Browsing by Author "Akkaya, Reyhan"

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Investigation Of Allosteric İnhibition Effect İn Pyruvate Kinase By Constrained Molecular Dynamics Simulation Method Piruvat Kinazın Allosterik Olarak İnhibe Edilmesinin Kısıtlanmış Moleküler Dinamik Similasyon Methodu Kullanılarak İncelenmesi
(Kadir Has Üniversitesi, 2021) Akkaya, Reyhan; Akdoğan, Ebru Demet
In previous studies, our research group identified species-specific allosteric sites in glycolytic enzymes from different organisms and identified candidate inhibitory molecules that strongly interact with the residues at these sites. In this study, a Molecular Dynamics simulation study was performed on one of the glycolytic enzymes, bacterial pyruvate kinase (S. aureus PK), by employing bond restraints between selected pairs of residues at the suggested allosteric region in order to mimic the presence of a drug molecule. At the same time, interacting residues in an ex- perimentally identified allosteric region were also restricted and compared with the proposed area. Three 100 ns long independent runs were conducted for each of three different states of the receptor; apo state (no restraints), constr-1 (restriction on proposed allosteric site) and constr-2 (restriction on known allosteric site) which amount to a total of nine runs, e.g., 900 ns. Several analytical methods were used to elucidate the effect of restricted regions on protein dynamics and the allosteric character of pyruvate kinase. While structural changes were examined with RMSD-RMSF analysis, correlations between global movements and structural components were analysed with principal component analysis. From PCA results, it was observed that both restricted allosteric regions led to decreased correlations of positional fluctuations in comparison to apo state. Investigation of changes in the secondary structure at the catalytic site showed that the α′6 helix, which has an essential role in the stabilization of the active structure, shifted to a coil-turn structure in the apo state more frequently than in the con- strained states. Additionally, domain rotations identified via principal axes analysis, showed that the constrained state disrupted the domain rotations more often. Finally, the distance fluctuation analysis was performed to observe the effect of the restricted residues in the allosteric signal transduction. The communications be- tween residues increased in the constr-1 state while there was slight decrease in the communications of the constr-2 state.