Computational simulation strategies for analysis of multisubunit RNA polymerases.
Computational simulation strategies for analysis of multisubunit RNA polymerases.
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DOI：
10.1021/cr400046x
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发表时间：
2013-11-13
期刊：
影响因子：
62.1
通讯作者：
Burton, Zachary F.
中科院分区：
文献类型：
--
作者：
Wang, Beibei;Feig, Michael;Cukier, Robert I.;Burton, Zachary F.
多亚基 RNA 聚合酶 (RNAP) 机制由于其体积大、模拟核酸和金属的复杂性以及系统的动态方面，对当前的计算技术提出了挑战。本综述的目的是讨论已应用于 RNAP 的计算方法并评估所获得的见解。此外，本次审查旨在预测一些未来的方法，以提供更多的理解。由于 RNAP 对现有计算技术提出了挑战，这些研究可能需要改进应用于包括蛋白质和核酸成分的大型多原子系统的方法和硬件。最近出现了有关 RNAP 结构/功能的其他评论，但通常关注点不同。 1本综述是在 Feig、Cukier、Burton、Kashlev 和 Coulombe 实验室合作的基础上制定的。我们的尝试是将复杂的计算分析与多亚基 RNAP 的生化和遗传结构/功能研究结合起来。我们希望整合这些广泛的方法可以丰富科学，从而更深入地描述已知生命系统中的复杂、模板化聚合机制的中心和全局。到目前为止，这种协作方法已经促进了理解的进步，并表明模拟和实验之间的来回应该被证明是解决生物学中一个非常大问题的深刻方法。本次审查可以被视为一份进度报告，着眼于光明和富有启发性的未来。
Multisubunit RNA polymerase (RNAP) mechanisms present challenges for current computational techniques because of their large size, complications of simulating nucleic acids and metals, and also dynamic aspects of the system. The purpose of this review is to discuss computational methods that have been applied to RNAPs and to evaluate the insight gained. Furthermore, this review seeks to anticipate some future approaches expected to give additional understanding. Because RNAPs pose challenges to available computation technology, these studies may necessitate improvements in methods and hardware applied to very large multiatom systems that include protein and nucleic acid components. Other reviews on RNAP structure/function have recently appeared but generally with a different focus. 1This review was developed on the basis of collaborations involving the Feig, Cukier, Burton, Kashlev, and Coulombe laboratories. The attempt has been to combine sophisticated computational analyses with biochemical and genetic structure/function studies of multisubunit RNAPs. The hope was that integrating these broad approaches might enrich the science, leading to a deeper description of a complex, templated polymerization mechanism central and global in known living systems. So far, this collaborative approach has led to advances in understanding and an indication that going back and forth between simulation and experiment should prove an incisive approach to a very big problem in biology. This review can be viewed as a progress report with an eye to a bright and revealing future.
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影响因子：
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作者：
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影响因子：
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作者：
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通讯作者：
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影响因子：
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作者：
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DOI：
10.1073/pnas.0608952104
发表时间：
2007-03-13
影响因子：
11.1
作者：
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通讯作者：
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作者：
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