The main goal of this project is to ensure, at the molecular level, the experiments of developing "nanobiosensors" using advanced computer simulation techniques. Nanobiosensors are made by functionalizing tips of the atomic force microscopes (AFM) with organic monolayers. The nanoprototypes currently developed at Nanoneurobiophysic Research Group (GNN) are able to detect the presence of contaminants, and allows to understand the physical and chemical processes involved in studies of autoimmune diseases and neurodegenerative diseases. The computational studies will be responsible for quantify interaction energies between the immobilization surface and enzymes as well as the enzyme and inhibitors. The steps in this molecular study will be: i) study of the electronic structure of the enzyme and exact location of the active site; II) study of the effect of specific interactions on the electronic structure of the enzyme; III) parameterization of inhibitors molecules; IV) simulation of the system enzyme monomer/dimer + inhibitor, in order to obtain information about the mechanical stability of the system and the behavior of the active site in the presence of the herbicide; and V) binding free energy calculation of the following solvated systems: enzyme-inhibitor and enzyme-surface. Some of the enzymes studied by the GNN are: Acetyl-CoA Carboxylase (ACCase), shikimate 5-enol-piruvil-shiquimato-3-fosfato sintase (EPSPs) and AcetolactatoSintase (ALS). A combination of molecular docking calculations, electrostatic potential, molecular dynamics simulations and hybrid calculations using quantum mechanics and molecular mechanics QM/MM will delineate the specific interactions of the system.
News published in Agência FAPESP Newsletter about the scholarship: