Gap junction structures: Analysis of the x-ray diffraction data

Models for the spatial distribution of protein, lipid and water in gap junction structures have been constructed from the results of the analysis of X-ray diffraction data described here and the electron microscope and chemical data presented in the preceding paper (Caspar, D. L. D., D. A. Goodenough, L. Makowski, and W.C. Phillips. 1977. 74:605-628). The continuous intensity distribution on the meridian of the X-ray diffraction pattern was measured, and corrected for the effects of the partially ordered stacking and partial orientation of the junctions in the X-ray specimens. The electron density distribution in the direction perpendicular to the plane of the junction was calculated from the meridional intensity data. Determination of the interference function for the stacking of the junctions improved the accuracy of the electron density profile. The pair-correlation function, which provides information about the packing of junctions in the specimen, was calculated from the interference function. The intensities of the hexagonal lattice reflections on the equator of the X-ray pattern were used in coordination with the electron microscope data to calculate to the two-dimensional electron density projection onto the plane of the membrane. Differences in the structure of the connexons as seen in the meridional profile and equatorial projections were shown to be correlated to changes in lattice constant. The parts of the junction structure which are variable have been distinguished from the invariant parts by comparison of the X-ray data from different specimens. The combination of these results with electron microscope and chemical data provides low resolution three- dimensional representations of the structures of gap junctions.     

Evaluation of the electron density profile of the frog rod outer segment disc-membrane in vivo using x-ray diffraction

The structure of the rod outer segment disc-membrane in vivo was studied by X-ray low-angle scattering. The experiments were made on frogs under narcosis. Diffraction patterns corresponding to a resolution of 1.5 nm could be obtained from the membrane stacks of the rod outer segment discs. For the analysis of the measured diffraction pattern a new special computer procedure was elaborated. Among other generalizations of the theory, it was taken into account that the electron densities in the inter- and intra-disc spaces differ from the mean electron density of the whole stack. The consideration of this possibility, together with an exact experimental measurement of the isotrope background scattering, led to a mathematically unique solution. The calculated electron density profile apparently is a distinct asymmetric bilayer. The electron density of the side of the membrane which is in contact with the disc lumen is higher than the electron density on the side in contact with the cytoplasm. Therefore, a localization of rhodopsin or of other high molecular proteins mainly on the cytoplasmatic edge of the membrane can be excluded for the rod outer segment discs in vivo.     

X-ray diffraction analysis of cytochrome b5 reconstituted in egg phosphatidylcholine vesicles.

Cytochrome b5 was reconstituted asymmetrically into large unilamellar egg phosphatidylcholine vesicles. Asymmetry was preserved after sedimentation and partial dehydration to form oriented stacks of membranes. The periodicity of the centrosymmetric unit cell ranged between 145 and 175 A, depending upon the water content of the oriented multilayer. X-ray diffraction data were collected to a resolution of 12 A and phase factors were unambiguously assigned by a swelling analysis to a resolution of 15 A. The lower-resolution profile structures clearly showed a highly asymmetric single membrane containing the heme peptide segment of the cytochrome on one side of the membrane bilayer. The higher-resolution data were also analyzed and profile structures were compared with various models for the distribution of cytochrome b5 nonpolar peptide within the membrane bilayer region. The data favor an asymmetric distribution of protein mass within the membrane bilayer.     

Formation of crystalline arrays of chlorophyll a/b - light-harvesting protein by membrane reconstitution.

The structure of the major protein constituent of photosynthetic membranes in higher plants, the chlorophyll a/b-light harvesting complex (LHC), was studied by x-ray diffraction and electron microscopy. The LHC was purified from Triton X-100 solubilized thylakoid membranes of the pea, and contained 6 mol of chlorophylls a and b per mole of a polypeptide of 27,000 molecular weight. X-ray diffraction showed that in the presence of 10 mM MgCl2, purified LHC forms planar aggregates that stack with a period of 51 A. Within each layer, LHC molecules pack with a center-to-center distance of 85 A but without long-range order. However, when LHC is incorporated into single-walled vesicles of plant lecithin, the addition of NaCl above 10 mM, or MgCl2 above 2 mM, led to the formation of plaques of hexagonal lattices, with a lattice constant of 125 A. The large domain size and high degree of order in the plane of the membrane are evident from the sharp lattice lines observed to 7 A resolution on the equator of the x-ray pattern. Freeze-fracture electron micrographs demonstrated an aligned stacking of the lattices in adjacent membranes, resulting in crystallinity in the third dimension over short distances. Micrographs of negatively stained membranes revealed a hexagonal lattice of the same lattice constant, formed by surface-exposed parts of the LHC molecules which are probably responsible for the ordered stacking of lattices. In both the LHC aggregates and in the reconstituted membrane lattices the diffracted x-ray intensities at 10-A spacing on the equator indicate that the LHC molecule contains paralled alpha-helices or beta-sheets that are oriented perpendicular to the planar arrays.     

