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

Prontipa Nokthai,Vannajan Sanghiran Lee,Lalida Shank

doi:10.3390/ijms11093266

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.

Highlights

Browning of vegetables, fruits and flowers alter their appearances, flavors, textures, and lower their marketing values
1APX—with the highest sequence similarity to grape peroxidase (80% sequence identity and an E-value of 2.62E-116)—was chosen as the template
The quality of the residue backbone conformations in the grape peroxidase model was checked by PROCHECK

Summary

Introduction

Fruits and flowers alter their appearances, flavors, textures, and lower their marketing values. Appearance, which is significantly impacted by color, is one of the first attributes used by consumers to evaluate the quality of goods [1]. The browning process can be caused by both enzymatic and non-enzymatic biochemical reactions [2]. Polyphenol oxidase (PPO) and peroxidase (POD) are two well known enzymes involved in the browning process [1,2,3]. PPO catalyzes the conversion of phenolic compounds to quinones and assists their products’ polymerization. In the presence of oxygen, leads to the formation of undesirable brown pigments and off-flavored products [4]. The browning of injured, peeled or diseased fruit tissues can causes undesirable quality changes during handling, processing and storage

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