Title

Insights from the docked DoxDA Model with Thiosulphate

Authors

Sujay Ray & Angshuman Bagchi *

Affiliation

Department of Biochemistry and Biophysics, University of Kalyani - 741245, Nadia, West Bengal, India,

Email

Angshuman Bagchi - E-mail: angshumanb@gmail.com; *Corresponding author

Article Type

Hypothesis

Date

Received February 25, 2016; Accepted March 30, 2016; Published April 10, 2016

Redox reaction of inorganic sulphur compound is very essential to maintain a global sulphur cycle. Certain experimental evidences suggest that gamma-proteobacterial Acidothiobacillus thiooxidans; lacking the sulphur-oxidizing (sox) operon, has an alternative thiosulphate oxidation pathway. Dox operon having essentially participating proteins; DoxD and DoxA serves as the central
players for this alternative pathway of thiosulphate oxidation. So, to identify their role in thiosulphate oxidation process, functional 3D model of DoxD and DoxA protein’s independently functioning conserved domains were built after the contentment of necessary stereochemical features. After formation of the best suited DoxDA protein-complex, DoxDA was MD simulated in
several steps and finally through MD simulation run utilizing GROMACS. Even after running beyond 20ns, 18ns simulated protein complex was the most stable and was selected for further study. Residual binding mode conferred mainly two ionic and twelve Hbonded interactions in DoxDA. Astonishingly, Asp167 and Arg18 from DoxA and DoxD, respectively was observed to hold a
pivotal role in 6 H-bonds accompanied by a separate ionic interaction. Interestingly, four residues from DoxD; Trp32, Met33, Lys36 and Asn140 strengthened the DoxD–thiosulphate interaction. Interaction energy (ΔG= (-) 222.016kcal/mol) and net solvent accessibility calculations depicts spontaneous and fervent residual participation in DoxDA, which is essential for thiosulphate
interaction and further sulphur oxidation. Conformational flexibility in DoxD with increased coil percentage benefits DoxD and makes its susceptible for the interaction with thiosulphate even after spontaneous interaction with DoxA. Therefore, this study serves as an insight at computational basis for sulphur oxidation even in organisms lacking sox operon.

Varied Molecular Modeling, Molecular Dynamics Simulated Protein-Protein Residual Participation, Protein-Ligand Interactions, Energy Estimation, Conformational Fluctuations and Alternative Sulphur Oxidation Pathway.

Citation

Ray & Bagchi,  Bioinformation 12(2): 69-73 (2016)
 

Edited by

P Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.