Cell Signaling Dynamics in Time and Space

Boris Kholodenko (Thomas Jefferson University)

Abstract

Extracellular information received by membrane receptors, such as G-protein coupled receptors (GPCRs) and receptor tyrosine kinases (RTKs), is encoded into complex temporal and spatial patterns of phosphorylation and topological relocation of signaling proteins. Processing and integration of this information through kinase cascades leads to important decisions that determine cell’s fate. We employ computational and experimental approaches to reveal kinetic and molecular factors that control the spatio-temporal dynamics of RTK signaling networks, including transient versus sustained phosphorylation patterns, bistable dynamics and oscillations.

Quantitative analysis of signal transduction is confronted by the combinatorial explosion in the number of feasible molecular species presenting different states of protein complexes that are formed by receptors and scaffolds. We show that a mechanistic description of a highly combinatorial network may be drastically reduced using a “domain-oriented” macro-modeling framework. Using this approach, we explored the role of the scaffold protein GAB1 in the control of mitogenic (Ras/MAPK) and survival (PI3K/Akt) signaling. Our findings demonstrate that the essential function of GAB1 is to enhance PI3K/Akt activation and extend the duration of Ras/MAPK signaling.

Cells have developed mechanisms for precise sensing of the positional information. The spatial separation of opposing reactions in covalent-modification cycles results in the intracellular gradients of protein activities. These gradients provide positional cues for pivotal cellular processes, such as mitosis, motility and migration. The membrane confinement of the initiating kinase (e.g., Ras/Raf in the MAPK cascade) and cytosolic localization of phosphatases result in precipitous spatial gradients of phosphorylated kinases down the cascade, with high concentration near the membrane and low in the perinuclear area. This suggests a need for additional (besides diffusion) mechanisms that facilitate signaling, such as vesicular and non-vesicular trafficking of phosphorylated kinases driven by molecular motors. Rapid survival signals in neurons might be transmitted by waves of protein phosphorylation emerging in kinase/phosphatase cascades, such as MAPK, PI3K/Akt and GTPase cascades.

In addition to mechanistic modeling, a top-down approach to inferring the structure of cellular signaling and gene networks will be presented. We demonstrate how dynamic connections leading to a particular network node can be retrieved from experimentally measured network responses to perturbations influencing other nodes.

References

1. Kholodenko, B.N. (2006) Cell-signalling dynamics in time and space. Nat Rev Mol Cell Biol, 7, 165-176.
2. Kiyatkin, A.B., Aksamitiene E, Markevich, N.I., Borisov, NM., Hoek, J.B. & Kholodenko, B.N. (2006) Scaffolding protein GAB1 sustains epidermal growth factor-induced mitogenic and survival signaling by multiple positive feedback loops. J. Biol. Chem. 281, 19925-19938.
3. Borisov N.M., Markevich, N.I., Hoek J.B. & Kholodenko B.N. (2005) Signaling through receptors and scaffolds: independent interactions reduce combinatorial complexity. Biophys J. 89, 951-966.
4. Sontag, E., Kiyatkin, A. and Kholodenko, B.N. (2004) Inferring dynamic architecture of cellular networks using time series of gene expression, protein and metabolite data. Bioinformatics, 20, 1877-1886.

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