Prevention of thermal aggregation of an allosteric protein by small molecules: some mechanistic insights

Detailed knowledge of conformation and dynamics of native, intermediate and unfolded states of a protein is essential in searching for effective small molecules to prevent its aggregation. In a recent study we have demonstrated how allosteric effectors may influence protein-protein interactions at high temperatures using glutamate dehydrogenase (GDH) as a model allosteric protein. In the present study, thermal aggregation of this well-characterized enzyme was investigated in the presence of a number of amino acids (including Gly, Glu, Trp, Pro, Lys, Arg), polyamines (putrescine and spermidine) and chaperone-like molecules (cyclodextrins and caseins) as non-specific effectors. It was shown that some amino acids and polyamines may suppress aggregation via interaction with native species and may preserve the activity of the enzyme while cyclodextrins and caseins may exert their anti-aggregation potential via binding to aggregation-prone intermediates, without having any capacity to protect its native structure from unfolding. Observations describing the similarities and differences between the specific ligands and non-specific small molecules related to their interaction with native and aggregation-prone states of GDH are presented and discussed. It is argued that the type of studies described in the present communication is useful for the development of effective strategies for prevention of aggregation by small molecules.     

Morphology and fine structure of Acipenser persicus (Acipenseridae, Chondrostei) spermatozoon: Inter-species comparison in Acipenseriformes

This study describes morphology and fine structure of the Persian sturgeon (Acipenser persicus) (Acipenseridae, Chondrostei) spermatozoon. The results show that the spermatozoon of A. persicus is differentiated into an elongated head (length: mean±SD: 7.1±0.5μm) with an acrosome (length: 1.2±0.2μm), a cylindrical midpiece (length: 1.8±0.5μm), a flagellum (length: 50.3±5.9μm) and a total length of 59.2±6.2μm. Ten posterolateral projections (PLPs) arise from the posterior edge of the acrosome and there were 3 endonuclear canals that traversed the nucleus from the acrosomal end to the basal nuclear fossa region. Three to six mitochondria were in peripheral midpiece and the proximal and distal centrioles were located near to "implantation fossa" and basement of the flagellum. The axoneme has a typical eukaryotic structure composed of 9 peripheral microtubules and a central pair of single microtubule surrounded by the plasma membrane. Lateral fins were observed along the flagellum. The fins started and ended at 0.5-1μm from midpiece and at 4-6μm from the end of flagellum. There were significant differences in the size of almost all measured morphological parameters between males and flagellar, midpiece and nucleus characters were more isolated parameters that can be considered for detecting inter-individual variations. This study showed that sperm morphology and fine structure are similar among sturgeon species, but the dimensions of the parameters may differ.     

Identification of tubular heparan sulfate as a docking platform for the alternative complement component properdin in proteinuric renal disease

Properdin binds to proximal tubular epithelial cells (PTEC) and activates the complement system via the alternative pathway in vitro. Cellular ligands for properdin in the kidney have not yet been identified. Because properdin interacts with solid-phase heparin, we investigated whether heparan sulfate proteoglycans (HSPG) could be the physiological ligands of properdin. Kidneys from proteinuric rats showed colocalization of syndecan-1, a major epithelial HSPG, and properdin in the apical membranes of PTEC, which was not seen in control renal tissue. In vitro, PTEC did not constitutively express properdin. However, exogenous properdin binds to these cells in a dose-dependent fashion. Properdin binding was prevented by heparitinase pretreatment of the cells and was dose-dependently inhibited by exogenous heparin. ELISA and surface plasmon resonance spectroscopy (BIAcore) showed a strong dose-dependent interaction between heparan sulfate (HS) and properdin (K(d) = 128 nm). Pretreatment of HSPG with heparitinase abolished this interaction in ELISA. Competition assays, using a library of HS-like polysaccharides, showed that sulfation pattern, chain length, and backbone composition determine the interaction of properdin with glycosaminoglycans. Interestingly, two nonanticoagulant heparin derivatives inhibited properdin-HS interaction in ELISA and BIAcore. Incubation of PTEC with human serum as complement source led to complement activation and deposition of C3 on the cells. This C3 deposition is dependent on the binding of properdin to HS as shown by heparitinase pretreatment of the cells. Our data identify tubular HS as a novel docking platform for alternative pathway activation via properdin, which might play a role in proteinuric renal damage. Our study also suggests nonanticoagulant heparinoids may provide renoprotection in complement-dependent renal diseases.     

Dielectric properties of tissues; variation with age and their relevance in exposure of children to electromagnetic fields; state of knowledge

This paper reviews and summarises the state of knowledge on dielectric properties of tissues; in particular those obtained as a function of age. It also examines the impact of variation in dielectric data on the outcome of recent dosimetric studies assessing the exposure of children to electromagnetic fields.     

