Familial defective apoB-100 is a genetic mutation that is characterized by abnormal low density lipoprotein (LDL) and moderate hypercholesterolemia. Heterozygotes for this disorder possess two populations of LDL. One has normal receptor binding, and the other, which can be isolated by monoclonal antibody 19 immunoaffinity chromatography, has almost no binding activity. The mutation that disrupts binding is a Gln for Arg substitution of apoB-100 residue 3500. NMR spectra of LDL containing (13CH3)2Lys residues show that chemically modified Lys exist in two microenvironments. In normal human LDL, there are about 50 Lys with pK 8.9 and 170 Lys with pK 10.5; an upper limit of 10 pK 8.9 Lys may be particularly involved in binding to the LDL receptor. Examination of the mixture of normal LDL and mutant LDL from five patients shows that the latter have fewer pK 8.9 Lys. In purified defective LDL at least seven Lys are redistributed from the active to normal pool. The CD spectra of mutant and normal LDL are identical. Therefore, substitution of Gln for Arg at position 3500 induces a change in local conformation which disrupts the receptor-binding domain of apoB-100.