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5.4: Lipid Probes

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  • Lipids are characteristically different from proteins, making in vivo identification and labeling more difficult. Compared to protons that are character by unique sequences of amino acids and that are often interfaced with hydrophilic regions, lipids are less recognizable due to their relatively inconspicuous hydrocarbon structures and their preference for hydrophobic environments. Additionally, the complexity of lipid biosynthesis prevents the use of techniques analogous to simplifying protein research, such as overexpression and radiolabeling, as many different downstream lipid species may be affected due to reliance on the original biosynthesis pathway. These major differences contribute to the difficulty of finding and using lipid probes. One of the first notable techniques for tagging lipids originated in the early 1980’s when several experiments involving one of the fatty acids in phospholipid and glycosphingolipids-like analogues, which were replaced by 6 carbon tethers that were also connected to a fluorescent probe (see research associated with Klausner and Karnovsky or Stierr and Stackmann [1,2,3,4]). Lipid labeling offers an alternative to destructive methods that use detergents, such as the formation of homogeneous vesicles that are characteristically different than the native environments for most lipids, to induce phase separation or separate membranes, allowing for measurement made in native environments without immobilization [5]. There are three major types of lipid probes: fluorescent probes can be used for identifying target membranes or lipids [1,2,3,4], spin-probes are useful for measuring membrane dynamics [27], and isotopic probes are often used for membrane composition analysis [33].

    Fluorescent Lipid Probes

    Fluorescent probes are molecules associated with lipid systems that can be excited to emit energy that can be measured to identify and track specific lipids. They can be divided into three categories: probes that target lipid components (such as gangliosides), probes that flexibly associate with lipids despite their phase, and probes that have ordered or disordered phase preferentiality [5]. Commonly used fluorescent probes are shown below in Table 1, where the spectroscopic properties and phase preference are included, and Figure \(\PageIndex{1}\) above demonstrates the visual response of fluorescent probes.

    Fluorescent Organelles.jpg
    Figure \(\PageIndex{1}\). Subcellular organelles in yeast. The membranes in question are made visible under the fluorescence microscope by staining with specific dyes. The cell size is 5–7 µm. Top row, from left to right: vacuoles, endoplasmic reticulum, mitochondria. Bottom row: cell nucleus, lipid droplet, plasma membrane [34]

    The first of these more specific groups consists mainly of fluorescent proteins that target lipid components, like cholesterol, through inactivation mechanisms; this is the least populated group of lipid probes [6,7]. These offer bright and photostable characteristics that are not very sensitive to environmental polarity or viscosity and are often the optimum dye to use when working with fluorescence correlation spectroscopy, single molecule imaging and other super-resolution techniques [8,9,10,11].

    The second group includes lipid-like dyes that associate with lipid membranes due to labeling of lipids or lipophilic structures of non-lipid molecules that can demonstrate similar phases of biological membranes, such as the ordered and disordered phases seen with lipid rafts [12]. Fluorescent lipid probes are chemical markers that can bind to certain functional groups that belong to one of the two amphiphilic structures found in lipids: the hydrophilic headgroup or the hydrophobic tail. The function of study for the lipid will depend on the choice of dye as the additional probe will chemically affect the local functionalization by changing hydrophilic/phobic balance while also sterically impeding lipid packing in membranes [13]. Head group-associated probes are useful for research where lipid head groups play a significant role, such as lipid sorting, while chain-associated probes are useful for cases when chain regions are important, like studying membrane fluidity [14, 15]. The insertion of these marked lipids into the membrane or system of study is then facilitated by the lipid base of the probe. These tagged lipids have preferential association with certain membrane phases and thus will show varying fluorescence depending on the environment, as well as affecting membrane stability [16, 17, 18]. Additionally, lipophilic probes that consist of non-lipid structures can take the form of long-chain hydrocarbons (LCH dyes) or poly-cyclic aromatic hydrocarbons (PAH dyes) can also be used [5]. LCH dyes include alkylated cyanines and rhodamines, which have more similar structures to lipids than PAH dyes that consist mainly of neutral aromatic compounds that lack alkyl chains [5]. These probes are often used with fluorescence correlation spectroscopy and single molecule imaging [19, 20].

