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61.
Ala PJ Gonneville L Hillman MC Becker-Pasha M Wei M Reid BG Klabe R Yue EW Wayland B Douty B Polam P Wasserman Z Bower M Combs AP Burn TC Hollis GF Wynn R 《The Journal of biological chemistry》2006,281(43):32784-32795
Crystal structures of protein-tyrosine phosphatase 1B in complex with compounds bearing a novel isothiazolidinone (IZD) heterocyclic phosphonate mimetic reveal that the heterocycle is highly complementary to the catalytic pocket of the protein. The heterocycle participates in an extensive network of hydrogen bonds with the backbone of the phosphate-binding loop, Phe(182) of the flap, and the side chain of Arg(221). When substituted with a phenol, the small inhibitor induces the closed conformation of the protein and displaces all waters in the catalytic pocket. Saturated IZD-containing peptides are more potent inhibitors than unsaturated analogs because the IZD heterocycle and phenyl ring directly attached to it bind in a nearly orthogonal orientation with respect to each other, a conformation that is close to the energy minimum of the saturated IZD-phenyl moiety. These results explain why the heterocycle is a potent phosphonate mimetic and an ideal starting point for designing small nonpeptidic inhibitors. 相似文献
62.
Alaña I Parker JC Gault VA Flatt PR O'Harte FP Malthouse JP Hewage CM 《The Journal of biological chemistry》2006,281(24):16370-16376
Glucose-dependent insulinotropic polypeptide (GIP) is an incretin hormone that stimulates the secretion of insulin after ingestion of food. GIP also promotes the synthesis of fatty acids in adipose tissue. Therefore, it is not surprising that numerous literature reports have shown that GIP is linked to diabetes and obesity-related diseases. In this study, we present the solution structure of GIP in water determined by NMR spectroscopy. The calculated structure is characterized by the presence of an alpha-helical motif between residues Ser(11) and Gln(29). The helical conformation of GIP is further supported by CD spectroscopic studies. Six GIP-(1-42)Ala(1-7) analogues were synthesized by replacing individual N-terminal residues with alanine. Alanine scan studies of these N-terminal residues showed that the GIP-(1-42)Ala(6) was the only analogue to show insulin-secreting activity similar to that of the native GIP. However, when compared with glucose, its insulinotropic ability was reduced. For the first time, these NMR and modeling results contribute to the understanding of the structural requirements for the biological activity of GIP. 相似文献
63.
Mengel B Hunziker A Pedersen L Trusina A Jensen MH Krishna S 《Current opinion in genetics & development》2010,20(6):656-664
Oscillations are commonly observed in cellular behavior and span a wide range of timescales, from seconds in calcium signaling to 24 hours in circadian rhythms. In between lie oscillations with time periods of 1-5 hours seen in NF-κB, p53 and Wnt signaling, which play key roles in the immune system, cell growth/death and embryo development, respectively. In the first part of this article, we provide a brief overview of simple deterministic models of oscillations. In particular, we explain the mechanism of saturated degradation that has been used to model oscillations in the NF-κB, p53 and Wnt systems. The second part deals with the potential physiological role of oscillations. We use the simple models described earlier to explore whether oscillatory signals can encode more information than steady-state signals. We then discuss a few simple genetic circuits that could decode information stored in the average, amplitude or frequency of oscillations. The presence of frequency-detector circuit downstream of NF-κB or p53 would be a strong clue that oscillations are important for the physiological response of these signaling systems. 相似文献
64.
65.
Tadas Jako?iūnas L?rke Rebekka Holm Janne Verhein-Hansen Ala Trusina Geneviève Thon 《PLoS genetics》2013,9(10)
Mating-type switching in fission yeast results from gene conversions of the active mat1 locus by heterochromatic donors. mat1 is preferentially converted by mat2-P in M cells and by mat3-M in P cells. Here, we report that donor choice is governed by two portable recombination enhancers capable of promoting use of their adjacent cassette even when they are transposed to an ectopic location within the mat2-mat3 heterochromatic domain. Cells whose silent cassettes are swapped to mat2-M mat3-P switch mating-type poorly due to a defect in directionality but cells whose recombination enhancers were transposed together with the cassette contents switched like wild type. Trans-acting mutations that impair directionality affected the wild-type and swapped cassettes in identical ways when the recombination enhancers were transposed together with their cognate cassette, showing essential regulatory steps occur through the recombination enhancers. Our observations lead to a model where heterochromatin biases competitions between the two recombination enhancers to achieve directionality. 相似文献
66.
Ala Qabaja Mohammed Alshalalfa Tarek A Bismar Reda Alhajj 《EURASIP Journal on Bioinformatics and Systems Biology》2013,2013(1):3
BackgroundThere is a growing body of evidence associating microRNAs (miRNAs) with human diseases. MiRNAs are new key players in the disease paradigm demonstrating roles in several human diseases. The functional association between miRNAs and diseases remains largely unclear and far from complete. With the advent of high-throughput functional genomics techniques that infer genes and biological pathways dysregulted in diseases, it is now possible to infer functional association between diseases and biological molecules by integrating disparate biological information.ResultsHere, we first used Lasso regression model to identify miRNAs associated with disease signature as a proof of concept. Then we proposed an integrated approach that uses disease-gene associations from microarray experiments and text mining, and miRNA-gene association from computational predictions and protein networks to build functional associations network between miRNAs and diseases. The findings of the proposed model were validated against gold standard datasets using ROC analysis and results were promising (AUC=0.81). Our protein network-based approach discovered 19 new functional associations between prostate cancer and miRNAs. The new 19 associations were validated using miRNA expression data and clinical profiles and showed to act as diagnostic and prognostic prostate biomarkers. The proposed integrated approach allowed us to reconstruct functional associations between miRNAs and human diseases and uncovered functional roles of newly discovered miRNAs.ConclusionsLasso regression was used to find associations between diseases and miRNAs using their gene signature. Defining miRNA gene signature by integrating the downstream effect of miRNAs demonstrated better performance than the miRNA signature alone. Integrating biological networks and multiple data to define miRNA and disease gene signature demonstrated high performance to uncover new functional associations between miRNAs and diseases. 相似文献
67.
