title: Insight into the dynamic interaction between different flavonoids and bovine serum albumin using molecular dynamics simulations and free energy calculations.
abstract: In this study, the binding of Bovine serum albumin (BSA) with three flavonoids, kaempferol-3-O-a-L-rhamnopyranosyl-(1-3)-a-L-rhamnopyranosyl-(1-6)-b-D-galacto- pyranoside (drug 1),kaempfol-7-O-rhamnosyl-3-O-rutinoside (drug 2)andkaempferide-7-O-(4"-O-acetylrhamnosyl)-3-O-ruti- noside (drug 3) is investigated by molecular docking, molecular dynamics (MD) simulation, and binding free energy calculation. The free energies are consistent with available experimental results and suggest that the binding site of BSA-drug1 is more stable than those of BSA-drug2 and BSA-drug3. The energy decomposition analysis is performed and reveals that the electrostatic interactions play an important role in the stabilization of the binding site of BSA-drug1 while the van der Waals interactions contribute largely to stabilization of the binding site of BSA-drug2 and BSA-drug3. The key residues stabilizing the binding sites of BSA-drug1, BSA-drug2 and BSA-drug3 are identified based on the residue decomposition analysis.
authors.affiliation: Department of Food quality and Safety, Jilin University, Changchun 130062, People's Republic of China. niuxd@jlu.edu.cn
authors.forename: Xiaodi
authors.initials: X
authors.lastname: Niu
authors.forename: Xiaohan
authors.initials: X
authors.lastname: Gao
authors.forename: Hongsu
authors.initials: H
authors.lastname: Wang
authors.forename: Xin
authors.initials: X
authors.lastname: Wang
authors.forename: Song
authors.initials: S
authors.lastname: Wang
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001665:Binding Sites; D002417:Cattle; D005419:Flavonoids / Q000737:chemistry / Q000378:metabolism*; D008024:Ligands; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D016415:Sequence Alignment; D012710:Serum Albumin, Bovine / Q000737:chemistry / Q000378:metabolism*; D013816:Thermodynamics
chemical_list: D005419:Flavonoids; D008024:Ligands; D012710:Serum Albumin, Bovine