Protein-detergent Micelles Research Articles

Neutron Scattering Reveals Protein Fluctuations in GPCR Activation

Protein fluctuations are the key for activation of G-protein-coupled receptors (GPCRs) such as rhodopsin. X-ray crystallography reveals useful structural information about the intermediates in the photoactivation process; however, knowledge of protein dynamical changes is pivotal for understanding the activation mechanism of GPCRs. We hypothesized that rhodopsin activation leads to multiple activated states in accord with an ensemble-activation mechanism (EAM) [1]. Neutron scattering provides us with non-invasive techniques to study both structural and dynamical transitions associated with the function of physiologically important proteins such as rhodopsin. Here we describe a combined small-angle neutron scattering (SANS) and quasi-elastic neutron scattering (QENS) approach to investigate the structural fluctuations associated with rhodopsin activation. The samples were prepared by purifying rhodopsin in detergents such as CHAPS from rhodopsin disk membranes. In SANS the intensity of the neutrons scattered is measured as a function of momentum transfer (Q). The experiments conducted on detergent contrast-matched conditions allowed us to probe the light-induced structural changes in rhodopsin exclusively in protein-detergent micelles. The SANS study unveiled a volumetric expansion of the protein upon photoactivation of rhodopsin. In QENS, the energy spectrum of the neutron scattered as a function of transfer-energy (ω) is measured for partially hydrated (h ≈ 0.27) rhodopsin samples. The QENS data in conjunction with the mode-coupling theory (MCT) revealed that the β-fluctuations in ligand-free opsin are substantially slower than in the dark-state rhodopsin, which indicates an increase in protein flexibility upon rhodopsin photoactivation. The volumetric expansion (from SANS experiments) and increased protein flexibility (from QENS experiments) are consistent with an increase in the number of configurations upon rhodopsin photoactivation as previously suggested by an EAM. Hence, neutron scattering provides insights into protein fluctuations crucial for GPCR activation. [1] A.V. Struts et al. (2011) PNAS 108, 8263-8268.

High-throughput Crystallization of Membrane Proteins Using the Lipidic Bicelle Method

Membrane proteins (MPs) play a critical role in many physiological processes such as pumping specific molecules across the otherwise impermeable membrane bilayer that surrounds all cells and organelles. Alterations in the function of MPs result in many human diseases and disorders; thus, an intricate understanding of their structures remains a critical objective for biological research. However, structure determination of MPs remains a significant challenge often stemming from their hydrophobicity. MPs have substantial hydrophobic regions embedded within the bilayer. Detergents are frequently used to solubilize these proteins from the bilayer generating a protein-detergent micelle that can then be manipulated in a similar manner as soluble proteins. Traditionally, crystallization trials proceed using a protein-detergent mixture, but they often resist crystallization or produce crystals of poor quality. These problems arise due to the detergent's inability to adequately mimic the bilayer resulting in poor stability and heterogeneity. In addition, the detergent shields the hydrophobic surface of the MP reducing the surface area available for crystal contacts. To circumvent these drawbacks MPs can be crystallized in lipidic media, which more closely simulates their endogenous environment, and has recently become a de novo technique for MP crystallization. Lipidic cubic phase (LCP) is a three-dimensional lipid bilayer penetrated by an interconnected system of aqueous channels. Although monoolein is the lipid of choice, related lipids such as monopalmitolein and monovaccenin have also been used to make LCP. MPs are incorporated into the LCP where they diffuse in three dimensions and feed crystal nuclei. A great advantage of the LCP is that the protein remains in a more native environment, but the method has a number of technical disadvantages including high viscosity (requiring specialized apparatuses) and difficulties in crystal visualization and manipulation. Because of these technical difficulties, we utilized another lipidic medium for crystallization-bicelles (Figure 1). Bicelles are lipid/amphiphile mixtures formed by blending a phosphatidylcholine lipid (DMPC) with an amphiphile (CHAPSO) or a short-chain lipid (DHPC). Within each bicelle disc, the lipid molecules generate a bilayer while the amphiphile molecules line the apolar edges providing beneficial properties of both bilayers and detergents. Importantly, below their transition temperature, protein-bicelle mixtures have a reduced viscosity and are manipulated in a similar manner as detergent-solubilized MPs, making bicelles compatible with crystallization robots. Bicelles have been successfully used to crystallize several membrane proteins (Table 1). This growing collection of proteins demonstrates the versatility of bicelles for crystallizing both alpha helical and beta sheet MPs from prokaryotic and eukaryotic sources. Because of these successes and the simplicity of high-throughput implementation, bicelles should be part of every membrane protein crystallographer's arsenal. In this video, we describe the bicelle methodology and provide a step-by-step protocol for setting up high-throughput crystallization trials of purified MPs using standard robotics.

