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Homology modeling and structure prediction of thioredoxin (TRX) protein in wheat (Triticum aestivum L.)

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Author(s): M. Prabhavathi 1 , K. Ashokkumar 2* , N. Geetha 1 , K.M. Saradha Devi 3

Journal: International Journal of Biosciences
ISSN 2220-6655

Volume: 1;
Issue: 1;
Start page: 20;
Date: 2011;
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Keywords: Antioxidant | function prediction | homology modeling | procheck validation | structure comparison | thioredoxin and Triticum aestivum.

ABSTRACT
Wheat is an important dietary cereal often associated with beneficial health effects. A study was carried out to investigate the in silico analysis of homology modeling and 3D structure prediction of Thioredoxin (TRX) protein in Triticum aestivum. Primary structure prediction and physicochemical characterization were performed by computing theoretical isoelectric point (pI), molecular weight, total number of positive and negative residues, extinction coefficient, instability index, aliphatic index and grand average hydropathy (GRAVY). In this study homology modeling, a high quality of protein 3D structure has been predicted for the hypothetical amino acid sequence. Thioredoxin of Triticum aestivum was compared to the 1XFL solution structure of Thioredoxin h1 from Arabidopsis thaliana predicted structure through ROSETTA. However, the quality of the homology model performed through SWISS-MODEL depended on the quality of the sequence alignment by BLAST and template structure. Comparative assessment of secondary structure modeled using GOR IV, HNN and SOPMA revealed greater percentage of residues as alpha helix and random coils against the beta sheets. Structure comparison by VAST for the ROSETTA modeled structure indicated no hits for the entire sequence unlike that of SWISS modeled structure, which indicated 60 structure neighbours for the entire residues. Tertiary structure was predicted using homology modeling by taking template PDB-1fxl and the modeled protein energy were minimized. The models were validated using protein structure checking tools PROCHECK. These structures will provide a good foundation for functional analysis of experimentally derived crystal structures.
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