X-ray diffraction and electron microscopy studies of frozen erythrocyte membrane preparations

Well-defined X-ray diffraction patterns have been recorded from erythrocyte membranes in the frozen state. At ?40°C, lamellar periodicities range from 19 to 95 nm depending on the glycerol content (0–40%, respectively). Freeze-fracture electron micrographs of samples frozen in two stages to approximate to the diffraction conditions show ice formation external to membrane stacks. The membrane stacks have periodicities of the same order of magnitude as those obtained by X-ray diffraction.     

Structure of sarcoplasmic reticulum membranes at low resolution (17A)

Vesicles of fragmented sarcoplasmic reticulum membranes have been prepared and centrifuged into a multilayered form suitable for analysis by X-ray diffraction. X-ray diffraction has been recorded from a regular stacking of flattened vesicles in the presence of excess fluid. Discrete orders of a lamellar repeat distance ranging from 220 to 270 Å have been recorded. The diffraction data extend out to a minimum Bragg spacing of 33 Å. An electron density profile at a resolution of 17 Å has been derived using direct methods of structure analysis. The membrane has a bilayer construction (similar to nerve myelin and retina at low resolution) but the profile is markedly asymmetrical. The protein molecules are predominantly on the inside of the vesicle. A striking resemblance between the disc membranes in retina and the sarcoplasmic reticulum membranes has been noted and is described. X-ray diffraction has been recorded from the protein molecules in the surface of the sarcoplasmic reticulum membrane. The protein molecules are not in an ordered array but appear to have a liquid-like ordering. The observation that vesicles can be prepared in a suitable form for X-ray analysis has importance for membrane research for many different membranes form vesicles and it follows that these membranes can now be profitably studied by X-ray diffraction using a similar method.     

An analysis of lamellar x-ray diffraction from disordered membrane multilayers with application to data from retinal rod outer segments.

Oriented multilayers containing a membrane pair within the unit cell potentially possess both lattice disorder and substitution disorder. Lattice disorder occurs when there is a lack of long-range order in the lattice spacings produced by a variation in the nearest neighbor distances between unit cells. A simple form of substitution disorder can arise from a variation in the separation of the two membranes within the unit cells in the multilayer. Lattice disorder produces a monotonically increasing width for higher order lamellar "reflections" while simple substitution disorder produces an incoherent intensity underlying the coherent intensity. A generalized Patterson function analysis has been developed for treating lamellar diffraction from lattice disordered multilayers. This analysis allows the identification of the autocorrelation function of the unit cell electron density profile and its subsequent deconvolution to provide the unit cell electron density profile. A recursive procedure has been developed for separating the incoherent intensity from the coherent intensity via a Gaussian probability model of the membrane intra-pair separation. In cases studied so far both disorders can be quantitatively accounted for and eliminated from interfering with the phasing of the coherent intensity or distorting the derived electron density profile. Lamellar X-ray diffraction data from intact retinal rods, using either film or position sensitive detectors, shows severe effects of both forms of disorder which have not been taken into account in past analysis of such data. We have applied our analysis to the data on dark adapted rod outer segments in electrophysiologically intact retinas of Chabre and Cavaggioni (unpublished). An electron density profile is derived at 25 A resolution. The lattice nearest neighbor spacing has a variation of +/- 19 A out of a 295 A repeat. The intra-unit cell membrane pair center to center distance of 88 A varies +/-8 A.     

Lateral packing of mineral crystals in bone collagen fibrils

Combined small-angle x-ray scattering and transmission electron microscopy studies of intramuscular fish bone (shad and herring) indicate that the lateral packing of nanoscale calcium-phosphate crystals in collagen fibrils can be represented by irregular stacks of platelet-shaped crystals, intercalated with organic layers of collagen molecules. The scattering intensity distribution in this system can be described by a modified Zernike-Prins model, taking preferred orientation effects into account. Using the model, the diffuse fan-shaped small-angle x-ray scattering intensity profile, dominating the equatorial region of the scattering pattern, could be quantitatively analyzed as a function of the degree of mineralization. The mineral platelets were found to be very thin (1.5 nm ∼ 2.0 nm), having a narrow thickness distribution. The thickness of the organic layers between adjacent mineral platelets within a stack is more broadly distributed with the average value varying from 6 nm to 10 nm, depending on the extent of mineralization. The two-dimensional analytical scheme also leads to quantitative information about the preferred orientation of mineral stacks and the average height of crystals along the crystallographic c axis.     

