Identical Structural Changes Research Articles

Connecting particle interactions to agglomerate morphology and rheology of boehmite nanocrystal suspensions

HypothesisThe rheology of complex suspensions, such as nuclear waste slurries at the Hanford and Savannah River sites, imposes significant challenges on industrial-scale processing. Investigating the rheology and connecting it to the agglomerate morphology and underlying particle interactions in slurries will provide important fundamental knowledge, as well as prescriptive data for practical applications. Here, we use suspensions of nano-scale aluminum oxyhydroxide minerals in the form of boehmite as an analog of the radioactive waste slurry to investigate the correlation between particle interactions, agglomerate morphology, and slurry rheology. ExperimentsA combination of Couette rheometry and small-angle scattering techniques (independently and simultaneously) were used to understand how agglomerate structure of slurry changes under flow and how these structural changes manifest themselves in the bulk rheology of the suspensions. FindingsOur experiments show that the boehmite slurries are thixotropic, with the rheology and structure of the suspensions changing with increasing exposure to flow. In the slurries, particle agglomerates begin as loose, system-spanning clusters, but exposure to moderate shear rates causes the agglomerates to irreversibly consolidate into denser clusters of finite size. The structural changes directly influence the rheological properties of the slurries such as viscosity and viscoelasticity. Our study shows that solution pH affects the amount of structural rearrangement and the kinetics of the rearrangement process, with an increase in pH leading to faster and more dramatic changes in bulk rheology, which can be understood via correlations between particle interactions and the strength of particle network. Nearly identical structural changes were also observed in Poiseuille flow geometries, implying that the observed changes are relevant in pipe flow as well.

Determination of Gas-Phase Ion Structures of Locally Polar Homopolymers Through High-Resolution Ion Mobility Spectrometry-Mass Spectrometry.

The strong synergy arising from coupling two orthogonal analytical techniques such as ion mobility and mass spectrometry can be used to separate complex mixtures and determine structural information of analytes in the gas phase. A tandem study is performed using two systems with different gases and pressures to ascertain gas-phase conformations of homopolymer ions. Aside from spherical and stretched configurations, intermediate configurations formed by a multiply charged globule and a "bead-on-a-string" appendix are confirmed for polyethylene-glycol (PEG), polycaprolactone (PCL), and polydimethylsiloxane (PDMS). These intermediate configurations are shown to be ubiquitous for all charge states and masses present. For each charge state, configurations evolve in two distinctive patterns: an inverse evolution which occurs as an elementary charge attached to the polymer leaves the larger globule and incorporates itself into the appendage, and a forward evolution which reduces the globule without relinquishing a charge while leaving the appendix relatively constant. Forward evolutions are confirmed to form self-similar family shapes that transcend charge states for all polymers. Identical structural changes occur at the same mass over charge regardless of the system, gas or pressure strongly suggesting that conformations are only contingent on number of charges and chain length, and start arranging once the ion is at least partially ejected from the droplet, supporting a charge extrusion mechanism. Configurational changes are smoother for PDMS which is attributed to the larger steric hindrance caused by protruding pendant groups. This study has implications in the study of the configurational space of more complex homopolymers and heteropolymers. Graphical Abstract.

Structural changes arising from different thawing protocols on cryopreserved human allograft's aortic valve leaflets.

The aim of our experimental work was to assess the impact and morphological changes that arise during different thawing protocols on human aortic valve (AV) leaflets resected from cryopreserved aortic root allografts (CARAs). Two thawing protocols were tested: 1. CARAs were thawed at a room temperature (23°C); 2. CARAs were placed directly into a water bath at a temperature of 37°C. After all the samples were thawed, non-coronary AV leaflets were sampled from each specimen and fixed in a 4% formaldehyde solution before they were sent for morphological analysis. All the samples were washed in distilled water for 5 min and dehydrated in a graded ethanol series (70%, 85%, 95%, and 100%) for 5 min at each level. The tissue samples were then immersed in 100% hexamethyldisilazane (HMDS) for 10 min, and then air-dried in an exhaust hood at room temperature. Processed samples were mounted on stainless steel stubs and coated with gold. Histological analysis was performed with the use of an electron microscope on a scanning mode operating at 25 kV - BS 301. Thawing protocol 1 (room temperature at 23°C): 6 (100%) samples showed loss of the endothelial covering of the basal membrane with no damage to the basal lamina. Thawing protocol 2 (water bath at 37°C): 5 (83%) samples showed loss of the endothelial covering of the basal membrane with no damage to the basal lamina. One (17%) sample showed loss of the endothelial covering the basal membrane with significant damage to the basal membrane. Based on our experimental work, we can clearly conclude that cryopreserved AV leaflet allografts show identical structural changes at different rates of thawing.

