(4ch) From Materials to Peptide Design: a Short Trip through Computational Techniques

Sustained advances in algorithms together with increased computer power and decreasing costs make computational techniques attractive for all types of molecular research. Today's simulations of millions of particles can span many microseconds, and although experimental investigations remain a primary source of information, computational studies are increasingly providing explanation of meso-scale properties and processes.

My research interests have always been focused on computational methods but in a range of topics from materials to peptide design. I will present my latest work going from a rough (coarse grained) to full atomic description of the systems. Coarse-grained molecular dynamics are used to describe a bilayer composed of polymer mixtures that exhibit lateral segregation and spatial colocalization of domains across the membrane (registration): simulations depict the mechanism by which the registration is achieved and suggest possibles causes. The concomitant use of different techniques such as normal mode analysis and molecular dynamics (MD) allow us to test hypothesized mechanisms for one membrane protein among the neurotransmitter sodium symporter (NSS) family. These proteins are of major biological importance as they are associated with various diseases and addictions. The results confirm the mechanism and show that the response of a protein to a mechanical perturbation is directly linked to its topology. Lastly I will show our efforts to design a peptide that functions as "self"-marker to macrophages. This peptide would make particles invisible to macrophages. The use of MD techniques together with docking algorithms lead us to a prediction of sequence that indeed shows, via affinity essays, to have the desired activity.