Ultrastructure of secretory and high-polymer serum immunoglobulin A of human and rabbit origin

Electron micrographs of immunoglobulins A from human and rabbit colostrum, which were purified on tall agarose columns, revealed Y-shaped molecules (125 by 140 angstroms). The linear dimensions of the arms were 55 to 75 by 25 to 30 angstroms. A molecular model is postulated in which two immunoglobulin A monomers are superimposed on each other in a close-packed state with the secretory piece inserted in the constant region of the alpha-chains. High-polymer (11 or 13S) immunoglobulin A molecules (total span 100 to 110 angstroms) from human serum were composed of four arms (50 to 55 by 20 angstroms) joined at a contrast-rich center.     

A monoclinic post-stishovite polymorph of silica in the shergotty meteorite

A post-stishovite phase of silica was identified in the Shergotty meteorite by x-ray diffraction and field emission scanning electron microscopy. The diffraction pattern revealed a monoclinic lattice, similar to the baddeleyite-structured polymorph with the cell parameters a = 4.375(1) angstroms, b = 4.584(1) angstroms, c = 4. 708(1) angstroms, beta= 99.97(3), rho = 4.30(2) grams per cubic centimeter, where the numbers in parentheses are the maximum deviations. Transmission electron microscopy investigations indicate the presence of the alpha-lead dioxide-like polymorph, stishovite, and secondary cristobalite in the same silica grain. The mixture of high-density polymorphs suggests that several post-stishovite phases were formed during the shock event on the Shergotty parent body.     

Aqueous central cavity in aspartate transcarbamylase from Escherichia coli

A three-dimensional x-ray diffraction study of aspartate transcarbamylase to 5.5-angstrom resolution, with the aid of four isomorphous heavy atom derivatives, indicates the presence of a central aqueous cavity approximating an oblate spheroid about 25 by 50 by 50 angstroms in dimension, within a molecule about 90 by 110 by 110 angstroms in largest dimensions.     

Neutron diffraction of cell membranes (myelin)

Small-angle neutron diffraction (wavelength 4.05 angstroms) of human and rabbit sciatic nerve has been carried out by means of the Brookhaven high flux beam reactor with an automated slit camera. Most of the free water of the nerves was substituted in order to minimize incoherent scatter of hydrogen atoms. The differences in amplitude and phase shifts between neutrons and x-rays resulted in a neutron diffraction pattern that was completely different from the x-ray pattern. The neutron pattern consisted of a single peak of about 89-angstrom spacing in the region examined (up to 6-angstrom spacing). The strong third, fourth, and fifth order reflections (about 60, 45, and 36 angstroms) seen in the x-ray pattern were suppressed. The neutron data indicated a strong scattering from one portion of the membrane.     

Atomic-resolution microscopy in water

The scanning tunneling microscope is revolutionizing the study of surfaces. In ultra-high vacuum it is capable not only of imaging individual atoms but also of determining energy states on an atom-by-atom basis. It is now possible to operate this instrument in water. Aqueous optical microscopy is confined to a lateral resolution limit of about 2000 angstroms, and aqueous x-ray microscopy has yielded a lateral resolution of 75 angstroms. With a scanning tunneling microscope, an image of a graphite surface immersed in deionized water was obtained with features less than 3 angstroms apart clearly resolved. Further, an image measured in saline solution demonstrated that the instrument can be operated under conditions useful for many biological samples.     

Porous, crystalline, covalent organic frameworks

Covalent organic frameworks (COFs) have been designed and successfully synthesized by condensation reactions of phenyl diboronic acid {C6H4[B(OH)2]2} and hexahydroxytriphenylene [C18H6(OH)6]. Powder x-ray diffraction studies of the highly crystalline products (C3H2BO)6.(C9H12)1 (COF-1) and C9H4BO2 (COF-5) revealed expanded porous graphitic layers that are either staggered (COF-1, P6(3)/mmc) or eclipsed (COF-5, P6/mmm). Their crystal structures are entirely held by strong bonds between B, C, and O atoms to form rigid porous architectures with pore sizes ranging from 7 to 27 angstroms. COF-1 and COF-5 exhibit high thermal stability (to temperatures up to 500 degrees to 600 degrees C), permanent porosity, and high surface areas (711 and 1590 square meters per gram, respectively).     

