Dynamics of pyrophosphate ion release and its coupled trigger loop motion from closed to open state in RNA polymerase II.
Dynamics of pyrophosphate ion release and its coupled trigger loop motion from closed to open state in RNA polymerase II.
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DOI：
10.1021/ja210656k
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发表时间：
2012-02-01
影响因子：
15
通讯作者：
Huang, Xuhui
中科院分区：
文献类型：
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作者：
Da, Lin-Tai;Wang, Dong;Huang, Xuhui
核苷酸掺入后焦磷酸根离子（PPi）的释放是RNA聚合酶II（pol II）在转录延伸过程中进入下一个核苷酸添加循环的必要步骤。然而，pol II残基在PPi释放中的作用，以及PPi释放与触发环构象变化之间的机制关系仍不清楚。在这项研究中，我们构建了一个马尔可夫状态模型（MSM）从广泛的全原子分子动力学（MD）模拟在显式溶剂中模拟PPi释放过程沿着pol II二级通道。我们的研究结果表明，触发环在催化和形成PPi后具有显著更大的内在运动，这反过来又主要通过触发环残基H1085和（Mg-PPi）2−基团之间的氢键来帮助PPi释放。一旦PPi离开活性位点，它采用跳跃模型通过几个高度保守的带正电荷的残基，如K752和K619，从二级通道的pol II孔区域释放。这些积极的跳跃网站形成有利的相互作用与PPi，并产生四个动力学亚稳态确定我们的MSM。此外，我们的单突变体模拟表明，H1085和K752援助PPi退出催化后的活性位点，而K619促进其通过二级通道。最后，我们建议，PPi释放可以帮助触发环的开放运动，即使PPi释放之前，由于更快的PPi动态触发环的完全开放。我们的模拟提供了预测，以指导未来的实验测试。
Pyrophosphate ion (PPi) release after nucleotide incorporation is a necessary step for RNA polymerase II (pol II) to enter the next nucleotide addition cycle during transcription elongation. However, the role of pol II residues in PPi release, and the mechanistic relationship between PPi release and the conformational change of the trigger loop remain unclear. In this study, we constructed a Markov State Model (MSM) from extensive all-atom Molecular Dynamics (MD) simulations in the explicit solvent to simulate the PPi release process along the pol II secondary channel. Our results show that the trigger loop has significantly larger intrinsic motion after catalysis and formation of PPi, which in turn, aids PPi release mainly through the hydrogen bonding between the trigger loop residue H1085 and (Mg-PPi)2− group. Once PPi leaves the active site, it adopts a hopping model through several highly conserved positively charged residues such as K752 and K619 to release from the pol II pore region of the secondary channel. These positive hopping sites form favorable interactions with PPi and generate four kinetically meta-stable states as identified by our MSM. Furthermore, our single mutant simulations suggest that H1085 and K752 aid PPi exit from the active site after catalysis, whereas K619 facilitates its passage through the secondary channel. Finally, we suggest that PPi release could help the opening motion of the trigger loop, even though PPi release precedes full opening of the trigger loop due to faster PPi dynamics. Our simulations provide predictions to guide future experimental tests.
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影响因子：
16.8
作者：
通讯作者：
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影响因子：
56.9
作者：
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通讯作者：
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DOI：
10.1073/pnas.0608952104
发表时间：
2007-03-13
影响因子：
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作者：
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通讯作者：
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通讯作者：
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