Computationally modelled structure of type IV pilus PilA of Aggregatibacter actinomycetemcomitans
Vahvelainen, Nelli; Bozkurt, Esra; Ihalin, Riikka (2022), Computationally modelled structure of type IV pilus PilA of Aggregatibacter actinomycetemcomitans, Dryad, Dataset, https://doi.org/10.5061/dryad.w6m905qqz
Some bacterial type IV pili structures have been determined with Cryo-EM, X-ray diffraction or similar method. The type IVa pilus PilA of Aggregatibacter actinomycetemcomitans, an oral pathogen, shares sequence identity with other bacterial type IVa pili. To understand the structure of AaPilA at the molecular level, we performed computational modeling studies. To model the filament, we utilized the GalaxyGemini web server using different monomer conformations from molecular dynamics simulations as a seed; then, we extended the structure to 14-mer by employing the cryo-EM map file of type IV pilus from enterohemorrhagic E. coli. The structures were predicted for a full-length monomer PilA_D7S, N-terminally truncated monomer PilA_D7S_Δ1-27 and 14-homo-oligomer PilA_D7S_14mer. PilAD7S_Δ1-27 and PilAD7S share the same secondary structural elements: an N-terminal α-helix, four antiparallel β-strands, a hypervariable segment and a flexible C-terminus. The homo-oligomeric PilAD7S from our computational model resembles the interface seen in the cryo-EM structure of N. meningitidis type IV pili.
Methods are described in detail in Vahvelainen et al. 2022 (https://doi.org/10.1016/j.micpath.2022.105843).
README file describes the dataset.
Academy of Finland, Award: 322817