Membrane Proteins In Detergent Research Articles

A novel high-throughput screen for identifying lipids that stabilise membrane proteins in detergent based solution.

Membrane proteins have a range of crucial biological functions and are the target of about 60% of all prescribed drugs. For most studies, they need to be extracted out of the lipid-bilayer, e.g. by detergent solubilisation, leading to the loss of native lipids, which may disturb important protein-lipid/bilayer interactions and thus functional and structural integrity. Relipidation of membrane proteins has proven extremely successful for studying challenging targets, but the identification of suitable lipids can be expensive and laborious. Therefore, we developed a screen to aid the high-throughput identification of beneficial lipids. The screen covers a large lipid space and was designed to be suitable for a range of stability assessment methods. Here, we demonstrate its use as a tool for identifying stabilising lipids for three membrane proteins: a bacterial pyrophosphatase (Tm-PPase), a fungal purine transporter (UapA) and a human GPCR (A2AR). A2AR is stabilised by cholesteryl hemisuccinate, a lipid well known to stabilise GPCRs, validating the approach. Additionally, our screen also identified a range of new lipids which stabilised our test proteins, providing a starting point for further investigation and demonstrating its value as a novel tool for membrane protein research. The pre-dispensed screen will be made commercially available to the scientific community in future and has a number of potential applications in the field.

Detergent Titration as an Efficient Method for NMR Resonance Assignments of Membrane Proteins in Lipid-Bilayer Nanodiscs.

Lipid bilayer nanodiscs are an attractive tool to study membrane proteins in a detergent-free lipid-bilayer environment. In the case of NMR studies, a sequence-specific resonance assignment is required in order to gain structural and functional insights with atomic resolution. Although NMR backbone assignments of membrane proteins in detergents are available, they are largely absent for membrane proteins in nanodiscs due to unfavorable relaxation properties of the slowly tumbling membrane protein-nanodisc complex. The necessary residue-specific reassignment of resonances in nanodiscs is therefore extremely time and sample consuming and represents the fundamental bottleneck in the application of nanodiscs for NMR studies. Here we present an elegant and fast solution to the problem. We show that a resonance assignment in detergent micelles can be transferred to a spectrum recorded in nanodiscs via detergent titration. The procedure requires that lipid-detergent exchange kinetics are in the fast exchange regime in order to follow linear and nonlinear peak shift trajectories with increasing detergent concentration. We demonstrate the feasibility of the approach on the 148-residue membrane protein OmpX. The titration method is then applied to VDAC, a 19-stranded β-barrel with 283 residues, for which 67% of the detergent assignment could be transferred to the nanodisc spectrum. We furthermore show that this method also works for the largest currently assigned membrane protein, BamA with 398 residues. The method is applicable for backbone amide and side chain methyl groups and represents a time and cost-effective assignment method, for example, to investigate membrane protein allostery and drug binding in a more natural and detergent-free lipid bilayer.

Membrane Protein Cryo-EM: Cryo-Grid Optimization and Data Collection with Protein in Detergent.

Cryo-electron microscopy (cryo-EM) is a powerful tool for investigating the structure of macromolecules under near-native conditions. Especially in the context of membrane proteins, this technique has allowed researchers to obtain structural information at a previously unattainable level of detail. Specimen preparation remains the bottleneck of most cryo-EM research projects, with membrane proteins representing particularly challenging targets of investigation due to their universal requirement for detergents or other solubilizing agents. Here we describe preparation of negative staining and cryo-EM grids and downstream data collection of membrane proteins in detergent, by far the most common solubilization agent. This protocol outlines a quick and straightforwardprocedure for screening and determining the structure of a membrane protein of interest under biologically relevant conditions.

Thermostability Assays: a Generic and Versatile Tool for Studying the Functional and Structural Properties of Membrane Proteins in Detergents.

There are very few generic methods to assess the stability and functional properties of membrane proteins solubilized in detergent. For this purpose, a thiol-reactive fluorochrome N-[4-(7-diethylamino-4-methyl-3-coumarinyl)phenyl]maleimide (CPM) can be used. An unfolding profile is obtained when the fluorochrome becomes fluorescent on reaction with cysteine residues that have been exposed during thermal denaturation of the protein population. The method was initially developed to optimize the stability of membrane proteins for crystallization studies, but in the course of our work we found many other applications. First, the assay can be used to study the binding of inhibitors, substrates, lipids, and other effectors to membrane proteins. Second, the assay can be used to understand the dynamics of proteins, allowing states to be defined by changes in accessibility of cysteine residues or by changes in specific amino acid interactions. Finally, the assay can be used to study state-dependent domain interactions, for example, as part of regulatory mechanisms. The CPM thermostability assay represents a broadly applicable and versatile tool for a wide range of applications in the functional and structural analysis of membrane proteins.

