2,565 research outputs found

    Coarse-graining protein energetics in sequence variables

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    We show that cluster expansions (CE), previously used to model solid-state materials with binary or ternary configurational disorder, can be extended to the protein design problem. We present a generalized CE framework, in which properties such as energy can be unambiguously expanded in the amino-acid sequence space. The CE coarse grains over nonsequence degrees of freedom (e.g., side-chain conformations) and thereby simplifies the problem of designing proteins, or predicting the compatibility of a sequence with a given structure, by many orders of magnitude. The CE is physically transparent, and can be evaluated through linear regression on the energies of training sequences. We show, as example, that good prediction accuracy is obtained with up to pairwise interactions for a coiled-coil backbone, and that triplet interactions are important in the energetics of a more globular zinc-finger backbone.Comment: 10 pages, 3 figure

    Use of an oocyte expression assay to reconstitute inductive signaling.

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    Hormonal adaptations to different training intensities during the preparation of elite judokas for competition

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    Many efforts are made to quantify objectively the balance between training load and the athlete’s tolerance. The aim of the present study was to evaluate the balance between anabolic (i.e. testosterone and IGF-I) and catabolic (i.e. cortisol) hormones in elite judokas during their preparations (4 months) for the European championships. Five healthy elite Israeli judokas (four male, one female, age range 17–26 years) were tested at baseline, after two months of moderate training, after another one month of intense training, after one month of tapering down prior to the competition, and during the week after the championships. Hormonal level remained relatively unchanged during period of moderate training. Circulating levels of IGF-I and testosterone decreased and the cortisol/testosterone ratio increased during intense training. However, only the decrease in circulating IGF-I level reached statistical significance. Both levels of IGF-I and testosterone increased significantly, and the cortisol/testosterone ratio decreased significantly following tapering down, prior to the championships, compared to the levels during intense training. Changes in the balance of anabolic and catabolic hormones during the training season may help elite athletes and assist their coaches in their preparation for the competition

    How well-proportioned are lens and prism spaces?

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    The CMB anisotropies in spherical 3-spaces with a non-trivial topology are analysed with a focus on lens and prism shaped fundamental cells. The conjecture is tested that well proportioned spaces lead to a suppression of large-scale anisotropies according to the observed cosmic microwave background (CMB). The focus is put on lens spaces L(p,q) which are supposed to be oddly proportioned. However, there are inhomogeneous lens spaces whose shape of the Voronoi domain depends on the position of the observer within the manifold. Such manifolds possess no fixed measure of well-proportioned and allow a predestined test of the well-proportioned conjecture. Topologies having the same Voronoi domain are shown to possess distinct CMB statistics which thus provide a counter-example to the well-proportioned conjecture. The CMB properties are analysed in terms of cyclic subgroups Z_p, and new point of view for the superior behaviour of the Poincar\'e dodecahedron is found
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