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Topological analysis of MAPK cascade for kinetic ErbB signaling.

Nakakuki T, Yumoto N, Naka T, Shirouzu M, Yokoyama S, Hatakeyama M - PLoS ONE (2008)

Bottom Line: Ligand-induced homo- and hetero-dimer formation of ErbB receptors results in different biological outcomes irrespective of recruitment and activation of similar effector proteins.We found that the pathway structure is characterized by ERK-mediated positive feedback regulation of B-Raf and B-Raf-mediated negative regulation of Raf-1.From a sensitivity analysis of the detailed upstream model for Ras activation, we concluded that Ras activation dynamics is dominated by heterodimer-mediated signaling coordination with a large initial speed of dimerization when the concentration of the ErbB4 receptor is considerably high.

View Article: PubMed Central - PubMed

Affiliation: Cellular Systems Biology Team, Computational and Experimental Systems Biology Group, RIKEN Genomic Sciences Center, Tsurumi-ku, Yokohama, Kanagawa, Japan.

ABSTRACT
Ligand-induced homo- and hetero-dimer formation of ErbB receptors results in different biological outcomes irrespective of recruitment and activation of similar effector proteins. Earlier experimental research indicated that cells expressing both EGFR (epidermal growth factor receptor) and the ErbB4 receptor (E1/4 cells) induced E1/4 cell-specific B-Raf activation and higher extracellular signal-regulated kinase (ERK) activation, followed by cellular transformation, than cells solely expressing EGFR (E1 cells) in Chinese hamster ovary (CHO) cells. Since our experimental data revealed the presence of positive feedback by ERK on upstream pathways, it was estimated that the cross-talk/feedback pathway structure of the Raf-MEK-ERK cascade might affect ERK activation dynamics in our cell system. To uncover the regulatory mechanism concerning the ERK dynamics, we used topological models and performed parameter estimation for all candidate structures that possessed ERK-mediated positive feedback regulation of Raf. The structure that reliably reproduced a series of experimental data regarding signal amplitude and duration of the signaling molecules was selected as a solution. We found that the pathway structure is characterized by ERK-mediated positive feedback regulation of B-Raf and B-Raf-mediated negative regulation of Raf-1. Steady-state analysis of the estimated structure indicated that the amplitude of Ras activity might critically affect ERK activity through ERK-B-Raf positive feedback coordination with sustained B-Raf activation in E1/4 cells. However, Rap1 that positively regulates B-Raf activity might be less effective concerning ERK and B-Raf activity. Furthermore, we investigated how such Ras activity in E1/4 cells can be regulated by EGFR/ErbB4 heterodimer-mediated signaling. From a sensitivity analysis of the detailed upstream model for Ras activation, we concluded that Ras activation dynamics is dominated by heterodimer-mediated signaling coordination with a large initial speed of dimerization when the concentration of the ErbB4 receptor is considerably high. Such characteristics of the signaling cause the preferential binding of the Grb2-SOS complex to heterodimer-mediated signaling molecules.

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Time courses of Ras- and Rap1-GTPs.The input signal generator reproduced the time-course data of Ras- and Rap1-GTPs with 10 nM EGF. (A) Normalized time-course data of Ras-GTP. (B) Normalized time-course data of Rap1-GTP. The graphs represent the normalized activity of Ras- and Rap-1 GTPs in which the data are divided by the value for E1/4 cells at 1 min. Blue and red lines correspond to simulation data for E1 and E1/4 cells, respectively. The filled squares and circles correspond to experimental data concerning E1 and E1/4 cells, respectively.
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pone-0001782-g004: Time courses of Ras- and Rap1-GTPs.The input signal generator reproduced the time-course data of Ras- and Rap1-GTPs with 10 nM EGF. (A) Normalized time-course data of Ras-GTP. (B) Normalized time-course data of Rap1-GTP. The graphs represent the normalized activity of Ras- and Rap-1 GTPs in which the data are divided by the value for E1/4 cells at 1 min. Blue and red lines correspond to simulation data for E1 and E1/4 cells, respectively. The filled squares and circles correspond to experimental data concerning E1 and E1/4 cells, respectively.

Mentions: For each of the 29 structures, we estimated the model parameters to reproduce the experimental data. Here, we employed the hypothesis that appropriate structures could explain experimental results using suitable kinetic parameters. Additionally, we also hypothesized that a biological pathway is robust against small parameter changes, and that the parameter should therefore be easily searched when the pathway structure is solid. For parameter estimation, we prepared 29 ODE (ordinary differential equation) models and six time-course datasets each from the Western blot analyses of E1 and E1/4 cells (Table 1, nos. 1–3). Additionally, we developed an input signal generator to reproduce the experimental data relating to Ras- and Rap1-GTPs (Figure 4 and Table 1, nos. 4 and 5). Detailed information relating to the input signal generator is provided in Text S1, Tables S2, S3, S4 and Figures S2 and S3. Moreover, we experimentally measured the time course of B-Raf activation (Table 1, no. 6), which showed sustained activation, for validation of the model. The procedure of model selection based on parameter estimation is provided in Materials and Methods.


