Name: co-translational insertion of membrane proteins into preformed nanodiscs
Uploaded: 2020-11-19T14:30:00.000+00:00
Duration: 8 min 24 s
Description: Watch this Scientific Journal Video about Co-Translational Insertion of Membrane Proteins into Preformed Nanodiscs at JoVE.com

We would like to thank the Deutsche Forschungsgemeinschaft (DFG) grant BE1911/8-1, the LOEWE project GLUE, and the collaborative research center Transport and Communication across Membranes (SFB807) for financial support.

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The authors have nothing to disclose.

The setup and strategies to optimize the CF expression and co-translational insertion of functional MPs into nanodiscs are described. The required equipment comprises a bioreactor, a French press device or similar, an UV/VIS and fluorescence reader, CF reaction vessels suitable for a two-compartment configuration setup, and a temperature-controlled incubator. Further standard equipment are centrifuges for harvesting E. coli cells as well as tabletop centrifuges reaching at least 30,000 x g for preparati...

Membrane proteins (MPs) are challenging targets in protein production studies due to their insolubility in aqueous environments. Conventional MP production platforms comprise cell-based systems such as E. coli, yeast, or eukaryotic cells. The synthesized recombinant MPs are either extracted from cell membranes or refolded from inclusion bodies1. After detergent solubilization, MPs can be transferred into suitable membrane environments by established in vitro reconstitution protocols. Besides vesicles and liposomes, MP reconstitution into planar membranes in the form of nanodiscs2 or salipro3 particles have become routine techniques in recent times. However, all these strategies imply detergent contact with MPs that can result in destabilization, dissociation of oligomers, and even loss of protein structure and activity4. Screening for optimal detergent solubilization and reconstitution conditions can therefore be tedious and time consuming5.
The open nature of cell-free (CF) systems allows the expression reaction to be directly supplied with preformed membranes with a defined lipid composition. In this lipid-based expression mode (L-CF), the synthesized MPs have the opportunity to co-translationally insert into the provided bilayers6,7 (Figure 1). Nanodiscs consisting of a membrane scaffold protein (MSP) surrounding a planar lipid bilayer disc8 appear to be particularly suitable for this strategy9,10. Nanodiscs can routinely be assembled in vitro with a variety of different lipids, they are very stable, and stocks can be concentrated up to 1 mM. However, MSP expression in E. coli and its purification is necessary. As an alternative strategy, MSP can be co-expressed together with the target MP in CF reactions supplied with liposomes11,12,13. DNA templates for both MSP and MP are added into the reaction and MP/nanodiscs can form upon expression. While MSP production is avoided, the co-expression strategy requires careful fine-tuning of the final DNA template concentrations and higher variations in the efficiency of sample production can be expected.
The co-translational insertion of MPs into membranes of preformed nanodiscs is a non-physiological and still largely unknown mechanism independent from translocon machineries and signal sequences13,14,15,16. Major determinants of the insertion efficiency are the type of membrane protein as well as the lipid composition of the provided membrane, with a frequent preference for negatively charged lipids15,17. As the nanodisc membranes are relatively confined in size, a substantial amount of lipids is released upon MP insertion18. Variation of nanodisc size enables insertion and tuning of higher oligomeric MP complexes15,18. Among others, the correct assembly of homooligomeric complexes was shown for the ion channel KcsA, for the ion pump proteorhodopsin (PR) and for the multidrug transporter EmrE15,18. MPs are likely to enter the symmetric nanodisc membrane from both sides at relatively equal frequency. It should therefore be considered that different monomers or oligomers inserted into one nanodisc may have opposite orientations. However, a bias in orientation could be caused by cooperative insertion mechanisms as reported for the formation of PR hexamers and KcsA tetramers18. A further bias in MP orientation might result from orientation switches of inserted MPs probably at the rim of the nanodisc membranes.
The production of CF lysates from E. coli strains is a reliable routine technique and can be performed in almost any biochemical laboratory19,20. It should be considered that besides disulfide bridge formation, most other post-translational modifications are absent if a MP is synthesized using E. coli lysates. While this might generate more homogenous samples for structural studies, it may be necessary to exclude potential effects on the function of individual MP targets. However, the efficient production of high quality samples of G-protein coupled receptors (GPCR)14,21,22, eukaryotic transporters23 or large heteromeric assemblies24 in E. coli CF lysates indicates their suitability for even complex targets. Preparative scale amounts (&#8776; 1 mg/mL) of a sample can be obtained with the two-compartment continuous exchange cell-free (CECF) configuration, composed of a reaction mixture (RM) and a feeding mixture (FM) compartment. The FM volume exceeds the RM volume 15 to 20-fold and provides a reservoir of low-molecular weight energy compounds and precursors19. The expression reaction is thus extended for several hours and the final yield of the MP target is increased. The RM and FM compartments are separated by a dialysis membrane with a 10-14 kDa cutoff. The two compartments require a special design of the CECF reaction container (Figure 1). Commercial dialysis cassettes as RM containers in combination with tailored plexiglass containers holding the FM are suitable examples. MP yields can further be manipulated by modifying the RM:FM ratios or by exchanging the FM after a certain period of incubation.
