Calculating Biomolecular Condensate Nucleation Barriers Using Simulations

Abstract

Biomolecular condensates are an active area of research that offers tremendous promise, and research is helping to uncover their function in cellular biology and the potential for therapeutic intervention in pathological condensates. Experiments and simulations have led to continuous improvement in our understandings of biomolecular condensate thermodynamics, but the kinetic properties of condensation remain under-explored. In this project, we explore the nucleation properties of the intrinsically-disordered region (IDR) of human Ribonucleoprotein A1, also known as A1LCD. This protein’s thermodynamic properties are well-characterized by experimental studies, but its energetic barrier to nucleation is unknown. We propose a workflow to broadly resolve nucleation barriers for A1LCD from simulations alone, taking advantage of the Mpipi coarse-grained intrinsically disordered protein (IDP) model’s accuracy and performance to run microsecond-long simulations enabling the calculation of kinetic barriers to rare events. We make predictions of condensate nucleation barriers and correlate nucleation barrier height with known critical temperature values across six A1LCD mutants. We find that energetic barriers to nucleation are relatively constant across these mutant strains that condense at different critical temperatures, and additionally see that nucleation barriers rise as we approach the critical temperature for low system densities. In addition, we offer insights to future calculation of nucleation barriers for other IDPs.