predicts elongation and misincorporation rates in close agreement with experiment and provides mechanistic hypotheses for how NTP entry and exit via the secondary pore is feasible and a key feature for achieving high elongation and low misincorporation rates during RNA elongation.