Molecular Dynamical Investigation of a YodA Protein Signifies Zinc Ion-Residues Interactions

Abstract

YodA protein is well known lipocalin-like protein which shows interaction with Zinc (Zn²⁺) ions, so called metal binding protein. The synchronization of Zn²⁺ ions on protein surface was investigated by molecular dynamics (MD) simulation. A systematic MD study of crystal structure (1OEK.pdb) of YodA protein was taken into account. Moreover, simulations of two more systems, i.e. entry of free (i) 4 Zn²⁺ ions (ii) and 2 Zn²⁺ ions in the bulk of Apo form of YodA protein were considered to emphasize the binding event and encounter of ions on residues of protein surface. Stabilities of each system were probed and further investigations revealed, Zn²⁺ ions show  robust interactions with glutamate and histidine residues. This revelation was corroborated by distance calculation during simulation. By comparing with other amino acid residues, glutamate and histidine demonstrate the better coordination with Zn²⁺ ions. This study might enhance to understand the Zinc interaction with YodA protein and investigation can propose significant hypothesis on metal resistance and bioremediation strategy.