A Chemical Strategy for Amphiphile Replacement in Membrane

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A Chemical Strategy for Amphiphile Replacement in Membrane Protein Research Dongxiang Xue, Jingjing Wang, Xiyong Song, Wei Wang, Lintao Ye, Yang Liu, Qingtong Zhou, Zhong-Xing Jiang, Zhijie Liu, and Houchao Tao Langmuir, Just Accepted Manuscript • DOI: 10.1021/acs.langmuir.8b04072 • Publication Date (Web): 19 Feb 2019 Downloaded from http://pubs.acs.org on February 23, 2019

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A Chemical Strategy for Amphiphile Replacement in Membrane Protein Research Dongxiang Xue1,2,3,4, Jingjing Wang1,3,4,5, Xiyong Song3,6, Wei Wang7, Lintao Ye1, Yang Liu1, Qingtong Zhou1, Zhong-Xing Jiang7, Zhi-Jie Liu1,4* and Houchao Tao1* 1iHuman

Institute, ShanghaiTech University, Ren Building, 393 Middle Huaxia Road, Pudong

New District, Shanghai, 201210, China 2Shanghai

Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road,

Building 3, Room 426, Shanghai, 201203, China 3University

4School

of Chinese Academy of Sciences, No. 19A, Yuquan Road, Beijing, 100049, China

of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China

5Institute

of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese

Academy of Sciences, Shanghai, 200031, China 6

National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of

Sciences, Beijing 100101, China 7Hubei

Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals,

School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China

ACS Paragon Plus Environment

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ABSTRACT: Membrane mimics are indispensable tools in the structural and functional understanding of membrane proteins (MPs). Given stringent requirements of integral MP manipulations, amphiphile replacement is often required in sample preparation for various biophysical purposes. Current protocols generally rely on physical methodologies and rarely reach complete replacement. In comparison, we report herein a chemical alternative that facilitates the exhaustive exchange of membrane mimicking systems for MP reconstitution. This method, namely sacrifice-replacement strategy, was enabled by a class of chemically cleavable detergent (CCD), derived from the disulfide incorporation in the traditional detergent n-dodecyl-β-Dmaltopyranoside (DDM). The representative CCD behaved well in both solubilizing the diverse α-helical human G protein-coupled receptors (GPCRs) and refolding of the β-barrel bacterial outer-membrane protein X (OmpX), and more importantly it could also be readily degraded under mild conditions. By this means, the A2A adenosine receptor was successfully reconstituted into a series of commercial detergents for stabilization screening and nanodiscs for electron microscopy (EM) analysis. Featured by the simplicity and the compatibility, this CCD mediated strategy would later find more applications when being integrated in other biophysics study.


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INTRODUCTION Membrane proteins (MPs) are highly pursued pharmaceutical targets due to their important biological roles in information and material exchange between and within cells.1, 2 Nevertheless, the exploration of MPs has been challenging compared to soluble proteins, as indicated in the protein data bank (PDB) where MPs only contribute to about 2% of known protein structures.3 One particular challenge is the reconstitution of MP in a proper mimicking membrane system that facilitates subsequent biochemical and biophysical characterization.4-7 Over the past decades, various membrane mimic cassettes have been developed to prompt in vitro MP studies. Detergents are the most commonly used lipid surrogates, which usually have unmatched solubilization but suboptimal stabilization to MPs.8 Though some conceptually novel detergents exhibited favorable stabilization properties, their applications suffer from poor solubilization or accessibility.3,

9-11

Similarly, bilayer systems like liposomes, bicelles and

nanodiscs, are deemed to maintain MPs in a more native-like state, which however are neither amenable to extraction and thus MP reconstitution has to commence with a detergent-solubilized mixture.3, 9-13 Therefore, amphiphile replacement is often required in reconstitution of challenging MPs in an ideal mimic system to facilitate further studies. Current detergent replacement protocols primarily involve in a physical methodology by means of dilution, dialysis or BioBeads adsorption.3,

