Towards a Coarse-Grained Model for Unfolded Proteins

Abstract

It is widely accepted that many biological systems benefit from the specific and unique properties of unfolded proteins. In order to study the conformational dynamics of these proteins, we propose an implicit solvent one-bead per amino-acid coarse-grained (CG) model. For the local backbone interactions, experimentally-obtained Ramachandran plots for the coil regions of proteins are converted into distributions of pseudo-bond and pseudo-dihedral angles between neighboring alpha-carbons in the CG chain. The obtained density plots are then used to derive bending and torsion potentials, which are residue- and sequence-specific. Our results show that the local interactions can be captured by specifically accounting for the presence of Proline and Glycine in the amino-acid sequence. An upper and lower bound is suggested for the radius of gyration of denatured proteins based on their specific sequence composition.