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Computational Molecular Biology 2014, Vol. 4, No. 13, 1-6
http://cmb.biopublisher.ca
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Research Report Open Access
In-silico analysis predicting the best model for photosystemIID2 Protein of
Spinaciaolearacea using multiple templates
Pranati Swain
Orissa university of agriculture and technology, India
Corresponding author email
Computational Molecular Biology, 2014, Vol.4, No.13 doi: 10.5376/cmb.2014.04.0013
Received: 04 Dec., 2014
Accepted: 26 Dec., 2014
Published: 30 Dec., 2014
© 2014
Swain, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use,
distribution, and reproduction in any medium, provided the original work is properly cited.
Preferred citation for this article:
Swain, 2014,
In-silico analysis predicting the best model for photosystemIID2 Protein of Spinaciaolearacea using multiple templates
,
Computational Molecular Biology, Vol.4, No.13, 1-6
(doi
Abstract
Spinach is a natural medicine against diabetes, prostate cancer, asthma, constipation, high blood pressure. Spinach acts as
anti-inflammatory, antiproliferative, antioxidative. In this study the PHOTOSYSTEMII D2 protein has considered for in-silico
analysis. Models of the protein were generated using 1IZLD, 3A0B, 3WU2, 4IL6 templates. The sequence retrieved from uniprot,
templates were predicted by usingblastP tool, physico-chemical analysis showed the properties of protein using prot-param tool ,
secondary structure prediction showed helices, turns and sheets using CFFSP server, homologous models were generated using
modeller9.12 tool, backbone confirmation was performed by using Rampage server and finally the best model generated by using
3A0B template having 94.0% of residues lying in favored region, 2.0% residues lying in outlier region, with 91% of query coverage
and 95% of identity with photosystemQ (B) protein of Thermosynechocuccus vulcanus.
Keywords
PHOTOSYSTEMII D2 protein; Template prediction; Homology modeling; Model validation; Best model prediction
Introduction
The common name of Spinaciaolearacea is spinach
which belongs to the family
Amaranthaceae-
Chenopodiaceae
and
plays an important role as a
source of energy. Most commonly this green leavesare
used as food . from a research it has been proved that
the spinach is full of vitamin C, which helps to protect
all of the oxygen-sensitive phytonutrients in the
spinach leaves for which the leaves look vibrant and
alive. The main health-supportive nutrients found in
spinach isglycerolipids. Naturally spinach is
anti-inflammatory
(Lomnitski
et
al.,
2000),
antiproliferative (Bergman et al., 2011), antioxidative
(Sani et al., 2004). From a research among broccoli,
spinach, cauliflower, cabbage, mustard greens, collard
and kale the spinach showed significant protection
against the occurrence of aggressive prostate cancer in
male. The spinach is blessed with a natural anti-cancer
carotenoid i.e, epoxyxanthophylls. It contains
carotenoids i.e, beta carotene, lutein, zeaxanthin along
with antioxidants i.e, flavonoid. Spinach is quite
healthy as it is composed of vit.K, vit.A, vit.B1, vit.B3,
vitB2, vit.E, vit.B6, iron, copper, folate, manganese,
calcium, fiber, potassium, zinc, protein, choline,
omega-3 fats, selenium, pantothenic acid etc. the
vit.K1 and vit.K2 helps in activating the osteocalcin
leading to bone-up. However spinach is full of oxalate
too which is dangerous to health if taken in a huge
amount. Spinach contains natural purine which causes
kidney stone and gout disease if taken in a huge a
amount. Basically spinach helps to fight against weak
bone, high blood pressure, diabetes, asthma, prostate
cancer in male, constipation,human pancreatic cancer
cells (Lomnitski et al., 2000). Spinach is also helpful
for energy metabolism, maintaining muscle and nerve
function, heart rhythm, a healthy immune system and
maintaining blood pressure. In this study we have
considered the Photosystem II D2 of spinach. This
protein is a plastoquinone oxidoreductase that uses
light energy to abstract electrons from H
2
O producing
oxygen and proton gradient in order to produce ATP.
Photosystem II D2 is a membrane protein. PSII is
composed of 1 copy each of membrane proteins PsbA,
PsbB, PsbC, PsbD, PsbE, PsbF, PsbH, PsbI, PsbJ,
PsbK, PsbL, PsbM, PsbT, PsbX, PsbY, PsbZ, Ycf12.
In the study the physico-chemical analysis of protein
has been done along with homology modeling, model
validation and optimization leading in prediction of