Solubilization Of Integral Membrane Proteins Research Articles

Strategies for the Purification of Membrane Proteins.

Membrane proteins account for approximately 30% of the coding regions of all sequenced genomes, and they play crucial roles in many fundamental cell processes. However, there are relatively few membrane proteins with known three-dimensional structures. This is likely due to technical challenges associated with membrane protein extraction, solubilization, and purification. Membrane proteins are classified based on the level of interaction with membrane lipid bilayers, with peripheral membrane proteins associating non-covalently with the membrane, and integral membrane proteins associating more strongly by means of hydrophobic interactions. Generally speaking, peripheral membrane proteins can be purified by milder techniques than integral membrane proteins, with the latter's extraction requiring phospholipid bilayer disruption using detergents or organic solvents. In this chapter, important considerations for membrane protein purification are addressed, with a focus on the initial stages of membrane protein solubilization, where problems are most frequently encountered. Protocols are outlined for the extraction of peripheral membrane proteins, solubilization of integral membrane proteins, and sample clean-up and concentration.

A water-soluble DsbB variant that catalyzes disulfide-bond formation in vivo.

Escherichia coli DsbB is a transmembrane enzyme that catalyzes the re-oxidation of the periplasmic oxidase DsbA by ubiquinone. Here, we sought to convert membrane-bound DsbB into a water-soluble biocatalyst by leveraging a previously described method for in vivo solubilization of integral membrane proteins (IMPs). When solubilized DsbB variants were co-expressed with an export-defective copy of DsbA in the cytoplasm of wild-type E. coli cells, artificial oxidation pathways were created that efficiently catalyzed de novo disulfide bond formation in a range of substrate proteins and in a manner that depended on both DsbA and quinone. Hence, DsbB solubilization was achieved with preservation of both catalytic activity and substrate specificity. Moreover, given the generality of the solubilization technique, the results presented here should pave the way for unlocking the biocatalytic potential of other membrane-bound enzymes whose utility has been limited by poor stability of IMPs outside of their native lipid bilayer context.

Solubilization of G protein-coupled receptors: a convenient strategy to explore lipid-receptor interaction.

G protein-coupled receptors (GPCRs) are the largest class of molecules involved in signal transduction across cell membranes and are major drug targets. Since GPCRs are integral membrane proteins, their structure and function are modulated by membrane lipids. In particular, membrane cholesterol is an important lipid in the context of GPCR function. Solubilization of integral membrane proteins is a process in which the proteins and lipids in native membranes are dissociated in the presence of a suitable amphiphilic detergent. Interestingly, solubilization offers a convenient approach to monitor lipid-receptor interaction as it results in differential extents of lipid solubilization, thereby allowing to assess the role of specific lipids on receptor function. In this review, we highlight how this solubilization strategy is utilized to decipher novel information about the structural stringency of cholesterol necessary for supporting the function of the serotonin(1A) receptor. We envision that insight in GPCR-lipid interaction would result in better understanding of GPCR function in health and disease.

Modeling Detergent Organization around Aquaporin-0 Using Small-Angle X-ray Scattering

Solubilization of integral membrane proteins in aqueous solutions requires the presence of amphiphilic molecules like detergents. The transmembrane region of the proteins is then surrounded by a corona formed by these molecules, ensuring a hydrophilic outer surface. The presence of this corona has strongly hampered structural studies of solubilized membrane proteins by small-angle X-ray scattering (SAXS), a technique frequently used to monitor conformational changes of soluble proteins. Through the online combination of size exclusion chromatography, SAXS, and refractometry, we have determined a precise geometrical model of the n-dodecyl β-d-maltopyranoside corona surrounding aquaporin-0, the most abundant membrane protein of the eye lens. The SAXS data were well-fitted by a detergent corona shaped in an elliptical toroid around the crystal structure of the protein, similar to the elliptical shape recently reported for nanodiscs (Skar-Gislinge et al. J. Am. Chem. Soc. 2010, 132, 13713-13722). The torus thickness determined from the curve-fitting protocol is in excellent agreement with the thickness of a lipid bilayer, while the number of detergent molecules deduced from the volume of the torus compares well with those obtained on the same sample from refractometry and mass analysis based on SAXS forward scattering. For the first time, the partial specific volume of the detergent surrounding a protein was measured. The present protocol is a crucial step toward future conformational studies of membrane proteins in solution.

