Elucidating the Functional Roles of Spatial Organization in Cross-Membrane Signal Transduction by a Hybrid Simulation Method

Jiawen Chen, Zhong Ru Xie, Yinghao Wu

Research output: Contribution to journalArticle

Abstract

The ligand-binding of membrane receptors on cell surfaces initiates the dynamic process of cross-membrane signal transduction. It is an indispensable part of the signaling network for cells to communicate with external environments. Recent experiments revealed that molecular components in signal transduction are not randomly mixed, but spatially organized into distinctive patterns. These patterns, such as receptor clustering and ligand oligomerization, lead to very different gene expression profiles. However, little is understood about the molecular mechanisms and functional impacts of this spatial-temporal regulation in cross-membrane signal transduction. In order to tackle this problem, we developed a hybrid computational method that decomposes a model of signaling network into two simulation modules. The physical process of binding between receptors and ligands on cell surfaces are simulated by a diffusion-reaction algorithm, while the downstream biochemical reactions are modeled by stochastic simulation of Gillespie algorithm. These two processes are coupled together by a synchronization framework. Using this method, we tested the dynamics of a simple signaling network in which the ligand binding of cell surface receptors triggers the phosphorylation of protein kinases, and in turn regulates the expression of target genes. We found that spatial aggregation of membrane receptors at cellular interfaces is able to either amplify or inhibit downstream signaling outputs, depending on the details of clustering mechanism. Moreover, by providing higher binding avidity, the co-localization of ligands into multi-valence complex modulates signaling in very different ways that are closely related to the binding affinity between ligand and receptor. We also found that the temporal oscillation of the signaling pathway that is derived from genetic feedback loops can be modified by the spatial clustering of membrane receptors. In summary, our method demonstrates the functional importance of spatial organization in cross-membrane signal transduction. The method can be applied to any specific signaling pathway in cells.

Original languageEnglish (US)
Pages (from-to)566-584
Number of pages19
JournalJournal of Computational Biology
Volume23
Issue number7
DOIs
StatePublished - Jul 1 2016

Fingerprint

Hybrid Simulation
Signal transduction
Signal Transduction
Hybrid Method
Simulation Methods
Receptor
Membrane
Ligands
Membranes
Cluster Analysis
Cell
Cell Surface Receptors
Signaling Pathways
Receptor Aggregation
Physical Phenomena
Clustering
Spatial Clustering
Protein Kinase
Oligomerization
Phosphorylation

Keywords

  • adnotation
  • algorithms
  • artificial life
  • biochemical networks
  • computational molecular biology

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics
  • Computational Mathematics
  • Modeling and Simulation
  • Computational Theory and Mathematics

Cite this

Elucidating the Functional Roles of Spatial Organization in Cross-Membrane Signal Transduction by a Hybrid Simulation Method. / Chen, Jiawen; Xie, Zhong Ru; Wu, Yinghao.

In: Journal of Computational Biology, Vol. 23, No. 7, 01.07.2016, p. 566-584.

Research output: Contribution to journalArticle

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