Constructing homology models is facilitated by the fact that the transmembrane region of Class A GPCRs is relatively well conserved. The accuracy of homology models is limited, however, by the uncertainty of modeling the extra- and intracellular loops, which greatly vary in length and amino acid composition, even between otherwise closely related GPCRs. In this study, we tested the utility of homology models for docking and selecting compounds with reasonable affinity for the investigated receptor subtype. We intentionally restricted the amount of existing ligand data used to refine the binding site during model building to mimic a situation where few ligands are known. In fact, except for the very first steps of model building and optimization, only the affinity data obtained in this study was used to improve the homology models. Three sequential cycles of model refinement, docking, and ligand testing were applied, using the data acquired in previous rounds to guide the receptor model optimization in the following rounds. In parallel, we also probed the tendency of the screen to identify novel ligands of other subtypes within the same receptor family, i.e. the selectivity of a homology model-based screen against a single GPCR subtype. These findings were compared with the distribution of selectivity ratios of known ligands for the same subtypes. The adenosine receptors, which consist of the four subtypes A1, A2A, A2B, and A3, have been chosen as a suitable test case for the application of virtual screening to a closely related subtype of a known GPCR structure. There are both antagonistbound and agonist-bound X-ray structures known for the A2AAR subtype, with various ligands co-crystallized for each case. Thus, the region for orthosteric AR ligand binding has been well characterized. The first antagonist-bound structure to be determined was co-crystallized with the high affinity ligand 4- triazin-5-yl-amino]ethylphenol. An unexpected orientation of the ligand perpendicular to the plane of the membrane bilayer was observed. Extracellular loops, as well as helical TM domains, are involved in coordinating the ligand. In silico virtual screening for A2AAR antagonists has already been demonstrated to be successful based on the inactive conformation of the A2AAR, as determined by crystallography. Among the different subtypes, the A1AR is also an attractive pharmaceutical target. Its antagonists have been explored as kidney-protective agents, compounds for treating cardiac failure, cognitive enhancers, and antiasthmatic agents. Structurally diverse antagonists, such as the pyrazolopyridine derivative 2 and the 7-deazaadenine derivative 3, were previously identified, and some of these compounds were under consideration for clinical use. The prototypical AR antagonists, i.e. the 1,3- dialkylxanthines, have provided numerous high affinity antagonists with selectivity for the A1AR. One such antagonist, rolofylline 4, an alkylxanthine derivative of high content screening abmole bioscience nanomolar affinity, was previously in clinical trials for cardiac failure. The human A1AR subtype was investigated in this study because it shares a high level of sequence identity with the A2AAR. It should thus be possible to model the A1AR by homology with high confidence. While this homology model was the only three-dimensional structure of a protein employed in the screening, all compounds were also tested in receptor binding assays against two other AR subtypes in order to investigate the intrinsic selectivity of the model.. We did not exclude the molecules tested in earlier rounds of screening during the subsequent ones, yet the vast majority of ligands identified in one model did not appear in the top ranks of a screen against another one.

