Kathleen Wood

Translational diffusion of hydration water correlates with functional motions in folded and intrinsically disordered proteins

Hydration water is the natural matrix of biological macromolecules and is essential for their activity in cells. The coupling between water and protein dynamics has been intensively studied, yet it remains controversial. Here we combine protein perdeuteration, neutron scattering and molecular dynamics simulations to explore the nature of hydration water motions at temperatures between 200 and 300 K, across the so-called protein dynamical transition, in the intrinsically disordered human protein tau and the globular maltose binding protein. Quasi-elastic broadening is fitted with a model of translating, rotating and immobile water molecules. In both experiment and simulation, the translational component markedly increases at the protein dynamical transition (around 240 K), regardless of whether the protein is intrinsically disordered or folded. Thus, we generalize the notion that the translational diffusion of water molecules on a protein surface promotes the large-amplitude motions of proteins that are required for their biological activity.

Mesoporous metallic rhodium nanoparticles

Mesoporous noble metals are an emerging class of cutting-edge nanostructured catalysts due to their abundant exposed active sites and highly accessible surfaces. Although various noble metal (e.g. Pt, Pd and Au) structures have been synthesized by hard- and soft-templating methods, mesoporous rhodium (Rh) nanoparticles have never been generated via chemical reduction, in part due to the relatively high surface energy of rhodium (Rh) metal. Here we describe a simple, scalable route to generate mesoporous Rh by chemical reduction on polymeric micelle templates [poly(ethylene oxide)-b-poly(methyl methacrylate) (PEO-b-PMMA)]. The mesoporous Rh nanoparticles exhibited a ∼2.6 times enhancement for the electrocatalytic oxidation of methanol compared to commercially available Rh catalyst. Surprisingly, the high surface area mesoporous structure of the Rh catalyst was thermally stable up to 400 °C. The combination of high surface area and thermal stability also enables superior catalytic activity for the remediation of nitric oxide (NO) in lean-burn exhaust containing high concentrations of O2.

Guanidine hydrochloride denaturation of dopamine-induced α-synuclein oligomers: A small-angle X-ray scattering study

Alpha‐synuclein (α‐syn) forms the amyloid‐containing Lewy bodies found in the brain in Parkinsons disease. The neurotransmitter dopamine (DA) reacts with α‐syn to form SDS‐resistant soluble, non‐amyloid, and melanin‐containing oligomers. Their toxicity is debated, as is the nature of their structure and their relation to amyloid‐forming conformers of α‐syn. The small‐angle X‐ray scattering technique in combination with modeling by the ensemble optimization method showed that the un‐reacted native protein populated three broad classes of conformer, while reaction with DA gave a restricted ensemble range suggesting that the rigid melanin molecule played an important part in their structure. We found that 6 M guanidine hydrochloride did not dissociate α‐syn DA‐reacted dimers and trimers, suggesting covalent linkages. The pathological significance of covalent association is that if they are non‐toxic, the oligomers would act as a sink for toxic excess DA and α‐syn; if toxic, their stability could enhance their toxicity. We argue it is essential, therefore, to resolve the question of whether they are toxic or not. Proteins 2014; 82:10–21.

QUOKKA, the pinhole small-angle neutron scattering instrument at the OPAL Research Reactor, Australia: design, performance, operation and scientific highlights

QUOKKA is a 40 m pinhole small-angle neutron scattering instrument in routine user operation at the OPAL research reactor at the Australian Nuclear Science and Technology Organisation. Operating with a neutron velocity selector enabling variable wavelength, QUOKKA has an adjustable collimation system providing source–sample distances of up to 20 m. Following the large-area sample position, a two-dimensional 1 m2 position-sensitive detector measures neutrons scattered from the sample over a secondary flight path of up to 20 m. Also offering incident beam polarization and analysis capability as well as lens focusing optics, QUOKKA has been designed as a general purpose SANS instrument to conduct research across a broad range of scientific disciplines, from structural biology to magnetism. As it has recently generated its first 100 publications through serving the needs of the domestic and international user communities, it is timely to detail a description of its as-built design, performance and operation as well as its scientific highlights. Scientific examples presented here reflect the Australian context, as do the industrial applications, many combined with innovative and unique sample environments.

Complex precipitation phenomena in strip cast steels with high sulfur and copper contents

A series of three steel alloys with increasing Cu and S concentrations has been prepared by simulated direct strip casting. It was found that the rapid solidification that occurs during direct strip casting results in the formation of a high number density of fine MnS precipitates, while Cu was retained in solid solution above equilibrium concentration. Upon ageing the MnS particles were found to coarsen and increase in volume fraction, indicating that some S was retained in solid solution in the as-cast condition. Ageing also resulted in the precipitation of Cu-rich precipitates. A new method to determine precipitate composition from small-angle neutron scattering is presented. This methodology, in conjunction with atom-probe tomography, has been used to show that the composition of the Cu-rich precipitates depends on the alloys bulk Cu content.

