Toward Accurate Simulation of Coupling between Protein Secondary Structure and Phase Separation

Abstract

Intrinsically disordered proteins (IDPs) frequently mediate phase separation that underlies the formation of a biomolecular condensate. Together with theory and experiment, efficient coarse-grained (CG) simulations have been instrumental in understanding the sequence-specific phase separation of IDPs. However, the widely used Cα-only models are limited in capturing the peptide nature of IDPs, particularly backbone-mediated interactions and effects of secondary structures, in phase separation. Here, we describe a hybrid resolution (HyRes) protein model toward a more accurate description of the backbone and transient secondary structures in phase separation. With an atomistic backbone and coarse-grained side chains, HyRes can semiquantitatively capture the residue helical propensity and overall chain dimension of monomeric IDPs. Using GY-23 as a model system, we show that HyRes is efficient enough for the direct simulation of spontaneous phase separation and, at the same time, appears accurate enough to resolve the effects of single His to Lys mutations. HyRes simulations also successfully predict increased β-structure formation in the condensate, consistent with available experimental CD data. We further utilize HyRes to study the phase separation of TPD-43, where several disease-related mutants in the conserved region (CR) have been shown to affect residual helicities and modulate the phase separation propensity as measured by the saturation concentration. The simulations successfully recapitulate the effect of these mutants on the helicity and phase separation propensity of TDP-43 CR. Analyses reveal that the balance between backbone and side chain-mediated interactions, but not helicity itself, actually determines phase separation propensity. These results support that HyRes represents an effective protein model for molecular simulation of IDP phase separation and will help to elucidate the coupling between transient secondary structures and phase separation.

Backbone-mediated weakening of pairwise interactions enables percolation in mimics of protein condensates

“…Our results emphasize the importance of backbone-mediated interactions as drivers of weakened pairwise interactions (which we take as a proxy for fluidity) and percolation within dense phases. This highlights the need for using coarse-grained models with explicit representations of polypeptide backbones as recently introduced by Zhang et al, 60 . Alternatively, one can use all-atom descriptions if computational resources are available 61 .…”

Vitamin C Drives Reentrant Actin Phase Transition: Biphasic Exocytosis Regulation Revealed by Single-Vesicle Electrochemistry

“…In addition, our work shows a V C -induced reversive structural transition in myosin II between α-helices and β-sheets. As predicted by molecular docking simulations, low-concentration V C preferentially interacts with the α-helices on the heavy chain of myosin II to disturb its actin-binding activity, while high-concentration V C also interacts with the light chains, which may alter the motor capacity of heavy chain to partially recover the actin-binding ability. , Even so, V C -regulated myosin dynamics is still less understood and is worth in-depth investigations.…”

Fundamental Aspects of Phase-Separated Biomolecular Condensates

“…The foregoing methods can all work with a coarse-grained representation of solute molecules with solvent treated implicitly. Many slab-geometry simulations at the coarse-grained level have been carried out for biomolecular condensates. ,,,,,− FMAP has been used to calculate binodals for proteins represented at the all-atom level, albeit with the proteins treated as rigid and the solvent treated implicitly. , Zhang et al . have developed a hybrid model for proteins, where the backbone is represented at the all-atom level whereas side chains are at the coarse-grained level, and the solvent is treated implicitly.…”