Quaternary Structure and Functional Unit of Energy Coupling Factor (ECF)-type Transporters

ATP-binding cassette (ABC) transporters mediate transport of diverse substrates across membranes. We have determined the quaternary structure and functional unit of the recently discovered ECF-type (energy coupling factor) of ABC transporters, which is widespread among prokaryotes. ECF transporters are protein complexes consisting of a conserved energizing module (two peripheral ATPases and the integral membrane protein EcfT) and a non-conserved integral membrane protein responsible for substrate specificity (S-component). S-components for different substrates are often unrelated in amino acid sequence but may associate with the same energizing module. Here, the energizing module from Lactococcus lactis was shown to form stable complexes with each of the eight predicted S-components found in the organism. The quaternary structures of three of these complexes were determined by light scattering. EcfT, the two ATPases (EcfA and EcfA'), and the S-components were found to be present in a 1:1:1:1 ratio. The complexes were reconstituted in proteoliposomes and shown to mediate ATP-dependent transport. ECF-type transporters are the smallest known ABC transporters.

NMR Characterization of Membrane Protein−Detergent Micelle Solutions by Use of Microcoil Equipment

Using microcoil NMR technology, the uniformly (2)H,(15)N-labeled integral membrane protein OmpX, and the phosphocholine derivative detergent Fos-10 (n-decylphosphocholine), we investigated solutions of mixed protein-detergent micelles to determine the influence of the detergent concentration on the NMR spectra of the protein. In a first step, we identified key parameters that influence the composition of the micelle solutions, which resulted in a new protocol for the preparation of well-defined concentrated protein solutions. This led to the observation that high-quality 2D [(15)N,(1)H]-transverse relaxation-optimized spectroscopy (TROSY) spectra of OmpX reconstituted in mixed micelles with Fos-10 were obtained only in a limited range of detergent concentrations. Outside of this range from about 90-180 mM, we observed a significant decrease of the average peak intensity. Relaxation-optimized NMR measurements of the rotational and translational diffusion coefficients of the OmpX/Fos-10 mixed micelles, D(r) and D(t), respectively, then showed that the stoichiometry and the effective hydrodynamic radius of the protein-containing micelles are not significantly affected by high Fos-10 concentrations and that the deterioration of NMR spectra is due to the increased viscosity at high detergent concentrations. The paper thus provides a basis for refined guidelines on the preparation of integral membrane proteins for structural studies.

Prion Protein-Detergent Micelle Interactions Studied by NMR in Solution

Cellular prion proteins, PrP(C), carrying the amino acid substitutions P102L, P105L, or A117V, which confer increased susceptibility to human transmissible spongiform encephalopathies, are known to form structures that include transmembrane polypeptide segments. Herein, we investigated the interactions between dodecylphosphocholine micelles and the polypeptide fragments 90-231 of the recombinant mouse PrP variants carrying the amino acid replacements P102L, P105L, A117V, A113V/A115V/A118V, K110I/H111I, M129V, P105L/M129V, and A117V/M129V. Wild-type mPrP-(90-231) and mPrP[M129V]-(91-231) showed only weak interactions with dodecylphosphocholine micelles in aqueous solution at pH 7.0, whereas discrete interaction sites within the polypeptide segment 102-127 were identified for all other aforementioned mPrP variants by NMR chemical shift mapping. These model studies thus provide evidence that amino acid substitutions within the polypeptide segment 102-127 affect the interactions of PrP(C) with membranous structures, which might in turn modulate the physiological function of the protein in health and disease.

