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

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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.

Original languageEnglish
Article numbere2111696118
JournalProceedings of the National Academy of Sciences of the United States of America
Volume118
Issue number44
Number of pages10
ISSN0027-8424
DOIs
Publication statusPublished - 2021

Bibliographical note

Publisher Copyright:
© 2021 National Academy of Sciences. All rights reserved.

    Research areas

  • Biomolecular condensates, Force field parameterization, Intrinsically disordered proteins, Liquid-liquid phase separation, Protein interactions

ID: 286414371