Molecular insights into the mechanisms of cation-type specific stability and denaturation of poly-l-glutamate: a simulation study

Cation-induced conformational changes of peptide as a guide to developing insights into human diseases-related proteins have received a lot of attention. The interactions between poly-l-glutamate (PGA) and different cations, including Na⁺, K⁺ and Mg²⁺, respectively, are studied in solvent at a concentration of 1 M, and the behaviours of peptide with different cations are investigated. For Na⁺, an oscillatory stabilising process to α-helix PGA is found, in accordance with the uniform free-energy landscape, whereas for K⁺, an extended α-helix structure is formed by the terminal turns, suggesting a weaker attraction to charged head groups. For Mg²⁺, the bridged charged side chains are responsible for the maximum probability of helix state. These distinct structural changes can be attributed to the different interactions between charged head groups and cations. Both Na⁺ and K⁺ are mainly attracted around head groups by direct ion binding while Mg²⁺ is centrally trapped among adjacent charged head groups. In addition, a surprising shift of the backbone hydrogen bond, from intact state to intermediate state, is observed. This is opposite to the stabilising effect of Na⁺ around negatively charged head groups.     

Ultrafast molecular dynamics of biofuel extraction for microalgae and bacteria milking: blocking membrane folding pathways to damaged lipid-bilayer conformations with nanomicelles

Cell milking is a 100% renewable green energy for CO₂ by extraction of biofuels inside the cytosol of photosynthetic micro-organisms as microalgae and bacteria. The cells are exposed to a hydrophobic solvent forming holes and cracks through their membranes from which the biofuels can leak out. In protein folding, the goal would be to find pathways to the unique functional protein conformer. However, in the lipid-bilayer interaction with the solvent for milking, the objective is to block the pathways for damaged membrane conformations of low free energy with undesired nanostructures, using the solvent properties, as shown with an ab initio structural bioinformatic model. Statistical thermodynamics is used to compute the free energy (including entropy) from the molecular dynamics trajectory of the biomolecular system with many conformational changes. This model can be extended to the general problem of biomolecules folding as for proteins and nucleic acids. Using an adaptation of the Einstein diffusion law, the conformational change dynamics of the lipid bilayer depends on the two diffusion coefficients of the solvent: D₁ before the irreversible folding transition time and the much smaller D₂ thereafter. In contrast to the n-hexane and n-heptane hydrocarbons of smaller size, the residual D₂?=?4.7?×?10^?7?cm²/s of the n-decane solvent, with the highest partition coefficient among the three extractors, is the only to present a D₂ value that is significantly below the critical threshold of 10^?6?cm²/s. Therefore, the membrane would resist to long hydrocarbons and the exposed cells would remain viable for milking.     

Studying the collective motions of the adenosine A2A receptor as a result of ligand binding using principal component analysis

Abstract

Adenosine receptors (ARs) belong to family A of GPCRs that are involved in many diseases, including cerebral and cardiac ischemic diseases, immune and inflammatory disorders, etc. Thus, they represent important therapeutic targets to treat these conditions. Computational techniques such as molecular dynamics (MD) simulations permit researchers to obtain structural information about these proteins, and principal component analysis (PCA) allows for the identification of collective motions. There are available structures for the active form (3QAK) and the inactive form (3EML) of A2AR which permit us to gain insight about their activation/inactivation mechanism. In this work, we have proposed an inverse strategy using MD simulations where the active form was coupled to the antagonist caffeine and the inactive form was coupled to adenosine agonist. Moreover, we have included four reported thermostabilizing mutations in the inactive form to study A2AR structural differences under different conditions. Some observations stand out from the PCA studies. For instance, the apo structures showed remarkable similarities, and the principal components (PCs) were rearranged in a ligand-dependent manner. Additionally, the active conformation was less stable compared to the inactive one. Some PCs inverted their direction in the presence of a ligand, and comparison of the PCs between 3EML and 3EML_ADN showed that adenosine induced major changes in the structure of A2AR. Rearrangement of PCs precedes and drives conformational changes that occur after ligand binding. Knowledge about these conformational changes provides important insights about the activity of A2AR.     

