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通过分子模拟对大肠杆菌RNA聚合酶与拓扑异构酶I之间分子相互作用的表征

Characterization of molecular interactions between Escherichia coli RNA polymerase and topoisomerase I by molecular simulations.

作者信息

Tiwari Purushottam B, Chapagain Prem P, Banda Srikanth, Darici Yesim, Üren Aykut, Tse-Dinh Yuk-Ching

机构信息

Department of Oncology, Georgetown University, Washington, DC, USA.

Department of Physics, Florida International University, Miami, FL, USA.

出版信息

FEBS Lett. 2016 Sep;590(17):2844-51. doi: 10.1002/1873-3468.12321. Epub 2016 Aug 4.

DOI:10.1002/1873-3468.12321
PMID:27448274
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5014613/
Abstract

Escherichia coli topoisomerase I (EctopoI), a type IA DNA topoisomerase, relaxes the negative DNA supercoiling generated by RNA polymerase (RNAP) during transcription elongation. Due to the lack of structural information on the complex, the exact nature of the RNAP-EctopoI interactions remains unresolved. Herein, we report for the first time, the structure-based modeling of the RNAP-EctopoI interactions using computational methods. Our results predict that the salt bridge as well as hydrogen bond interactions are responsible for the formation and stabilization of the RNAP-EctopoI complex. Our investigations provide molecular insights for understanding how EctopoI interacts with RNAP, a critical step for preventing hypernegative DNA supercoiling during transcription.

摘要

大肠杆菌拓扑异构酶I（EctopoI）是一种IA型DNA拓扑异构酶，在转录延伸过程中可缓解RNA聚合酶（RNAP）产生的负性DNA超螺旋。由于缺乏该复合物的结构信息，RNAP-EctopoI相互作用的确切性质仍未明确。在此，我们首次报道了使用计算方法对RNAP-EctopoI相互作用进行基于结构的建模。我们的结果预测，盐桥以及氢键相互作用负责RNAP-EctopoI复合物的形成和稳定。我们的研究为理解EctopoI如何与RNAP相互作用提供了分子见解，这是防止转录过程中产生过度负性DNA超螺旋的关键步骤。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3399/5014613/9e2042cbd1e8/nihms805856f4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3399/5014613/4a7f9a4df2ac/nihms805856f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3399/5014613/4cc29c2f088b/nihms805856f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3399/5014613/9806b8e80130/nihms805856f3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3399/5014613/9e2042cbd1e8/nihms805856f4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3399/5014613/4a7f9a4df2ac/nihms805856f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3399/5014613/4cc29c2f088b/nihms805856f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3399/5014613/9806b8e80130/nihms805856f3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3399/5014613/9e2042cbd1e8/nihms805856f4.jpg

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