Cholestasis: lamellar structure of the abnormal human serum lipoprotein

An abnormal lipoprotein was visualized directly in serum by electron microscopy of preparations negatively stained with potassium phosphotungstate. It appears as a unique disk-shaped particle with major axis measuring 400 to 600 angstroms and minor axis measuring about 100 angstroms. Chemical analysis, viscosity measurements, and x-ray diffraction analysis of purified preparations indicate that the particle, consisting of a one-to-one molar mixture of cholesterol and choline phosphatides associated with a small amount of protein, is a flattened vesicle, the wall of which is a continuous lipid bilayer.     

Tuning High-Tc Superconductors via Multistage Intercalation

Multistage intercalation has been used to tune the interaction between adjacent blocks of CuO(2) sheets in the bigh-T(c) (high superconducting transition temperature) superconductor Bi(2)Sr(2)CaCu(2)Ox. As revealed by atomic-resolution transmission electron microscopy images, foreign iodine atoms are intercalated into every nth BiO bilayer of the host crystal, resulting in structures of stoichiometry IBi2nSr2nCanCu2nOx with stage index n up to 4. An expansion of 3.6 angstroms for each intercalated BiO bilayer decouples the CuO(2) sheets in adjacent blocks. A comparison of the superconducting transition temperatures of the pristine host material and intercalated compounds of different stages suggests that the coupling between each pair of adjacent blocks contributes approximately 5 K to T(c) in Bi(2)Sr(2)CaCu(2)Ox.     

Vapor-Condensation Generation and STM Analysis of Fullerene Tubes

Fullerene tubular structures can be generated by vapor condensation of carbon on an atomically flat graphite surface. Scanning tunneling microscope (STM) images revealed the presence of tubes with extremely small diameters (from 10 to 70 angstroms), most of which are terminated by hemispherical caps. Atomic resolution images of such structures showed that the tubes have a helical graphitic nature. The formation of the tubes under the quasi-free conditions suggests that the growth to tubular rather than spherical configurations is preferred for "giant fullerenes."     

Triblock copolymer syntheses of mesoporous silica with periodic 50 to 300 angstrom pores

Use of amphiphilic triblock copolymers to direct the organization of polymerizing silica species has resulted in the preparation of well-ordered hexagonal mesoporous silica structures (SBA-15) with uniform pore sizes up to approximately 300 angstroms. The SBA-15 materials are synthesized in acidic media to produce highly ordered, two-dimensional hexagonal (space group p6mm) silica-block copolymer mesophases. Calcination at 500 degrees C gives porous structures with unusually large interlattice d spacings of 74.5 to 320 angstroms between the (100) planes, pore sizes from 46 to 300 angstroms, pore volume fractions up to 0.85, and silica wall thicknesses of 31 to 64 angstroms. SBA-15 can be readily prepared over a wide range of uniform pore sizes and pore wall thicknesses at low temperature (35 degrees to 80 degrees C), using a variety of poly(alkylene oxide) triblock copolymers and by the addition of cosolvent organic molecules. The block copolymer species can be recovered for reuse by solvent extraction with ethanol or removed by heating at 140 degrees C for 3 hours, in both cases, yielding a product that is thermally stable in boiling water.     

Control of the selectivity of the aquaporin water channel family by global orientational tuning

Aquaporins are transmembrane channels found in cell membranes of all life forms. We examine their apparently paradoxical property, facilitation of efficient permeation of water while excluding protons, which is of critical importance to preserving the electrochemical potential across the cell membrane. We have determined the structure of the Escherichia coli aquaglyceroporin GlpF with bound water, in native (2.7 angstroms) and in W48F/F200T mutant (2.1 angstroms) forms, and carried out 12-nanosecond molecular dynamics simulations that define the spatial and temporal probability distribution and orientation of a single file of seven to nine water molecules inside the channel. Two conserved asparagines force a central water molecule to serve strictly as a hydrogen bond donor to its neighboring water molecules. Assisted by the electrostatic potential generated by two half-membrane spanning loops, this dictates opposite orientations of water molecules in the two halves of the channel, and thus prevents the formation of a "proton wire," while permitting rapid water diffusion. Both simulations and observations revealed a more regular distribution of channel water and an increased water permeability for the W48F/F200T mutant.     

