This protocol describes a setup for the crystallization of the sterol transporter ABCG5/G8. ABCG5/G8 is reconstituted into bicelles for hanging-drop crystallization. The protocol does not require specialized materials or substrates, making it accessible and easy to adapt in any laboratory for determining the protein structure through X-ray crystallography.
ATP-binding cassette (ABC) transporters constitute lipid-embedded membrane proteins. Extracting these membrane proteins from the lipid bilayer to an aqueous environment is typically achieved by employing detergents. These detergents disintegrate the lipid bilayer and solubilize the proteins. The intrinsic habitat of membrane proteins within the lipid bilayer poses a challenge in maintaining their stability and uniformity in solution for structural characterization. Bicelles, which comprise a blend of long and short-chain phospholipids and detergents, replicate the natural lipid structure. The utilization of lipid bicelles and detergents serves as a suitable model system for obtaining high-quality diffraction crystals, specifically to determine the high-resolution structure of membrane proteins. Through these synthetic microenvironments, membrane proteins preserve their native conformation and functionality, facilitating the formation of three-dimensional crystals. In this approach, the detergent-solubilized heterodimeric ABCG5/G8 was reintegrated into DMPC/CHAPSO bicelles, supplemented with cholesterol. This setup was employed in the vapor diffusion experimental procedure for protein crystallization.
ATP-binding cassette (ABC) transporters constitute a superfamily of membrane proteins responsible for diverse ATP-dependent transport processes across biological membranes1,2,3,4,5. These transporter proteins are implicated in cardiovascular diseases and play a significant role in facilitating cholesterol efflux to the bile for subsequent excretion in the liver. Consequently, cholesterol metabolism and balance have garnered considerable interest over the years6. A specific mechanism involved in the elimination of cholesterol and other sterols from the body involves members of the human ABCG subfamily, notably the heterodimeric ABCG5/G87,8,9,10. Mutations in either of these genes disrupt the heterodimer, leading to loss of function and causing sitosterolemia, a disorder affecting sterol trafficking11,12,13. Given the disease's relevance and their role in promoting cholesterol efflux, sterol transporters have attracted significant attention. Nevertheless, the intricate details of their molecular mechanism and substrate selectivity remain largely undisclosed. Thus, the elucidation of the crystal structure of ABCG5/G8 is a crucial stride toward comprehending the mechanisms and downstream functions in cholesterol transport.
Membrane proteins require anchoring within membranes to fold and function correctly. Consequently, extracting membrane proteins from their natural environment often results in protein instability, misfolding, and loss of function14,15. These challenges underscore the primary hurdles faced in membrane protein crystallization. However, the reconstitution of proteins into synthetic detergent bilayers, like bicelles, has emerged as a solution to this predicament, enabling the maintenance of membrane proteins within a native-like bilayer milieu16. Bicelles are assemblies of synthetic phospholipids and detergents suspended and solubilized in water. Notably, they adopt a bilayer structure that mimics biological membranes16,17,18. Bicelles can transition between liquid and gel phases based on temperature and viscosity. Bicelle crystallization capitalizes on the small bilayer discs and low viscosity at reduced temperatures, facilitating thorough mixing of proteins and bicelle solutions. The size of the bicelles depends on the detergent-to-lipid ratio during preparation19,20. The prevalent detergents for bicelle formation include 3-[(3-cholamidopropyl)dimethylammonio]-2-hydroxy-1-propanesulfonate (CHAPSO), along with 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate (CHAPS) and 1,2-ditridecanoyl-sn-glycerol-3-phosphocholine (DHPC)21. These detergents are used in conjunction with lipids such as di-myristoyl-phosphatidylcholine (DMPC) and 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC). Furthermore, recent studies have demonstrated the full functionality of membrane proteins within bicelles under physiological conditions. For example, Lee and colleagues successfully crystallized and reported the crystal structure of ABCG5/ABCG8 based on a lipid bilayer22,23. In the crystallization process, protein-bicelle mixtures can be accommodated using standard equipment, including high-throughput crystallization robots24. The feasibility of utilizing bicelles, however, hinges on the proteins' thermostability due to the crystallization conditions at higher temperatures. Nevertheless, when compared to other techniques, the requisite crystallization conditions for membrane proteins generally remain mild, involving low concentrations of precipitant, salt, and buffer. This renders both protein-bicelle mixtures and vapor diffusion effective and easily implementable tools for structural studies of membrane proteins.
This protocol outlines essential steps in protein preparation and bicelle crystallization for determining the X-ray crystal structure of ABCG5/G8 at high resolution (Figure 1).
