A Study On The Homology Modeling And Interactions Of The SoxY, SoxZ And SoxB In Thiobacillus Denitrificans

With the rapid development of modern economy, flue gas and waste water from industrial production cause great environmental pollution. In the case of energy structure can’t be changed in the short term, how to deal with the waste gas and waste water from industry effectively, is a problem to be solved. Compared with traditional physical-chemical desulfurization methods, biological desulfurization method showed a series of advantages, and it has become a hotspot in studying desulfurization technology in recent years.As the facultatively anaerobeic bacterium, Thiobacillus denitrificans can oxidize the different sulfur compound molecules through a variety of metabolic pathways under aerobic and anaerobic conditions. Sox system encoded by the the sox（ sulfur oxidizing） gene cluster, is one of the most widely distributed sulfur oxidation pathways in both photosynthetic and nonphotosynthetic sulfur-oxidizing eubacteria, and it is important to the growth of bacterium and biogeochemical sulfur cycle. But there is still not having the structures of Sox protein of Thiobacillus denitrificans in PDB database.Based on the modern technology of molecular simulation, the three-dimensional structure of Sox Y, Sox Z and Sox B were constructed by homology modelling and were optimized by molecular mechanics in this study. The structure rationality evaluated through PROCHECK, ERRAT, VERIFY₃D and PROSA programs indicated that the Sox Y, Sox Z and Sox B protein monomer structures are reasonable.A stable dimer Sox YZ was constructed based on the native protein 2OXG as the template and was further optimized by molecular mechanics. Protein-protein interaction analysis showed that the hydrophobicity of Sox Y and Sox Z subunit in the formation of the dimer was 50.85%, and there were 12 short strong hydrogen bonds and a pi bond at the interface of Sox YZ to maintain the stability of dimer. The interaction energy analysis of the residues at the interface revealed binding pattern of two subunits and the key residues, and the electrostatic interaction was the driving force to promote the formation of the dimer Sox YZ. Residues THR28, ARG31, LYS32, SER64, GLY65, VAL66, SER67 of Sox Z subunit played an important role on the stability of active site of Sox Y subunit.Multiple sequence alignment revealed the residues of the active site of Sox B in Thiobacillus denitrificans, which were used in the Protein-protein docking. The Sox B-Y complex,which was constructed by ZDOCK,was further optimized and processed by RDOCK and molecular mechanics. The complex Sox B-Y-S2O3-was constructed based on the protein 2WDE as the template and was further optimized by molecular mechanics. Protein-protein interaction analysis found that the hydrophobic was similar in the formation of the compound Sox B-Y-S2O3-and dimer Sox YZ. There were eleven short strong hydrogen bonds and two salt bonds at the interface of Sox B-Y-S2O3-to maintain the stability of the complex.Electrostatic interaction analysis found there were15 amino acid residues at the active site of Sox B protein forming a new positive potential center, which was complementarity to the Sox Y protein and small molecule. The interaction energy analysis of the residues at the interface revealed binding pattern of two subunits and the important residues. Residues TRP206 and ARG454, which were not defined as the active site, played an important role on the stability of active site of Sox Y subunit.