To understand high-density lipoprotein (HDL) structure at the molecular level, the location and stability of α-helical segments in human apolipoprotein (apo) A-I in large (9.6 nm) and small (7.8 nm) discoidal HDL particles were determined by hydrogen-deuterium exchange (HX) and mass spectrometry methods. The measured HX kinetics of some 100 apoA-I peptides specify, at close to amino acid resolution, the structural condition of segments throughout the protein sequence and changes in structure and stability that occur on incorporation into lipoprotein particles. When incorporated into the large HDL particle, the nonhelical regions in lipid-free apoA-I (residues 45-53, 66-69, 116-146, and 179-236) change conformation from random coil to α-helix so that nearly the entire apoA-I molecule adopts helical structure (except for the terminal residues 1-6 and 237-243). The amphipathic α-helices have relatively low stability, in the range 3-5 kcalâmol, indicating high flexibility and dynamic unfolding and refolding in seconds or less. A segment encompassed by residues 125-158 exhibits bimodal HX labeling indicating co-existing helical and disordered loop conformations that interchange on a time scale of minutes. When incorporated around the edge of the smaller HDL particle, the increase in packing density of the two apoA-I molecules forces about 20% more residues out of direct contact with the phospholipid molecules to form disordered loops, and these are the same segments that form loops in the lipid-free state. The region of disc-associated apoA-I that binds the lecithin-cholesterol acyltransferase enzyme is well structured and not a protruding unstructured loop as reported by others.atherosclerosis | amphipathic α-helix | protein secondary structure T here is great interest in understanding the structure-function relationships of high-density lipoprotein (HDL) because of its important antiatherogenic properties. Because high-resolution structures of HDL microemulsion particles cannot be obtained by current X-ray crystallography and NMR methods, alternative biophysical approaches have been used to characterize various subspecies of HDL. Structural models that show the general lipid and protein organization in HDL particles are now available (for reviews, see refs. 1-6). To derive detailed understanding at the molecular level of how HDL functions in cholesterol transport (7) and in reducing the incidence of premature cardiovascular disease (8), higher-resolution structural information is required.Reconstituted discoidal HDL particles that are models of nascent HDL (9) created by the interaction of apolipoprotein (apo) A-I (3, 10), the principal protein of HDL, with the cellsurface ATP binding cassette transporter (ABCA1) (11, 12) have received a great deal of attention. A major advantage of model particles is the possibility of obtaining preparations that are sufficiently homogeneous for detailed structural investigation. The structure of a discoidal HDL particle (approximately 10 nm hydrodynamic diameter) comprising a 16...