Nanodisc

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Schematic illustration of a MSP nanodisc with a 7-transmembrane protein embedded. Diameter is about 10 nm. Picture from Sligar Lab NanodiscWith7TMMembraneProtein.jpg
Schematic illustration of a MSP nanodisc with a 7-transmembrane protein embedded. Diameter is about 10 nm. Picture from Sligar Lab

A nanodisc is a synthetic model membrane system which assists in the study of membrane proteins. [1] Nanodiscs are discoidal proteins in which a lipid bilayer is surrounded by molecules that are amphipathic molecules including proteins, peptides, and synthetic polymers. [2] It is composed of a lipid bilayer of phospholipids with the hydrophobic edge screened by two amphipathic proteins. These proteins are called membrane scaffolding proteins (MSP) and align in double belt formation. [3] [4] [5] Nanodiscs are structurally very similar to discoidal high-density lipoproteins (HDL) and the MSPs are modified versions of apolipoprotein A1 (apoA1), the main constituent in HDL. Nanodiscs are useful in the study of membrane proteins because they can solubilise and stabilise membrane proteins [6] and represent a more native environment than liposomes, detergent micelles, bicelles and amphipols.

Contents

The art of making nanodiscs has progressed past using only the MSPs and lipids to make particles, leading to alternative strategies like peptide nanodiscs that use simpler proteins and synthetic nanodiscs that do not need any proteins for stabilization.

MSP nanodisc

The original nanodisc was produced by apoA1-derived MSPs from 2002. [3] The size and stability of these discs depend on the size of these proteins, which can be adjusted by truncation and fusion. In general, MSP1 proteins consist of one repeat, and MSP2s are double-sized. [7] [8]

Peptide nanodisc

In peptide nanodiscs, the lipid bilayer is screened by amphipathic peptides instead of two MSPs. Peptide nanodiscs are structurally similar to MSP nanodiscs and the peptides also align in a double belt. They can stabilise membrane proteins, [9] but have higher polydispersity and are structurally less stable than MSP nanodiscs. Recent studies, however, showed that dimerization [10] and polymerization [11] of the peptides make them more stable.

Synthetic/Native nanodisc

Another way to mimic the native lipid membrane are synthetic polymers. Styrene-maleic acid co-polymers (SMAs) [12] [13] called SMALPs or Lipodisq and Diisobutylene-maleic acid (DIBMA) [14] are such synthetic polymers (DIBMALPs). They can solubilize membrane proteins directly from cells or raw extract. They also have been used to study the lipid composition of several organisms. [15] [16] [17] It was discovered that all synthetic polymers which contained a styrene and maleic acid group can solubilize proteins. [18] These SMA nanoparticles have also been tested as possible drug delivery vehicle [19] and for the study of folding, post-translational modifications and lipid interactions of membrane proteins by native mass spectrometry. [20]

Related Research Articles

<span class="mw-page-title-main">Biological membrane</span> Enclosing or separating membrane in organisms acting as selective semi-permeable barrier

A biological membrane, biomembrane or cell membrane is a selectively permeable membrane that separates the interior of a cell from the external environment or creates intracellular compartments by serving as a boundary between one part of the cell and another. Biological membranes, in the form of eukaryotic cell membranes, consist of a phospholipid bilayer with embedded, integral and peripheral proteins used in communication and transportation of chemicals and ions. The bulk of lipids in a cell membrane provides a fluid matrix for proteins to rotate and laterally diffuse for physiological functioning. Proteins are adapted to high membrane fluidity environment of the lipid bilayer with the presence of an annular lipid shell, consisting of lipid molecules bound tightly to the surface of integral membrane proteins. The cell membranes are different from the isolating tissues formed by layers of cells, such as mucous membranes, basement membranes, and serous membranes.

<span class="mw-page-title-main">Phospholipid</span> Class of lipids

Phospholipids are a class of lipids whose molecule has a hydrophilic "head" containing a phosphate group and two hydrophobic "tails" derived from fatty acids, joined by an alcohol residue. Marine phospholipids typically have omega-3 fatty acids EPA and DHA integrated as part of the phospholipid molecule. The phosphate group can be modified with simple organic molecules such as choline, ethanolamine or serine.