Yield and quality of a MP frequently require intense optimization of reaction parameters. An important advantage of CF expression is the possibility to modify and fine tune almost any compound according to the individual requirements of a MP. A straightforward strategy is to focus first on improving the yield of a MP by establishing a basic production protocol and then to optimize MP quality by fine tuning reaction and folding conditions. The absence of physiological processes in CF lysates and their reduced complexity result in high success rates for the efficient production of MPs25. Routine considerations for DNA template design and optimization of Mg2+ ion concentration are in most cases sufficient to obtain satisfactory yields26. Depending on expression mode, optimization of MP quality can become time consuming, as a larger variety of parameters need to be screened14,17,22.
To establish the described CF expression platform, protocols are necessary for the production of E. coli CF lysate (i), T7 RNA polymerase (ii), nanodiscs (iii), and the basic CECF reaction compounds (iv) (Figure 1). The E. coli K12 strain A1927 or BL21 derivatives are frequently used for the preparation of efficient S30 (centrifugation at 30,000 x g) lysates. Besides S30 lysates, corresponding lysates centrifuged at other g-forces (e.g. S12) may be used. The lysates differ in expression efficiency and in proteome complexity. The proteome of the S30 lysate prepared by the described protocol has been studied in detail28. The S30 proteome still contains some residual outer membrane proteins which could give background problems upon expression and analysis of ion channels. For such targets, the use of S80-S100 lysates is recommended. A valuable modification during lysate preparation is the induction of the SOS response by combined heat shock and ethanol supply at mid-log growth phase of the cells. The resulting HS30 lysates are enriched in chaperones and can be used in blends with S30 lysates for improved MP folding22. CF expression in E. coli lysates is operated as a coupled transcription/translation process with DNA templates containing promoters controlled by T7 RNA polymerase (T7RNAP). The enzyme can be efficiently produced in BL21(DE3) Star cells carrying the pAR1219 plasmid29.
Two copies of MSP1E3D1 assemble into one nanodisc with a diameter of 10-12 nm, but the protocol described below may also work for other MSP derivatives. However, nanodiscs larger than those formed with MSP1E3D1 tend to be less stable while smaller nanodiscs formed with MSP derivatives such as MSP1 may not accommodate larger MPs or MP complexes. MSP1E3D1 nanodiscs can be assembled in vitro with a large variety of different lipids or lipid mixtures. Preformed nanodiscs are usually stable for &#62; 1 year at -80 &#176;C, while stability may vary for different lipid components. For the screening of lipid effects on folding and stability of a MP, it is necessary to prepare a comprehensive set of nanodiscs assembled with a representative variety of lipids/lipid mixtures. The following lipids may give a good starting selection: 1,2-Dimyristoyl-sn-glycero-3-phospho-(1&#39;-rac-glycerol) (DMPG), 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), 1,2 dioleoyl-sn-glycero-3-phospho-rac-(1-glycerol) (DOPG), 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1&#39;-rac-glycerol) (POPG) and 1-palmitoyl-2-oleoyl-glycero-3-phosphocholine (POPC).
A protocol for the preparation of a 3 mL CECF reaction is described. Further up or down scaling in a 1:1 ratio is possible. For the two-compartment CECF configuration, a RM containing all compounds and a FM containing only the low-molecular weight compounds have to be prepared. Commercial 3 mL dialysis devices with 10-14 kDa MWCO can be used as RM containers, which are then placed into custom made plexiglass containers holding the FM (Figure 1D)30. The ratio of RM:FM is 1:20, so 60 mL of FM have to be prepared for 3 mL RM. Quality, concentration, or type of several components can be critical for the final yield and/or quality of the synthesized MP (Table 1). DNA templates should be prepared according to published guidelines and codon optimization of the reading frame of the target can further significantly improve product yield26. For preparative scale CECF reaction, an established protocol for the production of PR is described. To establish expression protocols for new MPs, it is usually necessary to perform optimization screens of certain compounds (Table 1) to improve yield and quality. For Mg2+ ions, a well-focused concentration optimum does exist that frequently shows significant variation for different DNA templates. Other CF reaction compounds such as new batches of T7RNAP or S30 lysates may further shift the optimal Mg2+ concentration. As an example, a typical Mg2+ screen within the range of 14-24 mM concentration and in steps of 2 mM is described. Each concentration is screened in duplicates and in analytical scale CECF reactions. As CECF reaction container, custom-made Mini-CECF Plexiglas containers30 holding the RM are used in combination with standard 24-well microplates holding the FM (Figure 1B). Alternatively, commercial dialysis cartridges in combination with 96-deep well microplates or other commercial dialyzer devices in appropriate setups may be used (Figure 1C).

