Homology modelling of RNA polymerase and associated transcription factors from Bacillus subtilis

Abstract

RNA polymerase (RNAP) is the central enzyme of transcription and requires interaction with transcription factors in vivo for correct processivity. Both the transcription initiation complex and the ternary elongation complex are stabilised by and require protein–protein interactions between the various components involved. These interactions may form the basis for rational design of small peptide mimics of one or more proteins involved in order to inhibit protein–protein interactions and thus transcription. Here, we present homology models of the model Gram positive organism Bacillus subtilis RNA polymerase in the core and holoenzyme forms. Interactions between RNA polymerase and the transcription factor σ A were investigated in order to design peptide mimics of the major interactions.