The biology of boundary conditions: cellular reconstitution in one, two, and three dimensions

Abstract

Reconstituting cellular behavior outside the complex environment of the cell allows the study of biological processes in simplified and controlled settings. Making the leap from cells to test tubes, however, carries the inevitable risk of removing too much context and therefore sacrificing the important biochemical, mechanical, or geometrical constraints that guide the system's behavior. In response to this challenge, reconstitution experiments have recently begun to focus not only on including the right molecules but also on faithfully recapitulating the constraints that are present within a cell. By setting the appropriate biological boundary conditions, these experiments are uncovering how dimensional constraints within the cellular environment guide biological processes.

Figure 1

Types of biological boundary conditions and approaches to control or monitor them experimentally. Imposed, embedded, and interfacial boundary conditions each present unique constraints that, when incorporated into reconstitution experiments, can enable more accurate reproductions of the cellular environment.

Figure 2

Boundary conditions on one-dimensional cytoskeletal polymers. Top: imposed boundary conditions can impart compressional forces, hold the filament's end stationary or allow it to glide, and can stabilize or destabilize growth through specific biochemical activities. Bottom: Internal constraints arise from different nucleotide states of the polymer's subunits and can influence the binding and activity of regulatory proteins.

Figure 3

Imposed and embedded boundary conditions in two-dimensional membrane systems. Top: supported membranes can be confined to defined sizes and shapes by patterning the underlying substrate, while free-standing membranes with defined curvatures offer confinement through the periodicity of their surfaces. Bottom: membranes support internal clusters of lipids and/or proteins, which can have different biochemical and mechanical properties than the membrane as a whole.

Figure 4

Reconstitutions in three dimensions. Top: encapsulation of proteins in defined shapes and sizes constrains symmetry and volume, and also allows differeing biochemical activities at the boundary. Bottom: compartmentalization of internal components (both with and without a surrounding membrane) creates embedded boundaries that freely exchange molecules with the surrounding environment (bottom right).