Protein ligand complexation: a computational and experimental approach

Abstract

Herein, we present an integrated computational and experimental study to tackle the interactions between proteins and ligands. As an example of a protein we have chosen fibrinogen, a blood serum protein related to coagulation processes. While as a ligand we have chosen a penicillin: cloxacillin. With respect to computational tools molecular docking simulation with elastic network based on collective low-frequency normal modes and perturbation response scanning maps were proposed to evaluate the conformational binding mechanism. With respect to the experimental part, the tools chosen were calorimetric (ITC and DSC) and spectroscopic (Raman and fluorescence). The combination of all these techniques will give us a broad and concise view of the bonding process between the two species.