4, 12, 14

Nevertheless, these physical approaches

usually fail to achieve a thorough and clean exchange. For example, dilution and dialysis can only minimize the concentration of the original detergents and thus the second mimic system will inevitably be contaminated with residual detergents. As for physical adsorption, BioBeads are supposedly able to distinguish detergents from lipids, but actually the selectivity is much less desirable (Figure S1). In addition, when dealing with fragile MPs such as GPCRs, laborious


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optimization might be required in a preliminary stage for MP reconstitution.12, 15 Tedious sample handling steps could easily arise protein aggregations. As an alternative to conventional physical methods, we present herein a chemical methodology—the sacrifice-replacement strategy—for facile and exhaustive detergent replacement during MP reconstitution. This strategy is enabled by a novel series of chemicallycleavable detergents (CCDs). In the sacrifice-replacement strategy (Figure 1), the selected CCD extracts MPs from biological membranes and then is readily replaced with new detergents or lipids by a mild decomposition. Using this strategy, we successfully conducted an economical detergent screening for A2A adenosine receptor (A2AR) and established a new nanodisc preparation protocol that facilitates further EM analysis. These proof-of-concept applications demonstrate the significant potential of this chemical methodology in reconstituting MPs for various applications.


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EXPERIMENTAL SECTION Synthesis and characterization of CCDs. Starting from the commercially available peracetylated maltosylbromide 1, CCDs with a variety of lengths (CCD-1-4) were easily obtained by a scalable three-step procedure with a total yield of 51-63% (Scheme S1). Nuclear magnetic resonance (NMR) spectra were recorded on a Bruker AVANCE III 500 or 800 spectrometer (FT, 500/800 MHz for 1H NMR; 126/201 MHz for

13C

NMR) at room temperature with CDCl3 or

CD3OD as the solvent. High-resolution mass spectra (HRMS) were recorded on an Agilent 6230 mass spectrometer using electrospray ionization. Synthetic procedures, characterization data and NMR spectra of all CCDs are shown in supplementary information. All other reagents applied in this context were obtained from commercial suppliers (Adamas, Anatrace, Accela, Aladdin, J&K, Sigma, etc.) and used without further purification. Protein expression and purification. Membrane scaffold protein (MSP). The MSP protein MSP2N2, which contains a 7-His-tag and a TEV protease site on N-terminus, is expressed and purified as previously described.16, 17 The plasmid pMSP2N2 (AddGene®) was transformed into Escherichia coli BL21GOLD (DE3) and the related protein expression was induced in Terrific Broth by addition of isopropyl β-D-1thiogalactopyranoside to 1 mM at an OD600 of 1. After about 3 hours, cells were harvested by centrifugation at 8,000 × g for 20 min and stored at −80 °C until purification. The cell pellet was lysed in the lysis buffer (100 mM NaCl, 0.5 mM ethylene diamine tetraacetic acid (EDTA), 20 mM Tris-HCl, pH 7.4) by sonication. The lysate was then clarified at 35,000 × g for 30 min and loaded onto a nickel NTA affinity column. Wash the column sequentially with 75 mL of each following buffer: (i) 100 mM NaCl, 0.5 mM EDTA, 30 mM imidazole, 20 mM Tris-HCl, pH 7.4; (ii) 100 mM NaCl, 0.5 mM EDTA, 50 mM imidazole, 20 mM Tris-HCl, pH 7.4; and (iii) 100 mM


