LASSI: A lattice model for simulating phase transitions of multivalent proteins

Author summary Spatial and temporal organization of molecular matter is a defining hallmark of cellular ultrastructure and recent attention has focused on membraneless organelles, which are also referred to as biomolecular condensates. Of interest are condensates that form via phase transitions that combine phase separation and networking of multivalent protein and nucleic acid molecules. Building on recently recognized analogies between associative polymers and multivalent proteins, we have developed and deployed LASSI, an open source computational engine that enables the calculation of architecture-specific phase diagrams for multivalent proteins. LASSI relies on a priori identification of stickers and spacers within a multivalent protein and mapping the stickers onto a 3-dimensional lattice. A Monte Carlo engine that incorporates a suite of novel and established move sets enables simulations that track density inhomogeneities and changes to the extent of networking among stickers as a function of protein concentration and interaction strengths. Calculation of distribution functions and other order parameters allow us to compute full phase diagrams for multivalent proteins modeled using a stickers-and-spacers representation on simple cubic lattices. These calculations allow us to rationalize experimental observations and open the door to the design of protein architectures with bespoke phase behavior. LASSI can be deployed to study the phase behavior of multicomponent systems, which allows us to make direct contact with the physical principles underlying cellular biomolecular condensates. Many biomolecular condensates form via spontaneous phase transitions that are driven by multivalent proteins. These molecules are biological instantiations of associative polymers that conform to a so-called stickers-and-spacers architecture. The stickers are protein-protein or protein-RNA interaction motifs and / or domains that can form reversible, non-covalent crosslinks with one another. Spacers are interspersed between stickers and their preferential interactions with solvent molecules determine the cooperativity of phase transitions. Here, we report the development of an open source computational engine known as LASSI (LAttice simulation engine for Sticker and Spacer Interactions) that enables the calculation of full phase diagrams for multicomponent systems comprising of coarse-grained representations of multivalent proteins. LASSI is designed to enable computationally efficient phenomenological modeling of spontaneous phase transitions of multicomponent mixtures comprising of multivalent proteins and RNA molecules. We demonstrate the application of LASSI using simulations of linear and branched multivalent proteins. We show that dense phases are best described as droplet-spanning networks that are characterized by reversible physical crosslinks among multivalent proteins. We connect recent observations regarding correlations between apparent stoichiometry and dwell times of condensates to being proxies for the internal structural organization, specifically the convolution of internal density and extent of networking, within condensates. Finally, we demonstrate that the concept of saturation concentration thresholds does not apply to multicomponent systems where obligate heterotypic interactions drive phase transitions. This emerges from the ellipsoidal structures of phase diagrams for multicomponent systems and it has direct implications for the regulation of biomolecular condensates in vivo.