By the efficient generation of favorable interactions, and this prediction has been supported by recent docking-simulation studies. In contrast, less attention has been paid to the minor population of ring oligomers having simple n-fold rotational symmetry. In our statistical analysis of the PDB, we found that such ring complexes may contain even or odd numbers of subunits, and there is no bias toward even numbers. Ring-shaped oligomers have a wide variety of symmetry. Prime numbers of subunits give the “lowest” symmetry, and highly composite numbers having many divisors give the “highest” symmetry. A question then arises whether there is a biological or physical reason for rings to evolve with a prime number or highly composite number of subunits. To answer this question, we studied trp RNA binding attenuation protein as an illustrative case. TRAP is a ring-form homooligomer for which crystal structures are available of 11-mer and 12-mer forms. TRAP is found in various species of Bacillus, and plays a central role in the regulation of transcription and translation of the trp operon. The monomers of TRAP form a ring-form homo 11-mer with a minor component of 12-mer depending on the solution conditions. Each subunit of TRAP is composed of seven-stranded anti-parallel b-sheets and a bound tryptophan molecule. Recently, Tame et al. solved the crystal structure of 12-mer TRAP, which was produced artificially by joining the subunits of B. stearothermophilus TRAP in tandem with linkers of alanine residues. The crystal structure of TRAP. Allatom root mean square displacement between the monomer of the 11-mer and that of 12-mer was only 0.26 A˚. Despite their structural similarity, however, 12-mer TRAP is significantly less stable, as shown from the population of 12-mer in solution. In this study, we tried to address the influence of the differences in symmetry on the dynamics of the oligomers. The 12-mer structure was modeled with subunits carrying no peptide linkers to stabilize the 12-mer form. We performed 100 ns fully-atomistic MD simulations with an explicit water environment for both forms of TRAPs as well as normal mode analysis using an elastic network model. The normal mode analysis with group theory allows a clear description of symmetry in the thermal vibration. Based on the results of the normal mode analysis, we looked into the details of the fluctuations observed in the trajectories of the MD simulations. The vibrational dynamics of the two TRAPs, the wild-type the engineered 12-mer, were investigated by focusing on their differences in rotational symmetry. First, the normal mode analysis of the perfectly symmetric TRAP system with the group theoretical approach showed that the normal modes on the ring can be viewed as a stationary wave characterized by wave nodes, and that the low frequency normal modes tended to select relatively soft regions, the subunit interfaces, as the wave nodes. Because commensurable with 12 but not with 11, the wave nodes were located at the subunit interfaces in the 12-mer, but were frequently situated at the rigid core region of the subunits in the 11-mer. This observation was BYL719 PI3K inhibitor utilized to study the thermally-fluctuating pseudo-symmetric systems through fullyatomistic MD simulations. In the MD snapshots, we observed similar vibrational motions as in the normal modes. In particular, large subunit interfacial deformations in the 12-mer caused larger displacements of entire subunits, while in the 11-mer, wave modes located at the subunit cores caused larger. Generalization of these observations leads to a hypothesis that ring-form proteins of higher symmetry, with a highly composite number of subunits, undergo relatively large global deformations of the ring.

Syntrophin binds to a variety of signaling molecules including sodium channels, neuronal nitric oxide synthase, aquaporin-4 and serine/threonine kinases. Mice lacking a1-syntrophin display aberrations in neuromuscular synapses with undetectable levels of postsynaptic utrophin and reduced levels of acetylcholine receptor and acetylcholinesterase. MAP1B deficiency did not appear to alter syntrophin expression or localization in Schwann cells, nor did it alter the characteristic organization of DRP2 in clusters at the abaxonal Schwann cell membrane, nor the internodal distance or the organization of the nodes of Ranvier as analyzed by staining for ezrin and Caspr1/paranodin. Thus, the previously observed reduction in nerve conductance velocity and the reduced myelination in MAP1B deficient sciatic nerves do not appear to be reflected by changes in syntrophin expression or intracellular organization. Originally, MAPs were thought to regulate neuronal microtubule dynamics, CPI-613 95809-78-2 stability, and spacing between individual microtubules in a microtubule bundle as well as modulating access and activity of microtubule-dependent motor proteins and thus axonal and dendritic transport through their direct interaction with microtubules. In a more recent development, classical MAPs have been found to bind to a wide variety of proteins with diverse functions. For example, proteins of the MAP1 family bind to receptors and ion channels, postsynaptic density proteins PSD-93 and PSD-95, signaling molecules and proteins involved in intracellular traffic. Thus, our findings presented here add to a growing body of evidence that classical MAPs can play a role in signal transduction not only by directly modulating microtubule function, but also through their interaction with a variety of signal transduction proteins. Exosomes are secreted membrane vesicles of nanometer size formed by inward budding of late endosomes