Role of electrostatic interactions in 2,2,2-trifluoroethanol-induced structural changes and aggregation of alpha-chymotrypsin

It has been recently demonstrated that alpha-chymotrypsin (CT) can be driven toward amyloid aggregation by addition of 2,2,2-trifluoroethanol (TFE), at intermediate concentrations. In the present article, the process of TFE-induced CT aggregation was investigated in more detailed kinetic terms where the effects of medium conditions, such as temperature, presence of kosmotropic and chaotropic salts, pH and chemical modification of lysine residues were examined. Various techniques, including light scattering, fluorescence and circular dichroism spectroscopy, were used to follow and characterize this process. The kinetics of aggregation was found to obey a second-order reaction with respect to protein concentration. The aggregation-prone A-state and aggregation-deficient TFE- or T-state of CT were found to be induced at lower TFE concentrations in the presence of salts. Use of acidic and alkaline conditions and lysine modification also promoted the formation of the T-state. Results presented suggest a role for electrostatic interactions in the aggregation process.     

A novel method of spectral clustering in attributed networks by constructing parameter-free affinity matrix

The most basic and significant issue in complex network analysis is community detection, which is a branch of machine learning. Most current community detection approaches, only consider a network's topology structures, which lose the potential to use node attribute information. In attributed networks, both topological structure and node attributed are important features for community detection. In recent years, the spectral clustering algorithm has received much interest as one of the best performing algorithms in the subcategory of dimensionality reduction. This algorithm applies the eigenvalues of the affinity matrix to map data to low-dimensional space. In the present paper, a new version of the spectral cluster, named Attributed Spectral Clustering (ASC), is applied for attributed graphs that the identified communities have structural cohesiveness and attribute homogeneity. Since the performance of spectral clustering heavily depends on the goodness of the affinity matrix, the ASC algorithm will use the Topological and Attribute Random Walk Affinity Matrix (TARWAM) as a new affinity matrix to calculate the similarity between nodes. TARWAM utilizes the biased random walk to integrate network topology and attribute information. It can improve the similarity degree among the pairs of nodes in the same density region of the attributed network, without the need for parameter tuning. The proposed approach has been compared to other primary and new attributed graph clustering algorithms based on synthetic and real datasets. The experimental results show that the proposed approach is more effective and accurate compared to other state-of-the-art attributed graph clustering techniques.

     

Fermented soybean meal extract improves oxidative stress factors in the lung of inflammation/infection animal model

Context

Fermented soybean products have been used in various ways, and more research is being conducted on them to reveal their benefit.

Objective

The objective of this study was to evaluate the antioxidative activity of fermented soybean meal extract by Lactobacillus plantarum in vitro and in vivo tests.

Materials and methods

A Lactobacillus plantarum strain RM10 was selected through plate and fermentation experiment, which increased the degree of protein hydrolysis (1.015 μg/mL) and antioxidant activity in soybean meal fermented by selected bacteria (FSBM). In vivo study was done on septic rats as an inflammation/infection model, and then the trial groups were treated with different concentrations of fermented soybean meal extracts (FSBM, 5, 10, and 20%).

Results

DPPH radical-scavenging and ferrozine ion-chelating activity enhanced (P < 0.05) after fermentation of soybean meal compared to control group. Reduced (P < 0.05) expression of inflammatory genes and enzymes was detected in the lungs of rats treated with fermented soybean meal extract.

Discussion and conclusions

These results demonstrated that a diet containing fermented soybean meal extract improved extreme inflammatory response in an infectious disease like sepsis by reducing inflammatory factors.

     

Evaluation of HYDRUS-1D and modified PRZM-3 models for tribenuron methyl herbicide transport in soil profile under vetiver cultivation

Abstract

Tribenuron methyl (TBM) is widely used in weed control. Due to its phytotoxicity, concerns on TBM pollution to soil have been raised. In this research, TBM concentration in the soil profile and vetiver grass were measured and simulated using HYDRUS-1D and modified PRZM-3 models. The treatments were two herbicide concentrations to soil with vetiver (C₁V and C₂V) and without vetiver (C₁S and C₂S). In control treatment (C_o) no herbicide was applied to the soil. In general, according to the measured data, TBM soil residues in C₁V and C₂V treatments were 39.8% and 30.1% lower than that obtained in C₁S and C₂S treatments, respectively. The TBM was leached to 90?cm soil depth and it was limited to about 50?cm in the treatments with vetiver grass. The simulated herbicide residue in the soil profile in modified PRZM-3 model was more accurate than the HYDRUS-1D model. The dissipation processes of herbicides in soil and solving method of water movement in soil, considered in the modified PRZM-3 model, are more precise than that obtained in the HYDRUS-1D model. However, the prediction of TBM uptake by vetiver in the HYDRUS-1D model was closer to the measured values than that obtained in the modified PRZM-3 model.