To identify residues and segments in the central region of apolipoprotein A-I (apoA-I) that are important for the protein structure and stability, we studied the effects of four double charge ablations, D102A/D103A, E110A/E111A, R116V/K118A, and R160V/H162A, and two deletion mutations, Δ(61-78) and Δ(121-142), on the conformation and stability of apoA-I in the lipid-free state and in reconstituted discoidal phospholipid:cholesterol:apoA-I particles (rHDL). The findings suggest that D102/D103 and E110/E111 located in helix 4, and segment(s) between residues 61 and 78 are involved in maintenance of the conformation and stability of apoA-I in both the lipid-free state and in rHDL. R116/K118 located in helix 4 are essential for the conformation and stabilization of apoA-I in rHDL, but not vital for the lipid-free state of the protein. The R160V/H162A substitutions in helix 6 lead to a less compact tertiary structure of lipid-free apoA-I without notable effects on the lipid-free or lipid-bound secondary conformation suggesting involvement of R160/H162 in important inter-helical interactions. The results on the Δ(121-142) mutant, together with our earlier findings, suggest disordered structure of a major segment between residues 121 and 143, likely including residues 131-143, in lipid-free apoA-I. Our findings provide the first experimental evidence for stabilization of rHDL by electrostatic inter-helical interactions, in agreement with the double belt model. The effects of alterations in the conformation and stability of the apoA-I mutants on in vitro and in vivo functions of apoA-I and lipid homeostasis are discussed.Apolipoprotein A-I (apoA-I) is the major protein component of high density lipoprotein (HDL) that plays a key role in the biogenesis and atheroprotective functions of HDL and in reverse cholesterol transport (1-3). Lipid-free apoA-I secreted by cells can interact functionally with ATP binding cassette transporter 1 (ABCA1) to promote efflux of cholesterol and phospholipids from cells. This process leads to the lipidation of apoA-I and formation of discoidal HDL (4,5). ApoA-I in discoidal HDL activates the enzyme lecithin:cholesterol acyltransferase (LCAT) converting cholesterol to cholesterol ester and thereby promoting the maturation of HDL particles from discoidal to spherical. ApoA-I bound to discoidal and spherical HDL also interacts functionally with scavenger receptor class B type I (SR-BI) (4, 6,7). On binding HDL, SR-BI mediates selective uptake of cholesterol esters and other lipids χ This work was supported by PO1HL 26335 and grant HL 48739 from the National Institute of Heath *To whom correspondence should be addressed at Department of Physiology and Biophysics, Boston University School of Medicine, 715 Albany Street, W-322, Boston, MA 02118. Fax: (617) from HDL by cells and net efflux of excess cholesterol (4,6). In the course of apoA-I metabolism, the protein function is modulated by alterations in its structure and stability (5,(8)(9)(10)(11)(12)(13)(14)(15). Therefore, detail...