The Importance of Detail: How Differences in Ligand Structures Determine Distinct Functional Responses in Integrin ?v?3

Ligand-based control of protein functional motions can provide novel opportunities in the study of fundamental biological mechanisms and in the development of novel therapeutics. Here, we address ligand-based modulation of integrin functions. Inhibitors of integrin ?v?3 are interesting anticancer agents but their molecular mechanisms are still unclear: peptides and peptidomimetics characterized by the RGD or isoDGR binding motifs have shown controversial agonist/antagonist effects. We investigate the differential mechanisms of integrin activation/deactivation by three distinct ligands (cyclo-RGDf(NMe)V (Cilengitide), cyclo[DKP3-RGD], cyclo[DKP3-isoDGR]), through comparative analysis of ligand-controlled protein internal dynamics: while RGD facilitates the onset of dynamic states leading to activation, isoDGR induces a diffuse rigidification of the complex consistent with antagonist activities. Computational predictions are experimentally probed by showing that antibody AP5, selective for active integrin conformations, binds specifically to the RGD complexes and not to the isoDGR one, supporting opposite functional roles for the two motifs targeting the same binding site.