<span class="mw-page-title-main">Pardaxin</span> Type of peptide

Pardaxin is a peptide produced by the Red Sea sole and the Pacific Peacock sole that is used as a shark repellent. It causes lysis of mammalian and bacterial cells, similar to melittin.

<span class="mw-page-title-main">Lipid bilayer</span> Membrane of two layers of lipid molecules

The lipid bilayer is a thin polar membrane made of two layers of lipid molecules. These membranes are flat sheets that form a continuous barrier around all cells. The cell membranes of almost all organisms and many viruses are made of a lipid bilayer, as are the nuclear membrane surrounding the cell nucleus, and membranes of the membrane-bound organelles in the cell. The lipid bilayer is the barrier that keeps ions, proteins and other molecules where they are needed and prevents them from diffusing into areas where they should not be. Lipid bilayers are ideally suited to this role, even though they are only a few nanometers in width, because they are impermeable to most water-soluble (hydrophilic) molecules. Bilayers are particularly impermeable to ions, which allows cells to regulate salt concentrations and pH by transporting ions across their membranes using proteins called ion pumps.

<span class="mw-page-title-main">Peripheral membrane protein</span> Membrane proteins that adhere temporarily to membranes with which they are associated

Peripheral membrane proteins, or extrinsic membrane proteins, are membrane proteins that adhere only temporarily to the biological membrane with which they are associated. These proteins attach to integral membrane proteins, or penetrate the peripheral regions of the lipid bilayer. The regulatory protein subunits of many ion channels and transmembrane receptors, for example, may be defined as peripheral membrane proteins. In contrast to integral membrane proteins, peripheral membrane proteins tend to collect in the water-soluble component, or fraction, of all the proteins extracted during a protein purification procedure. Proteins with GPI anchors are an exception to this rule and can have purification properties similar to those of integral membrane proteins.

<span class="mw-page-title-main">Liposome</span> Composite structures made of phospholipids and may contain small amounts of other molecules

A liposome is a small artificial vesicle, spherical in shape, having at least one lipid bilayer. Due to their hydrophobicity and/or hydrophilicity, biocompatibility, particle size and many other properties, liposomes can be used as drug delivery vehicles for administration of pharmaceutical drugs and nutrients, such as lipid nanoparticles in mRNA vaccines, and DNA vaccines. Liposomes can be prepared by disrupting biological membranes.

<span class="mw-page-title-main">Antimicrobial peptides</span> Class of peptides that have antimicrobial activity

Antimicrobial peptides (AMPs), also called host defence peptides (HDPs) are part of the innate immune response found among all classes of life. Fundamental differences exist between prokaryotic and eukaryotic cells that may represent targets for antimicrobial peptides. These peptides are potent, broad spectrum antimicrobials which demonstrate potential as novel therapeutic agents. Antimicrobial peptides have been demonstrated to kill Gram negative and Gram positive bacteria, enveloped viruses, fungi and even transformed or cancerous cells. Unlike the majority of conventional antibiotics it appears that antimicrobial peptides frequently destabilize biological membranes, can form transmembrane channels, and may also have the ability to enhance immunity by functioning as immunomodulators.

<span class="mw-page-title-main">Amphiphile</span> Chemical compound with both hydrophilic and lipophilic properties

In chemistry, an amphiphile, or amphipath, is a chemical compound possessing both hydrophilic and lipophilic properties. Such a compound is called amphiphilic or amphipathic. Amphiphilic compounds include surfactants and detergents. The phospholipid amphiphiles are the major structural component of cell membranes.

<span class="mw-page-title-main">Dipalmitoylphosphatidylcholine</span> Chemical compound

Dipalmitoylphosphatidylcholine (DPPC) is a phospholipid (and a lecithin) consisting of two C16 palmitic acid groups attached to a phosphatidylcholine head-group.

