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1.
Docking algorithms predict the structure of protein–protein interactions. They sample the orientation of two unbound proteins to produce various predictions about their interactions, followed by a scoring step to rank the predictions. We present a statistical assessment of scoring functions used to rank near‐native orientations, applying our statistical analysis to a benchmark dataset of decoys of protein–protein complexes and assessing the statistical significance of the outcome in the Critical Assessment of PRedicted Interactions (CAPRI) scoring experiment. A P value was assigned that depended on the number of near‐native structures in the sampling. We studied the effect of filtering out redundant structures and tested the use of pair‐potentials derived using ZDock and ZRank. Our results show that for many targets, it is not possible to determine when a successful reranking performed by scoring functions results merely from random choice. This analysis reveals that changes should be made in the design of the CAPRI scoring experiment. We propose including the statistical assessment in this experiment either at the preprocessing or the evaluation step. Proteins 2010. © 2010 Wiley‐Liss, Inc. 相似文献
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Cantó C Suárez E Lizcano JM Griñó E Shepherd PR Fryer LG Carling D Bertran J Palacín M Zorzano A Gumà A 《The Journal of biological chemistry》2004,279(13):12260-12268
Neuregulin-1, a growth factor that potentiates myogenesis induces glucose transport through translocation of glucose transporters, in an additive manner to insulin, in muscle cells. In this study, we examined the signaling pathway required for a recombinant active neuregulin-1 isoform (rhHeregulin-beta(1), 177-244, HRG) to stimulate glucose uptake in L6E9 myotubes. The stimulatory effect of HRG required binding to ErbB3 in L6E9 myotubes. PI3K activity is required for HRG action in both muscle cells and tissue. In L6E9 myotubes, HRG stimulated PKBalpha, PKBgamma, and PKCzeta activities. TPCK, an inhibitor of PDK1, abolished both HRG- and insulin-induced glucose transport. To assess whether PKB was necessary for the effects of HRG on glucose uptake, cells were infected with adenoviruses encoding dominant negative mutants of PKBalpha. Dominant negative PKB reduced PKB activity and insulin-stimulated glucose transport but not HRG-induced glucose transport. In contrast, transduction of L6E9 myotubes with adenoviruses encoding a dominant negative kinase-inactive PKCzeta abolished both HRG- and insulin-stimulated glucose uptake. In soleus muscle, HRG induced PKCzeta, but not PKB phosphorylation. HRG also stimulated the activity of p70S6K, p38MAPK, and p42/p44MAPK and inhibition of p42/p44MAPK partially repressed HRG action on glucose uptake. HRG did not affect AMPKalpha(1) or AMPKalpha(2) activities. In all, HRG stimulated glucose transport in muscle cells by activation of a pathway that requires PI3K, PDK1, and PKCzeta, but not PKB, and that shows cross-talk with the MAPK pathway. The PI3K, PDK1, and PKCzeta pathway can be considered as an alternative mechanism, independent of insulin, to induce glucose uptake. 相似文献
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Varun B. Kothamachu Elisenda Feliu Carsten Wiuf Luca Cardelli Orkun S. Soyer 《PLoS computational biology》2013,9(11)
Achieving a complete understanding of cellular signal transduction requires deciphering the relation between structural and biochemical features of a signaling system and the shape of the signal-response relationship it embeds. Using explicit analytical expressions and numerical simulations, we present here this relation for four-layered phosphorelays, which are signaling systems that are ubiquitous in prokaryotes and also found in lower eukaryotes and plants. We derive an analytical expression that relates the shape of the signal-response relationship in a relay to the kinetic rates of forward, reverse phosphorylation and hydrolysis reactions. This reveals a set of mathematical conditions which, when satisfied, dictate the shape of the signal-response relationship. We find that a specific topology also observed in nature can satisfy these conditions in such a way to allow plasticity among hyperbolic and sigmoidal signal-response relationships. Particularly, the shape of the signal-response relationship of this relay topology can be tuned by altering kinetic rates and total protein levels at different parts of the relay. These findings provide an important step towards predicting response dynamics of phosphorelays, and the nature of subsequent physiological responses that they mediate, solely from topological features and few composite measurements; measuring the ratio of reverse and forward phosphorylation rate constants could be sufficient to determine the shape of the signal-response relationship the relay exhibits. Furthermore, they highlight the potential ways in which selective pressures on signal processing could have played a role in the evolution of the observed structural and biochemical characteristic in phosphorelays. 相似文献
