Lysine (Lys) residues in apolipoprotein (apo) E are known to be involved in binding of apoE-containing lipoproteins to the low density lipoprotein (LDL) receptor. To examine the microenvironments of the Lys residues of apoE-3 in a variety of lipid-associated states, we have used a high resolution 13C-NMR method in which Lys were reductively methylated with [13C] formaldehyde. Over a wide pH range, the spectrum of apoE in canine HDLc, a spherical lipoprotein particle, exhibited two peaks from Lys epsilon-amino groups. The two pools of Lys in HDLc titrate with pK alpha values of 10.4 ("normal") and 9.3 ("active"). In contrast, eight epsilon-[13CH3]2Lys peaks (delta = 42.5-44.5 parts/million) with pK alpha values ranging from 8.2 to 10.1 and 7.8 to 10.5 were observed at pH 9.5 for human and canine apoE, respectively, in discoidal complexes with dimyristoyl glycerophosphocholine. A single Lys microenvironment was observed for apoE present in a disordered, lipid-free, state in 8 M urea, confirming the fact that the lipid environment is modulating the conformation of apoE. The above data demonstrate that the conformation of apoE, as reflected by the Lys microenvironments, on spherical HDLc particles is different from that on discoidal complexes.