Self-propagating, molecular-level polymorphism in Alzheimer's beta-amyloid fibrils

Amyloid fibrils commonly exhibit multiple distinct morphologies in electron microscope and atomic force microscope images, often within a single image field. By using electron microscopy and solid-state nuclear magnetic resonance measurements on fibrils formed by the 40-residue beta-amyloid peptide of Alzheimer's disease (Abeta(1-40)), we show that different fibril morphologies have different underlying molecular structures, that the predominant structure can be controlled by subtle variations in fibril growth conditions, and that both morphology and molecular structure are self-propagating when fibrils grow from preformed seeds. Different Abeta(1-40) fibril morphologies also have significantly different toxicities in neuronal cell cultures. These results have implications for the mechanism of amyloid formation, the phenomenon of strains in prion diseases, the role of amyloid fibrils in amyloid diseases, and the development of amyloid-based nano-materials.     

Atomlike, hollow-core-bound molecular orbitals of C60

The atomic electron orbitals that underlie molecular bonding originate from the central Coulomb potential of the atomic core. We used scanning tunneling microscopy and density functional theory to explore the relation between the nearly spherical shape and unoccupied electronic structure of buckminsterfullerene (C60) molecules adsorbed on copper surfaces. Besides the known pi* antibonding molecular orbitals of the carbon-atom framework, above 3.5 electron volts we found atomlike orbitals bound to the core of the hollow C60 cage. These "superatom" states hybridize like the s and p orbitals of hydrogen and alkali atoms into diatomic molecule-like dimers and free-electron bands of one-dimensional wires and two-dimensional quantum wells in C60 aggregates. We attribute the superatom states to the central potential binding an electron to its screening charge, a property expected for hollow-shell molecules derived from layered materials.     

Characterization of step-edge barriers in organic thin-film growth

Detailed understanding of growth mechanisms in organic thin-film deposition is crucial for tailoring growth morphologies, which in turn determine the physical properties of the resulting films. For growth of the rodlike molecule para-sexiphenyl, the evolution of terraced mounds is observed by atomic force microscopy. Using methods established in inorganic epitaxy, we demonstrate the existence of an additional barrier (0.67 electron volt) for step-edge crossing-the Ehrlich-Schwoebel barrier. This result was confirmed by transition state theory, which revealed a bending of the molecule at the step edge. A gradual reduction of this barrier in the first layers led to an almost layer-by-layer growth during early deposition stage. The reported phenomena are a direct consequence of the complexity of the molecular building blocks versus atomic systems.     

Atomic and molecular manipulation with the scanning tunneling microscope

The prospect of manipulating matter on the atomic scale has fascinated scientists for decades. This fascination may be motivated by scientific and technological opportunities, or from a curiosity about the consequences of being able to place atoms in a particular location. Advances in scanning tunneling microscopy have made this prospect a reality; single atoms can be placed at selected positions and structures can be built to a particular design atom-by-atom. Atoms and molecules may be manipulated in a variety of ways by using the interactions present in the tunnel junction of a scanning tunneling microscope. Some of these recent developments and some of the possible uses of atomic and molecular manipulation as a tool for science are discussed.     

Progress in modeling of protein structures and interactions

The prediction of the structures and interactions of biological macromolecules at the atomic level and the design of new structures and interactions are critical tests of our understanding of the interatomic interactions that underlie molecular biology. Equally important, the capability to accurately predict and design macromolecular structures and interactions would streamline the interpretation of genome sequence information and allow the creation of macromolecules with new and useful functions. This review summarizes recent progress in modeling that suggests that we are entering an era in which high-resolution prediction and design will make increasingly important contributions to biology and medicine.     

Molecular dynamics of a cytochrome c-cytochrome b5 electron transfer complex

Cytochrome c and cytochrome b5 form an electrostatically associated electron transfer complex. Computer models of this and related complexes that were generated by docking the x-ray structures of the individual proteins have provided insight into the specificity and mechanism of electron transfer reactions. Previous static modeling studies were extended by molecular dynamics simulations of a cytochrome c-cytochrome b5 intermolecular complex. The simulations indicate that electrostatic interactions at the molecular interface results in a flexible association complex that samples alternative interheme geometries and molecular conformations. Many of these transient geometries appear to be more favorable for electron transfer than those formed in the initial model complex. Of particular interest is a conformational change that occurred in phenylalanine 82 of cytochrome c that allowed the phenyl side chain to bridge the two cytochrome heme groups.     

