Virtual high-throughput screening of natural compounds in-search of potential inhibitors for protection of telomeres 1 (POT1)

Communicated by Ramaswamy H. Sarma     

Characterization of antifungal metabolites produced by Lactobacillus plantarum and Lactobacillus coryniformis isolated from rice rinsed water

Molecular Biology Reports - A recent spike in demand for chemical preservative free food has derived the scientific community to develop natural ways of food preservation. Therefore,...     

Biophysical insights into the binding characteristics of bovine serum albumin with dipyridamole and the influence of molecular interaction with β cyclodextrin

Abstract

The binding characteristic of anti-platelet drug dipyridamole has been investigated with a transport protein, serum albumin. A multi-spectroscopic approach has been employed, and the results were well supported by in silico molecular docking and simulation studies. The fluorescence quenching of serum albumin at three different temperatures revealed that the mechanism involved is static and the binding constant of the interaction was found to be of the order of 10⁴ M^?1. The reaction was found to be spontaneous and involved hydrophobic interactions. Synchronous, 3D fluorescence and CD spectroscopy indicated a change in conformation of bovine serum albumin (BSA) on interaction with DP. Using site-selective markers, the binding site of DP was found to be in subdomain IB. Molecular docking studies further corroborated these results. Molecular dynamic (MD) simulations showed lower RMSD values on interaction, suggesting the existence of a stable complex between DP and BSA. Furthermore, since β-Cyclodextrin (βCD) is used to improve the solubility of DP in ophthalmic solutions, therefore, the effect of (βCD) on the interaction of BSA and DP was also studied, and it was found that in the presence of βCD, the binding constant for BSA-DP interaction decreased. The present study is an attempt to characterize the transport of DP and to improve its bioavailability, consequently helping in dosage design to achieve optimum therapeutic levels.

Communicated by Ramaswamy H. Sarma     

Does hydatid disease have protective effects against lung cancer?

We hypothesized that solid tumors rarely occur in patients with hydatid disease. We obtained the serum of 14 patients diagnosed with hydatid disease, the serum of 10 patients who did not have a history of hydatid disease, and the hydatid cyst fluid from six patients. These sera and fluid samples were added at different concentrations to NCI-H209/An1 human lung small cell carcinoma cells and L929 mouse fibroblasts as a control group. Sera of patients with hydatid diseases had cytotoxic effects on NCI-H209/An1 cells, but they did not have cytotoxic effects on fibroblast cells. Sera from healthy subjects did not have a cytotoxic effect on the tumor cell line or control fibroblasts. Cyst fluid, also, did not have toxic effects on the NCI-H209/An1 cell line, but was toxic to fibroblasts up to a 1:32 dilution. Sera from patients with hydatid disease had cytotoxic effects on human small cell lung cancer cells in vitro.     

Identification of a novel mutation in ZAP70 and prenatal diagnosis in a Turkish family with severe combined immunodeficiency disorder

Protein tyrosine kinases (PTKs) play an important role in T cell development and activation. In vitro and in vivo defects, resulting in variable deficiencies in thymic development and in T cell antigen receptor (TCR) signal transduction, in PTKs have been shown. ZAP70, one of those PTKs, is a 70-kDa tyrosine phosphoprotein and associates with the ζ chain and undergoes tyrosine phosphorylation following TCR stimulation. It is expressed in T and natural killer (NK) cells. Several mutations were shown to lead to an autosomal recessive form of severe combined immunodeficiency disease (SCID).     

Exceptional complex chromosomal rearrangement and microdeletions at the 4q22.3q23 and 14q31.1q31.3 regions in a patient with azoospermia

In this report we describe the first patient ever found to have azoospermia in association with both exceptional complex chromosomal rearrangements and microdeletions at two translocation breakpoints. A 36-year-old male who had been suffering from male factor infertility was admitted to our clinic. The patient also displayed mild dysmorphia. An analysis of the patient's semen revealed azoospermia. GTG banding revealed the presence of an exceptional complex chromosomal rearrangement involving chromosomes 1, 4, 10 and 14. Using subtelomeric FISH analysis, the patient's karyotype was designated as 46,XY,t(1;10)(q43q44;q21q26.1)(CEB108/T7+,D1S3738-;10PTEL006+,D10S2290+, D1S3738+), ins(14;4) (q31.3;q23q33)(D14S1420+; D4S3359+, D4S2930+). Array-CGH analysis revealed two microdeletions at the 4q22.3q23 and 14q31.1q31.3 chromosomal regions. We suggest that microdeletions at the 4q22.3q23 and 14q31.1q31.3 chromosomal regions associated with both an exceptional complex chromosomal rearrangement and the Homo sapiens chromosome 4 open reading frame 37 (C4orf37) gene located at the 4q22.3q23 region might be associated with male factor infertility.     