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NaCl, 0.5 mM EDTA, 100 mM imidazole, 20 mM Tris-HCl, pH 7.4. Finally, the MSP2N2 was eluted from the resin with buffer (100 mM NaCl, 0.5 mM EDTA, 400 mM imidazole, 20 mM TrisHCl, pH 7.4), and dialyzed against the dialysis buffer (100 mM NaCl, 0.5 mM EDTA, 20 mM Tris-HCl, pH 7.4) overnight at 4 °C. Meanwhile, the N-terminal His-tag was removed using TEV protease. The cleaved MSP2N2 was separated from His-tag by an additional Ni-NTA purification step. The MSP2N2 protein was further filtered through a 0.22 μm syringe filter and stored at −80 °C until use. GPCRs. The MBP-A2AR-BRIL-ΔC construct was designed based on the sequence of A2ARBRIL-ΔC construct18 (PDB ID: 4EIY) by adding maltose binding protein (MBP) as a fusion protein at the N-terminal. The modified thermostabilizing apocytochrome b562RIL (BRIL) acting as a fusion partner was inserted into the third intracellular loop (IL3) between Lys209 to Gly218. Recombinant baculovirus was made from pFastbac1-MBP-A2AR-BRIL-ΔC using the Bac-to-Bac system (Invitrogen).19 The MBP-A2AR-BRIL-ΔC protein was expressed in baculovirus-infected Sf9 insect cells as described previously.20 Sf9 insect cells were prepared at a density of 2 × 106 cells/mL with P1 virus at MOI (multiplicity of infection) of 5 and suspended in 5 litres of the IPL41/SF900 II complex media or ESF921 insect media. After 48 hours, the remaining cells were centrifuged at 6,000 × g for 10 min and harvested. The other engineered constructs of GPCRs in this context were expressed as previously described.18, 21, 22 In brief of purification, cell pellets were homogenized by douncing in a hypotonic buffer (10 mM MgCl2, 20 mM KCl, protease inhibitor cocktail tablets (Roche), 10 mM HEPES, pH 7.5), and then precipitated by centrifugation at 35,000 rpm for 30 min. Repeat the above homogenization procedures again in hypotonic buffer and three times in osmotic buffer (1 M NaCl, 10 mM MgCl2, 20 mM KCl, 10 mM HEPES, pH 7.5) to give GPCR-containing membrane preparations. Membrane preparations were resuspended


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in suspension buffer (10 mM MgCl2, 20 mM KCl and 30% (v/v) glycerol, 100 μM ligand, 2 mg/mL iodoacetamide, 10 mM HEPES, pH 7.5) and incubated at 4 °C for 1 hour before being solubilized in buffer (800 mM NaCl, 1% (w/v) detergent, 50 mM HEPES, pH 7.5) for 3 hours. Supernatants were isolated by ultracentrifugation and incubated overnight in 20 mM imidazole with TALON IMAC resin (Clontech). The protein bounded resin was sequentially washed with the wash buffers: (i) 800 mM NaCl, 10% glycerol, 8 mM ATP, 10 mM MgCl2, 20 mM imidazole, 100 μM ligand, 10 × CMC detergent, 50 mM HEPES, pH 7.5; (ii) 500 mM NaCl, 10% glycerol, 10 mM MgCl2, 20 mM imidazole, 50 μM ligand, 10 × CMC detergent, 50 mM HEPES, pH 7.5; (iii) 500 mM NaCl, 10% glycerol, 20 mM imidazole, 100 μM ligand, 5 × CMC detergent, 50 mM HEPES, pH 7.5) before GPCRs were eluted with elute buffer (500 mM NaCl, 10% glycerol, 250 mM imidazole, 100 μM ligand, 2.5 × CMC detergent, 25 mM HEPES, pH 7.5) in a minimal volume. The ligands for A2AR (A2A adenosine receptor), GLP-1R (glucagon-like peptide-1 receptor) and SMO (smoothened receptor) were ZM241385 (4-[2-[[7-Amino-2-(2-furanyl)[1,2,4]triazolo[1,5a][1,3,5]triazin-5-yl]amino]ethyl]phenol), PF-06372222 (N-{4-[(R)-(3,3-dimethylcyclobutyl)({6[4-(trifluoromethyl)-1H-imidazol-1-yl]pyridin-3-yl}15amino)methyl]benzene-1-carbonyl}-betaalanine)

