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

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.

Effect of basil leaves and wheat bran water extracts on enzymatic browning of shredded storage iceberg lettuce

“…Peroxidases (POD) are oxidoreductases that are highly resistant to high temperatures. They catalyse the oxidation of various substrates, including phenolic compounds, in the presence of hydrogen peroxide to final dark-pigment products (Nokthai et al, 2010). Most importantly, these enzymes are induced by stress conditions, for example wounding that usually take places in the food production chain.…”

Relationship between polyphenol oxidase activity and phenolics degradation on ambient air-drying of herbal plants

“…Hence, as there is high amount of a particular phenolics, it is natural that the amount of PPO enzymes present will react accordingly resulting in a correlation. However, despite having low amount of both rutin and chlorogenic acid, P. americana still fitted in the correlation curve, as its PPO activity was already very low, hence, its capability to degrade/react with polyphenols are also limited, and therefore in this case, the amount of enzyme is a limiting factor for enzymatic reaction (Nokthai, Lee, & Shank, ).…”

The presentation of a new inhibitor to prevent enzymatic browning in mushroom, banana, and apple

“…1, was the best. Nokthai et al (2010) analyzed the active site of PPO by molecular modeling. They found that epicatechin and catechin had high affinity with the enzyme.…”