<span class="mw-page-title-main">Tyrocidine</span> Chemical compound

Tyrocidine is a mixture of cyclic decapeptides produced by the bacteria Brevibacillus brevis found in soil. It can be composed of 4 different amino acid sequences, giving tyrocidine A–D. Tyrocidine is the major constituent of tyrothricin, which also contains gramicidin. Tyrocidine was the first commercially available antibiotic, but has been found to be toxic toward human blood and reproductive cells. The function of tyrocidine within its host B. brevis is thought to be regulation of sporulation.

<span class="mw-page-title-main">Surfactin</span> Chemical compound

Surfactin is a cyclic lipopeptide, commonly used as an antibiotic for its capacity as a surfactant. It is an amphiphile capable of withstanding hydrophilic and hydrophobic environments. The Gram-positive bacterial species Bacillus subtilis produces surfactin for its antibiotic effects against competitors. Surfactin showcases antibacterial, antiviral, antifungal, and hemolytic effects.

Cell-penetrating peptides (CPPs) are short peptides that facilitate cellular intake and uptake of molecules ranging from nanosize particles to small chemical compounds to large fragments of DNA. The "cargo" is associated with the peptides either through chemical linkage via covalent bonds or through non-covalent interactions.

Orientations of Proteins in Membranes (OPM) database provides spatial positions of membrane protein structures with respect to the lipid bilayer. Positions of the proteins are calculated using an implicit solvation model of the lipid bilayer. The results of calculations were verified against experimental studies of spatial arrangement of transmembrane and peripheral proteins in membranes.

<span class="mw-page-title-main">Lipid bilayer fusion</span>

In membrane biology, fusion is the process by which two initially distinct lipid bilayers merge their hydrophobic cores, resulting in one interconnected structure. If this fusion proceeds completely through both leaflets of both bilayers, an aqueous bridge is formed and the internal contents of the two structures can mix. Alternatively, if only one leaflet from each bilayer is involved in the fusion process, the bilayers are said to be hemifused. In hemifusion, the lipid constituents of the outer leaflet of the two bilayers can mix, but the inner leaflets remain distinct. The aqueous contents enclosed by each bilayer also remain separated.

A model lipid bilayer is any bilayer assembled in vitro, as opposed to the bilayer of natural cell membranes or covering various sub-cellular structures like the nucleus. They are used to study the fundamental properties of biological membranes in a simplified and well-controlled environment, and increasingly in bottom-up synthetic biology for the construction of artificial cells. A model bilayer can be made with either synthetic or natural lipids. The simplest model systems contain only a single pure synthetic lipid. More physiologically relevant model bilayers can be made with mixtures of several synthetic or natural lipids.

Membrane curvature is the geometrical measure or characterization of the curvature of membranes. The membranes can be naturally occurring or man-made (synthetic). An example of naturally occurring membrane is the lipid bilayer of cells, also known as cellular membranes. Synthetic membranes can be obtained by preparing aqueous solutions of certain lipids. The lipids will then "aggregate" and form various phases and structures. According to the conditions and the chemical structures of the lipid, different phases will be observed. For instance, the lipid POPC tends to form lamellar vesicles in solution, whereas smaller lipids, such as detergents, will form micelles if the CMC was reached. There are five commonly proposed mechanisms by which membrane curvature is created, maintained, or controlled: lipid composition, shaped transmembrane proteins, protein motif insertion/BAR domains, protein scaffolding, and cytoskeleton scaffolding.

<span class="mw-page-title-main">WALP peptide</span> Class of peptides used for studying lipid membranes

WALP peptides are a class of synthesized, membrane-spanning α-helices composed of tryptophan (W), alanine (A), and leucine (L) amino acids. They are designed to study properties of proteins in lipid membranes such as orientation, extent of insertion, and hydrophobic mismatch.

<span class="mw-page-title-main">Cell membrane</span> Biological membrane that separates the interior of a cell from its outside environment

The cell membrane is a biological membrane that separates and protects the interior of a cell from the outside environment. The cell membrane consists of a lipid bilayer, made up of two layers of phospholipids with cholesterols interspersed between them, maintaining appropriate membrane fluidity at various temperatures. The membrane also contains membrane proteins, including integral proteins that span the membrane and serve as membrane transporters, and peripheral proteins that loosely attach to the outer (peripheral) side of the cell membrane, acting as enzymes to facilitate interaction with the cell's environment. Glycolipids embedded in the outer lipid layer serve a similar purpose.

