Molecular dynamics approaches in the study of biomolecular systems of increasing complexity: peptides, proteins and membranes

Molecular dynamics (MD) simulations are a powerful tool to study biochemical processes at the atomic level and to complement experiments by providing otherwise unattainable structural and dynamic information. In this thesis, different simulative approaches were applied to two classes of problems. The first regards the mechanism of lipid bilayer perturbation by antimicrobial peptides (AMPs), which kill bacteria by disrupting their membranes. Our computational results on peptides temporin L, LAH4, trichogin GAIV and PMAP-23 clarified several aspects of the mechanism of action of AMPs, illustrating how peptide sequence modulates aggregation and insertion in the lipid bilayer, and showing several facets of membrane disruption by AMPs, such as formation of bilayer defects, membrane thinning and perturbation of lipid dynamics. Overall, these data indicate that AMPs activity is regulated by several complex equilibria that should be taken into account in the rational design of new antibiotic drugs. Other studies focused on RRAS and SHP-2, two proteins involved in the MAPK pathway and in a family of disorders called RASopathies. We analyzed an RRAS mutation, isolated in a patient affected by Noonan syndrome, causing an enhancement in the rate of GDP dissociation. MD simulations revealed that this effect is related to the perturbation of the conformational transitions of the RRAS molecular switch. Similarly, simulations showed that the motions of an α-helix resulted to be essential in the function of SHP-2, thus providing new indications on the possible molecular effects of several pathogenic mutations. These studies underline once more the importance of conformational fluctuations in the physiological and aberrant function of proteins. All MD simulations reported in this thesis were consistent with the available experimental data, thus confirming the reliability of in silico approaches in obtaining novel insights in the characterization of complex biomolecular systems.