The C-terminal domain of apolipoprotein (apo) A-I plays an important role in lipid binding. ApoA-I Nichinan, a naturally occurring human apoA-I variant with a deletion of E235 located in the C-terminus, is associated with low high-density lipoprotein (HDL) cholesterolemia. In the present study, a series of variant peptides corresponding to residues 220-241 of human apoA-I were examined to clarify the influences of E235 deletion (DeltaE235) on the structure and lipid interaction of the C-terminal region. NMR studies demonstrated that in trifluoroethanol, apoA-I 220-241/DeltaE235 peptide forms the alpha-helical structure similar to wild-type (WT) peptide. Circular dichroism measurements revealed that the interaction with phospholipid vesicles induced structural changes from random coil to alpha-helix both in apoA-I 220-241 WT and E235A, a variant with a negative charge ablation, peptides. These peptides also showed abilities to form HDL-like particles through microsolubilization of phospholipid vesicles, indicating that the negative charge ablation in E235 has no effect on the lipid interaction. By contrast, neither lipid binding-induced alpha-helix formation nor microsolubilization of vesicles were observed in apoA-I 220-241/DeltaE235 and L230P, a helix-breaking variant, peptides. In addition, fluorescence measurements showed that tryptophan fluorescence intensity of apoA-I 220-241/F225W greatly increased upon lipid binding, while only a little increase was observed for the corresponding DeltaE235 variant. Taken together, these results suggest that the deletion of E235 causes defective lipid binding of apoA-I Nichinan because of the impaired helix-forming ability of the C-terminal residues.