and

LY2940680

(4-Fluoro-N-methyl-N-[1-[4-(1-methyl-1H-pyrazol-5-yl)-1-

phthalazinyl]-4-piperidinyl]-2-(trifluoromethyl)benzamide) respectively. The detergent refers to DDM or CCDs. Refolding of OmpX. OmpX was expressed and purified in denature buffer (20 mM Tris, 6 M urea, pH 8.5) according to previous reported procedures.23-25 1 μL denatured OmpX (~ 20 mg/ml) was slowly diluted into 30 μL refolding buffer (1% (w/v) Fos-choline 12 (Fos12) or CCD-2, 50 mM Tris-HCl, pH 9.0) at 4 °C. The refolding mixture was incubated at 4 °C for 2 hours and then heated at 70 °C with water bath for 10 min. After incubation at 4 °C for another 20 min, all OmpX


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samples were loaded to a 12% polyacrylamide gel and analyzed by SDS-gel electrophoresis in MES buffer. The refolding yields of OmpX in each group were determined by the band densitometry using ImageLab (Bio-Rad). Thermal shift assay. Each sample comprised of approximately 1 μg A2AR in a total volume of 50 μL buffer (500 mM NaCl, 10% glycerol, 50 μM ZM241385, 0.2% (w/v) detergent, 25 mM HEPES, pH 7.5). The CPM (N-([4-(7-diethylamino-4-methyl-3-coumarinyl) phenyl] maleimide) dye (λex = 365 nm, λem = 460 nm) was dissolved in DMSO at 4 mg/mL and diluted into each sample with final concentration of 2 μg/mL. After incubation at 4 °C for 15 minutes, all samples were subjected to thermal denaturation with a ramp rate of 1 °C/min from 25 °C to 90 °C in a RotorGene Q spectrofluorometer (Qiagen). All data were processed with GraphPad Prism program and the melting temperature (Tm °C) of each sample was determined in terms of the Bolzmann sigmoidal fitted curve of the raw data. Detergent screening. 20 μL A2AR (~ 0.1 mg/mL) in CCD-2 (0.05%, w/v) was added to 10 μL screening buffer (500 mM NaCl, 10% glycerol, 50 μM ZM241385, 20 mM or 20 × CMC detergent, 25 mM HEPES, pH 7.5) and incubated at 4 °C for 1 hour with constant rotation. 10 μL tris (2carboxyethyl) phosphine (TCEP) (10 mM, pH 7.5) was then added and the mixture was incubated for another 2 hours before centrifugation at 14,000 rpm for 15 min. The homogeneity of all A2AR samples were then evaluated through analytical size-exclusion chromatography (aSEC, HPLC: Agilent, Bioinert 1100 series; column: Nanofilm SEC-250, 4.6 × 250 mm, 5 μm, Sepax Technologies Inc.), which run at 0.5 mL/min in SEC buffer (150 mM NaCl, 2% glycerol, 0.05% DDM, 0.01% CHS (cholesterol hemisuccinate), 25 mM HEPES, pH 7.5) from UV absorbance at 280 nm. All above steps were carried out at 4 °C. As for thermal stability SEC assay, the above reconstitution samples were heated at 40 °C for another 3 min using metal bath before the aSEC


