title: Molecular dynamics simulations of the adipocyte lipid binding protein reveal a novel entry site for the ligand.
abstract: The adipocyte lipid binding protein (ALBP) binds fatty acids (FA) in a cavity that is inaccessible from the bulk. Therefore, the penetration of the FA necessitates conformational changes whose nature is still unknown. It was suggested that the lipid first enters through a "portal region" which consists of the alphaII helix and the adjacent tight turns. The initial event in the ligand binding must be the interaction of the lipid with the protein surface. To analyze this interaction, we have carried out three molecular dynamics simulations of the apo-ALBP, with a palmitate ion initially located at different positions near the protein surface. The simulation indicated that the ligand could adsorb to the protein in more than one location. Yet, in one case, the ligand managed to penetrate the protein by entering a newly formed cavity some 10 A deep. The entry site is located near the N-terminus, at the junction between the loops connecting the beta-strands. Further progression of the penetration seems to be arrested by the need for desolvation of the COOH end of the headgroup. Evolutionary analysis showed that amino acids in this entry site are well conserved. On the basis of these observations, we suggest that the ligand may enter the protein from a site other than the portal region. Furthermore, the rate-limiting step is proposed to be the desolvation of the FA polar headgroup.
authors.affiliation: Laser Laboratory for Fast Reactions in Biology, Department of Biochemistry, The George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978 Ramat-Aviv, Tel Aviv, Israel.
authors.forename: Ran
authors.initials: R
authors.lastname: Friedman
authors.forename: Esther
authors.initials: E
authors.lastname: Nachliel
authors.forename: Menachem
authors.initials: M
authors.lastname: Gutman
mesh_terms: D017667:Adipocytes / Q000737:chemistry / Q000378:metabolism*; D001059:Apoproteins / Q000737:chemistry / Q000378:metabolism; D001665:Binding Sites; D002352:Carrier Proteins / Q000737:chemistry* / Q000378:metabolism*; D003198:Computer Simulation; D017124:Conserved Sequence; D019143:Evolution, Molecular; D050556:Fatty Acid-Binding Proteins; D057927:Hydrophobic and Hydrophilic Interactions; D008024:Ligands; D008958:Models, Molecular; D019308:Palmitic Acid / Q000737:chemistry* / Q000378:metabolism*; D011485:Protein Binding; D011522:Protons; D012997:Solvents; D013499:Surface Properties; D013816:Thermodynamics
chemical_list: D001059:Apoproteins; D002352:Carrier Proteins; D050556:Fatty Acid-Binding Proteins; D008024:Ligands; D011522:Protons; D012997:Solvents; D019308:Palmitic Acid