title: Design of biomolecular network modifications to achieve adaptation.
abstract: A biomolecular network is called adaptive if its output returns to the original value after a transient response even under a persisting stimulus. The conditions for adaptation have been investigated thoroughly with systems theory approaches in the literature and it is easy to check whether they are satisfied in the linear approximation. In contrast, it is in general not easy to modify a non-adaptive network model such that it gains adaptive behaviour, especially for medium- and large-scale networks. The authors present a systematic approach based on the notion of kinetic perturbations to construct adaptive biomolecular network models from non-adaptive ones. An advantage of kinetic perturbations in this application is that neither the stoichiometry nor the steady state of the system is changed. Furthermore, the method covers both parameter and network structure modifications and can be applied to any reaction rate formalism and even to medium-scale or partially unknown models. The approach is exemplified at a small- and a medium-sized biomolecular network, illustrating its potential to systematically evaluate the different network modifications for adaptation. The proposed method will be useful either in iterative model building to construct mathematical models of adaptive biomolecular networks, or in synthetic biology where it can be applied to design or modify synthetic networks for adaptation.
authors.affiliation: Institute for Systems Theory and Automatic Control, Universität Stuttgart, Pfaffenwaldring 9, 70550 Stuttgart, Germany. waldherr@ist.uni-stuttgart.de
authors.forename: S
authors.initials: S
authors.lastname: Waldherr
authors.forename: S
authors.initials: S
authors.lastname: Streif
authors.forename: F
authors.initials: F
authors.lastname: Allgöwer
mesh_terms: D000222:Adaptation, Physiological; D000818:Animals; D003198:Computer Simulation; D053263:Gene Regulatory Networks; D007700:Kinetics; D020928:Mitogen-Activated Protein Kinases / Q000378:metabolism; D008954:Models, Biological; D058615:Synthetic Biology; D049490:Systems Biology / Q000379:methods*; D014981:Xenopus
chemical_list: D020928:Mitogen-Activated Protein Kinases