The ability of apolipoprotein E (apoE) to bind to cell-surface glycosaminoglycans (GAG) is important for lipoprotein remnant catabolism. Using surface plasmon resonance, we previously showed that the binding of apoE to heparin is a two-step process; the initial binding involves fast electrostatic interaction, followed by a slower hydrophobic interaction. Here we examined the contributions of the N-and C-terminal domains to each step of the binding of apoE isoforms to heparan sulfate (HS) and dermatan sulfate (DS). ApoE3 bound to less sulfated HS and DS with a decreased favorable free energy of binding in the first step compared to heparin, indicating that the degree of sulfation has a major effect on the electrostatic interaction of GAG with apoE. Mutation of a key Lys residue in the N-terminal heparin binding site of apoE significantly affected this electrostatic interaction. Progressive truncation of the C-terminal α-helical regions which favors the monomeric form of apoE3 greatly reduced the binding ability of apoE3 to HS, with much reduced favorable free energy of binding of the first step, suggesting that the C-terminal domain contributes to the GAG binding of apoE by the oligomerization effect. Supporting this, dimerization of the apoE3 N-terminal fragment via disulfide linkage restored the electrostatic interaction of apoE with HS. Significantly, apoE4 showed much greater binding to HS and DS than apoE2 or apoE3 in both lipidfree and lipidated states, perhaps resulting from enhanced electrostatic interaction through the Nterminal domain. This isoform difference in GAG binding of apoE may be physiologically significant such as in the retention of apoE-containing lipoproteins in the arterial wall.Heparan sulfate proteoglycan (HSPG) is a common constituent of cell surfaces and the extracellular matrix, and is involved in a wide range of biological functions (1). Normal uptake and catabolism of atherogenic lipoproteins is mediated by the interaction of lipoproteins with