Protein-protein interaction and quaternary structure

Protein-protein recognition plays an essential role in structure and function. Specific non-covalent interactions stabilize the structure of macromolecular assemblies, exemplified in this review by oligomeric proteins and the capsids of icosahedral viruses. They also allow proteins to form complexes that have a very wide range of stability and lifetimes and are involved in all cellular processes. We present some of the structure-based computational methods that have been developed to characterize the quaternary structure of oligomeric proteins and other molecular assemblies and analyze the properties of the interfaces between the subunits. We compare the size, the chemical and amino acid compositions and the atomic packing of the subunit interfaces of protein-protein complexes, oligomeric proteins, viral capsids and protein-nucleic acid complexes. These biologically significant interfaces are generally close-packed, whereas the non-specific interfaces between molecules in protein crystals are loosely packed, an observation that gives a structural basis to specific recognition. A distinction is made within each interface between a core that contains buried atoms and a solvent accessible rim. The core and the rim differ in their amino acid composition and their conservation in evolution, and the distinction helps correlating the structural data with the results of site-directed mutagenesis and in vitro studies of self-assembly.     

Applications of LC-MS in the study of the uptake, distribution, metabolism and excretion of bioactive polyphenols from dietary supplements

Specific and quantitative analyses of the bioactive components and their metabolites in body fluids are essential to assess the interaction between groups of compounds in dietary supplements and preparations of psychoactives. Reverse-phase LC separations combined with tandem mass spectrometry provide the necessary specificity and sensitivity. In this paper, applications of these methods are described for the analysis of isoflavones, salvinorin A, synephrine isomers and their metabolites in serum, urine and aqueous humor.     

Mineral Release Dynamics of Tricalcium Phosphate and Waste Muscovite by Mineral-Solubilizing Rhizobacteria Isolated from Indo-Gangetic Plain of India

The aim of the present investigation was to evaluate the mineral release abilities of ten rhizobacterial strains isolated from rhizosphere of various crops growing in the Indo-Gangetic Plain (IGP) of India. Their abilities to solubilize inorganic phosphorus (P) and potassium (K) minerals from insoluble tricalcium phosphate (TCP) and waste muscovite (WM) revealed that rhizobacteria significantly solubilized different levels of inorganic P and fixed K, respectively. Some of the rhizobacterial stains have the ability to produce ammonia, indole-3-acetic acid (IAA), and hydrogen cyanide (HCN). The identification based on the 16S rDNA gene sequencing of selected mineral-solubilizing rhizobacteria (MSR) having greater potential to serve as bioagents were identified as Bacillus subtilis (BRHU01, BRHU03, and BHU20), Bacillus tequilensis (BRHU02), Bacillus licheniformis (BRHU04), Bacillus pumilus (BRHU05), Bacillus flexus (BHU02), Brevibacillus formosus (BHU16), Bacillus methylotrophicus (BHU29), and Bacillus amyloliquefaciens (BHU30). Interestingly, inorganic P and K solubilization by these strains belonging to genera Bacillus and Brevibacillus showed significant variations from 0.52 to 14.49 and from 1.62 to 8.60 µg mL^?1, respectively. However, generally, pH values of culture media decreased from near neutral (6.43) to acidic (3.83) with increasing incubation period, and this was inversely correlated with quantities of K solubilized by these rhizobacterial strains. Meanwhile, the electrical conductivity (EC) of broth culture increased from 0.09 to 0.23 dS m^?1 with increasing incubation period. Principal component analysis (PCA) of the MSR revealed three clusters, which exhibited high variance with respect to nutrient release. Taken together, these results suggest that Bacillus and Brevibacillus sp. identified in this study solubilized varying levels of inorganic P and fixed K from insoluble TCP and WM by acidolysis mechanisms.     

2-Chlorophenyl-substituted benzofuro[3,2-b]pyridines with enhanced topoisomerase inhibitory activity: The role of the chlorine substituent

A new series of 2-chloropheny-substituted benzofuro[3,2-b]pyridines were designed, synthesized, and evaluated for topoisomerase I and II inhibition and antiproliferative activity. Compounds 17–19, 23, 24, 26, and 27 exhibited excellent topo II inhibitory activity. A systematic structure-activity relationship study revealed the important role of chlorine substitution in the strong topoisomerase inhibitory activity.     

