Dissection, residue conservation, and structural classification of protein-DNA interfaces

The basic DNA-binding modules of 128 protein-DNA interfaces have been analyzed. Although these are less planar, like the protein-protein interfaces, the protein-DNA interfaces can also be dissected into core regions in which all the fully-buried atoms are located, and rim regions having atoms with residual accessibilities. The sequence entropy of the core residues is smaller than those in the rim, indicating that the former are better conserved and possibly contribute more towards the binding free energy, as has been implicated in protein-protein interactions. On the protein side, 1014 A(2) of the surface is buried of which 63% belong to the core. There are some differences in the propensities of residues to occur in the core and the rim. In the DNA strands, the nucleotide(s) containing fully-buried atoms in all three components usually occupy central positions of the binding region. A new classification scheme for the interfaces has been introduced based on the composition of secondary structural elements of residues and the results compared with the conventional classification of DNA-binding proteins, as well as the protein class of the molecule. It appears that a common framework may be developed to understand both protein-protein and protein-DNA interactions.     

A Novel Copper Chelate Modulates Tumor Associated Macrophages to Promote Anti-Tumor Response of T Cells

BackgroundAt the early stages of carcinogenesis, the induction of tumor specific T cell mediated immunity seems to block the tumor growth and give protective anti-tumor immune response. However, tumor associated macrophages (TAMs) might play an immunosuppressive role and subvert this anti tumor immunity leading to tumor progression and metastasis.Conclusion/SignificanceOur results show the potential usefulness of CuNG in immunotherapy of drug-resistant cancers through reprogramming of TAMs that in turn reprogram the T cells and reeducate the T helper function to elicit proper anti-tumorogenic Th1 response leading to effective reduction in tumor growth.     

Prorenin has high affinity multiple binding sites for (pro)renin receptor

An important role of the decoy peptide sequence has recently been suggested in vitro for the binding of prorenin to the (pro)renin receptor [(P)RR]. In this study, other prospective crucial regions in renin and prorenin responsible for their interaction with (P)RR were investigated using various kinds of peptides, e.g., the “hinge” S¹⁴⁹QGVLKEDVF¹⁵⁸ designed from the structure of renin also common to prorenin, L^1PPTDTTTF^8P, L^1PPTDTTTFKRIFLKR^15P and the decoy (R^10PIFLKRMPSI^19P) designed from the predicted structure of prorenin. For the kinetic analysis, the recombinant h(P)RR was immobilized on the biosensor surface through a specific anti-(P)RR antibody. In case of the equilibrium state analysis, the (P)RR was directly adsorbed on plastic wells for observing the bindings of renin/prorenin. The dissociation constants (K_D) for the bindings of renin and prorenin to the pre-adsorbed receptors were 4.5 and 1.0 nM, respectively, similar to those stated in the kinetic study by BIAcore assay. The “hinge” region peptide bound to (P)RR in a dose-dependent manner with a K_D estimated 17.0 nM which was five times higher than that of the decoy. The K_D values for L^1PPTDTTTF^8P and L^1PPTDTTTFKRIFLKR^15P were 52 and 7.6 nM, respectively. The “hinge” peptide, as the decoy, inhibited the bindings of renin and prorenin to (P)RR. The inhibition constant (K_i) for the binding of renin and prorenin by the decoy and “hinge” were 16.7 and 15.1, and 37.1 and 30.7 nM, respectively. These in vitro studies suggest that renin has a single and prorenin has at least two high affinity binding sites for the (P)RR.     

Chronotherapeutically Modulated Pulsatile System of Valsartan Nanocrystals—an <Emphasis Type="Italic">In Vitro</Emphasis> and <Emphasis Type="Italic">In Vivo</Emphasis> Evaluation

The objective was to improve the dissolution of valsartan by developing valsartan nanocrystals and design a pulsed release system for the chronotherapy of hypertension. Valsartan nanocrystals were prepared by sonication—anti-solvent precipitation method and lyophilized to obtain dry powder. Nanocrystals were directly compressed to minitablets and coated to achieve pulsatile valsartan release. Pharmacokinetic profiles of optimized and commercial formulations were compared in rabbit model. The mean particle size and PDI of the optimized nanocrystal batch V4 was reported as 211 nm and 0.117, respectively. DSC and PXRD analysis confirmed the crystalline nature of valsartan in nanocrystals. The dissolution extent of valsartan was markedly enhanced with both nanocrystals and minitablets as compared to pure valsartan irrespective of pH of the medium. Core minitablet V4F containing 5% w/w polyplasdone XL showed quickest release of valsartan, over 90% within 15 min. Coated formulation CV4F showed two spikes in release profile after successive lag times of 235 and 390 min. The pharmacokinetic study revealed that the bioavailability of optimized formulation (72.90%) was significantly higher than the commercial Diovan tablet (30.18%). The accelerated stability studies showed no significant changes in physicochemical properties, release behavior, and bioavialability of CV4F formulation. The formulation was successfully designed to achieve enhanced bioavailability and dual pulsatile release. Bedtime dosing will more efficiently control the circadian spikes of hypertension in the morning.     

