Boronic Acid Resin for Selective Immobilization of Canonically Encoded Proteins.

The use of transition-metal-mediated boronic acid chemistry presents a novel method of protein immobilization on a solid support. This is a one-step method that site-selectively immobilizes pyroglutamate-histidine (pGH)-tagged proteins. Herein, we describe the synthesis of alkenylboronic acid-functionalized poly(ethylene glycol) acrylamide (PEGA) resin and its subsequent reactions with pGH-tagged proteins to produce covalent linkages. The selectivity of immobilization is demonstrated within fluorescent studies, model mixtures, and lysates.

Design of Oscillatory Networks through Post-Translational Control of Network Components.

Many essential functions in biological systems, including cell cycle progression and circadian rhythm regulation, are governed by the periodic behaviors of specific molecules. These periodic behaviors arise from the precise arrangement of components in biomolecular networks that generate oscillatory output signals. The dynamic properties of individual components of these networks, such as maturation delays and degradation rates, often play a key role in determining the network's oscillatory behavior. In this study, we explored the post-translational modulation of network components as a means to generate genetic circuits with oscillatory behaviors and perturb the oscillation features. Specifically, we used the NanoDeg platform-A bifunctional molecule consisting of a target-specific nanobody and a degron tag-to control the degradation rates of the circuit's components and predicted the effect of NanoDeg-mediated post-translational depletion of a key circuit component on the behavior of a series of proto-oscillating network topologies. We modeled the behavior of two main classes of oscillators, namely relaxation oscillator topologies (the activator-repressor and the Goodwin oscillator) and ring oscillator topologies (repressilators). We identified two main mechanisms by which non-oscillating networks could be induced to oscillate through post-translational modulation of network components: an increase in the separation of timescales of network components and mitigation of the leaky expression of network components. These results are in agreement with previous findings describing the effect of timescale separation and mitigation of leaky expression on oscillatory behaviors. This work thus validates the use of tools to control protein degradation rates as a strategy to modulate existing oscillatory signals and construct oscillatory networks. In addition, this study provides the design rules to implement such an approach based on the control of protein degradation rates using the NanoDeg platform, which does not require genetic manipulation of the network components and can be adapted to virtually any cellular protein. This work also establishes a framework to explore the use of tools for post-translational perturbations of biomolecular networks and generates desired behaviors of the network output.

A platform for post-translational spatiotemporal control of cellular proteins.

Mammalian cells process information through coordinated spatiotemporal regulation of proteins. Engineering cellular networks thus relies on efficient tools for regulating protein levels in specific subcellular compartments. To address the need to manipulate the extent and dynamics of protein localization, we developed a platform technology for the target-specific control of protein destination. This platform is based on bifunctional molecules comprising a target-specific nanobody and universal sequences determining target subcellular localization or degradation rate. We demonstrate that nanobody-mediated localization depends on the expression level of the target and the nanobody, and the extent of target subcellular localization can be regulated by combining multiple target-specific nanobodies with distinct localization or degradation sequences. We also show that this platform for nanobody-mediated target localization and degradation can be regulated transcriptionally and integrated within orthogonal genetic circuits to achieve the desired temporal control over spatial regulation of target proteins. The platform reported in this study provides an innovative tool to control protein subcellular localization, which will be useful to investigate protein function and regulate large synthetic gene circuits.

Input-dependent post-translational control of the reporter output enhances dynamic resolution of mammalian signaling systems.

Mammalian cells rely on complex and highly dynamic networks that respond to environmental stimuli and intracellular signals and maintain homeostasis. The use of synthetic orthogonal circuits for detection of dynamic behaviors has been limited by the remarkable stability of conventional reporters. While providing an appealing feature for signal amplification, the long half-life of reporters such as GFP is typically not ideal to measure transient signals and dynamic behaviors. This chapter explores the use of post-translational regulation for the design of input-dependent circuits that produce output signals with enhanced dynamic range and superior dynamic resolution of the input. Specifically, we report the use of the NanoDeg-a bifunctional system that mediates proteasomal degradation of a cellular target with high specificity and control over rate of decay-to achieve input-dependent depletion of a GFP reporter. Feedforward loop topologies were explored and compared to conventional reporters placed directly under control of the input to identify the ideal circuit architecture that allows placing both the GFP output and the GFP-specific NanoDeg under control of a common input and regulate GFP levels not only through input-dependent transcriptional activation but also input-dependent degradation. The circuit design was implemented experimentally by building a heat-sensitive reporter and exploring the design features that result in detection of the cell response with maximal output dynamic range and dynamic resolution of the heat shock. The method reported provides the design rules of a novel synthetic biology module that will be generally useful to build complex genetic networks for enhanced detection of highly dynamic behaviors.