Three-dimensional structure at 0.86 A of the uncomplexed form of the transmembrane ion channel peptide gramicidin A

The crystal structure of the uncomplexed orthorhombic form of gramicidin A has been determined at 120 K and at 0.86 angstrom resolution. The pentadecapeptide crystallizes as a left-handed antiparallel double-stranded helical dimer with 5.6 amino acid residues per turn. The helix has an overall length of 31 angstroms and an average inner channel diameter of 4.80 angstroms. The channel of this crystalline form is void of ions or solvent molecules. The channel diameter varies from a minimum of 3.85 angstroms to a maximum of 5.47 angstroms and contains three pockets where the cross-channel contacts are 5.25 angstroms or greater. The range of variation seen for the phi and psi torsion angles of the backbone of the helix suggests that these potential ion binding sites can be induced to travel the length of the channel in a peristaltic manner by cooperatively varying these angles. The indole rings of the eight tryptophan residues of the dimer are overlapped in three separate regions on the outer surface of the helix when viewed down the barrel of the channel. This arrangement would permit long-chained lipid molecules to nest parallel to the outer channel surface between these protruding tryptophan regions and act like molecular splines to constrain helical twist deformations of the channel.     

Structural studies on transfer RNA: preliminary crystallographic analysis

Single-crystal diffraction patterns from Escherichia coli leucine tRNA and yeast formylmethionine tRNA show a tetragonal lattice for the former, with a = 46 angstroms and c = 137 angstroms, and a hexagonal lattice for the latter, with a = 115 angstroms and c = 137 angstroms. Initial analysis suggests a molecule with a long, double helix parallel to the c-axis for both crystals.     

Molecular structure of DNA by scanning tunneling microscopy

Uncoated DNA molecules marked with an activated tris(l-aziridinyl) phosphine oxide (TAPO) solution were deposited on gold substrates and imaged in air with the use of a high-resolution scanning tunneling microscope (STM). Constant-current and gap-modulated STM images show clear evidence of the helicity of the DNA structure: pitch periodicity ranges from 25 to 35 angstroms, whereas the average diameter is 20 angstroms. Molecular structure within a single helix turn was also observed.     

Images of the DNA double helix in water

The scanning tunneling microscope can image uncoated DNA submerged in water. The grooves of the double helix were clearly resolved in images of the 146-base pair fragment extracted from calf thymus nucleosome. In contrast to images obtained with dry DNA, the helix pitch varied only a small amount (36 +/- 5 angstroms). The path of the helix shows considerable variation. It is quite straight when the molecules are densely packed, but it curves and bends in isolated molecules.     

DNA structure: evidence from electron microscopy

The contour lengths of phiX174 DNA duplex and RNA-DNA hybrid molecules were measured by several commonly used electron microscopic techniques. The countour length of the hybrid molecules corresponds to a rise of 2.5 to 2.6 angstroms per base pair, as expected for the A conformation, while the length of phiX174 duplex DNA similarly measured corresponds to a 2.9-angstrom rise, very different from 3.4 angstroms of the classic B form. Thus any chromatin structure parameter based on electron microscopy and a rise of 3.4 angstroms must be reappraised. The possibility that DNA in dilute solution also has a rise of 2.9 angstroms and a screw of 10.5 base pairs per turn is discussed.     

Crystallographic structure of the octameric histone core of the nucleosome at a resolution of 3.3 A

The structure of the (H2A-H2B-H3-H4)2 histone octamer has been determined by means of x-ray crystallographic techniques at a resolution of 3.3 angstroms. The octamer is a prolate ellipsoid 110 angstroms long and 65 to 70 angstroms in diameter, and its general shape is that of a rugby ball. The size and shape are radically different from those determined in earlier studies. The most striking feature of the histone octamer is its tripartite organization, that is, a central (H3-H4)2 tetramer flanked by two H2A-H2B dimers. The DNA helix, placed around the octamer in a path suggested by the features on the surface of the protein, appears like a spring holding the H2A-H2B dimers at either end of the (H3-H4)2 tetramer.     

Cartilage collagen: a staggered substructure in reconstituted fibrils

In contrast to the typical transverse banding pattern of native and reconstituted skin collagen fibrils, reconstituted fibrils of cartilage collagen have an oblique banding pattern that results from a regular axial shift (89 angstroms) of component "subfibrils." The 89-angstrom shift may be related to the major helix of the collagen molecule.     

Direct observation of native DNA structures with the scanning tunneling microscope

Uncoated double-stranded DNA dissolved in a salt solution was deposited on graphite and imaged in air with the scanning tunneling microscope (STM). The resolution was such that the major and minor grooves could be distinguished. The pitch of the helix varied between 27 and 63 angstroms in the images obtained. Thus the STM can be useful for structural studies of a variety of uncoated and isolated biomolecules.     

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.     

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.     

