Protein-protein interactions: principles, techniques, and their potential role in new drug development

A vast network of genes is inter-linked through protein-protein interactions and is critical component of almost every biological process under physiological conditions. Any disruption of the biologically essential network leads to pathological conditions resulting into related diseases. Therefore, proper understanding of biological functions warrants a comprehensive knowledge of protein-protein interactions and the molecular mechanisms that govern such processes. The importance of protein-protein interaction process is highlighted by the fact that a number of powerful techniques/methods have been developed to understand how such interactions take place under various physiological and pathological conditions. Many of the key protein-protein interactions are known to participate in disease-associated signaling pathways, and represent novel targets for therapeutic intervention. Thus, controlling protein-protein interactions offers a rich dividend for the discovery of new drug targets. Availability of various tools to study and the knowledge of human genome have put us in a unique position to understand highly complex biological network, and the mechanisms involved therein. In this review article, we have summarized protein-protein interaction networks, techniques/methods of their binding/kinetic parameters, and the role of these interactions in the development of potential tools for drug designing.     

Performance of suspended and attached growth MBR systems in treating high strength synthetic wastewater

The performance of laboratory-scale attached growth (AG) and suspended growth (SG) membrane bioreactors (MBRs) was evaluated in treating synthetic wastewater simulating high strength domestic wastewater. This study investigated the influence of sponge suspended carriers in AG-MBR system, occupying 15% reactor volume, on the removal of chemical oxygen demand (COD), total nitrogen (TN) and total phosphorus (TP), and compared it to that of SG-MBR. Results showed that the removal efficiencies of COD, TN and TP in AG-MBR were 98%, 89% and 58%, respectively as compared to 98%, 74% and 38%, respectively in SG-MBR. Improved TN removal in AG-MBR systems was primarily based on simultaneous nitrification and denitrification (SND) process. These results infer that the presence of small bio-particles having higher microbial activity and the growth of complex biomass captured within the suspended sponge carriers resulted in improved TN and TP removal in AG-MBR.     

Basic residues in the nucleocapsid domain of Gag are critical for late events of HIV-1 budding

The p6 region of HIV-1 Gag contains two late (L) domains, PTAP and LYPXnL, that bind the cellular proteins Tsg101 and Alix, respectively. These interactions are thought to recruit members of the host fission machinery (ESCRT) to facilitate HIV-1 release. Here we report a new role for the p6-adjacent nucleocapsid (NC) domain in HIV-1 release. The mutation of basic residues in NC caused a pronounced decrease in virus release from 293T cells, although NC mutant Gag proteins retained the ability to interact with cellular membranes and RNAs. Remarkably, electron microscopy analyses of these mutants revealed arrested budding particles at the plasma membrane, analogous to those seen following the disruption of the PTAP motif. This result indicated that the basic residues in NC are important for virus budding. When analyzed in physiologically more relevant T-cell lines (Jurkat and CEM), NC mutant viruses remained tethered to the plasma membrane or to each other by a membranous stalk, suggesting membrane fission impairment. Remarkably, NC mutant release defects were alleviated by the coexpression of a Gag protein carrying a wild-type (WT) NC domain but devoid of all L domain motifs and by providing alternative access to the ESCRT pathway, through the in trans expression of the ubiquitin ligase Nedd4.2s. Since NC mutant Gag proteins retained the interaction with Tsg101, we concluded that NC mutant budding arrests might have resulted from the inability of Gag to recruit or utilize members of the host ESCRT machinery that act downstream of Tsg101. Together, these data support a model in which NC plays a critical role in HIV-1 budding.     

Guanidinium chloride and urea denaturations of beta-lactoglobulin A at pH 2.0 and 25 degrees C: the equilibrium intermediate contains non-native structures (helix, tryptophan and hydrophobic patches)

We have carried out guanidinium chloride (GdmCl) and urea denaturations of bovine beta-lactoglobulin A (beta-lgA) at pH 2.0 and 25 degrees C, using far-UV and near-UV circular dichroism, near-UV absorption and tryptophan fluorescence spectroscopies. The stable intermediate state that occurs during GdmCl denaturation has been characterized by the far- and near-UV circular dichroism, tryptophan difference absorption, tryptophan fluorescence and 8-anilino-1-naphthalene sulphonic acid binding measurements. Following conclusions have been reached. (a) Urea-induced denaturation is not a two-state process. (b) GdmCl-induced denaturation is composed of two distinct two-state processes. (c) alpha-Helical content, burial of tryptophan residues and burial of hydrophobic surface area are more in the GdmCl-induced stable intermediate than those originally present in the native protein.     

microRNAs: New prognostic,diagnostic, and therapeutic biomarkers in cervical cancer

Cervical cancer is as a kind of cancer beginning from the cervix. Given that cervical cancer could be observed in women who infected with papillomavirus, regular oral contraceptives, and multiple pregnancies. Early detection of cervical cancer is one of the most important aspects of the therapy of this malignancy. Despite several efforts, finding and developing new biomarkers for cervical cancer diagnosis are required. Among various prognostic, diagnostic, and therapeutic biomarkers, miRNA have been emerged as powerful biomarkers for detection, treatment, and monitoring of response to therapy in cervical cancer. Here, we summarized various miRNAs as an employable platform for prognostic, diagnostic, and therapeutic biomarkers in the treatment of cervical cancer.     

