Secondary structure motifs and small protein domains can act as building blocks that are isolated and investigated to gain insights into protein global structure but can also modulate interactions with external partners. Most progress has been made in this field using synthetic peptides. Fragmentation of folded proteins by proteolytic enzymes that act preferentially on exposed and less structured sites can help to isolate shorter polypeptides with preserved secondary and tertiary structures that mimic the original protein architecture. Such mols. can be used as probes for structural studies and as tools for in vitro assays to select active fragments useful as agonists or antagonists of the original protein or as scaffolds for the design of more potent and selective ligands. This simple but effective proteolytic methodol. has been successfully applied to det. antagonists of protein-protein interactions, allowing the identification of inhibitors with high efficacy and specificity. Here, several studies are presented, including the complex between phosphoprotein enriched in diabetes/phosphoprotein enriched in astrocytes (PED/PEA-15)and phospholipase 1 (PLD1), believed to play a relevant role in the insulin resistance mechanism in phosphoprotein enriched in diabetes/phosphoprotein enriched in astrocytes-over-expressing tissues, the self-assocn. of BCL10 caspase recruitment domain that mediates a protein oligomerization process responsible for NF-.kappa.B activation, and the self-assocn. of growth arrest and DNA damage-inducible factor 45.beta. (GADD45.beta.), a major player of the endogenous NF-.kappa.B-mediated resistance to apoptosis.
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