Cellular Senescence,Epigenetic Switches and c-Myc

In response to hyperproliferative signaling elicited by transforming oncogenes some normal human cells can enter replicative senescence as a tumor defense mechanism. We recently found that human fibroblasts or endothelial cells with genetically-engineered reduction of proto-oncogene c-Myc expression switched with an increased frequency to a senescent state by a telomere-independent mechanism involving the polycomb group repressor Bmi-1 and the cyclin-dependent kinase inhibitor p16^INK4a. The same regulatory circuit was triggered upon exposure to mild oxidative stress. These findings point to the existence of a mechanism for monitoring hypoproliferative signaling, whose function may be to limit the proliferation and accretion of physiologically compromised cells. This mechanism may be another example of antagonistic pleiotropy leading to organismal aging.     

生物分子开关研究进展

分子开关是建立在分子水平上的一个可逆过程,外界条件的改变能使分子的结构或构型会有一些改变,从而表现出一些特殊的性质.其在生物体内的信号传导和信息调控等方面发挥着重要作用,成为近年来国内外的一大研究热点.本文介绍了胚胎干细胞分化的重要分子开关:Oct-3/4、神经突起相关分子开关Rho族GTP酶、控制肌卫星细胞激活的分子开关转录因子RBP-J、慢性疼痛的分子开关蛋白激酶G(PKG)、脂肪控制分子开关Wnt蛋白、调节核糖体翻译功能的分子开关L11蛋白、控制饥饿的分子开关巨噬细胞因子MIC-1、调节人体生理节奏的分子开关BMAL1基因、癌症相关的分子开关Wnt蛋白家族以及糖尿病相关的活性开关蛋白TORC2等生物学领域调控功能分子开关的作用机理以及相关研究进展情况.     

Attentional Switches and Dual-Task Interference

In four experiments, we studied the time course of interference between detection of an oddball orientation target (OT) in an 8-item circular search display, and identification of a letter target (LT) in a central stream of distractor letters. Dual-task performance for different temporal lags between targets was compared to single-task performance. When the LT preceded the OT, dual-task performance levels were reduced at short inter-target intervals of 0 and 166 ms; when the OT preceded the LT, the dual-task interference was unexpectedly stronger and lasted for up to 500 ms. Resource competition due to temporally overlapping target processing cannot account for this result, because the feature search task is easier than the letter identification task, and therefore would have generated less interference when presented first. Two alternative explanations were explored. First, by manipulating the spatial inter-target distance, we investigated to what degree there is a penalty associated with directing the attentional window from a large object (the search display) to a smaller object (the central letter stream). Second, by varying the duration of the OT and subsequent mask, we studied whether the interference was caused by the difficulty of disengaging attention from the search display. Results support this second explanation and thus indicate that switching attention to the letter stream is hampered by the continuing presence of (masked) search display items. This result shows that attentional effects may play a major role in dual-task execution and can easily obscure interference due to other factors such as resource competition.     

Cooperative Changes in Solvent Exposure Identify Cryptic Pockets,Switches, and Allosteric Coupling

Proteins are dynamic molecules that undergo conformational changes to a broad spectrum of different excited states. Unfortunately, the small populations of these states make it difficult to determine their structures or functional implications. Computer simulations are an increasingly powerful means to identify and characterize functionally relevant excited states. However, this advance has uncovered a further challenge: it can be extremely difficult to identify the most salient features of large simulation data sets. We reasoned that many functionally relevant conformational changes are likely to involve large, cooperative changes to the surfaces that are available to interact with potential binding partners. To examine this hypothesis, we introduce a method that returns a prioritized list of potentially functional conformational changes by segmenting protein structures into clusters of residues that undergo cooperative changes in their solvent exposure, along with the hierarchy of interactions between these groups. We term these groups exposons to distinguish them from other types of clusters that arise in this analysis and others. We demonstrate, using three different model systems, that this method identifies experimentally validated and functionally relevant conformational changes, including conformational switches, allosteric coupling, and cryptic pockets. Our results suggest that key functional sites are hubs in the network of exposons. As a further test of the predictive power of this approach, we apply it to discover cryptic allosteric sites in two different β-lactamase enzymes that are widespread sources of antibiotic resistance. Experimental tests confirm our predictions for both systems. Importantly, we provide the first evidence, to our knowledge, for a cryptic allosteric site in CTX-M-9 β-lactamase. Experimentally testing this prediction did not require any mutations and revealed that this site exerts the most potent allosteric control over activity of any pockets found in β-lactamases to date. Discovery of a similar pocket that was previously overlooked in the well-studied TEM-1 β-lactamase demonstrates the utility of exposons.     

