An adaptive coarse graining method for signal transduction in three dimensions

Abstract

The spatio-temporal landscape of the plasma membrane regulates activation and signal transduction of membrane bound receptors by restricting their two-dimensional mobility and by inducing receptor clustering. This regulation also extends to complex formation between receptors and adaptor proteins, which are the intermediate signaling molecules involved in cellular signaling that relay the received cues from cell surface to cytoplasm and eventually to the nucleus. Although their investigation poses challenging technical difficulties, there is a crucial need to understand the impact of the receptor diffusivity, clustering, and spatial heterogeneity, and of receptor-adaptor protein complex formation on the cellular signal transduction patterns. Building upon our earlier studies, we have developed an adaptive coarse-grained Monte Carlo method that can be used to investigate the role of diffusion, clustering and membrane corralling on receptor association and receptor-adaptor protein complex formation dynamics in three dimensions. The new Monte Carlo lattice based approach allowed us to introduce spatial resolution on the 2-D plasma membrane and to model the cytoplasm in three-dimensions. Being a multi-resolution approach, our new method makes it possible to represent various parts of the cellular system at different levels of detail and enabled us to utilize the locally homogeneous assumption when justified (e.g., cytoplasmic region away from the cell membrane) and avoid its use when high spatial resolution is needed (e.g., cell membrane and cytoplasmic region near the membrane) while keeping the required computational complexity manageable. Our results have shown that diffusion has a significant impact on receptor-receptor dimerization and receptor-adaptor protein complex formation kinetics. We have observed an "adaptor protein hopping" mechanism where the receptor binding proteins may hop between receptors to form short-lived transient complexes. This increased residence time of the adaptor proteins near cell membrane and their ability to frequently change signaling partners may explain the increase in signaling efficiency when receptors are clustered. We also hypothesize that the adaptor protein hopping mechanism can cause concurrent or sequential activation of multiple signaling pathways, thus leading to crosstalk between diverse biological functions.

Figure 1

Schematic layout of the coarse grained simulation framework representing the fine spatial resolution near the plasma membrane and coarse-graining in the cytoplasm where the resolution of the regions decreases in successive steps as moved away from the cell surface.

Figure 2

Workflow of the presented adaptive coarse-grained Monte Carlo method.

Figure 3

Cumulative counts of (A) receptor dimerization and (B) adaptor protein-receptor association events when receptors are clustered (cyan) and uniformly distributed (magenta) in the plasma membrane. The x-axis indicates elapsed time of the simulation and the y-axis shows number of occurred events (dimerization or association).

Figure 4

3D single particle tracking of cytosolic species (CS1) in the simulations, diffusing in the cytoplasm (green), diffusing on the plasma membrane while bound to receptor 1, R1-CS1 (red) or bound to receptor 2, R2-CS1 (blue). (A) Schematic illustration of the adaptor protein hopping mechanism. (B) Simulation of a rebinding event which is not an adaptor hopping event. (C) Simulation of an adaptor-hopping rebinding event. Inset shows the event’s projection onto the x-z plane. (D) Statistical distribution of the adaptor protein-receptor rebinding event counts as a function of the time (in second units) between rebinding events.