LASSI

LASSI simulates phase transitions of biomolecular condensates driven by multivalent "stickers-and-spacers" proteins using a lattice-based coarse-grained model.

Key Features:

• Stickers-and-Spacers Model: Implements a coarse-grained "stickers-and-spacers" representation where stickers are protein-protein or protein-RNA interaction motifs that form reversible non-covalent crosslinks and spacers preferentially interact with solvent to modulate cooperativity.
• Lattice-based Simulation: Uses a lattice-based simulation engine to represent spatial organization and interactions of multivalent proteins and RNA.
• Phase Diagram Calculation: Computes full phase diagrams for multicomponent systems containing coarse-grained multivalent proteins and RNA.
• Architecture Support: Supports modeling of both linear and branched multivalent protein structures.
• Dense Phase Modeling: Represents dense phases as droplet-spanning networks characterized by reversible physical crosslinks among multivalent proteins.
• Phenomenological Modeling: Enables computationally efficient phenomenological modeling of spontaneous phase transitions in complex mixtures.
• Correlative Analysis: Links apparent stoichiometry, condensate dwell times, and internal structural organization as proxies for internal density and networking extent.
• Multicomponent Interaction Effects: Captures effects of obligate heterotypic interactions and ellipsoidal phase diagram structures that challenge traditional saturation concentration thresholds.

Scientific Applications:

• Phase diagram analysis: Generating full phase diagrams for multicomponent mixtures of multivalent proteins and RNA.
• Mechanistic studies of condensate formation: Investigating how stickers, spacers, and multivalency drive spontaneous phase transitions and condensate architecture.
• Dense phase network analysis: Studying droplet-spanning networks and their relation to stoichiometry, dwell times, and internal density.
• Multicomponent interaction effects: Exploring how obligate heterotypic interactions alter saturation concentrations and phase behavior, including ellipsoidal phase diagram features.
• Architecture comparisons: Comparing phase behavior arising from linear versus branched multivalent protein structures.

Methodology:

LASSI performs lattice-based coarse-grained simulations of multivalent proteins and RNA, calculates full phase diagrams, and models reversible non-covalent crosslinks and droplet-spanning networks for linear and branched architectures.