Coarse-grained simulations of long intrinsically disordered proteins: a benchmark of Martini 3 force-fields

Abstract

Martini 3 is a force field ideally suited to simulating long intrinsically disordered proteins (IDPs) in cell-like surroundings. So far, most Martini 3 variations intended for IDPs have only been benchmarked on shorter IDPs of up to 140 amino acids. In this paper, we present a comprehensive benchmark including IDPs up to 809 amino acids in length and compare the behavior of four well-known Martini 3 variations for IDPs. Modifications to only the bonded parameters result in excessively compact conformations, thereby failing to reproduce the experimental radius of gyration observed for large IDPs. In contrast, general rescaling of interaction parameters, including tuning electrostatic interactions in the case of highly-charged long IDPs, yields acceptable levels of compaction at all tested length scales.