A Twist of Fate: The Helix–Turn–Helix Motif in Pseudomonas aeruginosa ExsA Can Allosterically Stabilize the Ligand-Binding Domain

TL;DR

The study explores how a specific protein structure in Pseudomonas aeruginosa could be targeted to reduce its harmful effects.

Contribution

The paper identifies novel druggable pockets in ExsA using molecular dynamics simulations.

Findings

A helix–turn–helix motif stabilizes the ligand-binding domain of ExsA.

Two new potentially druggable pockets were identified at the NTD/CTD interface of ExsA.

Molecular dynamics simulations revealed how ExsA interacts with DNA.

Abstract

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
injects effector toxins directly into host cells, thereby causing
cytotoxicity. The expression of all components of T3SS is regulated
by a master transcriptional regulator, ExsA. The inhibition of the
latter should therefore lead to the suppression of P. aeruginosa virulence. However, to date, no drugs
targeting ExsA have reached the market, and only static structural
models of the protein have been generated, focusing on the C-terminal
domain (CTD). Here, we used μs atomistic molecular dynamics
(MD) simulations to investigate the conformational dynamics of full-length
ExsA bound to DNA or DNA free, investigated as monomers or dimers.
Our data show how the CTD and NTD of ExsA likely interact with one
another and how ExsA binds to DNA. We also analyzed the MD trajectories
to predict potential druggable pocket(s) in the structure and relevant
geometry. This revealed a lipid-binding pocket within the β-sheet
bundle and identified two novel potentially 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 DNA recognition in each ExsA monomer and to stabilize
the putative ligand-binding domain.

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