Redox process is crucial for inhibitory properties of aurintricarboxylic acid against activity of YopH: virulence factor of Yersinia pestis

Kuban-Jankowska, Alicja; Sahu, Kamlesh K; Niedzialkowski, Pawel; Gorska, Magdalena; Tuszynski, Jack A; Ossowski, Tadeusz; Wozniak, Michal

The initial structure of YopH was imported from the RCSB protein data bank (http://www.pdb.org) with code 2YDU.pdb [28] . The structure was minimized using taff.ff forcefield of the Molecular Operating Environment software (MOE, chemical computing group). Chain A of this pdb file contains 306 residues. The ligand was removed from this pdb file and aurintricarboxylic acid (ATA) and phosphotyrosine (pTyr) were docked into the structure of YopH. A blind flexible docking simulation was performed, where the binding site was assumed to be the entire protein. The side chains were kept free to move during forcefield refinement. Alpha PMI is the placement method used with default settings (sample per conformation = 10, maximum poses = 250). London dG rescoring was used with Alpha PMI placement. Termination criteria for forcefield refinement were set as gradient = 0.001 and interactions = 500.