Structural and dynamic study of fungal cell wall degrading fungal chitinase and its interaction with chitooligosaccharide

Chitin, comprising of 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 chitooligomers which finds multifarious uses in various sectors and are gaining attention particularly as a biocontrol agent against chitin-containing insects and plant pathogens. Although fungi are a significant source of chitinases, the phylogenetic and functional diversity of the fungal enzymes 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 is rich in non-polar amino acid residues, while the active site contains more 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. Residual flexibility, hydrogen bonding, and structural packing showed consistent trajectories with no significant perturbations throughout the simulation. 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.