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Styliani Consta Anatoly Malevanets Myong In Oh Mahmoud Sharawy 《Molecular simulation》2018,44(13-14):1033-1043
AbstractThe free energy calculation method emerges as a viable technique for ‘in-silico’ calorimetry. Efficient sampling techniques and the good choice of a reaction path connecting the reactant and the product state enable accurate computations of the free energy differences. We argue that in many cases the thermodynamic integration technique has the lowest variance when the transformation between the reactant and the product state proceeds along the natural path of the studied chemical reaction. We provide examples of free energy calculations for the fragmentation of the charged clusters and the swapping reaction of oligomer formation in proteins that follow a tentative reaction mechanism. 相似文献
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Roussakis E Voutsadaki S Pinakoulaki E Sideris DP Tokatlidis K Katerinopoulos HE 《Cell calcium》2008,44(3):270-275
A new fluorescent Zn2+ indicator, namely, ICPBCZin was synthesized and the spectral profile of its free and Zn2+ bound forms was studied. The newly synthesized zinc indicator incorporates as chromophore the chromeno [3′,2′:3,4]pyrido[1,2a] [1,3]benzimidazole moiety and belongs to the dicarboxylate-type of zinc probes. The compound is excited with visible light, exhibits high selectivity for zinc in the presence of calcium and other common biological ions, and its Zn2+ dissociation constant is 4.0 nM. Fluorescence spectra studies of ICPBCZin indicated a clear shift in its emission wavelength maxima upon Zn2+ binding, as it belongs to the class of Photoinduced Charge Transfer (PCT) indicators, along with changes in fluorescence intensity that enable the compound to be used as a ratiometric, visible-excitable Zn2+ probe. 相似文献
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A drug-inducible transgenic system for direct reprogramming of multiple somatic cell types 总被引:1,自引:0,他引:1
Wernig M Lengner CJ Hanna J Lodato MA Steine E Foreman R Staerk J Markoulaki S Jaenisch R 《Nature biotechnology》2008,26(8):916-924
The study of induced pluripotency is complicated by the need for infection with high-titer retroviral vectors, which results in genetically heterogeneous cell populations. We generated genetically homogeneous 'secondary' somatic cells that carry the reprogramming factors as defined doxycycline (dox)-inducible transgenes. These cells were produced by infecting fibroblasts with dox-inducible lentiviruses, reprogramming by dox addition, selecting induced pluripotent stem cells and producing chimeric mice. Cells derived from these chimeras reprogram upon dox exposure without the need for viral infection with efficiencies 25- to 50-fold greater than those observed using direct infection and drug selection for pluripotency marker reactivation. We demonstrate that (i) various induction levels of the reprogramming factors can induce pluripotency, (ii) the duration of transgene activity directly correlates with reprogramming efficiency, (iii) cells from many somatic tissues can be reprogrammed and (iv) different cell types require different induction levels. This system facilitates the characterization of reprogramming and provides a tool for genetic or chemical screens to enhance reprogramming. 相似文献
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The Hierarchy of Exon-Junction Complex Assembly by the Spliceosome Explains Key Features of Mammalian Nonsense-Mediated mRNA Decay 下载免费PDF全文
Exon junction complexes (EJCs) link nuclear splicing to key features of mRNA function including mRNA stability, translation, and localization. We analyzed the formation of EJCs by the spliceosome, the physiological EJC assembly machinery. We studied a comprehensive set of eIF4A3, MAGOH, and BTZ mutants in complete or C-complex–arrested splicing reactions and identified essential interactions of EJC proteins during and after EJC assembly. These data establish that EJC deposition proceeds through a defined intermediate, the pre-EJC, as an ordered, sequential process that is coordinated by splicing. The pre-EJC consists of eIF4A3 and MAGOH-Y14, is formed before exon ligation, and provides a binding platform for peripheral EJC components that join after release from the spliceosome and connect the core structure with function. Specifically, we identified BTZ to bridge the EJC to the nonsense-mediated messenger RNA (mRNA) decay protein UPF1, uncovering a critical link between mRNP architecture and mRNA stability. Based on this systematic analysis of EJC assembly by the spliceosome, we propose a model of how a functional EJC is assembled in a strictly sequential and hierarchical fashion, including nuclear splicing-dependent and cytoplasmic steps. 相似文献
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Tet1 is dispensable for maintaining pluripotency and its loss is compatible with embryonic and postnatal development 总被引:4,自引:0,他引:4
Dawlaty MM Ganz K Powell BE Hu YC Markoulaki S Cheng AW Gao Q Kim J Choi SW Page DC Jaenisch R 《Cell Stem Cell》2011,9(2):166-175
The Tet family of enzymes (Tet1/2/3) converts 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). Mouse embryonic stem cells (mESCs) highly express Tet1 and have an elevated level of 5hmC. Tet1 has been implicated in ESC maintenance and lineage specification in?vitro but its precise function in development is not well defined. To establish the role of Tet1 in pluripotency and development, we have generated Tet1 mutant mESCs and mice. Tet1(-/-) ESCs have reduced levels of 5hmC and subtle changes in global gene expression, and are pluripotent and support development of live-born mice in tetraploid complementation assay, but display skewed differentiation toward trophectoderm in?vitro. Tet1 mutant mice are viable, fertile, and grossly normal, though some mutant mice have a slightly smaller body size at birth. Our data suggest that Tet1 loss leading to a partial reduction in 5hmC levels does not affect pluripotency in ESCs and is compatible with embryonic and postnatal development. 相似文献
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The main objective of the present study was to meticulously investigate an inclusive set of physicochemical and handle properties (determined through Kawabata evaluation system) of bioscoured cotton fabrics. The application of a commercial pectinase preparation, Bioprep 3000L, for a range of concentrations and treatment times, could create a pectin-free textile with low wax content. Multiple regression analysis was used to describe the effect of enzymatic process variables on pectin and waxes removal. Comparison of fabrics' properties such as wettability, whiteness, crystallinity index, and dyeing behaviour, confirmed that bioscouring could be as much effective as the conventional alkaline process. Uncovering the relationship between the composition of materials and their physicochemical properties was attempted. The application of higher enzyme concentrations generated fabrics with improved low-stress mechanical properties. Bending and shear rigidity, compressional resilience, as well as, extensibility of enzymatically treated cotton fabrics could be efficiently predicted by means of a single independent variable, the crystallinity index. 相似文献