Amphipols are a class of amphiphilic polymers designed to keep membrane proteins soluble in water without the need for detergents, which are traditionally used to this end but tend to be denaturing. Amphipols adsorb onto the hydrophobic transmembrane surface of membrane proteins thanks to their hydrophobic moieties and keep the complexes thus formed water-soluble thanks to the hydrophilic ones. Amphipol-trapped membrane proteins are, as a rule, much more stable than detergent-solubilized ones, which facilitates their study by most biochemical and biophysical approaches. Amphipols can be used to fold denatured membrane proteins to their native form and have proven particularly precious in the field of single-particle electron cryo-microscopy .The properties and uses of amphipols and other non-conventional surfactants are the subject of a book by Jean-Luc Popot.

<span class="mw-page-title-main">Amphipathic lipid packing sensor motifs</span>

AmphipathicLipid Packing Sensor (ALPS) motifs were first identified in 2005 in ARFGAP1 and have been reviewed.

References

  1. ↑ Liszewski K (1 October 2015). "Dissecting the Structure of Membrane Proteins". Genetic Engineering & Biotechnology News . 35 (17): 16–18, 21. doi:10.1089/gen.35.07.09. Nanodiscs are self-assembling nanoscale phospholipid bilayers that are stabilized using engineered membrane scaffold proteins.
  2. ↑ Anada, Chiharu; Ikeda, Keisuke; Egawa, Ayako; Fujiwara, Toshimichi; Nakao, Hiroyuki; Nakano, Minoru (April 2021). "Temperature- and composition-dependent conformational transitions of amphipathic peptide–phospholipid nanodiscs". Journal of Colloid and Interface Science. 588: 522–530. doi:10.1016/j.jcis.2020.12.090. ISSN   0021-9797. PMID   33429348.
  3. 1 2 Bayburt TH, Grinkova YV, Sligar SG (2002). "Self-Assembly of Discoidal Phospholipid Bilayer Nanoparticles with Membrane Scaffold Proteins". Nano Letters. 2 (8): 853–856. Bibcode:2002NanoL...2..853B. doi:10.1021/nl025623k.
  4. ↑ Bayburt TH, Sligar SG (May 2010). "Membrane protein assembly into Nanodiscs". FEBS Letters. 584 (9): 1721–7. doi:10.1016/j.febslet.2009.10.024. PMC   4758813 . PMID   19836392.
  5. ↑ Skar-Gislinge N, Simonsen JB, Mortensen K, Feidenhans'l R, Sligar SG, Lindberg Møller B, et al. (October 2010). "Elliptical structure of phospholipid bilayer nanodiscs encapsulated by scaffold proteins: casting the roles of the lipids and the protein". Journal of the American Chemical Society. 132 (39): 13713–22. doi:10.1021/ja1030613. PMC   4120756 . PMID   20828154.
  6. ↑ Denisov IG, Sligar SG (January 2011). "Cytochromes P450 in nanodiscs". Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics. 1814 (1): 223–9. doi:10.1016/j.bbapap.2010.05.017. PMC   2974961 . PMID   20685623.
  7. ↑ Denisov IG, Grinkova YV, Lazarides AA, Sligar SG (March 2004). "Directed self-assembly of monodisperse phospholipid bilayer Nanodiscs with controlled size". Journal of the American Chemical Society. 126 (11): 3477–87. doi:10.1021/ja0393574. PMID   15025475.
  8. ↑ Grinkova YV, Denisov IG, Sligar SG (November 2010). "Engineering extended membrane scaffold proteins for self-assembly of soluble nanoscale lipid bilayers". Protein Engineering, Design & Selection. 23 (11): 843–8. doi:10.1093/protein/gzq060. PMC   2953958 . PMID   20817758.
