Lipid-Binding Protein Cavity

In the members of the iLBP family whose function is to bind fatty acids, the cavity does not mirror the shape of the ligand. This should be apparent in Fig. 8. Note that the overall shape is ellipsoidal despite the fact that the protein mainly binds fatty acids and other generally elongated molecules. In CRBP and CRBPII, the cavity has a closer fit to the ligand (Cowan et ai, 1993). Except for MFB2, the bottom of the cavity is close to the center of the molecule and the top is near helix all and turns between /3C and /8D, j8 , and )8F. 

The cavity is lined by 35 to 38 residues from al, all, j8B-/3E, and /3G-/8J. In the text that follows, two different aspects of the ligandbinding site will be discussed (1) the number of amino acids in contact with the cavity and (2) the number of amino acids in contact with the bound ligand. The reader should note that they are not the same and that ligand contacts are always less than the number of amino acids contributing to the cavity. 

For the various iFBPs, the cavity volume that is available to other atoms 

An opening exists to the surface. For the closed surface volume calculation, Phe-57 and Lys-58 were moved to close the portal. 

In the two cases cited above, the cavity water molecules make extensive hydrogen bonds to internal polar atoms and other water molecules. They should be considered as an integral part of the protein structure. Allowing 12 per water molecule, these water molecules will occupy a space 

---

In summary, the overall structures of the LBPs have a motif common to a variety of other proteins. Different forms of the /8 barrel have been observed in other lipid-binding proteins as well as in other globular proteins. The unique feature of the LBPs should be visible in Fig. 2. The distinctive feature of the LBPs is their /8-barrel architecture that gives rise to a cavity accommodating a hydrophobic ligand. 

Lipid transfer peptides and proteins occur in eukaryotic and prokaryotic cells. In vitro they possess the ability to transfer phospholipids between lipid membranes. Plant lipid transfer peptides are unspecific in their substrate selectivity. They bind phosphatidylcholine, phosphatidylethanolamine, phosphatidylinositol, and glycolipids. Some of these peptides have shown antifungal activity in vitro The sequences of lipid transfer proteins and peptides contain 91-95 amino acids, are basic, and have eight cysteine residues forming four disulfide bonds. They do not contain tryptophan residues. About 40% of the sequence adopts a helical structure with helices linked via disulfide bonds. The tertiary structure comprises four a-helices. The three-dimensional structure of a lipid transfer peptide from H. vulgare in complex with palmitate has been solved by NMR. In this structure the fatty acid is caged in a hydrophobic cavity formed by the helices. 

Many larger lipid carrier proteins are known. The 476-residue plasma cholesteryl ester transfer protein is discussed briefly in Chapter 22. Plasma phospholipid transfer proteins are of similar size.t/U A 456-residue human phospholipid-binding protein interacts with the lipopolysaccharide of the surfaces of gram-negative bacteria (Fig. 8-30) and participates in the immune response to the bacteria. It has an elongated boomerang shape with two cavities, both of which bind a molecule of phosphatidylcholine. Other plasma lipid transfer proteins may have similar structures/... 

In addition, the carboxylate group of bound fatty acid was in a solvent-accessible environment, suggesting a lipid-binding mode different from that of wild-type protein. Furthermore, this mutant had an affinity for retinol when the wild-type IFABP had none (Jakoby el al, 1993). These experiments show that it is possible to switch the binding specificity of iLBP proteins by mutating individual amino acids associated with the specificity motif. These results do not, however, indicate that the mutated positions are singularly responsible for ligand selectivity. Substitution of other cavity residues may have similar or contributory effects. 

Although three dimensional crystal structures of maize LTP1 with various lipids13 showed only one monomer embedded in the protein cavity, we recently demonstrated that this protein is also capable of binding two monomers of double chained lipids (Douliez et al, in preparation). In that case, the fluorescence behaviour was slightly different than for wheat or barley LTP1 since the fluorescence intensity only increases after Ri = 0.5. This revealed a potential different mode of binding in case of this protein. 

---