ELECTRON SHADOW MICROGRAPHY OF THE TOBACCO MOSAIC VIRUS PROTEIN

Two improvements are described in the use of shadow electron micrography for the observation of particles of macromolecular dimensions. One involves the substitution of gold for chromium as shadowing metal. The thinner gold film that can be employed gives a truer representation of the shape of particles so small that shape and size are significantly altered by the thickness of the shadowing metal deposited on them. The other consists in metal-shadowing small particles deposited on a very smooth surface such as that of polished glass and the handling of this metal film as a replica of the glass surface and the particles resting on it. This technique permits the photography of particles whose direct observation is disturbed by the fine structure that is brought out by shadowing a collodion substrate. Application of these methods to the electron micrography of the tobacco mosaic virus protein shows that its fibrils are rods about 125A both in height and breadth. Though the rods appear segmented, these segments have not been found to have a length that is constant or a small integral multiple of an underlying unit.     

Dislocations in complex materials

Deformation of metals and alloys by dislocations gliding between well-separated slip planes is a well-understood process, but most crystal structures do not possess such simple geometric arrangements. Examples are the Laves phases, the most common class of intermetallic compounds and exist with ordered cubic, hexagonal, and rhombohedral structures. These compounds are usually brittle at low temperatures, and transformation from one structure to another is slow. On the basis of geometric and energetic considerations, a dislocation-based mechanism consisting of two shears in different directions on adjacent atomic planes has been used to explain both deformation and phase transformations in this class of materials. We report direct observations made by Z-contrast atomic resolution microscopy of stacking faults and dislocation cores in the Laves phase Cr2Hf. These results show that this complex dislocation scheme does indeed operate in this material. Knowledge gained of the dislocation core structure will enable improved understanding of deformation mechanisms and phase transformation kinetics in this and other complex structures.     

The structure of ferrihydrite, a nanocrystalline material

Despite the ubiquity of ferrihydrite in natural sediments and its importance as an industrial sorbent, the nanocrystallinity of this iron oxyhydroxide has hampered accurate structure determination by traditional methods that rely on long-range order. We uncovered the atomic arrangement by real-space modeling of the pair distribution function (PDF) derived from direct Fourier transformation of the total x-ray scattering. The PDF for ferrihydrite synthesized with the use of different routes is consistent with a single phase (hexagonal space group P6(3)mc; a = approximately 5.95 angstroms, c = approximately 9.06 angstroms). In its ideal form, this structure contains 20% tetrahedrally and 80% octahedrally coordinated iron and has a basic structural motif closely related to the Baker-Figgis delta-Keggin cluster. Real-space fitting indicates structural relaxation with decreasing particle size and also suggests that second-order effects such as internal strain, stacking faults, and particle shape contribute to the PDFs.     

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.     

Crystalline transfer RNA: the three-dimensional Patterson function at 12-angstrom resolution

An orthorhombic form of crystalline formylmethionine transter RNA has been obtained which contains one molecule as the asymmetric unit of the unit cell. Three-dimensional x-ray diffraction data have been collected up to a resolution of 12 angstroms, and from this a Patterson function has been calculated. The function contains an elongated ridge of interatomic vectors parallel to the c-axis of the crystal. Analysis of the function suggests that the molecules are elogated and dimerized in an overlapping antiparrael fashion along the c-axis. The dimer has a length near 109 angstroms and a width of 35 angstroms in one direction. The individual molecular length is approximately 80 angstroms with an irregular cross section measuring 25 by 35 angstrms.     

Supertetrahedral sulfide crystals with giant cavities and channels

Although aluminosilicates and metal phosphates can form porous open-framework materials such as zeolites, sulfide analogs usually form high-density phases because of the relatively small tetrahedral angle at sulfur atoms. One strategy to overcome this limitation is to use tetrahedral clusters as the building blocks to achieve porous sulfide-based networks. The preparation and crystal structures of two indium sulfide open frameworks (ASU-31 and ASU-32) built of supertetrahedral clusters around organic template and water guests are described. ASU-31, based on the sodalite-tetrahedrite network, contains cavities 25.6 angstroms in diameter, and ASU-32, based on the tetragonal CrB4 network, contains channels with a minimum diameter of 14.7 angstroms. The organic cations can be completely exchanged with sodium ions in aqueous solution at room temperature without degradation of the crystals.     

