Packing of transmembrane helices in bacteriorhodopsin folding: structure and thermodynamics

We propose a coarse-grained (CG) model to study the native structure and physical properties of helical membrane proteins (HMPs) using off-lattice computer simulations. Instead of considering sequence heterogeneity explicitly, we model its effect on the packing of helices by employing a mean packing parameter r(0), which is calculated from an all-atom (AA) model. Specifically, this CG model is applied to investigate the packing of helices in bacteriorhodopsin (BR), and predicts the seven helix bundle structure of BR with a root mean square deviation (RMSD) in coordinates of helix backbone atoms (N, C, C(alpha)) of 3.99 A from its crystal structure. This predicted structure is further refined in an AA model by Amber and the refined structure has a RMSD (in coordinates of helix backbone atoms) of 2.64 A. The predicted packing position, tilting angle, and orientation angle of each helix in the refined structure are consistent with experimental data and their physical origins can be well understood in our model. Our results show that a reasonably good structure of BR can be predicted by using such a dual-scale approach, provided that its secondary structure is known. Starting from a random initial configuration, the folded structure can be obtained in days using a regular desktop computer. Various thermodynamic properties of helix packing of BR are also investigated in this CG model.     

Ratio of Wnt3a to BMP4 doses is critical to their synergistic effects on proliferation of differentiating mouse embryonic stem cells

Abstract. Objectives : To investigate potential interactions between bone morphogenetic protein (BMP) and Wnt signalling on differentiating mouse embryonic stem cells (mESC). Materials and methods : Mouse embryonic stem cells were cultured with differing combinations of Wnt3a, BMP4 and inhibitors of Wnt, BMP, PI-3K (phosphoinositide 3-kinase), p38, ERK1/2 (extracellular signal-regulated kinase 1/2) and JNK (c-Jun N-terminal kinase) pathways. Results : We found that Wnt3a synergized with BMP4 to promote mESC proliferation. Furthermore, the relative ratio of Wnt3a to BMP4 doses was critical to their synergistic effects, which could be abolished by using Dkk-1, noggin or the inhibitors of PI-3K, p38, ERK1/2 and JNK pathways. We also demonstrated that combination of Wnt3a and BMP4 could suppress ectodermal differentiation of mESCs. Moreover, inhibitors of PI-3K, p38, ERK1/2 and JNK pathways could negate this effect. Conclusion : Relative ratio of Wnt3a to BMP4 doses is critical to their synergistic effect on differentiating mESC proliferation, which may work through PI-3K, p38, ERK1/2 and JNK pathways.     

Beta-L-(-)-dioxolane Cytidine (β-L-(-)-OddC) as a Potent Compound for the Treatment of Cancer

Abstract

L-(-)-OddC is the first nucleoside analog with the unnatural L-configuration and the first chain-terminator shown to have anti-cancer activity. This compound was found to be highly active against solid tumor growth in several human xenograft models. L-(-)-OddC exerts its activity be terminating DNA chain elongation after its incorporation.     

Characterizing the three-dimensional organization of telomeres.

BACKGROUND: Quantitative analysis can be used in combination with fluorescence microscopy. Although the human eye is able to obtain good qualitative results, when analyzing the spatial organization of telomeres in interphase nuclei, there is a need for quantitative results based on image analysis. METHODS: We developed a tool for analyzing three-dimensional images of telomeres stained by fluorescence in situ hybridization in interphase nuclei with DNA counterstained with 4',6-diamidino-2-phenylindole. After deconvolution of the image, we segmented individual telomeres. From the location of the telomeres we derived a distribution parameter rhoT, which indicated whether the telomeres were in a disk (rhoT > 1) or not (rhoT approximately 1). We sorted mouse lymphocyte nuclei and measured rhoT. We also performed a bromodeoxyuridine synchronous cell sorting experiment on live cells and measured rhoT at several instances. RESULTS: Measuring rhoT for nuclei in G0/G1, S, and G2 produced 1.4 +/- 0.1, 1.5 +/- 0.2, and 14 +/- 2, respectively, showing a significant difference between G2 and G0/G1 or S. For the bromodeoxyuridine synchronous cell sorting experiment, we found a cell cycle dependency of rhoT and a correlation between rhoT and an observer. CONCLUSIONS: In this study we present a quantitative method to characterize the organization of telomeres using three-dimensional imaging, image processing, and image analysis.     

