Integrated TEM, XRD and electron-microprobe investigation of mixed-layer chlorite smectite from the Point-Sal ophiolite, California

Five basalt samples from the Point Sal ophiolite, California, were examined using HRTEM and AEM in order to compare observations with interpretations of XRD patterns and microprobe analyses. XRD data from ethylene-glycol-saturated samples indicate the following percentages of chlorite in mixed-layer chlorite-smectite identified for each specimen: (i) L2036 almost-equal-to 50%, (ii) L2035 almost-equal-to 70 and 20%, (iii) 1A-13 almost-equal-to 70%, (iv) 1B-42 almost-equal-to 70%, and (v) 1B-55 = 100%. Detailed electron microprobe analyses show that 'chlorite' analyses with high Si, K, Na and Ca contents are the result of interlayering with smectite-like layers. The Fe/(Fe + Mg) ratios of mixed-layer phyllosilicates from Point Sal samples are influenced by the bulk rock composition, not by the percentage of chlorite nor the structure of the phyllosilicate. Measurements of lattice-fringe images indicate that both smectite and chlorite layers are present in the Point Sal samples in abundances similar to those predicted with XRD techniques and that regular alternation of chlorite and smectite occurs at the unit-cell scale. Both 10- and 14-angstrom layers were recorded with HRTEM and interpreted to be smectite and chlorite, respectively. Regular alternation of chlorite and smectite (24-angstrom periodicity) occurs in upper lava samples L2036 and 1A-13, and lower lava sample 1B-42 for as many as seven alternations per crystallite with local layer mistakes. Sample L2035 shows disordered alternation of chlorite and smectite, with juxtaposition of smectite-like layers, suggesting that randomly interlayered chlorite (< 0.5)-smectite exists. Images of lower lava sample 1B-55 show predominantly 14-angstrom layers. Units of 24 angstrom tend to cluster in what may otherwise appear to be disordered mixtures, suggesting the existence of a corrensite end-member having thermodynamic significance.

High resolution transmission electron microscopy of the Murchison Carbonaceous Chondrite and the Kenna Ureilite

Fine-grained matrices in carbonaceous chondrites and small, micron-sized inclusions in achondrites can be characterized effectively using high resolution transmission electron micro­scopy (HRTEM).

A High-Resolution Transmission of the Precipitation Process in a Electron Microscopy Study Dilute Ti-N Alloy

The precipitation processes in dilute nitrogen alloys of titanium have been examined in detail by conventional transmission electron microscopy (CTEM) and high-resolution electron microscopy (HREM). The alloy Ti-2 at. pct N on quenching from its high-temperature beta phase field has been found to undergo early stages of decomposition. The supersaturated solid solution (alpha''-hcp) on decomposition gives rise to an intimately mixed, irresolvable product microstructure. The associated strong tweed contrast presents difficulties in understanding the characteristic features of the process. Therefore, HREM has been carried out with a view to getting a clear picture of the decomposition process. Studies on the quenched samples of the alloy suggest the formation of solute-rich zones of a few atom layers thick, randomly distributed throughout the matrix. On aging, these zones grow to a size beyond which the precipitate/matrix interfaces appear to become incoherent and the alpha' (tetragonal) product phase is seen distinctly. The structural details, the crystallography of the precipitation process, and the sequence of precipitation reaction in the system are illustrated.

On the variety of electron diffraction patterns from quasicrystals

A new exciting era in the study of rapidly solidified alloys has been ushered in by the discovery of a quasicrystalline phase in an Al-1O%Mn alloy by Shechtman et al. (l). The fact that a quasicrystal diffracts electrons and X-rays like a single crystal provides a powerful approach for exploring the atomic configuration in these alloys. Shechtman et al deduced the icosahedral point group symmetry exhibited by quasicrystals on the basis of a set of three electron diffraction patterns showing 5-fold, 3-fold and 2-fold axes of symmetry with appropriate angular relationships. The exotic crystallography of quasicrystals has been recently reviewed by Nelson and Halperin (2).

Engineering multi-step electron tunneling systems in proteins

Multi-step electron tunneling, or “hopping,” has become a fast-developing research field with studies ranging from theoretical modeling systems, inorganic complexes, to biological systems. In particular, the field is exploring hopping mechanisms in new proteins and protein complexes, as well as further understanding the classical biological hopping systems such as ribonuclease reductase, DNA photolyases, and photosystem II. Despite the plethora of natural systems, only a few biologically engineered systems exist. Engineered hopping systems can provide valuable information on key structural and electronic features, just like other kinds of biological model systems. Also, engineered systems can harness common biologic processes and utilize them for alternative reactions. In this thesis, two new hopping systems are engineered and characterized.