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analysis. Pursuant to preliminary results (Figure S2), the final concentration of the test detergent was set at 5 mM (for detergents whose CMC is lower than 1 mM) or 5 × CMC (for detergents whose CMC is higher than 1 mM). Nanodisc preparation. The elution mixture of MBP-A2AR-BRIL-ΔC was desalted by a 5 mL HiTrap desalting column (Amersham/GE) with buffer (500 mM NaCl, 10% glycerol, 250 mM imidazole, 100 μM ZM241385, 3 × CMC detergent, 25 mM HEPES, pH 7.5). The MBP-A2ARBRIL-ΔC protein (0.7 mg/mL) mixture was then incubated with MSP2N2 (~17 mg/mL) and the lipid stock (POPC, 2-oleoyl-1-palmitoyl-sn-glycero-3-phosphocholine; POPS, 2-oleoyl-1palmitoyl-sn-glycero-3-phospho-L-serine) at a molar ratio of 1:5:180:420 (A2AR: MSP2N2: POPC: POPS). The mixture was incubated at 4 °C for 1 hour with constant rotation. Then reconstitution was initiated by removal of detergents from the system according to the following traditional physical protocols12, 26 or the alternative chemical protocols. Traditional physical protocols for removal of detergents. BioBeads SM-2 (Bio-Rad) was prepared by suspending in methanol, washing with several volumes of methanol, and rinsing with large amounts of Milli-Q treated water (Millipore). The above prepared BioBeads SM2 were added to A2AR-DDM mixture (0.2~0.3 g BioBead/mL mixture) and incubated at 4 °C overnight with constant rotation. Finally, BioBeads were removed by centrifugation. Chemical protocols for removal of detergents. TCEP (5 equiv. to the molar concentration of CCD-2 in A2AR-CCD2 mixture) was added to the protein mixture and incubated at 4 °C with constant rotation for 2 hours before further purification and analysis. The nanodiscs containing receptors were loaded onto a nickel NTA column, and washed with buffer (25 mM HEPES, 150 mM NaCl, 20 mM imidazole and 100 μM ZM241385, pH 7.5). Then reconstitution mixture was eluted by 10 column volumes of elute buffer (150 mM NaCl, 200 mM


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imidazole and 100 μM ZM241385, 25 mM HEPES, pH 7.5). The elution mixture was further purified by SEC (column: gel filtration column superdex 200; buffer: 100 mM NaCl, 250 mM EDTA, 20 mM Tris-HCl, pH 7.5). The fraction corresponding to MBP-A2AR-BRIL-ΔC reconstituted in lipid nanodiscs was collected for further analysis by dynamic light scattering (DLS) and negative-stained EM. Negative-stained EM data acquisition and analysis. 5.0 μL of nanodisc samples prepared as described above with the concentration of 0.03 mg/mL were applied to a glow-discharged holey carbon grid and stained with 2% (w/v) uranyl formate.27 The data of negative stained samples were acquired on a transmission EM (FEI, USA) operated at 120 KV equiped with a 4k × 4k scintillatorbased charge-coupled device camera (UltraScan 4000, Gatan). Images were recorded at a nominal magnification of × 57,000 or × 73,000 with a defocus range of -2.5 to -3.5 μm. A total of 118 micrographs with a magnification of × 73,000 (corresponding to 1.918 Å pixel−1 on the specimen ) were used for the 2D classification of the MBP-A2AR-BRIL-ΔC-nanodiscs samples. First of all, the CTF parameters of each image were determined by Gctf.28 Then, the particles were picked automatically by Gautomatch software and bad particles were excluded by manual selection. Finally, about 103,053 particles were used for 2D classification analysis with Relion 2.0 software.29


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RESULTS AND DISCUSSION Design and physical characterization of CCDs. Using the conventional detergent DDM as the template, we incorporated a disulfide bond between the hydrophilic maltose and the hydrophobic alkyl chain (Figure 2). In this design, the mild maltose head and the alkyl tail were supposed to retain the nature of DDM and the disulfide linker was expected to endow CCDs with the unique chemically cleavable property. Among this series of CCDs, CCD-1 and CCD-2 were highly water-soluble (>10%, w/v) while the other two detergents bearing longer alkyl chains were of poor solubility (10%) and similar CMC value (0.2 mM) to DDM, was chosen as a promising candidate for further investigation of potential applications in MP studies. Solubilization to diverse GPCRs. To evaluate the solubilization efficiency of CCD-2 on αhelix proteins, three engineered GPCRs, including class A receptor A2AR (A2AR-BRIL-ΔC)