Endocytosis and recycling of subunit H1 of the asialoglycoprotein receptor is independent of oligomerization with H2.

The human asialoglycoprotein receptor is composed of two homologous subunits, H1 and H2. By expressing the two subunits in transfected fibroblast cell lines, it has been shown previously that the formation of a hetero-oligomeric complex is necessary for the transport of H2 to the plasma membrane and for high-affinity ligand binding. Here we show that subunit H1, when expressed in the absence of H2, is capable of internalization through coated pits and recycling. The kinetics of these processes are very similar to those of the H1-H2 complex. To study endocytosis in the absence of ligand binding, the cell surface was labeled at 4 degrees C with the 125I-iodinated impermeant reagent sulfosuccinimidyl-3-(4-hydroxyphenyl) propionate, the cells were incubated at 37 degrees C for different times and the amount of internalized receptor was determined by protease digestion of surface proteins and immunoprecipitation. Similarly, recycling of surface-labeled and then internalized receptor protein was studied by monitoring its reappearance on the surface in the presence of exogenous protease. Our results show that subunit H1 contains all the signals necessary for receptor endocytosis and recycling independent of ligand binding.     

Altered dynamics of ubiquitin hybrid proteins during tumor cell apoptosis

The ubiquitin hybrid genes Uba80 and Uba52 encode ubiquitin (Ub), which is fused to the ribosomal proteins S27a (RPS27a) and L40 (RPL40), respectively. Here, we show that these genes are preferentially over-expressed during hepatoma cell apoptosis. Experiments using the tet-inducible transgenic system revealed that over-expression of the ubiquitin hybrid genes sensitized the cells to apoptosis. Further analysis suggested that Ub, and not RPS27a or RPL40, was associated with apoptotic cell death. Cleavage-resistant mutation analysis revealed that the N-terminal portion and the last two amino acids (GG) of Ub are critical for cleavage at the junction between the two protein moieties. An apoptogenic stimulus enhances the nuclear targeting and aggregation of Ub in the nucleus, resulting in histone H2A deubiquitylation followed by abnormal ubiquitylation of the nuclear envelope and the lamina. These events accompany the apoptotic nuclear morphology in the late stage of apoptosis. Each fused RP is localized in the nucleoli. These results suggest a role for Ub hybrid proteins in the altered nuclear dynamics of Ub during tumor cell apoptosis induced by apoptogenic stimuli.     

Efficacy of electrolysed oxidizing water in inactivating Vibrio parahaemolyticus on kitchen cutting boards and food contact surfaces

AIM: To determine the efficacy of electrolysed oxidizing (EO) water in inactivating Vibrio parahaemolyticus on kitchen cutting boards and food contact surfaces. METHODS AND RESULTS: Cutting boards (bamboo, wood and plastic) and food contact surfaces (stainless steel and glazed ceramic tile) were inoculated with V. parahaemolyticus. Viable cells of V. parahaemolyticus were detected on all cutting boards and food contact surfaces after 10 and 30 min, respectively, at room temperatures. Soaking inoculated food contact surfaces and cutting boards in distilled water for 1 and 3 min, respectively, resulted in various reductions of V. parahaemolyticus, but failed to remove the organism completely from surfaces. However, the treatment of EO water [pH 2.7, chlorine 40 ppm, oxidation-reduction potential 1151 mV] for 30, 45, and 60 s, completely inactivated V. parahaemolyticus on stainless steel, ceramic tile, and plastic cutting boards, respectively. CONCLUSIONS: EO water could be used as a disinfecting agent for inactivating V. parahaemolyticus on plastic and wood cutting boards and food contact surfaces. SIGNIFICANCE AND IMPACT OF THE STUDY: Rinsing the food contact surfaces with EO water or soaking cutting boards in EO water for up to 5 min could be a simple strategy to reduce cross-contamination of V. parahaemolyticus during food preparation.