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

被引：17

作者：

Tiwari, Purushottam B. ^{[1
]}

Chapagain, Prem P. ^{[2
,3
]}

Banda, Srikanth ^{[3
,4
]}

Darici, Yesim ^{[2
]}

Uren, Aykut ^{[1
]}

Tse-Dinh, Yuk-Ching ^{[3
,4
]}

机构：

[1] Georgetown Univ, Dept Oncol, Washington, DC 20057 USA

[2] Florida Int Univ, Dept Phys, Miami, FL 33199 USA

[3] Florida Int Univ, Biomol Sci Inst, Miami, FL 33199 USA

[4] Florida Int Univ, Dept Chem & Biochem, Miami, FL 33199 USA

来源：

FEBS LETTERS | 2016年 / 590卷 / 17期

基金：

美国国家卫生研究院;

关键词：

E. coli topoisomerase I; hydrogen bonds; MD simulations; RNA polymerase; salt bridge; SPR; SURFACE-PLASMON RESONANCE; FAST INTERACTION REFINEMENT; R-LOOP FORMATION; DYNAMICS SIMULATIONS; DNA; TRANSCRIPTION; DOCKING; PROTEIN; DOMAINS; BINDING;

D O I：

10.1002/1873-3468.12321

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：2844 / 2851

页数：8

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