The plasma low-density lipoprotein (LDL) profile in coronary artery disease patients is characterized by a predominance of small, dense LDL. Small, dense LDL exhibit both high susceptibility to oxidation and low binding affinity for the LDL receptor, suggesting that these particles may be of elevated atherogenic potential. Here we examine whether the variation in biological function is due to differences in apo B-100 conformation that alter the interaction with the cellular LDL receptor. The microenvironments (pKa) of Lys residues in apo B-100 in small, dense, intermediate, and light human LDL subspecies have been compared by 13C NMR, and the net surface charge of these particles has been characterized. Relative to the total LDL fraction, small, dense, and light LDL subspecies have a decreased number of pKa 8.9 Lys, while intermediate density LDL has a consistently higher number of pKa 8.9 Lys. It follows that differences in protein conformation, as reflected in the Lys microenvironments, exist in the different LDL subspecies. Electrophoretic mobility measurements revealed that the light LDL subfractions exhibit a surface charge at pH 8.6 that is from -26 to -34e more negative than the intermediate density LDL subfraction. For the small, dense LDL particles the increments in negative charge range from -7 to -17e relative to the intermediate density LDL subfraction. These results suggest that differences in the conformation of apo B-100 and surface charge between LDL subspecies are major determinants of their catabolic fate. The lower number of pKa 8.9 Lys leads to a reduction in binding of small, dense, and light LDL to the cellular LDL receptor and prolongs their plasma residence time, thereby elevating the atherogenicity of these particles. These data support the proposal that the intermediate LDL subspecies constitute the optimal ligand for the LDL receptor among human LDL particle subpopulations.