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Molecular Level Insight into the Interactions of SoxC and SoxD from Epsilonproteobacteria Sulfurimonas denitrificans: A Biomolecular Computational Approach

  • Sujay Ray
  • Arundhati Banerjee
  • Angshuman Bagchi
Conference paper
Part of the Advances in Intelligent Systems and Computing book series (AISC, volume 379)

Abstract

In deep seabeds, sulfide oxidation is essential for metabolism by microbes all through the seafloor. For the purpose, the organism Sulfurimonas denitrificans utilizes the gene cluster-sox (sulfur oxidizing). It comprises two units: soxXYZAB and soxZYCD. SoxCD complex formation is paramount for entire oxidation of sulfide and thiosulfate to sulfate. Herein for a computational molecular-level analysis, 3D models of SoxC and SoxD proteins were constructed by discrete molecular modeling techniques. Protein–protein docking generated SoxCD complex. Few stability calculating parameters revealed the simulated final protein complex as a highly stable one. Solvent accessibility value of the MD-simulated complex also disclosed it as the most interactive one. Identification of responsible amino acids for protein–protein interactions investigated that Asn145 from SoxD and His8 from SoxC played pivotal roles for the interactions to turn out stronger. Current study thereby provides a proposal for molecular mechanism and biophysical analysis of sulfur oxidation process to render a safe biota.

Keywords

Sulfur oxidation Molecular modeling Sox operon Protein–Protein interaction Molecular docking And energy optimization 

Notes

Acknowledgments

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. The author is also thankful to the DBT sponsored Bioinformatics Infrastructure Facility in the Department of Biochemistry and Biophysics, University of Kalyani for the necessary support.

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Copyright information

© Springer India 2016

Authors and Affiliations

  • Sujay Ray
    • 1
  • Arundhati Banerjee
    • 2
  • Angshuman Bagchi
    • 1
  1. 1.Department of Biochemistry and BiophysicsUniversity of KalyaniNadiaIndia
  2. 2.Department of BiotechnologyNational Institute of TechnologyDurgapurIndia

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