Rationally designed protein bandpass filters for controlling cellular signaling with chemical inputs

Abstract

Biological mechanisms that rely on signal integration and processing are fundamental for cell function. These types of capabilities are analogous to those found in electronic circuits where individual components perform operations on input signals. In electronics, bandpass filters are crucial components to narrow frequencies within a specified range and reject frequencies outside of that range. However, no generalizable protein-based components are currently available to mimic such processes in engineered biological systems, representing an unmet need in controllable modules. Here, we propose a rational design approach to create protein-based chemically responsive bandpass filters (CBP) which pass chemical concentrations within a range and reject concentrations outside of that range, showing an OFF-ON-OFF regulatory pattern. The CBPs were designed using structure-based approaches where we created a heterodimeric construct which the assembly is triggered by low concentration of a small-molecule, and this interaction is inhibited at high concentrations of the drug, effectively creating a bandpass filter. The CBPs have a multidomain architecture where we used known drug-receptors, a computationally designed protein binder and small-molecule inhibitors. Owing to the modularity of the system, each domain of the CBPs can be rationally fine-tuned to optimize its performance, including bandwidth, maximum response, cutoff concentration and fold changes. These CBPs were used to regulate cell surface receptor signaling pathways showing the capability to control cellular activities in engineered cells.