<table><tbody><tr><td>1,2-dimyristoyl-sn-glycero-3-phospho-(1&#039;-rac-glycerol) (sodium salt) (DMPG)</td><td>Avanti Polar Lipids (USA)</td><td>840445P</td><td></td></tr><tr><td>1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC)</td><td>Avanti Polar Lipids (USA)</td><td>850345C</td><td></td></tr><tr><td>1,2-dioleoyl-sn-glycero-3-phosphocholine (sodium salt) (DOPC)</td><td>Avanti Polar Lipids (USA)</td><td>850375C</td><td></td></tr><tr><td>1,2 dioleoyl-sn-glycero-3-phospho-rac-(1-glycerol) (sodium salt) (DOPG)</td><td>Avanti Polar Lipids (USA)</td><td>840475C</td><td></td></tr><tr><td>1-palmitoyl-2-oleoyl-glycero-3-phosphocholine (POPC)</td><td>Avanti Polar Lipids (USA)</td><td>850457C</td><td></td></tr><tr><td>1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1&#039;-rac-glycerol) (sodium salt) (POPG)</td><td>Avanti Polar Lipids (USA)</td><td>840034C</td><td></td></tr><tr><td>2-Amino-2-(hydroxymethyl)-propan-1,3-diol (Tris)</td><td>Carl Roth (Germany)</td><td>4855</td><td></td></tr><tr><td>2-Mercaptoethanol</td><td>Carl Roth (Germany)</td><td>4227</td><td></td></tr><tr><td>2-Propanol</td><td>Carl Roth (Germany)</td><td>9781</td><td></td></tr><tr><td>[&lt;sup&gt;3&lt;/sup&gt;H]-dihydroalprenolol Hydrochloride</td><td>American Radiolabeled Chemicals (USA)</td><td>ART0134</td><td></td></tr><tr><td>Acetyl phosphate lithium potassium salt (ACP)</td><td>Merck (Germany)</td><td>1409</td><td></td></tr><tr><td>Adenosine 5&amp;rsquo;-triphosphate (ATP)</td><td>Sigma Aldrich (Germany)</td><td>A9251</td><td></td></tr><tr><td>Alprenolol hydrochloride</td><td>Merck (Germany)</td><td>A0360000</td><td></td></tr><tr><td>Anion exchange chromatography column material: Q-sepharose&amp;reg;</td><td>Sigma-Aldrich (Germany)</td><td>Q1126</td><td></td></tr><tr><td>Autoclave Type GE 446EC-1</td><td>Gettinge (Germany)</td><td></td><td></td></tr><tr><td>Bioreactor Type 884 124/1</td><td>B.Braun (Germany)</td><td></td><td></td></tr><tr><td>Centrifuge</td><td>Sorvall RC12BP+; Thermo Scientific (Germany); Sorvall RC-5C; Thermo Scientific (Germany); Mikro 22 R; Hettich (Germany)</td><td></td><td></td></tr><tr><td>Cholic acid</td><td>Carl Roth (Germany)</td><td>8137</td><td></td></tr><tr><td>Coomassie Brilliant Blue R250</td><td>Carl Roth (Germany)</td><td>3862</td><td></td></tr><tr><td>Culture flasks 500 ml baffled flasks, 2 l baffled flasks</td><td>Schott Duran (Germany)</td><td></td><td></td></tr><tr><td>Cytidine 5&#039;-triphosphate disodium salt</td><td>Sigma-Aldrich (Germany)</td><td>C1506</td><td></td></tr><tr><td>D-glucose monohydrate</td><td>Carl Roth (Germany)</td><td>6780</td><td></td></tr><tr><td>Di-potassiumhydrogen phosphate trihydrate</td><td>Carl Roth (Germany)</td><td>6878</td><td></td></tr><tr><td>Dialysis tubing Spectrum&lt;sup&gt;TM&lt;/sup&gt; Labs Spectra/Por&lt;sup&gt;TM&lt;/sup&gt; 12-14 kD MWCO Standard RC tubing</td><td>Fisher Scientific (Germany)</td><td>8700152</td><td></td></tr><tr><td>Dithiothreit</td><td>Carl Roth (Germany)</td><td>6908</td><td></td></tr><tr><td>Ethanol</td><td>Carl Roth (Germany)</td><td>K928</td><td></td></tr><tr><td>Folinic acid calcium salt hydrate</td><td>Sigma-Aldrich (Germany)</td><td>47612</td><td></td></tr><tr><td>French pressure cell disruptor</td><td>SLM; Amico Instruments (USA)</td><td></td><td></td></tr><tr><td>Glycerol</td><td>Carl Roth (Germany)</td><td>3783</td><td></td></tr><tr><td>Guanosine 5&#039;-triphosphate di-sodium salt (GTP)</td><td>Sigma-Aldrich (Germany)</td><td>G8877</td><td></td></tr><tr><td>Hydrochloric Acid</td><td>Carl Roth (Germany)</td><td>K025</td><td></td></tr><tr><td>IMAC column: HiTrap IMAC HP 5 mL</td><td>GE Life Sciences (Germany)</td><td>GE17-5248</td><td></td></tr><tr><td>Imidazole</td><td>Carl Roth (Germany)</td><td>3899</td><td></td></tr><tr><td>Isopropyl-&amp;beta;-D-thiogalactopyranosid (IPTG)</td><td>Carl Roth (Germany)</td><td>2316</td><td></td></tr><tr><td>Kanamycin</td><td>Carl