Reconstitution of Semliki forest virus membrane

The spike glycoproteins of the Semliki forest virus membrane have been incorporated into vesicular phospholipid bilayers by a detergent- dialysis method. The detergent used was beta-D-octylglucoside which is nonionic and has an exceptionally high critical micellar concentration which facilitates rapid removal by dialysis. The vesicles obtained were of varying sizes and had spikes on their surface. Two classes of vesicles were preferentially formed, small protein-rich and large lipid- rich (average lipid to protein weight ratios, 0.22 and 3.5, respectively). Both classes of vesicles retained the hemagglutinating activity of the virus. The proteins were attached to the lipid bilayer by hydrophobic peptide segments, as in the viral membrane. Most of the proteins were accessible to proteolytic digestion from the outside, suggesting an asymmetric orientation.     

Detergent removal by non-polar polystyrene beads

Detergent removal from lipid-protein-detergent micellar solutions is the most successful strategy for reconstitution of integral membrane proteins into proteoliposomes or into two-dimensional crystals. This review establishes the potential of polystyrene beads as a simple alternative to other conventional detergent removing strategies such as dialysis, gel chromatography and dilution. Kinetics and equilibrium aspects of removal of different detergents by hydrophobic adsorption onto polystyrene beads have been systematically investigated. A mechanism of adsorption onto polystyrene beads is proposed and provide useful information about the use of these beads in reconstitution experiments. The usefulness of this detergent removal strategy to produce quasi-ideal proteoliposomes is evaluated by considering the morphology and the size of the reconstituted vesicles, the homogeneity in size and protein distribution, the final protein orientation and the permeability of resulting proteoliposomes. Finally, the advantages of detergent removal by polystyrene beads as an alternative to conventional dialysis in two-dimensional crystallization trials are evaluated through review of recent structural reconstitution studies. Received: 1 December 1997 / Revised version: 6 February 1998 / Accepted: 6 February 1998     

Two-dimensional crystallization of Escherichia coli lactose permease

A chimeric protein consisting of lactose permease with cytochrome b562 in the middle cytoplasmic loop and six His residues at the C terminus (LacY/L6cytb562/417H6 or "red permease") was overexpressed in Escherichia coli and isolated by nickel affinity chromatography after solubilization with dodecyl-beta,d-maltopyranoside. Red permease was then reconstituted in the presence of phospholipids, yielding densely packed vesicles and well-ordered two-dimensional (2D) crystals as shown by electron microscopy of negatively stained specimens. Single-particle analysis of 16 383 protein particles in densely packed vesicles reveals a 5.4-nm-long trapeziform protein of 4.1 to 5.1 nm width, with a central stain-filled indentation. Depending on reconstitution conditions, trigonal and rectangular crystallographic packing arrangements of these elongated particles assembled into trimers are observed. The best ordered 2D crystals exhibit a rectangular unit cell, of dimensions a = 9.9 nm, b = 17.4 nm, that houses two trimeric complexes. Projection maps calculated to a resolution of 2 nm show that these crystals consist of two layers.     

Electron cryomicroscopy of bacteriorhodopsin vesicles: mechanism of vesicle formation.

We obtained vesicles from purple membrane of Halobacterium halobium at different suspension compositions (pH, electrolytes, buffers), following the procedure of Kouyama et al. (1994) (J. Mol. Biol. 236:990-994). The vesicles contained bacteriorhodopsin (bR) and halolipid, and spontaneously formed during incubation of purple membrane suspension in the presence of detergent octylthioglucoside (OTG) if the protein:OTG ratio was 2:1 by weight. The size distribution of the vesicles was precisely determined by electron cryomicroscopy and was found to be almost independent on the incubation conditions (mean radius 17.9-19 nm). The size distribution in a given sample was close to the normal one, with a standard deviation of approximately +/- 1 nm. During dialysis for removal of the detergent, the vesicles diminished their radius by 2-2.5 nm. The results allow us to conclude that the driving force for the formation of bR vesicles is the preferential incorporation of OTG molecules in the cytoplasmic side of the membrane (with possible preferential delipidation of the extracellular side), which creates spontaneous curvature of the purple membrane. From the size distribution of the vesicles, we calculated the elasticity bending constant, K(B) approximately 9 x 10(-20) J, of the vesicle wall. The results provide some insight into the possible formation mechanisms of spherical assembles in living organisms. The conditions for vesicle formation and the mechanical properties of the vesicles could also be of interest with respect to the potential technological application of the bR vesicles as light energy converters.     

