(551b) Development of a Top-Down Coarse-Grained Model for Protein Assemblies

In this talk, I will describe ongoing efforts in my group aimed at developing an accurate simulation model to study the thermodynamics and kinetics of multiprotein assembly. As opposed to using a "bottom-up" coarse-graining approach such as the relative entropy framework of Shell and co-workers, we use a "top-down" approach for constructing a Calpha-based (one interaction site per amino acid) protein model. Development of the proposed model involves comparisons with experimental data available from the recent literature as well as comparisons with atomistic simulations of a single protein chain. The usefulness of our approach will be demonstrated by discussing results on a couple of systems. Of particular importance is the formation of liquid-like assemblies of disordered proteins that have been found to be important for the physiological function of membraneless compartments in living cells including the nucleolus and ribonucleoprotein (RNP) granules as well as many organelles in prokaryotic cells.