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Elisenda Amat Josefina Palou Celia Sanchez JoséMaría Rodriguez Mellado Francisco García Blanco 《International journal of biological macromolecules》1985,7(5):307-310
Using fluorescence and SH-groups titration techniques we have proved existence of an inverse relationship betweenthe rate constants of bimolecular deactivation of phosphorylase b coenzyme by iodide ion in the presence of AMP and its analogues and the shielding rate constants of slow cysteine, C-108, by the diverse nucleotides, The greater the shielding rate constants, the smaller the rate constant of deactivation by iodied ion. The analogues we have used were AMP, IMP, 2′dAMP, 2′AMP and 3′AMP. 相似文献
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The preparation of the thymine peptide nucleicacid (PNA) monomer carrying a 2-nitrophenyl group in position4 is described. This monomer is incorporated into PNAoligomers and reacted with amines to yield PNA oligomerscarrying 5-methylcytosine derivatives. During thedeprotection-modification step two side reactions weredetected: degradation of PNA oligomer from the N-terminal residue and modification of N
4-tert-butylbenzoyl cytosine residue. Protection of the N-terminal position and the use of N
4-acetyl group for the protection of cytosine eliminate these side reactions. 相似文献
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Michael Marcondes de Freitas Carsten Wiuf Elisenda Feliu 《Bulletin of mathematical biology》2017,79(7):1662-1686
Known graphical conditions for the generic and global convergence to equilibria of the dynamical system arising from a reaction network are shown to be invariant under the so-called successive removal of intermediates, a systematic procedure to simplify the network, making the graphical conditions considerably easier to check. 相似文献
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Iglesias-Guimarais V Gil-Guiñon E Gabernet G García-Belinchón M Sánchez-Osuna M Casanelles E Comella JX Yuste VJ 《The Journal of biological chemistry》2012,287(10):7766-7779
Apoptotic cell death is characterized by nuclear fragmentation and oligonucleosomal DNA degradation, mediated by the caspase-dependent specific activation of DFF40/CAD endonuclease. Here, we describe how, upon apoptotic stimuli, SK-N-AS human neuroblastoma-derived cells show apoptotic nuclear morphology without displaying concomitant internucleosomal DNA fragmentation. Cytotoxicity afforded after staurosporine treatment is comparable with that obtained in SH-SY5Y cells, which exhibit a complete apoptotic phenotype. SK-N-AS cell death is a caspase-dependent process that can be impaired by the pan-caspase inhibitor q-VD-OPh. The endogenous inhibitor of DFF40/CAD, ICAD, is correctly processed, and dff40/cad cDNA sequence does not reveal mutations altering its amino acid composition. Biochemical approaches show that both SH-SY5Y and SK-N-AS resting cells express comparable levels of DFF40/CAD. However, the endonuclease is poorly expressed in the cytosolic fraction of healthy SK-N-AS cells. Despite this differential subcellular distribution of DFF40/CAD, we find no differences in the subcellular localization of both pro-caspase-3 and ICAD between the analyzed cell lines. After staurosporine treatment, the preferential processing of ICAD in the cytosolic fraction allows the translocation of DFF40/CAD from this fraction to a chromatin-enriched one. Therefore, the low levels of cytosolic DFF40/CAD detected in SK-N-AS cells determine the absence of DNA laddering after staurosporine treatment. In these cells DFF40/CAD cytosolic levels can be restored by the overexpression of their own endonuclease, which is sufficient to make them proficient at degrading their chromatin into oligonucleosome-size fragments after staurosporine treatment. Altogether, the cytosolic levels of DFF40/CAD are determinants in achieving a complete apoptotic phenotype, including oligonucleosomal DNA degradation. 相似文献
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Xavier Rojano i Luque Elisenda Serra Marsal Olga Soler Cors Antoni Salvà Casanovas 《Revista espa?ola de geriatría y gerontología》2021,56(1):29-34
IntroductionThe aging of the population has led to the introduction of qualitative and quantitative changes in healthcare resources, among which are the introduction of models of person-centred care (PCC), although there is a lack of information on their impact. The objective of this study is to assess the impact of a PCC model on the quality of life, well-being and thriving, in people living in nursing homesMethodsCross-sectional study. Population: all persons who lived indefinitely in the two participating centres that gave their consent. Impact of PCC vs. traditional model was assessed in terms of quality of life, well-being and thriving. Effect size was estimated with Cohen d adjusted for health problems, Charlson index, and presence of depression.ResultsOverall participation was 78% (59/77 persons from the conventional centre and 66/88 from the PCC). The people of the PCC centre had better well-being (d = 0.378) and thriving (d = 0.566). No differences were found in quality of life.ConclusionThe PCC model can have a positive impact on well-being and thriving in persons living in nursing homes. 相似文献