Shahram Ala Mohammad Shokrzadeh Masoud Golpour Ebrahim Salehifar Mitra Alami Amirhossein Ahmadi 《Biological trace element research》2013,153(1-3):22-27
Zinc and copper are important cofactors and modulators of many critical biological functions in many dermatological diseases including psoriasis. Studies must be performed in different societies to organize a governmental health organization nutritional program. Due to the lack of information related to these trace elements in Iranian psoriasis patients, the aim of this observational case–control study was to compare the serum zinc and copper levels and the zinc/copper ratio in psoriatic patients and healthy volunteers in Northern Iran. Zinc and copper serum concentrations were assayed in 25 selected psoriasis patients and compared with sex- and age-matched healthy volunteers. The mean copper level in psoriatic patients was significantly higher than in healthy volunteers (p?=?0.003), but no significant difference was observed in the zinc concentration between the two groups (p?=?0.57). This study was the first one among Iranian society, and no information have been published in the field yet. The results bring some new information related to Iranian psoriatic patients in contrast to some other studies in different region so that preventive programs could be made in this regard particularly for Iranian population. With respect to the high copper concentration in the Iranian psoriatic population, using copper-chelating agents, such as penicillamine may be suggested for Iranian patients following further comprehensive investigations. 相似文献
68.
Inbreeding reveals mode of past selection on male reproductive characters in Drosophila melanogaster
Outi Ala‐Honkola David J. Hosken Mollie K. Manier Stefan Lüpold Elizabeth M. Droge‐Young Kirstin S. Berben William F. Collins John M. Belote Scott Pitnick 《Ecology and evolution》2013,3(7):2089-2102
Directional dominance is a prerequisite of inbreeding depression. Directionality arises when selection drives alleles that increase fitness to fixation and eliminates dominant deleterious alleles, while deleterious recessives are hidden from it and maintained at low frequencies. Traits under directional selection (i.e., fitness traits) are expected to show directional dominance and therefore an increased susceptibility to inbreeding depression. In contrast, traits under stabilizing selection or weakly linked to fitness are predicted to exhibit little‐to‐no inbreeding depression. Here, we quantify the extent of inbreeding depression in a range of male reproductive characters and then infer the mode of past selection on them. The use of transgenic populations of Drosophila melanogaster with red or green fluorescent‐tagged sperm heads permitted in vivo discrimination of sperm from competing males and quantification of characteristics of ejaculate composition, performance, and fate. We found that male attractiveness (mating latency) and competitive fertilization success (P2) both show some inbreeding depression, suggesting they may have been under directional selection, whereas sperm length showed no inbreeding depression suggesting a history of stabilizing selection. However, despite having measured several sperm quality and quantity traits, our data did not allow us to discern the mechanism underlying the lowered competitive fertilization success of inbred (f = 0.50) males. 相似文献
69.
Ala Barakat Bettie Mercer Emilie Cooper Hui‐Min Chung 《Genesis (New York, N.Y. : 2000)》2009,47(3):161-168
Presenilin (Psn) is a multipass transmembrane protein that functions as the catalytic subunit of γ‐secretase for mediating intramembrane cleavage of type 1 transmembrane proteins. Normally active Psn is in the form of a heterodimer composed by its N‐terminal and C‐terminal fragments that are generated from a Presenilinase‐mediated endoproteolytic cleavage within its large cytosolic loop during assembly of the protease complex. Using the Psn forms that either bypass or disable Presenilinase‐mediated endoproteolysis, and a Psn form that has most of the large cytosolic loop deleted, we have established an in vivo system to enable investigations of Psn functional domains in Drosophila. We show that the Presenilinase‐mediated endoproteolytic event is not essential for producing Psn activity during animal development, and is regulated by integrity of the large cytosolic loop of Psn in Drosophila. The Psn transgenic flies described here could be applied to a broad range of studies on Psn functioning and its related γ‐secretase activity at any developmental stage. genesis 47:161–168, 2009. © 2009 Wiley‐Liss, Inc. 相似文献
70.
Febrile seizures, or febrile convulsions (FEB), represent the most common form of childhood seizures and are believed to be influenced by variations in several susceptibility genes. Most of the associated loci, however, remain 'orphan', i.e. the susceptibility genes they contain still remain to be identified. Further orphan loci have been mapped for a related disorder, genetic (generalized) epilepsy with febrile seizures plus (GEFS+).We show that both spatially mapped and 'traditional' gene expression data from the human brain can be successfully employed to predict the most promising candidate genes for FEB and GEFS+, apply our prediction method to the remaining orphan loci and discuss the validity of the predictions. For several of the orphan FEB/GEFS+ loci we propose excellent, and not always obvious, candidates for mutation screening in order to aid in gaining a better understanding of the genetic origin of the susceptibility to seizures. 相似文献