Coarse‐grained and all‐atom modeling of structural states and transitions in hemoglobin

Hemoglobin (Hb), an oxygen‐binding protein composed of four subunits (α1, α2, β1, and β2), is a well‐known example of allosteric proteins that are capable of cooperative ligand binding. Despite decades of studies, the structural basis of its cooperativity remains controversial. In this study, we have integrated coarse‐grained (CG) modeling, all‐atom simulation, and structural data from X‐ray crystallography and wide‐angle X‐ray scattering (WAXS), aiming to probe dynamic properties of the two structural states of Hb (T and R state) and the transitions between them. First, by analyzing the WAXS data of unliganded and liganded Hb, we have found that the structural ensemble of T or R state is dominated by one crystal structure of Hb with small contributions from other crystal structures of Hb. Second, we have used normal mode analysis to identify two distinct quaternary rotations between the α1β1 and α2β2 dimer, which drive the transitions between T and R state. We have also identified the hot‐spot residues whose mutations are predicted to greatly change these quaternary motions. Third, we have generated a CG transition pathway between T and R state, which predicts a clear order of quaternary and tertiary changes involving α and β subunits in Hb. Fourth, we have used the accelerated molecular dynamics to perform an all‐atom simulation starting from the T state of Hb, and we have observed a transition toward the R state of Hb. Further analysis of crystal structural data and the all‐atom simulation trajectory has corroborated the order of quaternary and tertiary changes predicted by CG modeling. Proteins 2013. © 2012 Wiley Periodicals, Inc.     

Reverse Relationship Between Blood Boron Level and Body Mass Index in Humans: Does It Matter for Obesity?

The exact role of boron in humans is not known although its supplementation causes several important metabolic and inflammatory changes. The objective of this study is to evaluate the possibility of an association between blood boron level and obesity in normal, overweight, obese, and morbidly obese subjects. A total number of 80 subjects, categorized into four groups based on their body mass index as normal, overweight, obese, and morbidly obese, were enrolled in this study. Age, sex, body mass index, and blood boron levels were recorded for each subject. Although the distribution of female and male subjects and blood boron levels were similar between groups, the mean age of normal subjects was significantly lower than the others (p?=?0.002). There was a significant relationship between age and quantitative values of body mass index for each subject (β?=?0.24; p?=?0.003). In addition, between blood boron levels and quantitative values of body mass index for each subject, a significant reverse relationship was detected (β?=??0.16; p?=?0.043). Although age seemed to be an important variable for blood boron level and body mass index, blood boron levels were shown to be lower in obese subjects in comparison to non-obese subjects.     

Biofilm-producing abilities of Salmonella strains isolated from Turkey

In the present study the biofilm-forming characteristics of 99 serotyped (DMC strains) and 41 genus level-identified (IS strains) Salmonella strains originating from Turkey were investigated. The strains were selected based on their ability to show the biofilm morphotype on Congo red agar plates. In addition, all strains were evaluated with regard to properties related to forming pellicle structures, physical differences of pellicles, any changes in the media associated with the formation of pellicles, and the presence of cellulose within the formed biofilm matrix as determined using 366 nm UV light. The Salmonella Typhimurium DMC4 strain was the best producer of biofilm grown on polystyrene microtiter plates (optical density at 595 nm: 3.418). In subsequent experiments industrial process conditions were used to investigate different morphotyped Salmonella strains’ biofilm-forming capability on stainless steel, a commonly preferred surface for the food industries, and on polystyrene surfaces. The effect of other important industrial conditions, such as temperature (5, 20, 37°C), pH (4.5, 5.5, 6.5, 7.4) and NaCl concentration (0.5, 1.5, 5.5, 10.5%) on the production of biofilm of the different morphotyped Salmonella strains (DMC4; red, dry and rough morphotyped S. Typhimurium, DMC12; brown, dry and rough morphotyped S. Infantis, DMC13; pink, dry and rough morphotyped S. subsp. Roughform) were also assessed. On the other hand, pH values exhibited variable effects on biofilm-forming features for different Salmonella strains on both polystyrene and stainless steel surfaces.