The three-dimensional structure of the regular surface protein of Comamonas acidovorans derived from native outer membranes and reconstituted two-dimensional crystals

The three-dimensional structure of the regular surface protein (p4 symmetry, lattice constant a = b = 10.5 nm) of Comamonas acidovorans has been determined to a resolution of about 1.5 nm by means of electron microscopy and image processing. Three-dimensional reconstructions were performed using native outer membranes and artificial two-dimensional crystals of the surface protein, which was selectively solubilized by deoxycholate and recrystallized on carbon films. The two-fold symmetric morphological complex is composed of two identical monomers which are in tight contact with the outer membrane and presumably anchored to it by a small hydrophobic domain.     

MAL facilitates the incorporation of exocytic uroplakin-delivering vesicles into the apical membrane of urothelial umbrella cells

The apical surface of mammalian bladder urothelium is covered by large (500-1000 nm) two-dimensional (2D) crystals of hexagonally packed 16-nm uroplakin particles (urothelial plaques), which play a role in permeability barrier function and uropathogenic bacterial binding. How the uroplakin proteins are delivered to the luminal surface is unknown. We show here that myelin-and-lymphocyte protein (MAL), a 17-kDa tetraspan protein suggested to be important for the apical sorting of membrane proteins, is coexpressed with uroplakins in differentiated urothelial cell layers. MAL depletion in Madin-Darby canine kidney cells did not affect, however, the apical sorting of uroplakins, but it decreased the rate by which uroplakins were inserted into the apical surface. Moreover, MAL knockout in vivo led to the accumulation of fusiform vesicles in mouse urothelial superficial umbrella cells, whereas MAL transgenic overexpression in vivo led to enhanced exocytosis and compensatory endocytosis, resulting in the accumulation of the uroplakin-degrading multivesicular bodies. Finally, although MAL and uroplakins cofloat in detergent-resistant raft fractions, they are associated with distinct plaque and hinge membrane subdomains, respectively. These data suggest a model in which 1) MAL does not play a role in the apical sorting of uroplakins; 2) the propensity of uroplakins to polymerize forming 16-nm particles and later large 2D crystals that behave as detergent-resistant (giant) rafts may drive their apical targeting; 3) the exclusion of MAL from the expanding 2D crystals of uroplakins explains the selective association of MAL with the hinge areas in the uroplakin-delivering fusiform vesicles, as well as at the apical surface; and 4) the hinge-associated MAL may play a role in facilitating the incorporation of the exocytic uroplakin vesicles into the corresponding hinge areas of the urothelial apical surface.     

Preparation of reconstituted acetylcholine receptor membranes suitable for AFM imaging of lipid–protein interactions

The nicotinic acetylcholine receptor (nAChR) has been reconstituted in POPC vesicles at high lipid–protein (L/P) ratios for the preparation of supported lipid bilayers with a low protein density for studies of protein–lipid interactions using atomic force microscopy (AFM). Initial reconstitutions using a standard dialysis method with bulk L/P ratios ranging from 20:1 to 100:1 (w/w) gave heterogeneous samples that contained both empty vesicles and proteoliposomes with a range of L/P ratios. This is problematic because empty vesicles adsorb and rupture to form bilayer patches more rapidly than do protein-rich vesicles, resulting in the loss of protein during sample washing. Although it was not possible to find reconstitution conditions that gave homogeneous populations of vesicles with high L/P ratios, an additional freeze–thaw cycle immediately after dialysis did reproducibly yield a fraction of proteoliposomes with L/P ratios above 100:1. These proteoliposomes were separated by sucrose gradient centrifugation and used to prepare supported bilayers with well-separated individual receptors and minimal adsorbed proteoliposomes. AFM images of such samples showed many small features protruding from the bilayer surface. These features range in height from 1 to 5 nm, consistent with the smaller intracellular domain of the protein exposed, and have lateral dimensions consistent with an individual receptor. Some bilayers with reconstituted protein also had a small fraction of higher features that are assigned to nAChR with the larger extracellular domain exposed and showed evidence for aggregation to give dimers or small oligomers. This work demonstrates the importance of using highly purified reconstituted membranes with uniform lipid–protein ratios for AFM studies of integral membrane protein–lipid interactions.     

