An Adaptive Coarse Graining Method for Signal Transduction in Three Dimensions

Issue title: Watching the Daisies Grow: from Biology to Biomathematics and Bioinformatics — Alan Turing Centenary Special Issue

Article type: Research Article

Authors: Archuleta, Michelle N. | McDermott, Jason E. | Edwards, Jeremy S. | Resat, Haluk

Affiliations: Chemical and Nuclear Engineering Department, University of New Mexico, Albuquerque, NM 87131, USA | Computational Biology and Bioinformatics Group, Pacific Northwest National Laboratory, Richland, WA 99352, USA | Chemical and Nuclear Engineering Department, University of New Mexico, Albuquerque, NM 87131, USA | Computational Biology and Bioinformatics Group, Pacific Northwest National Laboratory, Richland, WA 99352, USA

Note: [] Address for correspondence: Broad Institute of MIT and Harvard, Program in Medical and Population Genetics, Cambridge, MA 02142, USA

Note: [] Also work: Molecular Genetics and Microbiology Department, University of New Mexico Albuquerque, NM 87131, USA Current address: Broad Institute of MIT and Harvard, Program in Medical and Population Genetics, Cambridge, MA 02142 USA

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.

DOI: 10.3233/FI-2012-720

Journal: Fundamenta Informaticae, vol. 118, no. 4, pp. 371-384, 2012