Roth (Germany)</td><td>T832</td><td></td></tr><tr><td>L-Alanine</td><td>Carl Roth (Germany)</td><td>3076.1</td><td></td></tr><tr><td>L-Arginine</td><td>Carl Roth (Germany)</td><td>6908</td><td></td></tr><tr><td>L-Asparagine</td><td>Carl Roth (Germany)</td><td>HN23</td><td></td></tr><tr><td>L-Aspartic Acid</td><td>Carl Roth (Germany)</td><td>T202</td><td></td></tr><tr><td>L-Cysteine</td><td>Carl Roth (Germany)</td><td>T203</td><td></td></tr><tr><td>L-Glutamic Acid</td><td>Carl Roth (Germany)</td><td>3774</td><td></td></tr><tr><td>L-Glutamine</td><td>Carl Roth (Germany)</td><td>3772</td><td></td></tr><tr><td>L-Glycine</td><td>Carl Roth (Germany)</td><td>3187</td><td></td></tr><tr><td>L-Histidine</td><td>Carl Roth (Germany)</td><td>3852</td><td></td></tr><tr><td>L-Isoleucine</td><td>Carl Roth (Germany)</td><td>3922</td><td></td></tr><tr><td>L-Leucine</td><td>Carl Roth (Germany)</td><td>1699</td><td></td></tr><tr><td>L-Lysine</td><td>Carl Roth (Germany)</td><td>4207</td><td></td></tr><tr><td>L-Methionine</td><td>Carl Roth (Germany)</td><td>9359</td><td></td></tr><tr><td>L-Proline</td><td>Carl Roth (Germany)</td><td>1713</td><td></td></tr><tr><td>L-Phenylalanine</td><td>Carl Roth (Germany)</td><td>1709</td><td></td></tr><tr><td>L-Serine</td><td>Carl Roth (Germany)</td><td>4682</td><td></td></tr><tr><td>L-Threonine</td><td>Carl Roth (Germany)</td><td>1738</td><td></td></tr><tr><td>L-Tryptophane</td><td>Carl Roth (Germany)</td><td>7700</td><td></td></tr><tr><td>L-Tyrosine</td><td>Carl Roth (Germany)</td><td>T207</td><td></td></tr><tr><td>MD100 dialysis units</td><td>Scienova (Germany)</td><td>40077</td><td></td></tr><tr><td>&lt;em&gt;N-2&lt;/em&gt;-Hydroxyethylpiperazine-&lt;em&gt;N&#039;-2&lt;/em&gt;-ethansulfonic acid (HEPES)</td><td>Carl Roth (Germany)</td><td>6763</td><td></td></tr><tr><td>n-dodecylphosphocholine</td><td>Antrace (USA)</td><td>F308S</td><td></td></tr><tr><td>PAGE chamber: Mini-Protean Tetra Cell</td><td>Biorad (Germany)</td><td></td><td></td></tr><tr><td>PAGE gel casting system: Mini Protean Handcast systems</td><td>Biorad (Germany)</td><td></td><td></td></tr><tr><td>PAGE gel power supply: Power Pac 3000</td><td>Biorad (Germany)</td><td></td><td></td></tr><tr><td>Tryptone/peptone from caseine</td><td>Carl Roth (Germany)</td><td>6681</td><td></td></tr><tr><td>Peristaltic pump: ip-12</td><td>Ismatec (Germany)</td><td></td><td></td></tr><tr><td>Phosphoenol pyruvate monopotassium salt</td><td>Sigma Aldrich (Germany)</td><td>860077</td><td></td></tr><tr><td>Potassium dihydrogen phosphate</td><td>Carl Roth (Germany)</td><td>P018</td><td></td></tr><tr><td>Potassium acetate</td><td>Carl Roth (Germany)</td><td>4986</td><td></td></tr><tr><td>Potassium chloride</td><td>Carl Roth (Germany)</td><td>6781</td><td></td></tr><tr><td>Pyruvate Kinase</td><td>Roche (Germany)</td><td>10109045001</td><td></td></tr><tr><td>Scintillation counter: Hidex 300 SL</td><td>Hidex (Finland)</td><td></td><td></td></tr><tr><td>SDS pellets</td><td>Carl Roth (Germany)</td><td>8029</td><td></td></tr><tr><td>Sodium azide</td><td>Sigma-Aldrich (Germany)</td><td>K305</td><td></td></tr><tr><td>Sodium chloride</td><td>Carl Roth (Germany)</td><td>P029</td><td></td></tr><tr><td>Spectrophotometer Nanodrop</td><td>Peqlab (Germany)</td><td></td><td></td></tr><tr><td>Spectrophotometer/fluorescence reader Spark&amp;reg;</td><td>Tecan (Switzerland)</td><td></td><td></td></tr><tr><td>tRNA (E. coli)</td><td>Roche (Germany)</td><td>10109550001</td><td></td></tr><tr><td>Ultra sonificator</td><td>Labsonic U, B. Braun (Germany)</td><td></td><td></td></tr><tr><td>Uridine 5&amp;rsquo;-triphosphate tri-sodium salt (UTP)</td><td>Sigma-Aldrich (Germany)</td><td>U6625</td><td></td></tr><tr><td>Y-30 antifoam</td><td>Sigma-Aldrich (Germany)</td><td>A6457</td><td></td></tr><tr><td>Yeast extract</td><td>Carl Roth (Germany)</td><td>2904</td><td></td></tr></tbody></table>

