Developing Bonded Potentials for a Coarse-Grained Model of Intrinsically Disordered Proteins.

ABSTRACT: Recent advances in residue-level coarse-grained (CG) computational models have enabled molecular-level insights into biological condensates of intrinsically disordered proteins (IDPs), shedding light on the sequence determinants of their phase separation. The existing CG models that treat protein chains as flexible molecules connected via harmonic bonds cannot populate common secondary-structure elements. Here, we present a CG dihedral angle potential between four neighboring beads centered at C_α atoms to faithfully capture the transient helical structures of IDPs. In order to parameterize and validate our new model, we propose C_α-based helix assignment rules based on dihedral angles that succeed in reproducing the atomistic helicity results of a polyalanine peptide a

SUBMITTER: Rizuan A 

PROVIDER: S-EPMC10165611 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature