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Signaling proteins comprise interaction and effector modules connected by linkers. Throughout evolution, these recurring modules have multiply been recombined to produce the present-day plethora of signaling proteins. Likewise, modular recombination lends itself to the engineering of hybrid signal receptors, whose functionality hinges on linker topology, sequence, and length. Often, numerous linkers must be assessed to obtain functional receptors. To expedite linker optimization, we devised the PATCHY strategy (primer-aided truncation for the creation of hybrid proteins) for the facile construction of hybrid gene libraries with defined linker distributions. Empowered by PATCHY, we engineered photoreceptors whose signal response was governed by linker length: whereas blue-light-repressed variants possessed linkers of 7n or 7n+5 residues, variants with 7n+1 residues were blue-light-activated. Related natural receptors predominantly displayed linker lengths of 7n and 7n+5 residues but rarely of 7n+1 residues. PATCHY efficiently explores linker sequence space to yield functional hybrid proteins including variants transcending the natural repertoire of signaling proteins.

As light-regulated actuators, sensory photoreceptors underpin optogenetics and numerous applications in synthetic biology. Protein engineering has been applied to fine-tune the properties of photoreceptors and to generate novel actuators. For the blue-light-sensitive light-oxygen-voltage (LOV) photoreceptors, mutations near the flavin chromophore modulate response kinetics and the effective light responsiveness. To probe for potential, inadvertent effects on receptor activity, we introduced these mutations into the engineered LOV photoreceptor YF1 and determined their impact on light regulation. While several mutations severely impaired the dynamic range of the receptor (e.g., I39V, R63K, and N94A), residue substitutions in a second group were benign with little effect on regulation (e.g., V28T, N37C, and L82I). Electron paramagnetic resonance and absorption spectroscopy identified correlated effects for certain of the latter mutations on chromophore environment and response kinetics in YF1 and the LOV2 domain from Avena sativa phototropin 1. Carefully chosen mutations provide a powerful means to adjust the light-response function of photoreceptors as demanded for diverse applications.

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Neurotransmitter-sensitive contrast agents for magnetic resonance imaging (MRI) have recently been used for mapping signaling dynamics in live animal brains, but paramagnetic sensors for T1-weighted MRI are usually effective only at micromolar concentrations that themselves perturb neurochemistry. Here we present an alternative molecular architecture for detecting neurotransmitters, using superparamagnetic iron oxide nanoparticles conjugated to tethered neurotransmitter analogs and engineered neurotransmitter binding proteins. Interactions between the nanoparticle conjugates result in clustering that is reversibly disrupted in the presence of neurotransmitter analytes, thus altering T2weighted MRI signals. We demonstrate this principle using tethered dopamine and serotonin analogs, together with proteins selected for their ability to competitively bind either the analogs or the neurotransmitters themselves. Corresponding sensors for dopamine and serotonin exhibit target-selective relaxivity changes of up to 20%, while also operating below endogenous neurotransmitter concentrations. Semisynthetic magnetic particle sensors thus represent a promising path for minimally perturbative studies of neurochemical analytes. ASSOCIATED CONTENT Supporting Information. Additional data, detailed methods, and characterization of synthetic compounds. This material is available free of charge at http://pubs.acs.org.