Dimeric Structure of Human Na+/H+ Exchanger Isoform 1 Overproduced in Saccharomyces cerevisiae

The Na(+)/H(+) exchanger isoform 1 (NHE1) is an integral membrane protein that regulates intracellular pH by extruding an intracellular H(+) in exchange for one extracellular Na(+). The human NHE1 isoform is involved in heart disease and cell growth and proliferation. Although details of NHE1 regulation and transport are being revealed, there is little information available on the structure of the intact protein. In this report, we demonstrate overexpression, purification, and characterization of the human NHE1 (hNHE1) protein in Saccharomyces cerevisiae. Overproduction of the His-tagged protein followed by purification via nickel-nitrilotriacetic acid-agarose chromatography yielded 0.2 mg of pure protein/liter of cell culture. Reconstitution of hNHE1 in proteoliposomes demonstrated that the protein was active and responsive to an NHE1-specific inhibitor. Circular dichroism spectroscopy of purified hNHE1 revealed that the protein contains 41% alpha-helix, 23% beta-sheet, and 36% random coil. Size exclusion chromatography indicated that the protein-detergent micelle was in excess of 200 kDa, consistent with an hNHE1 dimer. Electron microscopy and single particle reconstruction of negatively stained hNHE1 confirmed that the protein was a dimer, with a compact globular domain assigned to the transmembrane region and an apical ridge assigned to the cytoplasmic domain. The transmembrane domain of the hNHE1 reconstruction was clearly dimeric, where each monomer had a size and shape consistent with the predicted 12 membrane-spanning segments for hNHE1.

Yeast mitochondrial ADP/ATP carriers are monomeric in detergents.

Mitochondrial carriers are believed widely to be homodimers both in the inner membrane of the organelle and in detergents. The dimensions and molecular masses of the detergent and protein-detergent micelles were measured for yeast ADP/ATP carriers in a range of different detergents. The radius of the carrier at the midpoint of the membrane, its average radius, its Stokes' radius, its molecular mass, and its excluded volume were determined. These parameters are consistent with the known structural model of the bovine ADP/ATP carrier and they demonstrate that the yeast mitochondrial ADP/ATP carriers are monomeric in detergents. Therefore, models of substrate transport have to be considered in which the carrier operates as a monomer rather than as a dimer.

Simulation studies of the interactions between membrane proteins and detergents

Interactions between membrane proteins and detergents are important in biophysical and structural studies and are also biologically relevant in the context of folding and transport. Despite a paucity of high-resolution data on protein–detergent interactions, novel methods and increased computational power enable simulations to provide a means of understanding such interactions in detail. Simulations have been used to compare the effect of lipid or detergent on the structure and dynamics of membrane proteins. Moreover, some of the longest and most complex simulations to date have been used to observe the spontaneous formation of membrane protein–detergent micelles. Common mechanistic steps in the micelle self-assembly process were identified for both α-helical and β-barrel membrane proteins, and a simple kinetic mechanism was proposed. Recently, simplified (i.e. coarse-grained) models have been utilized to follow long timescale transitions in membrane protein–detergent assemblies.

Simulation studies of the interactions between membrane proteins and detergents

Interactions between membrane proteins and detergents are important in biophysical and structural studies and are also biologically relevant in the context of folding and transport. Despite a paucity of high-resolution data on protein-detergent interactions, novel methods and increased computational power enable simulations to provide a means of understanding such interactions in detail. Simulations have been used to compare the effect of lipid or detergent on the structure and dynamics of membrane proteins. Moreover, some of the longest and most complex simulations to date have been used to observe the spontaneous formation of membrane protein-detergent micelles. Common mechanistic steps in the micelle self-assembly process were identified for both alpha-helical and beta-barrel membrane proteins, and a simple kinetic mechanism was proposed. Recently, simplified (i.e. coarse-grained) models have been utilized to follow long timescale transitions in membrane protein-detergent assemblies.

Membrane protein-lipid interactions in mixed micelles studied by NMR spectroscopy with the use of paramagnetic reagents.

