Differential trypsin-accessibility and monoclonal antibodies (Mabs) to human apolipoprotein (apo) B-1 00 are both important tools for probing apoB structure and conformation on low-density lipoproteins (LDL). In this study, we have mapped > 80% of the C-terminal region (720 residues) of LDL apoB-100 using trypsin digestion.Our results extend our previous data Nature (Lond.) 323, confirming that the C-terminal region of about 420 residues of apoB-100 is largely inaccessible to trypsin, whereas the part just preceding this region has interspersed trypsin-accessible and inaccessible peptides. We have determined the amino acid sequence of specific apoB-100 peptides containing epitopes recognized by four separate Mabs: two epitopes have been mapped to within 20 residues, one has been mapped to 36 residues, and the last to 80 residues. We used polyclonal antisera to identify 16 overlapping clones of varying lengths of apoB-100 cDNAs extending from the C-terminus of apoB-100 cloned in the expression vector, Agtll . These clones were then tested against individual Mabs. By nucleotide sequence analysis of overlapping clones that show differential reactivities to different Mabs, we have mapped the individual epitopes of each Mab to within about 50 -150 amino acid residues predicted from the DNA sequences. Confirmation and further fine mapping were accomplished by competition for LDL binding using partially purified fusion proteins and chemically synthesized oligopeptides. Two epitopes (Mabs 7 and 22) were mapped to the C-terminal20 amino acids of apoB-100, one (Mab 16) to residues 4154-4189, and another (Mab 20) to residues 3926-4005. Mab 16 precipitates more than 80% of LDL particles. Mab 20 precipitates only denatured apoB but not native LDL apoB Mol. Zmmunol. 24, 4351. Mabs 7 and 22 are unique in that they precipitate LDL apoB modified by storage much better than freshly isolated LDLapoB. Although epitope expression and trypsin-accessibility represent two useful probes for the study of protein conformation, there was no obvious correlation between these two parameters when applied to LDL apoB for the antibodies we have examined Apolipoprotein (apo) B is the largest of the apolipoproteins. It is heterogeneous in size; apoB-100, a 512-kDa protein, is an obligatory component in very-low-density, intermediate-density, and low-density lipoproteins (LDL); apoB-48, a smaller protein of about 264 kDa, is present mainly on chylomicrons [l]. Because of the central role of apoB in lipid transport and in cholesterol homeostasis, it is important to understand the structure and conformation of apoB in the various classes of lipoprotein particles. The sequence analysis of cloned apoB-100 cDNAs has provided the complete primary sequence of the protein [2 -61. However, in order to understand fully the conformation of apoB-100 on the lipoprotein particles, additional molecular probes are needed to define the exposed vs the buried regions of the protein on these particles. One method is the trypsin digestion of apoB-I 00 on the lipop...