A protein-RNA docking benchmark (I): nonredundant cases

We have developed a nonredundant protein-RNA docking benchmark dataset, which is derived from the available bound and unbound structures in the Protein Data Bank involving polypeptide and nucleic acid chains. It consists of nine unbound-unbound cases where both the protein and the RNA are available in the free form. The other 36 cases are of unbound-bound type where only the protein is available in the free form. The conformational change upon complex formation is calculated by a distance matrix alignment method, and based on that, complexes are classified into rigid, semi-flexible, and full flexible. Although in the rigid body category, no significant conformational change accompanies complex formation, the fully flexible test cases show large domain movements, RNA base flips, etc. The benchmark covers four major groups of RNA, namely, t-RNA, ribosomal RNA, duplex RNA, and single-stranded RNA. We find that RNA is generally more flexible than the protein in the complexes, and the interface region is as flexible as the molecule as a whole. The structural diversity of the complexes in the benchmark set should provide a common ground for the development and comparison of the protein-RNA docking methods. The benchmark can be freely downloaded from the internet.     

Enzymatic synthesis of apigenin glucosides by glucosyltransferase (YjiC) from Bacillus licheniformis DSM 13

Apigenin, a member of the flavone subclass of flavonoids, has long been considered to have various biological activities. Its glucosides, in particular, have been reported to have higher water solubility, increased chemical stability, and enhanced biological activities. Here, the synthesis of apigenin glucosides by the in vitro glucosylation reaction was successfully performed using a UDP-glucosyltransferase YjiC, from Bacillus licheniformis DSM 13. The glucosylation has been confirmed at the phenolic groups of C-4′ and C-7 positions ensuing apigenin 4′-O-glucoside, apigenin 7-O-glucoside and apigenin 4′,7-O-diglucoside as the products leaving the C-5 position unglucosylated. The position of glucosylation and the chemical structures of glucosides were elucidated by liquid chromatography/mass spectroscopy and nuclear magnetic resonance spectroscopy. The parameters such as pH, UDP glucose concentration and time of incubation were also analyzed during this study.     

Sustainable approaches towards green synthesis of TiO2 nanomaterials and their applications in photocatalysis-mediated sensing to monitor environmental pollution

Nanomaterials are gaining enormous interests due to their novel applications that have been explored nearly in every field of our contemporary society. In this scenario, preparations of nanomaterials following green routes have attracted widespread attention in terms of sustainable, reliable, and environmentally friendly practices to produce diverse nanostructures. In this review, we summarize the fundamental processes and mechanisms of green synthesis approaches of TiO₂ nanoparticles (NPs). We explore the role of plants and microbes as natural bioresources to prepare TiO₂ NPs. Particularly, focus has been made to explore the potential of TiO₂-based nanomaterials to design a variety of sensing platforms by exploiting the photocatalysis efficiency under the influence of a light source. These types of sensing are of massive importance for monitoring environmental pollution and therefore for inventing advanced strategies to remediate hazardous pollutants and offer a clean environment.     

Effect of a single exposure to ultraviolet radiation on Mycobacterium bovis bacillus Calmette-Guerin infection in mice

BALB/c and C3H mice were exposed on the dorsal skin to 45 kJ/m2 of UVB radiation from FS-40 sunlamps 3 days before infection with 1 x 10(6) live units of Mycobacterium bovis bacillus Calmette-Guérin (BCG) (Tice strain) in the footpad. At regular intervals, groups of mice were tested for a delayed type hypersensitivity (DTH) response to the purified protein derivative (PPD) of tubercle bacilli, and the course of infection was monitored by measuring the size of the infected footpad, enlargement of the draining lymph node, and the number of bacteria in the spleen and lymph node. In both strains the DTH response to PPD was significantly delayed in UV-treated mice compared to unirradiated mice, when tested 21 and 42 days after BCG infection. By day 50, no significant difference was detected in the DTH response between irradiated and unirradiated mice. UV treatment reduced the size of the lymph node draining the site of BCG infection in both strains of mice and the size of the infected footpad in C3H mice but not in BALB/c mice. In both strains of mice the total number of bacteria in the spleen and the draining lymph node increased after UV irradiation. When irradiated 3, 5, 18, or 21 days after BCG infection, BALB/c mice also showed a significant decrease in their DTH response to PPD, indicating that the UV-induced suppression of BCG occurs both at the induction and the elicitation stages of the immune response. Thus, mice exposed to a single dose of UV radiation either before or after BCG infection showed an impaired DTH response to mycobacteria, which was accompanied by an increase in the multiplication of bacteria in the tissues, even though the organisms were introduced at an unirradiated site. These studies demonstrate that a systemic effect of UV irradiation can interfere with the development and expression of immunity to pathogenic bacteria in mice.     

Antiviral activity of substituted 5-chlorodiphenylamine-2-carboxylic acid hydrazides and their N-benzylidene derivatives

The substituted 5-chlorodiphenylamine-2-carboxylic acid hydrazides and their N-benzylidene derivatives were tested for their antiviral activity against gomphrena mosaic virus in a hypersensitive hostin vitro as well asin vivo. Most of the compounds exhibited potential antiviral activity. These compounds may be useful in controlling viral infections in garden as well as in field crops.