Mechanism and Function of Substrate Recognition by Fatty Acid Binding Protein 3

<p>Our research interests focus on the lipid-protein and/or lipid-lipid interactions, which are predominantly controlled in a non-directional manner; van der Waals forces, as well as electrostatic and water-molecule mediating interactions, play important roles there. Particularly, mechanism of molecular recognition in the hydrophobic region of lipid membranes is in high demand not only for protein science but also for natural products chemistry to gain a better understanding of molecular mechanism of bioactive compounds that target lipid membranes and membrane proteins. However, the estimation of the total effects of multiple non-directional interactions is far more difficult as compared to the effects of highly directional hydrogen bonds usually occurring in drug-target interactions.</p><p>In this study, we examined the molecular mechanism in the structure recognition of fatty acid by human fatty acid binding protein 3 (FABP3), by means of combination of thermodynamic and structural biological methods. Fatty acid is one of the simplest lipid molecules, and FABP3 is a small cytoplasmic protein (15 kDa) serving as a carrier of fatty acids. </p><p>A unified interaction analysis between fatty acids and FABP3 was implemented by isothermal titration calorimetry (ITC) using fatty acids bound to liposomes. The results showed that FABP3 possesses relatively high and similar affinity (K_d= ~1 mM) to fatty acids with a chain length of C10-C18. The analysis of thermodynamic parameters indicated FABP3-fatty acid interaction is enthalpy-driven.</p><p>The co-crystal structures of FABP3-fatty acids were obtained for C10:0-C18:0 at extremely high resolution by using SPring8 beam lines. The results showed that an additional network of ordered water molecules was found in the binding pocket of co-crystal with a C10:0 ligand to be forming hydrogen bonds with hydrophilic residues of FABP3. These water molecules were substituted by alkyl chains of longer fatty acids in C12:0-C18:0 co-crystals. These observations indicate that the water molecules in the new hydrogen bond network are involved in the retention of the similar binding affinity to C10-C18 fatty acids. Substitution of water molecules on a hydrophilic protein surface by a lipid alkyl chain may be one of the important models of lipid-protein interaction, which may lead to a better understanding of the molecular interactions among diverse constituents in cell membranes. </p>