High-symmetry ill-fitting subunits in 3D form aggregates of all dimensions

Abstract

Proteins can combine into functional elements in living cells or self-assemble into unwanted structures in a number of diseases. The resulting aggregates often display filamentous morphologies across a large range of protein shapes and molecular interactions. This has led to the suggestion that filament formation could be a generic outcome of the aggregation of geometrically complex, ill-fitting objects, although such a mechanism has not been demonstrated in three dimensions. To address this problem, we theoretically study the self-assembly of three-dimensional identical, ill-fitting deformable subunits mimicking globular proteins in solution. In our model, self-assembling subunits incur deformations that accumulate as the aggregate size increases and can eventually hamper further assembly. We analytically predict the ground state morphologies of the resulting aggregates as a function of the subunit adhesivity and elasticity by mapping their mechanics onto those of two incompatible, interconnected networks. We find that zero-dimensional clusters, three-dimensional bulks as well as symmetry-broken one-dimensional filaments and two-dimensional layers can all form depending on assembly parameters. Poorly compressible, moderately adhesive subunits favor filaments. These findings hint at a generic pathway to control self-assembly in three dimensions and suggests that such mechanisms could be investigated in more realistic protein models.