Abstract
Redox reaction of inorganic sulphur compound is very essential to maintain a global sulphur cycle. Certain experimental evidences suggest that gamma-proteobacterial Acidothiobacillus thiooxidans; lacking the sulphur-oxidizing (sox) operon, has an alternative thiosulphate oxidation pathway. Dox operon having essentially participating proteins; DoxD and DoxA serves as the central players for this alternative pathway of thiosulphate oxidation. So, to identify their role in thiosulphate oxidation process, functional 3D model of DoxD and DoxA protein’s independently functioning conserved domains were built after the contentment of necessary stereochemical features. After formation of the best suited DoxDA protein-complex, DoxDA was MD simulated in several steps and finally through MD simulation run utilizing GROMACS. Even after running beyond 20ns, 18ns simulated protein complex was the most stable and was selected for further study. Residual binding mode conferred mainly two ionic and twelve Hbonded interactions in DoxDA. Astonishingly, Asp167 and Arg18 from DoxA and DoxD, respectively was observed to hold a pivotal role in 6 H-bonds accompanied by a separate ionic interaction. Interestingly, four residues from DoxD; Trp32, Met33, Lys36 and Asn140 strengthened the DoxD–thiosulphate interaction. Interaction energy (deltaG = (-) 222.016kcal/mol) and net solvent accessibility calculations depicts spontaneous and fervent residual participation in DoxDA, which is essential for thiosulphate interaction and further sulphur oxidation. Conformational flexibility in DoxD with increased coil percentage benefits DoxD and makes its susceptible for the interaction with thiosulphate even after spontaneous interaction with DoxA. Therefore, this study serves as an insight at computational basis for sulphur oxidation even in organisms lacking sox operon.
Highlights
Hydrogen sulfide is typically unfavorable to various plants and creature tissues
A standout amongst the most imperative arrangements of biogeochemical responses are the redox reactions of environmental sulfur compounds and their steady turnover is highly important to adjust a biosystem with sulfur compounds [1]
Results & Discussion: This study explores the structural features of two competent proteins for sulphur oxidation; DoxD and DoxA
Summary
Hydrogen sulfide is typically unfavorable to various plants and creature tissues. At whatever point sulfide is produced, it is a prime need to oxidize the sulfide to essential sulfur [1]. With a broad range of oxidation states, sulfur gets oxidized variedly via the utilization of the respiratory electron transport chains [2]. This varied oxidization methods for sulphur is carried out by a wider and sundry faction of micro-organisms. These microorganisms are documented to maintain a specific gene family for the purpose, which is known as the sox operon [2]. This operon includes soxVW succeeded by soxXYZABCDEFGH [2]. Earlier experimentation involving in silico approaches were dealt to uncover the computational biochemistry for the oxidation of sulfur anion in distinct life forms like Paracoccus pantotrophus and others [3]
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