Cholesterol-wrapping lipoprotein gets a closer look

Despite decades of study, a pharmacopoeia of medicines, and untold millions in pharmaceutical research, heart disease remains the leading cause of death around the world. Excess cholesterol in low-density lipoproteins (LDL) is one of the strongest biomarkers for heart disease, but researchers have struggled to pin down the structure of apolipoprotein B100 (ApoB100), the protein component of LDL particles. In a recent pair of papers in Nature, two teams of structural biologists report high-resolution structures of ApoB100 (2024, DOIs: 10.1038/s41586-024-08467-w and 10.1038/s41586-024-08223-0). One structure shows how the protein wraps around the surface of LDL like a belt, with prongs extending into the lipid core. The other reveals that ApoB100 makes multiple contacts with the LDL receptor (LDLR) and may help explain why certain gene variants cause high cholesterol levels.

ApoB100 is a key protein in normal metabolism and in heart disease. Beginning before the protein’s synthesis is completed, it collects cholesterol and fats into particles that allow these hydrophobic molecules to circulate in plasma. When ApoB100 binds to LDLR, which is the target of cholesterol-lowering statin drugs, its fatty cargo can be delivered into cells. If they’re not absorbed, LDL particles can accumulate to harmful effect in artery walls.

ApoB100 has evaded structural characterization until now. At 550 kDa, it is one of the largest human proteins, and its structure depends on its interaction with lipids, which are tough to resolve using most structural biology approaches. In addition, LDL particles range in diameter from about 20 nm to 100 nm, meaning ApoB100 can adopt a lot of conformations.

To get around these problems, a two-person research team at the University of Missouri solved the structure of ApoB100 in the very smallest LDL particles. Soon after starting his laboratory, Zachary Berndsen collected cryoelectron micrographs of hundreds of thousands of LDL particles. Berndsen handed the data off to Keith Cassidy, another new professor, who focuses on simulation. “AlphaFold frankly can’t account for the lack of a lipid particle,” Cassidy says; given the peptide sequence of ApoB100 without the lipids it binds, the program tends to predict a protein collapsed in on itself like a crumpled piece of paper. But by using Berndsen’s electron density maps to guide molecular dynamics simulations, Cassidy could resolve the protein’s structure, including a β-sheet that wraps around the outside of the particle like a sash and prongs that extend deep into the lipid core.

Another group, led by Joseph Marcotrigiano and Alan Remaley at the US National Institutes of Health (NIH), describes the cryoEM structure of a complex of ApoB100 bound to LDLR, which was stabilized with a nanobody reagent they added. Surprisingly, the NIH team found two points of contact between ApoB100 and LDLR. This finding might help explain why gene variants linked to familial hypercholesterolemia can disrupt the ApoB100-LDLR interaction, even though the mutations map to distant points on each protein’s surface.

Increased structural insight into ApoB100 could be useful for future drug developers, says Berndsen. “The first step to rational drug design is to have a structure.”

Jan Nilsson is a professor at Lund University and founder and chief scientific officer of the biotech company Abcentra, which is developing drugs to target oxidized ApoB100. Nilsson says the studies are extremely important and will certainly change the field. But, he adds, “we have so many affordable and effective cholesterol-lowering drugs already” that it may be challenging for new antibody-based therapies to compete.