Versatility in ligand recognition by LDL receptor family proteins: advances and frontiers

Abstract

Proteins of the low-density lipoprotein receptor family transport cholesterol-carrying particles into cells, clear protease-inhibitor complexes from the circulation, participate in biological signaling cascades, and even serve as viral receptors. These receptors utilize clusters of cysteine-rich LDL receptor type-A (LA) modules to bind many of their ligands. Recent structures show that these modules typically exhibit a characteristic binding mode to recognize their partners, relying primarily on electrostatic complementarity and avidity effects. The dominant contribution of electrostatic interactions with small interface areas in these complexes allows binding to be regulated by changes in pH via at least two distinct mechanisms. The structure of the subtilisin/kexin family protease PCSK9, a newly identified molecular partner of the LDLR also implicated in LDL-cholesterol homeostasis, also raises the possibility that the LDLR and its related family members may employ other strategies for pH-sensitive binding that have yet to be uncovered.

Figure 1

X-ray Structure of LA module five (LA5) from the LDL receptor [32] (PDB ID code 1AJJ). A. Ribbon representation. Side chains are superimposed on a gray ribbon trace of the module backbone, with the bound calcium ion illustrated as a red sphere. Cysteines and additional residues are labeled as reference points. B. Surface electrostatic potential. The negative surface potential (red) around the bound calcium ion is indicated with a black oval. Panel A reproduced from reference [33] with permission (www.annualreviews.org).

Figure 2

A. Overall structure of the LA3-4/RAP-D3 complex (PDB ID code 2FCW). The LA3-4 (red) and RAP-D3 (blue) polypeptide chains are illustrated as ribbons, and a transparent molecular surface of LA3-4 is shown in light gray. The calcium ions bound by LA3 and LA4 are shown as yellow spheres. Disulfide bonds in LA3-4 are rendered as sticks, with sulfur atoms colored orange. B. Interactions between LA4 and lysine 256 of RAP-D3 in the LA3-4/RAP-D3 structure. LA module backbone traces are illustrated as crimson ribbons, and interacting side chains (carbon: salmon, oxygen: red) are rendered as sticks. The RAP-D3 polypeptide backbone is shown as a blue ribbon, with the lysine side-chain (carbon: cyan, nitrogen: blue) in stick form. The calcium ions bound by LA3 (C) and LA4 (D) are shown as yellow spheres. Hydrogen bonds are shown as dashed black lines. Adapted from reference [13], and reproduced with permission (www.molecule.org).

Figure 3

Comparison of the LA4/RAP-D3 interface (A–D, gray) with other LA module interfaces. A. Comparison with the LA3/RAP-D3 interface (backbone: cyan ribbon). B. Comparison with the LDLR intramolecular interface [14] between LA4 and the YWTD β-propeller (backbone: magenta ribbon; PDB ID code:1N7D). C. Comparison with the LDLR intramolecular interface between LA5 and the YWTD β-propeller (backbone: orange ribbon). (D) Comparison with the interface between VLDLR repeat three and HRV2 [15] (backbone: green ribbon; PDB ID code: 1V9U).

Figure 4

A. Four helix bundle structure of the N-terminal domain of apoE in its lipid-free form (pdb ID code 1BZ4; [34]). Ribbons representing the four helices in the N-terminal domain are colored red (helix 1), blue (helix 2), green (helix 3) and yellow (helix 4), and ribbons of the connecting regions are colored gray. Side chains are illustrated as sticks, with K143 and K146, two lysines of the fourth helix implicated in receptor binding [35], explicitly indicated. B. Model of the α-helical hairpin conformation of apoE–DPPC HDL-like particles derived from X-ray diffraction studies. The residues implicated in receptor binding are located on helix 4 and R172 is in the cyan-colored region. Figure 4B adapted from page 450 of reference [36], and reproduced with permission (www.elsevier.com).

Figure 5

Structure of the PCSK9 protein after self-cleavage (PDB ID code 2P4E). A. Ribbon representation illustrating the three domains: prodomain (olive), catalytic domain (blue), and C-terminal domain (purple). The C-terminal end of the prodomain is occluding the catalytic site (black circle). B. Clustered histidines (labeled) lie on one face of the C-terminal domain, suggesting a potential role in enhancing the affinity of PCSK9 for the LDLR at endosomal pH [29,31].