A comparative investigation of predicted protein structures of a histidine acid phosphatase from Saccharomyces cerevisiae through molecular docking and MD simulations

This study compares four predicted models of histidine acid phosphatase (HAP) from Saccharomyces cerevisiae generated using SWISS-MODEL, YASARA, AlphaFold2, and DMFold. Structural validation revealed that AlphaFold2 and DMFold had the highest ERRAT values (92.711 and 92.955, respectively), with AlphaFold2 demonstrating the best Ramachandran plot results (90.2% of residues in favored regions). Molecular docking indicated that DMFold formed 16 hydrogen bonds with phytic acid, the most among the models, and exhibited the strongest docking score (-6.9 kcal/mol). YASARA was the only model to depict critical catalytic interactions between His59, Asp322, and phytic acid. Molecular dynamics (MD) simulations demonstrated that SWISS-MODEL exhibited the highest structural stability, with the lowest RMSD (1.664328 ± 0.12 Å), Rg (33.2908 ± 0.61 Å), and SASA (51,908.99 ± 135.92 Å2), while DMFold displayed the most flexibility. Binding energy analysis revealed that DMFold had the strongest binding affinity ( – 89.2612 ± 2.93 kJ/mol), followed by YASARA ( – 122.101 ± 11.25 kJ/mol). Despite DMFold’s superior binding, YASARA is considered the most functionally accurate due to its depiction of the correct catalytic interactions.

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