title: Characterization of molecular interactions between Escherichia coli RNA polymerase and topoisomerase I by molecular simulations.
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.
authors.affiliation: Department of Oncology, Georgetown University, Washington, DC, USA.
authors.forename: Purushottam B
authors.initials: PB
authors.lastname: Tiwari
authors.affiliation: Department of Physics, Florida International University, Miami, FL, USA.|Biomolecular Sciences Institute, Florida International University, Miami, FL, USA.
authors.forename: Prem P
authors.initials: PP
authors.lastname: Chapagain
authors.affiliation: Biomolecular Sciences Institute, Florida International University, Miami, FL, USA.|Department of Chemistry and Biochemistry, Florida International University, Miami, FL, USA.
authors.forename: Srikanth
authors.initials: S
authors.lastname: Banda
authors.affiliation: Department of Physics, Florida International University, Miami, FL, USA.
authors.forename: Yesim
authors.initials: Y
authors.lastname: Darici
authors.affiliation: Department of Oncology, Georgetown University, Washington, DC, USA.
authors.forename: Aykut
authors.initials: A
authors.lastname: Üren
authors.affiliation: Biomolecular Sciences Institute, Florida International University, Miami, FL, USA.|Department of Chemistry and Biochemistry, Florida International University, Miami, FL, USA.
authors.forename: Yuk-Ching
authors.initials: YC
authors.lastname: Tse-Dinh
mesh_terms: D004264:DNA Topoisomerases, Type I / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D004926:Escherichia coli / Q000737:chemistry / Q000201:enzymology; D006860:Hydrogen Bonding; D046912:Multiprotein Complexes / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D011485:Protein Binding; D011487:Protein Conformation; D014158:Transcription, Genetic
chemical_list: D046912:Multiprotein Complexes; D012321:DNA-Directed RNA Polymerases; D004264:DNA Topoisomerases, Type I
keywords: E. coli topoisomerase I; MD simulations; RNA polymerase; SPR; hydrogen bonds; salt bridge