Cometary particles: thin sectioning and electron beam analysis

Thin sections (500 to 1000 angstroms thick) of individual micrometeorites (5 to 15 micrometers) have been prepared with an ultramicrotome equipped with a diamond knife. Electron microscopic examination of these sections has revealed the internal structures of chondritic micrometeorites, and a subset of highly porous, fragile particles has been identified. Delicate meteoritic materials such as these are characteristic of debris from cometary meteors.     

A potent and broad neutralizing antibody recognizes and penetrates the HIV glycan shield

The HIV envelope (Env) protein gp120 is protected from antibody recognition by a dense glycan shield. However, several of the recently identified PGT broadly neutralizing antibodies appear to interact directly with the HIV glycan coat. Crystal structures of antigen-binding fragments (Fabs) PGT 127 and 128 with Man(9) at 1.65 and 1.29 angstrom resolution, respectively, and glycan binding data delineate a specific high mannose-binding site. Fab PGT 128 complexed with a fully glycosylated gp120 outer domain at 3.25 angstroms reveals that the antibody penetrates the glycan shield and recognizes two conserved glycans as well as a short β-strand segment of the gp120 V3 loop, accounting for its high binding affinity and broad specificity. Furthermore, our data suggest that the high neutralization potency of PGT 127 and 128 immunoglobulin Gs may be mediated by cross-linking Env trimers on the viral surface.     

Atomic-level models of the bacterial carboxysome shell

The carboxysome is a bacterial microcompartment that functions as a simple organelle by sequestering enzymes involved in carbon fixation. The carboxysome shell is roughly 800 to 1400 angstroms in diameter and is assembled from several thousand protein subunits. Previous studies have revealed the three-dimensional structures of hexameric carboxysome shell proteins, which self-assemble into molecular layers that most likely constitute the facets of the polyhedral shell. Here, we report the three-dimensional structures of two proteins of previously unknown function, CcmL and OrfA (or CsoS4A), from the two known classes of carboxysomes, at resolutions of 2.4 and 2.15 angstroms. Both proteins assemble to form pentameric structures whose size and shape are compatible with formation of vertices in an icosahedral shell. Combining these pentamers with the hexamers previously elucidated gives two plausible, preliminary atomic models for the carboxysome shell.     

Crystallography of the hexagonal ferrites

The hexagonal ferrites form an unusual group of complex, ferrimagnetic oxides embodying some 60 known crystal structures. These include phases for which the structural unit cell is larger than that in any known inorganic materials. The various hexagonal ferrite modifications fall into two distinct structural series, each formed by the ordered interlayering (stacking) of two discrete building blocks; these blocks stack along the c crystallographic axis in varying ratios and varying permutations to form strictly coherent, reproducible crystal structures. This mixed-layering aspect of the hexagonal ferrites permits direct, visual observation of the sequence of their subunit-cell stacking elements, after etching, by means of electron microscopy. The sequence of stacked blocks in such structures constitutes the only information lacking for a complete, three-dimensional structure determination. Direct access to this information provides an immediate, unique solution of the crystal structure problem in each case and thereby avoids the dilemmas of a classical diffraction approach to such large unit cells. Ferrite structures with hexagonal c dimensions of 1455 and 1577 angstroms have been uniquely solved by direct electron microscopic readout of surface etch features. One must exercise caution, however, in generalizing these findings to other materials. The method is successful in the case of the hexagonal ferrites because these are mixed-layer structures, wherein the building blocks react at different rates to a specific etchant. Mixed-layer systems are not uncommon in crystallography, and it is likely that similar techniques can be developed for other such materials. Regardless of the validity of this prognosis, however, it is quite evident that high-resolution replica electron microscopy is a most promising tool for the direct observation of surface structure on an ultramicro scale. During the studies reported here replica resolution capability was improved to about 10 angstroms; final resolution is limited by the particle size of the platinum shadowing material. Careful control of experimental conditions during replica preparation or an alternate choice of shadowing material, or both, might reasonably improve the resolution by a factor of 2. This resolution is within the range of most unit cell dimensions and approaches interatomic distances in solid-state materials. The potential of such an experimental capability needs no elaboration.     

