Molecular Dynamics Simulation and Molecular Docking Study on the Conversion of Ginsenosides by β-Glucanase

Abstract

Abstract Enzymatic conversion is an important method for producing rare ginsenosides. In order to explore the molecular mechanisms underlying the interaction of β-Glucanase during the conversion process of rare ginsenoside CK, this study employed high-performance liquid chromatography, infrared spectroscopy, ultraviolet spectroscopy, and fluorescence spectroscopy to investigate the ability of β-Glucanase to convert ginsenoside Rb1 into ginsenoside CK. Changes in the secondary structure quantity of the enzyme before and after conversion were characterized. Additionally, this study accurated binding sites of β-Glucanase with ginsenoside Rb1, as well as optimal conformations, were identified through molecular dynamics simulations and molecular docking. Spectroscopic experiments revealed a reduction in the α-helix and β-fold content of β-Glucanase in acetic acid buffer. Molecular dynamics and docking results indicated that spontaneous interactions between β-Glucanase and ginsenosides Rb1, Rd, and F2, characterized by strong binding forces and high dissociation rates. In summary, the spectroscopic experiments, molecular simulations, and docking validations collectively demonstrate structural changes in the enzyme itself and the generation of some secondary bonds between the enzyme and ginsenosides during the process of converting ginsenoside Rb1 to CK. This study provides theoretical support for the conversion of ginsenoside Rb1 by β-Glucanase, elucidating the mechanisms of enzyme immobilization and catalytic reactions of β-Glucanase, offering new insights into the interaction between proteins and small molecule ligands.