Molecular Level Insight into the Interactions of SoxC and SoxD from Epsilonproteobacteria Sulfurimonas denitrificans: A Biomolecular Computational Approach

Ray, Sujay; Banerjee, Arundhati; Bagchi, Angshuman

doi:10.1007/978-81-322-2517-1_39

Cited by 1 publication

(6 citation statements)

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“…In our previous investigation, we analyzed the residual interaction pattern between two essential proteins, SoxC and SoxD, from Sulfurimonas denitrificans for global sulphur oxidation [ 4 ]. For that purpose, we modeled the 3D structures of SoxC and SoxD protein and further disclosed the residue-level binding strength between two modeled proteins [ 4 ]. The comparative study was examined for the stability of SoxC and SoxD protein after the duo-protein was simulated.…”

Section: Methodsmentioning

confidence: 99%

“…Two different groups can be categorized for the microbial metabolic reactions of sulphur anions. Either they possess the “ sox multienzyme complex” within their genes coding for the necessary proteins or few of them follow the pathway for “reverse sulphate reduction” [ 4 ]. The “ sox multienzyme complex organization” encodes a cluster of genes ( sox operon, sulphur oxidizing operon) and is the most widely predominant one [ 4 – 7 ].…”

Section: Introductionmentioning

confidence: 99%

“…This is, moreover, based upon the wet-laboratory experiments and their documentation, which states SoxYZ to be crucial and to serve as an important interacting partner for SoxCD to complete the thiosulphate oxidation process [ 8 , 9 ]. In the presence of SoxYZCD, sox system is proficient to oxidize elemental sulphur, sulphide, and explicitly sulfane sulphur (-S-) in thiosulphate [ 4 , 6 , 7 , 9 ]. Within the complex, SoxY solely participates with thiosulphate.…”

Section: Introductionmentioning

confidence: 99%

“…Within the complex, SoxY solely participates with thiosulphate. Further SoxCD aids in recycling the thiosulphate-bound protein SoxY from SoxYZ complex via releasing of the sulphate group from SoxY protein, hydrolytically [ 4 , 6 , 7 , 9 ].…”

Section: Introductionmentioning

confidence: 99%

“…Formerly, the modeling of SoxC and SoxD protein from Sulfurimonas denitrificans was performed via simulation. A comparable study was examined for the pre- and postsimulated complexes [ 4 ]. But hitherto, there was no such molecular and residual disclosure for the analysis of the entire pattern of interaction in SoxYZCD with thiosulphate for the oxidation of thiosulphate in Wadden Sea and deep ocean belts.…”

Section: Introductionmentioning

confidence: 99%

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Structural Stability, Transitions, and Interactions within SoxYZCD-Thiosulphate from Sulfurimonas denitrificans: An In Silico Molecular Outlook for Maintaining Environmental Sulphur Cycle

Ray

Banerjee

2016

Journal of Biophysics

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Thiosulphate oxidation (an essential mechanism) serves to maintain the global sulphur cycle. Earlier experimental and computational studies dealt with environmental thiosulphate oxidation but none dealt with thiosulphate oxidation from deep ocean belts. Wet-laboratory experimental research shows that epsilon-proteobacteria Sulfurimonas denitrificans possess sox (sulphur-oxidizing) operon and perform thiosulphate oxidation efficiently underneath the oceans. From this specific sox operon, SoxCD complex recycles the thiosulphate-bound SoxY from SoxYZ complex to balance the environmental sulphur cycle. So, four chief proteins were variedly modeled and relevant simulated interactive structures were obtained. The final simulated tetraprotein complex (SoxYZCD) from docked SoxYZ and SoxCD complexes was disclosed to be a highly interactive one with predominant ionic residues. Free energy of folding, solvent accessibility, and conformational shifts (coil-like conformation to helices and sheets) were observed in SoxYZ complex after interacting with SoxCD. The stability of the complex (SoxYZCD) after simulation was also observed through the electrostatic surface potential values. These evaluations were rationalized via biostatistics. This aids SoxCD for recycling SoxY along with thiosulphate, which remains interconnected by four H-bonds with SoxY. Therefore, this novel exploration is endowed with the detailed molecular viewpoint for maintaining the sulphur cycle (globally) including the ocean belts.

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Section: Methodsmentioning

confidence: 99%