Enzyme Sequestration as a Tuning Point in Controlling Response Dynamics of Signalling Networks

Signalling networks result from combinatorial interactions among many enzymes and scaffolding proteins. These complex systems generate response dynamics that are often essential for correct decision-making in cells. Uncovering biochemical design principles that underpin such response dynamics is a prerequisite to understand evolved signalling networks and to design synthetic ones. Here, we use in silico evolution to explore the possible biochemical design space for signalling networks displaying ultrasensitive and adaptive response dynamics. By running evolutionary simulations mimicking different biochemical scenarios, we find that enzyme sequestration emerges as a key mechanism for enabling such dynamics. Inspired by these findings, and to test the role of sequestration, we design a generic, minimalist model of a signalling cycle, featuring two enzymes and a single scaffolding protein. We show that this simple system is capable of displaying both ultrasensitive and adaptive response dynamics. Furthermore, we find that tuning the concentration or kinetics of the sequestering protein can shift system dynamics between these two response types. These empirical results suggest that enzyme sequestration through scaffolding proteins is exploited by evolution to generate diverse response dynamics in signalling networks and could provide an engineering point in synthetic biology applications.Author Summary: Biological systems utilise signalling networks that are composed of multiple interacting proteins to process environmental information. The function of these networks is critical for cells to respond and adapt to their environment by converting environmental signals to appropriate cellular response dynamics. As results of evolution, these signalling networks display certain evolutionary design principles (i.e. common structural and dynamical features) that allow them to implement specific functions. Here, we use an in silico evolution approach to simulate the emergence of signalling networks that are capable of two specific types of response dynamics: switch-like and/or adaptive response dynamics. These two response dynamics underpin cellular decision-making and homeostasis. By analysing the evolved networks, we discover that enzyme sequestration is a key feature involved in achieving both types of response dynamics. Based on this finding, we design a minimalistic signalling motif featuring enzyme sequestration through a scaffold protein. We demonstrate that this motif can achieve both response dynamics and furthermore the type of response can be controlled through the concentration level of the scaffold protein. These results highlight enzyme sequestration as a potential evolutionary design principle to achieve key response dynamics in natural signalling networks and as an engineering route in synthetic biology.