18,

class B receptor GLP-1R (glucagon-like peptide-1 receptor, GLP-1R-T4L)22 and class F receptor SMO (smoothened receptor, SMO-FLA)21, were solubilized and purified by CCD-2. It turned out that CCD-2 was efficient in solubilizing A2AR with comparable yield and even superior homogeneity when compared to DDM (Figure 3A). Significantly, A2AR in CCD-2 remained consistently homogeneous even after storage at 4 °C for 10 days while obvious aggregation was observed in the corresponding DDM sample (Figure S4). Moreover, the other two engineered GPCRs (GLP-1R-T4L and SMO-FLA) that were extracted from the membrane by CCD-2 also exhibited comparable protein yield and homogeneity to that of DDM (Figure 3B, 3C), implying that CCD-2 could be a perfect surrogate of DDM for solubilization of various GPCRs. Refolding of OmpX. To further explore the versatility of CCD-2 for β-barrel membrane protein, the bacterial outer-membrane protein OmpX was applied (Figure 3D). OmpX is an eight-stranded


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β-barrel membrane protein that plays an important role in bacterial interactions with the host.24, 25, 36, 37

Well-folded OmpX can be conveniently distinguished from the denatured one in standard gel

electrophoresis, based on which the refolding efficacy in diverse detergents can be readily analyzed by the readout of SDS-PAGE.38 Accordingly, refolding of denatured OmpX in 1% CCD2 accomplished a comparable efficacy (73 %) to its favorable detergent Fos12 (67 %), indicating that CCD-2 is also amenable to the β-barrel protein research. Chemical cleavage of CCD-2. According to the design, the disulfide bond of CCDs that locates close to the hydrophilic area would be liable to aqueous reductants. Among various common reductive conditions (Table S1), CCD-2 was found to be readily decomposed by the treatment of tris (2-carboxyethyl) phosphine (TCEP). The exhaustive cleavage of CCD-2 (Figure 4A) was confirmed in the HPLC profiles detected by an evaporative light scattering detector (ELSD) (Figure 4B) and led to the complete disappearance of micelles, as detected by the fluorophore encapsulation assay (Figure S5A) and dynamic light scattering (DLS) (Figure S5B). Moreover, under the optimal cleavage condition (Entry 10, Table S1), complete degradation of CCD-2 was also achieved in the presence of commercial detergents (lauryl maltose neopentyl glycol, LMNG; DTM and n-octyl-β-D-gluopyranoside, OG) or lipid (2-Oleoyl-1-palmitoyl-sn-glycero-3phosphocholine, POPC) and resulted in a unitary mimetic system (Figure S6, S7). Of note, TCEP, as well as the thiol debris, showed minimal interference on the property of commercial amphiphiles, as exemplified by the consistent CMC value of DDM under different conditions (Figure S8). More importantly, the whole cleavage process of CCD-2 was also well compatible with various tested MPs (Figure 4C, 4D, S9, S10). All three fragile GPCRs (~ 5 μM), notably including SMO-FLA with a cysteine-rich domain (CRD), were well preserved in DDM under 5 mM TCEP for 6 hours (Figure S11). We speculated that those critical disulfide bonds of


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MPs should be buried in the hydrophobic interior of protein-detergent complexes (PDCs), where is hardly accessible to the aqueous reductant. In all, the chemical cleavage of CCD-2 is rapid, complete and biorthogonal and should facilitate a chemical methodology for in situ detergent replacement in diverse MP studies. Detergent screening for the stabilization of A2AR. It is well known that the stability of MPs, as well the compatibility on the biophysical studies are highly dependent on the detergents used.3, 8

