Novel crystalline sheets of Na,K-ATPase induced by phospholipase A2

Structural Study of H,K-ATPase by Electron Microscopy and Image Reconstruction

H,K-ATPase is an integral protein of the plasma membrane of parietal cells. It is believed to constitute the pump responsible for secretion of acid into stomach. Its catalytic subunit (Mr 110,000) shows striking sequence homology to those of other transport ATPases. Recent studies suggest that there is also a glycoprotein (ca 300 amino acids) associated with the H,K pump, which is very homologous to the β subunit of the Na,K-ATPase.

The enzyme is isolated in protein-rich membrane vesicles from hog stomachs. Formation of two-dimensional crystals is induced in suspensions of the enzyme by methods that had proved successful for crystallization of the Na,K-ATPase.

Structure and function of the calcium pump

Active transport of cations is achieved by a large family of ATP-dependent ion pumps, known as P-type ATPases. Various members of this family have been targets of structural and functional investigations for over four decades. Recently, atomic structures have been determined for Ca2+-ATPase by X-ray crystallography, which not only reveal the architecture of these molecules but also offer the opportunity to understand the structural mechanisms by which the energy of ATP is coupled to calcium transport across the membrane. This energy coupling is accomplished by large-scale conformational changes. The transmembrane domain undergoes plastic deformations under the influence of calcium binding at the transport site. Cytoplasmic domains undergo dramatic rigid-body movements that deliver substrates to the catalytic site and that establish new domain interfaces. By comparing various structures and correlating functional data, we can now begin to associate the chemical changes constituting the reaction cycle with structural changes in these domains.

Reconstitution of detergent-solubilized Na,K-ATPase and formation of two-dimensional crystals

Very pure, detergent-solubilized Na,K-ATPase from dog or lamb kidneys has been successfully reconstituted at high protein-to-lipid weight ratios. Studies have been conducted to establish the orientation of the Na,K-ATPase molecules in the reconstituted membranes and to assess the functional activity and the conformational state of the reconstituted enzyme. Results indicate that reincorporation of the Na,K-ATPase molecules in the lipid bilayer is unidirectional and that the reconstituted enzyme retains its functional and structural integrity. Two-dimensional crystals have been induced in these preparations by vanadate ions. The arrays, with a dimeric structure in the unit cell, have a morphology similar to that of the crystals that had previously formed in the native membranes. Filtered images show that in projection, the molecule had an asymmetrical mass distribution, which at the resolution of 2.5 nm is identical to that of the earlier crystals. These sheets, although small, represent the first crystals of Na, K-ATPase to be formed by reconstitution. We expect that optimization of the reconstitution and crystallization parameters will lead to larger and better-ordered sheets, suitable for electron crystallography.

Two-dimensional crystallization of Ca-ATPase by detergent removal

By using Bio-Beads as a detergent-removing agent, it has been possible to produce detergent-depleted two-dimensional crystals of purified Ca-ATPase. The crystallinity and morphology of these different crystals were analyzed by electron microscopy under different experimental conditions. A lipid-to-protein ratio below 0.4 w/w was required for crystal formation. The rate of detergent removal critically affected crystal morphology, and large multilamellar crystalline sheets or wide unilamellar tubes were generated upon slow or fast detergent removal, respectively. Electron crystallographic analysis indicated unit cell parameters of a = 159 A, b = 54 A, and gamma = 90 degrees for both types of crystals, and projection maps at 15-A resolution were consistent with Ca-ATPase molecules alternately facing the two sides of the membrane. Crystal formation was also affected by the protein conformation. Indeed, tubular and multilamellar crystals both required the presence of Ca2+; the presence of ADP gave rise to another type of packing within the unit cell (a = 86 A, b = 77 A, and gamma = 90 degrees), while maintaining a bipolar orientation of the molecules within the bilayer. All of the results are discussed in terms of nucleation and crystal growth, and a model of crystallogenesis is proposed that may be generally true for asymmetrical proteins with a large hydrophilic cytoplasmic domain.

Three-dimensional structure of the porcine gastric H,K-ATPase from negatively stained crystals

A low-resolution three-dimensional model of membrane-bound H,K-ATPase from pig gastric mucosa has been reconstructed by electron microscopy and image processing of two-dimensional crystals in negative stain. The crystal formation is induced by magnesium and vanadate, which stabilize the E2 conformation of the enzyme. The unit cell, with a size of a = b = 123 A, gamma = 90 degrees, has tetragonal p4 symmetry. There are four separate alpha beta protomers within each unit cell. The high-contrast region is limited to the cytoplasmic part of the protein. The total volume of the observed asymmetric protein domain corresponds to a molecular mass of 80-90 kDa. It consists mainly of a large pear-shaped domain measuring 60 x 45 A2, with a height of 50 A as measured perpendicular to the membrane plane. A small stalk segment, 20 A in length, forms a connection to the transmembrane region.