    The third group of dyes, commonly referred to as environment-sensitive dyes, respond spectroscopically to local environment properties like polarity, hydration, viscosity and pH while also being able to distinguish between ordered and disordered membrane phases [21, 22]. These can be further categorized into solvatochromic probes that have fluorescence that responds to the environmental polarity and viscosity-sensitive, molecular rotor probes that vary their fluorescence intensity and duration with local viscosity. Solvatochromic dyes rely on changes in dipole-dipole or hydrogen bonding interactions with their environment that affect the maxima of their excitation/emission spectra to give optical responses. These probes are used most often with ratiometric or lifetime measurements due to the change in their emission spectra and lifetime as a response to their local membrane phase [15, 23]. Molecular rotors rely on local lipid interactions, which are directly related to membrane viscosity to affect the intramolecular rotation of the fluorophore and thus the fluorescence quantum yield (or the ratio of number of photons emitted to the number of photons absorbed) [24, 16]. These probes are also used with fluorescence lifetime measurements due to the relationship between their fluorescence lifetime and local viscosity [25, 26].

    Spin Probes

    A spin probe is molecule with an unpaired electron that can associated to another molecule and can be used with electron paramagnetic resonance (EPR) spectroscopy to identify lipid membrane dynamics. Common species include nitroxide radicals associated with either the hydrophilic headgroup or the hydrophobic chains of the lipid molecules that can then be identified by EPR to determine membrane fluidity through correlation with line-width and line-shape, which can describe local environmental influences on the labeled lipids, as shown in Figure \(\PageIndex{2}\) [27]. Other available spin probes applicable to lipids include TEMPO ((2,2,6,6-tetramethylpiperidin-1-yl)oxyl) and DTBN (di-tert-butyl nitroxide), which are notably water-soluble and can interact with the aqueous-hydrocarbon interface [28]. The main targeting mechanism for introducing these spin probes to native environments involves adding spin labeled precursors that will be used in lipid biosynthesis pathways, which will then be integrated in target membranes [29]. Spin labels are used in low concentrations in lipid systems to avoid spin-spin interactions and prevent membrane disruption. Common experiments involve measuring the response of chain-labeled lipids as the labeling group moves down the acyl chain of lipid segments away from the headgroup, which demonstrates an increase in spin the further away with increasing distance from the headgroup [30, 31, 32].

