What are nanodiscs - the basics

The term nanodiscs describes a small (7-50 nm in diameter) disc-shaped structure that finds use in proteomics and biomedicine. It consists of two main components:
  1. Phospholipids, either of the artificial origin or from the cell membrane
  2. stabilizing belt that holds the phospholipids together. This is either an MSP protein or a synthetic polymer.
MSPNanodisc ImageSchematic depiction of a nanodisc stabilizing a membrane protein.
Green: The stabilizing belt - A MSP protein in this case
Grey: phospholipids
Orange: Stabilized membrane protein

The purpose of nanodiscs

Their aim is to mimic the native phospholipid bilayer of cells for target molecules (often membrane proteins). Membrane proteins are the key to communication between cells. They mediate fundamental biological processes such as signal transduction, transport processes across membranes, sensing of chemical signals, and coordination of cell-cell interactions.
Numerous diseases in humans are linked to membrane proteins, making them important targets for drug development. So it seems surprising, that membrane proteins are encoded by up to ∼23% of genes but represent <1 % of known protein structures (1).

stabilisation of membrane proteins with nanodiscFigure 1: Membrane proteins have hydrophobic and hydrophilic parts. Nanodiscs make them soluble in aqueous solutions.
The problem is, that membrane proteins, unlike soluble proteins, are difficult to analyze in their native environment, due to their insertion in the lipid membrane. Surfaces of membrane proteins in the hydrophobic core of the lipid bilayer are also hydrophobic, whereas surface areas in contact with the aqueous membrane environment are as hydrophilic as the surfaces of ordinary soluble proteins (2). The presence of extensive hydrophobic and hydrophilic surfaces on the same molecule is characteristic of membrane proteins. As a result, membrane proteins are not soluble in standard aqueous buffers without a solubilizing agent. For example, nanodiscs are required to solubilize them to mimic the amphipathic environment of a lipid bilayer whilst maintaining the structure of the membrane protein in a physiologically relevant state.

Watch our "The purpose of nanodiscs" video guide, for an animated summary of this chapter.


Two types of nanodisc

MSP and synthetic nanodiscs comparedFigure 2: Two types of nanodiscs exist: Synthetic nanodiscs (blue stabilizer) and MSP nanodiscs (green stabilizer)

As mentioned before nanodiscs can be differentiated between their phospholipid composition and most importantly, their type of stabilizer. This stabilizer is the reason why nanodiscs in total are split into two main categories: MSP nanodiscs and Synthetic nanodiscs.
The respective names originate from the type of stabilizer that is used to keep the nanodiscs together and form them in the first place. It also decides what the lipid composition of the nanodisc is made up of. MSP nanodiscs always contain an artificial lipid composition. Meaning you have full control of it. In contrast: Synthetic nanodiscs use the native cell phospholipids to create the nanodisc. A direct comparison of the individual advantages of both nanodiscs can be found here.

Table 1: Small comparison between MSP and Synthetic nanodiscs
  Synthetic NanodiscMembrane scaffold protein (MSP) Nanodisc
Belt properties / Stabilizer synthetic polymers (e.g. DIBMA, SMA) MSP proteins
Lipids Native cell membrane lipids Artificial phospholipid environments (e.g. phospholipids)
Examples Diisobutylene-maleic acid (DIBMA), styrene-maleic acid (SMA), amphipols Pre-Assembled nanodiscs
But first, let us introduce both kinds of nanodiscs on their own, starting with the MSP nanodiscs.

MSP nanodiscs

MSP nanodiscs
Figure 3: Schematic depition of a MSP nanodisc. Similar to figure 1.
MSP nanodiscs are held together by membrane scaffold proteins (MSPs). MSPs can be truncated forms of apolipoprotein (apo) A-I which wrap around a patch of a lipid bilayer to form a disc-like particle or nanodisc (5). MSPs provide a hydrophobic surface facing the hydrophobic tail of the lipids, and a hydrophilic surface on the outside. This setup makes nanodiscs highly soluble in aqueous solutions. Once assembled into nanodiscs, membrane proteins can be kept in solution in the absence of detergents (5).

Size: The size of an MSP nanodisc can range between 7 - 17 nm. It is determined by the used membrane scaffolding protein. Table 2 depicts the membrane scaffold proteins that Cube Biotech offers and which nanodisc sizes it leads to. MSP nanodiscs of the same MSP protein are uniform in size and only differ +/- 1 nm in diameter. This suits them perfectly for Cryo-EM studies.

