©2021-2032  All Rights Reserved. Online Journal of Bioinformatics.  You may not store these pages in any form except for your own personal use. All other usage or distribution is illegal under international copyright treaties. Permission to use any of these pages in any other way besides  the before mentioned must be gained in writing from the publisher. This article is exclusively copyrighted in its entirety to onlinejournals@gmail.com publications. This article may be copied once but may not be, reproduced or  re-transmitted without the express permission of the editors. Linking: To link to this page or any pages linking to this page you must link directly to this page only here rather than put up your own page.

OJBTM

Online Journal of Bioinformatics©

Volume 22 (2): 70-81, 2021.

In silico copper and zinc superoxide dismutase in Dinococcus radiodurans.

 

Ashokan KV1 and Pillai MM2

 

Department(s) 1Biological Science,  PVP College, Kavathe Mahankal, Sangli, Mharashtrea, 2Biotechnology, KIIT’s Engineering College, Gokulshirgoan, Kolhapur, India.

                          

ABSTRACT

 

Ashokan KV, Pillai MM., In silico copper and zinc superoxide dismutase in Dinococcus radiodurans, Onl J Bioinform., 22 (2): 70-81, 2021. We characterized copper and zinc superoxide dismutase protein of Dinococcus radiodurans strain R1 by in silico tools and servers. We found that the primary sequence analysis of the protein’s net positive charge was due to arginine and lysine with an isoelectric point  >7, pH 9.8 and hydrophobicity of 53.5%. By PROSCAN we identified functional amino acid length, Myristylation, 3 phosphorylation and N-glycosylation sites. Secondary structure predicted by JPRED revealed β-turns with disulphide bonds. INTERPROSCAN revealed 3 integral domains of copper, zinc, superoxide dismutase 6 bladed propeller, TOIB and SMP-30/Gluconolaconase/LRE. Domains sequences were determined by EXPASY for extinction coefficient, half-life, instability, aliphatic indexes and grand average hydropathy (GRAVY). The sequence was used to generate tertiary structure using HHpred server which suggested that Cu, Zn SOD binding site was in an oxidoreductase fold metal family, with TOIB peptidoglycan lipoprotein and SMP-30 domain site hydrolyzing enzyme which protects stress associated with aging. 3D-structure was done with RAMPAGE, PROQ and Combinatorial Extension (CE) visualized with RASMOL.   

 

Key words: Cu, Zn superoxide dismutase, Dinococcus rdaiodurans, Radiation resistance, TOIB protein and SMP-30 protein and 3Dstructure. 

©2021-2032  All Rights Reserved. Online Journal of Bioinformatics.  You may not store these pages in any form except for your own personal use. All other usage or distribution is illegal under international copyright treaties. Permission to use any of these pages in any other way besides  the before mentioned must be gained in writing from the publisher. This article is exclusively copyrighted in its entirety to onlinejournals@gmail.com publications. This article may be copied once but may not be, reproduced or  re-transmitted without the express permission of the editors. Linking: To link to this page or any pages linking to this page you must link directly to this page only here rather than put up your own page.

OJBTM

Online Journal of Bioinformatics©

Volume 22 (2): 70-81, 2021.

In silico copper and zinc superoxide dismutase in Dinococcus radiodurans.

 

Ashokan KV1 and Pillai MM2

 

Department(s) 1Biological Science,  PVP College, Kavathe Mahankal, Sangli, Mharashtrea, 2Biotechnology, KIIT’s Engineering College, Gokulshirgoan, Kolhapur, India.

                          

ABSTRACT

 

Ashokan KV, Pillai MM., In silico copper and zinc superoxide dismutase in Dinococcus radiodurans, Onl J Bioinform., 22 (2): 70-81, 2021. We characterized copper and zinc superoxide dismutase protein of Dinococcus radiodurans strain R1 by in silico tools and servers. We found that the primary sequence analysis of the protein’s net positive charge was due to arginine and lysine with an isoelectric point  >7, pH 9.8 and hydrophobicity of 53.5%. By PROSCAN we identified functional amino acid length, Myristylation, 3 phosphorylation and N-glycosylation sites. Secondary structure predicted by JPRED revealed β-turns with disulphide bonds. INTERPROSCAN revealed 3 integral domains of copper, zinc, superoxide dismutase 6 bladed propeller, TOIB and SMP-30/Gluconolaconase/LRE. Domains sequences were determined by EXPASY for extinction coefficient, half-life, instability, aliphatic indexes and grand average hydropathy (GRAVY). The sequence was used to generate tertiary structure using HHpred server which suggested that Cu, Zn SOD binding site was in an oxidoreductase fold metal family, with TOIB peptidoglycan lipoprotein and SMP-30 domain site hydrolyzing enzyme which protects stress associated with aging. 3D-structure was done with RAMPAGE, PROQ and Combinatorial Extension (CE) visualized with RASMOL.   

 

Key words: Cu, Zn superoxide dismutase, Dinococcus rdaiodurans, Radiation resistance, TOIB protein and SMP-30 protein and 3Dstructure.

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