Electron crystallography of membrane proteins: two-dimensional crystallization and screening by electron microscopy

Structural and functional information of membrane proteins at ever-increasing resolution is being obtained by electron crystallography. While a large amount of work on the development of methods for electron microscopy and image processing has resulted in tremendous advances in terms of speed of data collection and resolution, general guidelines for crystallization are first starting to emerge. Yet two-dimensional crystallization itself will always remain the limiting factor of this powerful approach in structural biology. Two-dimensional crystallization through detergent removal by dialysis is the most widely used technique. Four main factors need to be considered for the dialysis method: the protein preparation, the detergent, the lipid added as well as any constituent lipid, and the buffer conditions. Equally important is proper and careful screening to identify two-dimensional crystals.     

Reassociation of disk components solubilized with deoxycholate.

Cattle disk membrane was solubilized in 2% deoxycholate in 0.05 m Tris-HCl buffer at pH 8.0. The sedimentation coefficient of rhodopsin in this solvent was 4.4 S. A sedimentation equilibrium study in H₂O-D₂O solvent showed that rhodopsin was mainly associated with deoxycholate and probably free of phospholipid when the deoxycholate concentration was higher than 0.8%. Bleaching of rhodopsin resulted in aggregation of the protein. Reduction of the deoxycholate concentration by dialysis promoted protein-phospholipid interaction in such a way that when the deoxycholate concentration was 0.2%, most of the rhodopsin present in the initial solution formed a soluble protein-phospholipid-deoxycholate complex with a molecular weight of 86,000. The complex, we believe, contains one molecule of rhodopsin, 50 to 55 molecules of phospholipid, and 20 to 25 molecules of deoxycholate.After dialysis against 0.05 m phosphate buffer at pH 6.5 that contained 20 mm MgCl₂ all the material was incorporated into vesicular membranes of diameters from 20 to 500 nm. Such results signify the dominance of rhodopsin-phospholipid interaction over either inter-rhodopsin or inter-phospholipid interactions in the initial decrease of deoxycholate concentration. The protein-phospholipid membrane was then formed by the two-dimensional aggregation of a rhodopsin-phospholipid complex. The presence of at least a part of the sugar moiety of rhodopsin on the outer surface of the vesicles was shown by using ferritin-labeled concanavalin A.     

A multichamber equilibrium dialysis apparatus

A method for inexpensively producing large quantities of equilibrium dialysis cells as well as two types of cell rotators is described. The method of production is simple enough that several hundred chambers can be produced in a single day. The assay procedure is flexible enough that any number of assays from one to several hundred may be completed in a short time. The chambers have proved extremely useful in the isolation and kinetic characterization of proteins which appear to be associated with membrane transport systems. They will also suffice for any of the other many uses for equilibrium dialysis. The large number of chambers available also provides an ideal means for determining the proper conditions for the growth of protein crystals by dialysis against the crystallizing agent. Microgram quantities of protein are easily crystallized by this technique.     

Outer membrane proteins and cell surface structure of Selenomonas ruminantium.

The protein compositions of the membrane preparations from Selenomonas ruminantium grown in glucose or lactate medium were determined by sodium dodecyl sulfate- and two-dimensional (first, isoelectric focusing; second, sodium dodecyl sulfate) polyacrylamide slab gel electrophoresis. The outer membrane from both glucose- and lactate-grown cells contained two major proteins with apparent molecular weights of 42,000 and 40,000. These proteins existed as peptidoglycan-associated proteins in the outer membrane. The critical temperature at which they were dissociated completely into the monomeric subunits of 42,000 and 40,000 daltons was found to be 85 degrees C. The amount of each protein varied considerably depending upon the cultural conditions. The absence of the lipoprotein of Braun in S. ruminantium was suggested in our preceding paper (Y. Kamio, and H. Takahashi, J. Bacteriol. 141:888--898, 1980), and the possible absence of the protein components corresponding to the Braun lipoprotein in this strain was confirmed by electrophoretic analysis of the outer membrane and the lysozyme-treated peptidoglycan fractions. Examination of the cell surface of S. ruminantium by electron microscopy showed that the outer membrane formed a wrinkled surface with irregular blebs, some of which pinched off forming vesicles of various sizes. Rapid cell lysis occurred with the addition of a low level of lysozyme to the cell suspension. These findings led us to conclude that the physiological and morphological properties of this strain were similar to those of "deep rough" and mlp or lpo mutants of Escherichia coli K-12, respectively.     

