Structural Origins of Misfolding Propensity in the Platelet Adhesive Von Willebrand Factor A1 Domain

AbstractThe von Willebrand factor (VWF) A1 and A3 domains are structurally isomorphic yet exhibit distinct mechanisms of unfolding. The A1 domain, responsible for platelet adhesion to VWF in hemostasis, unfolds through a molten globule intermediate in an apparent three-state mechanism, while A3 unfolds by a classical two-state mechanism. Inspection of the sequences or structures alone does not elucidate the source of this thermodynamic conundrum; however, the three-state character of the A1 domain suggests that it has more than one cooperative substructure yielding two separate unfolding transitions not present in A3. We investigate the extent to which structural elements contributing to intermediate conformations can be identified using a residue-specific implementation of the structure-energy-equivalence-of-domains algorithm (SEED), which parses proteins of known structure into their constituent thermodynamically cooperative components using protein-group-specific, transfer free energies. The structural elements computed to contribute to the non-two-state character coincide with regions where Von Willebrand disease mutations induce misfolded molten globule conformations of the A1 domain. This suggests a mechanism for the regulation of rheological platelet adhesion to A1 based on cooperative flexibility of the α2 and α3 helices flanking the platelet GPIbα receptor binding interface

Low pH immobilizes and kills human leukocytes and prevents transmission of cell-associated HIV in a mouse model

BACKGROUND: Both cell-associated and cell-free HIV virions are present in semen and cervical secretions of HIV-infected individuals. Thus, topical microbicides may need to inactivate both cell-associated and cell-free HIV to prevent sexual transmission of HIV/AIDS. To determine if the mild acidity of the healthy vagina and acid buffering microbicides would prevent transmission by HIV-infected leukocytes, we measured the effect of pH on leukocyte motility, viability and intracellular pH and tested the ability of an acidic buffering microbicide (BufferGel(®)) to prevent the transmission of cell-associated HIV in a HuPBL-SCID mouse model. METHODS: Human lymphocyte, monocyte, and macrophage motilities were measured as a function of time and pH using various acidifying agents. Lymphocyte and macrophage motilities were measured using video microscopy. Monocyte motility was measured using video microscopy and chemotactic chambers. Peripheral blood mononuclear cell (PBMC) viability and intracellular pH were determined as a function of time and pH using fluorescent dyes. HuPBL-SCID mice were pretreated with BufferGel, saline, or a control gel and challenged with HIV-1-infected human PBMCs. RESULTS: Progressive motility was completely abolished in all cell types between pH 5.5 and 6.0. Concomitantly, at and below pH 5.5, the intracellular pH of PBMCs dropped precipitously to match the extracellular medium and did not recover. After acidification with hydrochloric acid to pH 4.5 for 60 min, although completely immotile, 58% of PBMCs excluded ethidium homodimer-1 (dead-cell dye). In contrast, when acidified to this pH with BufferGel, a microbicide designed to maintain vaginal acidity in the presence of semen, only 4% excluded dye at 10 min and none excluded dye after 30 min. BufferGel significantly reduced transmission of HIV-1 in HuPBL-SCID mice (1 of 12 infected) compared to saline (12 of 12 infected) and a control gel (5 of 7 infected). CONCLUSION: These results suggest that physiologic or microbicide-induced acid immobilization and killing of infected white blood cells may be effective in preventing sexual transmission of cell-associated HIV

TRY plant trait database – enhanced coverage and open access

Plant traits - the morphological, anatomical, physiological, biochemical and phenological characteristics of plants - determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait‐based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits - almost complete coverage for ‘plant growth form’. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait–environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives

Floral odors and the interaction between pollinating Ceratopogonid midges and Cacao

Most plant species depend upon insect pollination services, including many cash and subsistence crops. Plants compete to attract those insects using visual cues and floral odor which pollinators associate with a reward. The cacao tree, Theobroma cacao, has a highly specialized floral morphology permitting pollination primarily by Ceratopogonid midges. However, these insects do not depend upon cacao flowers for their life cycle, and can use other sugar sources. To understand how floral cues mediate pollination in cacao we developed a method for rearing Ceratopogonidae through several complete lifecycles to provide material for bioassays. We carried out collection and analysis of cacao floral volatiles, and identified a bouquet made up exclusively of saturated and unsaturated, straight-chain hydrocarbons, which is unusual among floral odors. The most abundant components were tridecane, pentadecane, (Z)-7-pentadecene and (Z)-8-heptadecene with a heptadecadiene and heptadecatriene as minor components. We presented adult midges, Forcipomyia sp. (subgen. Forcipomyia), Culicoides paraensis and Dasyhelea borgmeieri, with natural and synthetic cacao flower odors in choice assays. Midges showed weak attraction to the complete natural floral odor in the assay, with no significant evidence of interspecific differences. This suggests that cacao floral volatiles play a role in pollinator behavior. Midges were not attracted to a synthetic blend of the above four major components of cacao flower odor, indicating that a more complete blend is required for attraction. Our findings indicate that cacao pollination is likely facilitated by the volatile blend released by flowers, and that the system involves a generalized odor response common to different species of Ceratopogonidae

