Sequence analysis and homology modeling of peroxidase from Medicago sativa |
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Authors: | Vinita Hooda Prasada babu Gundala Paramageetham Chinthala |
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Institution: | 1Department of Botany, Maharshi Dayanand University, Rohtak 124001, India;2Department of Botany, Sri Venkateswara University,Tirupati-517502, India;3Department of Microbiology, Sri Venkateshwara University, Tirupati-517502, India |
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Abstract: | Plant peroxidases are one of the most extensively studied group of enzymes which find applications in the environment, health,
pharmaceutical, chemical and biotechnological processes. Class III secretary peroxidase from alfalfa (Medicago sativa) has been
characterized using bioinformatics approach Physiochemical properties and topology of alfalfa peroxidase were compared with
that of soybean and horseradish peroxidase, two most popular commercially available peroxidase preparations. Lower value of
instability index as predicted by ProtParam and presence of extra disulphide linkages as predicted by Cys_REC suggested alfalfa
peroxidase to be more stable than either of the commercial preparations. Multiple Sequence Alignment (MSA) with other
functionally similar proteins revealed the presence of highly conserved catalytic residues. Three dimensional model of alfalfa
peroxidase was constructed based on the crystal structure of soybean peroxidase (PDB Id: 1FHF A) by homology modelling
approach. The model was checked for stereo chemical quality by PROCHECH, VERIFY 3D, WHAT IF, ERRAT, 3D MATCH AND
ProSA servers. The best model was selected, energy minimized and used to analyze structure function relationship with substrate
hydrogen peroxide by Autodock 4.0. The enzyme substrate complex was viewed with Swiss PDB viewer and one residue ASP43
was found to stabilize the interaction by hydrogen bonds. The results of the study may be a guiding point for further investigations
on alfalfa peroxidase. |
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Keywords: | Homology modeling Peroxidase alfalfa Docking Hydrogen peroxide |
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