Surface crystallisation of the plasma membrane H+-ATPase on a carbon support film for electron crystallography

Large two-dimensional crystals of H+-ATPase, a 100 kDa integral membrane protein, were grown directly onto the carbon surface of an electron microscope grid. This procedure prevented the fragmentation that is normally observed upon transfer of the crystals from the air-water interface to a continuous carbon support film. Crystals grown by this method measure approximately 5 microm across and have a thickness of approximately 240 A. They are of better quality than the monolayers previously obtained at the air-water interface, yielding structure factors to at least 8 A in-plane resolution by electron image processing. Unlike most other two-dimensional crystals of membrane proteins they do not contain a lipid bilayer, but consist of detergent-protein micelles of H+-ATPase hexamers tightly packed on a trigonal lattice. The crystals belong to the two-sided plane group p321 (a=b=165 A), containing two layers of hexamers related by an in-plane axis of 2-fold symmetry. The protein is in contact with the carbon surface through its large, hydrophilic 70 kDa cytoplasmic portion, yet due to the presence of detergent in the crystallizing buffer, the hydrophobicity of the carbon surface does not appear to affect crystal formation. Surface crystallisation may be a useful method for other proteins which form fragile two-dimensional crystals, in particular if conditions for obtaining three-dimensional crystals are known, but their quality or stability is insufficient for X-ray structure determination.     

A nuclear magnetic resonance study of the hydrogen-exchange behaviour of lysozyme in crystals and solution

Amide hydrogen/deuterium exchange behaviour has been studied for all of the peptide amides of hen lysozyme by means of two-dimensional n.m.r. spectroscopy. The amides have been grouped into four categories on the basis of their rates of exchange in solution at pH 4.2 and 7.5. The distribution of the amides into the different categories has been examined in the light of the crystallographic structural information, considering the type of secondary structure, the nature of hydrogen bonding and the distance from the protein surface. None of these features was found to determine uniquely the pattern of hydrogen exchange rates within the protein. The exchange behaviour of the individual amides could, however, in general be rationalized by a combination of these features. Hydrogen exchange was also monitored in both tetragonal and triclinic crystals of lysozyme, by allowing exchange to take place in the crystals prior to dissolution and recording of n.m.r. spectra under conditions where further exchange was minimized. This enabled direct comparison to be made of the exchange behaviour in the crystals and solution. A reduction in exchange rate was observed in the crystalline state relative to solution for a substantial number of amides and distinct differences between exchange in the different crystals could be observed. These differences between the solution and the different crystal states do not, however, correlate in a simple manner with proximity to intermolecular contacts in the crystals. However, the existence of these contacts, which are on the surface of the protein molecule, have a profound effect on the exchange of amides in the interior of the protein. The results indicate that the spectrum of fluctuations giving rise to hydrogen exchange may be significantly altered by the intermolecular interactions present within the crystalline state.     

A high-throughput strategy to screen 2D crystallization trials of membrane proteins

Electron microscopy of two-dimensional (2D) crystals has demonstrated potential for structure determination of membrane proteins. Technical limitations in large-scale crystallization screens have, however, prevented a major breakthrough in the routine application of this technology. Dialysis is generally used for detergent removal and reconstitution of the protein into a lipid bilayer, and devices for testing numerous conditions in parallel are not readily available. Furthermore, the small size of resulting 2D crystals requires electron microscopy to evaluate the results and automation of the necessary steps is essential to achieve a reasonable throughput. We have designed a crystallization block, using standard microplate dimensions, by which 96 unique samples can be dialyzed simultaneously against 96 different buffers and have demonstrated that the rate of detergent dialysis is comparable to those obtained with conventional dialysis devices. A liquid-handling robot was employed to set up 2D crystallization trials with the membrane proteins CopA from Archaeoglobus fulgidus and light-harvesting complex II (LH2) from Rhodobacter sphaeroides. For CopA, 1 week of dialysis yielded tubular crystals and, for LH2, large and well-ordered vesicular 2D crystals were obtained after 24 h, illustrating the feasibility of this approach. Combined with a high-throughput procedure for preparation of EM-grids and automation of the subsequent negative staining step, the crystallization block offers a novel pipeline that promises to speed up large-scale screening of 2D crystallization and to increase the likelihood of producing well-ordered crystals for analysis by electron crystallography.     