2D crystallization: from art to science

The techniques as well as the principles of the 2D crystallization of membrane and water-soluble proteins for electron crystallography are reviewed. First, the biophysics of the interactions between proteins, lipids and detergents is surveyed. Second, crystallization of membrane proteins in situ and by reconstitution methods is discussed, and the various factors involved are addressed. Third, we elaborate on the 2D crystallization of water-soluble proteins, both in solution and at interfaces, such as lipid monolayers, mica, carbon film or mercury surfaces. Finally, techniques and instrumentations that are required for 2D crystallization are described.

Na,K-ATPase in crystalline form investigated by scanning force microscopy

Na,K-ATPase has been isolated in purified membrane fragments from kidney tissue and crystallized by phospholipase treatment to obtain two-dimensional, membrane-bound protein crystals. Scanning force microscopy has been used to identify and analyze the topography of the membrane fragments. Specific patterns in accordance with electron microscopic images have been found. In biological material under physiological conditions the scanning force is a crucial parameter for the resulting image at high resolution.

Three-dimensional structure of Na,K-ATPase determined from membrane crystals induced by cobalt-tetrammine-ATP

The three-dimensional structure of Na,K-ATPase has been analyzed with electron microscopy and image processing. The enzyme, purified from pig kidney outer medulla, was arranged in a new form of tetragonal two-dimensional membrane crystals after incubation with cobalt-tetrammine-ATP, a stable MgATP complex analogue. Each continuous protein domain, as delineated by negative stain, consists of two alpha beta-protomers related by a dyad axis. The two rod-like regions are connected by a bridge displaced about 20 A away from the center of the structure toward the lipid bilayer. The domain connecting the two promoters is more constricted and closer to the center of the structure in the Co(NH3)4ATP-induced crystals than in the vanadate-induced p21 crystals. These observations suggest that the difference between previously analyzed dimers of two-dimensional p21 crystals induced with vanadate/magnesium and dimers of p4 crystals induced with Co(NH3)4ATP reflects two different conformational states of the enzyme.

Two-dimensional crystallization of membrane proteins

In spite of several great breakthroughs, the overall rate of progress in determining high-resolution structures of membrane proteins has been slow. This is entirely due to the scarcity of suitable, well-ordered crystals. Most membrane proteins are multimeric complexes with a composite molecular mass in excess of 50000 Da which puts them outside the range of current solution NMR techniques. For the foreseeable future, detailed information about the structure of large membrane proteins will therefore depend on crystallographic methods.

Configuration of subunits within crystals of Na, K-ATPase maintained in the frozen-hydrated state

Two-dimensional crystalline sheets of Na, K-ATPase were studied in the vitrified, frozen-hydrated state by electron microscopy and image processing. The technique of correlation averaging was used to determine the projected structure. The projection map shows asymmetry between the pair of "alpha beta" protomers comprising a dimer of Na, K-ATPase molecules. The two protomers differ in overall density as well as in shape. One protomer has an oblong shape, whereas the other with higher density has a head and a hook region. Such an asymmetry has not been reported by other laboratories. This asymmetry may either be due to the coexistence of two different conformations of the enzyme in the dimeric form or due to the simultaneous existence of two molecular species of Na, K-ATPase.

Coexistence of different forms of Na,K-ATPase in two-dimensional membrane crystals

Two-dimensional membrane crystals of renal Na,K-ATPase were analyzed by electron microscopy and image processing. The particular property of the crystals in this work was that they showed unit cell parameters similar to the previously studied p21 crystals but lacked the dyad axis as observed in nominal 0 degrees-projections. A three-dimensional reconstruction revealed that structural differences between alpha beta-units of the enzyme gave rise to the asymmetry. A high degree of two-fold rotational symmetry was observed in the middle of the structure while the protein units had different three-dimensional shapes at levels above and below the central sections. The simultaneous coexistence of different forms of Na,K-ATPase suggests that the conformational flexibility of the enzyme plays an important role in the pumping process.

Identification of monoclonal antibody binding domains of Na+,K(+)-ATPase by immunoelectron microscopy

Treatment of purified preparations of porcine Na+,K(+)-ATPase with phospholipase A2, MgCl2 and NaVO3 leads to the formation of two-dimensional crystals exclusively in a dimeric configuration. Two-dimensional computer-averaged projections of the electron microscopy images of the crystalline enzyme with bound Fab fragments of monoclonal antibody M10-P5-C11 were accomplished using image enhancement software and showed that the antibody fragments caused only a modest increase in the unit cell size, while reducing the extent of asymmetry of the two promoters in each unit cell. The digital imaging also showed that the antibody's epitope on the alpha subunit resides on the 'lobe' or 'hook' region of the intracellular portion of the enzyme. Since functional studies indicate that M10-P5-C11 binds near or between the ATP binding site and the phosphorylation site, this visualized 'lobe' region of alpha may comprise the catalytic site. In addition, the binding of another inhibitory antibody, 9-A5, has been found to prevent crystal formation and the presence of the carbohydrate sugars on the enzyme's beta subunit shown to be required for crystal formation.

