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Int. J. Mol. Sci. 2010, 11(9), 3266-3276; doi:10.3390/ijms11093266

Molecular Modeling of Peroxidase and Polyphenol Oxidase: Substrate Specificity and Active Site Comparison

1
Bioinformatics Research Laboratory (BiRL), Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
2
Computational Simulation and Modeling Laboratory (CSML), Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
3
Department of Chemistry and Center for Innovation in Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
4
Thailand Center of Excellence in Physics (ThEP), Commission Higher on Education, Ministry of Education, Bangkok 10400, Thailand
5
Phytochemica Research Unit, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
*
Authors to whom correspondence should be addressed.
Received: 30 July 2010 / Revised: 26 August 2010 / Accepted: 7 September 2010 / Published: 14 September 2010
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
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Abstract

Peroxidases (POD) and polyphenol oxidase (PPO) are enzymes that are well known to be involved in the enzymatic browning reaction of fruits and vegetables with different catalytic mechanisms. Both enzymes have some common substrates, but each also has its specific substrates. In our computational study, the amino acid sequence of grape peroxidase (ABX) was used for the construction of models employing homology modeling method based on the X-ray structure of cytosolic ascorbate peroxidase from pea (PDB ID:1APX), whereas the model of grape polyphenol oxidase was obtained directly from the available X-ray structure (PDB ID:2P3X). Molecular docking of common substrates of these two enzymes was subsequently studied. It was found that epicatechin and catechin exhibited high affinity with both enzymes, even though POD and PPO have different binding pockets regarding the size and the key amino acids involved in binding. Predicted binding modes of substrates with both enzymes were also compared. The calculated docking interaction energy of trihydroxybenzoic acid related compounds shows high affinity, suggesting specificity and potential use as common inhibitor to grape ascorbate peroxidase and polyphenol oxidase. View Full-Text
Keywords: peroxidase; polyphenol oxidase; browning reaction; molecular docking peroxidase; polyphenol oxidase; browning reaction; molecular docking
This is an open access article distributed under the Creative Commons Attribution License (CC BY 3.0).

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MDPI and ACS Style

Nokthai, P.; Lee, V.S.; Shank, L. Molecular Modeling of Peroxidase and Polyphenol Oxidase: Substrate Specificity and Active Site Comparison. Int. J. Mol. Sci. 2010, 11, 3266-3276.

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