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In-Silico Structural Analysis of SoxF Protein Through Molecular Modelling and Protein-Protein Docking from Hydrogenophilus thermoluteolus: An Approach to Understand the Molecular Mechanism of Thiosulfate Oxidation

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

Abstract

Microbial redox reactions of inorganic sulphur compounds play vital role for recycling of sulphur to maintain environmental sulphur balance. These important reactions are carried out by enzyme system encoded by sox operon. Central player of sulphur oxidation process is SoxY–Z protein complex. Thermophilic beta-proteobacterium-Hydrogenophilus thermoluteolus, oxidizes sulphur compounds including thiosulfate with the help of proteins encoded by sox operon. Protein SoxF having sulfide dehydrogenase activity has the ability to reactivate the inactivated SoxY–Z complex. Till date no structural details are available for SoxF protein from H. thermoluteolus. In present work, homology modeling has been used to build 3D structures of SoxY, SoxZ and SoxF of H. thermoluteolus. 3D structure of SoxY–Z–F complex was obtained by ClusPro2.0. Amino acid residues responsible for protein-protein interaction were identified. Interactions in SoxY–Z–F were found to be mediated through hydrogen bonding. Probable biophysical mechanism of the interactions of SoxF with SoxY–Z complex has been identified.

Keywords

Sulphur oxidation Homology modelling Sox operon Protein-protein interaction Molecular docking 

Abbreviations

SD

Steepest descend

CD

Conjugate gradient

Notes

Acknowledgment

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 2015

Authors and Affiliations

  1. 1.Department of Biochemistry and BiophysicsUniversity of KalyaniKalyani, NadiaIndia

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