    Spin Labeled.gif
    Figure \(\PageIndex{2}\): Spin-Labeling EPR of Lipid Membranes, ESEEM spectra at 77 K of 5-PCSL (upper) and of 15-PCSL (lower) in membranes of DPPC + 50 mol% cholesterol dispersed in \(\ce{D2O}\) [26]
    Table 1: Commonly studied fluorescent probes with associated spectroscopic properties and phase preferences [13]
    Name Absorbance Max (nm) Fluorescence Max (nm) Partitioning in giant unicellular vesicles Partitioning in giant plasma membrane vesicles
    Cholesterol derivatives
    TF-Chol 495 507 Lo (A, 80%) Lo (66%)
    NBD-Chol 470 538 Ld (A)
    Cholestatrienol 324 390 Lo (A)
    PE head group labeled
    NBD-DOPE 470 538 Ld (A) Ldb
    NBD-DPPE 470 538 Lo/Ld (A-C) Lo
    Rh-DOPE 560 583 Ld (A) Ldb
    Rh-DPPE 560 583 Ld (A) Ldb
    Texas Red-DPPE 595 614 Ld (A)
    DSPE-KK114 640 660 Ld (D)
    DSPE-PEG-KK114 640 660 Lo (D)
    PC acyl chain labeled
    5-BODIPY-PC 505 512 Ld (A)
    12-NBD-PC 470 538 Ld
    SM acyl chain labeled
    5-BODIPY-SM 505 512 Ld (A, 78%)
    12-BODIPY-SM 505 512 Ld (A, 69%) Lo (66%)
    6-NBD-SM 470 538 Ld (A, 88%) Ld (54%)
    12-NBD-SM 470 538 Ld (A, 95%) Ld (65%)
    4-Atto647N-SM 644 669 Ld (A, 97%) Ld (82%)
    4-Atto532-SM 532 552 Ld (A, 90%) Ld (53%)
    SM head group labeled
    SM-Atto647N 644 669 Ld (A, 97%) Ld (85%)
    SM-Atto532 532 552 Ld (A, 88%) Ld (62%)
    LCH dyes
    DiI-C18 550 568 Ld (A), Lo (B)
    DiD-C18 648 670 Ld (A) Ld
    FAST DiO 490 505 Ld (A)
    R18 554 627 Ld (A)
    DPH 350 452 Lo/Ld (A, B)
    LcTMA-DPH 350 452 Lo (A)
    PAH dyes
    Naphthopyrene 460 Lo (A)
    Perylene 436 447 Lo/Ld (A)
    Terrylene Lo (A)
    Solvatochromic probes
    Laurdan 363 460-520 Lo/Ld (A,E) Lo/Ld
    C-Laurdan 383 460-520 Lo/Ld (C) Lo/Ld
    di-4-ANEPPDHQ 482 681 Lo/Ld (C)
    F2N12S 416 490/580 Lo/Ld (A)*
    F66NS 416 490/580 Lo/Ld (A)*
    NR12S 550 626 Lo/Ld (A)*
    Molecular rotors
    FCVJ 433 500
    C-Laurdan-2 390 530 Lo/Ld (C)
    BODIPY-Ph-C12 500 512 Lo/Ld (A)
    GM1 derivatives
    5-BODIPY-GM1 505 512 Ld (A, 79%) Lo (65%)
    BODIPY-GM1 505 512 Lo (A)
    6-NBD GM1 470 538 Ld (A, 75%) Lo (67%)

    * demonstrate some preference for the lipid disordered phase. Partioning of probes in giant unicellular vesicles (GUVs) for the following lipid mixtures: A, SM/DOPC/cholesterol; B, DSPC/DOPC/cholesetrol; C, DPPC/DQPC/cholesterol; D, DPPC/PhyPC/cholesterol; Lo and Ld refer to lipid ordered and lipid disordered phases, respectively

    Isotopic Probes

    \(\ce{^2H}\), \(\ce{^{14}C}\), \(\ce{^{16}N}\) isotopes are introduced into specific metabolic pathways in biological systems and are used as labels for both lipid intermediate and products [33, 34, 36]. They replace the more commonly found atom (\(\ce{^1H}\), \(\ce{^{12}C}\), \(\ce{^{15}N}\)) in certain molecules generally without significantly affecting any biological processes while providing information for how those molecules are synthesized and transported. For plants and bacterial lipids, 34S provides another source of isotopic labelling due to the prevalence of sulfolipids [34]. These isotopic labels can be introduced through biosynthetic pathways [29] or by introduction of a pre-labeled lipid to the organism [35]. These isotopic labeled molecules can then be identified using nuclear magnetic resonance (NMR) or mass spectrometry (MS), which take advantage of non-zero net spins characteristic of deuterium and carbon-14 isotopes or the difference in mass/charge ratio attributable to the excess neutron in the isotope, respectively. A major benefit of using MS is being able to couple the use of several isotopic labels with chromatography methods to label the same molecule through comparison of mass/charge ratios and chromatographic retention times, which may be difficult with a single method due to the similarity in lipid structure and synthesis pathways [33].


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