engleski

Characterization of ligand binding to purine nucleoside phosphorylase from human pathogen Helicobacter pylori

Purine nucleoside phosphorylase (PNP) is the enzyme that has important role in nucleoside degradation metabolism. Bacterial and human PNPs show significant differences in oligomerization (bacterial PNPs are hexamers, human is trimer), primary amino acid sequence, and substrate specificity. Due to mentioned differences, Helicobacter pylori PNP (HpPNP) presents possible target for developing new antibiotics for treating Helicobacter pylori infection. Starting from the novel crystallographic structures of HpPNP, with and without inhibitor formycin A in active site(s), molecular dynamics (MD) simulation were applied with goal of investigating structural and dynamical properties of HpPNP enzyme. Enzyme complexes with known inhibitor formycin A, and complexes with substrate adenosine, as well as enzyme structures in different conformations without any ligand bound or only with hydrogenphosphate ion bound, were prepared and subjected to MD simulations. In an attempt to find possible allosteric effect between the subunits, extensive analysis of H-bond interactions during the simulations was accomplished. Further, results of MD simulations enabled structural and dynamical characterization of ligand binding and, for some ligands, a few different binding modes were identified. Also, conformational changes between these binding modes were observed during the MD simulations. Results of MD simulations were compared and validated with the results obtained from different experimental methods, such as X-ray crystallography, microscale thermophoresis, and kinetical measurements. Overall results on structural and dynamical properties of ligand binding to HpPNP enzyme might contribute to development of novel potential inhibitors.

molecular dynamics simulations; docking; Helicobacter pylori

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