Related Experiment Video
Updated: Jul 1, 2026

Spatiotemporal Control of Protein Activity through Optogenetic Allosteric Regulation
Published on: October 4, 2024
Modelling the dynamics of signalling pathways
Sree N Sreenath1, Kwang-Hyun Cho, Peter Wellstead
1Case Complex Systems Biology Center, Electrical Engineering and Computer Science Department, Case Western Reserve University, Cleveland, OH 44139, U.S.A. n.sreenath@case.edu
Abstract:
In the present chapter we discuss methodologies for the modelling, calibration and validation of cellular signalling pathway dynamics. The discussion begins with the typical range of techniques for modelling that might be employed to go from the chemical kinetics to a mathematical model of biochemical pathways. In particular, we consider the decision-making processes involved in selecting the right mechanism and level of detail of representation of the biochemical interactions. These include the choice between (i) deterministic and stochastic chemical kinetics representations, (ii) discrete and continuous time models and (iii) representing continuous and discrete state processes. We then discuss the task of calibrating the models using information available in web-based databases. For situations in which the data are not available from existing sources we discuss model calibration based upon measured data and system identification methods. Such methods, together with mathematical modelling databases and computational tools, are often available in standard packages. We therefore make explicit mention of a range of popular and useful sites. As an example of the whole modelling and calibration process, we discuss a study of the cross-talk between the IL-1 (interleukin-1)-stimulated NF-kappaB (nuclear factor kappaB) pathway and the TGF-beta (transforming growth factor beta)-stimulated Smad2 pathway.
Related Concept Videos
Interactions Between Signaling Pathways
Convergence and divergence, and cross-talk between signaling pathways
Two distinct signaling pathways can converge on a single functional unit, which may either be a single protein or a complex of proteins. The response is either functionally distinct or synergistic between the two pathways but different from the response...
Diversity in Cell Signaling Responses
Graded and Abrupt Responses
Some signaling systems generate...
Amplifying Signals via Enzymatic Cascade
Assembly of Signaling Complexes
Interaction domains in cell signaling
Interaction domains recognize exposed features of their binding partners containing post-translationally modified sequences,...
Signal Transduction: Overview
Typically, signal transduction involves three...
Cell Signaling Feedback Loops
Negative feedback loops
Most signaling systems have negative feedback loops that can perform different functions such as output limiter, and adaptation.
Output limiter
Upon receiving an input signal, the cellular response rapidly increases until a threshold is reached. Beyond this threshold, a negative feedback loop...

