Threading Modeling and Molecular Docking for Sulfur Oxidation Protein SoxAX of Thiobacillus denitrificans
Article
Figures
Metrics
Preview PDF
Reference
Related
Cited by
Materials
Abstract:
The sulfur oxidizing (Sox) enzyme complex plays a vital role in the sulfur metabolism of Thiobacillus denitrificans (Td), with the SoxAXYZB complex enzyme at its core. Inorganic sulfur compound substrates need to be successfully combined on the SoxAX complex and transferred to the carrier SoxYZ for further subsequent sulfur oxidation. However, the three-dimensional (3D) structure of Td SoxAX has not yet been elucidated. The protein threading method was adopted in this study in order to construct the Td SoxAX dimer, and the result was verified. Differences in the configuration and energy of binding between the SoxAX protein model and the substrates thiosulfate, hydrogen sulfide, and sulfite were then explored using molecular docking experiments. The result shows that the 3D structure of the constructed SoxAX dimer was relatively reliable. Hydrogen bonds were the major forces that maintained the interaction between SoxA and SoxX. Ten short and strong hydrogen bonds and one pi-pi interaction were involved in stabilizing the dimer structure, and six residues including Arg160 in SoxA and eight residues including Asn15 in SoxX played an important role in the stability of the dimer. Molecular docking studies showed that hydrogen bonds were the major force maintaining the binding between SoxAX and the three different substrates. The key residues for substrate binding were Arg210, Cys214, and Gln217. Among the three substrates, sulfide showed the highest binding energy, followed by thiosulfate and sulfite.
