Effect of metal ions on the internal motions of Adenylate Kinase: A Molecular dynamics simulation study

Adenylate Kinase (ADK) catalyzes the reversible interconversion between cytoplasmic nucleotides that is essential for energy homeostasis. We performed several Molecular Dynamics simulations on ADK, containing metal ions Mg+2 and Zn+2. The dynamics of the enzyme were computed on the ion-free structure, and the structures containing individual ions. RMSD and Rg data demonstrate that the coordination of Zn+2 does not significantly affect the overall stability of the enzyme. Decreasing the overall dynamics of the enzyme in the presence of both metal ions was explained by the cooperativity between the stabilizing interactions of metal ions. The high RMSF value of a specific segment in the presence of both ions, demonstrates that a fine balance between the conformational stability and local structural dynamics may be involved in the regulation of the enzyme catalysis. It was also concluded that the orientation of the structural domains is affected by the simultaneous presence of both ions.