Limits...
Computational Modelling of NF-κB Activation by IL-1RI and Its Co-Receptor TILRR, Predicts a Role for Cytoskeletal Sequestration of IκBα in Inflammatory Signalling.

Rhodes DM, Smith SA, Holcombe M, Qwarnstrom EE - PLoS ONE (2015)

Bottom Line: Simulations used a comprehensive agent-based model of the NF-κB pathway, which includes the type 1 IL-1 receptor (IL-1R1) complex and signalling intermediates, as well as cytoskeletal components.Agent based modelling relies on in silico reproductions of systems through the interactions of its components, and provides a reliable tool in investigations of biological processes, which require spatial considerations and involve complex formation and translocation of regulatory components.In silico simulations using the agent-based model predict that the cytoskeletal pool of IκBα is released to adjust signal amplification in relation to input levels.

View Article: PubMed Central - PubMed

Affiliation: Department of Cardiovascular Science, Medical School, University of Sheffield, United Kingdom; Department of Computer Science, University of Sheffield, Sheffield, United Kingdom.

ABSTRACT
The transcription factor NF-κB (nuclear factor kappa B) is activated by Toll-like receptors and controlled by mechanotransduction and changes in the cytoskeleton. In this study we combine 3-D predictive protein modelling and in vitro experiments with in silico simulations to determine the role of the cytoskeleton in regulation of NF-κB. Simulations used a comprehensive agent-based model of the NF-κB pathway, which includes the type 1 IL-1 receptor (IL-1R1) complex and signalling intermediates, as well as cytoskeletal components. Agent based modelling relies on in silico reproductions of systems through the interactions of its components, and provides a reliable tool in investigations of biological processes, which require spatial considerations and involve complex formation and translocation of regulatory components. We show that our model faithfully reproduces the multiple steps comprising the NF-κB pathway, and provides a framework from which we can explore novel aspects of the system. The analysis, using 3-D predictive protein modelling and in vitro assays, demonstrated that the NF-κB inhibitor, IκBα is sequestered to the actin/spectrin complex within the cytoskeleton of the resting cell, and released during IL-1 stimulation, through a process controlled by the IL-1RI co-receptor TILRR (Toll-like and IL-1 receptor regulator). In silico simulations using the agent-based model predict that the cytoskeletal pool of IκBα is released to adjust signal amplification in relation to input levels. The results suggest that the process provides a mechanism for signal calibration and enables efficient, activation-sensitive regulation of NF-κB and inflammatory responses.

No MeSH data available.


Related in: MedlinePlus

Cytoskeletal binding and release of IκBα controls NF-κB signalling and gene induction.A. Simulated IL-8 gene activity kinetics at varying IL-1 pathway stimulation levels, in the presence (Red) and absence (Blue) of cytoskeletal binding and release of IκBα. Simulations show that disabling cytoskeletal binding of the inhibitor abrogates activation at low levels of stimulation, causes delayed responses at medium stimulation, and results in a slightly delayed but significantly increased activation at high levels of stimulus. P < 0.05 at low and high stimulus. B. Simulated degradation of IκBα after stimulation with saturated levels of IL-1β (10-9M) with enabled (Red) or disabled (Blue) cytoskeletal binding and release of IκBα, in the presence WT TILRR, R425 TILRR or D448 TILRR. The model predicts that cytoskeletal binding of IκBα causes a reduction in its degradation in the presence of WT TILRR and both mutants, consistent with a greater IL-8 response at higher levels of stimulation. The low level of IκBα-degradation induced in the presence of the 448 mutant is similarly affected by cytoskeletal binding of the inhibitor. n = 4 p>0.05 at 60 min for all conditions. C. Predicted IL-8 activity at varying TILRR expression levels, with enabled (Red) or disabled (Blue) cytoskeleton: IκBα binding, and in the presence of WT TILRR, or TILRR mutants R425 or D448. As expected, inflammatory activity is higher in the presence of wild type TILRR or the 425 mutant. Comparing activity in the presence and absence of cytoskeletal binding, under these conditions, show a more pronounced effect at lower levels with inverse effects at higher levels of, activity, while effects at intermediate activities are less pronounced consistent with data in 5A. Levels in the presence of the 448 mutants correspond to the lower range of activity, only. (Mean±SEM, n = 3). WT, 425 0.0005< p< 0.05 at expression levels 0, 15, 120, 180, ns 30, 60. D448. 0.0005< p < 0.05 at expression levels 0–180.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4482363&req=5

