Consistent Force Field Captures Homolog Resolved HP1 Phase Separation

Abstract

Many proteins have been shown to function via liquid-liquid phase separation. Computational modeling could offer much needed structural details of protein condensates and reveal the set of molecular interactions that dictate their stability. However, the presence of both ordered and disordered domains in these proteins places a high demand on the model accuracy. Here, we present an algorithm to derive a coarse-grained force field, MOFF, that can model both ordered and disordered proteins with consistent accuracy. It combines maximum entropy biasing, least-squares fitting, and basic principles of energy landscape theory to ensure that MOFF recreates experimental radii of gyration while predicting the folded structures for globular proteins with lower energy. The theta temperature determined from MOFF separates ordered and disordered proteins at 300 K and exhibits a strikingly linear relationship with amino acid sequence composition. We further applied MOFF to study the phase behavior of HP1, an essential protein for posttranslational modification and spatial organization of chromatin. The force field successfully resolved the structural difference of two HP1 homologs, despite their high sequence similarity. We carried out large scale simulations with hundreds of proteins to determine the critical temperature of phase separation and uncover multivalent interactions that stabilize higher-order assemblies. In all, our work makes significant methodological strides to connect theories of ordered and disordered proteins and provides a powerful tool for studying liquid-liquid phase separation with near-atomistic details.

On the stability and layered organization of protein-DNA condensates

“…Protein-DNA interactions were adjusted to reproduce the binding free energy for a set of complexes (Figure S3). With this calibrated force field and the slab simulation methodology, 39,54 we constructed phase diagrams for each protein at different ratios of protein (dimers of HP1 or monomers of H1) to a 50-bp-long DNA, while keeping the total number of molecules fixed at 100.…”

“…Results for HP1 homologs are adapted with permission from Ref. 39 Copyright American Chemical Society. (C-E) Phase diagrams and critical temperatures of HP1α (C), HP1β (D), and H1 (E) at different mixing ratios with DNA.…”

“…We found that the radius of gyration of the heterodimer lies in between that of HP1α and HP1β (Figure S13). 39 We computed the phase diagram and T C for pure heterodimers, which we denote as HP1α/HP1β, and their DNA mixture (Figure S14). While the condensate formed by heterodimers is equally stable compared to that of HP1α and HP1β homodimers, the stability of the DNA mixture is significantly reduced.…”

“…We focused on the phase behavior of chromatin regulators that play crucial roles in heterochromatin formation and gene silencing, including heterochromatin protein 1 (HP1) and histone H1. 2,38 A recently developed force field, MOFF, 39 that is well suited for simulating both ordered and disordered proteins was combined with a chemically accurate DNA model 40 to study protein-DNA condensates. Our simulations resolved the difference of various chromatin regulators in their phase behaviors and their association with DNA molecules.…”

Size Conservation Emerges Spontaneously in Biomolecular Condensates Formed by Scaffolds and Surfactant Clients

“…Coarse-grained (CG) potentials have emerged as powerful tools for describing the phase behavior of biomolecules, such as proteins and nucleic acids, and delineating the underlying physicochemical features that drive LLPS 47,48 . Various levels of molecular resolution can be achieved with CG models; encompassing mean field models 49,50 , lattice-based simulations 51,52 , minimal models 44,45,[53][54][55][56] , and coarse-grained sequence-dependent simulations 42,[57][58][59][60][61] . Here, we employ our minimal protein model 43 , which has been previously applied to unveil the role of protein multivalency in multicomponent condensates 62 and multilayered condensate organization 63 , as well as to investigate the role of RNA in RNA-binding protein nucleation and stability 64 .…”