co-translational insertion of membrane proteins into preformed nanodiscs

Cell-free expression systems allow the tailored design of reaction environments to support the functional folding of even complex proteins such as membrane proteins. The experimental procedures for the co-translational insertion and folding of membrane proteins into preformed and defined membranes supplied as nanodiscs are demonstrated. The protocol is completely detergent-free and can generate milligrams of purified samples within one day. The resulting membrane protein/nanodisc samples can be used for a variety of functional studies and structural applications such as crystallization, nuclear magnetic resonance, or electron microscopy. The preparation of basic key components such as cell-free lysates, nanodiscs with designed membranes, critical stock solutions as well as the assembly of two-compartment cell-free expression reactions is described. Since folding requirements of membrane proteins can be highly diverse, a major focus of this protocol is the modulation of parameters and reaction steps important for sample quality such as critical basic reaction compounds, membrane composition of nanodiscs, redox and chaperone environment, or DNA template design. The whole process is demonstrated with the synthesis of proteorhodopsin and a G-protein coupled receptor.

The impact of fine-tuning reaction compounds on the final yield or quality of synthesized MPs is exemplified. A frequent routine approach is to adjust the optimal Mg2+ concentration in CF reactions by expression of green fluorescent protein (GFP) as a convenient monitor of system efficiency. As an example, GFP was synthesized from a pET-21a(+) vector at Mg2+ concentrations between 14 and 24 mM (Figure 2). SDS-PAGE analysis identified the optimal Mg2+ concentr...

Watch this Scientific Journal Video about Co-Translational Insertion of Membrane Proteins into Preformed Nanodiscs at JoVE.com

Co-Translational Insertion of Membrane Proteins into Preformed Nanodiscs

Co-translational insertion into pre-formed nanodiscs makes it possible to study cell-free synthesized membrane proteins in defined lipid environments without contact with detergents. This protocol describes the preparation of essential system components and the critical parameters for improving expression efficiency and sample quality.

Cell-free expression systems allow the tailored design of reaction environments to support the functional folding of even complex proteins such as ...

co-translational-insertion-membrane-proteins-into-preformed

Research

JoVE Journal

Biochemistry

3.3K Views.  Goethe University Frankfurt. Co-translational insertion into pre-formed nanodiscs makes it possible to study cell-free synthesized membrane proteins in defined lipid environments without contact with detergents. This protocol describes the preparation of essential system components and the critical parameters for improving expression efficiency and sample quality.

Video: Co-Translational Insertion of Membrane Proteins into Preformed Nanodiscs

Method to Visualize and Analyze Membrane Interacting Proteins by Transmission Electron Microscopy

Monotopic proteins exert their function when attached to a membrane surface, and such interactions depend on the specific lipid composition and on the availability of enough area to perform the function. Nanodiscs are used to provide a membrane surface of controlled size and lipid content. In the absence of bound extrinsic proteins, sodium phosphotungstate-stained nanodiscs appear as stacks of coins when viewed from the side by transmission electron microscopy (TEM). This protocol is therefore designed to intentionally promote stacking; consequently, the prevention of stacking can be interpreted as the binding of the membrane-binding protein to the nanodisc. In a further step, the TEM images of the protein-nanodisc complexes can be processed with standard single-particle methods to yield low-resolution structures as a basis for higher resolution cryoEM work. Furthermore, the nanodiscs provide samples suitable for either TEM or non-denaturing gel electrophoresis. To illustrate the method, Ca2+-induced binding of 5-lipoxygenase on nanodiscs is presented.

Many proteins perform their function when attached to membrane surfaces. The binding of extrinsic proteins on nanodisc membranes can be indirectly imaged by transmission electron microscopy. We show that the characteristic stacking (rouleau) of nanodiscs induced by the negative stain sodium phosphotungstate is prevented by the binding of extrinsic protein.

Monotopic proteins exert their function when attached to a membrane surface, and such interactions depend on the specific lipid composition and on the ...

Analysis of Endocytic Uptake and Retrograde Transport to the Trans-Golgi Network Using Functionalized Nanobodies in Cultured Cells

Transport of proteins and membranes from the cell surface to the Golgi and beyond is essential for homeostasis, organelle identity and physiology. To study retrograde protein traffic, we have recently developed a versatile nanobody-based toolkit to analyze transport from the cell surface to the Golgi complex, either by fixed and live cell imaging, by electron microscopy, or biochemically. We engineered functionalized anti-green fluorescent protein (GFP) nanobodies &#8212; small, monomeric, high-affinity protein binders &#8212; that can be applied to cell lines expressing membrane proteins of interest with an extracellular GFP moiety. Derivatized nanobodies bound to the GFP reporters are specifically internalized and transported piggyback along the reporters&#39; sorting routes. Nanobodies were functionalized with fluorophores to follow retrograde transport by fluorescence microscopy and live imaging, with ascorbate peroxidase 2 (APEX2) to investigate the ultrastructural localization of reporter-nanobody complexes by electron microscopy, and with tyrosine sulfation (TS) motifs to assess kinetics of trans-Golgi network (TGN) arrival. In this methodological article, we outline the general procedure to bacterially express and purify functionalized nanobodies. We illustrate the powerful use of our tool using the mCherry- and TS-modified nanobodies to analyze endocytic uptake and TGN arrival of cargo proteins.

