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Takalloo, Z.

Publications and source records attributed to Takalloo, Z..

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Stress-Dependent Conformational Changes of Artemin: Effects of Heat and Oxidant

Artemin is an abundant thermostable protein in Artemia embryos and considered as a highly efficient molecular chaperone against extreme environmental stress conditions. The dynamic conformational properties of artemin appear to play a critical role in its biological activities. In this study, we have investigated the conformational transitions and functional changes of artemin under heat and oxidative stress to find some evidence of the relationship between the structure and function of artemin. The tertiary and quaternary structures of artemin have been evaluated by fluorescence measurements, protein cross-linking analysis, and dynamic light scattering. Based on the structural analysis, artemin showed irreversible substantial conformational lability in response to heat and oxidant which mainly mediated through the hydrophobic interactions and dimerization of the chaperone. In addition, the chaperone-like activity of the heated and oxidized artemin was examined using lysozyme refolding assay and the experiments showed that although both factors, i.e. heat and oxidant, at specific levels improved artemin potency, simultaneous incubation with both stressors significantly triggered the activation of artemin. Moreover, the heat-induced dimerization of artemin was found to be the most critical factor for its activation. It was suggested that oxidation presumably acts through stabilizing the dimer structures of artemin through formation of disulfide bridges between the subunits and strengthens its chaperoning efficacy. Accordingly, it was proposed that artemin probably exists in a monomer-oligomer equilibrium in Artemia cysts and environmental stresses and intracellular portion of protein substrates may shift the equilibrium towards the active dimer forms of the chaperone. STATEMENT OF SIGNIFICANCEThere are a number of reports in which the chaperone-like activity of artemin, as a stress protein, has been confirmed in vivo and in vitro. Nonetheless, the details of structural changes of the protein have not been fully discovered yet. In the present work, we focused on conformational properties of artemin from A. urmiana upon exposing to heat and oxidation, by using various structural and functional analysis in order to predict the mechanisms of artemins activation. Notably, this is the first document on reporting the structural transitions of the chaperone in stress conditions.

biochemistry↗

afpCOOL: An Accurate Tool for Antifreeze Protein Detection

Various cold-adapted organisms produce antifreeze proteins (AFPs), which prevent to freeze of cell fluids by resisting the growth of the ice crystal. AFPs are currently being recognized in various organisms that are living in extremely low temperatures. AFPs have several important applications in increasing freeze tolerance of plants; maintain the tissue in frozen conditions and producing cold-hardy plants using transgenic technology. Substantial differences in the sequence and structure of the AFPs, pose a challenge for researcher to identify these proteins. In this paper, we proposed a novel method for identifying AFPs using support vector machine (SVM) by incorporating 4 types of features. Results on two benchmark datasets revealed the strength of the proposed method in AFP prediction. Also, according to the results on an independent test set, our method outperformed the current state-of-the-art methods. The further analysis showed the non-satisfactory performance of the BLAST in AFP detection: more than 62% of the BLAST searches have specificity less than 10% and there is no any BLAST search with sensitivity higher than 10%. These results reveal the urgent need for an accurate tool for AFP detection. In addition, the comparison results of the discrimination power of different feature types disclosed that evolutionary features and amino acid composition are the most contributing features in AFP detection. This method has been implemented as a stand-alone tool, namely afpCOOL, for various operating systems to predict AFPs with a user friendly graphical interface.\n\nAvailabilityafpCOOL is freely available at http://bioinf.modares.ac.ir:8080/AFPCOOL/page/afpcool.isp\n\nContactDr Zahiri zahiri@modares.ac.ir

bioinformatics↗