A tunnel in the large ribosomal subunit revealed by three-dimensional image reconstruction

A better understanding of the molecular mechanism of protein biosynthesis depends on the availability of a reliable model for the ribosome particle. The application of a diffraction technique, namely, three-dimensional image reconstruction from two-dimensional sheets of the large ribosomal subunits of Bacillus stearothermophilus at a resolution of 30 angstroms is described. The resulting three-dimensional model shows at least four projecting arms, arranged radially near the presumed interface with the 30S subunit. The projecting arms are positioned around a cleft, which turns into a tunnel with a length of 100 to 120 angstroms and a diameter of up to 25 angstroms. This tunnel spans the particle and may provide the path taken by the nascent polypeptide chain.     

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.     

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.     

Ultrastructure of gamma-M immunoglobulin and alpha macroglobulin: electron-microscopic study

Electron microscopy of purified Waldenstr?m macroglobulins and normal human and rabbit gammaM immunoglobulins revealed spider-like structures with five legs varying in length and often joining a central ring. Usually only the central more rigid part of this structure (about 150 by 170 angstroms) was clearly visible, but occasionally particles were seen with longer very flexible legs having a total span of about 350 angstroms. Molecules of gammaM antibody retained antibody activity during preparation for electron microscopy. Human and rabbit alpha macroglobulins revealed more rigid symmetric structures (100 by 200 angstroms) which resembled the Russian letter .     

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.     

Ultrahigh-Resolution X-ray Tomography

Ultrahigh-resolution three-dimensional images of a microscopic test object were made with soft x-rays collected with a scanning transmission x-ray microscope. The test object consisted of two different patterns of gold bars on silicon nitride windows that were separated by approximately 5 micrometers. Depth resolution comparable to the transverse resolution was achieved by recording nine two-dimensional images of the object at angles between -50 and +55 degrees with respect to the beam axis. The projections were then combined tomographically to form a three-dimensional image by means of an algorithm using an algebraic reconstruction technique. A transverse resolution of approximately 1000 angstroms was observed. Artifacts in the reconstruction limited the overall depth resolution to approximately 6000 angstroms; however, some features were clearly reconstructed with a depth resolution of approximately 1000 angstroms.     

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.     

Determination of the pore size of cell walls of living plant cells

The limiting diameter of pores in the walls of living plant cells through which molecules can freely pass has been determined by a solute exclusion technique to be 35 to 38 angstroms for hair cells of Raphanus sativus roots and fibers of Gossypium hirsutum, 38 to 40 angstroms for cultured cells of Acer pseudoplatanus, and 45 to 52 angstroms for isolated palisade parenchyma cells of the leaves of Xanthium strumarium and Commelina communis. These results indicate that molecules with diameters larger than these pores would be restricted in their ability to penetrate such a cell wall, and that such a wall may represent a more significant barrier to cellular communication than has been previously assumed.     

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.     

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.     

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.     

Crystallinity of the double layer of cadmium arachidate films at the water surface

A crystalline counterionic layer at the interface between an electrolyte solution and a charged layer of insoluble amphiphilic molecules was observed with grazing incidence synchrotron x-ray diffraction. Uncompressed arachidic films spread over 10(-3) molar cadmium chloride solution (pH 8.8) spontaneously form crystalline clusters with coherence lengths of approximately 1000 angstroms at 9 degrees C. Ten distinct diffraction peaks were observed, seven of which were attributed to scattering only from a crystalline Cd(2+) layer and the other three to scattering primarily from the arachidate layer. The reflections from the Cd(2+) layer were indexed according to a 2 x 3 supercell of the arachidate lattice with three Cd(2+) ions per cadmium unit cell.     

