Deciphering the Filamentous Organization of Human Liver Phosphofructokinase-1 through Highly-Coarse-Grained Modeling

Abstract Enzyme filamentation is an increasingly recognized mode of metabolic regulation and spatial organization, yet the relationship between filament-forming interactions, assembly morphology, and potential function remains insufficiently understood. Phosphofructokinase-1 (PFK1), a key glycolytic enzyme, provides a prominent example: its liver isoform, PFKL, forms higher-order filamentous assemblies with distinct experimentally resolved interaction modes. Here, we develop a shape-based rigid-body model of human PFKL tetramers with explicit interaction sites derived from these filament-forming interfaces. The model preserves the overall tetramer geometry while remaining sufficiently coarse-grained to simulate the collective assembly and organization of many PFKL tetramers. We use this framework to determine how the relative strengths of the Interface 1–Interface 1 and Interface 1–Interface 2 interaction modes influence filament formation and emergent assembly morphology. We further examine how an attractive membrane-like surface alters PFKL organization and how filament formation affects the spatial colocalization of generic client proteins representing potential components of glycolytic assemblies. The simulations reveal how protein shape, interface specificity, surface association, client size, and interaction strength influence higher-order organization. Together, these results establish a structure-informed framework for connecting experimentally defined enzyme interfaces to mesoscale assembly. This framework provides a computationally tractable approach for investigating enzyme filament formation and membrane-associated protein organization.