Fair Scheduling for Input Buffered Switches

Input buffered switch architecture has become attractive for implementing high performance switches for workstation clusters. It is challenging to provide a scheduling technique that is both highly efficient and fair in resource allocation. In this paper, we first introduce an iterative Fair Scheduling (iFS) scheme for input buffered switches that supports fair bandwidth distribution among the flows and achieves asymptotically 100% throughput. We then apply the idea of fair scheduling to switches with multicasting capability and propose an mFS scheme which allocates bandwidth to various flows according to their reservations. We show that mFS produces throughput comparable to the existing schemes while distributing the bandwidth as per the given reservations. Extensive simulation results are presented to validate the effectiveness of our proposed schemes.     

Switches, catapults, and chaperones: steady-state kinetic analysis of Hsp70-substrate interactions

Hsp70 chaperones are heterotropic allosteric systems in which ATP and misfolded or aggregated polypeptides are the activating ligands. To gain insight into the mechanism by which ATP and polypeptides regulate Hsp70 chaperone activity, the effect of a short peptide on the K(M) for ATP was analyzed using the Escherichia coli Hsp70 called DnaK. In the absence of peptide, the K(-P)(M) for ATP is 52 +/- 11 nM, whereas this value jumps to 14.6 +/- 1.6 microM in the presence of saturating peptide. This finding supports a mechanism in which ATP binding drives the chaperone in one direction and peptide binding pushes the chaperone back in the opposite direction (and thus increases K(M)), according to ATP + DnaK.P <==> ATP.DnaK.P <==> ATP.DnaK* + P, where ATP.DnaK.P is an intermediate from which competing ATP hydrolysis occurs (ATP.DnaK.P --> ADP.DnaK.P). We show that this branched mechanism can even explain how DnaK hydrolyzes ATP in the absence of peptide and that the true rate constant for DnaK-mediated ATP hydrolysis (k(hy)) in the absence of peptide may be as high as 0.5 s(-)(1) (rather than 5 x 10(-)(4) s(-)(1) as often stated in the literature). What happens is that a conformational equilibrium outcompetes ATP hydrolysis and effectively reduces the concentration of the intermediate by a factor of a thousand, resulting in the following relation: k(cat) = k(hy)/1000 = 5 x 10(-)(4) s(-)(1). How polypeptide substrates and the co-chaperone DnaJ modulate DnaK to achieve its theoretical maximal rate of ATP hydrolysis, which we suggest is 0.5 s(-)(1), is discussed.     

Plasmonic Electro-Optical Switches Operating at Telecom Wavelengths

Electro-optical (EO) switches with a subwavelength device length based on metal–dielectric–metal nanocavities waveguide combined with organic EO materials have been proposed and numerically investigated. The finite difference time domain (FDTD) method with perfectly matched layer absorbing boundary condition is adopted to simulate and study their properties. The FDTD simulation results reveal that these structures filled with EO materials can realize the function of switch with low-driving voltage. The wavelength conversion switch structure might become a choice for the design of integrated architectures for optical computing and communication, especially in WDM systems in the nanoscale.     

TXNIP Switches Tracks toward a Terminal UPR

During the progression of diabetes, crosstalk between ER stress and inflammation controls islet cell fate. In this issue, Lerner et?al. (2012) and Oslowski et?al. (2012) discover that thioredoxin-interacting protein (TXNIP) is a regulatory switch connecting the terminal unfolded protein response (UPR) and NLRP3 inflammasome to mediate β cell death.     

Exploring Performance Parameters of Artificial Allosteric Protein Switches

Biological information processing networks rely on allosteric protein switches that dynamically interconvert biological signals. Construction of their artificial analogues is a central goal of synthetic biology and bioengineering. Receptor domain insertion is one of the leading methods for constructing chimeric protein switches. Here we present an in vitro expression-based platform for the analysis of chimeric protein libraries for which traditional cell survival or cytometric high throughput assays are not applicable. We utilise this platform to screen a focused library of chimeras between PQQ-glucose dehydrogenase and calmodulin. Using this approach, we identified 50 chimeras (approximately 23% of the library) that were activated by calmodulin-binding peptides. We analysed performance parameters of the active chimeras and demonstrated that their dynamic range and response times are anticorrelated, pointing to the existence of an inherent thermodynamic trade-off. We show that the structure of the ligand peptide affects both the response and activation kinetics of the biosensors suggesting that the structure of a ligand:receptor complex can influence the chimera’s activation pathway. In order to understand the extent of structural changes in the reporter protein induced by the receptor domains, we have analysed one of the chimeric molecules by CD spectroscopy and hydrogen–deuterium exchange mass spectrometry. We concluded that subtle ligand-induced changes in the receptor domain propagated into the GDH domain and affected residues important for substrate and cofactor binding. Finally, we used one of the identified chimeras to construct a two-component rapamycin biosensor and demonstrated that core switch optimisation translated into improved biosensor performance.