Direct determination of ionic solvation from neutron diffraction

Much information on ionic solvation in electrolyte solutions has been inferred from macroscopic thermodynamic and transport properties and from spectroscopy. These ion-water interactions can now be probed directly and unambiguously by neutron diffraction. Such measurements have been done with neodymium trichloride solutions in heavy water that are identical in every respect except the isotopic state of the neodymium ions; these experiments yield in a straightforward manner the distribution of oxygen and deuterium atoms from the water molecules in the first hydration sphere of the neodymium ion. Each ion is surrounded by 8.6 oxygen atoms at a distance of 2.48 angstroms and 16.7 deuterium atoms at 3.13 angstroms indicating a well-defined first hydration sphere of water molecules, the deuterium atoms pointing away from the cation.     

Comet kohoutek: ultraviolet images and spectrograms

Emissions of atomic oxygen (1304 angstroms), atomic carbon (1657 angstroms), and atomic hydrogen (1216 angstroms) from Comet Kohoutek were observed with ultraviolet cameras carried on a sounding rocket on 8 January 1974. Analysis of the Lyman alpha halo at 1216 angstroms gave an atomic hydrogen production rate of 4.5 x 10(29) atoms per second.     

New phases of c60 synthesized at high pressure

The fullerene C(60) can be converted into two different structures by high pressure and temperature. They are metastable and revert to pristine C(60) on reheating to 300 degrees C at ambient pressure. For synthesis temperatures between 300 degrees and 400 degrees C and pressures of 5 gigapascals, a nominal face-centered-cubic structure is produced with a lattice parameter a(o) = 13.6 angstroms. When treated at 500 degrees to 800 degrees C at the same pressure, C(60) transforms into a rhombohedral structure with hexagonal lattice parameters of a(o) = 9.22 angstroms and c(o) = 24.6 angstroms. The intermolecular distance is small enough that a chemical bond can form, in accord with the reduced solubility of the pressure-induced phases. Infrared, Raman, and nuclear magnetic resonance studies show a drastic reduction of icosahedral symmetry, as might occur if the C(60) molecules are linked.     

Crystal structure of a complex of acridine, cytosine and water (1:1:1)

X-ray structural analysis of a crystalline complex between acridine C(13)H(9)N, cytosine C(4)H(5)N(3)O, and water (1:1:1) has been completed. The cytosine and water molecules form a sheet-like structure through a series of hydrogen bonds. The acridine molecules are bound to this layer through a hydrogen bridge from the water to the ring nitrogen. The acridine molecules stack in a parallel fashion normal to the cytosine-water sheets, with an average interplanar spacing of 3.5 angstroms.     

New low-dimensional molecular metals: single-crystal electrical conductivity of nickel phthalocyanine iodide

Single crystals of NiPcI(1.0) (Pc = phthalocyanine), which are composed of one-dimensional stacks of (NiPc)(+0.33) molecules and chains of I(3)(-) molecules, exhibit metallic electrical conductivity in the stacking direction. At room temperature the mean free path of the carrier is 3.3 to 8.2 angstroms.     

Anti-inflammatory activity of human IgG4 antibodies by dynamic Fab arm exchange

Antibodies play a central role in immunity by forming an interface with the innate immune system and, typically, mediate proinflammatory activity. We describe a novel posttranslational modification that leads to anti-inflammatory activity of antibodies of immunoglobulin G, isotype 4 (IgG4). IgG4 antibodies are dynamic molecules that exchange Fab arms by swapping a heavy chain and attached light chain (half-molecule) with a heavy-light chain pair from another molecule, which results in bispecific antibodies. Mutagenesis studies revealed that the third constant domain is critical for this activity. The impact of IgG4 Fab arm exchange was confirmed in vivo in a rhesus monkey model with experimental autoimmune myasthenia gravis. IgG4 Fab arm exchange is suggested to be an important biological mechanism that provides the basis for the anti-inflammatory activity attributed to IgG4 antibodies.     

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.     

2 types of lambda polypeptide chains in human immunoglobulins

Two antigenic subtypes of human lambda polypeptide chains were distinguished by rabbit antiserum produced to a lambda Bence Jones protein. Lambda Bence Jones proteins and G myeloma proteins with lambda light chains were identified as being in one or the other subtype. The Oz (+) lambda chain subtype is present in light chains from pooled normal human immunoglobulin G and in whole normal immunoglobulin G molecules.