Structural Analysis of the Mode of Interactions of SoxB Protein with SoxYZ Complex from Allochromatium vinosum in the Global Sulfur Oxidation Cycle  

Sujay Ray , Angshuman Bagchi
Department of Biochemistry and Biophysics University of Kalyani, Kalyani, Nadia, India
Author    Correspondence author
Computational Molecular Biology, 2013, Vol. 3, No. 1   doi: 10.5376/cmb.2013.03.0001
Received: 12 Jun., 2013    Accepted: 19 Jun., 2013    Published: 30 Aug., 2013
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Preferred citation for this article:

Bagchi et al., 2013, Structural Analysis of the Mode of Interactions of SoxB Protein with SoxYZ Complex from Allochromatium vinosum in the Global Sulfur Oxidation Cycle, Computational Molecular Biology, Vol.3, No.1 1-5 (doi: 10.5376/cmb.2013.03.0001)

Abstract

Microbial redox reaction is a very essential reaction to maintain for the recycling of sulphur to maintain the environmental sulphur balance. These oxidation process is conducted by a large number of phylogenitically diversed sulphur oxidizing bacteria. The sox gene cluster of α-proteobacteria, Allochromacium vinosum (A. vinosum or A. vino) are mainly responsible for microbial redox reaction. The main proteins of this process are SoxY, SoxZ and SoxB. SoxY binds to sulfur anions with the help of SoxZ. SoxB is a heterodimeric protein, which then hydrolytically releases one molecule of sulfate to yield a SoxY-persulfide. In the present work, homology modeling has been used to build the three dimensional structures of SoxY, SoxZ. Due to large sequence length only 5'-nucleotidase C-terminal domain of SoxB has been modelled by homology modeling. With the help of protein-protein docking complex structure of SoxYZB is formed and using Protein interaction calculator (P.I.C) webserver the amino acid residues of these proteins involved in the interactions have been identified. The interactions between the SoxY, SoxZ and 5'-nucleotidase, C-terminal domain of SoxB proteins are mediated mainly through hydrogen bonding. The probable biophysical mechanism of SoxB interaction with SoxYZ complex has been identified.

Keywords
Docking simulations; Environmental sulphur balance; Homology modelling; Sox operon; Sulphur oxidation
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