The G551D CFTR chloride channel spurs the development of personalized medicine.

The G551D CFTR chloride channel spurs the development of personalized medicine.

A Local, Interactive Network of 3′ RNA Elements Supports Translation and Replication of Turnip Crinkle Virus

The majority of the 3' untranslated region (UTR) of Turnip crinkle virus (TCV) was previously identified as forming a highly interactive structure with a ribosome-binding tRNA-shaped structure (TSS) acting as a scaffold and undergoing a widespread conformational shift upon binding to RNA-dependent RNA polymerase (RdRp). Tertiary interactions in the region were explored by identifying two highly detrimental mutations within and adjacent to a hairpin H4 upstream of the TSS that reduce translation in vivo and cause identical structural changes in the loop of the 3' terminal hairpin Pr. Second-site changes that compensate for defects in translation/accumulation and reverse the structural differences in the Pr loop were found in the Pr stem, as well as in a specific stem within the TSS and within the capsid protein (CP) coding region, suggesting that the second-site changes were correcting a conformational defect and not restoring specific base pairing. The RdRp-mediated conformational shift extended upstream through this CP open reading frame (ORF) region after bypassing much of an intervening, largely unstructured region, supporting a connection between 3' elements and coding region elements. These data suggest that the Pr loop, TSS, and H4 are central elements in the regulation of translation and replication in TCV and allow for development of an RNA interactome that maps the higher-order structure of a postulated RNA domain within the 3' region of a plus-strand RNA virus.

Charge Effects in the Selection of NPF Motifs by the EH Domain of EHD1

The Eps15 homology (EH) domain is found in proteins associated with endocytosis and vesicle trafficking. EH domains bind to their target proteins through an asparagine-proline-phenylalanine (NPF) motif. We have measured the interaction energetics of the EH domain from EHD1 with peptides derived from two of its binding partners: Rabenosyn-5 (Ac-GPSLNPFDEED-NH(2)) and Rab11-Fip2 (Ac-YESTNPFTAK-NH(2)). Heteronuclear single quantum coherence (HSQC) spectroscopy shows that both peptides bind in the canonical binding pocket of EHD1 EH and induce identical structural changes, yet the affinity of the negatively charged Ac-GPSLNPFDEED-NH(2) (K(a) = 8 x 10(5) M(-1)) is tighter by 2 orders of magnitude. The thermodynamic profiles (DeltaG, DeltaH, DeltaS) were measured for both peptides as a function of temperature. The enthalpies of binding are essentially identical, and the difference in affinity is a consequence of the difference in entropic cost. Ac-GPSLNPFDEED-NH(2) binding is salt-dependent, demonstrating an electrostatic component to the interaction, whereas Ac-YESTNPFTAK-NH(2) binding is independent of salt. Successive replacement of acidic residues in Ac-GPSLNPFDEED-NH(2) with neutral residues showed that all are important. Lysine side chains in EHD1 EH create a region of strong positive surface potential near the NPF binding pocket. Contributions by lysine epsilon-amino groups to complex formation with Ac-GPSLNPFDEED-NH(2) was shown using direct-observe (15)N NMR spectroscopy. These experiments have enabled us to define a new extended interaction motif for EHD proteins, N-P-F-[DE]-[DE]-[DE], which we have used to predict new interaction partners and hence broaden the range of cellular activities involving the EHD proteins.