Retrograde transport of proteins from the cell surface to the Golgi is essential to maintain membrane homeostasis. Here, we describe a method to biochemically analyze cell surface-to-Golgi transport of recombinant proteins using functionalized nanobodies in HeLa cells.

Transport of proteins and membranes from the cell surface to the Golgi and beyond is essential for homeostasis, organelle identity and physiology. To ...

Native Cell Membrane Nanoparticles System for Membrane Protein-Protein Interaction Analysis

Protein-protein interactions in cell membrane systems play crucial roles in a wide range of biological processes- from cell-to-cell interactions to signal transduction; from sensing environmental signals to biological response; from metabolic regulation to developmental control. Accurate structural information of protein-protein interactions is crucial for understanding the molecular mechanisms of membrane protein complexes and for the design of highly specific molecules to modulate these proteins. Many in vivo and in vitro approaches have been developed for the detection and analysis of protein-protein interactions. Among them the structural biology approach is unique in that it can provide direct structural information of protein-protein interactions at the atomic level. However, current membrane protein structural biology is still largely limited to detergent-based methods. The major drawback of detergent-based methods is that they often dissociate or denature membrane protein complexes once their native lipid bilayer environment is removed by detergent molecules. We have been developing a&#160;native cell membrane nanoparticle system for membrane protein structural biology. Here, we demonstrate the use of this system in the analysis of protein-protein interactions on the cell membrane with a case study of the oligomeric state of AcrB.

Presented here is a protocol for the determination of oligomeric state of membrane proteins that utilizes a native cell membrane nanoparticle system in conjunction with electron microscopy.

Protein-protein interactions in cell membrane systems play crucial roles in a wide range of biological processes- from cell-to-cell interactions to signal ...

Formulation and Characterization of Bioactive Agent Containing Nanodisks

The term nanodisk refers to a discrete type of nanoparticle comprised of a bilayer forming lipid, a scaffold protein, and an integrated bioactive agent. Nanodisks are organized as a disk-shaped lipid bilayer whose perimeter is circumscribed by the scaffold protein, usually a member of the exchangeable apolipoprotein family. Numerous hydrophobic bioactive agents have been efficiently solubilized in nanodisks by their integration into the hydrophobic milieu of the particle&#39;s lipid bilayer, yielding a largely homogenous population of particles in the range of 10-20 nm in diameter. The formulation of nanodisks requires a precise ratio of individual components, an appropriate sequential addition of each component, followed by bath sonication of the formulation mixture. The amphipathic scaffold protein spontaneously contacts and reorganizes the dispersed bilayer forming lipid/bioactive agent mixture to form a discrete, homogeneous population of nanodisk&#160;particles. During this process, the reaction mixture transitions from an opaque, turbid appearance to a clarified sample that, when fully optimized, yields no precipitate upon centrifugation. Characterization studies involve the determination of bioactive agent solubilization efficiency, electron microscopy, gel filtration chromatography, ultraviolet visible (UV/Vis) absorbance spectroscopy, and/or fluorescence spectroscopy. This is normally followed by an investigation of biological activity using cultured cells or mice. In the case of nanodisks harboring an antibiotic (i.e., the macrolide polyene antibiotic amphotericin B), their ability to inhibit the growth of yeast or fungi as a function of concentration or time can be measured. The relative ease of formulation, versatility with respect to component parts, nanoscale particle size, inherent stability, and aqueous solubility permits myriad in vitro and in vivo applications of nanodisk technology. In the present article, we describe a general methodology to formulate and characterize nanodisks containing amphotericin&#160;B as the hydrophobic bioactive agent.

Here, we describe the production and characterization of bioactive agents containing nanodisks. Amphotericin B nanodisks are taken as an example to describe the protocol in a stepwise manner.

The term nanodisk refers to a discrete type of nanoparticle comprised of a bilayer forming lipid, a scaffold protein, and an integrated bioactive agent. ...

A Step-by-step Method for the Reconstitution of an ABC Transporter into Nanodisc Lipid Particles

The nanodisc is a discoidal particle (~ 10-12 nm large) that trap membrane proteins into a small patch of phospholipid bilayer. The nanodisc is a particularly attractive option for studying membrane proteins, especially in the context of ligand-receptor interactions. The method pioneered by Sligar and colleagues is based on the amphipathic properties of an engineered highly a-helical scaffold protein derived from the apolipoprotein A1. The hydrophobic faces of the scaffold protein interact with the fatty acyl side-chains of the lipid bilayer whereas the polar regions face the aqueous environment. Analyses of membrane proteins in nanodiscs have significant advantages over liposome because the particles are small, homogeneous and water-soluble. In addition, biochemical and biophysical methods normally reserved to soluble proteins can be applied, and from either side of the membrane. In this visual protocol, we present a step-by-step reconstitution of a well characterized bacterial ABC transporter, the MalE-MalFGK2 complex. The formation of the disc is a self-assembly process that depends on hydrophobic interactions taking place during the progressive removal of the detergent. We describe the essential steps and we highlight the importance of choosing a correct protein-to-lipid ratio in order to limit the formation of aggregates and larger polydisperse liposome-like particles. Simple quality controls such as gel filtration chromatography, native gel electrophoresis and dynamic light scattering spectroscopy ensure that the discs have been properly reconstituted.