There are nearly one hundred of commercially available detergents (www.anatrace.com), which

is ever-expanding as a result of ongoing research. However, rational design or selection of detergents for a given MP has been difficult, since the understanding of the fundamental behavior of detergent around MP is still limited, though the recent efforts have pushed forward in this field.17, 39, 40

Based on our sacrifice-replacement strategy, we set out to conduct a comprehensive detergent

screening on the stabilization of A2AR. Accordingly, the A2AR protein purified by CCD-2 was successfully reconstituted into a group of selected detergents (Table S2) by the chemical replacement strategy and the monodispersity of A2AR samples was then evaluated through aSEC. As a result, seven nonionic maltoside detergents (DDM, LMNG, DTM, decyl maltose neopentyl glycol (DMNG), n-undecyl-β-D-maltopyranoside (UDM), n-decyl-β-D-maltopyranoside (DM) and CYMAL-7) stood out from 23 commercial detergents for the maintenance of A2AR (Figure 5, S11), which suggests the neutral maltose group in detergents plays a key role in the stabilization of A2AR. In comparison, A2AR in the other detergents, including glucosides (n-nonyl-β-D-glucopyranoside, NG), PEG derivatives (C12E8, tetraethylene glycol monooctyl ether, TX-100), amino oxides (n-dodecyl-N,N-dimethylamine-Noxide, LDAO) and zwitterionic detergents (CHAPS, Tripao, Fos-Choline), displayed high


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aggregation peaks in aSEC (Figure S12), indicating these detergents are either too weak to stabilize A2AR or so harsh that they denatured the fragile protein. For a further comparison, these optimal A2AR samples, encapsulated in the seven promising maltoside detergents, were subjected to thermal denaturation by heating at 40 °C for 3 min before aSEC analysis. As a result, DDM and its thio-glycosylated homolog, DTM, outperformed the other detergents by maintaining more than half the A2AR in a native monotropic state (Figure 5 and Table S3). Another commonly used detergent, LMNG, a seemingly dimerized homolog of DDM, also performed well with about 50% of A2AR remaining in monomer after heating. In comparison, A2AR in shorter-chained maltosides, both traditional DM and two-head-two-tailed DMNG, almost totally denatured after thermal treatment. In addition, the cyclohexanyl terminated detergent CYMLA-7 apparently exhibited comparable stabilization to the linear chained maltoside detergent UDM (Figure 5). These screening results were in good agreement with the detergent priority of previous structural biology studies on A2AR, indicating that this facile and economical detergent screening methodology could provide reliable guidance for the selection of proper amphiphile candidates for MP structure determination. Nanodisc preparation using CCD-2 as the sacrifice detergent. The nanodisc is a discoidal lipid nanostructure where phospholipid bilayers are encircled by two membrane scaffolding proteins (MSPs) aligned in double belt formation. Thanks to their well-defined size, good stability and more native-like lipid environment when compared to other membrane mimics, nanodiscs have recently been recognized as a versatile tool that has enabled structure-function investigations of MPs in solution.41 However, nanodiscs are usually unable to extract MPs from the biological membrane. Traditional protocols for incorporating a target MP in nanodiscs commences with the gradual removal of initial detergents through BioBeads adsorption or dialysis, which usually need


