Computational Analysis of the Tripartite Interaction of Phasins (PhaP4 and 5)-Sigma Factor (σ²⁴)-DNA of Azospirillum brasilense Sp7

Azospirillum brasilense Sp7 produces PHB, which is covered by granule-associated proteins (GAPs). Phasins are the main GAPs. Previous studies have shown phasins can regulate PHB synthesis. When A. brasilense grows under stress conditions, it uses sigma factors to transcribe genes for survival. One of these factors is the σ²⁴ factor. This study determined the possible interaction between phasins and the σ²⁴ factor or phasin-σ²⁴ factor complex and DNA. Three-dimensional structures of phasins and σ²⁴ factor structures were predicted using the I-TASSER and SWISS-Model servers, respectively. Subsequently, a molecular docking between phasins and the σ²⁴ factor was performed using the ClusPro 2.0 server, followed by molecular docking between protein complexes and DNA using the HDOCK server. Evaluation of the types of ligand–receptor interactions was performed using the BIOVIA Discovery Visualizer for three-dimensional diagrams, as well as the LigPlot server to obtain bi-dimensional diagrams. The results showed the phasins (Pha4_Abs7 or Pha5_Abs7)-σ²⁴ factor complex was bound near the −35 box of the promoter region of the phaC gene. However, in the individual interaction of PhaP5_Abs7 and the σ²⁴ factor, with DNA, both proteins were bound to the −35 box. This did not occur with PhaP4_Abs7, which was bound to the −10 box. This change could affect the transcription level of the phaC gene and possibly affect PHB synthesis.