Prediction of the Binding Site of Kryptofix-۲۲۱ to Na-dependent β-Galactosidase: A Molecular Docking study

Due to its nutritional, biotechnological and therapeutic applications, β-D-Galactosidase (E.C.۳.۲.۱.۲۳) has been extensively studied. It catalyzes the hydrolysis of lactose to glucose and galactose.β -galactosidase from E.coli is a ۴۶۴kDa homotetramer. Each subunit (۱,۰۲۳ residues) consists of five domains, the third being an alpha/beta barrel that contains most of the active site residues. Sodium ion is critical for generating the action potential in nervous and cardiac tissues, and its level in blood is an excellent biomarker to show electrolyte imbalance and provide valuable information regarding an individual’s physical and mental situation Accordingly, measurement of Na+ level in blood is of great clinical importance. Measuring serum level of Na+ is based on the sodium-dependent activity ofβ-galactosidase. In this method, Kryptofix-۲۲۱ (Na+-binding agent) is used to prevent the enzyme reaction from being saturated with excessive sodium ions. Pre-incubation of the enzyme with Kryptofix-۲۲۱ leads to a decrease in enzyme stability. Regarding this problem, efforts were raised to analyze the ligand interaction with β-galactosidase. The ۳D structures of the enzyme and Kryptofix-۲۲۱ were obtained from PDB (ID:۱D۰P) and PubChem (ID:۱۲۳۴۳۸), respectively. It was checked by Chimera v.۱.۱۶ for hydrogen and charge addition. The active site pocket of the enzyme was evaluated using CASTp web server, and YASARA was used for energy minimization of the protein. Docking studies between Kryptofix-۲۲۱ and β-galactosidase were carried out using Autodock vina v.۱.۱.۲. The ligand interaction plots of protein-ligand complexes were illustrated by Ligplot+ v.۲.۲.۷ program. Enzyme showed optimum binding a nity to target ligand with the binding energy of ۵.۶ kcal/mol. Based on docking analyses, seven residues, including Val-۱۰۳, His-۴۱۸, Glu-۴۶۱, Met-۵۰۲, Tyr-۵۰۳, Phe-۵۱۲, and Trp-۹۹۹ are involved in non-bonding interactions with Kryptofix-۲۲۱. Moreover, Kryptofix-۲۲۱ can form one hydrogen bond with Lys-۵۱۷.

کلیدواژه ها:

β-Galactosidase ، Sodium sensing ، Molecular docking ، Kryptofix