Molecular Dynamics Simulation of the Effect of Deep Eutectic Solvent on the Structural Stability of Uricase

Predicting enzyme properties typically relies on two methodologies: experimental assays, which are often time-consuming and costly, and computational simulations that alleviate these constraints by providing insights into the structural changes of proteins. Molecular dynamics (MD) simulation stands as one of the most significant computational tools for studying protein structures, enabling theorists to model and predict outcomes based on theoretical frameworks. Uricase (urate oxidase), an enzyme within the oxidoreductase class, is responsible for the oxidation of uric acid to allantoin and plays a pivotal role in conditions such as hyperuricemia and gout by reducing uric acid levels. To investigate the impact of a deep eutectic solvent synthesized from glycerol, fructose, and sucrose on the stability of this enzyme, uricase was overexpressed in E. coli BL۲۱ and purified using a nickel affinity column. Analysis of root mean square deviation (RMSD), root mean square fluctuation (RMSF), solvent-accessible surface area (SASA), and radius of gyration (Rg) revealed a decrease in these parameters in the presence of the eutectic solvent, suggesting enhanced structural compactness and stability conferred by the solvent. Additionally, radial distribution function (RDF) analysis and total energy calculations (incorporating electrostatic and Lennard-Jones potentials) were performed for each component, with the strongest interactions attributed to sucrose.

کلیدواژه ها:

Simulation ، Molecular Dynamics ، Uricase ، Deep Eutectic Solvent