Structural bioinformatic analyses of (macro)molecular interactions of biomedical relevance: an experimental validation

Structural bioinformatics, like many other subdisciplines within bioinformatics, is characterized by the establishment of general purpose methods for manipulating information about biological macromolecules, and the application of these methods to solving problems in biology and creating new knowledge. Among its capabilities, structural bioinformatics can analyse the feasible (macro)molecular interactions and assists, or sometimes anticipates, the experimental approaches in biological research, even starting from a prediction analysis of the three-dimensional structures of the partners. This thesis reports on the in silico and in vitro characterization of a selection on physiologically relevant processes involving binding between proteins and endogenous and exogenous ligands, with results confirming the well-founded capability of the bioinformatic methods to clarify these issues. The general approach consisted in: (i) the in silico derivation of the predictive structural and equilibrium parameters for the ligand-receptor complexes starting from either deposited crystallographic (where available) or homology modeled structures; (ii) the experimental validation of the computational data according to both "in solution" and "on surface" in vitro studies; (iii) the final evaluation of the effects of the interactions on cell based models. Specifically, during the PhD period my interest was mainly focused on the characterization of the molecular basis of the systemic sclerosis (SSc), a rare human auto-immune disease, with particular emphasis on the interaction between platelet-derived growth factor receptor and a selection of human autoantibodies expressed in SSc patients (the revised version of this manuscript is currently under evaluation in Nature Communications). This project was paralleled by several other studies, among which the modulation by natural polyphenols of two human enzymes, HMG-CoA reductase and plasmin, involved in cholesterol biosynthetic pathway and in cellular adhesion and mobility, respectively. The results of these studies were published in impacted scientific journals.