Stability and membrane interactions of an autotransport protein: MD simulations of the Hia translocator domain in a complex membrane environment

Hia is a trimeric autotransporter found in the outer membrane of Haemphilus influenzae. The X-ray structure of Hia translocator domain revealed each monomer to consist of an α-helix connected via a loop to a 4-stranded β-sheet, thus the topology of the trimeric translocator domain is a 12-stranded β-barrel containing 3 α-helices that protrude from the mouth of the β-barrel into the extracellular medium. Molecular dynamics simulations of the Hia monomer and trimer have been employed to explore the interactions between the helices, β-barrel and connecting loops that may contribute to the stability of the trimer. In simulations of the Hia monomer we show that the central α-helix may stabilise the fold of the 4-stranded β-sheet. In simulations of the Hia trimer, a H-bond network involving residues in the β-barrel, α-helices and loops has been identified as providing stability for the trimeric arrangement of the monomers. Glutamine residues located in the loops connecting the α-helices to the β-barrel are orientated in a triangular arrangement such that each forms 2 hydrogen bonds to each of the corresponding glutamines in the other loops. In the absence of the loops, the β‐barrel becomes distorted. Simulations show that while the trimeric translocator domain β-barrel is inherently flexible, it is unlikely to accommodate the passenger domain in a folded conformation. Simulations of Hia in an asymmetric model of the outer membrane have revealed membrane–protein interactions that anchor the protein within its native membrane environment.