Characterization of early and late transition states of the folding pathway of a SH2 domain

Albeit SH2 domains are abundant protein–protein interaction modules with fundamental roles in the regulation of several physiological and molecular pathways in the cell, the available information about the determinants of their thermodynamic stability and folding properties are still very limited. In this work, we provide a quantitative characterization of the folding pathway of the C‐terminal SH2 domain of SHP2, conducted through a combination of site‐directed mutagenesis and kinetic (un)folding experiments (Φ‐value analysis). The energetic profile of the folding reaction of the C‐SH2 domain is described by a three‐state mechanism characterized by the presence of two transition states and a high‐energy intermediate. The production of 29 site‐directed variants allowed us to calculate the degree of native‐like interactions occurring in the early and late events of the folding reaction. Data analysis highlights the presence of a hydrophobic folding nucleus surrounded by a lower degree of structure in the early events of folding, further consolidated as the reaction proceeds towards the native state. Interestingly, residues physically located in the functional region of the domain reported unusual Φ‐values, a hallmark of the presence of transient misfolding. We compared our results with previous ones obtained for the N‐terminal SH2 domain of SHP2. Notably, a conserved complex folding mechanism implying the presence of a folding intermediate arise from comparison, and the relative stability of such intermediate appears to be highly sequence dependent. Data are discussed under the light of previous works on SH2 domains.     

Nitrogen deposition outweighs climatic variability in driving annual growth rate of canopy beech trees: Evidence from long‐term growth reconstruction across a geographic gradient

In this study, we investigated the role of climatic variability and atmospheric nitrogen deposition in driving long‐term tree growth in canopy beech trees along a geographic gradient in the montane belt of the Italian peninsula, from the Alps to the southern Apennines. We sampled dominant trees at different developmental stages (from young to mature tree cohorts, with tree ages spanning from 35 to 160 years) and used stem analysis to infer historic reconstruction of tree volume and dominant height. Annual growth volume (G_V) and height (G_H) variability were related to annual variability in model simulated atmospheric nitrogen deposition and site‐specific climatic variables, (i.e. mean annual temperature, total annual precipitation, mean growing period temperature, total growing period precipitation, and standard precipitation evapotranspiration index) and atmospheric CO₂ concentration, including tree cambial age among growth predictors. Generalized additive models (GAM), linear mixed‐effects models (LMM), and Bayesian regression models (BRM) were independently employed to assess explanatory variables. The main results from our study were as follows: (i) tree age was the main explanatory variable for long‐term growth variability; (ii) GAM, LMM, and BRM results consistently indicated climatic variables and CO₂ effects on G_V and G_H were weak, therefore evidence of recent climatic variability influence on beech annual growth rates was limited in the montane belt of the Italian peninsula; (iii) instead, significant positive nitrogen deposition (N_dep) effects were repeatedly observed in G_V and G_H; the positive effects of N_dep on canopy height growth rates, which tended to level off at N_dep values greater than approximately 1.0 g m^?2 y^?1, were interpreted as positive impacts on forest stand above‐ground net productivity at the selected study sites.     

Deoxynivalenol and 3-acetyldeoxynivalenol — mycotoxins associated with wheat head fusariosis in Poland

Samples of wheat naturally infected in the field byFusarium culmorum (W.G.Sm.) Sacc. andFusarium graminearum Schwabe were analyzed for deoxynivalenol, 3-acetyldeoxynivalenol, and zearalenone. No zearalenone was detected at levels higher than 0.5mg/kg. Deoxynivalenol was present in 100% and 3-acetyldeoxynivalenol in 80% of the examined samples at levels of 0.21 to 30.4 mg/kg and 0.54 to 29.54 mg/kg, respectively. The mycotoxin levels in the chaff were 5 to 50 times higher than in the kernels. This is the first report on natural occurrence of 3-acetyldeoxynivalenol in wheat. This toxin, in addition to deoxynivalenol, was highly correlated with wheat head fusariosis. These findings suggest that more attention should be given to the occurrence of 3-acetyldeoxynivalenol in cereal grains during the growth as well as during storage.     

Variations in total ozone column and biologically effective solar UV exposure doses in Bologna, Italy during the period 2005–2010

Variations in total ozone column and sun exposures able to cause erythema and damage the DNA molecules were observed by the narrow-band filter radiometer UV-RAD in Bologna, Italy from 2005 to 2010. The ozone columns determined from the UV-RAD measurements were found to be close to those provided by the satellite Ozone Monitoring Instrument (OMI) showing an average discrepancy of 1 % with standard deviation of ± 6 %. Analysis of the data highlights a well-marked annual cycle of the ozone column variations while the oscillations with periods of 8, 18 and 34 months present much smaller amplitudes. The influence of the frequency of solar irradiance measurements on the accuracy of the evaluated daily exposure dose has been studied and it was found that time intervals no longer than 5–10 min between the measurements of erythema and DNA damage effective UV irradiances provide a satisfactory assessment of the corresponding daily exposures. The latter do not present significant year-to-year variations for the period under study, while their annual distributions show slight changes likely due to the specific cloud cover and ozone column variability for different years. The annual erythemal exposure dose for 2007–2010 varied between 603.7 and 638.1 kJ?m^?2, while the corresponding sun exposure affecting DNA changed from 6.38 to 7.91 kJ?m^?2.     