For solution NMR studies of the structure and function of membrane proteins, these macromolecules have to be reconstituted and solubilized in detergent micelles. Detailed characterization of the mixed detergent/protein micelles is then of key importance to validate the results from such studies, and to evaluate how faithfully the natural environment of the protein in the biological membrane is mimicked by the micelle. In this paper, a selection of paramagnetic probes with different physicochemical properties are used to characterize the 60 kDa mixed micelles consisting of about 90 molecules of the detergent dihexanoylphosphatidylcholine (DHPC) and one molecule of the Escherichia coli outer-membrane protein X (OmpX), which had previously been extensively studied by solution NMR techniques. The observation of highly selective relaxation effects on the NMR spectra of OmpX and DHPC from a water-soluble relaxation agent and from nitroxide spin labels attached to lipophilic molecules, confirmed data obtained previously with more complex NMR studies of the diamagnetic OmpX/DHPC system, and yielded additional novel insights into the protein-detergent interactions in the mixed micelles. The application of paramagnetic probes to the well-characterized OmpX/DHPC system indicates that such probes should be widely applicable as an efficient support of NMR studies of the topology of mixed membrane protein-detergent micelles.

LV006 Polymorphisms in virulence-associated genes among clinical and environmental strains of Legionella pneumophila

The whole cell vaccine (WCV) of Bordetella pertussis is protective in the intracerebral (i.c.) mouse protection assay. We found a correlation between the i.c. mouse protection assay potency and the presence of the virulence-associated outer membrane proteins (OMPs) in outer membrane complexes (OMC). The virulence-associated 92, 32 and 30 kDa OMPs were purified and the N-terminal amino acid sequences were determined. The N-terminal amino acid sequences of the 30 and 32 kDa OMPs show homology with the C-terminal fragment of the P.93 precursor of the 69 kDa OMP (pertactin). The purified 32 kDa OMP was protective in the i.c. test when presented as mixed protein-detergent micelles. The 92 kDa OMP became a protective antigen when nonprotective levels of pertussis toxin were added. We found a correlation between the i.c. mouse protection value and the 92 kDa38 kDa (porin) ratio in OMC preparations.

Three-dimensional crystallization of the light-harvesting complex from Mantoniella squamata (Prasinophyceae) requires an adequate purification procedure

We present a new purification procedure for the light-harvesting complex of Mantoniella squamata whereupon three-dimensional crystallization succeeded. Previous purification methods were based on density centrifugations as the only separating principle. We have extended this preparation procedure by applying anion-exchange and molecular-sieve chromatography techniques. Purity and stability of the complex were proved by denaturing and non-denaturing polyacrylamide-gel electrophoresis, and spectroscopic measurements. With respect to contaminating lipids the purified pigment-protein complex was examined by thin-layer chromatography and the aggregation and/or oligomeric states were investigated by gel filtration, fluorescence emission, and electron microscopy. Molecular-mass determination by gel filtration gave evidence for a trimeric organization of the purified native complex. Our purification procedure resulted in mixed protein-detergent micelles, small and homogeneous, the ideal material to start crystallization trials. We found involuntary aggregation to be easily detected by additional fluorescence emission at red-shifted wavelength (700 nm) as compared to the main emission at 680 nm. Electron-microscopic images proved this emission at 700 nm to be really due to aggregation, which could be prevented if sufficient detergent were present in the samples during the whole purification procedure. The ultimate proof that our efforts have been successful was the appearance of hexagonal crystals.

The purification and protective capacity of Bordetella pertussis outer membrane proteins

The whole cell vaccine (WCV) of Bordetella pertussis is protective in the intracerebral (i.c.) mouse protection assay. We found a correlation between the i.c. mouse protection assay potency and the presence of the virulence-associated outer membrane proteins (OMPs) in outer membrane complexes (OMC). The virulence-associated 92, 32 and 30 kDa OMPs were purified and the N-terminal amino acid sequences were determined. The N-terminal amino acid sequences of the 30 and 32 kDa OMPs show homology with the C-terminal fragment of the P.93 precursor of the 69 kDa OMP (pertactin). The purified 32 kDa OMP was protective in the i.c. test when presented as mixed protein-detergent micelles. The 92 kDa OMP became a protective antigen when nonprotective levels of pertussis toxin were added. We found a correlation between the i.c. mouse protection value and the 92 kDa 38 kDa (porin) ratio in OMC preparations.

