General CG Modeling

Although the EVB and other microscopic models allows us to explore the coupling of the conformational and chemical coordinates in some regions, we need to explore a wider range of the conformational landscape and to perform long time simulations. Thus we developed a coarse grained (CG) model of the type used in simulations of protein folding1 but with emphasize on reliable description of electrostatic effects2,3 we also developed a renormalization model 4,5 which allows us to obtain the effective friction for a drastically reduced model by applying strong forces to both the full and reduced model, while adjusting the free energy surface and friction of the lower dimensionality model until the time dependence response of both models becomes similar. This model, that has been validated systematically5, allows us to perform long time simulations on the effective landscapes of various proteins and to explore their functional properties2. Overall our CG model is quite unique in its ability to reproduce and analyze the properties of large biological systems. In particular most other CG models do not have a proper description of the electrostatic energetic s, that appear to control functional properties. Furthermore, our renormalization approach, which is still not widely used, provides arguably the most powerful way of obtaining long time CG simulations which reliably reproduce the features of the underlining microscopic system. Finally, our paradynamics (PD) strategy of using the CG model as a reference potential for sampling the corresponding microscopic surface.