Structural Analyses of SoxY and SoxZ Proteins from Epsilonproteobacterium Sulfurimonas denitrificans: A Structural Bioinformatics Approach

Abstract

Abstract:

Molecular level participation of epsilonproteobacteria for the global sulfur oxidation phenomena is an essential zone to be indulged with. Epsilonproteobacteria aids in the microbial sulfur metabolism both at and beneath the seafloor. For the recycling of the inorganic sulfur compounds, microbial redox reactions are one of the responsible and most important reactions to maintain the environmental sulfur balance. These reactions are carried out by phylogenetically diverse sets of microorganisms. The sulfur oxidizing gene cluster (Sox) of epsilonproteobacterium Sulfurimonas denitrificans isolated from the coastal sediments and hydrothermal vents are known to perform sulfur oxidation. This bacterium comprises two gene clusters—soxXYZAB and soxCD. There are practically no reports regarding the structural biology of the sulfur oxidation process in this organism. In the present context, homology modeling was employed to construct the three dimensional structures of SoxY and SoxZ from S. denitrificans. The stereochemical properties of the individual protein structures were examined properly. With the help of docking simulations, the amino acid residues of these proteins involved in the interactions were identified. The stability of the energy minimized protein complex structure has also been analyzed through calculation of net interaction energy and net solvent accessibility. The energy minimized final complex structure revealed to serve as the most interactive phase. Interactive bonds that strengthened the SoxYZ complex was also determined and elucidated herein. Therefore, this study provides a novel platform to understand the basic initial molecular mechanism of the sulfur oxidation biochemistry for the family of epsilonproteobacteria.

Keywords: homology modeling, Sox operon, epsilonproteobacteria, molecular docking, stability

Cite this Article:
Sujay Ray, Arundhati Banerjee, Angshuman Bagchi. Structural Analyses of SoxY and SoxZ Proteins from Epsilonproteobacterium Sulfuri-monas denitrificans: A Structural Bioinformatics Approach. Research & Reviews: Journal of Biotech-nology. 2015; 5(1): 35–44p.