Variation at the apolipoprotein E locus on chromosome 19 plays a role in more cases of Alzheimer's disease than does any other identified genetic determinant. We have previously reported the isoform-specific interaction of native human apolipoprotein E (APOE, gene; apoE, protein) epsilon 3 with the amyloid-ss peptide, Ass(1-40), the major component of the cerebral amyloid deposits that appear to cause Alzheimer's disease.In order to investigate the apoE: A beta interaction further, a modified assay was developed based on co-immunoprecipitation of the complex using an anti-apoE antibody (anti-apoE IP assay).Application of this assay demonstrated that the interaction of Ass(1-40) and apoE can be distinguished into two types: sodium dodecyl sulfate (SDS) -resistant and SDS-releasable. The SDS-resistant interaction between epsilon;3 and Ass(1-40) is apparently maximal at an Ass(1-40) concentration of approximately 75 micro M, and an Ass(1-40) /epsilon 3 molar ratio of about 250:1. The major apoE-isoform-specific difference in interaction with Ass(1-40) is the ability of Ass(1-40) to form SDS- resistant complexes with epsilon 3 but not with epsilon 4. Using the anti-apoE co-IP assay, we found that human cerebrospinal fluid (CSF) epsilon 3 can also form an SDS-resistant complex with Ass(1-40) but human CSF epsilon;4 cannot. However, when compared with apoE epsilon;3 collected from the conditioned medium of APOE epsilon 3-transfected cells, the competence of equal concentrations of CSF apoE epsilon 3 to form SDS-resistant complexes with Ass(1-40) is apparently diminished. A 1:1 mixture of CSF plus apoE epsilon 3-containing conditioned medium is associated with diminished Ass(1-40) /epsilon;3 complex formation to a greater extent than that observed when an identical volume of phosphate-buffered saline is added to apoE epsilon;3 medium.These results suggest the presence in CSF of factors that interfere with the formation of complexes between synthetic Ass(1-40) and apoE epsilon 3.