Computational study of conformational changes in human 3-hydroxy-3-methylglutaryl coenzyme reductase induced by substrate binding

Abstract

The enzyme 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR) is mainly involved in the regulation of cholesterol biosynthesis. HMGR catalyses the reduction of 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) to mevalonate at the expense of two NADPH molecules in a two-step reversible reaction. In the present study, we constructed a model of human HMGR (hHMGR) to explore the conformational changes of HMGR in complex with HMG-CoA and NADPH. In addition, we analysed the complete sequence of the Flap domain using molecular dynamics (MD) simulations and principal component analysis (PCA). The simulations revealed that the Flap domain plays an important role in catalytic site activation and substrate binding. The apo form of hHMGR remained in an open state, while a substrate-induced closure of the Flap domain was observed for holo hHMGR. Our study also demonstrated that the phosphorylation of Ser872 induces significant conformational changes in the Flap domain that lead to a complete closure of the active site, suggesting three principal conformations for the first stage of hHMGR catalysis. Our results were consistent with previous proposed models for the catalytic mechanism of hHMGR.

Communicated by Ramaswamy H. Sarma     

The effect of immersion cleansers on gloss,colour and sorption of acetal denture base material

doi: 10.1111/j.1741‐2358.2012.00657.x The effect of immersion cleansers on gloss, colour and sorption of acetal denture base material Objective: To study the effect of peroxide and hypochlorite cleansers on gloss, colour and sorption of acetal denture resins. Materials and methods: Pink acetal and thermoplastic acrylic resins were evaluated. Thirty‐five specimens 39 × 39 × 1.8 mm of each resin were prepared. Each group of specimens (n = 7) was then immersed into cleansers for 100 days. Group I immersed in tap water, Group II in Corega Extradent for 5 min, Group III in Corega Extradent for 8 h, Group IV in NitrAdine? Seniors for 15 min and Group V in NaOCl 5.25%. Gloss, colour and weight measurements were taken initially and after 100 days. Data subjected to two‐way anova and Tukey’s test at α = 0.05. Results: Acrylic resin showed reductions of glossiness from ?5 to ?15 and acetal from ?0.2 to ?6. Colour changes (ΔΕ*) ranged from 2.64 to 7.64 for acrylic and 2.77 to 26.54 for acetal resin. Sorption for acrylic ranged from 11.64 to 17.06 μg/mm³ and 9.18 to 24.79 μg/mm³ for acetal resin. The results of (ΔΕ*) and sorption showed an interaction between denture resins and cleansers. Conclusions: The gloss of acetal resin was less affected by water, peroxides and NaOCl 5.25% compared with acrylic resin. Acetal resin showed clinically acceptable (ΔΕ*) whereas acrylic resin unacceptable ones for water and peroxide solutions. The immersion of acetal resin in NaOCl 5.25% showed clinically unacceptable (ΔΕ*) and higher sorption and should be avoided or should be managed with care.     