Integral Membrane Proteins in Nanodiscs Can Be Studied by Solution NMR Spectroscopy

We present a two-dimensional solution NMR spectrum of an integral membrane protein (IMP) in a nanodisc. Solution NMR relies on rapid isotropic tumbling of the analyte with correlation times in the nanosecond range. IMPs in a cellular membrane do not satisfy this condition. Previous liquid-state NMR studies on IMPs were conducted in organic solvent or artificial membrane mimicking particles like detergent micelles. Nanodiscs are relatively small (150 kDa), detergent-free model membranes that are suitable for functional reconstitution of IMPs. Nanodiscs allow solubilization of integral membrane proteins in a nearly native lipid bilayer environment. The 70 residue polypeptide CD4mut was incorporated into nanodiscs. CD4mut features one transmembrane helix. The aliphatic (1)H-(13)C HSQC spectrum of nanodiscs with inserted, ((13)C, (15)N)-labeled CD4mut exhibits reasonably dispersed protein and lipid NMR signals. Our results demonstrate that IMPs in nanodiscs are amenable to liquid-state NMR methodology.

Thematic Review Series: Proteomics. Proteomic analysis of lipid-protein complexes

There is intense interest in comprehensive proteomic approaches for analyzing integral membrane proteins and lipoproteins. Key features of mass spectrometric analysis center on enriching biological material for proteins of interest, efficiently digesting them, extracting the resulting peptides, and using fractionation methods to comprehensively sample proteins or peptides by tandem mass spectrometry. However, lipid-associated proteins are generally rich in hydrophobic domains and are often low in abundance. These features, together with the associated lipid, make their mass spectrometric analysis technically challenging. In this article, we review analytical strategies for successful proteomic analysis of lipid-associated proteins.

Blue Native/SDS-PAGE Analysis Reveals Reduced Expression of the mClCA3 Protein in Cystic Fibrosis Knock-out Mice

Cystic fibrosis (CF) is a frequent autosomal recessive disorder caused by mutation of a gene encoding a multifunctional transmembrane protein, the cystic fibrosis transmembrane conductance regulator (CFTR), located in the apical membrane of epithelial cells lining exocrine glands. In an attempt to get a more complete picture of the pleiotropic effects of the CFTR defect on epithelial cells and particularly on the membrane compartment, a bidimensional blue native (BN)/SDS-PAGE-based proteomic approach was used on colonic crypt samples from control and CFTR knock-out mice (cftr-/-). This approach overcomes the difficulties of membrane protein analysis by conventional two-dimensional PAGE and is able to resolve multiprotein complexes. Used here for the first time on crude membrane proteins that were extracted from murine colonic crypts, BN/SDS-PAGE allows effective separation of protein species and complexes of various origins, including mitochondria, plasma membrane, and intracellular compartments. The major statistically significant difference in protein maps obtained with samples from control and cftr-/- mice was unambiguously identified as mClCA3, a member of a family of calcium-activated chloride channels considered to be key molecules in mucus secretion by goblet cells. On the basis of this finding, we evaluated the overall expression and localization of mClCA3 in the colonic epithelium and in the lung of mice by immunoblot analysis and immunohistochemistry. We found that mClCA3 expression was significantly decreased in the colon and lung of the cftr-/- mice. In an ex vivo assay, we found that the Ca2+-dependent (carbachol-stimulated) glycoprotein secretion strongly inhibited by the calcium-activated chloride channel blocker niflumic acid (100 microm) was impaired in the distal colon of cftr-/- mice. These results support the conclusion that a ClCA-related function in the CF colon depends on CFTR expression and may be correlated with the impaired expression of mClCA3.

Membrane Protein Solubilization: Recent Advances and Challenges in Solubilization of Serotonin1A Receptors

Solubilization of integral membrane proteins is a process in which the proteins and lipids that are held together in native membranes are suitably dissociated in a buffered detergent solution. The controlled dissociation of the membrane results in formation of small protein and lipid clusters that remain dissolved in the aqueous solution. Effective solubilization and purification of membrane proteins, especially heterologously-expressed proteins in mammalian cells in culture, in functionally active forms represent important steps in understanding structure-function relationship of membrane proteins. In this review, critical factors determining functional solubilization of membrane proteins are highlighted with the solubilization of the serotonin 1A receptor taken as a specific example.

Application of zwitterionic detergents to the solubilization of integral membrane proteins for two-dimensional gel electrophoresis and mass spectrometry.

Comparative analysis has long been utilized in biological research to interpret protein interactions in both drug naïve versus drug challenged and normal versus diseased tissues. The technology of proteomics today allows researchers to provide insight into old and still open questions related to biological mechanisms while offering the opportunity to discover novel details in cellular lifecycles. Perhaps the most powerful way to execute these differential displays is in the combination of two-dimensional (2-D) gel electrophoresis and mass spectrometry. While these two techniques together are well suited for abundant and soluble proteins found in cells, rare proteins and integral membrane proteins are still problematic. Recently, a series of novel zwitterionic detergents has been reported in the literature that shows a substantial improvement in solubilizing integral membrane proteins. We show that the amidosulfobetaine, 4-octylbenzol amidosulfobetaine, is better than 3-[(3-cholamidopropyl)dimethylamino]-1-propanesulfonate (CHAPS) at solubilizing both an ion channel and a G-protein coupled receptor (GPCR), while another amidosulfobetaine, myristic amidosulfobetaine (ASB-14), was better than CHAPS at solubilizing a GPCR. Neither membrane protein was visible after staining with colloidal Coomassie blue, silver nor Sypro Ruby. However, a comparison against a duplicate immunoblot allowed for the localization and identification of the ion channel from a 2-D gel by liquid chromatography-tandem mass spectrometry.

