Investigating the Conformational Structure and Potential Site Interactions of SOD Inhibitors on Ec-SOD in Marine Mud Crab Scylla serrata: A Molecular Modeling Approach

Paital, B; Sablok, G; Kumar, S; Singh, SK; Chainy, GBN

Investigating the Conformational Structure and Potential Site Interactions of SOD Inhibitors on Ec-SOD in Marine Mud Crab Scylla serrata: A Molecular Modeling Approach

Paital, B Sablok, G

Kumar, S Singh, SK Chainy, GBN

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Publication Type:: Journal Article
Citation:: Interdisciplinary Sciences: Computational Life Sciences, 2016, 8 (3), pp. 312 - 318
Issue Date:: 2016-09-01

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Field	Value	Language
dc.contributor.author	Paital, B	en_US
dc.contributor.author	Sablok, G https://orcid.org/0000-0002-4157-9405	en_US
dc.contributor.author	Kumar, S	en_US
dc.contributor.author	Singh, SK	en_US
dc.contributor.author	Chainy, GBN	en_US
dc.date.available	2015-02-26	en_US
dc.date.issued	2016-09-01	en_US
dc.identifier.citation	Interdisciplinary Sciences: Computational Life Sciences, 2016, 8 (3), pp. 312 - 318	en_US
dc.identifier.issn	1913-2751	en_US
dc.identifier.uri	http://hdl.handle.net/10453/37633
dc.description.abstract	© 2015, International Association of Scientists in the Interdisciplinary Areas and Springer-Verlag Berlin Heidelberg. Superoxide dismutases (SODs) act as a first line of the enzymatic antioxidant defense system to control cellular superoxide anion toxicity. Previously, several inhibitors have been widely identified and catalogued for inhibition of SOD activity; however, still the information about the mechanism of interaction and points toward the inhibitor interactions in structures of SODs in general and in extracellular (Ec)-SOD in particular is still in naive. In the present research, we present an insight to elucidate the molecular basis of interactions of SOD inhibitors with Ec-SOD in mud crab Scylla serrata using molecular modeling and docking approaches. Different inhibitors of SOD such as hydrogen peroxide ( H 2O2) , potassium cyanide, sodium dodecyl sulfate (SDS), β-mercaptoethanol and dithiocarbamate were screened to understand the potential sites that may act as sites for cleavage or blocking in the protein. SOD–SDS and SOD - H 2O2 complex interactions indicate residues Pro72 and Asp102 of the predicted crab Ec-SOD as common targets. The GOLD result indicates that Pro72, Asp102 and Thr103 are commonly acting as the site of interaction in Ec-SOD of S. serrata with SOD inhibitors. For the first time, the results of this study provide an insight into the structural properties of Ec-SOD of S. serrata and define the possible involvements between the amino acids present in its active sites, i.e., in the regions from 70 to 84 and from 101 to 103 and different inhibitors.	en_US
dc.relation.ispartof	Interdisciplinary Sciences: Computational Life Sciences	en_US
dc.relation.isbasedon	10.1007/s12539-015-0110-2	en_US
dc.subject.mesh	Animals	en_US
dc.subject.mesh	Brachyura	en_US
dc.subject.mesh	Hydrogen Peroxide	en_US
dc.subject.mesh	Potassium Cyanide	en_US
dc.subject.mesh	Sodium Dodecyl Sulfate	en_US
dc.subject.mesh	Superoxide Dismutase	en_US
dc.subject.mesh	Enzyme Inhibitors	en_US
dc.subject.mesh	Amino Acid Sequence	en_US
dc.subject.mesh	Catalytic Domain	en_US
dc.subject.mesh	Models, Molecular	en_US
dc.title	Investigating the Conformational Structure and Potential Site Interactions of SOD Inhibitors on Ec-SOD in Marine Mud Crab Scylla serrata: A Molecular Modeling Approach	en_US
dc.type	Journal Article
utslib.citation.volume	3	en_US
utslib.citation.volume	8	en_US
pubs.embargo.period	Not known	en_US
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Science
pubs.organisational-group	/University of Technology Sydney/Strength - C3 - Climate Change Cluster
utslib.copyright.status	closed_access
pubs.issue	3	en_US
pubs.publication-status	Published	en_US
pubs.volume	8	en_US

Abstract:

© 2015, International Association of Scientists in the Interdisciplinary Areas and Springer-Verlag Berlin Heidelberg. Superoxide dismutases (SODs) act as a first line of the enzymatic antioxidant defense system to control cellular superoxide anion toxicity. Previously, several inhibitors have been widely identified and catalogued for inhibition of SOD activity; however, still the information about the mechanism of interaction and points toward the inhibitor interactions in structures of SODs in general and in extracellular (Ec)-SOD in particular is still in naive. In the present research, we present an insight to elucidate the molecular basis of interactions of SOD inhibitors with Ec-SOD in mud crab Scylla serrata using molecular modeling and docking approaches. Different inhibitors of SOD such as hydrogen peroxide ( H 2O2) , potassium cyanide, sodium dodecyl sulfate (SDS), β-mercaptoethanol and dithiocarbamate were screened to understand the potential sites that may act as sites for cleavage or blocking in the protein. SOD–SDS and SOD - H 2O2 complex interactions indicate residues Pro72 and Asp102 of the predicted crab Ec-SOD as common targets. The GOLD result indicates that Pro72, Asp102 and Thr103 are commonly acting as the site of interaction in Ec-SOD of S. serrata with SOD inhibitors. For the first time, the results of this study provide an insight into the structural properties of Ec-SOD of S. serrata and define the possible involvements between the amino acids present in its active sites, i.e., in the regions from 70 to 84 and from 101 to 103 and different inhibitors.

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http://hdl.handle.net/10453/37633