Functional and structural comparison of the ABC exporter MsbA studied in detergent and reconstituted in nanodiscs

Purified membrane proteins are most frequently studied solubilized in detergent, but the properties of detergent micelles are very different from those of lipid bilayers. Therefore, there is an increasing interest in studying membrane proteins under conditions that resemble the membrane protein native environment more closely. Although there are indications of differences between membrane proteins in detergent and in lipid bilayers, direct functional and structural comparisons are very hard to find. Nanodiscs have been established as a new platform that consists of two molecules of a membrane scaffold protein that surround a small lipid-bilayer patch. Here, we undertook the task of comparing the function and conformational states of the transport protein MsbA in detergent and nanodiscs using ATPase activity and luminescence resonance energy transfer (LRET) measurements to assess differences in activity and conformational states, respectively. MsbA is a prototypical member of the ATP binding cassette protein superfamily. MsbA activity was higher in nanodiscs vs detergent, which had clear structural correlates: an increase in the fraction of molecules displaying closed nucleotide-binding domain dimers in the apo state, and a decrease in the distance of the “dissociated” nucleotide-binding domains. Our LRET studies support the notion that the widely separated nucleotide binding domains observed in the MsbA x-ray structures in detergent do not correspond to physiological conformations. Although our studies focus on a particular ABC exporter, the possibility of similar environment effects on other membrane proteins should be carefully considered.

Perturbations of Native Membrane Protein Structure in Alkyl Phosphocholine Detergents: A Critical Assessment of NMR and Biophysical Studies.

Membrane proteins perform a host of vital cellular functions. Deciphering the molecular mechanisms whereby they fulfill these functions requires detailed biophysical and structural investigations. Detergents have proven pivotal to extract the protein from its native surroundings. Yet, they provide a milieu that departs significantly from that of the biological membrane, to the extent that the structure, the dynamics, and the interactions of membrane proteins in detergents may considerably vary, as compared to the native environment. Understanding the impact of detergents on membrane proteins is, therefore, crucial to assess the biological relevance of results obtained in detergents. Here, we review the strengths and weaknesses of alkyl phosphocholines (or foscholines), the most widely used detergent in solution-NMR studies of membrane proteins. While this class of detergents is often successful for membrane protein solubilization, a growing list of examples points to destabilizing and denaturing properties, in particular for α-helical membrane proteins. Our comprehensive analysis stresses the importance of stringent controls when working with this class of detergents and when analyzing the structure and dynamics of membrane proteins in alkyl phosphocholine detergents.

Biomolecular Interaction Determination and Quantification by Microscale Thermophoresis

MicroScale Thermophoresis (MST), an immobilization-free technology, is used to rapidly quantify biomolecular interactions (pM-mM). MST, the directed movement of molecules in optically generated microscopic temperature gradients, is monitored by fluorescence. Thermophoretic movement is highly sensitive to binding reactions, which affect the size, charge, conformation, and/or hydration shell of target molecules. Here, we demonstrate that MST can be used to quantify interactions between biomolecules of interest, including proteins, nucleic acids, ions, and more. In one example, the binding site of a protein-protein interaction is investigated via protein engineering. As MST is suitable for probe interactions with membrane proteins in detergent or liposomes, we also demonstrate the quantification of interactions with GPCRs in a label free format using tryptophan fluorescence. Thus, MST is a critical addition to the biophysical toolbox allowing greater user-flexibility for analyzing molecular interactions.

Feasibility of Cryo-EM for Structural Characterization of Small Membrane Proteins

