Simulation of protein misfolding using a lattice model

The structure of the tightly bound complex of the globular myosin head with F-actin is the key to understanding important details of the mechanism of how the actin-myosin motor functions. The current notion on this complex is based on the docking of known atomic structures of constituent proteins into low-resolution electron-density maps. The atomic structure of the complex was refined by the molecular mechanics method, which consists in minimizing the energy of molecular interaction and which makes it possible to optimize not only the relative position of protein backbones as rigid bodies, but also the position of side chains on the protein interface. The structure calculated using ICM-Pro software, on the one hand, is close to the model obtained using electron microscopy; on the other hand, it ensures the best calculated interaction energy and accounts for the results of mutagenesis experiments. On the basis of the structure obtained, we can suggest the molecular mechanisms underlying the actin-activated release of ATP hydrolysis products from myosin and the decrease in the affinity of myosin for actin upon binding of nucleotides.     

White-rot fungal conversion of wheat straw to energy rich cattle feed

In order to improve the digestibility and nutrient availability in rumen, wheat straw was subjected to solid state fermentation (SSF) with white-rot fungi (i.e. Pleurotus ostreatus and Trametes versicolor) and the fermented biomass (called myco-straw) was evaluated for biochemical, enzymatic and nutritional parameters. The fungal treatment after 30 days led to significant decrease (P < 0.05) in cell wall constituents viz, acid detergent fiber (ADF), neutral detergent fiber (NDF), hemicellulose, lignin and cellulose to the extent of 35.00, 38.88, 45.00, 37.48 and 37.86%, respectively in P. ostreatus fermented straw, while 30.04, 33.85, 39.90, 31.29 and 34.00%, respectively in T. versicolor fermented straw. However, maximum efficiency of fermentation in terms of low carbohydrate consumption per unit of lignin degradation, favoring cattle feed production was observed for P. ostreatus on the 10th day (17.12%) as compared with T. versicolor on the 30th day (16.91%). The myco-straw was found to contain significantly high (P < 0.05) crude protein (CP; 4.77% T. versicolor, 5.08% P. ostreatus) as compared to control straw (3.37%). Metabolizable energy (ME, MJ/kg DM), percent organic matter digestibility (OMD) and short chain fatty acids (SCFAs; mmol) production also increased considerably from control straw (4.40, 29.91 and 0.292) to a maximum up to P. ostreatus fermented straw (4.92, 33.39 and 0.376 on 20th day) and T. versicolor fermented straw (4.66, 31.74 and 0.334 on 10th day), respectively. Moreover, the myco-straw had lower organic carbon and was rich in nitrogen with lower C/N ratio as compared to control wheat straw. Results suggest that the fungal fermentation of wheat straw effectively improved CP content, OM digestibility, SCFAs production, ME value and simultaneously lowered the C/N ratio, thus showing potential for bioconversion of lignin rich wheat straw into high energy cattle feed.     

Cr(VI) Imposed Toxicity in Maize Seedlings Assessed in Terms of Disruption in Carbohydrate Metabolism

The present study examined the toxic effects of Cr(VI; 100, 250 and 500 μM) in maize seedlings by investigating the changes in carbohydrate metabolism after 48, 96, and 144 h of exposure. Cr-stress results in severe alterations in the contents of carbohydrates and reducing sugars and the activities of carbohydrate metabolizing enzymes, amylases, phosphatases and phosphorylases, and invertases in maize seedlings. Under Cr stress, the contents of carbohydrates and reducing sugars declined in roots, whereas an increase was noticed in leaves. The catalytic activity of carbohydrate metabolizing enzymes, except invertases, in roots declined in the presence of Cr(VI) in a concentration- and exposure time-dependent manner. In contrast, the activities of these enzymes were enhanced in leaves under Cr(VI) stress. The activity of invertases increased with increasing amount of Cr(VI) but declined with an increase in the time interval. In conclusion, our results show that carbohydrate metabolism is severely affected under Cr(VI) toxicity. The study suggests that Cr-induced perturbations in the carbohydrate metabolism are one of the factors resulting in growth inhibition under Cr(VI) stress.     

Graphical representation of the salient conformational features of protein residues.

A composite plot for depicting in two dimensions the conformation and the secondary structural features of protein residues has been developed. Instead of presenting the exact values of the main- and side-chain torsion angles (φ, psi and chi(1)), it indicates the region in the three-dimensional conformational space to which a residue belongs. Other structural aspects, like the presence of a cis peptide bond and disulfide linkages, are also displayed. The plot may be used to recognize patterns in the backbone and side-chain conformation along a polypeptide chain and to compare protein structures derived from X-ray crystallography, NMR spectroscopy or molecular modelling studies and also to highlight the effect of mutation on structure.     

Effect of ruthenium red upon Ca2+ and Mn2+ uptake in Saccharomyces cerevisiae. Comparison with the effect of La3+

The initial rate of both Ca2+ and Mn2+ uptake is inhibited by ruthenium red to about the same extent as by equivalent concentrations of La3+. The inhibition of Ca2+ uptake, however, is relieved during further incubation with ruthenium red. On preincubating the cells with ruthenium red even a stimulation of divalent cation uptake can be found. Relieve of the inhibition of divalent cation uptake is accompanied by K+ efflux. Both ruthenium red and La3+ displace Ca2+ very effectively from binding sites at the cell surface. The inhibition of initial Ca2+ uptake is accompanied by a reduction in the binding of Ca2+.     

Nucleoside uptake in macrophages from various murine strains: a short-time and a two-step stimulation model

Kinetics of [3H]-uridine uptake by murine peritoneal macrophages (pM phi) is early altered after exposure to a variety of stimuli. Alterations caused by Candida albicans, lipopolysaccharide (LPS) and recombinant interferon-gamma (rIFN-gamma) were similar in SAVO, C57BL/6, C3H/HeN and C3H/HeJ mice, and were not correlated with an activation process as shown by the amount of tumor necrosis factor-alpha (TNF-alpha) being released. Short-time exposure to all stimuli resulted in an increased nucleoside uptake by SAVO pM phi, suggesting that the tumoricidal function of this cell either depends from the type of stimulus or the time when the specific interaction with the cell receptor is taking place. Experiments with priming and triggering signals confirmed the above findings, indicating that the increase or the decrease of nucleoside uptake into the cell depends essentially on the chemical nature of the priming stimulus. The triggering stimulus, on the other hand, is only able to amplify the primary response.