Electron density profile of two-dimensionally crystalline membranous cytochrome c oxidase at low resolution.

Unilamellar vesicles of membranous cytochrome c oxidase have been isolated whose distribution of protein in the membrane plane was predominantly crystalline. The vesicles were collapsed via controlled partial dehydration, resulting, at first, in the formation of unoriented, mostly unstacked, membrane pairs. Further controlled partial dehydration resulted in the formation of oriented multilayers of stacks of membrane pairs, retaining the in-plane crystallinity. The above were monitored by electron microscopy and x-ray diffraction. Analysis of the x-ray diffraction from unoriented, unstacked membrane pairs by two independent methods provided the membrane electron density profile to 30 A resolution.     

Nucleosomes stacked with aligned dyad axes are found in native compact chromatin in vitro

In this study, electron tomograms of plunge-frozen isolated chromatin in both open and compacted form were recorded. We have resolved individual nucleosomes in these tomograms in order to provide a 3D view of the arrangement of nucleosomes within chromatin fibers at different compaction states. With an optimized template matching procedure we obtained accurate positions and orientations of nucleosomes in open chromatin in "low-salt" conditions (5 mM NaCl). The mean value of the planar angle between three consecutive nucleosomes is 70°, and the mean center-to-center distance between consecutive nucleosomes is 22.3 nm. Since the template matching approach was not effective in crowded conditions, for nucleosome detection in compact fibers (40 mM NaCl and 1 mM MgCl(2)) we developed the nucleosome detection procedure based on the watershed algorithm, followed by sub-tomogram alignment, averaging, and classification by Principal Components Analysis. We find that in compact chromatin the nucleosomes are arranged with a predominant face-to-face stacking organization, which has not been previously shown for native isolated chromatin. Although the path of the DNA cannot be directly seen in compact conditions, it is evident that the nucleosomes stack with their dyad axis aligned in forming a "double track" conformation which is a consequence of DNA joining adjacent nucleosome stacks. Our data suggests that nucleosome stacking is an important mechanism for generating chromatin compaction in vivo.     

A direct analysis of lamellar x-ray diffraction from hydrated oriented multilayers of fully functional sarcoplasmic reticulum.

The profile structure of functional sarcoplasmic reticulum (SR) membranes was investigated by X-ray diffraction methods to a resolution of 10 A. The lamellar diffraction data from hydrated oriented multilayers of SR vesicles showed monotonically increasing widths for higher order lamellar reflections, indicative of simple lattice disorder within the multilayer. A generalized Patterson function analysis, previously developed for treating lamellar diffraction from lattice-disordered multilayers, was used to identify the autocorrelation function of the unit cell electron density profile. Subsequent deconvolution of this autocorrelation function provided the most probable unit cell electron density profile of the SR vesicle membrane pair. The resulting single membrane profile possesses marked asymmetry, suggesting that a major portion of the Ca++ -ATPase resides on the exterior of the vesicle. The electron density profile also suggests that the Ca++-dependent ATPase penetrates into the lipid hydrocarbon core of the SR membrane. Under conditions suitable for X-ray analysis, SR vesicles prepared as partially dehydrated oriented multilayers are shown to conserve most of their ATP-induced Ca++ uptake functionality, as monitored spectrophotometrically with the Ca++ indicator arsenazo III. This has been verified both in resuspensions of SR after centrifugation and slow partial dehydration, and directly in SR multilayers in a partially dehydrated state (20-30 percent water). Therefore, the profile structure of the SR membrane that we have determined may closely resemble that found in vivo.     

Cellular compartments in mitotic cells: ultrahistochemical identification of Golgi elements in PtK-1 cells

This investigation focuses on the identification, distribution, and transport of intracellular membrane systems during mitosis. The membranes of the Golgi apparatus can be identified cytochemically by staining for acid phosphatase (acPase) and thiamine pyrophosphatase (TPPase) activity. Using this approach we are able to study the disintegration of the Golgi apparatus during mitosis and to follow the dislocation as well as the organized reappearance of Golgi elements after the completion of mitosis. We are able to demonstrate that during mitosis the activity of both enzymes is strong enough to react with the substrate applied during the staining procedure. Furthermore, we observe a characteristic pattern of membrane distribution in mitotic cells. During interphase the TPPase reaction is characteristically limited to one or two cisternae of a dictyosomal stack. The acPase reaction stains the membranes of the total stack, of the GERL, of some vesicles and cisternae near the dictyosomes and lysosomes. After the mitotic breakdown of the dictyosomal stacks the forming vesicles still stain positively and are distributed over the entire cytoplasm. At late anaphase and early telophase the enzyme activity occurs not only in the reconstituting dictyosomes but also in the nuclear envelope and in some ER cisternae. The extended spectrum of membrane structures indicating Golgi enzyme activity becomes obvious. This phenomenon favors the idea that at least some functions of the Golgi apparatus persist during mitosis.     

