Nucleation of Biomolecular Condensates from Finite-Sized Simulations

Abstract

The nucleation of protein condensates is a concentration-driven process of assembly. When modelled in the canonical ensemble, condensation is affected by finite-size effects. Here, we present a general and efficient route to obtain ensemble properties of protein condensates in the macroscopic limit from finite-sized nucleation simulations. The approach is based on a theoretical description of droplet nucleation in the canonical ensemble and enables estimating thermodynamic and kinetic parameters, such as the macroscopic equilibrium density of the dilute protein phase, the condensates surface tension and nucleation free energy barriers. We apply the method to coarse-grained simulations of NDDX4 and FUS-LC, two phase-separating disordered proteins with different physicochemical characteristics. Our results show that NDDX4 condensate droplets, characterised by lower surface tension, higher solubility, and faster monomer exchange dynamics than FUS-LC, form with negligible nucleation barriers. In contrast, FUS-LC condensates form via an activated process over a wide range of concentrations. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=196 SRC="FIGDIR/small/515961v2_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@15306c9org.highwire.dtl.DTLVardef@1e2927forg.highwire.dtl.DTLVardef@1ffe65borg.highwire.dtl.DTLVardef@16c74e1_HPS_FORMAT_FIGEXP M_FIG Graphical Table of Contents. C_FIG