High resolution X-ray studies of mammalian intestinal and muscle fatty acid-binding proteins provide an opportunity for defining the chemical nature of fatty acid: protein interactions

The structure of E. coli-derived rat intestinal fatty acid-binding protein has recently been refined to 1.2 Å without bound fatty acid and to 2.0 Å and 1.75 Å with bound hexadecanoate (palmitate) and 9Z-octadecenoate (oleate), respectively. The structure of E. coli-derived human muscle fatty acid-binding protein has also been solved to 2.1 Å with a C16 bacterial fatty acid. Both proteins contain 10 anti-parallel β-strands in a+1, +1, +1... motif. The strands are arranged in two β-pleated sheets that are orthogonally oriented. In each case, the fatty acid is enclosed by the β-sheets and is bound to the proteins by feeble forces. These feeble forces consist of (i) a hydrogen bonding network between the fatty acid's carboxylate group, ordered solvent, and side chains of polar/ionizable amino acid residues; (ii) van der Waals contacts between the methylene chain of the fatty acid and the side chain atoms of hydrophobic and aromatic residues; (iii) van der Waals interactions between the π{variant} methyl and the component methenyls of the phenyl side chain of a Phe which serves as an adjustable terminal sensor situated over a surface opening or portal connecting interior and exterior solvent; and (iv) van der Waals contacts between methylenes of the alkyl chain and oxygens of ordered waters that have been located inside the binding cavity. These waters are positioned over one face of the ligand and are held in place by hydrogen bonding with one another and with the side chains of protein's polar and ionizable residues. Binding of the fatty acid ligand is associated with minimal adjustments of the positions of main chain or side chain atoms. However, acquisition of ligand is associated with removal of ordered interior solvent suggesting that the free energy of dehydration of the binding site may be as important for the energy of the binding reaction as the free energy of stabilization of the fatty acid: protein complex.