A Flexible Docking Scheme Efficiently Captures the Energetics of Glycan-Cyanovirin Binding

Cyanovirin-N (CVN), a cyanobacterial lectin, exemplifies a class of antiviral agents that inhibit HIV by binding to the highly glycosylated envelope protein gp120. Here, we investigate the energetics of glycan recognition using a computationally inexpensive flexible docking approach, backbone perturbation docking (BP-Dock). We benchmarked our method using two mutants of CVN: P51G-m4-CVN, which binds dimannose with high affinity through domain B, and CVN^(mutDB), in which binding to domain B has been abolished through mutation of five polar residues to small nonpolar side chains. We investigated the energetic contribution of these polar residues along with the additional position 53 by docking dimannose to single-point CVN mutant models. Analysis of the docking simulations indicated that the E41A/G and T57A mutations led to a significant decrease in binding energy scores due to rearrangements of the hydrogen-bond network that reverberated throughout the binding cavity. N42A decreased the binding score to a level comparable to that of CVN^(mutDB) by affecting the integrity of the local protein structure. In contrast, N53S resulted in a high binding energy score, similar to P51G-m4-CVN. Experimental characterization of the five mutants by NMR spectroscopy confirmed the binding affinity pattern predicted by BP-Dock. Despite their mostly conserved fold and stability, E41A, E41G, and T57A displayed dissociation constants in the millimolar range. N53S showed a binding constant in the low micromolar range, similar to that observed for P51G-m4-CVN. No binding was observed for N42A. Our results show that BP-Dock is a useful tool for rapidly screening the relative binding affinity pattern of in silico-designed mutants compared with wild-type, supporting its use to design novel mutants with enhanced binding properties.     

Effect of an intervention to improve the cardiovascular health of family members of patients with coronary artery disease: a randomized trial

Background:

Family members of patients with coronary artery disease (CAD) have higher risk of vascular events. We conducted a trial to determine if a family heart-health intervention could reduce their risk of CAD.

Methods:

We assessed coronary risk factors and randomized 426 family members of patients with CAD to a family heart-health intervention (n = 211) or control (n = 215). The intervention included feedback about risk factors, assistance with goal setting and counselling from health educators for 12 months. Reports were sent to the primary care physicians of patients whose lipid levels and blood pressure exceeded threshold values. All participants received printed materials about smoking cessation, healthy eating, weight management and physical activity; the control group received only these materials. The main outcomes (ratio of total cholesterol to high-density lipoprotein [HDL] cholesterol; physical activity; fruit and vegetable consumption) were assessed at 3 and 12 months. We examined group and time effects using mixed models analyses with the baseline values as covariates. The secondary outcomes were plasma lipid levels (total cholesterol, low-density lipoprotein cholesterol, HDL cholesterol and triglycerides); glucose level; blood pressure; smoking status; waist circumference; body mass index; and the use of blood pressure, lipid-lowering and smoking cessation medications.

Results:

We found no effect of the intervention on the ratio of total cholesterol to HDL cholesterol. However, participants in the intervention group reported consuming more fruit and vegetables (1.2 servings per day more after 3 mo and 0.8 servings at 12 mo; p < 0.001). There was a significant group by time interaction for physical activity (p = 0.03). At 3 months, those in the intervention group reported 65.8 more minutes of physical activity per week (95% confidence interval [CI] 47.0–84.7 min). At 12 months, participants in the intervention group reported 23.9 more minutes each week (95% CI 3.9–44.0 min).

Interpretation:

A health educator–led heart-health intervention did not improve the ratio of total cholesterol to HDL cholesterol but did increase reported physical activity and fruit and vegetable consumption among family members of patients with CAD. Hospitalization of a spouse, sibling or parent is an opportunity to improve cardiovascular health among other family members. Trial registration: clinicaltrials.gov, no {"type":"clinical-trial","attrs":{"text":"NCT00552591","term_id":"NCT00552591"}}NCT00552591.People with a family history of coronary artery disease (CAD) among their first-degree relatives have an increased risk of vascular events.^1–5 This risk is greater if more than 1 relative has heart disease, or if the onset of disease in relatives occurred before age 55.^1–3,5 A concordance of coronary risk factors between patients with heart disease and their spouses has also been reported.^6–10 Although genetic factors are important, familial aggregation of coronary risk factors also plays a role.^9,11,12 Guidelines recommend screening individuals with a positive family history,^13–15 but screening rates are low (< 15%), and interventions are rarely initiated.^16,17 Family members of patients with heart disease may benefit from focused interventions to improve cardiovascular health. Counselling that address physical inactivity and dietary behaviours is central to these interventions; clinical management of risk factors such as tobacco addiction, dyslipidemia, hypertension and dysglycemia are also important. We developed and evaluated a year-long family-based heart-health intervention for the siblings, offspring and spouses of patients admitted to hospital with an acute coronary event.