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Characterization of molecular interactions between Escherichia coli RNA polymerase and topoisomerase I by molecular simulations
Author(s) -
Tiwari Purushottam B.,
Chapagain Prem P.,
Banda Srikanth,
Darici Yesim,
Üren Aykut,
TseDinh YukChing
Publication year - 2016
Publication title -
febs letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.593
H-Index - 257
eISSN - 1873-3468
pISSN - 0014-5793
DOI - 10.1002/1873-3468.12321
Subject(s) - topoisomerase , dna supercoil , rna polymerase , escherichia coli , transcription (linguistics) , polymerase , dna , biophysics , chemistry , biology , rna , microbiology and biotechnology , biochemistry , gene , dna replication , linguistics , philosophy
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.