Nanodiscs are small discoid particles that incorporate membrane proteins into a small patch of phospholipid bilayer. We provide a visual protocol that shows the step-by-step incorporation of the MalFGK2 transporter into a disc.

The nanodisc is a discoidal particle (~ 10-12 nm large) that trap membrane proteins into a small patch of phospholipid bilayer. The nanodisc is a ...

Biology

Light-Controlled Reversible Protein Patterning on Lipid Membranes

Dynamic Light-Induced Protein Patterns at Model Membranes

The precise localization and activation of proteins at the cell membrane at a certain time gives rise to many cellular processes, including cell polarization, migration, and division. Thus, methods to recruit proteins to model membranes with subcellular resolution and high temporal control are essential when reproducing and controlling such processes in synthetic cells. Here, a method is described for fabricating light-regulated reversible protein patterns at lipid membranes with high spatiotemporal precision. For this purpose, we immobilize the photoswitchable protein iLID (improved light-inducible dimer) on supported lipid bilayers (SLBs) and on the outer membrane of giant unilamellar vesicles (GUVs). Upon local blue light illumination, iLID binds to its partner Nano (wild-type SspB) and allows the recruitment of any protein of interest (POI) fused to Nano from the solution to the illuminated area on the membrane. This binding is reversible in the dark, which provides dynamic binding and release of the POI. Overall, this is a flexible and versatile method for regulating the localization of proteins with high precision in space and time using blue light.

Author Spotlight: Photo Switchable Protein Recruitment for Reversible Patterning in Artificial Cellular Systems

Here, a protocol is described for generating light-regulated and reversible protein patterns with high spatiotemporal precision at artificial lipid membranes. The method consists of the localized photoactivation of the protein iLID (improved light-inducible dimer) immobilized on model membranes that, under blue light, binds to its partner protein Nano (wild-type SspB).

The precise localization and activation of proteins at the cell membrane at a certain time gives rise to many cellular processes, including cell ...

Bioengineering

Protein Translocation Machinery on the ER Membrane

The translocon complex situated on the ER membrane is the main gateway for the protein secretory pathway. It facilitates the transport of nascent peptides into the ER lumen and their insertion into the ER membrane.
Sec61 protein conducting channel
In eukaryotes, the translocon complex comprises a core heterotrimeric translocator channel called the Sec61 complex. This channel includes three transmembrane proteins, Sec61&#945;, Sec61&#946;, and Sec61&#947;, and is the largest subunit of the translocon complex. In higher eukaryotes, such as mammals, the channel is capped in its resting state to prevent the leakage of ions like calcium into the cytosol.
Accessory protein complexes associated with the Sec61 channel
Sec62 and Sec63 are integral transmembrane proteins associated with the Sec61 complex. They are primarily involved in the functioning of the Sec61 channel&#39;s lateral gate and aid in the exit of the signal sequence and transmembrane domains into the lipid bilayer.
The translocon-associated protein or TRAP complex is a hetero-tetrameric constitutive subunit of the translocon complex, present behind the Sec61 channel. It assists in the binding of signal peptides having low hydrophobicity to the Sec61 channel. The oligosaccharyltransferase (OST) complex is another closely associated complex, which transfers pre-assembled glycans to select asparagine residues.
Some proteins, like the signal peptidase complex, associate with the translocon complex under specific conditions. For instance, the signal recognition particle receptor (SR) only interacts with the Sec61 channel to hand over the ribosome-nascent peptide complex during active translocation. Other proteins like lectin chaperones (calnexin and malectin) and sensor molecules (IRE1) associate with the translocon to correctly fold the incoming polypeptide or signal misfolded proteins.

The translocon complex situated on the ER membrane is the main gateway for the protein secretory pathway. It facilitates the transport of nascent peptides ...

