Developing coarse-grained models to understand physical principles underlying phase separation of intrinsically disordered proteins (IDPs) with lower critical solution temperatures (LCST)

Macromolecular phase separation has emerged as a new principle for understanding different cellular functions, e.g., signaling transduction. Phase separation is the process in which a homogeneous solution separates into two coexisting phases if the solute concentration is above the saturation concentration: a dense phase termed biomolecular condensates and a dilute phase. Membraneless organelles are examples of biomolecular
condensates. These membraneless organelles provide temporal and spatial control of different cellular compartments. Dysregulation of phase separation is implicated in manyhuman diseases, including neurodegenerative diseases and cancers. Thus, phase separation provides a molecular-level framework for understanding many diseases and exploring new therapeutic opportunities.

Driven by multivalent interactions, certain classes of intrinsically disordered proteins (IDPs) can undergo phase separation with an upper critical solution temperature (UCST) or a lower critical solution temperature (LCST). For UCST-type phase behavior, phase separation occurs if the temperature is lower than a system-specific transition temperature. For LCST-type phase behavior, phase separation occurs if the temperature is lower than the transition temperature. The large length- and timescales of phase separation of IDPs are beyond the current capability of all-atom simulations. Thus, coarse-grained (CG) simulations become important and necessary tools for understanding the physics of phase separation of IDPs. Although CG models have
provided important insights into the phase separation of IDPs, they cannot be used to simulate LCST-type phase behavior, as they do not account for driving forces for this process.

To address this challenge, we propose to develop a new coarse-grained model that can be used to simulate both UCST- and LCST-type phase behavior. This model accounts for driving forces for LCST-type phase behavior, namely the temperature-dependent free energy of solvation and the release and binding of ions. Our preliminary results show that the proposed model can capture the single-chain behavior of IDPs with LCST-type phase behavior. The optimal force field parameters for this model will be explored. This model can be used to study the thermodynamics and kinetics of phase
separation. Using NUP98, CTD PolII and ELPs as model systems, we will apply the model to investigate the molecular grammar governing the LCST-type phase behavior. We believe our new model will generate new insights into the LCST-type phase behavior of IDPs. In addition, we will apply this model to design sequences with LCST-type phase behaviors, which will be further validated by our experimental collaborator. These designed sequences hold great potential for designing biomaterials.