title: Fatty acid binding into the highest affinity site of human serum albumin observed in molecular dynamics simulation.
abstract: Multiple molecular dynamics simulations were performed to investigate the association of stearic acid into the highest affinity binding site of human serum albumin. All binding events ended with a rapid (<10 ps) lock-in of the fatty acid due to formation of a hydrogen bond with Tyr401. The kinetics and energetics of the penetration process both depended linearly on the positional shift of the fatty acid, with an average insertion time and free energy reduction of, respectively, 32 ± 20 ps and 0.70 ± 0.15 kcal/mol per methylene group absorbed. Binding events of longer duration (tbind>1 ns) were characterized by a slow exploration of the pocket entry and, frequently, of a nearby protein crevice corresponding to a metastable state along the route to the binding site. Taken all together, these findings reconstruct the following pathway for the binding process of stearic acid: (i) contact with the protein surface, possibly facilitated by the presence of an intermediate location, (ii) probing of the site entry, (iii) insertion into the protein, and (iv) lock-in at the final position. This general description may also apply to other long-chain fatty acids binding into any of the high-affinity sites of albumin, or to specific sites of other lipid-binding proteins.
authors.affiliation: Licryl Laboratory, CNR-NANOTEC and CEMIF.Cal, University of Calabria, 87036 Rende, Italy. Electronic address: bruno.rizzuti@cnr.it.
authors.forename: Bruno
authors.initials: B
authors.lastname: Rizzuti
authors.affiliation: Molecular Biophysics Laboratory and CNISM Unit, Department of Physics, University of Calabria, 87036 Rende, Italy.
authors.forename: Rosa
authors.initials: R
authors.lastname: Bartucci
authors.affiliation: Molecular Biophysics Laboratory and CNISM Unit, Department of Physics, University of Calabria, 87036 Rende, Italy.
authors.forename: Luigi
authors.initials: L
authors.lastname: Sportelli
authors.affiliation: Molecular Biophysics Laboratory and CNISM Unit, Department of Physics, University of Calabria, 87036 Rende, Italy.
authors.forename: Rita
authors.initials: R
authors.lastname: Guzzi
mesh_terms: D001665:Binding Sites; D006801:Humans; D007700:Kinetics; D008956:Models, Chemical; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D011487:Protein Conformation; D012709:Serum Albumin / Q000737:chemistry* / Q000648:ultrastructure*; D013229:Stearic Acids / Q000737:chemistry*
chemical_list: D012709:Serum Albumin; D013229:Stearic Acids; C031183:stearic acid
keywords: Association; Binding site; Human serum albumin; Kinetics; Molecular dynamics; Stearic acid