Education

JoVE Core

Cell Biology

Unit 1

Transmembrane Transport in Endoplasmic Reticulum and Peroxisomes

KEY TERMS AND CONCEPTS

Cotranslational Protein Translocation

Translocation of proteins across membranes is an ancient process that occurs even in bacteria and archaebacteria. In fact, the components of the translocation machinery are still conserved between prokaryotes and eukaryotes.
Sec61 channel partners for cotranslational translocation
During cotranslational translocation, the Sec61 channel partners with the signal recognition particle (SRP), the signal recognition particle receptor (SR), and the ribosomes to transport the nascent polypeptide chain into the lumen.
SRP mediates ribosome attachment to the Sec61 complex via the polypeptide exit tunnel of the large ribosomal subunit. The GTPase domains on both SRP and SR carry out GTP hydrolysis, which supports the transfer of the target polypeptide to the Sec61 channel. Subsequently, the ribosomes act as primary translocation motors and push the protein towards the ER lumen. Except for the GTPs spent during peptide chain elongation, no additional energy is expended for the protein to descend through the channel.&#160;
Accessory translocon complex proteins involved in cotranslational translocation
The translocating chain-associating membrane (TRAM) protein and translocon-associated protein (TRAP) complex are auxiliary components associated with the Sec61 channel during SRP-mediated translocation. The TRAP complex is a substrate-specific complex essential for secure anchoring of the signal sequences having low hydrophobicity. Its proteins directly interact with Sec61 and keep the channel in open confirmation to compensate for the weak interaction with the signal sequence.
On the other hand, TRAM is a membrane protein that acts as a chaperone. It assists in folding and membrane integration of cotranslationally translocating proteins.

Translocation of proteins across membranes is an ancient process that occurs even in bacteria and archaebacteria. In fact, the components of the ...

Post-translational Translocation of Proteins to the RER

A sizable fraction of proteins destined for ER are first synthesized in the cell cytosol and then transported across the ER membrane&#8211;a process called post-translational translocation. Similar to cotranslationally translocated proteins, these proteins also use the Sec translocon complex to enter the ER lumen.
Targeting proteins to the ER
Hsp40 and Hsp70 chaperone molecules bind the translated proteins in the cytosol to prevent their folding. The chaperone binding helps to keep the signal sequence present on the target proteins available for interaction with the recognition site on the Sec61 channel.
The ER signal sequence of proteins translocating post-translation has characteristic features that distinguish them from cotranslationally translocated proteins. For example, in yeast, the signal sequence of post-translationally translocated proteins is relatively less hydrophobic compared to the signal sequence of cotranslationally translocating proteins. In contrast, in mammalian systems, the target proteins have a characteristic short positively charged N-terminal.
Translocon partners for post-translational translocation
All proteins enter the ER lumen using the Sec61 channel but the channel partners vary depending on whether it is a cotranslational or a post-translational translocation process. Sec62 and Sec63 play an important role during post-translational translocation. Sec62 has a strong affinity for the ER signal sequence present on the cytosol-translated proteins, while Sec63 has a specialized domain that hydrolyzes the ATP to allow the BiP chaperone to bind to the incoming protein. BiP chaperone is a lumenal chaperone that keeps the protein loosely folded or unfolded till it has attained the appropriate secondary structure. Together, the Sec62/63 complex and the BiP chaperone are involved in actively pulling the protein into the ER lumen by a Brownian ratcheting mechanism.
Other functions of the Sec proteins
Besides their central role in translocating proteins, Sec proteins are essential in other cell functions and diseases. For example,&#160; Sec62 is involved in the stress recovery of cells, while the Sec61 channel can double up as a passive ER calcium leak channel. Additionally, mutations and overexpression of the SEC genes are linked to diabetes, cancer, and various kidney and liver disorders in humans.

A sizable fraction of proteins destined for ER are first synthesized in the cell cytosol and then transported across the ER membrane&#8211;a process ...

Insertion of Single-pass Transmembrane Proteins in the RER

Integral membrane proteins are proteins adhered to the lipid bilayer of a cell organelle or membrane. They can be of two types: transmembrane integral proteins that span the lipid bilayer and monotopic proteins that are attached to either side of the membrane but do not pass through it.
Integral transmembrane proteins possess transmembrane and extra membrane domains. The transmembrane domains are primarily made of 20-25 hydrophobic amino acids arranged in a helical secondary confirmation. These domains are stable enough to be embedded in the phospholipid interior of the membrane and are critical in determining the protein&#39;s topology. Such proteins are inserted into the ER membrane co-translationally and are broadly categorized as single-pass and multipass transmembrane proteins. There are three types of single-pass transmembrane proteins with a single domain traversing through the membrane.
Type I membrane proteins have a cleavable ER-signal sequence, a single transmembrane domain, the N terminal placed in the ER lumen. It has two distinct sequences to start and stop the polypeptide transfer through the translocon on the ER membrane. The human growth hormone receptor is a type I transmembrane protein.
Type II membrane proteins also have a single transmembrane domain, but it acts as a non-cleavable signal sequence and a membrane anchor, unlike type I membrane proteins. The transmembrane domain of the type II proteins is also called the signal anchor sequence. This sequence is always preceded by positive amino acid residues that prevent the N terminal of the polypeptide chain from slipping down into the translocon. Hence, the C terminal of type II proteins is oriented inside the ER lumen. The transferrin receptor and the Golgi galactosyltransferase are examples of a type II membrane protein.
Type III membrane proteins are similar to type II proteins in terms of the transmembrane domain structure; however, the positive amino acid residues are placed after the signal-anchor sequence. Thus, their N terminal is inserted into the translocon, and the C terminal is left out in the cytosol. Cytochrome P40 is a type III membrane protein.

Integral membrane proteins are proteins adhered to the lipid bilayer of a cell organelle or membrane. They can be of two types: transmembrane integral ...