In situ two-dimensional crystallization of a polytopic membrane protein: the cardiac gap junction channel.

In situ crystallization of rat ventricular gap junctions was accomplished by sequential dialysis of membranes against low concentrations of deoxycholate and dodecyl-beta-D-maltoside. Lipids are removed without solubilizing the protein, and the increased protein concentration in the membrane plane facilitates two-dimensional crystallization in the native membrane environment. The two-dimensional crystals have a nominal resolution of 16 A and display plane group symmetry p6 with a = b = 85 A and gamma = 120 degrees. Electron crystallography reveals that the cardiac gap junction membrane channel is formed by a hexameric cluster of protein subunits, and this hexameric design appears to be a recurring quaternary motif for the multigene family of gap junction proteins. Exposure of membranes to low concentrations of detergents may provide an approach for in situ two-dimensional crystallization of other connexins as well as other membrane proteins, especially those that are labile when solubilized as protein-detergent micelles.

The effect of dissociation of Bacteroides nososus pili on their efficacy as a protective antigen against ovine footrot

Previous studies have shown that pili from homologous Bacteroides nodosus provide protective immunity in sheep against footrot, whereas denatured pilin subunits are ineffective. The aim of the present study was to examine whether pili that were dissociated into pilin subunits under less vigorous, non-denaturing treatment conditions, would provide an effective level of protective immunity. Using the techniques of gel permeation chromatography, light scattering and susceptibility to proteolysis as measures of disruption, it was shown that pili were dissociated either by the neutral detergents n- octyl-β- D - glucopyranoside (NOG) and Tween 80 or by lowering the pH with 1 M phosphoric acid to pH 2.2. Circular dichroic spectra indicated, however that the samples were not denatured by these treatments. Electron microscopic monitoring of detergent dissociated material following exhaustive dialysis showed the presence of protein-detergent micelles and “in-line” aggregates which gave the appearance of short fibres. Within these monitored preparations, there was no evidence of native undissociated pili. Pili dissociated by NOG or acid were tested in protection trials and shown to provide protective immunity, although agglutination titres of serum taken from the vaccinated sheep were significantly lower than those of animals inoculated with intact pili.

Application of high-performance liquid chromatography to the purification of the putative intestinal peptide transporter

A membrane protein of relative molecular mass ( M r) 127 000 was identified by photoaffinity labelling as (a component of) the uptake system for small peptides and β-lactam antibiotics in rabbit small intestine. This binding protein is a microheterogeneous glycosylated integral membrane protein which could be solubilized with non-ionic detergents and enriched by lectin affinity chromatography on wheat germ lectin agarose. For the final purification of this protein and separation from aminopeptidase N of M r 127 000, fast protein liquid chromatography (FPLC) was used. Gel permeation, hydroxyapatite and hydrophobic interaction chromatography were not successful for the purification of the 127 000-dalton binding protein. By anion-exchange chromatography on a Mono Q column with either Triton X-100 or n-octylglucoside as detergent, a partial separation of the 127 000-dalton binding protein from aminopeptidase N was achieved. By cation-exchange chromatography on a Mono S HR 5 5 column at pH 4.5 using Triton X-100 as detergent also only a partial separation from aminopeptidase N could be achieved. If, however, Triton X-100 was replaced with n-octylglucoside, the binding protein for β-lactam antibiotics and small peptides of M r 127 000 could be completely separated from aminopeptidase N. These results indicate that Triton X-100 should be avoided for the purification of integral membrane proteins because mixed protein-detergent micelles of high molecular weight prevent a separation into the individual membrane proteins. The putative peptide transport protein was finally purified by rechromatography on Mono S and was obtained more than 95% pure as determined densitometrically after sodium dodecyl sulphate gel electrophoresis. By application of FPLC even microheterogeneous membrane glycoproteins from the intestinal mucosa can be purified to such an extent that a sequence analysis and immunohistochemical localization with antibodies prepared from the purified protein is possible.

