Physics

Organic chemistry

Chain (unit)

Astronomy

Chemistry

Materials science

Intrinsically disordered proteins

Liquid liquid

Phase (matter)

Liquid phase

Chromatography

Biochemistry

Thermodynamics

Proceedings of the National Academy of Sciences

Many intrinsically disordered proteins (IDPs) may undergo liquid- liquid phase separation (LLPS) and participate in the formation of membraneless organelles in the cell, thereby contributing to the regulation and compartmentalization of intracellular biochemical reactions. The phase behavior of IDPs is sequence dependent, and its investigation through molecular simulations requires protein models that combine computational efficiency with an accurate description of intramolecular and intermolecular interactions. We developed a general coarse-grained model of IDPs, with residuelevel detail, based on an extensive set of experimental data on single-chain properties. Ensemble-averaged experimental observables are predicted from molecular simulations, and a data-driven parameter-learning procedure is used to identify the residuespecificmodel parameters thatminimize the discrepancy between predictions and experiments. The model accurately reproduces the experimentally observed conformational propensities of a set of IDPs. Through two-body as well as large-scale molecular simulations, we show that the optimization of the intramolecular interactions results in improved predictions of protein selfassociation and LLPS.

Accurate model of liquid–liquid phase behavior of intrinsically disordered proteins from optimization of single-chain properties