Simulation of FUS Protein Condensates with an Adapted Coarse-Grained Model

Abstract

Disordered proteins and nucleic acids can condense into droplets that resemble the membraneless organelles observed in living cells. MD simulations offer a unique tool to characterize the molecular interactions governing the formation of these biomolecular condensates, their physicochemical properties, and the factors controlling their composition and size. However, biopolymer condensation depends sensitively on the balance between different energetic and entropic contributions. Here, we develop a general strategy to fine-tune the potential energy function for molecular dynamics simulations of biopolymer phase separation. We rebalance protein–protein interactions against solvation and entropic contributions to match the excess free energy of transferring proteins between dilute solution and condensate. We illustrate this formalism by simulating liquid droplet formation of the FUS low-complexity domain (LCD) with a rebalanced MARTINI model. By scaling the strength of the nonbonded interactions in the coarse-grained MARTINI potential energy function, we map out a phase diagram in the plane of protein concentration and interaction strength. Above a critical scaling factor of α c ≈ 0.6, FUS-LCD condensation is observed, where α = 1 and 0 correspond to full and repulsive interactions in the MARTINI model. For a scaling factor α = 0.65, we recover experimental densities of the dilute and dense phases, and thus the excess protein transfer free energy into the droplet and the saturation concentration where FUS-LCD condenses. In the region of phase separation, we simulate FUS-LCD droplets of four different sizes in stable equilibrium with the dilute phase and slabs of condensed FUS-LCD for tens of microseconds, and over one millisecond in aggregate. We determine surface tensions in the range of 0.01–0.4 mN/m from the fluctuations of the droplet shape and from the capillary-wave-like broadening of the interface between the two phases. From the dynamics of the protein end-to-end distance, we estimate shear viscosities from 0.001 to 0.02 Pa s for the FUS-LCD droplets with scaling factors α in the range of 0.625–0.75, where we observe liquid droplets. Significant hydration of the interior of the droplets keeps the proteins mobile and the droplets fluid.

Improved coarse‐grained model for studying sequence dependent phase separation of disordered proteins

“…The single‐chain properties of DDX4 and FUS LC (see Figure 2d) suggest that the Urry scale may be more appropriate to study the phase behavior of these IDPs. Recently, experimentally derived coexistence densities were used to scale the interaction strengths in the MARTINI CG forcefield 34 for capturing the LLPS of the FUS LC sequence 50 . We want to test if our optimized Urry scale‐based CG model above can capture the concentrations of coexisting phases of FUS LC and DDX4 without any further modifications.…”

On the stability and layered organization of protein-DNA condensates

“…We represented protein and DNA molecules with one coarsegrained bead per amino acid or nucleotide. Models of similar resolutions have been widely used to study IDPs [64][65][66][67][68] and protein-DNA complexes [69][70][71][72][73][74][75][76][77] with great success. The MOFF force field for proteins 39 and molecular renormalization group coarse-graining model (MRG-CG) for the DNA 40 were combined together to describe protein-DNA interactions under implicit solvation.…”

Macromolecular regulators have matching effects on the phase equilibrium and interfacial tension of biomolecular condensates

“…The calculation of interfacial tensions for phase‐separated model systems has a long history 21–23 . Here we note only a few studies that have direct relevance to the present work.…”