Investigating Escherichia coli Colicin E9 immunity protein interactions with DNA gyrase of Pseudomonas aeruginosa: advanced computational approach for developing novel antimicrobial strategies

Protein-protein interactions (PPIs) are essential to numerous cellular processes, making a thorough investigation of these interactions crucial for a deeper understanding of molecular mechanisms. This research initiative aims to elucidate the complex relationship between the Colicin E9 immunity protein from Escherichia coli (E. coli) and DNA gyrase from Pseudomonas aeruginosa, a significant target for antimicrobial strategies. By inhibiting DNA gyrase, the immunity protein Colicin E9, produced by E. coli, allows the host to generate a protective protein that lowers the risk of self-toxicity from this interaction. Understanding this relationship can aid the development of antibacterial strategies to combat resistant infections. Molecular docking, molecular dynamics (MD) simulations, and binding energy analyses were integral to the computational approach used in this study. MD simulations were employed to assess the stability and dynamics of the protein complex after docking was conducted using ClusPro and LightDock. The MM-GBSA method was used to evaluate binding free energies and to characterise structural features through hydrogen-bond analysis to uncover key stabilising interactions. Several important residues were identified that help stabilise the interface between the two proteins: HIS40, MET27, LYS105, GLU44, ASP47, and three others. The ClusPro complex displayed impressive interactions, featuring between six and ten hydrogen bonds along with a binding free energy of ΔG = -3.88 kcal/mol, indicating a strong protein interaction. Despite some variations, both complexes maintained stable interfaces throughout the MD simulations, and DNA gyrase retained its structural integrity. This study concludes that the protein complex formed between the Colicin E9 immunity protein and DNA gyrase is stable, paving the way for future experiments and the development of new antimicrobial agents targeting DNA gyrase in P. aeruginosa infections.