Molecular Dynamics Investigations of Aspergillus nigerα-α-L-rhamnosidase with Naringin

Abstract:

α--L-Rhamnosidase generates prunin and L-rhamnose by hydrolyzing naringin，which can be used to debittering citrus juices. In the present study，the α--L-rhamnosidase，previously identified from Aspergillus niger JMU-TS528，was docked with naringin and the binding energy was calculated by molecular dynamics simulation and MM-PBSA method. The results of binding energy indicate that var der Waalsforce is the main driving force for enzyme-substrate combination；whereas the electrostatic interaction and non-polar solvents contribute less. In addition，the critical amino acid residues for hydrophobic effect are Trp236，Ala340，Ile462，Phe461，Tyr516，Val522 and Trp528. Ser286，Phe465 and Pro520 are important amino acid residues which could form steady hydrogen bonds with naringin. The key amino acid residues identified in the study provides valuable targeting sites for remoulding α--L-rhamnosidase in protein engineering.