Abstract
Protein self-assembly is a critical step in many biological processes, including endocytosis and virion formation. Standard computational methods to study self-assembly are limited in their ability to reach the long, biologically-relevant timescales required to observe the formation these assemblies within the cell, or to couple self-assembly with critical nonequilibrium events such as chemical reactions. Methods for studying cell-scale dynamics, such as single-particle reaction-diffusion, are typically not applied to self-assembly, as they neglect the geometry of the species being simulated. We detail here generalized software for performing reaction-diffusion simulations of self-assembly through recently developed algorithms that include interface resolution and rigid-body structure while simplifying position updates of species, to accurately reproduce kinetics, and equilibrium, of association in an efficient manner. Each protein is represented as a set of center of mass and interface coordinates and are propagated individually to provide spatiotemporal resolution at both single-particle and interface levels. Interface interactions are provided by the user in a simple, rule-based format along with predefined angles for rigid-body association, enabling formation of multi-protein structures and definitions of chemical reactions. This software represents a powerful tool for studying nonequilibrium self-assembly at biologically-relevant timescales, which is demonstrated here through simulations of clathrin-coated structure formation on membranes.
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