Three-dimensional tertiary structure of yeast phenylalanine transfer RNA

The 3-angstrom electron density map of crystalline yeast phenylalanine transfer RNA has provided us with a complete three-dimensional model which defines the positions of all of the nucleotide residues in the moleclule. The overall features of the molecule are virtually the same as those seen at a resolution of 4 angstroms except that many additional details of tertiary structure are now visualized. Ten types of hydrogen bonding are identified which define the specificity of tertiary interactions. The molecule is also stabilized by considerable stacking of the planar purines and pyrimidines. This tertiary structure explains, in a simple and direct fashion, chemical modification studies of transfer RNA. Since most of the tertiary interactions involve nucleotides which are common to all transfer RNA 's, it is likely that this three-dimensional structure provides a basic pattern of folding which may help to clarify the three-dimensional structure of all transfer RNA's.     

Direct determination of local lattice polarity in crystals

With current advances in sub-angstrom resolution scanning transmission electron microscopy (STEM), it is now possible to image directly local crystal structures of materials where dramatically different atoms are separated from each other at distances about or less than 1 angstrom. We achieved direct imaging of atomic columns of nitrogen in close proximity to columns of aluminum in wurtzite aluminum nitride by using annular dark field imaging in an aberration-corrected STEM. This ability allows direct determination of the local polarity in nanoscale crystals and crystal defects.     

Ammonioborite: new borate polyion and its structure

The mineral ammonioborite is monoclinic with unit cell dimensions (in angstroms): a = 25.27, b = 9.65, and c = 11.56; beta = 94 degrees 17', and the space group is C 2/c. Analysis of the crystal structure revealed the crystallo-chemical formula (NH(4))(3)B(15)O(20)(OH)(8).4H(2)O, with four such formula units in the unit cell. The basic structural unit is the double ring consisting of one BO(4) tetrahedron and four BO(3) triangles: in ammonioborite three of these units are connected to give trimeric ions [B(15)O(20)(OH)(8)](3-).     

Crystal structure of cobra-venom phospholipase A2 in a complex with a transition-state analogue

The crystal structure of a complex between a phosphonate transition-state analogue and the phospholipase A2 (PLA2) from Naja naja atra venom has been solved and refined to a resolution of 2.0 angstroms. The identical stereochemistry of the two complexes that comprise the crystal's asymmetric unit indicates both the manner in which the transition state is stabilized and how the hydrophobic fatty acyl chains of the substrate are accommodated by the enzyme during interfacial catalysis. The critical features that suggest the chemistry of binding and catalysis are the same as those seen in the crystal structure of a similar complex formed with the evolutionarily distant bee-venom PLA2.     

Crystal structure of serotonin picrate, a donor-acceptor complex

The crystal structure of the red picric acid salt of serotonin was determined by x-ray diffraction methods. The structure consists of parallel hydroxyindole and picrate planes which are intimately stacked with an interplanar separation of 3.3 to 3.4 angstroms. The stacking interaction appears to be of the donor-acceptor (charge-transfer) type, involving specific contacts between picrate nitro groups and atoms of the hydroxyindole moieties. Similar interactions might mediate biological processes involving serotonin.     

Orientational disorder in solvent-free solid c70

The high-temperature structure of solvent-free C(70) has been determined with high-resolution x-ray powder difraction and electron microscopy. Samples crystallized from solution form hexagonal close-packed crystals that retain an appreciable amount of residual toluene, even after prolonged heating. Samples prepared by sublimation, which contain no detectable solvent, are primarily face-centered cubic with some admixture of a hexagonal phase. The relative volume of the hexagonal phase can be further reduced by annealing. The structures of both phases are described by a model of complete orientational disorder. The cubic phase contains an appreciable density of stacking faults along the [111] direction.     

