Fatty acid binding proteins (FABPs) act as intracellular shuttles for fatty acids as well as lipophilic xenobiotics to the nucleus, where these ligands are released to a group of nuclear receptors called the peroxisome proliferator activated receptors (PPARs). PPAR mediated gene activation is ultimately involved in maintenance of cellular homeostasis through the transcriptional regulation of metabolic enzymes and transporters that target the activating ligand. Here we show that liver- (L-) FABP displays a high binding affinity for PPAR subtype selective drugs. NMR chemical shift perturbation mapping and proteolytic protection experiments show that the binding of the PPAR subtype selective drugs produces conformational changes that stabilize the portal region of L-FABP. NMR chemical shift perturbation studies also revealed that L-FABP can form a complex with the PPAR ligand binding domain (LBD) of PPARα. This protein-protein interaction may represent a mechanism for facilitating the activation of PPAR transcriptional activity via the direct channeling of ligands between the binding pocket of L-FABP and the PPARαLBD. The role of L-FABP in the delivery of ligands directly to PPARα via this channeling mechanism has important implications for regulatory pathways that mediate xenobiotic responses and host protection in tissues such as the small intestine and the liver where L-FABP is highly expressed. 1. Introduction Intracellular long-chain fatty acids (FAs) are key components in the synthesis of cellular membranes as well as being utilized as signaling molecules and for energy delivery [1, 2]. The preservation of a proper balance between absorption, secretion, and storage of FA is therefore, integral for cellular physiology [1]. Increasingly prominent diseases such as obesity, cardiovascular diseases, type II diabetes, and atherosclerosis, to a large extent, all evolve from disorders of lipid metabolism. In vivo, due to their poor aqueous solubility, FAs are bound and transported by a class of intracellular lipid binding proteins (iLBPs) termed fatty acid binding proteins (FABPs) [1–4]. Structurally, FABPs possess a similar tertiary fold, consisting of ten antiparallel β-strands, which form a clam shell-like β-barrel structure (cf. Figure 3(c)) [3, 5, 6]. The β-barrel is capped by a pair of α-helices that enclose an internal cavity, which forms the ligand binding pocket. A mechanism for ligand binding termed the “portal hypothesis” has been proposed, where the FA molecule enters the protein through a dynamic structure formed by the α-helical region, before
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