1. Cloning and protein expression
2. Preparation of microsomal membrane
3. Protein preparation-purification of heterodimers
4. Protein preparation-pre-crystallization treatment
5. Protein crystallization in bicelles
Recombinant ABC half-transporters, human ABCG5, and ABCG8, are co-expressed in Pichia pastoris yeast. The yeast membrane fraction is then fractionated through centrifugation. As outlined in this protocol, the heterodimeric proteins are extracted using tandem column chromatography. Subsequently, chemically pre-treated proteins are crystallized by incubating them with phospholipid/cholesterol bicelles. Schematic overviews of the purification and crystallization processes are provided in Figure 1.
To assess the monodispersity of the purified proteins, samples containing 0.01-0.05 mg/mL of proteins are stained with 1%-2% uranyl acetate. These samples are then examined using negative-stain TEM (Figure 2A). In order to evaluate protein stability without undergoing freeze-thaw cycles, analytical gel filtration chromatography is employed. This analysis involves monitoring the time-course storage of purified proteins through the use of small, equal-volume aliquots of the proteins (Figure 2B). There might be a slight loss of proteins at the peak fractions after a week of incubation at 4 °C, possibly due to residual soluble protein aggregates. Nonetheless, the overall protein yield remains sufficient for crystal growth. The use of negative stain TEM and analytical gel filtration chromatography is a standard practice to assess the suitability of proteins for crystallization, particularly from different engineered constructs.
For the assessment of protein quality at each step of the column chromatography process, as well as after the pre-crystallization chemical treatment, aliquots of fractions corresponding to two Ni-NTA columns, two CBP columns, one gel filtration, and reductive alkylation are loaded onto a 10% SDS-PAGE gel (Figure 3). Additionally, the same reaction environment utilized for alkylation can be applied for mercury labeling with ethyl mercury (EMTS), although this is beyond the scope of the current study.
The growth of crystals is monitored daily using a tabletop stereo microscope equipped with a polarizer. Crystals that are mature and suitable for data collection generally attain dimensions of 50 µm x 100 µm x 2 µm (Figure 4). During the crystal harvesting process, smaller crystals or clusters are deliberately avoided.
Figure 1: Schematic overviews for purification (A) and bicelle crystallization (B) of heterodimeric ABCG5/G8. Constructs of recombinant human ABCG5 (hG5) and ABCG8 (hG8) carry RGS-H6-G-H6 and 3C-CBP tags, respectively (A, top). Tandem affinity column chromatography, followed by gel filtration chromatography to achieve heterodimeric purification (A, bottom). Please click here to view a larger version of this figure.
Figure 2: Evaluation of mono-dispersity (A) and stability (B) of purified proteins. (A) Electron micrograph of negatively stained ABCG5/G8 (G5G8) heterodimers using TEM. Representative particles are highlighted in solid white circles. Scale bar = 100 nm. (B) Alkylated proteins stored at 4 °C analyzed by analytical gel filtration chromatography over the course of a month with a slight loss of proteins after a week. Please click here to view a larger version of this figure.
Figure 3: SDS-PAGE analysis of protein eluates of column chromatography and reductive alkylation. Various volumes (1-10 µL) of protein fractions were loaded onto a 10% Tris/Glycine gel and ran for 45 min at a constant voltage of 200 V. The gel was stained with Coomassie blue, destained, air-dried, and scanned by a tabletop scanner. 1° & 2° Ni: first and second Ni-NTA columns; 1° & 2° CBP: first and second CBP columns; Peak Fractions solid line: pooled fractions for crystallization; Peak Fractions dashed line: shoulder fractions; EMTS: ethyl mercury thiosalicynate; IA: iodoacedamide. Please click here to view a larger version of this figure.
Figure 4: Assessment of protein crystal maturation by light microscopy. Mature crystals of ABCG5/G8 from a crystallization drop were visualized under a tabletop and polarizer-equipped stereo microscope. Scale bar = 100 µm. Please click here to view a larger version of this figure.
The challenges associated with crystallizing membrane proteins have prompted the development of lipid-bilayer-driven crystallization methods, such as the bicelle27 or lipid cubic phase (LCP)14 approaches. However, achieving successful crystallization of membrane proteins still hinges on the critical and sometimes bottlenecked step of protein preparation. Notably, ABC transporters present a formidable hurdle in growing crystals suitable for X-ray crystallography. This protocol provides comprehensive hands-on guidance for streamlining the preparation of human ABCG5/G8 sterol transporter and fostering crystal growth through the bicelle crystallization approach.
A key consideration in devising this protocol was the imperative for a substantial protein yield in the initial phases of protein purification, allowing for a certain degree of protein loss during pre-crystallization treatment (Figure 3). Common strategies for addressing this challenge involve extensive protein engineering, utilization of diverse expression hosts, and exploration of orthologs or homologs, among other approaches. Nevertheless, with this seemingly intricate procedure, a number of pivotal steps have been identified that underpin the protocol’s success and also provide insights into potential limitations that may arise when studying other ABC transporters or membrane proteins in general.