Apolipoprotein C-II Adopts Distinct Structures in Complex with Micellar and Submicellar Forms of the Amyloid-Inhibiting Lipid-Mimetic Dodecylphosphocholine.

The formation of amyloid deposits is a common feature of a broad range of diseases, including atherosclerosis, Alzheimers disease, and Parkinsons disease. The basis and role of amyloid deposition in the pathogenesis of these diseases is still being defined, however an interesting feature of amyloidogenic proteins is that the majority of the pathologically associated proteins are involved in lipid homeostasis, be it in lipid transport, incorporation into membranes, or the regulation of lipid pathways. Thus, amyloid-forming proteins commonly bind lipids, and lipids are generally involved in the proper folding of these proteins. However, understanding of the basis for these lipid-related aspects of amyloidogenesis is lacking. Thus, we have used the apolipoprotein C-II amyloid model system in conjunction with x-ray and neutron scattering analyses to address this problem. Apolipoprotein C-II is a well-studied model system of systemic amyloid fibril formation, with a clear and well-defined pathway for fibril formation, where the effects of lipid interaction are characterized, particularly for the lipid mimetic dodecylphosphocholine. We show that the micellar state of an inhibitory lipid can have a very significant effect on protein conformation, with micelles stabilizing a particular α-helical structure, whereas submicellar lipids stabilize a very different dimeric, α-helical structure. These results indicate that lipids may have an important role in the development and progression of amyloid-related diseases.

Substrate Locking Promotes Dimer-Dimer Docking of an Enzyme Antibiotic Target

Protein dynamics manifested through structural flexibility play a central role in the function of biological molecules. Here we explore the substrate-mediated change in protein flexibility of an antibiotic target enzyme, Clostridium botulinum dihydrodipicolinate synthase. We demonstrate that the substrate, pyruvate, stabilizes the more active dimer-of-dimers or tetrameric form. Surprisingly, there is little difference between the crystal structures of apo and substrate-bound enzyme, suggesting protein dynamics may be important. Neutron and small-angle X-ray scattering experiments were used to probe substrate-induced dynamics on the sub-second timescale, but no significant changes were observed. We therefore developed a simple technique, coined protein dynamics-mass spectrometry (ProD-MS), which enables measurement of time-dependent alkylation of cysteine residues. ProD-MS together with X-ray crystallography and analytical ultracentrifugation analyses indicates that pyruvate locks the conformation of the dimer that promotes docking to the more active tetrameric form, offering insight into ligand-mediated stabilization of multimeric enzymes.

Mesoporous Metallic Iridium Nanosheets

Two-dimensional (2D) metals are an emerging class of nanostructures that have attracted enormous research interest due to their unusual electronic and thermal transport properties. Adding mesopores in the plane of ultrathin 2D metals is the next big step in manipulating these structures because increasing their surface area improves the utilization of the material and the availability of active sites. Here, we report a novel synthetic strategy to prepare an unprecedented type of 2D mesoporous metallic iridium (Ir) nanosheet. Mesoporous Ir nanosheets can be synthesized with close-packed assemblies of diblock copolymer (poly-(ethylene oxide)- b-polystyrene, PEO- b-PS) micelles aligned in the 2D plane of the nanosheets. This novel synthetic route opens a new dimension of control in the synthesis of 2D metals, enabling new kinds of mesoporous architectures with abundant catalytically active sites. Because of their unique structural features, the mesoporous metallic Ir nanosheets exhibit a high electrocatalytic activity toward the oxygen evolution reaction (OER) in acidic solution as compared to commercially available catalysts.

Atom probe tomography data analysis procedure for precipitate and cluster identification in a Ti-Mo steel

An atom probe tomography data analysis procedure for identification of particles in a Ti-Mo steel is presented. This procedure has been used to characterise both carbide precipitates (larger particles) and solute clusters (smaller particles), as reported in an accompanying Mater. Sci. Eng. A paper [1]. Particles were identified using the maximum separation method (cluster-finding algorithm) after resolving peak overlaps at several locations in the mass spectrum. The cluster-finding algorithm was applied to the data in a two-stage process to properly identify particles having a bimodal size distribution. Furthermore, possible misidentification of matrix atoms (mainly Fe) due to the local magnification effect (from the difference in field evaporation potential between the matrix and precipitates) has been resolved using an atomic density approach, comparing that measured experimentally using APT to the theoretical density of both the matrix and particles.