Structure of Golgi apparatus

Summary Golgi apparatus (GA) of eukaryotic cells consist of one or more stacks of flattened saccules (cisternae) and an array of fenestrae and tubules continuous with the peripheral edges of the saccules. Golgi apparatus also are characterized by zones of exclusion that surround each stack and by an assortment of vesicles (or vesicle buds) associated with both the stacks and the peripheral tubules of the stack cisternae. Each stack (sometimes referred to as Golgi apparatus, Golgi complex, or dictyosome) is structurally and functionally polarized, reflecting its role as an intermediate between the endoplasmic reticulum, the cell surface, and the lysosomal system of the cell. There is probably only one GA per cell, and all stacks of the GA appear to function synchronously. All Golgi apparatus are involved in the generation and movement of product and membrane within the cell or to the cell exterior, and these functions are often reflected as structural changes across the stacks. For example, in plants, both product and membrane appear to maturate from the cis to the trans poles of the stacks in a sequential, or serial, manner. However, there is also strong ultrastructural evidence in plants for a parallel input to the stack saccules, probably through the peripheral tubules. The same modes of functioning probably also occur in animal GA; although here, the parallel mode of functioning almost surely predominates. In some cells at least, GA stacks give rise to tubular-vesicular structures that resemble the trans Golgi network. Rudimentary GA, consisting of tubular-vesicular networks, have been identified in fungi and may represent an early stage of GA evolution.     

Stacking behavior of an intertidal abalone: an adaptive response or a consequence of space limitation?

Intertidal populations of black abalone Haliotis cracherodii Leach at Santa Cruz Island, California, vary in density among surge channels from < 1 to 126 abalone/m². Dense populations are characterized by high levels of intraspecific secondary substratum use (“stacking”) for attachment surfaces, though it is rare in low density areas. Use of shell surfaces by black abalone appears not to be an evolved adaptive strategy. Individuals in stacks fed significantly more than expected, yet solitary abalone next to stacks shared food trapped by stacks. In the laboratory, starvation did not increase the propensity of an abalone to stack. Stacks were equally common in the breeding and non-breeding seasons, suggesting that stacking behavior was not a mechanism to enhance reproductive success. Stacking did not enhance avoidance of predators or competitors. Laboratory experiments showed that stacking is density dependent and probably the result of limitation of primary attachment space. Removals of significant predators (sea otters and Chumash Indians) of adult abalone during the past two centuries probably led to increased densities of black abalone, which in turn has had an indirect effect on the prevalence of stacking.     

Structure and packing of microfibrils in collagen

X-ray diffraction, patterns suggest that the five-stranded microfibrils in the collagen of rat tail tendon are supercoiled and packed together on a square lattice with a statistical distribution of axial displacements between nearest neighbours.     

Structure and Function of Chloroplast Membrane III. The Effects of Mg++ and K+ Ions Toward the Ultrastructure of Two Kinds of Chloroplast Thylakoid Membranes

Based upon our previous work on the relationship between structure and function of chloroplast of wheat in connection with PSⅡ reaction, we studied the effects of MgCl2 and KC1 toward two kinds of thylakoid membranes. After exposing etiolated wheat seedlings to intermittent light (cycle of 2 min. light, 118 min. dark) for 24 hr, we obtain ed an incompletely developed chleroplast membrane. Completely developed chloroplast membrane was obtained from wheat seedlings grown under normal light-dark regime. Thylakoid membranes of plants grown under intermittent light failed to form grana stacks they remained as single lamellae in the suspension containing Mg++ or K+ of high concentration although simple stackings not more than two thylakoids c.ould be found. However, thylakoids grown under normal light-dark regime showed well developed grand stacks. Isolated chloroplast samples from two kinds of seedlings were suspended in 5 mM MgCl2 and 100 mM KC1 solutions for a definite time, portions of each samples were processed for electron microscopic observations and their photosynthetic activities were measured at the same time (It will be dealt with in another article). When these two kinds of isolated plastids were suspended either in MgCl2 (5 mM) or KC1 (100), the normally developed grana thylakoids stacked closely but the incompletely developed thylakoid- membranes did not stack. The incompletely developed chloroplast thylakoid membranes,, in either Mg++ or K+ ions could not induce stacking of the scattered thylakoid membranes to form grana. Therefore, we presume that light- harvesting chlorophyll a/b protein complex is on internal factor to induce thylakoid- membranes stacking and a definite concentration of caionions is an important factor in maintaining the stacking of thylakoid membranes. These results further prove the close association between structure and function in our previous studies on the mesophyll cell of the winter wheat.     