The present state of two-dimensional crystallization of membrane proteins

This review summarizes the present literature on two-dimensional crystallization of membrane proteins, with emphasis on the technical aspects. It includes all the intrinsic membrane proteins that have been crystallized after solubilization. Four general ways of making crystals are described in detail. Furthermore, suggestions for improving crystallization conditions are presented.

Fusion of the mitochondrial outer membrane: use in forming large, two-dimensional crystals of the voltage-dependent, anion-selective channel protein

Phospholipase A2 induces crystallization of the channel protein, VDAC (also called mitochondrial porin), in the outer membrane of Neurospora crassa mitochondria. The channel crystals formed in native membranes typically contain a few hundred unit cells. To increase the size of these membrane crystals for low-contrast electron microscopic imaging and diffraction studies, fusion of the isolated mitochondrial outer membranes was attempted before and after phospholipase treatment. Successful fusion of the untreated membranes was achieved by a procedure involving slow dehydration at acid pH. Single crystals of channels obtained by subsequent action of soluble phospholipase A2 on fused mitochondrial outer membranes may contain several thousand unit cells.

Digital image analysis of two-dimensional Na,K-ATPase crystals: dissimilarity between pump units

Two-dimensional crystals of purified Na,K-ATPase were induced by treatment with phospholipase-A2 and vanadate. The negatively stained crystals were imaged by electron microscopy and analysed by digital image processing. Two-dimensional averaged projections of the crystals were calculated by the technique of correlation analysis, utilizing SPIDER (System for Processing of Image Data in Electron microscopy and Related fields) image processing software. The calculated dimensions of the unit cell were found to be 13.3 X 4.59 nm with included angle of 98 degrees, comparable to those reported by others. However, the two protomers of the unit cell were found always to be dissimilar in shape and in orientation. All protomers of one side of the dimer ribbon had a triangular outline, and all protomers of the opposing side had a comma shape. This dissimilarity could be explained by two orientations of identical protomers: one orientation for one side of the dimer ribbon, and another orientation for the protomers of the opposing side of the ribbon. An alternative explanation is that the protomers of one side of the dimer ribbon are actually in a conformation different from that of the protomers of the opposing of the ribbon.

Assembly of two-dimensional membrane crystals of Na,K-ATPase

The assembly of vanadate-induced two-dimensional membrane crystals of Na,K-ATPase was analyzed by electron microscopy and image processing. Electron micrographs of negatively stained linear arrays of protein molecules were recorded and processed by correlation averaging methods. The arrays were compared with fully developed p21 crystals of the enzyme. On the basis of similarity in protein form, symmetry, and packing arrangement it was concluded that the fully developed crystals are built of tightly packed ribbons. Assembly pathways for two-dimensional membrane crystals of Na,K-ATPase are proposed.

Lateral segregation of sterol and channel proteins in the mitochondrial outer membrane induced by phospholipase A2: evidence from negative-stain electron microscopy using filipin

The channel protein in the mitochondrial outer membrane of Neurospora crassa aggregates laterally into crystalline arrays by the action of phospholipase A2. When mitochondrial outer membranes are reacted with filipin and examined by negative-stain electron microscopy, filipin-sterol complexes are found everywhere on the membranes except on the crystalline channel arrays. This suggests that the channel-rich membrane domains may have a relatively low content of accessible sterol. It is proposed that in vitro segregation of protein and lipid membrane components by phospholipase A2 may reflect a mechanism by which the endogenous enzyme organizes the native mitochondrial membrane into functional domains.

The three-dimensional structure of the Na,K-ATPase from electron microscopy

The structure of Na,K-ATPase has been studied by electron microscopy and image reconstruction. A three-dimensional structure of this enzyme has been obtained to an overall resolution of 2.5 nm using data from specimens of negatively stained dimer sheets tilted through a range of angles +/- 60 degrees. The reconstruction shows a complex mass distribution consisting of ribbons of paired molecules extending approximately 6.0 nm from the cytoplasmic side of the membrane. The molecular envelope consists of a massive "body" with "lobe" and "arm" structures projecting from it. The body has a columnar shape and is tilted with respect to the plane of the membrane. The region of interaction responsible for dimer formation is located between two bodies and is clearly visible in the reconstruction. It has been identified as a segment in the amino-terminal portion of the alpha subunit. The arms that interconnect the ribbons are located close to the membrane and are most probably formed by the beta subunits.