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Sequence and 3D structure based analysis of TNT degrading proteins in Arabidopsis thaliana

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Abstract

TNT, accidentally released at several manufacturing sites, contaminates ground water and soil. It has a toxic effect to algae and invertebrate, and chronic exposure to TNT also causes harmful effects to human. On the other hand, many plants including Arabidopsis thaliana have the ability to metabolize TNT either completely or at least to a reduced less toxic form. In A. thaliana, the enzyme UDP glucosyltransferase (UDPGT) can further conjugate the reduced forms 2-HADNT and 4-HADNT (2-hydroxylamino-4, 6- dinitrotoluene and 4-hydroxylamino-2, 6- dinitrotoluene) of TNT. Based on the experimental analysis, existing literature and phylogenetic analysis, it is evident that among 107 UDPGT proteins only six are involved in the TNT degrading process. A total of 13 UDPGT proteins including five of these TNT degrading proteins fall within the same group of phylogeny. Thus, these 13 UDPGT proteins have been classified into two groups, TNT-degrading and TNT-non-degrading proteins. To understand the differences in TNT-degrading capacities; using homology modeling we first predicted two structures, taking one representative sequence from both the groups. Next, we performed molecular docking of the modeled structure and TNT reduced form 2-hydroxylamino-4, 6- dinitrotoluene (2-HADNT). We observed that while the Trp residue located within the active site region of the TNT- degrading protein showed π-Cation interaction; such type of interaction was absent in TNT-non-degrading protein, as the respective Trp residue lay outside of the pocket in this case. We observed the conservation of this π-Cation interaction during MD simulation of TNT–degrading protein. Thus, the position and the orientation of the active site residue Trp could explain the presence and absence of TNT-degrading capacity of the UDPGT proteins.

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Acknowledgments

The author AB acknowledges UGC, RFSMS, and Department of Biophysics, Molecular Biology and Bioinformatics for the financial support and Rahul Shubhra Mandal is thankful to ICMR [extramural project (IRIS ID: 2013-1551G)] for funding. We also thank the reviewers for their useful comments.

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Authors and Affiliations

  1. Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92 APC Road, Kolkata, 700009, India

    Amrita Bhattacherjee & Sudip Kundu

  2. Biomedical Informatics Centre, National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme XM, Beleghata, Kolkata, 700 010, India

    Rahul Shubhra Mandal & Santasabuj Das

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  1. Amrita Bhattacherjee
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  2. Rahul Shubhra Mandal
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Correspondence to Sudip Kundu.

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894_2014_2174_MOESM1_ESM.doc

All the supplementary data (Supplementary Tables T1-T3, Supplementary Figs. S1-S8) is provided as a single doc file entitled Supplementary_data.doc. (DOC 2487 kb)

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Bhattacherjee, A., Mandal, R.S., Das, S. et al. Sequence and 3D structure based analysis of TNT degrading proteins in Arabidopsis thaliana . J Mol Model 20, 2174 (2014). https://doi.org/10.1007/s00894-014-2174-z

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