Coarse-Grained Potentials for Local Interactions in Unfolded Proteins

Recent studies have revealed the key role of natively unfolded proteins in many important biological processes. In order to study the conformational changes of these proteins, a one-bead-per-amino-acid coarse grained (CG) model is developed, and a method is proposed to extract the potential functions for the local interactions between CG beads. Experimentally obtained Ramachandran data for the coil regions of proteins are converted into distributions of pseudo-bond and pseudo-dihedral angles between neighboring alpha-carbons in the polypeptide chain. These are then used to derive bending and torsion potentials, which are residue and sequence specific. The validity of the developed model is testified by studying the radius of gyration as well as the hydrodynamic properties of chemically denatured proteins.