Biomolecular condensates underlain by liquid-liquid phase separation (LLPS) of proteins and nucleic acids can serve important biological functions; yet current understanding of the effects of amino acid sequences on LLPS is limited. Endeavoring toward a transferable, predictive coarse-grained explicit-chain model for biomolecular LLPS, we used the N-terminal intrinsically disordered region (IDR) of the DEAD-box helicase Ddx4  as a test case to conduct extensive multiple-chain simulations to assess the roles of electrostatic, hydrophobic, cation-\pi, and aromatic interactions in sequence-specific phase behaviors. Three different residue-residue interaction schemes sharing the same electrostatic potentialwere evaluated. We found that neither a common scheme based on amino acid hydrophobicity nor one augmented with arginine/lysine-aromatic cation-\pi interactions can consistently account for the available experimental LLPS data on the wildtype, a charge-scrambled mutant, a phenylalanine-to-alanine (FtoA) mutant and an arginine-to-lysine (RtoK ) mutant of the Ddx4 IDR. In contrast, an interaction scheme based on contact statistics among folded globular protein structures reproduces the overall experimental trend, including that the RtoK mutant has a much diminished LLPS propensity. This finding underscores the important role of \pi-related interactions in LLPS and that their effects are embodied to a degree in classical statistical potentials.  Protein-protein electrostatic interactions are modulated by relative permittivity, which in general depends on protein concentration in the aqueous medium . Analytical theory suggests that this dependence entails enhanced inter-protein interactions in the condensed phase but more favorable protein-solvent interactions in the dilute phase. The opposing trends lead to only a modest overall impact on LLPS.
 Endeavoring toward a transferable, predictive coarse-grained explicit-chain model for biomolecular condensates underlain by liquid-liquid phase separation (LLPS), we conducted multiple-chain simulations of the N-terminal intrinsically disordered region (IDR) of DEAD-box helicase Ddx4 , as a test case , to assess the roles of electrostatic, hydrophobic, cation-\pi, and aromatic interactions in amino acid sequence-dependent LLPS. We evaluated 3 residue-residue interaction schemes with a shared electrostatic potential. Neither a common hydrophobicity scheme nor one augmented with arginine/lysine-aromatic cation-\pi interactions consistently accounted for the experimental LLPS data on the wildtype, a charge-scrambled , an FtoA, and an RtoK mutant of Ddx4 IDR. In contrast, interactions based on contact statistics among folded globular protein structures reproduce the overall experimental trend, including that the RtoK mutant has a much diminished LLPS propensity. Consistency between simulation and LLPS experiment was also found for RtoK mutants of P-granule protein LAF-1, underscoring that, to a degree, the important LLPS-driving \pi-related interactions are embodied in classical statistical potentials. Further elucidation will be necessary, however, especially of phenylalanine's role in condensate assembly because experiments on FtoA and YtoF mutants suggest that LLPS-driving phenylalanine interactions are significantly weaker than those posited by common statistical potentials. Protein-protein electrostatic interactions are modulated by relative permittivity, which depends on protein concentration . Analytical theory suggests that this dependence entails enhanced inter-protein interactions in the condensed phase but more favorable protein-solvent interactions in the dilute phase. The opposing trends lead to a modest overall impact on LLPS.
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