Entrapment of lipid vesicles and membrane protein-lipid vesicles in gel bead pores

Phospholipid vesicles were entrapped in gel beads of Sepharose 6B and Sephacryl S-1000 during vesicle preparation by dialysis. Egg-yolk phospholipids solubilized with cholate or octyl glucoside were dialysed together with gel beads for 2.5 days in a flat dialysis bag. Some vesicles were formed in gel bead pores and vesicles of sufficient size became trapped. Red cell membrane protein-phospholipid vesicles could be immobilized in the same way. Non-trapped vesicles were carefully removed by chromatographic procedures and by centrifugation. The amount of entrapped vesicles increased with the initial lipid concentration and was dependent on the relative sizes of vesicles and gel pores. The largest amount of trapped vesicles, corresponding to 9.5 mumol of phospholipids per ml gel, was achieved when Sepharose 6B gel beads were dialysed with cholate-solubilized lipids at a concentration of 50 mM. In this case the vesicles had an average diameter of 60 nm and an internal volume of 15 microliters/ml gel. The amount of vesicles trapped in Sephacryl S-1000 gel beads upon dialysis under the same conditions was smaller: 2.2 mumol of phospholipids per ml gel. Probably most of the gel pores were too large to trap such vesicles. Larger vesicles, with an average diameter of 230 nm, were entrapped in the Sephacryl S-1000 matrix in an amount corresponding to 3.0 mumol phospholipids per ml gel upon dialysis of the gel beads and octyl glucoside-solubilized lipids at a concentration of 20 mM. The internal volume of these vesicles was 22 microliters/ml gel. The yield of immobilized phospholipids was up to 19%. The entrapped vesicles were somewhat unstable: 9% of the phospholipids were released during 9 days of storage at 4 degrees C. By the dialysis entrapment method vesicles can be immobilized in the gel beads without using hydrophobic ligands or covalent coupling.     

Functional reconstitution of the integral membrane proteins of influenza virus into phospholipid liposomes

The integral membrane proteins of influenza virus, a hemagglutinin and a neuraminidase, have been incorporated into liposomes composed of either phosphatidylcholine or a mixture of phosphatidylcholine and phosphatidylethanolamine (2:1 w/w) using detergent dialysis. The virus spike glycoproteins for reconstitution were selectively solubilized by using cetyltrimethylammonium bromide to leave a "core particle", which lacked a lipid bilayer but possessed quaternary structure as observed by electron microscopy. The viral spike proteins were combined with exogenous phospholipid in excess sodium cholate followed by exhaustive dialysis for 150 h. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis showed that only the viral glycoproteins were associated with all the complexes formed. The level of sodium cholate remaining after dialysis was shown to be reduced to less than 1 molecule per 80 protein molecules. Viral proteins reconstituted into dimyristoylphosphatidylcholine liposomes were shown to have retained hemagglutination, low-pH-dependent hemolysis, and neuraminidase activities and were associated with a lipid bilayer in two types of complexes with average lipid to protein mole ratios after sucrose density gradient purification of either 590:1 or 970:1. The bilayer vesicles formed were of similar sizes and were shown by negative-stain electron microscopy to be 150-300 nm in diameter with well-defined spikes on their surface. Reconstituted liposomes of dimyristoylphosphatidylcholine were found to be unstable with respect to their trapped volume and therefore were unsuitable for fusion studies, unlike complexes formed with phosphatidylcholine or a mixture of phosphatidylcholine/phosphatidylethanolamine derived from hen eggs.(ABSTRACT TRUNCATED AT 250 WORDS)     

Crystallization of p68 on lipid monolayers and as three-dimensional single crystals

