Megalin is an endocytic lipoprotein receptor expressed widely throughout the body, ranging from the proximal tubule in the kidneys to the cochlea in the inner ear. Megalin is known to bind over 50 different ligands and is involved in protein clearance of the renal ultrafiltrate via endocytosis. The extracellular domain of megalin consists of several modular domains, of which the most abundant are the ligand binding complement type (CR) domains, that are divided into four clusters separated by YWTD -propeller domains. The broad ligand binding profile has associated megalin with the unwanted cellular uptake of aminoglycosides during
antibacterial treatment, which can lead to nephro- and ototoxic side-effects.
This thesis presents new insights into the structure-function relation of the megalin receptor. The interaction between megalin and several natural protein ligands as well as the aminoglycoside gentamicin was studied using NMR spectroscopy. The structure of the tenth CR domain from the human megalin receptor was solved using NMR spectroscopy and a HADDOCK model of the complex between this domain and gentamicin was determined. The structural complex showed that a Trp residue and three Asp residues from megalin were involved in binding, which utilizes the commonly found ligand binding motif. The details of the atomic resolutionmodel will aid the future design of effective megalin antagonists, however, since the common ligand binding motif of CR domains is used to bind gentamicin this may
not be a trivial task. Recently, structural data has provided direct proof that the -propeller domains from the lipoprotein receptor family actively engage in ligand binding. Previously,
these domains were thought to serve as ’spacer regions’ in the extracellular domain. By analyzing the structural data a number of simple ligand binding motifs were identified and an analysis of the distribution of these simple motifs in -propeller domains throughout the LRP family was performed in order to identify -propellers capable of ligand binding. The analysis showed that several -propeller domains have ligand binding motifs, indicating that other receptors from the family, including megalin, may bind ligands using their -propeller domains as well.