Effects of PEG on detergent micelles: implications for the crystallization of integral membrane proteins.

The solubilization of integral membrane proteins with detergents produces protein-detergent complexes (PDCs). Interactions between the detergent moieties of PDCs contribute significantly to their behavior. The effects of the precipitating agent polyethylene glycol (PEG) upon these detergent-detergent interactions have been examined, focusing on the detergent system used to crystallize the bacterial outer membrane protein OmpF porin. Static and dynamic light scattering were used to assess the effects of temperature and concentration upon the hydrodynamic size distribution and the aggregation state of detergent micelles and a phase diagram for micellar solutions was mapped. Estimates of the second osmotic virial coefficient obtained from static light-scattering measurements on micelles were shown to accurately reflect the thermodynamic quality of the solvent. Solvent quality decreases as the consolute boundary is approached, suggesting micelle-micelle attractive forces help to organize PDCs into crystalline aggregates near the cloud point. An apparent increase in micelle mass is observed as the solution approaches the cloud point. These results raise the possibility that the detergent-mediated aggregation of PDCs and/or slight changes in micelle geometry may prove to be important in the nucleation of membrane protein crystals.

Purification and reconstitution of an integral membrane protein, the photoreaction center of Rhodobacter sphaeroides, using synthetic sugar esters.

Detergents are indispensable reagents for the extraction and solubilization of integral membrane proteins, but their removal from a reconstituted phospholipid-protein complex is usually desirable. In this paper, we describe a novel method in which the synthetic sugar esters 6-O-octanoyl-beta-D-glucose (OG) or 6-O-octanoyl-beta-D-mannose (OM) are used as detergents for both the isolation and the rapid reconstitution of the photosynthetic reaction center protein of Rhodobacter sphaeroides. Following solubilization of the reaction center with OG or OM and reconstitution of this protein in liposomes, a convenient removal of these detergents was achieved within less than two hours by hydrolytic cleavage of the sugar esters using immobilized lipases. Best results were achieved with lipase from Bacillus sp. immobilized on silica gel.

Reduction of membrane protein hydrophobicity by site-directed mutagenesis: introduction of multiple polar residues in helix D of bacteriorhodopsin.

Introduction of polar and charged residues on the lipid-exposed face of transmembrane proteins using site-directed mutagenesis represents a novel approach to render membrane proteins more soluble in aqueous solution. We have sequentially introduced as many as five polar and charged amino acids onto the lipid-exposed face of helix D of bacteriorhodopsin from Halobacterium salinarium. The most polar mutant (Q4D) has four glutamine residues at positions 113, 116, 120 and 124 and an aspartate at position 117. In combination with wild-type residues Gln105, Thr107, Thr121 and Thr128, the Q4D mutant has a nearly uninterrupted stripe of polar residues on the surface of helix D. All of the mutants refold, bind retinal and the resulting pigments exhibit light- and dark-adapted UV and visible spectroscopic properties that are similar to the wild-type pigment, indicating that the secondary, tertiary and active site structures are similar to the wild-type protein. These results demonstrate that micelle-solubilized bacteriorhodopsin can tolerate multiple non-conservative substitution of amino acids that face the non-polar portion of the lipid bilayer in vivo, thus lending credence to the notion of partial or complete solubilization of integral membrane proteins by site-directed mutagenesis.

Pitfalls in the use of commercial nonionic detergents for the solubilization of integral membrane proteins: Sulfhydryl oxidizing contaminants and their elimination

For studies of isolated integral membrane proteins, nonionic detergents are an essential class of chemicals. A serious handicap, however, is that purified detergents which have been chemically analyzed are not available commercially. One type of contaminant that complicates studies of membrane-bound proteins acts as a sulfhydryl oxidizing agent. We have developed a convenient spectrophotometric assay to detect sulfhydryl oxidizing agents and have examined a number of nonionic detergents frequently used in biochemical studies. The method involves incubation of 1% detergent solutions with a known amount of dithiothreitol for 20 h followed by back-titration of unreacted dithiothreitol with 5,5′-dithiobis(2-nitrobenzoic acid). Many of the detergents assayed were found to contain significant amounts of oxidizing agents. The amount varied between different lots of the detergent and increased upon standing in aqueous solution, presumably due to peroxide formation initiated by light and oxygen. A method for purifying commercial nonionic detergents is proposed in which sulfhydryl oxidizing contaminants are eliminated by reaction with sodium borohydride followed by silica gel column chromatography and passage through a mixed bed ion-exchange resin.