New insights into structural determinants of prion protein folding and stability

Prions are the etiological agent of fatal neurodegenerative diseases called prion diseases or transmissible spongiform encephalopathies. These maladies can be sporadic, genetic or infectious disorders. Prions are due to post-translational modifications of the cellular prion protein leading to the formation of a β-sheet enriched conformer with altered biochemical properties. The molecular events causing prion formation in sporadic prion diseases are still elusive. Recently, we published a research elucidating the contribution of major structural determinants and environmental factors in prion protein folding and stability. Our study highlighted the crucial role of octarepeats in stabilizing prion protein; the presence of a highly enthalpically stable intermediate state in prion-susceptible species; and the role of disulfide bridge in preserving native fold thus avoiding the misfolding to a β-sheet enriched isoform. Taking advantage from these findings, in this work we present new insights into structural determinants of prion protein folding and stability.     

Rooting strategy of naturally regenerated beech in Silver birch and Scots pine woodlands

This study investigated the belowground development and strategy of late-successional European beech (Fagus sylvatica L.) in ageing natural Scots pine (Pinus sylvestris L.) and Silver birch (Betula pendula Roth.) woodlands in a French volcanic mid-elevation area. For this purpose root biomass, root profile and fine-root architecture of competitor trees were examined in 53 mixed pine–beech and 42 birch–beech woodlands along a stand maturation gradient, using the root auger technique (0–75-cm). The total beech fine-root biomass highly correlated with aerial dimensions such as stem height and girth, whereas it moderately correlated with its age, thus indicating the effects of competition. Basic stand biometric data such as stand density and basal area had no significant effect on beech root biomass. Conversely, competition indices taking into account the vertical dimensions of competitor trees were efficient, probably due to redundancy with beech height. At similar age and height, beeches under birch had a greater belowground development than beeches under pine. Each species exhibited specific rooting pattern and plasticity of fine-root architecture along the gradients of stand maturation and competition. Beech had a heart-shaped rooting habit in both mixings, which strongly increased along stand maturation. Its fine-root system adopted a foraging strategy to respond to increasing stand competition. The Scots pine fine-root system was plate-like and showed a low morphological plasticity, thus presumably a conservative strategy. Silver birch exhibited a high biomass and a foraging capacity in the topsoil but a loose root system in the subsoil. The coexistence of pine and beech roots in the upper soil presumably leads to a high belowground competition. Beech root system becomes predominant throughout the soil profile and it adopts an efficient foraging strategy, but at the expense of its belowground development. Conversely, the niche partitioning strategy between beech and birch may explain why beech develops strongly belowground in spite of the fact that birch has a dense rooting and a competitive fine-root architecture. As a consequence, beech mid-term regeneration and development may be facilitated under birch as compared with pine.     

Quantifying and Understanding Voltage Losses Due to Nonradiative Recombination in Bulk Heterojunction Organic Solar Cells with Low Energetic Offsets

Open‐circuit voltage (V_OC) losses in organic photovoltaics (OPVs) inhibit devices from reaching V_OC values comparable to the bandgap of the donor–acceptor blend. Specifically, nonradiative recombination losses (?V_nr) are much greater in OPVs than in silicon or perovskite solar cells, yet the origins of this are not fully understood. To understand what makes a system have high or low loss, an investigation of the nonradiative recombination losses in a total of nine blend systems is carried out. An apparent relationship is observed between the relative domain purity of six blends and the degree of nonradiative recombination loss, where films exhibiting relatively less pure domains show lower ?V_nr than films with higher domain purity. Additionally, it is shown that when paired with a fullerene acceptor, polymer donors which have bulky backbone units to inhibit close π–π stacking exhibit lower nonradiative recombination losses than in blends where the polymer can pack more closely. This work reports a strategy that ensures ?V_nr can be measured accurately and reports key observations on the relationship between ?V_nr and properties of the donor/acceptor interface.     

A hidden aggregation‐prone structure in the heart of hypoxia inducible factor prolyl hydroxylase

Prolyl hydroxylase domain‐containing protein 2 (PHD2), as one of the most important regulators of angiogenesis and metastasis of cancer cells, is a promising target for cancer therapy drug design. Progressive studies imply that abnormality in PHD2 function may be due to misfolding. Therefore, study of the PHD2 unfolding pathway paves the way for a better understanding of the influence of PHD2 mutations and cancer cell metabolites on the protein folding pathway. We study the unfolding of the PHD2 catalytic domain using differential scanning calorimetry (DSC), fluorescence spectroscopy, and discrete molecular dynamics simulations (DMD). Using computational and experimental techniques, we find that PHD2 undergoes four transitions along the thermal unfolding pathway. To illustrate PHD2 unfolding events in atomic detail, we utilize DMD simulations. Analysis of computational results indicates an intermediate species in the PHD2 unfolding pathway that may enhance aggregation propensity, explaining mutation‐independent PHD2 malfunction. Proteins 2016; 84:611–623. © 2016 Wiley Periodicals, Inc.     