Table 2: Overview of MSP proteins and the resulting nanodisc sizes.
MSP typeSize (diameter in nm)Ref
MSP1D1ΔH5 8.2 (+/- 0.6) (5)
MSP1D1 9.5 (+/- 1.1) (5)
MSP1E3D1 13 (+/-1) (15)
MSP2N2 17 (+/-1) (21)
Other advantages of MSP nanodiscs
MSP nanodiscs have a number of advantages compared to other systems for membrane protein solubilization and reconstitution, in particular for ligand binding studies, analysis of conformational dynamics, and protein interaction studies (6). Nanodiscs can be used to reconstitute membrane proteins such as GPCRs or transporters in an artificial environment resembling the native membrane.
These nanodisc-stabilized proteins can be directly purified by standard chromatographic procedures. The resulting purified membrane protein-nanodisc complex can be used in applications that require access to both the physiologically intracellular and extracellular surfaces of the protein and thus allows unrestricted access to antagonists, agonists, G proteins, and other interaction partners (7).

How to generate MSP nanodisc + protein - complexes

2 ways for nanodisc assemblyFigure 4: Schematic image of two ways to reconstitute proteins into nanodiscs. A: Assembled nanodiscs are added to a cell-free reaction. The nascent protein can insert spontaneously. B: Detergent and MSP are added to cells expressing the protein of interest. A complex of membrane phospholipids, proteins, and MSP forms.
A: Combining nanodiscs and cell-free expression systems
Starting from an expression plasmid, membrane proteins can be produced in cell-free systems. Pre-assembled nanodiscs are supplied in the mixture that integrate the nascent membrane protein (8). The addition of detergents is not required, which minimizes possible artifacts. Optionally, modifications such as biotinylation or isotope labeling can be included.
B: Two-step reconstitution of detergent-solubilized proteins
Starting from a purified membrane protein in suitable detergent, membrane scaffold proteins and phospholipids are added. Nanodiscs containing the membrane protein form spontaneously, and can be purified by affinity or size exclusion chromatography (6, 7).
C: Direct solubilization from membranes
Starting from membranes expressing the protein of interest, detergent and membrane scaffold protein are added. Membrane phospholipids, membrane protein, and MSP assemble to form the nanodisc complex (5). Here, a mixture of nanodisc complexes representing the membrane protein population is obtained, which may be used for proteomics studies. If required, individual membrane protein-nanodisc complexes can be purified by affinity chromatography. Compared to method B, exposure time to detergents is significantly shorter (hours vs. days).

Choice of phospholipids - the key to proper protein activity

As already mentioned the phospholipids composition of an MSP nanodisc is artificial. Meaning the used phospholipids that should make up the artificial membrane environment for the membrane protein of interest must be decided before. But there are numerous phospholipids to choose from out there, so which to choose?

Refer to this list of our most commonly used phospholipids for MSP nanodiscs, when faced with this question.

Dimyristoyl-glycero-phosphocholine (DMPC) DMPC phospholipid structure

Palmitoyl-oleoyl-phosphatidylcholine (POPC) POPC phospholipid structure

Phosphatidylglycerol (DMPG) DMPG phospholipid structure
This selection, but also many other phospholipids have been successfully used alone or in combination (8,25). The choice of lipids has been shown to be crucial for protein activity (8), for example in cases where lipids promote protein oligomerization (25). Cell-free expression using assembled nanodiscs is a fast and easy way to screen a variety of lipids and lipid mixtures for their effect on the protein. When proteins are solubilized directly from the membrane fraction, endogenous phospholipids are carried along and incorporated into the nanodisc complex, which may enhance protein activity.

Examples of MSP nanodisc applications in science

MSP Nanodiscs were first described by Sligar and coworkers (3,4). They provide the perfect environment to stabilize membrane proteins to study the binding of ligands, agonists, or antagonists by methods such as NMR and SPR (9,10). Nanodiscs were shown to increase the resolution of membrane-spanning protein regions in Cryo-EM (22,26). Membrane scaffold proteins can be tagged with histidines to facilitate purification, detection, and immobilization of the protein-nanodisc complex. Other nanodisc applications include resonance Raman (11), MALDI (13), non-covalent mass spectrometry (25), protein activation studies (14), time-resolved fluorescence spectroscopy (15), and protein crystallization (24). Antigens reconstituted into nanodiscs have been used to raise immunogenic responses in mice, showing their potential to be used as vaccines (16). In addition, the entire membrane proteome of E.coli was reconstituted into nanodiscs, thereby creating a solubilized membrane protein library (15). Proteins reconstituted in nanodiscs can be transferred to bicelles to improve NMR resolution (23). Even soluble, lipid-interacting proteins were analyzed with the help of nanodiscs (20). Table 3 lists examples for nanodisc applications.
Table 3: Publications that include MSP proteins:

Synthetic nanodiscs

SMALP ImageFigure 5: Schematic depiction of a synthetic nanodisc that stabilizes a hypothetical membrane protein. The figure legend mentions SMA as the used stabilizing polymer, but e.g. DIBMA could fill this role as well.
Synthetic nanodiscs are the second big option in the field of nanodisc. They differ in certain key aspects from their MSP counterparts, but also share certain similarities.