Topological analysis of MAPK cascade for kinetic ErbB signaling.

Nakakuki T, Yumoto N, Naka T, Shirouzu M, Yokoyama S, Hatakeyama M - PLoS ONE (2008)

Time courses of Ras- and Rap1-GTPs.The input signal generator reproduced the time-course data of Ras- and Rap1-GTPs with 10 nM EGF. (A) Normalized time-course data of Ras-GTP. (B) Normalized time-course data of Rap1-GTP. The graphs represent the normalized activity of Ras- and Rap-1 GTPs in which the data are divided by the value for E1/4 cells at 1 min. Blue and red lines correspond to simulation data for E1 and E1/4 cells, respectively. The filled squares and circles correspond to experimental data concerning E1 and E1/4 cells, respectively.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2262155&req=5

pone-0001782-g004: Time courses of Ras- and Rap1-GTPs.The input signal generator reproduced the time-course data of Ras- and Rap1-GTPs with 10 nM EGF. (A) Normalized time-course data of Ras-GTP. (B) Normalized time-course data of Rap1-GTP. The graphs represent the normalized activity of Ras- and Rap-1 GTPs in which the data are divided by the value for E1/4 cells at 1 min. Blue and red lines correspond to simulation data for E1 and E1/4 cells, respectively. The filled squares and circles correspond to experimental data concerning E1 and E1/4 cells, respectively.
Mentions: For each of the 29 structures, we estimated the model parameters to reproduce the experimental data. Here, we employed the hypothesis that appropriate structures could explain experimental results using suitable kinetic parameters. Additionally, we also hypothesized that a biological pathway is robust against small parameter changes, and that the parameter should therefore be easily searched when the pathway structure is solid. For parameter estimation, we prepared 29 ODE (ordinary differential equation) models and six time-course datasets each from the Western blot analyses of E1 and E1/4 cells (Table 1, nos. 1–3). Additionally, we developed an input signal generator to reproduce the experimental data relating to Ras- and Rap1-GTPs (Figure 4 and Table 1, nos. 4 and 5). Detailed information relating to the input signal generator is provided in Text S1, Tables S2, S3, S4 and Figures S2 and S3. Moreover, we experimentally measured the time course of B-Raf activation (Table 1, no. 6), which showed sustained activation, for validation of the model. The procedure of model selection based on parameter estimation is provided in Materials and Methods.

Bottom Line: Ligand-induced homo- and hetero-dimer formation of ErbB receptors results in different biological outcomes irrespective of recruitment and activation of similar effector proteins.We found that the pathway structure is characterized by ERK-mediated positive feedback regulation of B-Raf and B-Raf-mediated negative regulation of Raf-1.From a sensitivity analysis of the detailed upstream model for Ras activation, we concluded that Ras activation dynamics is dominated by heterodimer-mediated signaling coordination with a large initial speed of dimerization when the concentration of the ErbB4 receptor is considerably high.

View Article: PubMed Central - PubMed

Affiliation: Cellular Systems Biology Team, Computational and Experimental Systems Biology Group, RIKEN Genomic Sciences Center, Tsurumi-ku, Yokohama, Kanagawa, Japan.

ABSTRACT
Ligand-induced homo- and hetero-dimer formation of ErbB receptors results in different biological outcomes irrespective of recruitment and activation of similar effector proteins. Earlier experimental research indicated that cells expressing both EGFR (epidermal growth factor receptor) and the ErbB4 receptor (E1/4 cells) induced E1/4 cell-specific B-Raf activation and higher extracellular signal-regulated kinase (ERK) activation, followed by cellular transformation, than cells solely expressing EGFR (E1 cells) in Chinese hamster ovary (CHO) cells. Since our experimental data revealed the presence of positive feedback by ERK on upstream pathways, it was estimated that the cross-talk/feedback pathway structure of the Raf-MEK-ERK cascade might affect ERK activation dynamics in our cell system. To uncover the regulatory mechanism concerning the ERK dynamics, we used topological models and performed parameter estimation for all candidate structures that possessed ERK-mediated positive feedback regulation of Raf. The structure that reliably reproduced a series of experimental data regarding signal amplitude and duration of the signaling molecules was selected as a solution. We found that the pathway structure is characterized by ERK-mediated positive feedback regulation of B-Raf and B-Raf-mediated negative regulation of Raf-1. Steady-state analysis of the estimated structure indicated that the amplitude of Ras activity might critically affect ERK activity through ERK-B-Raf positive feedback coordination with sustained B-Raf activation in E1/4 cells. However, Rap1 that positively regulates B-Raf activity might be less effective concerning ERK and B-Raf activity. Furthermore, we investigated how such Ras activity in E1/4 cells can be regulated by EGFR/ErbB4 heterodimer-mediated signaling. From a sensitivity analysis of the detailed upstream model for Ras activation, we concluded that Ras activation dynamics is dominated by heterodimer-mediated signaling coordination with a large initial speed of dimerization when the concentration of the ErbB4 receptor is considerably high. Such characteristics of the signaling cause the preferential binding of the Grb2-SOS complex to heterodimer-mediated signaling molecules.

Show MeSH
Related in: MedlinePlus