The protein Pseudomonas aeruginosa azurin is used as a building block to create the two new hopping systems. Besides being well studied and amenable to mutation, azurin already has been used to successfully engineer a hopping system. The two hopping systems presented in this thesis have a histidine-attached high potential rhenium 4,7-dimethyl-1,10-phenanthroline tricarbonyl [Re(dmp)(CO)3] + label which, when excited, acts as the initial electron acceptor. The metal donor is the type I copper of the azurin protein. The hopping intermediates are all tryptophan, an amino acid mutated into the azurin at select sites between the photoactive metal label and the protein metal site. One system exhibits an inter-molecular hopping through a protein dimer interface; the other system undergoes intra-molecular multi-hopping utilizing a tryptophan “wire.” The electron transfer reactions are triggered by excitation of the rhenium label and monitored by UV-Visible transient absorption, luminescence decays measurements, and time-resolved Infrared spectroscopy (TRIR). Both systems were structurally characterized by protein X-ray crystallography.

Electron tomography of cryofixed, isometrically contracting insect flight muscle reveals novel actin-myosin interactions.

BACKGROUND: Isometric muscle contraction, where force is generated without muscle shortening, is a molecular traffic jam in which the number of actin-attached motors is maximized and all states of motor action are trapped with consequently high heterogeneity. This heterogeneity is a major limitation to deciphering myosin conformational changes in situ. METHODOLOGY: We used multivariate data analysis to group repeat segments in electron tomograms of isometrically contracting insect flight muscle, mechanically monitored, rapidly frozen, freeze substituted, and thin sectioned. Improved resolution reveals the helical arrangement of F-actin subunits in the thin filament enabling an atomic model to be built into the thin filament density independent of the myosin. Actin-myosin attachments can now be assigned as weak or strong by their motor domain orientation relative to actin. Myosin attachments were quantified everywhere along the thin filament including troponin. Strong binding myosin attachments are found on only four F-actin subunits, the "target zone", situated exactly midway between successive troponin complexes. They show an axial lever arm range of 77°/12.9 nm. The lever arm azimuthal range of strong binding attachments has a highly skewed, 127° range compared with X-ray crystallographic structures. Two types of weak actin attachments are described. One type, found exclusively in the target zone, appears to represent pre-working-stroke intermediates. The other, which contacts tropomyosin rather than actin, is positioned M-ward of the target zone, i.e. the position toward which thin filaments slide during shortening. CONCLUSION: We present a model for the weak to strong transition in the myosin ATPase cycle that incorporates azimuthal movements of the motor domain on actin. Stress/strain in the S2 domain may explain azimuthal lever arm changes in the strong binding attachments. The results support previous conclusions that the weak attachments preceding force generation are very different from strong binding attachments.

Imaging domains in BaTiO3 single crystal nanostructures: comparing information from transmission electron microscopy and piezo-force microscopy

This article compares and contrasts information
obtained, using transmission electron microscopy (TEM)
and piezo-force microscopy (PFM), on domain configurations
adopted in single crystal lamellae of BaTiO3, that had
been cut directly from bulk using a focused ion beam
microscope with top and bottom surfaces parallel to
{100}pseudocubic. Both forms of imaging reveal domain
walls parallel to {110}pseudocubic, consistent with sets of 90
domains with dipoles oriented parallel to the two
\001[pseudocubic directions in the plane of the lamellae.
However, the domain width was observed to be dramatically
larger using PFM than it was using TEM. This suggests
significant differences in the surface energy densities
that drive the domain formation in the first place, that could
relate to differences in the boundary conditions in the two
modes of imaging (TEM samples are imaged under high
vacuum, whereas PFM imaging was performed in air).
Attempts were made to map local dipole orientations
directly, using a form of ‘vector’ PFM. However, information
inferred was largely inconsistent with the known
crystallography of the samples, raising concern about the
levels of care needed for accurate interpretation of PFM
images.

