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

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

Author information

1
Department of Oncology, Georgetown University, Washington, DC, USA.
2
Department of Physics, Florida International University, Miami, FL, USA.
3
Biomolecular Sciences Institute, Florida International University, Miami, FL, USA.
4
Department of Chemistry and Biochemistry, Florida International University, Miami, FL, USA.

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.

KEYWORDS:

E. coli topoisomerase I; MD simulations; RNA polymerase; SPR; hydrogen bonds; salt bridge

PMID:
27448274
PMCID:
PMC5014613
DOI:
10.1002/1873-3468.12321
[Indexed for MEDLINE]
Free PMC Article

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