Interaction of non‐classical detergents with the mitochondrial porin

The effect of different families of detergents on the solubilization and purification of the pore-forming protein (porin) of the mitochondrial outer membrane of bovine heart was investigated in detail. With Tritons, dimethylamine oxides and zwittergents, porin solubilization with respect to total mitochondrial membrane protein was more efficient with the more hydrophobic members of each series. With most detergents the protein eluted as protein-detergent micelles in the void volume of hydroxyapatite/celite columns. In contrast, the protein was bound to the column material and was eluted after the addition of salt to the elution buffer when the detergents octylglucoside, zwittergent Z-314 and lauryl(dimethyl)-amine oxide were used. The protein purified in the presence of the latter detergent had a higher pore-forming activity in lipid bilayer membranes compared to porin isolated in the presence of Triton X-100. The binding of porin to the hydroxyapatite/celite column was used to study the lipid content of the active pore-forming complex. The analysis revealed that the complex contained no phospholipid but rather five molecules of cholesterol/polypeptide chain.

Effect of Triton X-100 on the inhibition of human erythrocyte acetylcholinesterase by organophosphorus insecticide DDVP

This paper describes the inhibition of membrane-bound and Triton X-100-solubilized acetylcholinesterase from human erythrocytes by organophosphorus insecticide DDVP. The enzyme in nonionic detergent solutions exhibits full catalytic activity and nonchanged kinetics. In these conditions, however, the acetylcholinesterase is more susceptible to inhibition by DDVP. The results reported here suggest that the hydrophobic surrounding of the membrane protects the enzyme from insecticide inhibition. The relation between enzyme structure in membrane and in protein detergent micelle and insecticide action are discussed.

Expression and characterization of hepatitis B virus surface antigen polypeptides in insect cells with a baculovirus expression system.

The baculovirus Autographa californica nuclear polyhedrosis virus was used as an expression vector to produce hepatitis B virus surface antigen with and without the pre-S domain. The S gene product was expressed as both fusion and nonfusion polypeptides. No difference was observed in the posttranslational modification of the fusion and nonfusion polypeptides. The S proteins were not secreted into the medium but were inserted into the endoplasmic reticulum, glycosylated, and partially extruded into the lumen of the endoplasmic reticulum as 22-nm lipoprotein particles. The oligosaccharide chains on the insect cell-derived S protein were of the N-linked high-mannose form, in contrast to the complex-type oligosaccharides detected on plasma-derived hepatitis B virus surface antigen. The pre-S-S polypeptides were inserted into the endoplasmic reticulum, glycosylated, and modified by fatty acid acylation with myristic acid. A procedure was developed to purify the S protein from cellular membranes by using detergent extraction and immunoaffinity chromatography. The purified S protein was in the form of protein-detergent micelles and was highly antigenic and immunogenic.

29] Critical micellar concentrations of detergents

Publisher Summary This chapter describes the critical micellar concentrations (CMC) of detergents. Membrane-spanning proteins are amphiphilic macromolecules that are incorporated vectorially in the lipid membrane in a quasi-solid state. On disruption of the membrane and removal of the lipids, such proteins tend to aggregate unspecifically and precipitate in bulk, thus avoiding an entropically unfavorable exposure of their hydrophobic parts to water. The easiest and least disruptive method to achieve this is the replacement of membrane lipids by detergents that do not form membrane-like structures. Solubilized membrane proteins form mixed micelles with the detergent. Under appropriate conditions, their hydrophobic surface parts are covered by a (curved) monolayer film of the detergent. Because this film only forms at an adequate detergent concentration, the final solution after membrane solubilization contains mixed protein–detergent micelles, mixed lipid–detergent micelles, pure detergent micelles, and detergent monomers. However, just below or at the CMC, mixed micelles may contain more than one protein molecule in the same complex. To avoid this situation of incomplete and evasive solubilization, experiments should be performed at a detergent concentration at which the free-to-mixed micelle ratio is at least 10.