Structure of a dinucleotide: thymidylyl-(5'-3')-thymidylate-5' (pTpT)

The crystal and molecular structure of the naturally occurring deoxyribose dinucleotide sodium thymidylyl-(5'-->3')-thymidylate-5' has been determined by x-ray diffraction. There are four molecules of dinucleotide and 52 water molecules in an orthorhombic unit cell of dimensions (in angstroms) a = 16.06, b = 15.13, c = 15.65, space group P2(1)2(1)2. There is a very high degree of conformational consistency between the two halves of the molecule when the dinucleotide is viewed as the combination of two 5'-mononucleotides. The planes of the two thymines are not parallel, but are tilted 38 degrees with respect to each other. An extensive system of hydrogen bonding exists involving the bases, waters, phosphates, and sodiums; no base-base hydrogen bonding occurs. The dinucleotide structural parameters should be of assistance in interpreting DNA fiber diagrams in terms of possible structures.     

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.     

Stabilizing isopeptide bonds revealed in gram-positive bacterial pilus structure

Many bacterial pathogens have long, slender pili through which they adhere to host cells. The crystal structure of the major pilin subunit from the Gram-positive human pathogen Streptococcus pyogenes at 2.2 angstroms resolution reveals an extended structure comprising two all-beta domains. The molecules associate in columns through the crystal, with each carboxyl terminus adjacent to a conserved lysine of the next molecule. This lysine forms the isopeptide bonds that link the subunits in native pili, validating the relevance of the crystal assembly. Each subunit contains two lysine-asparagine isopeptide bonds generated by an intramolecular reaction, and we find evidence for similar isopeptide bonds in other cell surface proteins of Gram-positive bacteria. The present structure explains the strength and stability of such Gram-positive pili and could facilitate vaccine development.     

Hexagonal pattern in cell walls of Escherichia coli B

Cell walls, isolated from Escherichia coli B, as examined by electron microscopy and optical diffraction contain a hexagonal lattice structure, the (1,0) planes of which are separated by 140 +/- 8 angstroms. Unless the walls are briefly heated (10 minutes, 90 degrees C) early in the isolation, the hexagonal array cannot always be observed. Enzymatic digestion with pancreatin and amylase improves visualization of the lattice; subsequent treatment with pepsin and sodium dodecylsulfate removes the hexagonal pattern. Protein or lipoprotein globular units within the wall may thus be arranged in a hexagonal array uponthe mucopeptide layer.     

Thyroglobulin: evidence for crystallization and association

Crystals of thyroglobulin have been obtained from ammonium sulfate solutions and have been examined by electron microscopy as shadowed carbon replicas. Unit size in the crystal is 228 +/- 9 angstroms, which corresponds to a molecular weight of 5,300,000. Data are in accord with the possibility that this unit represents a polymer of thyroglobulin.     

Hexagonal Domain-Like Charge Density Wave Phase of TaS2 Determined by Scanning Tunneling Microscopy

The structure of the room-temperature charge density wave (CDW) phase in octahedrally coordinated tantalum disulfide, 1T-TaS2, has been a controversial issue for over 15 years. Large-scale scanning tunneling microscope images of the intralayer structure of this phase exhibit a domain-like pattern defined by a variation in the maximum CDW amplitude. The circular domains, consisting of high-amplitude CDWs, are arranged in a regular hexagonal lattice (period 73+/-3 angstroms) that is rotated relative to the CDWs. In addition, from the analysis of atomic resolution images it was determined that there is a well-defined phase shift between the CDWs in adjacent domains, and that within a domain the CDW superlattice is commensurate with the atomic lattice. These results provide evidence for the hexagonal discommensurate CDW phase in 1T-TaS2 and also suggest an explanation for the long-standing controversy concerning the structure of this phase.