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A Computational Structural Biology of SoxR and DNA: A Modelling and Interactive Discern to Express the Sox Operon in Pseudaminobacter salicylatoxidans (KCT001) for Global Sulphur Oxidation

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Intelligent Computing and Applications

Part of the book series: Advances in Intelligent Systems and Computing ((AISC,volume 343))

Abstract

Computational and microbial molecular-level participation of sox operon and its repressor protein (SoxR) in sulphur oxidation from Pseudaminobacter salicylatoxidans (KCT001) was investigated. Documentation reveals that P. salicylatoxidans (KCT001) has sox TRSVWXYZABCD operon that is regulated by a repressor protein (SoxR). Previously, various experimental procedures such as DMS-mediated DNA methylations and hydroxyl radical footprinting have disclosed that SoxR interacts first with an operator region-sv (present in between soxS and soxV). Detailed computational studies were accomplished in the present study. 3D models of repressor protein and the DNA sequence from operon’s promoter region were demonstrated using molecular modelling techniques. Molecular docking simulation was performed to predict DNA–protein interaction. Amino acid residues and nucleotide bases responsible for interaction were identified by PyMOL and Discovery Studio software suite. This novel residue-level study is paramount for initiating transcription in the operon, thereby leading to sulphur oxidation.

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Abbreviations

SD:

Steepest Descent

CG:

Conjugate Gradient

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Acknowledgment

Authors are deeply indebted to DST-PURSE program 2012–2015 and DBT sponsored Bioinformatics Infrastructure Facility in Department of Biochemistry and Biophysics, University of Kalyani, for providing different equipments and essential infrastructural support.

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Authors and Affiliations

  1. Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, Nadia, India

    Sujay Ray & Angshuman Bagchi

  2. Department of Biotechnology, National Institute of Technology, Mahatma Gandhi Avenue, Durgapur, West Bengal, India

    Arundhati Banerjee

Authors
  1. Sujay Ray
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  2. Arundhati Banerjee
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  3. Angshuman Bagchi
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Corresponding author

Correspondence to Angshuman Bagchi .

Editor information

Editors and Affiliations

  1. Electronics & Communication Engineering, NIT, Durgapur, Durgapur, West Bengal, India

    Durbadal Mandal

  2. Electronics & Communication Engineering, NIT, Durgapur, Durgapur, West Bengal, India

    Rajib Kar

  3. Machine Intelligence Unit, ISI, Kolkata, West Bengal, India

    Swagatam Das

  4. Electrical Engineering, IIT Delhi, New Delhi, India

    Bijaya Ketan Panigrahi

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Ray, S., Banerjee, A., Bagchi, A. (2015). A Computational Structural Biology of SoxR and DNA: A Modelling and Interactive Discern to Express the Sox Operon in Pseudaminobacter salicylatoxidans (KCT001) for Global Sulphur Oxidation. In: Mandal, D., Kar, R., Das, S., Panigrahi, B. (eds) Intelligent Computing and Applications. Advances in Intelligent Systems and Computing, vol 343. Springer, New Delhi. https://doi.org/10.1007/978-81-322-2268-2_61

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  • DOI: https://doi.org/10.1007/978-81-322-2268-2_61

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  • Publisher Name: Springer, New Delhi

  • Print ISBN: 978-81-322-2267-5

  • Online ISBN: 978-81-322-2268-2

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