Firstly, this protocol employs thorough centrifugation at each step to minimize protein aggregation. Additionally, continuous monitoring of the thermostability of the purified proteins is crucial. Electron microscopy is utilized to verify protein monodispersity, while analytical gel filtration tracks protein stability over time (Figure 2). Alternative techniques like circular dichroism (CD) or differential scanning calorimetry (DSC) could also be incorporated. Furthermore, the incorporation of lipids at specific stages is essential to maximize both the activity and crystallogenesis of the purified ABCG5/G8. For instance, cholate and CHS are necessary to exhibit measurable ATP hydrolysis; phospholipids are indispensable for maintaining the stability of methylated proteins; and cholesterol is a requisite component of the bicelle solution, fostering crystal growth suitable for high-resolution X-ray diffraction (Figure 4).
In essence, the entire procedure can be accomplished within a week’s worth of effort. In contrast to LCP, the retrieval of crystals from hanging-drop crystallization trays is straightforward. Looking ahead, with a substantial protein yield (approximately 10 mg), this protocol is readily adaptable for developing crystallographic investigations involving ABCG5/G8 mutants or other transporter proteins. This is particularly pertinent for cases that currently evade visualization through electron microscopy.
The authors have nothing to disclose.
This work is supported by a Natural Sciences and Engineering Research Council Discovery Grant (RGPIN 2018-04070) and a Canadian Institutes of Health Research Project Grant (PJT-180640) to JYL. This protocol is based on the original reports in ABCG5/G8 crystal structures reported earlier by Farhat et al.22 and Lee et al.23.
(NH4)2SO4 | MilliporeSigma | A4915 | |
ABCG5 | National Institute of Health collection | NCBI accession number NM_022436 | |
ABCG8 | National Institute of Health collection | NCBI accession number NM_022437 | |
ÄKTA FPLC system | Cytiva (formerly GE Healthcare Life Sciences) | ||
CaCl2 | Wisent | 600-024-CG | Anhydrous |
CBP | Agilent | 214303 | Calmodulin binding peptide affinity resin |
Centrifugal concentrators (Vivaspin) | Sartorius | ||
CHAPSO | Anatrace | C317 | Anagrade |
Cholesterol | Anatrace | CH200 | |
CHS | Steraloids | C6823-000 | |
DMAB | MilliporeSigma | 180238 | 97% |
DMNG | Anatrace | NG322 | |
DMPC | Anatrace | D514 | |
DOPC | Avanti | 850375 | |
DOPC | Anatrace | D518 | |
DOPE | Avanti | 850725 | |
DTT | Fisher | BP172 | |
Dual Thickness MicroLoops | MiTeGen | ||
EDTA | BioShop | EDT003 | Disodium salt, dihydrate |
EGTA | MilliporeSigma | 324626 | |
Emulsifier (EmulsiFex-C3) | Avestin | ||
Endo H | New England Biolabs | P0702 | |
Ethanol | Greenfield | P016EAAN | Ethyl Alcohol Anhydrous |
Formaldehyde | MilliporeSigma | 252549 | ACS Reagent |
Glycerol | BioShop | GLY004 | |
HEPES | BioShop | HEP001 | |
HRV-3C protease | Homemade | ||
Imidazole | BioShop | IMD510 | Reagent grade |
Iodoacetamide | MilliporeSigma | I1149 | BioUltra |
Isopropanol | Fisher | BP2618212 | |
Leupeptin | BioShop | LEU001 | |
MES | MilliporeSigma | 69892 | BioUltra |
Methanol | Fisher | A412P | |
MgCl2 | Wisent | 800-070-CG | Hydrated |
microfluidizer (LM 20) | Microfluidics | ||
NaCl | BioShop | SOD002 | |
NH4OH | Fisher | A669-212 | ACS Reagent |
Ni-NTA superflow | Qiagen | 30430 | Nickel-charged resins |
PEG 400 | MilliporeSigma | 202398 | |
Pepstatin | BioShop | PEP605 | |
PMSF | MilliporeSigma | P7626 | |
pSGP18 and pLIC | Homemade (derived from pPICZ, Invitrogen) | ||
SDS | BioShop | SDS003 | |
Sodium cholate | Fisher | 229101 | |
Sodium malonate | MilliporeSigma | 63409 | |
Sucrose | Wisent | 800-081-WG | Ultra pure |
Superdex 200 30/100 GL | Cytiva (formerly GE Healthcare Life Sciences) | 28990944 | Prepacked gel-filtration column |
TCEP | |||
TEM | FEI, Technai | ||
Tris Base | Fisher | BP152 | |
β-DDM | Anatrace | D310S | Sol Grade |
β-mercaptoethanol | MilliporeSigma | ||
ε-aminocaproic acid | Fisher | AAA1471936 |