An In-Silico Structural Analysis of the Interactions of SoxY and SoxZ from Moderately Thermophilic Betaproteobacterium, Hydrogenophilus thermoluteolus in the Global Sulfur Oxidation Cycle

  • Sujay Ray
  • Angshuman Bagchi
Conference paper
Part of the Advances in Intelligent Systems and Computing book series (AISC, volume 340)


Microbial redox reactions are mediated by a diverse set of sulfur-oxidising bacteria. These redox reactions are important to maintain the environmental sulfur balance. The sulfur oxidation reactions are performed by sulfur-oxidizing gene cluster called the sox operon comprising of genes soxEFCDYZAXBH. However, the mechanistic details of sulfur oxidation process by Hydrogenophilus thermoluteolus are yet to be determined. In this study, the three-dimensional structures of SoxY and SoxZ proteins were constructed by homology modeling. Protein-protein docking generated SoxY–Z complex. Responsible amino acid residues for the protein interactions were identified after molecular dynamics simulation of SoxY–Z complex. The best binding mode of thiosulfate with SoxY–Z complex was identified through their molecular docking. Current study thereby, provides a rational frame-work to discern molecular mechanism and biophysical characterization of sulfur-oxidation process.


Sulfur oxidation Homology modelling Sox operon Protein-protein interaction Molecular docking Molecular dynamics simulation 


Hydrogenophilus thermoluteolus


Protein interaction calculator




The authors would like to thank the DST-PURSE programme 2012–2015 going on in the Department of Biochemistry and Biophysics, University of Kalyani for providing different instrumental and infrastructural support. Authors are also thankful to the DBT sponsored Bioinformatics Infrastructure Facility in the Department of Biochemistry and Biophysics, University of Kalyani for the necessary support.

Conflict of Interest



  1. 1.
    Friedrich, C.G., Bardischewsky, F., Rother, D., Quentmeier, A., Fischer, J.: Prokaryotic sulfur oxidation. Curr. Opin. Microbiol. 8, 253–259 (2005)Google Scholar
  2. 2.
    Freidrich, C.G.: Physiology and genetics of sulfur- oxidizing bacteria. Adv. Microb. Physiol. 39, 235–289 (1998). doi: 10.1016/S0065-2911(08)60018-1 CrossRefGoogle Scholar
  3. 3.
    Appia-Ayme, C., et al.: Cytochrome complex essential for photosynthetic oxidation of both thiosulfate and sulfide in Rhodovulum sulfidophilum. J. Bacteriol. 183, 6107–6118 (2001)CrossRefGoogle Scholar
  4. 4.
    Bagchi, A., Ghosh, T.C.: Structural insight into the interactions of SoxV, SoxW and SoxS in the process of transport of reductants during sulfur oxidation by the novel global sulfur oxidation reaction cycle. Biophys. Chem. 119, 7–13 (2006)CrossRefGoogle Scholar
  5. 5.
    Bagchi, A., et al.: Homology modeling of a tran-scriptional regulator SoxR of the lithotrophic sulfur oxidation (Sox) operon in α-proteobacteria. J. Biomol. Struct. Dyn. 22, 571–578 (2005)CrossRefGoogle Scholar
  6. 6.
    Bagchi, A.; and Roy, P.; Structural insight into SoxC and SoxD interaction and their role in electron transport process in the novel global sulfur cycle in Paracoccus pantotrophus. Biochem. Biophys. Res. Commun. 331:1107–1103 (2005)Google Scholar
  7. 7.
    Bagchi, A.: Structural modeling of SoxF protein from Chlorobium tepidum: an approach to understand the molecular basis of thiosulfate oxidation. Biochem. Biophys. Res. Commun. 414, 409–411 (2011)CrossRefGoogle Scholar
  8. 8.
    Bagchi, A., Ghosh, T.C.: Structural analyses of the interactions of SoxY and SoxZ from thermo-neutrophilic Hydrogenobacter thermophiles. J. Biophys. Chem. 2(4), 408–413 (2011)CrossRefGoogle Scholar
  9. 9.
    Bagchi, A.: Structural insight into the mode ofinteractions of SoxL from Allochromatium vinosum in the global sulfur oxidation cycle. Mol. Biol. Rep. 39(12), 10243–10248 (2012)CrossRefGoogle Scholar
  10. 10.
    Sali, A., Potterton, L., Yuan, F., Van Vlijmen, H., Karplus, M.: Evaluation of comparative protein modeling by MODELLER. Proteins 23(3), 318–326 (1995)Google Scholar
  11. 11.
    Berman, M.H., et al.: The protein data bank. Nucleic Acids Res 28, 235–242 (2000)CrossRefGoogle Scholar
  12. 12.
    Altschul, S.F., et al.: Basic local alignment search tool. J. Mol. Biol. 25, 403–410 (1990)CrossRefGoogle Scholar
  13. 13.
    Brooks, B.R., Bruccoleri, R.E., Olafson, B.D. States, D.J., Swaminathan, S., Karplus, M.: CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J. Comp. Chem. 4,187–217 (1983)Google Scholar
  14. 14.
    Sippl, M.J.: Recognition of errors in three-dimen- sional structures in proteins. Proteins 17, 355–362 (1993)CrossRefGoogle Scholar
  15. 15.
    Eisenberg, D., et al.: VERIFY3D: assessment of protein models with three-dimensional profiles. Methods Enzymol. 277, 396–404 (1997)CrossRefGoogle Scholar
  16. 16.
    Laskowski, R.A., et al.: PROCHECK: a program to check the stereochemistry of protein structures. J. Appl. Crystallogr. 26, 283–291 (1993)CrossRefGoogle Scholar
  17. 17.
    Ramachandran, G.N., Sashisekharan, V.: Con- formation of polypeptides and proteins. Adv. Protein Chem. 23, 283–438 (1968)CrossRefGoogle Scholar
  18. 18.
    Comeau, S.R., et al.: ClusPro: an automated docking and discrimination method for the prediction of protein complexes. Bioinformatics 20, 45–50 (2004)CrossRefGoogle Scholar
  19. 19.
    Hess, B., Kutzner, C., Van Der Spoel, D., Lindahl, E.: GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J. Chem. Theor. Comput. 4(3), 435–447 (2008)CrossRefGoogle Scholar
  20. 20.
    Tina, K.G., Bhadra, R., Srinivasan, N.: PIC: protein interactions calculator. Nucleic Acids Res. 35, W473–W476 (2007)Google Scholar
  21. 21.
    Morris, G.M., Huey, R., Lindstrom, W., Sanner, M.F., Belew, R.K., Goodsell, D.S., Olson, A.J.: Autodock4 and AutoDockTools4: automated docking with selective receptor flexiblity. J. Comput. Chem. 30, 2785–2791 (2009)Google Scholar
  22. 22.
    Cosconati, S., Forli, S., Perryman, A.L., Harris, R., Goodsell, D.S., Olson, A.J.: Virtual screening with AutoDock: theory and practice. Expert Opin. Drug Discovery 5, 597–607 (2010)Google Scholar

Copyright information

© Springer India 2015

Authors and Affiliations

  1. 1.Department of Biochemistry and BiophysicsUniversity of KalyaniKalyaniIndia

Personalised recommendations