Minimal Models for Proteins and RNA: From Folding to Function

Abstract

Publisher Summary This chapter describes insights into the folding mechanisms of proteins and RNA that have come from using coarse-grained (CG) models. In principle, many of the important questions in biomolecular folding and their functions can be addressed using all-atom molecular dynamics (MD) simulations in explicit water. While this approach is valuable in many contexts, it is difficult to simulate the processes of interest for longer times to obtain insights or make testable predictions. As a result, there has been a great emphasis on developing CG models that capture the essential physics of the processes of interest. In the context of biopolymers, phenomenological theories have helped rationalize the use of CG models. The misfolding of proteins and their subsequent aggregation are linked to fatal neurodegenerative diseases like Alzheimer's and prion diseases.