  9. ↑ Midtgaard SR, Pedersen MC, Kirkensgaard JJ, Sørensen KK, Mortensen K, Jensen KJ, Arleth L (February 2014). "Self-assembling peptides form nanodiscs that stabilize membrane proteins". Soft Matter. 10 (5): 738–52. doi:10.1039/c3sm51727f. PMID   24651399.
  10. ↑ Larsen AN, Sørensen KK, Johansen NT, Martel A, Kirkensgaard JJ, Jensen KJ, et al. (July 2016). "Dimeric peptides with three different linkers self-assemble with phospholipids to form peptide nanodiscs that stabilize membrane proteins". Soft Matter. 12 (27): 5937–49. Bibcode:2016SMat...12.5937L. doi: 10.1039/c6sm00495d . PMID   27306692.
  11. ↑ Kondo H, Ikeda K, Nakano M (October 2016). "Formation of size-controlled, denaturation-resistant lipid nanodiscs by an amphiphilic self-polymerizing peptide". Colloids and Surfaces B: Biointerfaces. 146: 423–30. doi:10.1016/j.colsurfb.2016.06.040. PMID   27393815.
  12. ↑ Bada Juarez JF, Harper AJ, Judge PJ, Tonge SR, Watts A (July 2019). "From polymer chemistry to structural biology: The development of SMA and related amphipathic polymers for membrane protein extraction and solubilisation". Chemistry and Physics of Lipids. 221: 167–175. doi:10.1016/j.chemphyslip.2019.03.008. PMID   30940445.
  13. ↑ Knowles TJ, Finka R, Smith C, Lin YP, Dafforn T, Overduin M (June 2009). "Membrane proteins solubilized intact in lipid containing nanoparticles bounded by styrene maleic acid copolymer". Journal of the American Chemical Society. 131 (22): 7484–5. doi:10.1021/ja810046q. PMID   19449872.
  14. ↑ Oluwole AO, Klingler J, Danielczak B, Babalola JO, Vargas C, Pabst G, Keller S (December 2017). "Formation of Lipid-Bilayer Nanodiscs by Diisobutylene/Maleic Acid (DIBMA) Copolymer". Langmuir. 33 (50): 14378–14388. doi:10.1021/acs.langmuir.7b03742. PMID   29160078.
  15. ↑ Lavington S, Watts A (November 2020). "Lipid nanoparticle technologies for the study of G protein-coupled receptors in lipid environments". Biophysical Reviews. 12 (6): 1287–1302. doi: 10.1007/s12551-020-00775-5 . PMC   7755959 . PMID   33215301.
  16. ↑ Barniol-Xicota M, Verhelst SH (February 2021). "Lipidomic and in-gel analysis of maleic acid co-polymer nanodiscs reveals differences in composition of solubilized membranes". Communications Biology. 4 (1): 218. doi: 10.1038/s42003-021-01711-3 . PMC   7886889 . PMID   33594255.
  17. ↑ Bada Juarez JF, O'Rourke D, Judge PJ, Liu LC, Hodgkin J, Watts A (August 2019). "Lipodisqs for eukaryote lipidomics with retention of viability: Sensitivity and resistance to Leucobacter infection linked to C.elegans cuticle composition". Chemistry and Physics of Lipids. 222: 51–58. doi:10.1016/j.chemphyslip.2019.02.005. PMID   31102583.
  18. ↑ "Diisobutylene-maleic acid (DIBMA)". Cube Biotech. Retrieved 2019-02-21.
  19. ↑ Torgersen ML, Judge PJ, Bada Juarez JF, Pandya AD, Fusser M, Davies CW, et al. (April 2020). "Physicochemical Characterization, Toxicity and In Vivo Biodistribution Studies of a Discoidal, Lipid-Based Drug Delivery Vehicle: Lipodisq Nanoparticles Containing Doxorubicin". Journal of Biomedical Nanotechnology. 16 (4): 419–431. doi:10.1166/jbn.2020.2911. hdl: 10852/85267 . PMID   32970975.
  20. ↑ Hoi KK, Bada Juarez JF, Judge PJ, Yen HY, Wu D, Vinals J, et al. (March 2021). "Detergent-free Lipodisq Nanoparticles Facilitate High-Resolution Mass Spectrometry of Folded Integral Membrane Proteins". Nano Letters. 21 (7): 2824–2831. doi:10.1021/acs.nanolett.0c04911. PMC   8050825 . PMID   33787280.
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