Comparative Roles of Charge, $\pi$ and Hydrophobic Interactions in Sequence-Dependent Phase Separation of Intrinsically Disordered Proteins

Abstract

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.

65 pages (main text and supporting information), 7 main-text figures, 7 supporting figures, 1 supporting table, 135 references; accepted for publication in the Proceedings of the National Academy of Sciences, U.S.A

References in corpus (15)

• Canonical sampling through velocity-rescaling
• Strong scaling of general-purpose molecular dynamics simulations on GPUs
• Phase separation and single-chain compactness of charged disordered proteins are strongly correlated
• Sequence-specific polyampholyte phase separation in membraneless organelles
• The Dielectric Constant of Ionic Solutions: A Field-Theory Approach
• Model for disordered proteins with strongly sequence-dependent liquid phase behavior
• Random-phase-approximation theory for sequence-dependent, biologically functional liquid-liquid phase separation of intrinsically disordered proteins
• Charge Pattern Matching as a "Fuzzy" Mode of Molecular Recognition for the Functional Phase Separations of Intrinsically Disordered Proteins
• Coarse-Grained Residue-Based Models of Disordered Protein Condensates: Utility and Limitations of Simple Charge Pattern Parameters
• A Lattice Model of Charge-Pattern-Dependent Polyampholyte Phase Separation
• A unified analytical theory of heteropolymers for sequence-specific phase behaviors of polyelectrolytes and polyampholytes
• Analytical Theory for Sequence-Specific Binary Fuzzy Complexes of Charged Intrinsically Disordered Proteins
• Novel physics arising from phase transitions in biology
• Finite-size scaling analysis of protein droplet formation
• Phase behavior of blocky charge lattice polymers: Crystals, liquids, sheets, filaments and clusters

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