Research article

A domain-oriented approach to the reduction of combinatorial complexity in signal transduction networks

Holger Conzelmann¹ , Julio Saez-Rodriguez² , Thomas Sauter¹ , Boris N Kholodenko³ and Ernst D Gilles^1,2

¹Institute for System Dynamics and Control Engineering, University of Stuttgart, Pfaffenwaldring 9, 70569 Stuttgart, Germany

²Max-Planck-lnstitute for Dynamics of Complex Technical Systems, Sandtorstr. 1, 39106 Magdeburg, Germany

³Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, 1020 Locust St., Philadelphia, PA 19107, USA

author email corresponding author email

BMC Bioinformatics 2006, 7:34doi:10.1186/1471-2105-7-34

Published:	23 January 2006

Abstract

Background:

Receptors and scaffold proteins possess a number of distinct domains and bind multiple partners. A common problem in modeling signaling systems arises from a combinatorial explosion of different states generated by feasible molecular species. The number of possible species grows exponentially with the number of different docking sites and can easily reach several millions. Models accounting for this combinatorial variety become impractical for many applications.

Results:

Our results show that under realistic assumptions on domain interactions, the dynamics of signaling pathways can be exactly described by reduced, hierarchically structured models. The method presented here provides a rigorous way to model a large class of signaling networks using macro-states (macroscopic quantities such as the levels of occupancy of the binding domains) instead of micro-states (concentrations of individual species). The method is described using generic multidomain proteins and is applied to the molecule LAT.

Conclusion:

The presented method is a systematic and powerful tool to derive reduced model structures describing the dynamics of multiprotein complex formation accurately.