Time-dependent material properties of ageing biomolecular condensates from different viscoelasticity measurements in molecular dynamics simulations

Abstract

Biomolecular condensates are important contrib-utors to the internal organization of the cell material. While initiallydescribed as liquid-like droplets, the term biomolecular con-densates is now used to describe a diversity of condensed phaseassemblies with material properties extending from low to highviscous liquids, gels, and even glasses. Because the materialproperties of condensates are determined by the intrinsic behaviorof their molecules, characterizing such properties is integral torationalizing the molecular mechanisms that dictate their functionsand roles in health and disease. Here, we apply and compare threedistinct computational methods to measure the viscoelasticity ofbiomolecular condensates in molecular simulations. Thesemethods are the Green−Kubo (GK) relation, the oscillatoryshear (OS) technique, and the bead tracking (BT) method. We find that, although all of these methods provide consistent results forthe viscosity of the condensates, the GK and OS techniques outperform the BT method in terms of computational efficiency andstatistical uncertainty. We thus apply the GK and OS techniques for a set of 12 different protein/RNA systems using a sequence-dependent coarse-grained model. Our results reveal a strong correlation between condensate viscosity and density, as well as withprotein/RNA length and the number of stickers vs spacers in the amino acid protein sequence. Moreover, we couple the GK and theOS technique to nonequilibrium molecular dynamics simulations that mimic the progressive liquid-to-gel transition of proteincondensates due to the accumulation of interprotein β-sheets. We compare the behavior of three different protein condensates, i.e.,those formed by either hnRNPA1, FUS, or TDP-43 proteins, whose liquid-to-gel transitions are associated with the onset ofamyotrophic lateral sclerosis and frontotemporal dementia. We find that both the GK and OS techniques successfully predict thetransition from functional liquid-like behavior to kinetically arrested states once the network of interprotein β-sheets has percolatedthrough the condensates. Overall, our work provides a comparison of different modeling rheological techniques to assess theviscosity of biomolecular condensates, a critical magnitude that provides information on the behavior of biomolecules insidecondensates.