Soft Matter and Complex Systems Seminar

The application of coarse-grained (CG) models in biophysics is essentially important due to the large length and time scales involved in the description of several biological processes. The versatile Martini force field allows the CG representation of proteins, sugars and lipids and hence it has been employed in biophysical simulations. The Martini protein model is based on the well-known elastic network (EN) model which maintains the secondary structure of the protein. Such model is inneficient for the sampling of large conformational changes in proteins due to the nature of unbreakable harmonic bonds associated with EN model. To overcome such limitation we have introduced a new description based on a different structure-based CG model. Our model shows a very good agreement with all-atom MD and former Martini protein simulations. Moreover, we show how our model captures the large-scale motion related to the catalytic activity in Man5B protein complex and it results in a smaller number of interactions compared to former Martini protein model description.