Performing all-atom molecular dynamics simulations of intrinsically disordered proteins with replica exchange solute tempering

TL;DR

This paper demonstrates how to set up, perform, and analyze all-atom molecular dynamics simulations of intrinsically disordered proteins using replica exchange solute tempering to efficiently sample their complex conformational space.

Contribution

It provides a detailed methodology for applying REST enhanced sampling to all-atom MD simulations of IDPs, addressing sampling challenges.

Findings

REST improves sampling efficiency for IDPs.

Methodology enables detailed conformational analysis.

Applicable to various IDP systems.

Abstract

All-atom molecular dynamics (MD) computer simulations are a valuable tool for characterizing the conformational ensembles of intrinsically disordered proteins (IDPs). IDP conformational ensembles are highly heterogeneous and contain structures with many distinct topologies separated by large free-energy barriers. Sampling the vast conformational space of IDPs in explicit solvent all-atom MD simulations is extremely challenging, and enhanced sampling methods are generally required to obtain statistically meaningful descriptions of IDP conformational ensembles. Replica exchange solute tempering (REST) methods, where multiple coupled simulations of a system are performed in parallel with selectively modified potential energy functions, are a powerful approach for efficiently sampling the conformational space of IDPs. In this chapter, we demonstrate how to set-up, perform and analyze all-atom MD simulations of IDPs with REST enhanced sampling methods.