Fig 1.
(A) Snapshots of a Direct Coexistence (DC) simulation used to calculate the phase diagram and critical temperature of A1-LCD (WT+NLS) protein, where each protein replica has a different colour. Top panel exhibits phase separation with a distinguishable condensed and diluted phase as depicted by the associated density profile. Bottom panel represents a system above the critical solution temperature where no phase separation occurs and a single phase is detected across the density profile. B-G Temperature–density phase diagrams of A1-LCD variants calculated via DC simulations employing the HPS (B), HPS-cation–π (C), HPS-Urry (D), CALVADOS2 (E), Mpipi (F) and Mpipi-Recharged (G) models. Critical temperatures are represented by empty circles while filled circles depict coexistence densities obtained from DC simulations. The lines serve as a guide to the eye. The colour coding is preserved throughout all the panels for all the variants as indicated in the legend of panel B.
Fig 2.
Experimental (solid stars) vs. simulated (empty circles) phase diagrams for the WT+NLS, allF, and allY variants of A1-LCD using different models: HPS (A), HPS-cation–π (B), HPS-Urry (C), CALVADOS2 (D), Mpipi (E), and Mpipi-Recharged (F).
Fig 3.
Comparison of the critical temperatures of WT+NLS (circles), allF (stars), and allY (triangles) calculated in simulations and estimated from experiments (by applying the law of rectilinear diameters and critical exponents [90] to measurements of saturation concentrations at several temperatures [77, 78]).
The black solid line indicates perfect correlation between experimental and simulation results.
Fig 4.
Predicted critical temperature (normalised by the critical temperature of the WT+NLS sequence) for the different models HPS (A), HPS-cation–π (B), HPS-Urry (C), CALVADOS2 (D), Mpipi (E), and Mpipi-Recharged (F) vs. the experimental saturation concentration at 298 K reported in Ref. [78] for the different A1-LCD mutants.
The panels include the Pearson correlation coefficient (r) and the slope (m) from a linear fit to the data. The error bars show the uncertainty in the critical temperature associated to its calculation using the laws of critical exponents and rectilinear diameters (see further details in Section 4.3).
Fig 5.
Simulated vs. experimental saturation concentration (Csat), normalised by the WT+NLS Csat [78], for the different variants and for the models CALVADOS2 (A), Mpipi (B) and Mpipi-Recharged (C).
The Pearson correlation coefficient (r) and the root mean square deviation from the experimental values (D) are displayed for each set of simulation data. The black lines indicate a perfect match between experimental and computational values, while the red dashed lines depict a linear regression for each set of data.
Fig 6.
(A) Snapshot of a bulk NVT simulation with 200 A1-LCD (WT+NLS) protein replicas (each of them depicted by a different tone of colour) employed to compute the condensate viscosity. (B) Shear stress relaxation modulus (G(t)) for the WT+NLS sequence at 298 K evaluated by different models. (C) G(t) for different A1-LCD mutants using the Mpipi-Recharged model. In both B and C panels, G(t) raw data obtained during the simulations are represented by filled symbols, while Maxwell’s mode fits to the data (as described in Section 4.5) are plotted with solid lines. D, E, and F: Predicted versus in vitro viscosity (both reduced by the corresponding WT+NLS value) for all variants under study and the CALVADOS, Mpipi, and Mpipi-Recharged models respectively. The meaning of r, D, and the red dashed and black solid lines is the same as in Fig 5.
Fig 7.
Correlation between the critical temperature (normalised by the Tc of the WT+NLS sequence) and the condensate viscosity (also normalised by η of the WT+NLS) for the different studied A1-LCD mutants as predicted by the CALVADOS2 (A), Mpipi (B), and Mpipi-Recharged (C) models.
Experimental data from Ref. [78] for the WT+NLS, allF and allY sequences have been also included as empty squares (see legend). A linear trend to the experimental correlation between these two quantities for the three sequences measured in vitro [78] is shown with a grey band.
Fig 8.
Contact energy maps of pairwise intermolecular interaction energy for allF (A), WT+NLS (B), and allW (C) condensates at T = 0.95 Tc as predicted by the Mpipi-Recharged model. The most frequent intermolecular amino acid pairwise interactions sustaining the condensates of allF (D), WT+NLS (E), and allW (F) are also displayed. Pairwise contacts have been both normalised by the highest value of residue-residue pairwise interactions and their abundance across their sequence (see Section 4.4 for further details on these calculations).
Table 1.
Table of equations used by each model.
The details of the equations are given below.