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laborious optimization in a preliminary stage. 12, 13, 42 Since CCD-2 can efficiently solubilize and stabilize diverse GPCRs and are readily degraded, we envisioned that CCD-2 would be an ideal initial detergent from which a simple and convenient protocol for the preparation of GPCR embedding nanodiscs could be established. Firstly, we investigated the self-assembly of empty nanodisc with different detergent removal methodologies. As showed in Figure 6A, the chemical cleavage methodology turned out to be perfectly compatible with the nanodisc assembly and yielded equal amount of empty nanodiscs to that of the control detergent-free group. By contrast, the traditional physical adsorption method seemingly brought in slightly more MSP aggregation and resulted in a lower nanodisc yield. Subsequently, an engineered construct of A2AR (MBP-A2AR-BRIL-ΔC) was applied to investigate the potential utility of this chemical strategy to deliver GPCRs into nanodiscs for electron microscopy studies. Since MBP-A2AR-BRIL-ΔC appeared to be less stable than the previous crystallization construct (A2AR-BRIL-ΔC), 20% CHS was applied to improve its thermostability during protein purification.5 Accordingly, both DDM/CHS and CCD-2/CHS yielded highly homogeneous monotopic A2AR samples (Figure S13). Following the complete decomposition of CCD-2 or physical adsorption of DDM, A2AR was in situ reconstituted into nanodiscs. The empty nanodiscs, redundant reagents as well as cleavage debris, were removed via immobilized metal affinity chromatography (IMAC) and the resulting reconstitution mixture was fractionated on SEC before EM analysis. Compared to the traditional physical protocol, the new reconstitution strategy produced a slightly better monodispersed peak of A2AR incorporated nanodiscs in FPLC profiles (Figure 6B). Of note, nanodiscs prepared according to the chemical protocol, both with and without the incorporated protein, showed the consistent size with those prepared according to the traditional physical method (Table S4). Furthermore, those A2AR


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incorporated nanodiscs prepared using the chemical approach were displayed as highly homogeneous particles in negative-stained EM (Figure 6C) and could be further clearly differentiated into nine representative classes with different orientations by 2D classification (Figure S14). So far, the chemical replacement strategy has proven to be a perfect complementary method to the existing physical approaches.

CONCLUSION In summary, we present here an alternative detergent replacement for MP reconstitution mediated by a class of chemically cleavable detergents. Thanks to the unique property of disulfide bonds, CCDs derived from DDM largely maintain the excellent capability in the manipulation of α-helix and β-barrel MPs while readily decompose for removal under mild condition. Based on this first proof-of-principle, other biocompatible bond-cleavage chemistry along with diverse triggering stimuli43, such as other reduction-induced cleavage reactions44, photo-induced decaging reactions45, metal-induced deallylation and depropargylation46-48, could potentially be used to expand the CCD repertoire. Compared to traditional physical methods, this chemical degradation is more a quantitative approach that facilitates MP reconstitution. In addition to detergent screening and nanodisc preparation, other speculative applications could also be investigated. For example, CCD-2 might be amenable to the precise bottom-up mass spectrometry proteomic studies of integral MPs by prompting full coverage digestion.49, 50 The CCD-based strategy should in the future speed up such innovation or upgrading of biophysics study.


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Figure 1. The in situ sacrifice-replacement strategy for reconstitution of MPs mediated by chemically cleavable detergents (CCDs).


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OH HO HO

O OH O HO

OH

O

X

OH

X = O n-Dodecyl-D-Maltopyranoside (DDM) X = S n-Dodecyl-D-Thiomaltoside (DTM) OH HO HO

O OH O HO

OH

O

S

OH

S

R

Chemically Cleavable Detergent (CCD) R= H Me Et n-Pr

CCD-1 CCD-2 CCD-3 CCD-4

Figure 2．Design of CCDs by the introduction of bioorthogonally cleavable disulfide bonds.


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Table 1. The molecular weight (MW), CMCs, the gyration radii (Rg) of their micelles and water solubility of DDM, DTM and CCDs.

Dets.

MWa CMCb (g/mol) (mM)

Rgc (Å)

Sol.d (w/v, %)

DDM

510.1

~ 0.17

31.7 ± 0.21

> 10

DTM

526.7

~ 0.05

37.7 ± 1.63

> 10

CCD-1

516.7

~ 0.50

23.8 ± 0.19

> 10

CCD-2

530.7

~ 0.20

28.9 ± 0.33

> 10

CCD-3

544.7

~ 0.07

30.0 ± 3.18

A Chemical Strategy for Amphiphile Replacement in Membrane

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