Disordered peptide chains in an {\alpha}-C-based coarse-grained model

TL;DR

This paper introduces a coarse-grained model for intrinsically disordered proteins that captures long-timescale dynamics and contact formation, aligning well with experimental data and revealing sequence-dependent geometric properties.

Contribution

The authors develop a one-bead-per-residue model that simulates disordered proteins at longer timescales, incorporating dynamic contact formation and dissociation.

Findings

Model reproduces experimental and all-atom data

Contact dynamics depend on residue types

Radius of gyration scales with sequence length

Abstract

We construct a one-bead-per-residue coarse-grained dynamical model to describe intrinsically disordered proteins at significantly longer timescales than in the all-atom models. In this model, inter-residue contacts form and disappear during the course of the time evolution. The contacts may arise between the sidechains, the backbones or the sidechains and backbones of the interacting residues. The model yields results that are consistent with many all-atom and experimental data on these systems. We demonstrate that the geometrical properties of various homopeptides differ substantially in this model. In particular, the average radius of gyration scales with the sequence length in a residue-dependent manner.