Insights into zinc-sensing metalloregulator ‘Zur’ deciphering mechanism of zinc transportation in Bacillus spp. by modeling, simulation and molecular docking

Abstract

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:

• Zinc
• Bacillus spp
• transportation
• modeling
• molecular docking
• molecular dynamics simulation

Acknowledgments

Authors are grateful to the Dean, Department of Botany and Microbiology, Gurukula Kangri University, Haridwar, Uttarakhand, India, for providing all necessary facilities to carry out this research.

Disclosure statement

The authors declare no conflicts of interest.