resulting in the formation of multivesicular bodies in the cell and subsequent release into the cytosol by exocytosis. These mechanisms were first described in the 1980s by the groups of Stahl and Johnstone when studying the maturation of erythrocytes. Since then exosomes have been shown to be released by several cell types including epithelial cells, dendritic cells, B cells, T cells, mast cells and tumor cells among others. The presence of exosomes has also been shown in human body fluids such as plasma, urine, breast milk, bronchoalveolar lavage and malignant effusions. They have also been suggested to play a role in tumor immunity both as tumor growth promoters and as inhibitors of tumor growth. Exosome secretion from different T cell types has been demonstrated by several groups e.g. from activated CD3+ cells, CD4+ T cells and CD8+ T cells. The exosomes from CD4+ T cells have been suggested to deliver antigen specific signals, atherogenic signals and co-stimulatory signals whereas exosomes from CD8+ T cells have been associated with non-cytotoxic suppression of HIV1 transcription. While many studies have demonstrated the impact of immune signaling from exosomes derived from antigen presenting cells on T cells, not many, to our knowledge, have demonstrated the role of T cell exosome communication with other T cells. However, it has been shown that activated human T cells can release microvesicles containing Fas and APO2 ligand. The cytokine IL-2 is a potent lymphokine which regulates immune responses. It stimulates the proliferation and differentiation of activated immune cell e.g. T cells, B cells, monocytes and natural killer cells. T cells, activated by T cell receptor engagement with an antigen together with costimulation, are the main IL-2 secreting cells which stimulate proliferation of themselves in an autocrine manner as well as other neighboring antigen activated T cells.

This may indicate that the exosomes carry information that together with IL-2 can induce resting T cells to respond similar to the cells that secreted them. The chemokine CCL4, also known as macrophage inflammatory protein 1b, has previously been shown to be secreted by CD8+ T cells which supports the notion of a preferential stimulation of cytotoxic T cells as also indicated by the shift in CD4/CD8 ratio. The cytokine profile of cells stimulated with exosomes+IL-2 reveals a high level of IL-5 and IL-13, which may indicate a Th2 skewing of the activated cells. In addition the exosomes seem to carry with them large amounts of CCL5, since the addition of exosomes to the culture media makes this cytokine immediately readily detectable. Interestingly RANTES has been shown to be secreted by activated CD8+ T cells from a specific storage compartment with exosome properties and exosomes carrying RANTES can actively inhibit HIV infection. There is also a previous report demonstrating that RANTES is present in CD8+ cytotoxic cell granules and that it can act as a mitogen upon cell surface aggregation followed by secretion of MIP-1b. These results correspond well with our observations. In summary, our result show that exosomes secreted from simulated CD3+ T cells can dramatically change the response of resting autologous T cells to IL-2. The exosomes carry RANTES and seem to favor a cytotoxic response, which could be of potential interest in anti-viral and anti-tumor treatment. The emphasis on studying the interaction of methylxanthines such as theophylline, PLX-4720 theobromine and caffeine with nucleic acids is mainly because of a) its dietary consumption b) their use as therapeutic agents. Interestingly these xanthine derivatives have interactions with steroid-receptor complex, DNA, RNA, adenosine receptor, protein kinases, and neurological behavior which are reckoned to be pivotal for their ability to modulate the biochemical reactions by interacting with the nucleic acids or through cell signaling molecules. While probing the spectroscopic analysis of methylxanthines interaction with nucleic acids, it has been understood that caffeine known to interact with 59-adenosine monophosphate and poly riboadenylate by a parallel arrangement outside-stacked selfassociation to DNA bases, and report from Nafisi et.al, indicate that caffeine and theophylline bind to DNA in aqueous solution. However a comparative analysis of caffeine, theophylline with the other structurally related compounds like theobromine has not yet been shown to understand their variance in binding efficacy with DNA, as all of them are having vital cellular activities. Moreover, the current study deals the binding interaction of all these three methylxanthines with DNA in the presence of divalent metal ions and during helix-coil transition state holding some key rationales are explicitly explored in detail. As far as the importance of theobromine is concerned it has been shown that theobromine enhanced the antitumor activity of adriamycin with reduced toxicity. It has also been reported that caffeine and theobromine inhibited the doxorubicin efflux from tumor cells and increased the tumoricidal activity with reduced side effect. From our earlier reports it could be understood that since xanthine derivatives can interact with DNA, they can reduce the DNA-directed toxicity of certain intercalating dyes such as ethidium bromide, acridine orange and antitumor agents like cisplatin, novantrone, actinomycin D etc. Moreover, co-administration of methylxanthines in cancer therapy used for the enhancement of anti-tumor agent’s activity and serving as candidates for radiosensitization are promising baseline for developing methylxanthines as potential secondary enhancers for future clinical trial.

