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Physics-driven coarse-grained model for biomolecular phase separation with near-quantitative accuracy.

Jerelle A JosephAleks ReinhardtAnne AguirrePin Yu ChewKieran O RussellJorge R EspinosaAdiran GaraizarRosana Collepardo-Guevara
Published in: Nature computational science (2021)
Various physics- and data-driven sequence-dependent protein coarse-grained models have been developed to study biomolecular phase separation and elucidate the dominant physicochemical driving forces. Here, we present Mpipi, a multiscale coarse-grained model that describes almost quantitatively the change in protein critical temperatures as a function of amino-acid sequence. The model is parameterised from both atomistic simulations and bioinformatics data and accounts for the dominant role of π - π and hybrid cation- π / π - π interactions and the much stronger attractive contacts established by arginines than lysines. We provide a comprehensive set of benchmarks for Mpipi and seven other residue-level coarse-grained models against experimental radii of gyration and quantitative in-vitro phase diagrams; Mpipi predictions agree well with experiment on both fronts. Moreover, it can account for protein-RNA interactions, correctly predicts the multiphase behaviour of a charge-matched poly-arginine/poly-lysine/RNA system, and recapitulates experimental LLPS trends for sequence mutations on FUS, DDX4 and LAF-1 proteins.
Keyphrases
  • molecular dynamics
  • amino acid
  • molecular dynamics simulations
  • high resolution
  • nitric oxide
  • binding protein
  • electronic health record
  • mass spectrometry
  • big data