Structural equivalence classes, biological

The classification of logical network structures imposed by the hypercube description depends on the signs of the focal point coordinates - associated with each orthant of phase space, which leads to the hypercube representation of the allowed flows. We consider that two different networks are in the same dynamical equivalence class if their directed A-cube representations can be superimiposed under a symmetry of the A-cube. For example, in three dimensions there is only one cyclic attractor (see Fig. 3b), but this can appear in eight different orientations on the 3-cube. From a dynamical perspective, exactly the same qualitative dynamics can be found in any of these networks provided the focal points are chosen in an identical fashion. However, from a biological... 

Ironically, SE or TSST-1 concentrations that cause T-cell proliferation do not always correlate with receptor affinity. For instance, SEE binds HLA-DR with 100-fold lower affinity relative to the very similarly structured SEA however, SEE stimulates T-cell proliferation to equivalent levels as SEA. The dose-response curves for cytokine and chemokine production in vitro by staphylococcal superantigen-stimulated cells are also very similar despite differences in affmity/specificity for major histocompatibility complex class II and T-cell receptor V/3 molecules. Overall, these observations suggest that the biological effects of staphylococcal superantigens are induced at rather low, nonsaturating occupancy rates not readily classified by typical biokinetics. 

Since oxazolidines and oxazolidinones are fiindamental structural classes in organic chemistry (chiral auxiliaries) and in medicinal chemistry (e.g., Linezolid) and since they mask P-hydroxy-a-amino acids, which are widespread in various biologically active compounds and in natural products, the enantioselective synthesis of oxazolidinones is a challenging topic. Indeed, a new method for the direct synthesis of chiral 4-carboxyl oxazolidinones 168 by the catalytic asymmetric aldol reaction of isocyanato-malonate diesters 166 with aldehydes 167 in the presence of a thiourea catalyst (TUC) was developed. Since the resulting chiral 4-carboxy oxazolidinones are the equivalent of P-hydroxy-a-amino acids, this procedure... 

If we consider that the role played by an amino acid inside a folded protein is equivalent to its interaction degree, then these plots show that despite a functional diversity between the 4 SCOP classes, there are globally the same amino acids which interact most, namely the Ala, Cys, Gly, Leu, Val. Therefore, the amino adds having a high connectivity interact independently of the protein biological function, we will explain this behavior further. Thus, the figure shows dearly that the amino add Ala plays a central role in the studied proteins independently of the classification of their secondary structure. 

On the basis of these data, epothilones A, B and some congeners have been widely pursued as lead structures for the development of a new generation of non-taxane-derived microtubule stabilizers for cancer treatment [5]. Five representatives of this class are currently undergoing clinical evaluation in humans. This outcome confirms the view that natural products provide a vast pool of potential lead structures for drug discovery. In a very general sense, the strategy that resulted in 12-aza-epothilones could be viewed as the synthesis-based equivalent to the discovery of a new natural product with a specific biological activity. 

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