GPCR structure, function, drug discovery and crystallography: report from Academia-Industry International Conference (UK Royal Society) Chicheley Hall, 1-2 September 2014

G-protein coupled receptors (GPCRs) are the targets of over half of all prescribed drugs today. The UniProt database has records for about 800 proteins classified as GPCRs, but drugs have only been developed against 50 of these. Thus, there is huge potential in terms of the number of targets for new therapies to be designed. Several breakthroughs in GPCRs biased pharmacology, structural biology, modelling and scoring have resulted in a resurgence of interest in GPCRs as drug targets. Therefore, an international conference, sponsored by the Royal Society, with world-renowned researchers from industry and academia was recently held to discuss recent progress and highlight key areas of future research needed to accelerate GPCR drug discovery. Several key points emerged. Firstly, structures for all three major classes of GPCRs have now been solved and there is increasing coverage across the GPCR phylogenetic tree. This is likely to be substantially enhanced with data from x-ray free electron sources as they move beyond proof of concept. Secondly, the concept of biased signalling or functional selectivity is likely to be prevalent in many GPCRs, and this presents exciting new opportunities for selectivity and the control of side effects, especially when combined with increasing data regarding allosteric modulation. Thirdly, there will almost certainly be some GPCRs that will remain difficult targets because they exhibit complex ligand dependencies and have many metastable states rendering them difficult to resolve by crystallographic methods. Subtle effects within the packing of the transmembrane helices are likely to mask and contribute to this aspect, which may play a role in species dependent behaviour. This is particularly important because it has ramifications for how we interpret pre-clinical data. In summary, collaborative efforts between industry and academia have delivered significant progress in terms of structure and understanding of GPCRs and will be essential for resolving problems associated with the more difficult targets in the future.

DOMINANCE OF SHORT-RANGE-ORDER EFFECTS IN LOW-ENERGY ELECTRON-DIFFRACTION INTENSITY SPECTRA

Using low-energy electron-diffraction (LEED) formalism, we demonstrate theoretically that LEED I-V spectra are characterized mainly by short-range order. We also show experimentally that diffuse LEED (DLEED) I-V spectra can be accurately measured from a disordered system using a video-LEED system even at very low coverage. These spectra demonstrate that experimental DLEED I-V spectra from disordered systems may be used to determine local structures. As an example, it is shown that experimental DLEED I-V spectra from K/Co {1010BAR} at potassium coverages of 0.07, 0.1, and 0.13 monolayer closely resemble calculated and experimental LEED I-V spectra for a well-ordered Co{1010BAR}-c(2X2)-K superstructure, leading to the conclusion that at low coverages, potassium atoms are located in the fourfold-hollow sites and that there is no large bond-length change with coverage.

Purification and electron cryomicroscopy of coronavirus particles

Intact, enveloped coronavirus particles vary widely in size and contour, and are thus refractory to study by traditional structural means such as X-ray crystallography. Electron microscopy (EM) overcomes some problems associated with particle variability and has been an important tool for investigating coronavirus ultrastructure. However, EM sample preparation requires that the specimen be dried onto a carbon support film before imaging, collapsing internal particle structure in the case of coronaviruses. Moreover, conventional EM achieves image contrast by immersing the specimen briefly in heavy-metal-containing stain, which reveals some features while obscuring others. Electron cryomicroscopy (cryo-EM) instead employs a porous support film, to which the specimen is adsorbed and flash-frozen. Specimens preserved in vitreous ice over holes in the support film can then be imaged without additional staining. Cryo-EM, coupled with single-particle image analysis techniques, makes it possible to examine the size, structure and arrangement of coronavirus structural components in fully hydrated, native virions. Two virus purification procedures are described.

Monitoring one-electron photo-oxidation of guanine in DNA crystals using ultrafast infrared spectroscopy

To understand the molecular origins of diseases caused by ultraviolet and visible light, and also to develop photodynamic therapy, it is important to resolve the mechanism of photoinduced DNA damage. Damage to DNA bound to a photosensitizer molecule frequently proceeds by one-electron photo-oxidation of guanine, but the precise dynamics of this process are sensitive to the location and the orientation of the photosensitizer, which are very difficult to define in solution. To overcome this, ultrafast time-resolved infrared (TRIR) spectroscopy was performed on photoexcited ruthenium polypyridyl–DNA crystals, the atomic structure of which was determined by X-ray crystallography. By combining the X-ray and TRIR data we are able to define both the geometry of the reaction site and the rates of individual steps in a reversible photoinduced electron-transfer process. This allows us to propose an individual guanine as the reaction site and, intriguingly, reveals that the dynamics in the crystal state are quite similar to those observed in the solvent medium.

Simulation of electron density maps for two-dimensional crystal structures using Mathematica

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)