Direct use of unassigned resonances in NMR structure calculations with proxy residues

We present a method that significantly enhances the robustness of (automated) NMR structure determination by allowing the NOE data corresponding to unassigned NMR resonances to be used directly in the calculations. The unassigned resonances are represented by additional atoms or groups of atoms that have no interaction with the regular protein atoms except through distance restraints. These so-called "proxy" residues can be used to generate NOE-based distance restraints in a similar fashion as for the assigned part of the protein. If sufficient NOE information is available, the restraints are expected to place the proxies at positions close to the correct atoms for the unassigned resonance, which can facilitate subsequent assignment. Convergence can be further improved by supplying additional information about the possible identities of the unassigned resonances. We have implemented this approach in the widely used automated assignment and structure calculation protocols ARIA and CANDID. We find that it significantly increases the robustness of structure calculations with regard to missing assignments and yields structures of higher quality. Our approach is still able to find correctly folded structures with up to 30% randomly missing resonance assignments, and even when only backbone and beta resonances are present! This should be of significant value to NMR-based structural proteomics initiatives.     

Observation and modelling of barrel droplets on vertical fibres subjected to gravitational and drag forces

Extensive experimental investigation of the wetting processes of fibre/liquid systems during air filtration (when drag and gravitational forces are acting) has shown many important features, including droplet extension, oscillatory motion, and detachment or flow of drops from fibres as airflow velocity increases. A detailed experimental study of the aforementioned processes was conducted using glass filter fibres and H(2)O aerosol, which coalesce on the fibre to form barrel droplets with small contact angles. The droplets were predominantly observed in the Reynolds transition (or unsteady laminar) flow region. The droplet oscillation appears to be induced by the onset of vortexes in the flow field around the droplet as the increasing droplet size increases the Reynolds number. Flow in this region is usually modelled using the classical two-dimensional Karman vortex street, and there exist no 3D equivalents. Therefore to model such oscillation it was necessary to create a new conceptual model to account for the forces both inducing and inhibiting such oscillation. The agreement between the model and experimental results is acceptable for both the radial and transverse oscillations.     

Diffusivity of asphaltene molecules by fluorescence correlation spectroscopy

Using fluorescence correlation spectroscopy (FCS) we measure the translational diffusion coefficient of asphaltene molecules in toluene at extremely low concentrations (0.03-3.0 mg/L): where aggregation does not occur. We find that the translational diffusion coefficient of asphaltene molecules in toluene is about 0.35 x 10(-5) cm(2)/s at room temperature. This diffusion coefficient corresponds to a hydrodynamic radius of approximately 1 nm. These data confirm previously estimated size from rotational diffusion studied using fluorescence depolarization. The implication of this concurrence is that asphaltene molecular structures are monomeric, not polymeric.     

Reactivity of molecularly chemisorbed oxygen on a Au/TiO2 model catalyst

We present results of an investigation into the reactivity of molecularly chemisorbed oxygen with CO on a Au/TiO2 model catalyst at 77 K. We previously discovered that exposing the model catalyst sample to a radio-frequency-generated plasma jet of oxygen results in co-population of both atomically and molecularly chemisorbed oxygen species on the sample. We tested the reactivity of the molecularly chemisorbed oxygen by comparing the CO2 produced from a sample populated with both species to the CO2 produced from a sample that has been cleared of molecularly chemisorbed oxygen employing collision-induced desorption. Samples that are populated with both species consistently result in greater CO2 produced than samples with only atomic oxygen. We interpret this result to indicate that molecularly chemisorbed oxygen on the sample can directly participate in the CO oxidation reaction. The reactivity of molecularly chemisorbed oxygen has been investigated for five different gold coverages (0.5, 0.75, 1, 1.25, and 2 ML), and we observe that there is a greater fractional difference in the CO2 produced (difference between sample populated with both molecularly and atomically adsorbed oxygen and sample populated solely with atomically adsorbed oxygen) for the 1 ML Au coverage than for the other coverages for equivalent oxygen plasma-jet exposures. However, it is not possible to unambiguously conclude that this observation is directly related to a particle size effect on the chemistry since the absolute O(2,a) and O(a) content on the various surfaces is different for all the coverages studied because of the plasma-jet technique that we employed for populating the surfaces with oxygen. Unfortunately, this precludes a direct comparison of the reactivity of molecular oxygen in the carbon monoxide oxidation reaction as a function of gold coverage and hence particle size.     

Molecular orientation of asphaltenes and PAH model compounds in Langmuir-Blodgett films using sum frequency generation spectroscopy

Asphaltenes are an important class of compounds in crude oil whose surface activity is important for establishing reservoir rock wettability which impacts reservoir drainage. While many phenomenological interfacial studies with crude oils and asphaltenes have been reported, there is very little known about the molecular level interactions between asphaltenes and mineral surfaces. In this study, we analyze Langmuir-Blodgett films of asphaltenes and related model compounds with sum frequency generation (SFG) vibrational spectroscopy. In SFG, the polarization of the input (vis, IR) and output (SFG) beams can be varied, which allows the orientation of different functional groups at the interface to be determined. SFG clearly indicates that asphaltene polycyclic aromatic hydrocarbons (PAHs) are highly oriented in the plane of the interface and that the peripheral alkanes are transverse to the interface. In contrast, model compounds with oxygen functionality have PAHs oriented transverse to the interface. Computational quantum chemistry is used to support corresponding band assignments, enabling robust determination of functional group orientations.     

Dynamics of Ligand Binding to a Rigid Glycosidase**

The single-domain GH11 glycosidase from Bacillus circulans (BCX) is involved in the degradation of hemicellulose, which is one of the most abundant renewable biomaterials in nature. We demonstrate that BCX in solution undergoes minimal structural changes during turnover. NMR spectroscopy results show that the rigid protein matrix provides a frame for fast substrate binding in multiple conformations, accompanied by slow conversion, which is attributed to an enzyme-induced substrate distortion. A model is proposed in which the rigid enzyme takes advantage of substrate flexibility to induce a conformation that facilitates the acyl formation step of the hydrolysis reaction.     

Flux line lattice symmetries in the borocarbide superconductor LuNi2B2C

We compare the results of small angle neutron scattering on the flux line lattice (FLL) obtained in the borocarbide superconductor LuNi₂B₂C with the applied field along the c- and a-axes. For H‖c the temperature dependence of the FLL structural phase transition from square to hexagonal symmetry was investigated. Above 10 K the transition onset field. H ₂(T), rises sharply, bending away from H _c2(T) in contradiction to theoretical predictions of the two merging. For H‖a a first order FLL reorientation transition is observed at H _tr=3–3.5 kOe. Below H _tr the FLL nearest neighbor direction is parallel to the b-axis, and above H _tr to the c-axis. This transition cannot be explained using nonlocal corrections to the London model.