The standard coil or globule phases cannot describe the denatured state of structured proteins and intrinsically disordered proteins

Abstract

The concepts of globule and random coil were developed to describe the phases of homopolymers and then used to characterize the denatured state of structured cytosolic proteins and intrinsically disordered proteins. Using multi-scale molecular dynamics simulations, we were able to explore the conformational space of the disordered conformations of both types of protein under biological conditions in an affordable amount of computational time. By studying the size of the protein and the density correlations in space, we conclude that the standard phases of homopolymers and the tools to detect them cannot be applied straightforwardly to proteins.