Complex 1 (ferritin-HrpE/YscL family type III secretion apparatus protein).

The purple chain indicates the ferritin protein from P. vannamei, and the red chain indicates the HrpE/YscL family type III secretion apparatus protein from V. parahaemolyticus. (TIF)</p

Average of triplicate 100 ns MD simulation.

(a) RMSD, (b) Rg, (c) H-bond, and (d) distance. The purple plot indicates Complex 1 (Ferritin-HrpE/YscL family type III secretion apparatus protein), the red plot represents Complex 2 (Protein kinase domain-containing protein-Chemotaxis CheY protein), and the orange plot illustrates Complex 3 (GPCR-Chemotaxis CheY protein).</p

Superimposition of pre-MD and post-MD.

The pre-MD for Complex 1, Complex 2, and Complex 3 are represented with yellow, pink, and green, respectively. Meanwhile, the post-MD for Complex 1, Complex 2, and Complex 3, are illustrated with red, purple, and brown, respectively.</p

Protein-protein docking score using the HawkDock server.

Protein-protein docking score using the HawkDock server.</p

Workflow of the study.

The rectangle box represents the method. The parallelogram indicates the output.</p

Triplicate of 100 ns MD simulation of Complex 2.

(a) RMSD, (b) Rg, (c) Distance, (d) H-bond. The blue plot indicates replicate 1, the red plot represents replicate 2, and the yellow plot illustrates replicate 3.</p

Triplicate of 100 ns MD simulation of Complex 3.

(a) RMSD, (b) Rg, (c) Distance, (d) H-bond. The blue plot indicates replicate 1, the red plot represents replicate 2, and the yellow plot illustrates replicate 3.</p

3D models and 2D topology diagrams of <i>Vibrio parahaemolyticus</i> proteins.

(a) Chemotaxis CheY protein (Q79YX1), (b) HrpE/YscL family type III secretion apparatus protein (A0A6H0JL36). The red cylinder in the topology diagram represents α-helix, and the pink arrow indicates the β-strand to form β-sheet. A small blue arrow illustrates the direction of the protein chain from N- to C-terminal.</p

Protein structure validation using ERRAT, PROCHECK, MolProbity, ProQ, and ProSA.

Protein structure validation using ERRAT, PROCHECK, MolProbity, ProQ, and ProSA.</p

Comparative PPI of the top cluster coordinates from MD simulation trajectories.

Comparative PPI of the top cluster coordinates from MD simulation trajectories.</p