Flexibility analysis of Native Pyridoxal Kinase and its complexes with ATP and ADP: A Molecular Dynamics Simulation Study

Sachin Patodia, Anant Vijay, Subramanyam Swaminathan, Deepak Chopra, Ashima Bagaria

Abstract


Pyridoxal Kinase (PLK) phosphorylates vitamin B6, a step required for the conversion of Vitamin B6 into pyridoxal 5-phosphate. The protein is cytoplasmic and is active as a dimer. Molecular dynamics (MD) simulation studies using a 25ns scale for PLK and its complex with ATP (Adenosine triphosphate) and ADP (Adenosine diphosphate) were carried out and the trajectory analysis revealed that the flexibility of the entire PLK molecule increases. In present study we have investigated the conformational changes in pyridoxal kinase (PLK) after binding of ligands (ATP/ADP). The stability of native and PLK in complex with ATP and ADP, was ascertained by MD simulations and mechanism of ligand binding was explored by essential dynamics. Simulation results also indicated that the van der Waals contribution was greater than the electrostatic interaction between the protein residues and the ligands. Further, the ligand (ATP/ADP) binding results into decrement and increment of fluctuations in certain regions of protein.

 


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