Two-dimensional crystals of p68, a Ca2+ -binding protein that has homology with members of the lipocortin/calpactin family, were obtained by interaction with a phospholipid monolayer. By measuring surface pressure at constant surface area, p68 was found to interact in a Ca2+ -dependent manner specifically with phosphatidylethanolamine, less so with phosphatidylserine and not at all with phosphatidylcholine. With dimyristoyl-phosphatidylethanolamine, two-dimensional crystalline arrays were formed. Image analysis of electron micrographs of these crystals, which diffracted to about 50 A, revealed p3 symmetry with a unit cell of about 178 A by 178 A; the protein densities showed a two-domain structure giving a cylindrical molecule of about 100 A by 35 A diameter packed as trimers. Three-dimensional microcrystals obtained without lipid or Ca2+ were suitable for electron microscopy and gave a tetragonal unit cell of about 256 A by 68 A. The implications of these observations on the structure and lipid specificity of p68 binding are discussed.     

A model for water motion in crystals of lysozyme based on an incoherent quasielastic neutron-scattering study

This paper reports an incoherent quasielastic neutron scattering study of the single particle, diffusive motions of water molecules surrounding a globular protein, the hen egg-white lysozyme. For the first time such an analysis has been done on protein crystals. It can thus be directly related and compared with a recent structural study of the same sample. The measurement temperature ranged from 100 to 300 K, but focus was on the room temperature analysis. The very good agreement between the structural and dynamical studies suggested a model for the dynamics of water in triclinic crystals of lysozyme in the time range approximately 330 ps and at 300 K. Herein, the dynamics of all water molecules is affected by the presence of the protein, and the water molecules can be divided into two populations. The first mainly corresponds to the first hydration shell, in which water molecules reorient themselves fivefold to 10-fold slower than in bulk solvent, and diffuse by jumps from hydration site to hydration site. The long-range diffusion coefficient is five to sixfold less than for bulk solvent. The second group corresponds to water molecules further away from the surface of the protein, in a second incomplete hydration layer, confined between hydrated macromolecules. Within the time scale probed they undergo a translational diffusion with a self-diffusion coefficient reduced approximately 50-fold compared with bulk solvent. As protein crystals have a highly crowded arrangement close to the packing of macromolecules in cells, our conclusion can be discussed with respect to solvent behavior in intracellular media: as the mobility is highest next to the surface, it suggests that under some crowding conditions, a two-dimensional motion for the transport of metabolites can be dominant.     

Ultrastructure of reconstituted rat liver microsomal membranes and cytochrome b5- or P-450-containing proteoliposomes

Thin sectioning and freeze-fracture electron microscopy have been used to show that it is possible to obtain topologically closed vesicles by means of reconstitution of rat liver microsomal membrane "ghosts." The reconstitution by 15 hr dialysis resulted in the formation of vesicles with intramembrane particles (IMP) while after 40 hr dialysis no IMP were observed in the membranes. The protein/lipid ratio and functional activity of NADPH- and NADH-linked enzyme systems were similar in both cases. Cytochrome P-450 (LM2) was incorporated into liposomes of different composition (protein: lipid ratio--1:200). IMP were observed only when the incorporation of cytochrome P-450 was performed in the presence of detergent Emulgen 913 as specific additive to the initial protein-lipid-sodium cholate mixture or in the course of incubation of proteoliposomal suspensions at 37 degrees C. After the incorporation of cytochrome b5 into azolectin liposomes vesicular membranes contain IMP if the incorporated membrane protein: lipid ratio is at least 1:50. Pronase-induced splitting off of a 11 kDa heme-containing fragment of cytochrome b5 did not affect IMP content. The conditions of IMP formation in reconstituted membranes and in microsomal ghosts are discussed.     

Ultrastructure of cementum formation on partially formed teeth in dogs

Cementum crystals and matrix vesicles on the root surface of partially formed teeth in dogs were examined with a transmission electron microscope. Fine filamentous crystals were observed in the cementum calcifying fronts. The running pattern was mainly parallel to the root surface in the apical region and perpendicular to the root surface in lateral and coronal regions. Matrix vesicles were observed at the apical half of the periodontium, but not observed at the coronal region. These findings suggest that the parallel-arranged cementum would become the light-microscopic lamellar type and the perpendicular one the light-microscopic dense-line structure when fully developed. Moreover, cementum formation occurs due to two kinds of mechanisms: participation of matrix vesicles and secondary calcification (= additional cementogenesis).