The association of apolipoprotein B-100 (apoB-100) containing lipoproteins, low-density lipoproteins (LDL), very low density lipoproteins (VLDL) and lipoprotein(a) [Lp(a)] with chondroitin sulfate-rich proteoglycans (CSPG) of the arterial intima appears to contribute significantly to lipoprotein disposition during atherogenesis. Using frontal elution analysis and competition experiments, we have previously suggested that the apoB-100 segment RLTRKRGLK (3359-3367) is a mediator of the association between LDL and arterial CSPG. Here, with direct binding measurements and fluorescence titrations, we evaluated the effect of the lipid environment on the affinity of the above apoB-100 segment for chondrotin 6-sulfate (C6S). We synthesized a secondary model peptide with hydrophobic tails which allowed its binding to lipid vesicles and lipoproteins (VVWRLTRKRGLKVVV). When associated with lipid vesicles, this peptide showed a higher affinity (KD = 3.9 microM) for C6S than the free peptide (KD = 18.7 microM). However, the affinity was still lower than that of LDL (KD = 0.21 microM). The increase in affinity for the peptide after association with lipid vesicles indicates that the secondary structure induced by its association with lipid vesicles is a significant modulator of the affinity for glycosaminoglycans. When bound to LDL and VLDL subfractions, VVWRLTRKRGLKVVV increased the affinity of the lipoproteins for C6S. The results suggest that, with the proper secondary structure induced by the lipid environment, the segment RLTRKRRGLK of apoB-100 is an important determinant of the association of LDL and VLDL with glycosaminoglycans but that probably other basic segments contribute to this interaction.