The important role of Twist1 in promoting cell survival, cell invasion and immigration, and facilitating tumor angiogenesis. Both Twist1 and Twist2 are known to mediate EMT in human cancers. Twist1 is a key regulator of metastasis. It has been shown that Twist1 promotes EMT through down-regulation of E-cadherin in subsets of sporadic invasive human lobular breast cancer, but little is known about the expression pattern of Twist2. Twist2 activates EMT programs and facilitates a cancer stem cell phenotype in breast cancer. However, the role of Twist2 in promoting breast cancer invasion and metastasis has not been established in the context of the breast microenvironment. In addition, the identification and clinical relevance of Twist2 in breast cancer is not known. We showed that Twist2 was up-regulated in human primary breast carcinoma tissues compared with the matched normal breast tissues. Twist2 was expressed mostly in cytoplasm as demonstrated by immunohistochemical assay in tissue microarray. Cytoplasmic Twist2 was associated with tumor histological type, the TNM clinical stage and tumor metastasis. Our study showed that, in some cases of invasive ductal breast carcinoma, Twist2 were mainly localized in cytoplasm of cancer cells expressing E-cadherin at tumor center and the lymph metastases. In contrast, nuclear Twist2 were detected in cancer cells located at the invasive margins of primary breast cancer. In this study we report that Twist2 promotes breast cancer invasion through loss of E-cadherin. Our data suggested that there was a link between nuclear Twist2 and EMT and the EMT process depends on Twist2 cellular location. These results demonstrate an important role of Twist2 in breast cancer invasion and indicate that Twist2 may be a new EMT indicator for dissemination of breast cancer. It has been well recognized that EMT plays a critical role in cancer metastasis. However, the difficulty to directly demonstrate the role of EMT in metastasis in vivo is to validate cancer cells that have undergone an EMT in primary human tumor specimens. The molecular mechanism associated with the involvement of EMT in tumor metastasis is still highly debated. As clinical observations showed that the majority of human breast carcinoma cells in metastases express E-cadherin and maintain their epithelial morphology, cancer cells may have disseminated without switching to a mesenchymal phenotype. The master regulators of tumor invasion and metastasis were largely unknown. Twist1 is one of essential factors to promote tumor metastasis. The hypothesis that cancer cells routinely undergo a complete EMT program is likely to be simplistic. In breast cancer, Twist1 only partially induced an EMT program. Twists belong to bHLH transcription factor family which form either homo-or-heterodimers with other bHLH proteins to bind to a core E-box sequence on the promoter region of target genes such as E-cadherin. It has been reported that Twist2 could activate EMT programs to facilitate a cancer stem cell phenotype in breast cancer recently. But how Twist2 participates in EMT of breast cancer in vivo remains poorly understood. The present data indicate that Twist2 staining was a reliable Temozolomide predictor in the prognosis of breast cancer patients. Twist2 increased significantly with tumor metastasis, especially in cytoplasm of ductal carcinoma of breast cells. Additionally, cytoplasm Twist2 expression was mainly in ductal carcinoma of breast relative to lobular carcinoma. Twist1 has also been shown to be expressed in cytoplasm but not nucleus of human hepatocellular carcinoma, whereas E-cadherin was localized on membranes. Twist2 overexpression was significantly linked to cervical cancer progression recently.