Three-dimensional structures of the TAFII-containing complexes TFIID and TFTC

TBP (TATA-binding protein)-associated factors (TAF(II)s) are components of large multiprotein complexes such as TFIID, TFTC, STAGA, PCAF/GCN5, and SAGA, which play a key role in the regulation of gene expression by RNA polymerase II. The structures of TFIID and TFTC have been determined at 3.5-nanometer resolution by electron microscopy and digital image analysis of single particles. Human TFIID resembles a macromolecular clamp that contains four globular domains organized around a solvent-accessible groove of a size suitable to bind DNA. TFTC is larger and contains five domains, four of which are similar to TFIID.     

RNA structure: reading the ribosome

The crystal structures of the ribosome and its subunits have increased the amount of information about RNA structure by about two orders of magnitude. This is leading to an understanding of the principles of RNA folding and of the molecular interactions that underlie the functional capabilities of the ribosome and other RNA systems. Nearly all of the possible types of RNA tertiary interactions have been found in ribosomal RNA. One of these, an abundant tertiary structural motif called the A-minor interaction, has been shown to participate in both aminoacyl-transfer RNA selection and in peptidyl transferase; it may also play an important role in the structural dynamics of the ribosome.     

Imaging of single organic molecules in motion

High-resolution transmission electron microscopy revealed nearly atomically precise images of stepping conformational change and translational motion of single hydrocarbon molecules confined in carbon nanotubes. One or two C12 or C22 alkyl chains were tethered to a carborane end group and then embedded in the nanotubes. Images of the hydrocarbon chains interacting with each other and with a graphitic surface provide information on three-dimensional structures and dynamic molecular interactions that cannot be obtained by other analytical methods.     

The microbial engines that drive Earth's biogeochemical cycles

Virtually all nonequilibrium electron transfers on Earth are driven by a set of nanobiological machines composed largely of multimeric protein complexes associated with a small number of prosthetic groups. These machines evolved exclusively in microbes early in our planet's history yet, despite their antiquity, are highly conserved. Hence, although there is enormous genetic diversity in nature, there remains a relatively stable set of core genes coding for the major redox reactions essential for life and biogeochemical cycles. These genes created and coevolved with biogeochemical cycles and were passed from microbe to microbe primarily by horizontal gene transfer. A major challenge in the coming decades is to understand how these machines evolved, how they work, and the processes that control their activity on both molecular and planetary scales.     

Artificially structured thin-film materials and interfaces

The ability to artificially structure new materials on an atomic scale by using advanced crystal growth methods such as molecular beam epitaxy and metal-organic chemical vapor deposition has recently led to the observation of unexpected new physical phenomena and to the creation of entirely new classes of devices. In particular, the growth of materials of variable band gap in technologically important semiconductors such as GaAs, InP, and silicon will be reviewed. Recent results of studies of multilayered structures and interfaces based on the use of advanced characterization techniques such as high-resolution transmission electron microscopy and scanning tunneling microscopy will be presented.     

Nanoscale imaging of molecular adsorption

In situ atomic force microscope observations were made of the adsorption of anions (1- or 2-) of the organic diacid 5-benzoyl-4-hydroxy-2-methoxybenzenesulfonic acid from aqueous solution onto the (0001) surface of hydrotalcite (HT), a layered clay. This adsorption process is believed to mimic the ion-exchange reactions that occur within the layers of HT and other layered clays. Atomic force microscope images of the (0001) surfaces of HT, acquired in aqueous solutions, reveal an ordered structure with respect to magnesium and aluminum atoms. In the presence of the anions, atomic force microscopy indicates pH-dependent adsorption onto the formally cationic HT surface. The anion coverage is governed by electroneutrality and steric interactions between the bulky anions within the adsorbed layer, whereas the orientation of the anions with respect to the HT surface is dictated by coulombic interactions and hydrogen bonding between the anion's sulfonate moiety and clay hydroxyl triads. These observations reveal that the reversible adsorption of molecular species can be examined directly by in situ atomic force microscopy, providing details of surface stoichiometry and adlayer symmetry on the local, molecular level.     