Microalgae Versus Land Crops as Feedstock for Biodiesel: Productivity,Quality, and Standard Compliance

Despite certain environmental advantages over fossil diesel, land crop-derived biodiesels may not satisfy the increasing worldwide demand for transportation fuels. As an abundant photosynthesizer, algae could be an adequate surrogate for biodiesel production. Nevertheless, high production costs, scarce selected species, and inaccurate assumptions about production yields represent industrial uncertainties. In this study, a reliable approach to analyzing algal biodiesel production has been developed based on species-to-species variations in oil productivity and quality. This approach compares biodiesels from Chlorophyta strains with land crop feedstock according to (i) potential yields, (ii) oil quality, and (iii) compliance with biodiesel quality standards. Algal yields were assessed by (i) extrapolating the strain-specific laboratory results to commercial-scale growth systems; (ii) converting volumetric to areal biomass productivity; and (iii) estimating oil yields for each strain, as the product of their projected areal biomass productivity for each growth system, and the oil percentage in biomass as determined in the laboratory. Biodiesel fuel properties were estimated by using fatty acid methyl ester profile predictive models. The Chlorophyta strains in this study provided annual oil yields that were generally higher than those of land crops by one order of magnitude. Six strains yielding more than 40 mg oil l^?1 day^?1 were identified as adequate for sustaining biodiesel production. Trebouxiophyceae algae were the most productive. Critical biodiesel parameters from both feedstock types suggest that most microalgae-derived biodiesels meet international fuel quality standards with better values than those of land crops. Because some of the highly productive feedstock does not simultaneously meet all the standards for a high quality biodiesel, optimization solutions are discussed.     

Probing the Ca(2+) switch of the neuronal Ca(2+) sensor GCAP2 by time-resolved fluorescence spectroscopy

We report fluorescence lifetime and rotational anisotropy measurements of the fluorescent dye Alexa647 attached to the guanylate cyclase-activating protein 2 (GCAP2), an intracellular myristoylated calcium sensor protein operating in photoreceptor cells. By linking the dye to different protein regions critical for monitoring calcium-induced conformational changes, we could measure fluorescence lifetimes and rotational correlation times as a function of myristoylation, calcium, and position of the attached dye, while GCAP2 was still able to regulate guanylate cyclase in a Ca(2+)-sensitive manner. We observe distinct site-specific variations in the fluorescence dynamics when externally changing the protein conformation. A clear reduction in fluorescence lifetime suggests that in the calcium-free state a dye marker in amino acid position 131 senses a more hydrophobic protein environment than in position 111. Saturating GCAP2 with calcium increases the fluorescence lifetime and hence leads to larger exposure of position 111 to the solvent and at the same time to a movement of position 131 into a hydrophobic protein cleft. In addition, we find distinct, biexponential anisotropy decays reflecting the reorientational motion of the fluorophore dipole and the dye/protein complex, respectively. Our experimental data are well described by a "wobbling-in-a-cone" model and reveal that for dye markers in position 111 of the GCAP2 protein both addition of calcium and myristoylation results in a pronounced increase in orientational flexibility of the fluorophore. Our results provide evidence that the up-and-down movement of an α-helix that is situated between position 111 and 131 is a key feature of the dynamics of the protein-dye complex. Operation of this piston-like movement is triggered by the intracellular messenger calcium.     

Gibberellin-producing Promicromonospora sp. SE188 improves Solanum lycopersicum plant growth and influences endogenous plant hormones

Plant growth-promoting rhizobacteria (PGPR) producing gibberellins (GAs) can be beneficial to plant growth and development. In the present study, we isolated and screened a new strain of Promicromonospora sp., SE188, isolated from soil. Promicromonospora sp. SE188 secreted GAs into its growth medium and exhibited phosphate solubilization potential. The PGPR produced physiologically active (GA₁ and GA₄) and inactive (GA₉, GA₁₂, GA₁₉, GA₂₀, GA₂₄, GA₃₄, and GA₅₃) GAs in various quantities detected by GC/MS-SIM. Solanum lycopersicum (tomato) plants inoculated with Promicromonospora sp. SE188 showed a significantly higher shoot length and biomass as compared to controls where PGPR-free nutrient broth (NB) and distilled water (DW) were applied to plants. The presence of Promicromonospora sp. SE188 significantly up-regulated the non C-13 hydroxylation GA biosynthesis pathway (GA₁₂→GA₂₄→GA₉→GA₄→ GA₃₄) in the tomato plants as compared to the NB and DW control plants. Abscisic acid, a plant stress hormone, was significantly down-regulated in the presence of Promicromonospora sp. SE188. Contrarily, salicylic acid was significantly higher in the tomato plant after Promicromonospora sp. SE188 inoculation as compared to the controls. Promicromonospora sp. SE188 showed promising stimulation of tomato plant growth. From the results it appears that Promicromonospora sp. SE188 has potential as a bio-fertilizer and should be more broadly tested in field trials for higher crop production in eco-friendly farming systems.