Single-particle cryo-EM has recently emerged as a tool for characterization of protein structure at atomic resolution, with applications both to soluble and membrane proteins. Cryo-EM relies on computational alignment of single-particle images, permitting calculation of interpretable two-dimensional averages and three-dimensional reconstructions. Prior to data collection, cryo-EM samples are trapped in vitreous ice by plunge freezing, protecting biological macromolecules from radiation damage and high-vacuum, yet maintaining hydration and native structure. Soluble proteins are thus surrounded by water, which has a small electron scattering cross-section relative to the protein itself. However, membrane proteins in detergent or lipid nanoparticle systems (nanodiscs, saposin), are embedded in contrastive and predominantly unstructured material. The impact of this contrastive, unstructured mass on image alignment and three-dimensional reconstruction is unknown. Indeed, traditional cryoprotectants (glycerol) are not used in cryo-EM because their protein-like scattering is deleterious to particle contrast. Nevertheless, a growing number of membrane proteins have been characterized using cryo-EM. To date all such proteins bear large, soluble domains (often dwarfing the membrane bound component, e.g. nanodisc-anchored ribosomes), which are hypothesized to drive image alignment. Recent structures of TRPV1 (a tetrameric Ca2+ channel) reconstituted in lipid nanodiscs show that current cryo-EM pipelines can deliver high resolutions even when the ratio of structured to unstructured mass falls as low as 2:1. Here, we undertake to ascertain the limits to this ratio (if any), as well as the feasibility of reconstructing structures lacking any soluble extension.Starting from micrographs of TRPV1 in lipid nanodiscs, we use signal subtraction to simulate data for progressively smaller ratios of structured to unstructured mass, eventually eliminating all contributions from the soluble domains. Our results, including a 3.4 Angstrom structure of a hypothetical membrane protein with no soluble domain, suggest that high-resolution alignment and reconstruction is feasible for membrane proteins with no soluble extension, including when the ratio of structured to unstructured mass is less than 1:1. With continued technological development, it may be possible to adopt cryoprotectants that greatly enhance the formation of vitreous ice even during slow freezing. Finally, this work also serves as a tutorial for precise signal subtraction using open-source software, including creation of a suitable subtraction map, simulation of particle image contributions, recentering of subtracted particles, and per-particle normalization based on Fourier correlations.

A simple guide to the structural study on membrane proteins in detergents using solution NMR

Abstract NMR-based structural studies on membrane proteins are appreciated quite challenging due to various reasons, generally including the narrow dispersion of NMR spectra, the severe peak broadening, and the lack of long range NOEs. In spite of the poor biophysical properties, structural studies on membrane proteins have got to go on ,considering their functional importance in biological systems. In this review, we provide a simple overview of the techniques generally used in structural studies of membrane proteins by solution NMR, with experimental examples of a helical membrane protein, caveolin 3. Detergent screening is usually employed as the first step and the selection of appropriate detergent is the most important for successful approach to membrane proteins. Various tools can then be applied as NMR specializedtechniques in solution that include sample deteuration, amino-acid selective isotope labeling, residual dipolar coupling, and paramagnetic relaxation enhancement.

Reconstitution of membrane proteins: a GPCR as an example.

Membrane proteins are the gatekeepers to the cell and are essential to the function of all cells, controlling the flow of molecules and information across the cell membrane. Much effort has been put into the development of systems for studying membrane proteins in simplified environments that nevertheless mimic their native lipid environment. After isolation and production of purified membrane proteins in detergent, it is often necessary to reconstitute them into a lipid structure such as liposome, nanodisc, or lipodisq. Each of these has the advantage of returning the protein to a defined lipid environment, and the choice of system depends on the application. Regardless of the system to be used, the fundamental process involves the removal of detergent and incorporation of the protein into a stable lipid system. This chapter details methodologies we have developed, mainly focussed on the model G protein-coupled receptor (GPCR) neurotensin receptor 1, and the GPCR-homologue and model, bacteriorhopdopsin.

Identification and removal of nitroxide spin label contaminant: Impact on PRE studies of α‐helical membrane proteins in detergent

NMR paramagnetic relaxation enhancement (PRE) provides long-range distance constraints (~15-25 Å) that can be critical to determining overall protein topology, especially where long-range NOE information is unavailable such as in the case of larger proteins that require deuteration. However, several challenges currently limit the use of NMR PRE for α-helical membrane proteins. One challenge is the nonspecific association of the nitroxide spin label to the protein-detergent complex that can result in spurious PRE derived distance restraints. The effect of the nitroxide spin label contaminant is evaluated and quantified and a robust method for the removal of the contaminant is provided to advance the application of PRE restraints to membrane protein NMR structure determination.