pone.0129888.g005: Cytoskeletal binding and release of IκBα controls NF-κB signalling and gene induction.A. Simulated IL-8 gene activity kinetics at varying IL-1 pathway stimulation levels, in the presence (Red) and absence (Blue) of cytoskeletal binding and release of IκBα. Simulations show that disabling cytoskeletal binding of the inhibitor abrogates activation at low levels of stimulation, causes delayed responses at medium stimulation, and results in a slightly delayed but significantly increased activation at high levels of stimulus. P < 0.05 at low and high stimulus. B. Simulated degradation of IκBα after stimulation with saturated levels of IL-1β (10-9M) with enabled (Red) or disabled (Blue) cytoskeletal binding and release of IκBα, in the presence WT TILRR, R425 TILRR or D448 TILRR. The model predicts that cytoskeletal binding of IκBα causes a reduction in its degradation in the presence of WT TILRR and both mutants, consistent with a greater IL-8 response at higher levels of stimulation. The low level of IκBα-degradation induced in the presence of the 448 mutant is similarly affected by cytoskeletal binding of the inhibitor. n = 4 p>0.05 at 60 min for all conditions. C. Predicted IL-8 activity at varying TILRR expression levels, with enabled (Red) or disabled (Blue) cytoskeleton: IκBα binding, and in the presence of WT TILRR, or TILRR mutants R425 or D448. As expected, inflammatory activity is higher in the presence of wild type TILRR or the 425 mutant. Comparing activity in the presence and absence of cytoskeletal binding, under these conditions, show a more pronounced effect at lower levels with inverse effects at higher levels of, activity, while effects at intermediate activities are less pronounced consistent with data in 5A. Levels in the presence of the 448 mutants correspond to the lower range of activity, only. (Mean±SEM, n = 3). WT, 425 0.0005< p< 0.05 at expression levels 0, 15, 120, 180, ns 30, 60. D448. 0.0005< p < 0.05 at expression levels 0–180.

Mentions: To determine the effect of cytoskeletal sequestration and release of IκBα on receptor induced activation, we disabled the process and compared activation at three stimulus levels, using the inflammatory gene IL-8 as readout (Fig 5A). Simulations predict low levels of stimulation to be most sensitive to cytoskeletal release of the inhibitor, and activation to be abrogated in the absence of cytoskeleton: IκBα binding. At intermediate levels, lack of cytoskeletal binding of the inhibitor increases lag time and results in a moderate reduction in gene activity. At high stimulation, disabling the process causes an increased lag time, followed by pronounced signal-amplification and enhanced activation levels, which by 90 minutes exceed responses in the presence cytoskeletal binding and release of IκBα.


Computational Modelling of NF-κB Activation by IL-1RI and Its Co-Receptor TILRR, Predicts a Role for Cytoskeletal Sequestration of IκBα in Inflammatory Signalling.

Rhodes DM, Smith SA, Holcombe M, Qwarnstrom EE - PLoS ONE (2015)

Cytoskeletal binding and release of IκBα controls NF-κB signalling and gene induction.A. Simulated IL-8 gene activity kinetics at varying IL-1 pathway stimulation levels, in the presence (Red) and absence (Blue) of cytoskeletal binding and release of IκBα. Simulations show that disabling cytoskeletal binding of the inhibitor abrogates activation at low levels of stimulation, causes delayed responses at medium stimulation, and results in a slightly delayed but significantly increased activation at high levels of stimulus. P < 0.05 at low and high stimulus. B. Simulated degradation of IκBα after stimulation with saturated levels of IL-1β (10-9M) with enabled (Red) or disabled (Blue) cytoskeletal binding and release of IκBα, in the presence WT TILRR, R425 TILRR or D448 TILRR. The model predicts that cytoskeletal binding of IκBα causes a reduction in its degradation in the presence of WT TILRR and both mutants, consistent with a greater IL-8 response at higher levels of stimulation. The low level of IκBα-degradation induced in the presence of the 448 mutant is similarly affected by cytoskeletal binding of the inhibitor. n = 4 p>0.05 at 60 min for all conditions. C. Predicted IL-8 activity at varying TILRR expression levels, with enabled (Red) or disabled (Blue) cytoskeleton: IκBα binding, and in the presence of WT TILRR, or TILRR mutants R425 or D448. As expected, inflammatory activity is higher in the presence of wild type TILRR or the 425 mutant. Comparing activity in the presence and absence of cytoskeletal binding, under these conditions, show a more pronounced effect at lower levels with inverse effects at higher levels of, activity, while effects at intermediate activities are less pronounced consistent with data in 5A. Levels in the presence of the 448 mutants correspond to the lower range of activity, only. (Mean±SEM, n = 3). WT, 425 0.0005< p< 0.05 at expression levels 0, 15, 120, 180, ns 30, 60. D448. 0.0005< p < 0.05 at expression levels 0–180.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4482363&req=5