Diurnal and seasonal changes in semen quality of men in subfertile partnerships

ABSTRACT

Circadian and circannual rhythms influence not only the environment, but also human physiology. In times of increasing numbers of couples struggling with infertility, and thus increasing demand for successful assisted reproduction, the aim of our study was to evaluate circadian and circannual rhythms and their association with semen quality. A total of 12 245 semen samples from 7068 men, collected at the andrology laboratory of the Department of Reproductive Endocrinology, University Hospital Zurich, between 1994 and 2015, were uniformly analysed in terms of sperm concentration, total sperm count, progressive motility and normal morphology. On the basis of these four parameters, we retrospectively examined the circadian and circannual changes of semen quality. The Mann–Whitney U test and multiple linear regression analysis were used for the statistical evaluation. The semen samples collected in the early morning before 7:30 a.m. showed the highest levels in sperm concentration, total sperm count and normal morphology, all with statistical significance. Progressive motility did not show any significant alterations based on circadian rhythm. Furthermore, a significant increase in sperm concentration and total sperm count was found in spring, with significant decreases in the summer. The highest percentage of normal morphology was found in summer. For progressive motility, no significant seasonal variation could be demonstrated. Male semen quality varies with both circadian and circannual rhythms. Collection of semen in the early morning, where semen quality was highest, can be used to improve natural fertility as well as fertility resulting from assisted reproduction.     

Rest-activity rhythms characteristics and seasonal changes in seasonal affective disorder

ABSTRACT

Identifying objectively measurable seasonal changes in 24-h activity patterns (rest-activity rhythms or RARs) that occur in seasonal affective disorder (SAD) could help guide research and practice towards new monitoring tools or prevention targets. We quantified RARs from actigraphy data using non-parametric and extended cosine based approaches, then compared RARs between people with SAD and healthy controls in the summer (n = 70) and winter seasons (n = 84). We also characterized the within-person seasonal RAR changes that occurred in the SAD (n = 19) and control (n = 26) participants who contributed repeated measures. Only controls had significant winter increases in RAR fragmentation (intra-daily variability; in controls mean winter-summer changes (log scale) = 0.05, 0.21 standard deviation, p = 0.03). In SAD participants only, estimated evening settling times (down-mesor) were an average of 30 min earlier in the winter compared with the summer (1-h standard deviation, p = 0.045). These RAR characteristics correlated with greater fatigue (Spearman r = 0.36) but not depression symptom severity. Additional research is needed to ascertain why healthy controls, but not people with SAD, appear to have increased RAR fragmentation in the winter. People with SAD lacked this increase in RAR fragmentation, and instead had earlier evening setting in the winter. Prospective and intervention studies with greater temporal resolution are warranted to ascertain how these seasonal behavioral differences relate to fatigue pathophysiology in SAD. Future research is needed to determine whether extending the winter active period, even in relatively fragmented bouts, could help reduce the fatigue symptoms common in SAD.     

METAMORPHOSIS OF THE LARVA OF THE POLYCHAETE ARENICOLA CRISTATA. MORPHOLOGY OF THE ‘HOUR-GLASS’ STAGE

The constricted ‘waist’ of the metamorphosing larva of the polychaete Arenicola cristata is described, using light and electron microscopy. The constriction is shown to be the consequence of the discharge and collapse of a post-trochal ring of epithelial cells which remain as functional components of the post-metamorphic juvenile. Morphological differentiation of neuro-effector and interneuronal contacts is initiated at this time. Muscular and neural changes are discussed in terms of their role in effecting metamorphosis.     

Wild plants eaten in childhood: a retrospective of Estonia in the 1970s–1990s

In this ethnobotanical study, the authors provide the first quantitative analysis of the use of wild edible plants in Estonia, describing the domains and assessing the food importance of different species. The information was collected using free‐listing written questionnaires and concerned plants used by the respondents in their childhood. As part of a major study, this article covers the responses of professionals with some botanical education at vocational or university level, to ensure the greatest possible reliability without using voucher specimens. Fifty‐eight respondents provided information on the use of 137 plant taxa, corresponding to approximately 6% of the native and naturalized vascular plants of Estonia. According to use frequency, the most typical wild food plant of Estonia is a fruit, eaten raw as a snack. The results clearly signal that the majority of famine and food shortage plants had already been forgotten by the end of the 20^th century, but new plants have been introduced as green vegetables for making salads. Despite changes in the nomenclature of the plants, the use of wild food plants in Estonia was still thriving at the turn of the 20^th century, covering many domains already forgotten in urbanized modern Europe. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 172 , 239–253.