S3.13 Determination of the dimensions and mass of membrane proteins in detergents by size exclusion chromatography

S3.13 Determination of the dimensions and mass of membrane proteins in detergents by size exclusion chromatography

Effects of ionizing radiations on proteins. Evidence of non-random fragmentations and a caution in the use of the method for determination of molecular mass

We have reinvestigated the use of ionizing radiations to measure the molecular mass of water-soluble or membrane proteins. The test was performed by using the most straightforward aspect of the technique, which consists of SDS/PAGE analysis of the protein-fragmentation process. We found that exposure of purified standard proteins to increasing doses of ionizing radiation causes progressive fragmentation of the native protein into defined peptide patterns. The coloured band corresponding to the intact protein was measured on the SDS gel as a function of dose to determine the dose (D37.t) corresponding to 37% of the initial amount of unfragmented protein deposited on the gel. This led to a calibration curve between 1/D37.t and the known molecular mass of the standard proteins whose best fit gave Mr = 1.77 x 10(6)/D37.t at -78 degrees C, i.e. 35% higher than the generally accepted value at that temperature obtained from inactivation studies. However, we have to conclude that this method is useless to determine the state of aggregation of a protein, since, for all the oligomers tested, the best fit was obtained by using the protomeric molecular mass, suggesting that there is no energy transfer between promoters. Furthermore, SDS greatly increases the fragmentation rate of proteins, which suggests additional calibration problems for membrane proteins in detergent or in the lipid bilayer. But the main drawback of the technique arises from our observation that some proteins behaved anomalously, leading to very large errors in the apparent target size as compared with true molecular mass (up to 100%). It is thus unreliable to apply the radiation method for absolute molecular-mass determination. We then focused on the novel finding that discrete fragmentation of proteins occurs at preferential sites, and this was studied in more detail with aspartate transcarbamylase. N-Terminal sequencing of several radiolysis fragments of the catalytic chain of the enzyme revealed that breaks along the polypeptide chains are localized close to the C-terminal end. Examination of the three-dimensional structure of aspartate transcarbamylase suggests that radiolysis sites (fragile bonds) might be localized in connecting loops.

Isolation and characterization of a lipoprotein receptor from the fat body of an insect, Manduca sexta.

A lipoprotein receptor has been purified from the fat body of Manduca sexta larvae. The purification involves solubilization of membrane proteins in detergent, DEAE-, and hydroxyapatite chromatography, affinity chromatography on a concanavalin A column, and affinity chromatography on a lipoprotein-Sepharose column. An overall purification of 220-fold from the solubilized membranes was achieved. The receptor has an apparent molecular mass of 120 kDa. The receptor has an absolute requirement for Ca2+ and is inhibited by Suramin. The pH optimum of the receptor is 6.5, which is near the pH of the hemolymph. Binding data indicate a single high affinity binding site with a Kd = 4.1 +/- 0.19 x 10(-8) M as measured with the lipoprotein isolated from larval hemolymph. The major neutral lipid carried by insect lipoproteins is diacylglycerol, and it was shown that the affinity of the receptor for lipoprotein ligands correlates with their diacylglycerol content. It is proposed that the decrease in affinity of the receptor for lipoproteins depleted of diacylglycerol plays a key role in facilitating the transport of diacylglycerol from the midgut to the fat body during the larval feeding period. The insect receptor has some properties which are similar to those of vertebrate lipoprotein receptors, viz. molecular weight, requirement for Ca2+, and inhibition by Suramin. However, the insect receptor does not bind human low density lipoprotein.

Electrophoresis of membrane proteins in concentrated formic acid solutions

To obviate the difficulties resulting from partial solubility of membrane proteins in detergents or from the use of noxious solvent mixtures containing phenol or chloral, a simple procedure was devised for acrylamide gel electrophoresis of membrane proteins in 13 m formic acid. Polyacrylamide gels are equilibrated in 13 m formic acid and used in the electrophoresis assembly with 13 m formic acid as the electrolyte. Particulate proteinaceous preparations are dissolved in trifluoroacetic acid or in 24 m formic acid containing glycine to increase the density and to facilitate the solubilization of the protein. Protein samples (10 to 100 μg) migrate as polycations.

The size and detergent binding of membrane proteins.

Sucrose density gradient centrifugation has been used to measure the binding of Triton X-100 above its critical micellar concentration to a variety of purified membrane and non-membrane proteins. In addition, binding studies were done on the three proteins below the critical micellar concentration of detergent to distinguish between the interaction of proteins with detergent monomers and detergent micelles. A procedure is described for the calculation of the molecular weight of these Triton X-100 protein complexes and measurements were made for opsin, plasma low density lipoprotein, the (Na-+ plus K-+)-dependent adenosine triphosphatase, the human red blood cell major sialoglycoprotein (PAS-1) and the human red blood cell minor glycoprotein (bandIII). These proteins behave as monomers or dimers in detergent and bind between 0.28 and 1.12 g of detergent per g of protein. A general method is also present for calculating the molecular size and shape of impure membrane proteins in detergent. Finally, Triton X-100 was shown to replace bound Na dodecyl-SO4 on the minor glycoprotein of the red blood cell.