pone.0129888.g005: Cytoskeletal binding and release of IκBα controls NF-κB signalling and gene induction.A. Simulated IL-8 gene activity kinetics at varying IL-1 pathway stimulation levels, in the presence (Red) and absence (Blue) of cytoskeletal binding and release of IκBα. Simulations show that disabling cytoskeletal binding of the inhibitor abrogates activation at low levels of stimulation, causes delayed responses at medium stimulation, and results in a slightly delayed but significantly increased activation at high levels of stimulus. P < 0.05 at low and high stimulus. B. Simulated degradation of IκBα after stimulation with saturated levels of IL-1β (10-9M) with enabled (Red) or disabled (Blue) cytoskeletal binding and release of IκBα, in the presence WT TILRR, R425 TILRR or D448 TILRR. The model predicts that cytoskeletal binding of IκBα causes a reduction in its degradation in the presence of WT TILRR and both mutants, consistent with a greater IL-8 response at higher levels of stimulation. The low level of IκBα-degradation induced in the presence of the 448 mutant is similarly affected by cytoskeletal binding of the inhibitor. n = 4 p>0.05 at 60 min for all conditions. C. Predicted IL-8 activity at varying TILRR expression levels, with enabled (Red) or disabled (Blue) cytoskeleton: IκBα binding, and in the presence of WT TILRR, or TILRR mutants R425 or D448. As expected, inflammatory activity is higher in the presence of wild type TILRR or the 425 mutant. Comparing activity in the presence and absence of cytoskeletal binding, under these conditions, show a more pronounced effect at lower levels with inverse effects at higher levels of, activity, while effects at intermediate activities are less pronounced consistent with data in 5A. Levels in the presence of the 448 mutants correspond to the lower range of activity, only. (Mean±SEM, n = 3). WT, 425 0.0005< p< 0.05 at expression levels 0, 15, 120, 180, ns 30, 60. D448. 0.0005< p < 0.05 at expression levels 0–180.
Mentions: To determine the effect of cytoskeletal sequestration and release of IκBα on receptor induced activation, we disabled the process and compared activation at three stimulus levels, using the inflammatory gene IL-8 as readout (Fig 5A). Simulations predict low levels of stimulation to be most sensitive to cytoskeletal release of the inhibitor, and activation to be abrogated in the absence of cytoskeleton: IκBα binding. At intermediate levels, lack of cytoskeletal binding of the inhibitor increases lag time and results in a moderate reduction in gene activity. At high stimulation, disabling the process causes an increased lag time, followed by pronounced signal-amplification and enhanced activation levels, which by 90 minutes exceed responses in the presence cytoskeletal binding and release of IκBα.

Bottom Line: Simulations used a comprehensive agent-based model of the NF-κB pathway, which includes the type 1 IL-1 receptor (IL-1R1) complex and signalling intermediates, as well as cytoskeletal components.Agent based modelling relies on in silico reproductions of systems through the interactions of its components, and provides a reliable tool in investigations of biological processes, which require spatial considerations and involve complex formation and translocation of regulatory components.In silico simulations using the agent-based model predict that the cytoskeletal pool of IκBα is released to adjust signal amplification in relation to input levels.

View Article: PubMed Central - PubMed

Affiliation: Department of Cardiovascular Science, Medical School, University of Sheffield, United Kingdom; Department of Computer Science, University of Sheffield, Sheffield, United Kingdom.

ABSTRACT
The transcription factor NF-κB (nuclear factor kappa B) is activated by Toll-like receptors and controlled by mechanotransduction and changes in the cytoskeleton. In this study we combine 3-D predictive protein modelling and in vitro experiments with in silico simulations to determine the role of the cytoskeleton in regulation of NF-κB. Simulations used a comprehensive agent-based model of the NF-κB pathway, which includes the type 1 IL-1 receptor (IL-1R1) complex and signalling intermediates, as well as cytoskeletal components. Agent based modelling relies on in silico reproductions of systems through the interactions of its components, and provides a reliable tool in investigations of biological processes, which require spatial considerations and involve complex formation and translocation of regulatory components. We show that our model faithfully reproduces the multiple steps comprising the NF-κB pathway, and provides a framework from which we can explore novel aspects of the system. The analysis, using 3-D predictive protein modelling and in vitro assays, demonstrated that the NF-κB inhibitor, IκBα is sequestered to the actin/spectrin complex within the cytoskeleton of the resting cell, and released during IL-1 stimulation, through a process controlled by the IL-1RI co-receptor TILRR (Toll-like and IL-1 receptor regulator). In silico simulations using the agent-based model predict that the cytoskeletal pool of IκBα is released to adjust signal amplification in relation to input levels. The results suggest that the process provides a mechanism for signal calibration and enables efficient, activation-sensitive regulation of NF-κB and inflammatory responses.

No MeSH data available.


Related in: MedlinePlus