Measurements of free radical in vitamin E-doped ultra-high molecular weight polyethylene: Dependence on materials processing and irradiation environments

Ultra-high molecular weight polyethylene (UHMWPE), doped with vitamin E (α-tocopherol (α-T)), was irradiated with gamma rays in nitrogen (N 2) or air, and the resulting free radicals were detected in air using an electron spin resonance (ESR) technique. Two groups of samples were investigated. In one group, samples were prepared from blends of α-T (20 wt%) and UHMWPE powder (PPE-α-T) and, in the other, from compression molded blocks (CMPE-α-T). The CMPE-α-T blocks contained 0% (control), 0.5%, 1.0%, 10.0%, 15.0%, 20.0% and 25.0% α-T by weight. When irradiation was performed in air, the ESR spectrum of powder samples showed the presence of only vitamin E radical (tocopheroxyl, α-T-O ), and there was no detectable signal due to PE radicals (alkyl/allyl). Most likely, all PE radicals were quenched by vitamin E during irradiation in air. However, when irradiation was performed in N 2, composite ESR spectra showed the presence of both PE and α-T-O radicals. Compared to the control (PPE, 0% α-T) PE radicals in PPE-20% α-T were found to be significantly reduced or quenched by α-T. The presence of α-T in powder samples, however, did not affect the long-term (71 days in this study) oxidation behavior of the PE radicals. Compression molded samples, with and without α-T, produced identical ESR spectra irrespective of their irradiation environment N 2 or air. However, radical concentration, measured immediately after irradiation, was found to be an order of magnitude less in CMPE-α-T than in the control (CMPE-0% α-T). They also evidenced identical structural changes in the respective ESR spectra during subsequent oxidation for 24 days in open air. These observations suggest that α-T can effectively quench a significant fraction of PE radicals during irradiation, but has no measurable effect on subsequent reactions. No significant difference was found in the ESR spectra of samples containing different α-T concentration.

Atomic Level Insight into the Oxidative Half-reaction of Aromatic Amine Dehydrogenase

The quinoprotein aromatic amine dehydrogenase (AADH) uses a covalently bound tryptophan tryptophylquinone (TTQ) cofactor to oxidatively deaminate primary aromatic amines. Recent crystal structures have provided insight into the reductive half-reaction. In contrast, no atomic details are available for the oxidative half-reaction. The TTQ O7 hydroxyl group is protonated during reduction, but it is unclear how this proton can be removed during the oxidative half-reaction. Furthermore, compared with the electron transfer from the N-quinol form, electron transfer from the non-physiological O-quinol form to azurin is significantly slower. Here we report crystal structures of the O-quinol, N-quinol, and N-semiquinone forms of AADH. A comparison of oxidized and substrate reduced AADH species reveals changes in the TTQ-containing subunit, extending from residues in the immediate vicinity of the N-quinol to the putative azurin docking site, suggesting a mechanism whereby TTQ redox state influences interprotein electron transfer. In contrast, chemical reduction of the TTQ center has no significant effect on protein conformation. Furthermore, structural reorganization upon substrate reduction places a water molecule near TTQ O7 where it can act as proton acceptor. The structure of the N-semiquinone, however, is essentially similar to oxidized AADH. Surprisingly, in the presence of substrate a covalent N-semiquinone substrate adduct is observed. To our knowledge this is the first detailed insight into a complex, branching mechanism of quinone oxidation where significant structural reorganization upon reduction of the quinone center directly influences formation of the electron transfer complex and nature of the electron transfer process.

A Pseudoknot in a Preactive Form of a Viral RNA Is Part of a Structural Switch Activating Minus-Strand Synthesis

RNA can adopt different conformations in response to changes in the metabolic status of cells, which can regulate processes such as transcription, translation, and RNA cleavage. We previously proposed that an RNA conformational switch in an untranslated satellite RNA (satC) of Turnip crinkle virus (TCV) regulates initiation of minus-strand synthesis (G. Zhang, J. Zhang, A. T. George, T. Baumstark, and A. E. Simon, RNA 12:147-162, 2006). This model was based on the lack of phylogenetically inferred hairpins or a known pseudoknot in the "preactive" structure assumed by satC transcripts in vitro. We now provide evidence that a second pseudoknot (Psi(2)), whose disruption reduces satC accumulation in vivo and enhances transcription by the TCV RNA-dependent RNA polymerase in vitro, stabilizes the preactive satC structure. Alteration of either Psi(2) partner caused nearly identical structural changes, including single-stranded-specific cleavages in the pseudoknot sequences and strong cleavages in a distal element previously proposed to mediate the conformational switch. These results indicate that the preactive structure identified in vitro has biological relevance in vivo and support a requirement for this alternative structure and a conformational switch in high-level accumulation of satC in vivo.