Structural and Energetic Characterization of the Denatured State from the Perspectives of Peptides, the Coil Library, and Intrinsically Disordered Proteins

The α and polyproline II (PPII) basins are the two most populated regions of the Ramachandran map when constructed from the protein coil library, a widely used denatured state model built from the segments of irregular structure found in the Protein Data Bank. This indicates the α and PPII conformations are dominant components of the ensembles of denatured structures that exist in solution for biological proteins, an observation supported in part by structural studies of short, and thus unfolded, peptides. Although intrinsic conformational propensities have been determined experimentally for the common amino acids in short peptides, and estimated from surveys of the protein coil library, the ability of these intrinsic conformational propensities to quantitatively reproduce structural behavior in intrinsically disordered proteins (IDPs), an increasingly important class of proteins in cell function, has thus far proven elusive to establish. Recently, we demonstrated that the sequence dependence of the mean hydrodynamic size of IDPs in water and the impact of heat on the coil dimensions, provide access to both the sequence dependence and thermodynamic energies that are associated with biases for the α and PPII backbone conformations. Here, we compare results from peptide-based studies of intrinsic conformational propensities and surveys of the protein coil library to those of the sequence-based analysis of heat effects on IDP hydrodynamic size, showing that a common structural and thermodynamic description of the protein denatured state is obtained

Dietary intakes of children with Crohn\u27s disease

Approximately 25 % of individuals with Crohn\u27s disease (CD), a life-long relapsing-remitting disease, are diagnosed during childhood and adolescence. Symptoms of CD, including abdominal pain, nausea and diarrhoea, can lead to reduced food intake, which may negatively have an impact on nutritional status during this critical period of growth and development. The aims of the present study were to assess the growth and adequacy of dietary intakes of children with CD at Sydney Children\u27s Hospital, Randwick, and compare with healthy controls. Sixty-three subjects aged 10–16 years were recruited, including: children with active CD (n 18), children with CD in remission (n 23) and healthy controls (n 22). Dietary intake was assessed using a FFQ and compared with current Australian recommended dietary intakes (RDI). Growth and dietary intakes were compared between groups. Subjects with active CD had lower weight and BMI Z scores than children in remission and controls. The energy intakes of children with active CD and those in remission were significantly lower than estimated energy requirements (P = 0·001 and P = 0·03 respectively). Children with active CD did not meet the RDI for Fe and their Ca intake was lower than the RDI (P = 0·04). In conclusion, the dietary intake of children with active CD was impaired, with inadequate intakes of energy, Ca and Fe. Reduced energy intakes during active disease may contribute to poor weight gain and impaired growth. Quantifying nutrient intake and ascertaining requirements for nutritional supplementation are essential components of successful management in paediatric CD

Hydrodynamic Radii of Intrinsically Disordered Proteins Determined from Experimental Polyproline II Propensities

<div><p>The properties of disordered proteins are thought to depend on intrinsic conformational propensities for polyproline II (<i>PP</i>_<i>II</i>) structure. While intrinsic <i>PP</i>_<i>II</i> propensities have been measured for the common biological amino acids in short peptides, the ability of these experimentally determined propensities to quantitatively reproduce structural behavior in intrinsically disordered proteins (IDPs) has not been established. Presented here are results from molecular simulations of disordered proteins showing that the hydrodynamic radius (<i>R</i>_<i>h</i>) can be predicted from experimental <i>PP</i>_<i>II</i> propensities with good agreement, even when charge-based considerations are omitted. The simulations demonstrate that <i>R</i>_<i>h</i> and chain propensity for <i>PP</i>_<i>II</i> structure are linked via a simple power-law scaling relationship, which was tested using the experimental <i>R</i>_<i>h</i> of 22 IDPs covering a wide range of peptide lengths, net charge, and sequence composition. Charge effects on <i>R</i>_<i>h</i> were found to be generally weak when compared to <i>PP</i>_<i>II</i> effects on <i>R</i>_<i>h</i>. Results from this study indicate that the hydrodynamic dimensions of IDPs are evidence of considerable sequence-dependent backbone propensities for <i>PP</i>_<i>II</i> structure that qualitatively, if not quantitatively, match conformational propensities measured in peptides.</p></div

Correlation of normalized error in predicted <i>R</i>_<i>h</i> to <i>N</i> and net charge density.

<p>Normalized error and net charge density were calculated for each IDP using Eqs <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004686#pcbi.1004686.e007" target="_blank">(7)</a> and <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004686#pcbi.1004686.e008" target="_blank">(8)</a>, respectively. In both panels, red triangles show normalized error from <i>R</i>_<i>h</i> predicted using the Kallenbach reported propensities, blue squares from Creamer reported propensities, open circles from Hilser reported propensities, black dots from the composite propensity scale, and X is the null model. Lines are linear fits to the five prediction sets colored as the symbols (Kallenbach scale was red; Creamer was blue, Hilser was stippled black, composite was solid black, and null was dotted black).</p