Capturing secondary structure in coarse grained intrinsically disordered proteins with simulations driven by chemical shifts.

Abstract

A major challenge when investigating intrinsically disordered proteins (IDPs) pertains to understanding how secondary structure formation across otherwise disordered ensembles, relates to function. While coarse-grained (CG) simulation methods are instrumental to describe ensemble-to-function relationships in IDPs, they remain largely incapable of sampling secondary structure. We here present NapshiftC, an artificial neural network capable of modelling NMR chemical shifts from C-mapped CG protein conformations, leveraging its predictions to restrain simulations and yield experimentally-informed IDP ensembles that contain secondary structure. We applied NapshiftC on a large set of proteins in isolation or condensed phase, and found that, when secondary structure is present, CS incorporation yields improved agreements with smFRET spectroscopy and resolves the over-reliance of CG models on near linear conformers. By incorporating observables that are routinely collected for IDPs but never coupled to CG simulations, NapshiftC ultimately informs on both local and global conformational features of function-defining IDP ensembles.