Structure of the Reduced TiO2(110) Surface Determined by Scanning Tunneling Microscopy

The scanning tunneling microscope has been used to image a reduced TiO(2)(110) surface in ultrahigh vacuum. Structural units with periodicities rangng from 21 to 3.4 angstroms have been clearly imaged, demonstrating that atomic resolution imaging of an ionic, wide band gap (3.2 electron volts) semiconductor is possible. The observed surface structures can be explained by a model involving ordered arrangements of two-dimensional defects known as crystallographic shear planes and indicate that the topography of nonstoichiometric oxide surfaces can be complex.     

Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 A

The zinc finger DNA-binding motif occurs in many proteins that regulate eukaryotic gene expression. The crystal structure of a complex containing the three zinc fingers from Zif268 (a mouse immediate early protein) and a consensus DNA-binding site has been determined at 2.1 angstroms resolution and refined to a crystallographic R factor of 18.2 percent. In this complex, the zinc fingers bind in the major groove of B-DNA and wrap part way around the double helix. Each finger has a similar relation to the DNA and makes its primary contacts in a three-base pair subsite. Residues from the amino-terminal portion of an alpha helix contact the bases, and most of the contracts are made with the guanine-rich strand of the DNA. This structure provides a framework for understanding how zinc fingers recognize DNA and suggests that this motif may provide a useful basis for the design of novel DNA-binding proteins.     

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.     

Tunable Coherent X-rays

A modern 1- to 2-billion-electron-volt synchrotron radiation facility (based on high-brightness electron beams and magnetic undulators) would generate coherent (laser-like) soft x-rays of wavelengths as short as 10 angstroms. The radiation would also be broadly tunable and subject to full polarization control. Radiation with these properties could be used for phase- and element-sensitive microprobing of biological assemblies and material interfaces as well as reserch on the production of electronic microstructures with features smaller than 1000 angstroms. These short wavelength capabilities, which extend to the K-absorption edges of carbon, nitrogen, and oxygen, are neither available nor projected for laboratory XUV lasers. Higher energy storage rings (5 to 6 billion electron volts) would generate significantly less coherent radiation and would be further compromised by additional x-ray thermal loading of optical components.     

Ultrathin carbon support films for electron microscopy

Carbon support films only 4 to 6 angstroms thick have been made for use in electron microscopy. The determination of their thickness is based on geometrical calculation, electron scattering measurements, and elemental microanalysis.     

Palladium: preparation and catalytic properties of particles of uniform size

A method has been developed for the preparation of uniform palladium particles of diameter from 55 to 450 angstroms. Uniform particles of gold layered on palladium were also synthesized. Hydrothermal treatment of aluminum hydroxide sol was used to prepare rods of alumina with uniform cross section from 100 to 500 angstroms and of varying lengths. The palladium was adsorbed as individual particles on alumina rods, both present in aqueous suspension. Then the suspension was dried to give a catalyst containing metal particles of uniform size dispersed in open pores produced by the intermeshing of the alumina rods. This procedure guaranteed the absence of diffusion control in the rate of reactions observed experimentally. All stages of the preparation were monitored with the electron microscope. The kinetics of the ethylene-hydrogen reaction were examined by means of a pulse technique. The number of active sites determined by carbon monoxide titration of the surface was equal to the number of surface atoms as determined by the calculation of the quantities of compounds involved in the synthesis and electron microscope examination. Furthermore, the activity per site depended on the method of preparation, being four times smaller when sodium formate was used as a reducing agent instead of sodium citrate. This may be due to the fact that the shape of particles makes certain crystallographic planes more favorable. Decrease in the size of particles to 56 angstroms produced no effect on catalytic activity beyond that due to the increase in the number of surface atoms. The activity of commercial 5 percent palladium on alumina diluted 100-fold with alumina gave 80.4 percent conversion with propylene and 82.7 percent conversion with ethylene. Thus there was little difference in the behavior of the two olefins.     

Rapid electron tunneling through oligophenylenevinylene bridges

We measured rate constants of thermal, interfacial electron transfer through oligophenylenevinylene bridges between a gold electrode and a tethered redox species in contact with an aqueous electrolyte using the indirect laser-induced temperature jump technique. Analysis of the distance dependence indicates that, unlike other bridges studied to date, the rate constants are not limited by electronic coupling for bridges up to 28 angstroms long. The energy levels of the bridges relative to those of the redox species rule out hopping through the bridge. We conclude that, out to 28 angstroms, the transfer is limited by structural reorganization and that electron tunneling occurs in less than 20 picoseconds, suggesting that oligophenylenevinylene bridges could be useful for wiring molecular electronic elements.     

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.     

Shape analysis of the histone octamer in solution

The conformation of the histone octamer is shown to depend upon the specific salt used to solubilize it. In 2M sodium chloride the octamer is similar in size and shape to the histone component of crystallized core nucleosomes. In contrast, in 3.5M ammonium sulfate the octamer is elongated, resembling an ellipsoid with approximate dimensions of 114 by 62 by 62 angstroms. These results indicate that the elongated conformation seen in the 3.3 angstroms electron density map of the histone octamer crystallized in ammonium sulfate is due to the particular salt conditions used.