An investigation of molecular dynamics simulation and molecular docking: Interaction of citrus flavonoids and bovine [beta]-lactoglobulin in focus

• Published in: Computers in biology and medicine 2014-08, Vol.51, p.44
• Main Authors: Sahihi, M, Ghayeb, Y
• Format: Article
• Language: English
• Subjects: Binding sites; Citrus fruits; Ligands; Molecular biology; Molecular weight; Proteins; Studies
• ISSN: 0010-4825; 1879-0534
• DOI: 10.1016/j.compbiomed.2014.04.022

Citrus flavonoids are natural compounds with important health benefits. The study of their interaction with a transport protein, such as bovine β-lactoglobulin (BLG), at the atomic level could be a valuable factor to control their transport to biological sites. In the present study, molecular docking and molecular dynamics simulation methods were used to investigate the interaction of hesperetin, naringenin, nobiletin and tangeretin as citrus flavonoids and BLG as transport protein. The molecular docking results revealed that these flavonoids bind in the internal cavity of BLG and the BLG affinity for binding the flavonoids follows naringenin>hesperetin>tangeretin>nobiletin. The docking results also indicated that the BLG-flavonoid complexes are stabilized through hydrophobic interactions, hydrogen bond interactions and π-π stacking interactions. The analysis of molecular dynamics (MD) simulation trajectories showed that the root mean square deviation (RMSD) of various systems reaches equilibrium and fluctuates around the mean value at various times. Time evolution of the radius of gyration, total solvent accessible surface of the protein and the second structure of protein showed as well that BLG and BLG-flavonoid complexes were stable around 2500ps, and there was not any conformational change as for BLG-flavonoid complexes. Further, the profiles of atomic fluctuations indicated the rigidity of the ligand binding site during the simulation.