Direct imaging of reconstructed atoms on TiO2 (110) surfaces

Determining the atomic structures of oxide surfaces is critical for understanding their physical and chemical properties but also challenging because the breaking of atomic bonds in the formation of the surface termination can involve complex reconstructions. We used advanced transmission electron microscopy to directly observe the atomic structure of reduced titania (TiO2) (110) surfaces from directions parallel to the surface. In our direct atomic-resolution images, reconstructed titanium atoms at the top surface layer are clearly imaged and are found to occupy the interstitial sites of the TiO2 structure. Combining observations from two orthogonal directions, the three-dimensional positioning of the Ti interstitials is identified at atomic dimensions and allows a resolution of two previous models that differ in their oxygen stoichiometries.     

Direct sub-angstrom imaging of a crystal lattice

Despite the use of electrons with wavelengths of just a few picometers, spatial resolution in a transmission electron microscope (TEM) has been limited by spherical aberration to typically around 0.15 nanometer. Individual atomic columns in a crystalline lattice can therefore only be imaged for a few low-order orientations, limiting the range of defects that can be imaged at atomic resolution. The recent development of spherical aberration correctors for transmission electron microscopy allows this limit to be overcome. We present direct images from an aberration-corrected scanning TEM that resolve a lattice in which the atomic columns are separated by less than 0.1 nanometer.     

Preparation of amorphous boron nitride and its conversion to a turbostratic, tubular form

Amorphous boron nitride, BN, is obtained from the reaction of B-trichloroborazine, (BCINH)(3), with cesium metal. The amorphous product is converted to a turbostratic form upon heating to 1100 degrees C. Scanning electron microscopy reveals a previously unreported morphology composed of hollow tubular structures. The largest of these appear to be approximately 3 micrometers in external diameter and 50 to 100 micrometers in length. Transmission electron microscopy and selected-area electron diffraction also indicate the tube walls to be turbostratic in nature. The mechanism by which the tubes form is not known, although apparent sites of incipient tube growth have been observed.     

Spin coupling in engineered atomic structures

We used a scanning tunneling microscope to probe the interactions between spins in individual atomic-scale magnetic structures. Linear chains of 1 to 10 manganese atoms were assembled one atom at a time on a thin insulating layer, and the spin excitation spectra of these structures were measured with inelastic electron tunneling spectroscopy. We observed excitations of the coupled atomic spins that can change both the total spin and its orientation. Comparison with a model spin-interaction Hamiltonian yielded the collective spin configuration and the strength of the coupling between the atomic spins.     

Polarized electron probes of magnetic surfaces

The magnetic properties of surfaces are now being explored with electron spectroscopies that use electron spin polarization techniques. The increased activity in surface magnetic measurements with polarized electron beams is spurred by new scientific and technological challenges and is made feasible by recent advances in the technology of sources and detectors of polarized electrons. The ability to grow thin films and to engineer artificial structures permits new phenomena to be investigated at magnetic surfaces and interfaces. For such investigations, spin-polarized electron techniques-such as polarized electron scattering, polarized photoemission, polarized Auger spectroscopy, and scanning electron microscopy with polarization analysis-have been and will probably continue to be used to great advantage.     

Visualizing ribosome biogenesis: parallel assembly pathways for the 30S subunit

Ribosomes are self-assembling macromolecular machines that translate DNA into proteins, and an understanding of ribosome biogenesis is central to cellular physiology. Previous studies on the Escherichia coli 30S subunit suggest that ribosome assembly occurs via multiple parallel pathways rather than through a single rate-limiting step, but little mechanistic information is known about this process. Discovery single-particle profiling (DSP), an application of time-resolved electron microscopy, was used to obtain more than 1 million snapshots of assembling 30S subunits, identify and visualize the structures of 14 assembly intermediates, and monitor the population flux of these intermediates over time. DSP results were integrated with mass spectrometry data to construct the first ribosome-assembly mechanism that incorporates binding dependencies, rate constants, and structural characterization of populated intermediates.     

High-resolution three-dimensional imaging of dislocations

Dislocations and their interactions govern the properties of many materials, ranging from work hardening in metals to device pathology in semiconductor laser diodes. However, conventional electron micrographs are simply two-dimensional projections of three-dimensional (3D) structures, and even stereo microscopy cannot reveal the true 3D complexity of defect structures. Here, we describe an electron tomographic method that yields 3D reconstructions of dislocation networks with a spatial resolution three orders of magnitude better than previous work. We illustrate the method's success with a study of dislocations in a GaN epilayer, where dislocation densities of 1010 per square centimeter are common.