Unveiling the interaction between fungal biocontrol agent Paraphaeosphaeria minitans chitinase and chitotriose through molecular dynamics study
TL;DR
The free energy calculations for the PmChi-chitotriose complex indicated that MM/PBSA calculations are more accurate for analyzing enzyme-carbohydrate interactions and enhance the understanding of the structural properties and functional dynamics of chitinase from P. minitans.
Abstract
Chitin, comprising repeating units of N-acetyl-glucosamine, is the second most abundant polymer occurring in wide range of insects, fungi, yeasts and plants. Chitinases hydrolyze chitin into widely applicable chitooligomers and are gaining attention, particularly, as a biocontrol agent against insects and fungal plant pathogens. Although fungi are a significant source of chitinases, their phylogenetic and functional diversity is not well understood. In this study, we employed molecular modeling and simulation techniques to investigate the molecular characteristics of chitinase (PmChi) from a mycoparasitic fungus, Paraphaeosphaeria minitans, widely used as a biological control agent. The secondary structure of PmChi is predominantly random coil (51.24%), followed by alpha helices (28.44%) and extended strands (14.22%). PmChi contains the conserved chitinase sequence FDGLDIDWE at positions 178 to 186, where glutamic acid (E) acts as the catalytic proton donor, and aspartic acid (D) stabilizes the protein by accommodating substrate distortion. The protein surface of PmChi has non-polar amino acid residues, while the active site contains polar residues to facilitate the reaction. Key amino acids involved in catalytic activity include Trp146, Asp184, Glu186, Tyr187, Pro228, Met252, Tyr254, and Asp255. Molecular simulations demonstrated that PmChi maintained stability during interaction with chitotriose. After binding, PmChi revealed an increase in hydrophobic bonds from 702 to 827, showing a non-polar surface primed for intermolecular interactions alongside an active site rich in catalytic aspartate and glutamate residues. The free energy calculations for the PmChi-chitotriose complex indicated that MM/PBSA calculations are more accurate for analyzing enzyme-carbohydrate interactions. These findings enhance our understanding of the structural properties and functional dynamics of chitinase from P. minitans and provide a platform for future research and applications.