Abstract
The binding interactions of the surfactants: anionic sodium dodecyl sulphate (SDS), cationic cetyltrimethylammonium bromide (CTAB), non-ionic octyl glucoside (OG), and zwitterionic 3-[Hexadecyl(dimethyl)ammonio]-1-propanesulfonate (HPS), with bovine serum albumin (BSA) were investigated by computer simulation. The results disclosed that the surfactants bound stably between hydrophobic subdomain IIA and IIIA where tryptophan-213 residue, an important intrinsic fluorophore in BSA is housed. The interactions of the surfactants with the BSA were electrostatic and hydrophobic interactions. The head-groups of SDS, HPS and OG formed hydrogen bonds with the BSA, while that of CTAB was shielded from intermolecular hydrogen-bonding due to intervening methyl groups. Subsequently, molecular dynamics (MD) simulation of the protein-surfactant complexes revealed that hydrogen bonds formed by OG were stronger than those of SDS and HPS. However, the decomposed force-field energies showed that OG had the least interaction energy with the BSA. In addition to MD simulation, it was found by density functional theory (DFT) that the differences in the coulomb interaction energies can be attributed to charge distribution in the surfactants. Overall, free energies calculated by linear interaction energy (LIE) proved that the binding of each surfactant was dominated by differences between van der Waals interactions in bound and free states.
Highlights
The binding interactions of the surfactants: anionic sodium dodecyl sulphate (SDS), cationic cetyltrimethylammonium bromide (CTAB), non-ionic octyl glucoside (OG), and zwitterionic 3-[Hexadecyl(dimethyl)ammonio]-1-propanesulfonate (HPS), with bovine serum albumin (BSA) were investigated by computer simulation
To calibrate the simulation protocol discussed above, and to investigate the reliability of the docking program, we used the AutoDock Vina software to perform a test docking of SDS binding to LGB, which was followed by 100 ns molecular dynamics (MD) simulation of the highest ranked LGB-SDS complex
The binding of four major categories of surfactants to BSA has been studied by molecular docking and molecular dynamics simulation
Summary
The binding interactions of the surfactants: anionic sodium dodecyl sulphate (SDS), cationic cetyltrimethylammonium bromide (CTAB), non-ionic octyl glucoside (OG), and zwitterionic 3-[Hexadecyl(dimethyl)ammonio]-1-propanesulfonate (HPS), with bovine serum albumin (BSA) were investigated by computer simulation. We seek to use computer simulation to provide atomic-level interpretation of protein-surfactant interactions by decomposing the binding site residues for the protein-surfactant complexes, and the molecular mechanics energies. Owing to the limited capability of the conformational search methods and the scoring functions, the current trend is to carry out MD simulation of a docked protein-ligand complex in order to validate the ligand stability and the molecular interactions[21,22,23,24,25]. The use of molecular docking and MD simulations for the efficient screening of a large set of ligands and for the refining of the structures of the final complexes is a rational way to accurately study protein-ligand interactions[25]
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