International Journal of Computational Bioinformatics

Zinc-regulated transporter 1 (tzn-1) is a membrane protein that is mainly involved in transport of zinc and iron across the membrane, thereby helping in maintenance of the homeostasis. The previous in silico studies suggests that deletion of this protein coding gene results in aconidiation. Even though tzn-1 gene is not related to conidial formation pathway, still it resulted in aconidiation. To understand this mechanism and its interacting partners the tertiary structure of the protein is essential and hence this study was initiated. In the present study Fold recognition based model of tzn-1 was built using Photosynthetic Reaction Center from Rhodopseudomonas viridis (1PRC_M) as a template. The model was refined by optimization and step wise energy minimization process. The refined model was placed into a POPC/TIP3P membrane system and was simulated for 20ns at 300K temperature with NPT ensemble. Amino acid residues Asp 183, His 185, His 189 and Glu 179, His 199, His 200 are the key active sites for binding of zinc ion. The Root Mean Square Fluctuation from dynamic simulations at the active sites is less and the overall structure quality is 81.2% with 96.2% amino acids in the favorable regions of Ramachandran plot. This study reports the simulated tertiary structure of tzn-1 and dynamics study in the membrane and aqueous environment.