Cosmic dust and our origins

The small solid particles in the space between the stars provide the surfaces for the production of many simple and complex molecules. Processes involving the effects of ultraviolet irradiation of the thin (hundredth micron) mantles are shown to produce a wide range of molecules and ions also seen in comets. Some of the more complex ones inferred from laboratory experiments are expected to play an important role in the origin of life. An outline of the chemical evolution of interstellar dust as observed and as studied in the laboratory is presented. Observations of comets are shown to provide substantial evidence for their being fluffy aggregates of interstellar dust as it was in the protosolar nebula, i.e. the interstellar cloud which collapsed to form the solar system. The theory that comets may have brought the progenitors of life to the earth is summarized.     

Preprocessing of rotamers for protein design calculations

We have developed a process that significantly reduces the number of rotamers in computational protein design calculations. This process, which we call Vegas, results in dramatic computational performance increases when used with algorithms based on the dead-end elimination (DEE) theorem. Vegas estimates the energy of each rotamer at each position by fixing each rotamer in turn and utilizing various search algorithms to optimize the remaining positions. Algorithms used for this context specific optimization can include Monte Carlo, self-consistent mean field, and the evaluation of an expression that generates a lower bound energy for the fixed rotamer. Rotamers with energies above a user-defined cutoff value are eliminated. We found that using Vegas to preprocess rotamers significantly reduced the calculation time of subsequent DEE-based algorithms while retaining the global minimum energy conformation. For a full boundary design of a 51 amino acid fragment of engrailed homeodomain, the total calculation time was reduced by 12-fold.     

Exact rotamer optimization for protein design

Computational methods play a central role in the rational design of novel proteins. The present work describes a new hybrid exact rotamer optimization (HERO) method that builds on previous dead-end elimination algorithms to yield dramatic performance enhancements. Measured on experimentally validated physical models, these improvements make it possible to perform previously intractable designs of entire protein core, surface, or boundary regions. Computational demonstrations include a full core design of the variable domains of the light and heavy chains of catalytic antibody 48G7 FAB with 74 residues and 10(128) conformations, a full core/boundary design of the beta1 domain of protein G with 25 residues and 10(53) conformations, and a full surface design of the beta1 domain of protein G with 27 residues and 10(60) conformations. In addition, a full sequence design of the beta1 domain of protein G is used to demonstrate the strong dependence of algorithm performance on the exact form of the potential function and the fidelity of the rotamer library. These results emphasize that search algorithm performance for protein design can only be meaningfully evaluated on physical models that have been subjected to experimental scrutiny. The new algorithm greatly facilitates ongoing efforts to engineer increasingly complex protein features.     

Adaptation of a fast Fourier transform-based docking algorithm for protein design

Designing proteins with novel protein/protein binding properties can be achieved by combining the tools that have been developed independently for protein docking and protein design. We describe here the sequence-independent generation of protein dimer orientations by protein docking for use as scaffolds in protein sequence design algorithms. To dock monomers into sequence-independent dimer conformations, we use a reduced representation in which the side chains are approximated by spheres with atomic radii derived from known C2 symmetry-related homodimers. The interfaces of C2-related homodimers are usually more hydrophobic and protein core-like than the interfaces of heterodimers; we parameterize the radii for docking against this feature to capture and recreate the spatial characteristics of a hydrophobic interface. A fast Fourier transform-based geometric recognition algorithm is used for docking the reduced representation protein models. The resulting docking algorithm successfully predicted the wild-type homodimer orientations in 65 out of 121 dimer test cases. The success rate increases to approximately 70% for the subset of molecules with large surface area burial in the interface relative to their chain length. Forty-five of the predictions exhibited less than 1 A C(alpha) RMSD compared to the native X-ray structures. The reduced protein representation therefore appears to be a reasonable approximation and can be used to position protein backbones in plausible orientations for homodimer design.     

Concise Synthesis of (3Z)-Dodecen-12-olide,Pheromone Component of the Emerald Ash Borer

Emerald ash borer (EAB), Agrilus planipennis Fairmaire, is an invasive insect that has killed millions of ash trees in Canada and the USA. (3Z)-Dodecen-12-olide is a known female-produced pheromone of this insect, and a concise, three-step synthesis of a 2:1 blend of (3Z)-dodecen-12-olide and (3E)-dodecen-12-olide starting from commercially available (2-carboxyethyl)triphenylphosphonium bromide and 10-bromo-1-decene is described. The key steps in this synthesis are a lithium-salt-free Wittig reaction and an intramolecular S_N2 esterification. Both of these macrocyclic lactones are behaviorally active toward EAB, and the 2:1 blend whose synthesis is described here has the potential to be a detection agent, mating disruptor, or mass trapping agent, which could be used in the control of EAB.     

A feasibility study of X‐ray phase‐contrast mammographic tomography at the Imaging and Medical beamline of the Australian Synchrotron

Results are presented of a recent experiment at the Imaging and Medical beamline of the Australian Synchrotron intended to contribute to the implementation of low‐dose high‐sensitivity three‐dimensional mammographic phase‐contrast imaging, initially at synchrotrons and subsequently in hospitals and medical imaging clinics. The effect of such imaging parameters as X‐ray energy, source size, detector resolution, sample‐to‐detector distance, scanning and data processing strategies in the case of propagation‐based phase‐contrast computed tomography (CT) have been tested, quantified, evaluated and optimized using a plastic phantom simulating relevant breast‐tissue characteristics. Analysis of the data collected using a Hamamatsu CMOS Flat Panel Sensor, with a pixel size of 100 µm, revealed the presence of propagation‐based phase contrast and demonstrated significant improvement of the quality of phase‐contrast CT imaging compared with conventional (absorption‐based) CT, at medically acceptable radiation doses.     

Surface photochemistry: The photo-chlorination of aromatic hydrocarbons with ferric chloride on alumina

Irradiation of a number of aromatic hydrocarbons adsorbed on alumina in the presence of ferric chloride leads to monochlorination.     

A simple method to measure 13CH2 heteronuclear dipolar cross-correlation spectral densities

Here, we report a method to simultaneously determine CH2 cross-correlation spectral densities and T1 relaxation times in the laboratory and rotating frames. To accomplish this, we have employed an indirect approach that is based on measurement of differences in relaxation rates acquired with and without cross-correlation terms. The new method, which can be employed using multidimensional NMR and standard relaxation pulse sequences, is validated experimentally by investigation of a selectively 13C-enriched hexadecapeptide and the uniformly 13C-enriched immunoglobulin-binding domain of streptococcal protein G (GB1). Use of this approach makes determination of CH2 cross-correlation spectral densities in uniformly 13C-enriched proteins now routine and provides novel information concerning their internal motions.     

Quantitative quasi-local tomography using absorption and phase contrast

Possibilities are investigated for quantitative computed tomography (CT) reconstruction of the spatial distribution of refractive index in a region of interest (ROI) inside an object which is larger than the field of view. The analysis is presented for the case of conventional (absorption) CT, as well as diffraction (phase-contrast) CT. It is shown that in both cases an accurate reconstruction can be achieved using the projection data corresponding to rays passing through a sufficiently wide vicinity of a ROI. Our analysis also indicates that X-ray phase-contrast CT can typically be localized to smaller regions compared to absorption CT. In particular, quasi-local hard X-ray micro-CT of regions of the order of 100 μm or even smaller in size, appears feasible with the use of propagation-based phase contrast. Numerical and experimental tests confirm the possibility of accurate quantitative CT reconstruction from truncated projections.