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