Molecule of the Month: Nanodiscs and HDL

We're in the middle of a revolution in structural biology, and nanodiscs are playing a supporting role. New developments in cryoelectron microscopy are allowing researchers to determine structures of molecular machines much larger and more complex than ever before. This includes the trickiest class of molecular machines, membrane-bound proteins, which are difficult to study because they need to be protected in a lipid environment. This is where nanodiscs are proving to be useful. They are composed of a tiny disc of lipids, just big enough to hold one copy of a membrane-protein of interest, surrounded by a stabilizing belt of proteins.

Nanodiscs were engineered by looking to nature for inspiration. Cholesterol and other lipids are transported through our blood in small globules, surrounded and shaped by dedicated proteins called apolipoproteins. One particular class of these globules is termed "high-density lipoproteins" or “HDL”, since they contain a large percentage of protein and are denser than more lipid-rich varieties of lipoprotein particles. HDL particles are often termed "good cholesterol," since they are intimately involved with the transport of excess cholesterol to the liver, where it is removed from the blood stream. HDL has also been good for science, since one form of HDL has a disc-like shape that was the inspiration for engineering nanodiscs.

If you search for nanodisc structures in the PDB archive, you'll find dozens of different examples. However, very few of them include coordinates for the actual nanodisc. That's because the lipids are very mobile, and researchers typically focus their attention on the protein, causing the surrounding lipids to blur out in the cryoEM map. The enormous structure shown here, which includes a ribosome secreting a newly-synthesized protein chain through the protein export channel SecYE, is an exception (PDB entry 4v6m). The researchers used cryoelectron microscopy combined with molecular dynamics simulations to generate a structural model of the whole complex, including the nanodisc and its constituent lipids.

Since nanodiscs are small and soluble in water, they have also been a boon for structural biologists who use NMR to study proteins. The structure shown here (PDB entry 6clz) is the membrane-binding domain of MT1-MMP (membrane type 1 matrix metalloproteinase), a collagen-cutting enzyme that is needed to allow cells to migrate through existing extracellular matrix when new blood vessels are being built. This protein is also a target to fight cancer, since metastatic tumor cells often use this enzyme to spread. The structure allowed the researchers to explore two binding modes of the domain and their possible roles in regulating the action of the enzyme.