The reaction center profile structure derived from neutron diffraction

Both reaction center protein from the photosynthetic bacteria Rhodopseudomonas sphaeroides and egg phosphatidylcholine can be deuterium labelled; the reaction center protein can be incorporated into the phosphatidylcholine bilayers forming a homogeneous population of unilamellar vesicles. The lipid profile and the reaction center profile within these reconstituted membrane profiles were directly determined to 32 Å resolution using lamellar neutron diffraction from oriented membrane multilayers containing either deuterated or protonated reaction centers, and either deuterated or protonated phosphatidylcholine. The 32 Å resolution reaction center profile shows that the protein spans the membranes, and has an asymmetric mass distribution along the perpendicular to the membrane plane. These results were combined with previously described X-ray diffraction results in order to extend the resolution of the derived reaction center profile to 9 Å.     

A method on strain measurement of HAP in cortical bone from diffusive profile of X-ray diffraction

Bone tissue is a composite material composed of hydroxyapatite (HAp) and collagen matrix. As HAp is a crystalline structure, an X-ray diffraction method is available to measure the lattice strain of HAp crystals. However, mineral particles of HAp in bone have much lower crystallinity than usual crystalline materials, which show a diffusive intensity profile of X-ray diffraction. It is not easy to determine quantitatively an infinitesimal strain of HAp from the peak position of diffusive profile. In order to improve the accuracy of strain measurement of HAp in bone tissue and to obtain reproducible results, this paper proposes an X-ray diffraction method applied to a diffusive profile for low crystallinity. This method is to estimate the lattice strain of HAp using not a peak position but a whole diffraction profile. In this experiment, a strip specimen of 28 x 8 x 2 mm was made from bone axial, outside circumferential and cross-sectional circumferential region in the cortical bone of bovine femur. The X-ray diffraction measurements were carried out before and after applying an external load. As a result, the precision of strain measurement was much improved by this method. Although a constant value of macroscopic strain was applied in the specimen, the lattice strain had a lower value than the macroscopic strain and had a different value in each specimen.     

Structure of photosynthetic membranes of Euglena using X-ray diffraction

Novel X-ray diffraction results of membranes from chloroplasts of Euglena are presented, together with freeze-etch images obtained concurrently. Conditions were found for sharp lamellar reflections corresponding to ordered stacking of thylakoids. The periodicity measured by diffraction agrees well with that observed by microscopy. Intensities of diffraction were analysed in order to calculate the electron density distributions across the membranes. Some arguments in favour of the preferred phases of the reflection are given. The distributions indicate firstly the presence of 25 Å-wide regions where the hydrocarbon chains of the membrane lipids are concentrated. This result is discussed in terms of structural models for the chloroplast membrane. Comparison with results of freeze-etching indicates where in the density distribution are the regons inside and outside the membrane sacs. Secondly, the density distributions show maxima on the outside of the membranes only, corresponding possibly to an asymmetrical distribution of lipids.     

Transmission electron microscopy as a tool for nanocrystal characterization pre- and post-injector

Recent advancements at the Linac Coherent Light Source X-ray free-electron laser (XFEL) enabling successful serial femtosecond diffraction experiments using nanometre-sized crystals (NCs) have opened up the possibility of X-ray structure determination of proteins that produce only submicrometre crystals such as many membrane proteins. Careful crystal pre-characterization including compatibility testing of the sample delivery method is essential to ensure efficient use of the limited beamtime available at XFEL sources. This work demonstrates the utility of transmission electron microscopy for detecting and evaluating NCs within the carrier solutions of liquid injectors. The diffraction quality of these crystals may be assessed by examining the crystal lattice and by calculating the fast Fourier transform of the image. Injector reservoir solutions, as well as solutions collected post-injection, were evaluated for three types of protein NCs (i) the membrane protein PTHR1, (ii) the multi-protein complex Pol II-GFP and (iii) the soluble protein lysozyme. Our results indicate that the concentration and diffraction quality of NCs, particularly those with high solvent content and sensitivity to mechanical manipulation may be affected by the delivery process.