Creation of Synthetic nanodiscs
In contrast to the three creation ways of MSP nanodiscs (figure 4), synthetic nanodiscs can only be created directly from intact cells. The used synthetic polymer has a dual function during this process. First, it dissolves the cell membrane, similar to a detergent. Then it forms a nanodisc structure around membrane proteins using the native cell phospholipids. A good analogy to this process is a cookie cutter that stamps the cookies out of the dough.

Synthetic nanodiscs are variable in their size. The main factor that decides their diameter is the size of the membrane protein complex that they surround and stabilize. Therefore a definitive size cannot be given for a synthetic nanodisc. But they all range in the size range that can also be found in MSP nanodiscs (table 2). This applies to all established polymers so far. If uniformous nanodisc size is desired for a synthetic nanodiscs complex, a size-exclusion chromatography (SEC) has to be performed after the stabilized membrane protein of interest has been purified by e. g. affinity chromatography with the Rho1D4-tag.
Which polymer?
SMA and DIBMA comparisonFigure 6: DIBMA and SMA seem to be interchangeable in the first view, but there are some differences.
The selection of different polymers for synthetic nanodiscs is constantly growing. Each with its own benefits and downsides. DIBMA for example has protein-like absorption at a wavelength of 280 nm. Meanwhile, AASTY has quite fixed nanodiscs diameters compared to other polymers.

However, this is only a small extract from a long list of pros and cons of the different polymers. We dedicated this topic its own webpage. Have a look at it!
More in-depth information regarding the different polymers for synthetic nanodiscs can be found here:

MSP or Synthetic nanodiscs?

So after all of this, the question remains what type of nanodisc best suits your project? Both MSP and synthetic nanodiscs are meant for the solubilization & stabilization of membrane proteins by mimicking a cell-membrane environment. However, as mentioned before, there are some key differences between the two. Table 4 lists all differences and their respective advantages & disadvantages.

Table 4: Direct comparison between MSP and Synthetic nanodiscs.
MSP nanodiscsSynthetic nanodiscs

Depending on the used MSP protein. Uniformous (+/-1 nm) for each MSP protein)

Advantage: Uniformous sizes make MSP nanodiscs perfect tools for applications like Cryo-EM.

Variable, due to different lengths of the polymer chains.

Advantage: The variability of the diameter skips screening steps that are necessary when working with MSP nanodiscs.
Lipid composition

Artificial. Provided by the scientist.

Advantage: The scientist has complete control over the phospholipid composition.
Lipid composition

Made up of native cell membrane lipids.

Advantage: The membrane protein is stabilized in a part of its native environment.
UV absorption

Overlaps with membrane protein due to the presence of the MSP proteins.

Note: Due to the MSP proteins, the nanodisc itself has a UV signal at a wavelength of 280 nm and interferes with protein quantification attempts via absorbance.
UV absorption

SMA behaves like MSP nanodiscs, but DIBMA-based nanodiscs do not absorb at wavelengths of 280 nm.

Advantage: With DIBMA-based nanodiscs, the protein quantity can easily be determined by measuring the absorbance of the solution at a wavelength of 280 nm.

Able to be created in 3 different ways (see figure 4).

Advantage: The different situations in which MSP nanodiscs can stabilize membrane proteins make them the go-to option often.

Only directly from the cell.

Note: Since the synthetic polymers use native cell membrane material to create the nanodiscs, only membrane proteins from living cell material can be stabilized.
Involvement of detergents

Involved in the beginning before the MSP protein form the nanodisc around the protein of interest.

Note: A detergent has to be chosen that does not impact the folded protein's structure. This can result in some extra work.
Involvement of detergents

No detergent necessary.

Advantage: The polymers both act as solubilizers and stabilizers simultaneously. Therefore no additional detergents are needed.

Literature references
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MSP Nanodiscs are protected by US Patents 7,691,414; 7,662,410; 7,622,437; 7,592,008; 7,575,763; 7,083,958; 7,048,949