Systems biology and physical biology of clathrin-mediated endocytosis

Abstract

In this review, we describe the application of experimental data and modeling of intracellular endocytic trafficking mechanisms with a focus on the process of clathrin-mediated endocytosis. A detailed parts-list for the protein-protein interactions in clathrin-mediated endocytosis has been available for some time. However, recent experimental, theoretical, and computational tools have proved to be critical in establishing a sequence of events, cooperative dynamics, and energetics of the intracellular process. On the experimental front, total internal reflection fluorescence microscopy, photo-activated localization microscopy, and spinning-disk confocal microscopy have focused on assembly and patterning of endocytic proteins at the membrane, while on the theory front, minimal theoretical models for clathrin nucleation, biophysical models for membrane curvature and bending elasticity, as well as methods from computational structural and systems biology, have proved insightful in describing membrane topologies, curvature mechanisms, and energetics.

Fig. 1

Overview and “parts”-list of clathrin-mediated endocytosis.

Fig. 2

Green = clathrin; blue = AP-2; black = medium. (a) At normal concentrations, clathrin and adaptor for a stable coat. (b) Removal of the adaptor leads to coat disappearance. (c) At supra-physiological levels, clathrin can polymerize into cages independent of the adaptor. (d) In coats containing clathrin and adaptor, the amount of each coat component is dynamic throughout the simulation even after stable coat formation.

Fig. 3

Increasing levels of cargo within a coated pit (a)–(c) lead to larger stable coats, as predicted by the model. (d) Clathrin coat size dependence on cargo levels predicted by the model. In the color scale bar, H, M, Cr, correspond to high, medium, and critical (lower-bound) concentration of PIP₂.

Fig. 4

(Reproduced with permission from ref. 125) Left: membrane deformation profiles under the influence of imposed curvature of the epsin shell model for three different coat areas, here κ = 20 k_BT. For the largest coat area, the membrane shape is reminiscent of a clathrin-coated vesicle. Right: calculated (top) and experimentally measured (bottom) probability of observing a clathrin-coated vesicular bud of given size in WT cells (filled) and CLAP IgG injected cells (unfilled).

Fig. 5

Mean and Gaussian curvature profiles during early bud formation, medium membrane invagination, and deep membrane invagination.

Fig. 6

Left: angular distributions, probability P(θ) versus angle θ (°), of epsins; top corresponds to the mature bud, middle corresponds to the early intermediate, and bottom corresponds to a planar membrane. Middle: snapshot of a mature bud; red dots indicate fixed locations of epsins, where the angular distributions were sampled. Right: snapshot of an intermediate bud; red dots indicate fixed locations of epsins, where the angular distributions were sampled.