Polycrystalline echinoderm calcite and its fracture mechanics

Polycrystalline calcite was revealed by scanning electron microscopy of fractured skeletal ossicles of the sea star Echinaster spinulosus (Echinodermata, Asteroidea). Whisker-like calcite crystals were observed in specimens that were loaded in stress relaxation before being fractured; rapidly broken surfaces were smooth and glassy. The crystallites were 1300 angstroms wide and at least 3600 angstroms long and were packed together in lamellae. The lamellae were wound into spirals that formed the trabecular bars. All the crystallites in an ossicle appear to be aligned in the same direction. Geometric considerations indicate that the requirement for packing the crystallites smoothly may explain the high magnesium ion concentration of echinoderm calcite.     

Structure of langmuir-blodgett films of disk-shaped molecules determined by atomic force microscopy

Monolayer Langmuir-Blodgett films of a discotic mesogen have been studied with atomic force microscopy (AFM). These measurements confirm the "edge on" arrangement for the disk-shaped molecules suggested by surface pressure-area isotherms and show that the molecules form columns that are separated by 17.7 angstroms +/- 10 percent. Column alignment is found to be predominantly along the film deposition direction, with an angular spread of 35 degrees . The AFM images also show that the mean disk separation within the columns is 5.1 +/- 1.3 angstroms, in good agreement with x-ray diffraction (XRD) results. Roomtemperature XRD measurements on bulk samples of the same material indicate a disordered-hexagonal liquid crystalline mesophase, with a column-to-column spacing of 19.9 +/- 0.2 angstroms.     

Structural basis of multiple drug-binding capacity of the AcrB multidrug efflux pump

Multidrug efflux pumps cause serious problems in cancer chemotherapy and treatment of bacterial infections. Yet high-resolution structures of ligand transporter complexes have previously been unavailable. We obtained x-ray crystallographic structures of the trimeric AcrB pump from Escherichia coli with four structurally diverse ligands. The structures show that three molecules of ligands bind simultaneously to the extremely large central cavity of 5000 cubic angstroms, primarily by hydrophobic, aromatic stacking and van der Waals interactions. Each ligand uses a slightly different subset of AcrB residues for binding. The bound ligand molecules often interact with each other, stabilizing the binding.     

Immunoglobulins G, A, and M determined in single cells from human tonsil

The analysis of specific proteins in single cells is described and applied to the determination of immunoglobulins G, A, and M (gammaG, gammaA, and gammaM) in lymphoid cells of the human tonsil. The number of cells containing gammaA or gammaM was much less than the number of cells containing gammaG, but the average cell content of gammaA or gammaM was much greater than the average cell content of gammaG. Similarly, in one child where relatively few cells containing gammaG were found, the average cell content of gammaG in those cells was higher than that in the other children. The limit of sensitivity of the method for each of the three immunoglobulins with the antiserums used was less than 10(-14) gram of the specific protein.     

Mucopolysaccharides: comparison of chondroitin sulfate conformations with those of related polyanions

X-ray diffraction shows that chondroitin 6-sulfate, and some further rulfated derivatives, can occur in two ordered structures in stretched films. Both structures contain single helices with similar projected disaccharide lengths (9.6 and 9.8 angstroms) but with very different turn angles between successive disaccharides (120 and 45 degrees). In contrast, coaxial double helices of hyaluronates and t-carrageenates have shorter projected disaccharide lengths (8.5 and 8.9 angstroms).