To comprehend the molecular mechanism of zinc transportation by bacteria tends to be a very complicated and time-consuming method. To date, fragmented and scanty studies are available about the mechanism of zinc transportation at molecular level. So, the present study scrutinizes in silico pathways of zinc fractions transportation, specifically in Bacillus spp. stimulating dynamic performance of zinc. For this, the constructed model reveals Zur to be the prime regulatory transport protein maintaining bacterial survivability at fluctuation in zinc concentrations, thereby attaining zinc homeostasis. Topology for hub nodes displays appropriate evidence of the molecular basis of bacterial zinc imports and exports. Further, the molecular docking reveals interaction of Zur protein with the zinc ligands (ZnCO3 and ZnSO4). By validation of binding affinity, binding energy and docking score via Autodock Vina and X-Score, the ZnSO4 compound was found to possess excellent stability in the active pocket site of Zur, stating Zur-ZnSO4 complex to be the most potential. Owing to which, the Zur-ZnSO4 complex was selected and subjected to molecular dynamics simulation, revealing RMSD, RG, RMSF, SASA and interaction energy for 20 ns trajectory period. Henceforth,the study provides novel insight into revealing the unrecognized Zur protein pathway, assisting zinc transportation, besides retaining best interaction with ZnSO4 ligand. This is the first system biology where molecular docking and molecular dynamics simulation-based investigation decipher the role of Zur transport protein system and interaction of its amino acids with zinc ligands in a simpler and economical form via in silico techniques.Communicated by Ramaswamy H. Sarma.
Keywords: Bacillus spp; Zinc; modeling; molecular docking; molecular dynamics simulation; transportation.