Textural vs structural plastic instabilities in sheet metal forming

Negative work-hardening rates are precursors of plastic instabilities. The objective of the work is to determine the origin of the stress decrease in the case of prestrained sheet metals. Samples of low carbon steel and pure aluminium deformed in rolling and reloaded in simple shear exhibit softening for specific shear directions with respect to the rolling direction. Structural and textural evolutions are analysed with transmission electron microscopy and X-ray measurements, respectively. The low carbon steel shows clear evidence of intragranular structural destabilization while the Taylor factor, estimated by self-consistent calculations, remains nearly constant. It is deduced that for steel, the softening has a structural origin. By contrast the aluminium samples present identical structural changes whatever the sign of the work-hardening rate. It is shown that the latter is strongly correlated with Taylor factor evolutions. A textural instability is obtained in this case.

Identical structural changes in inherited albumin variants from different populations.

Alloalbuminemia is rare and has a cumulative frequency of only approximately 1 in 3,000 in Europeans and Japanese. The worldwide ethnic and geographic distribution of certain albumin genetic variants appears to be nonrandom. Moreover, we have found that structurally identical variants may occur at different frequencies in ethnically distinct populations, presumably owing to independent mutations. In this study, albumin B and two types of proalbumins, which as a group are the most common European albumin variants, have also been found in Asians. We have identified the amino acid substitution characteristic of albumin B (glutamic acid----lysine at position 570) in alloalbumins from six unrelated individuals of five different European descents and also in two Japanese and one Cambodian. The two types of proalbumins most common in Europe (Lille type, arginine----histidine at position -2; Christchurch type, arginine----glutamic acid at position -1) also occur in Japan. These results provide evidence for independent mutations at single sites in the albumin genome. The clustering of these and of several other amino acid exchanges in certain regions of the albumin molecule suggests two possibilities: that certain sites are hypermutable or that mutants involving certain sites are more subject to selection than mutants involving others.

Two hypolipidemic peroxisome proliferators increase the number of lamellar bodies in alveolar cells type II of the rat lung

Male rats treated with either clofibrate or nafenopin, two peroxisome proliferating compounds with potent hypolipidemic properties, show identical structural changes in their lungs. In both cases, two types of lung cells were affected by these agents: (i) the alveolar epithelial cells type II and (ii) the intraalveolar macrophages. These lung cells are known to be involved in the metabolism of the pulmonary surfactant which serves to reduce the surface tension within alveoli. The size of the alveolar cells type II was conspicuously increased in the treated lungs. Compared to controls, intraalveolar macrophages apparently were slightly more numerous. Their enlarged cytoplasm was strongly vacuolated. The osmiophilic lamellar bodies within alveolar cells type II represent the intracellular presecretory pulmonary surfactant. Their number per individual alveolar cell type II was estimated by means of light microscopic morphometry on Epon-embedded semithin sections. Compared to control lungs, the number was increased by about 30% in rats treated with clofibrate (11.4 ± 0.5 lamellar inclusions in the control cells; P < 0.001). The increase in the number of lamellar bodies per type II cell was close to 60% in animals fed the nafenopin diet. In contrast the frequency of alveolar cells type II, estimated per area of lung tissue, remained unchanged. These results demonstrate that clofibrate and nafenopin, two drugs with hypolipidemic properties, cause identical structural changes in the rodent lung. It is concluded from these data that (i) the morphological changes observed in the surfactant metabolizing cells represent a specific action of hypolipidemic agents at the lungs and (ii) hypolipidemic peroxisome proliferators influence the metabolism of the pulmonary surfactant.

Identical structural changes induced in glycogen phosphorylase by two nonexclusive allosteric inhibitors

Identical structural changes induced in glycogen phosphorylase by two nonexclusive allosteric inhibitors