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

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 unres...

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Bibliographic Details
Published in:FEBS letters 2016-09, Vol.590 (17), p.2844-2851
Main Authors: Tiwari, Purushottam B., Chapagain, Prem P., Banda, Srikanth, Darici, Yesim, Üren, Aykut, Tse‐Dinh, Yuk‐Ching
Format: Article
Language:English
Subjects:
DNA Topoisomerases, Type I - chemistry
DNA Topoisomerases, Type I - genetics
DNA Topoisomerases, Type I - metabolism
DNA-Directed RNA Polymerases - chemistry
DNA-Directed RNA Polymerases - genetics
DNA-Directed RNA Polymerases - metabolism
E. coli topoisomerase I
Escherichia coli - chemistry
Escherichia coli - enzymology
Hydrogen Bonding
hydrogen bonds
MD simulations
Multiprotein Complexes - chemistry
Multiprotein Complexes - genetics
Multiprotein Complexes - metabolism
Protein Binding
Protein Conformation
RNA polymerase
salt bridge
SPR
Transcription, Genetic
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Summary: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.
ISSN:0014-5793
1873-3468
DOI:10.1002/1873-3468.12321