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Tertiary structure of apolipoprotein A-I in nascent high-density lipoproteins

Significance High-density lipoprotein (HDL), popularly known as “good cholesterol,” is an assembly of lipids and proteins that is protective against cardiovascular diseases. HDL begins to develop when two copies of the protein apolipoprotein A-I (APOA1) mediate the removal of excess lipids from peripheral cells and form a nanodisc. How the proteins adjust their structures as the nanodisc increases in diameter, mediates the conversion of cholesterol to cholesteryl esters, and becomes spherical is crucial to understanding HDL maturation and relevant pathologies. This study combines multimicrosecond atomistic molecular dynamics simulations, molecular modeling, and cross-linking experiments to reveal APOA1 structure in two nascent HDLs. The structures provide a mechanistic understanding for HDL maturation and revise previous models of nascent HDL. Understanding the function of high-density lipoprotein (HDL) requires detailed knowledge of the structure of its primary protein, apolipoprotein A-I (APOA1). However, APOA1 flexibility and HDL heterogeneity have confounded decades of efforts to determine high-resolution structures and consistent models. Here, molecular dynamics simulations totaling 30 μs on two nascent HDLs, each with 2 APOA1 and either 160 phospholipids and 24 cholesterols or 200 phospholipids and 20 cholesterols, show that residues 1–21 of the N-terminal domains of APOA1 interact via strong salt bridges. Residues 26–43 of one APOA1 in the smaller particle form a hinge on the disc edge, which displaces the C-terminal domain of the other APOA1 to the phospholipid surface. The proposed structures are supported by chemical cross-linking, Rosetta modeling of the N-terminal domain, and analysis of the lipid-free ∆185APOA1 crystal structure. These structures provide a framework for understanding HDL maturation and revise all previous models of nascent HDL.