The helix-turn-helix motif in Pseudomonas aeruginosa ExsA monomer can recognize DNA and stabilize the putative ligand-binding domain

Pseudomonas aeruginosa is an opportunistic human pathogen. One of the most potent virulence factors in its arsenal is the Type III Secretion System (T3SS). This secretion apparatus transports effector toxins directly into host cells, thereby causing cell damage or death. Expression of the T3SS is regulated by a master transcriptional regulator, ExsA. To date, no drugs targeting ExsA are available and only static structural models of the protein have been generated, focusing on the C-terminal regulatory domain (CTD). Here, we used µsec atomistic molecular dynamics (MD) simulations to investigate the conformational dynamics in the full-length ExsA (bound to DNA) and in the N-terminal DNA-binding domain (NTD). These data show how the CTD and NTD likely interact with one other. We also subjected the MD trajectories to binding pocket prediction and geometry analyses. This revealed a lipid-binding pocket in the β-sheet bundle and also identified two novel potential druggable pockets at the NTD/CTD interface, which could be used in future structure-based drug discovery campaigns. Overall, a single helix-turn-helix motif seems to drive ExsA monomer DNA recognition and stabilize the putative ligand-binding domain.