Discovering adaptation-capable biological network structures using control-theoretic approaches

Constructing biological networks capable of performing specific biological functionalities has been of sustained interest in synthetic biology. Adaptation is one such ubiquitous functional property, which enables every living organism to sense a change in its surroundings and return to its operating condition prior to the disturbance. In this paper, we present a generic systems theory-driven method for designing adaptive protein networks. First, we translate the necessary qualitative conditions for adaptation to mathematical constraints using the language of systems theory, which we then map back as ‘design requirements’ for the underlying networks. We go on to prove that a protein network with different input–output nodes (proteins) needs to be at least of third-order in order to provide adaptation. Next, we show that the necessary design principles obtained for a three-node network in adaptation consist of negative feedback or a feed-forward realization. We argue that presence of a particular class of negative feedback or feed-forward realization is necessary for a network of any size to provide adaptation. Further, we claim that the necessary structural conditions derived in this work are the strictest among the ones hitherto existed in the literature. Finally, we prove that the capability of producing adaptation is retained for the admissible motifs even when the output node is connected with a downstream system in a feedback fashion. This result explains how complex biological networks achieve robustness while keeping the core motifs unchanged in the context of a particular functionality. We corroborate our theoretical results with detailed and thorough numerical simulations. Overall, our results present a generic, systematic and robust framework for designing various kinds of biological networks.
Author summary Biological systems display a remarkable diversity of functionalities, many of which can be conceived as the response of a large network composed of small interconnecting modules. Unravelling the connection pattern, i.e. design principles, behind important biological functionalities is one of the most challenging problems in systems biology. One such phenomenon is perfect adaptation, which merits special attention owing to its universal presence ranging from chemotaxis in bacterial cells to calcium homeostasis in mammalian cells. The present work focuses on finding the design principles for perfect adaptation in the presence of a stair-case type disturbance. To this end, the current work proposes a systems-theoretic approach to deduce precise mathematical (hence structural) conditions that comply with the key performance parameters for adaptation. The approach is agnostic to the particularities of the reaction kinetics, underlining the dominant role of the topological structure on the response of the network. Notably, the design principles obtained in this work serve as the most strict necessary structural conditions for a network of any size to provide perfect adaptation.