An in silico approach to understand the structure–function properties of a serine protease (Bacifrinase) from Bacillus cereus and experimental evidence to support the interaction of Bacifrinase with fibrinogen and thrombin

Microbial fibrinogenolytic serine proteases find therapeutic applications in the treatment of thrombosis- and hyperfibrinogenemia-associated disorders. However, analysis of structure–function properties of an enzyme is utmost important before its commercial application. In this study, an attempt has been made to understand the structure of a fibrinogenolytic protease enzyme, “Bacifrinase” from Bacillus cereus strain AB01. From the molecular dynamics trajectory analysis, the modelled three-dimensional structure of the protease was found to be stable and the presence of a catalytic triad made up of Asp102, His83 and Ser195 suggests that it is a serine protease. To understand the mechanism of enzyme–substrate and enzyme–inhibitor interactions, the equilibrated protein was docked with human fibrinogen (the physiological substrate of this enzyme), human thrombin and with ten selective protease inhibitors. The Bacifrinase–chymostatin interaction was the strongest among the selected protease inhibitors. The serine protease inhibitor phenyl methane sulphonyl fluoride was found to interact with the Ser134 residue of Bacifrinase. Furthermore, protein–protein docking study revealed the fibrinogenolytic property of Bacifrinase and its interaction with Aα-, Bβ- and Cγ-chains human fibrinogen to a different extent. However, biochemical analysis showed that Bacifrinase did not hydrolyse the γ-chain of fibrinogen. The in silico and spectrofluorometric studies also showed interaction of Bacifrinase with thrombin as well as fibrinogen with a Kd value of 16.5 and .81 nM, respectively. Our findings have shed light on the salient structural features of Bacifrinase and confirm that it is a fibrinogenolytic serine protease.     

Bisindole‐oxadiazole hybrids,T3P®‐mediated synthesis,and appraisal of their apoptotic,antimetastatic, and computational Bcl‐2 binding potential

In the pursuit of novel anticancer leads, new bisindole‐oxadiazoles were synthesized using propyl phosphonic anhydride as a mild and efficient reagent. The molecule, 3‐[5‐(1H‐indol‐3‐ylmethyl)‐1,3,4‐oxadiazol‐2‐yl]‐1H‐indole ( 3a ) exhibited selective cytotoxicity to MCF‐7 cells with a cell cycle arrest in the G1 phase. The mechanism of cytotoxicity of 3a involved caspase‐2‐dependent apoptotic pathway with characteristic apoptotic morphological alterations as observed in acridine orange/ethidium bromide and Hoechst staining. The wound healing migratory assay exhibited an intense impairment in the motility of MCF‐7 cells on incubation with 3a . Docking simulations with anti‐apoptotic protein Bcl‐2, which is also involved in cancer metastasis displayed good affinity and high binding energy of 3a into the well characterized BH3 binding site. The positive correlation between the Bcl‐2 binding studies and the results of in vitro investigations exemplifies compound 3a as a lead molecule exhibiting MCF‐7 differential cytotoxicity via apoptotic mode of cell death in addition to its anti‐metastatic activity.     

Circulating endothelium-enriched microRNA-126 as a potential biomarker for coronary artery disease in type 2 diabetes mellitus patients

Circulating microRNAs (miRNAs) have been shown as promising biomarkers for various diseases. We investigated the predictive potential of circulating endothelium-enriched miR-126 in type 2 diabetes patients (T2D) without chronic complications and T2D patients with coronary artery diseases (CAD). The expression levels of circulating miR-126, determined by quantitative real time PCR, were decrease in peripheral blood of T2D patients and T2D with CAD compared with healthy controls. MiR-126 strongly associated with T2D and CAD, negatively correlated with LDL in CAD patients and differentiated between T2D patients, T2D patients with CAD and healthy subjects. Circulating miR-126 may serve as a biomarker for predicting patients with T2D and diabetic CAD.     

Survival in Nuclear Waste,Extreme Resistance,and Potential Applications Gleaned from the Genome Sequence of Kineococcus radiotolerans SRS30216

Kineococcus radiotolerans {"type":"entrez-protein","attrs":{"text":"SRS30216","term_id":"1414251709","term_text":"SRS30216"}}SRS30216 was isolated from a high-level radioactive environment at the Savannah River Site (SRS) and exhibits γ-radiation resistance approaching that of Deinococcus radiodurans. The genome was sequenced by the U.S. Department of Energy''s Joint Genome Institute which suggested the existence of three replicons, a 4.76 Mb linear chromosome, a 0.18 Mb linear plasmid, and a 12.92 Kb circular plasmid. Southern hybridization confirmed that the chromosome is linear. The K. radiotolerans genome sequence was examined to learn about the physiology of the organism with regard to ionizing radiation resistance, the potential for bioremediation of nuclear waste, and the dimorphic life cycle. K. radiotolerans may have a unique genetic toolbox for radiation protection as it lacks many of the genes known to confer radiation resistance in D. radiodurans. Additionally, genes involved in the detoxification of reactive oxygen species and the excision repair pathway are overrepresented. K. radiotolerans appears to lack degradation pathways for pervasive soil and groundwater pollutants. However, it can respire on two organic acids found in SRS high-level nuclear waste, formate and oxalate, which promote the survival of cells during prolonged periods of starvation. The dimorphic life cycle involves the production of motile zoospores. The flagellar biosynthesis genes are located on a motility island, though its regulation could not be fully discerned. These results highlight the remarkable ability of K radiotolerans to withstand environmental extremes and suggest that in situ bioremediation of organic complexants from high level radioactive waste may be feasible.