I read with interest the review by Walden and Hegele [1]. The authors state that "apolipoprotein (apo) E is divided into two independently folded domains with different functions." The boundary between these two domains is the random-coil region spanning amino acids 165 to 201, which is subject to enzymatic cleavage [2]. Thus, the region encompassing approximately the first 160 to 210 amino acids contains the apo B-E receptor-binding domain (which is located approximately between amino acids 130 and 160), whereas the C-terminal region mediates the binding to lipids.

Evidence now suggests that apolipoproteins do specifically bind thyroid hormones with medium affinity [3-5]. Such a hormone interaction may serve several biological functions [4]. Studies of apo A-I and apo E have shown that the location is N-terminal and that it coincides with the respective exon 3-coded region of both apolipoproteins. Sequences of particular relevance to this hormone-binding function are those having the predicted secondary structure of a ß-sheet (amino acids 32 to 44 in apo E and amino acids 9 to 23, 28 to 33, and 43 to 47 in apo A-I). By contrast, the secondary structure of the lipid-binding region is the amphipathic -helix in the form of a 22-mer repeating unit. This location of the hormone site of apolipoproteins is supported by the recent finding that the exon 3-coded regions not only of apo A-I and apo E but also of the other apolipoproteins of the high-density lipoproteins share sequence homology with the regions of the three major thyroid hormone plasma transport proteins (thyroid-binding globulin, transthyretin, and albumin) known or postulated to contain the respective thyroid hormone sites [5]. The N-terminal position of the thyroid hormone site explains why the amino acid mutations at position 112 (apo E4) or 158 (E2) leave intact the thyroid hormone-binding property.

It can be concluded that the domain constituted by the first 160 to 210 residues is composed of three subdomains: the hormone-binding subdomain (approximately the first 61 amino acids), the apo B-E receptor-binding subdomain (approximately amino acids 130 to 160) and a lipid-binding subdomain between them. It seems more logical (and more justified on genetic grounds), however, to consider apo E (and the other high-density lipoprotein apolipoproteins) as comprising two distinct domains: the exon 3-coded domain and the exon-4 coded domain. The first represents the thyroid hormone-binding domain, and the second consists of the lipid-binding domain (amino acids 62 to 299 in apo E). In apo E, however, this domain evolved to contain a specialized region that interacts with the apo B-E receptor and that can be viewed as a subdomain separating two flanking lipid-binding subdomains.