Two steps in the transition between the native and acid states of bovine α-lactalbumin detected by circular polarization of luminescence: Evidence for a premolten globule state?

A few studies indirectly support the existence of an intermediate in the transition of Ca(2+)-saturated bovine alpha-lactalbumin (alpha-LA) from the native (N) to the acidic (A) state, known as the molten globule state. However, direct experimental evidence for the appearance of this intermediate has not been obtained. The signal of circular polarization of luminescence (CPL) is sensitive to fine conformational transitions because of its susceptibility to changes in the environmental asymmetry of fluorescent chromophores in their excited electronic states. In the present study, CPL measurements were applied using the intrinsic tryptophan fluorescence of alpha-LA as well as the fluorescence of 8-anilino-1-naphthalenesulfonic acid (ANS) bound to alpha-LA. CPL of tryptophan and ANS was measured in the pH range of 2.5-6 in order to find direct experimental evidence for the proposed intermediate. CPL (characterized by the emission anisotropy factor, g(em)) depends on the asymmetry of the protein molecular structure in the environment of the tryptophan and the ANS chromophores in the excited electronic state. The pH dependence of both the gab, absorption anisotropy factor determined by CD, and the ANS steady state fluorescence, showed a single transition at pH 3-3.7 as already reported elsewhere. This transition was interpreted as being a result of a change of the alpha-LA tertiary structure, which resulted in a loss of asymmetry of the environment of both the tryptophan residues and the ANS hydrophobic binding sites. The pH dependence of the tryptophan and ANS g(em) showed an additional conformational transition at pH 4-5, which coincided with the pKa of Ca2+ dissociation (pKa 5), as predicted by Permyakov et al. (1981, Biochem Biophys Res Commun 100:191-197). The titration curve showed that there is a pH range between 3.7 and 4.1 in which alpha-LA exists in an intermediate state between the N- and A-state. We suggest that the intermediate is the premolten globule state characterized by a reduced Ca2+ binding to the alpha-LA, native-like tertiary structure, and reduced asymmetric fluctuation of the tertiary structure on the nanosecond time scale. This intermediate resembles the "critical activated state" theoretically deduced by Kuwajima et al. (1989, J Mol Biol 206:547-561). The present study demonstrates the power of CPL measurements for the investigation of folding/unfolding transitions in proteins.     

Subtidal macrozoobenthic community resilience to change following natural mouth breaching of the temporarily open/closed East Kleinemonde Estuary,South Africa

The East Kleinemonde Estuary, on the south-east coast of South Africa, typically opens for only short periods, usually <10 days. During a nine-month study in 2006, marine influence persisted for a near-continuous period of three months. This provided an opportunity to explore potential changes in the structure and pattern of the subtidal estuarine macrozoobenthic community. Salinity changes were minimal after mouth opening, decreasing by c. 4 and 8 in the lower and upper estuary, respectively. Salinity decrease was due to river dominance over tidal influence. Two biotic assemblages, structured by sediment characteristics, typified the community throughout the study: a sand-associated group near the mouth and a mud-associated group upstream. Amphipods were proportionally the most abundant group within each assemblage and on each sampling occasion. At the species level, high variability typified the community, with no trends or patterns observed. However, species richness declined from 27–30 to 23 after mouth opening. The number of species returned to former levels at the time of the final survey and just before final mouth closure. An analysis of the subtidal macrozoobenthos in the East Kleinemonde and other temporarily open/closed estuaries (TOCEs) of similar size in the bioregion indicated that communities were typically composed of relatively few, broadly tolerant euryhaline species with no species unique to TOCEs.     

Control of Photosystem II in spinach leaves by continuous light and by light pulses given in the dark

The light-induced induction of components of non-photochemical quenching of chlorophyll fluorescence which are distinguished by different rates of dark relaxation (qNf, rapidly relaxing and qNs, slowly relaxing or not relaxing at all in the presence brief saturating light pulses which interrupt darkness at low frequencies) was studied in leaves of spinach.After dark adaptation of the leaves, a fast relaxing component developed in low light only after a lag phase. Quenching increased towards a maximum with increasing photon flux density. This fast component of quenching was identified as energy-dependent quenching qE. It required formation of an appreciable transthylakoid pH and was insignificant when darkened spinach leaves received 1 s pulses of light every 30 s even though zeaxanthin was formed from violaxanthin under these conditions.Another quenching component termed qNs developed in low light without a lag phase. It was not dependent on a transthylakoid pH gradient, decayed exponentially with a long half time of relaxation and was about 20% of total quenching irrespective of light intensity. When darkened leaves were flashed at frequencies higher than 0.004 Hz with 1 s light pulses, this quenching also appeared. Its extent was very considerable, and it did not require formation of zeaxanthin. Relaxation was accelerated by far-red light, and this acceleration was abolished by NaF.We suggest that qNs is the result of a so-called state transition, in which LHC II moves after its phosphorylation from fluorescent PS II to nonfluorescent PS I. This state transition was capable of decreasing in darkened leaves the potential maximum quantum efficiency of electron flow through Photosystem II by about 20%.Abbreviations PFD photon flux density - PS photosystem