System Concept
The collection is modeled after the principles of a synthetic immune cell. A modular unit that perceives extracellular signals, computes them through intracellular logic, and executes tailored functions.
Explore our part collection here!
Sensing
Our receptor layer converts diverse extracellular cues, including small molecules, soluble proteins, and surface-bound antigens, into phosphorylation events using synthetic GPCRs and MESA receptors. A key innovation is the dual receptor concept: Stimulatory receptors drive kinase activity, while inhibitory receptors activate phosphatases.
SalB-responsive GPCR gated by an anti-VEGF nanobody fused to a truncated ABL kinase; activation triggers arrestin binding and proximity-dependent substrate phosphorylation
SalB-responsive GPCR gated by an anti-VEGF nanobody fused to a truncated PTPN1 phosphatase; activation triggers arrestin binding and proximity-dependent substrate dephosphorylation.
SalB-inducible GPCR directly fused to a truncated ABL kinase; activation triggers arrestin binding and proximity-dependent substrate phosphorylation.
SalB-inducible GPCR fused to a truncated PTPN1 phosphatase; activation triggers arrestin binding and proximity-dependent substrate dephosphorylation.
Adapter that binds activated GPCRs and recruits bZipRR-containing modules, bringing kinase or phosphatase fusion proteins into catalytic proximity.
MESA receptor half, containing an extracellular FKBP dimerization domain and an intracellular truncated kinase; dimerization with the bZipEE half brings both domains into proximity to enable phosphorylation.
MESA receptor half, containing an extracellular FKBP domain and an intracellular truncated phosphatase; dimerization with the bZipEE partner subunit enables proximity-driven substrate dephosphorylation.
Complementary MESA receptor half with an extracellular FRB domain and intracellular bZipEE; dimerization with the kinase or phosphatase subunit positions the enzyme for substrate modification.
Cell-free platform for rapid screening of de novo designed binders, validated with successful BindCraft binder design against GDF15
Temperature-responsive adaptor that drives transcriptional activation above 40 °C.
Processing
The intracellular core performs immune-like logic integration, computing the opposing effects of kinase and phosphatase inputs on a shared substrate. This phosphorylation logic operates with fast, reversible kinetics, unlike transcriptional circuits that rely on slower protein expression, and ensures that switching occurs only once a defined phosphorylation threshold is reached. This translates to dynamic and precise adaptation to the rapidly changing tumor environment.
Truncated, modular kinase engineered for use in phosphorylation-based signaling circuits; transfers phosphate groups to compatible SynSubstrates when brought into proximity via bZipEE or receptor complexes.
Truncated, modular phosphatase engineered for use in phosphorylation-based signaling circuits; removes phosphate groups from compatible SynSubstrates when brought into proximity via bZipEE or receptor complexes.
Modular SH2 domain recognizing phosphorylated CD3ζ motifs; serves as a dynamic output linker or transcriptional activator in phosphorylation-dependent signaling circuits.
Synthetic substrate derived from the CD3ζ signaling chain; contains defined tyrosine motifs that mediate phosphorylation-dependent SH2 recruitment and circuit output activation.
Responding
Upon activation, PHOENICS translates the computed signal into therapeutic action. Beyond expression-based effectors, the central innovation is the rapid secretion platform. Effector proteins are pre-synthesized, retained in the ER, and released only upon circuit activation. This minimizes delay and provides immediate secretion of therapeutic proteins directly at the tumor site.
Links phosphorylation to gene expression; SH2 binds phosphorylated CD3ζ, recruiting VP64 to activate minimal promoter
CD3ζ-based substrate fused to Gal4 DNA-binding domain; upon phosphorylation, complexes with SH2-VP64 to bind UAS target sequence and drive transcription.
Effector coupling phosphorylation to cytokine secretion; PhosphoTEV activation removes ER retention, releasing pre-synthesized IL-12.
Split TEV protease activated by substrate phosphorylation; converts phosphorylation inputs into proteolytic or secretion outputs.
Integration with SPARC
The collection was co-developed with SPARC (Simulator for Phosphorylation and Receptor Characterization), a computational framework that accelerates circuit design through the integration of iterative wet-lab and dry-lab processes. SPARC combines deep learning–based de novo binder design with physics-based molecular dynamics (MD) simulations to prototype new protein binders, receptor architectures, and phosphorylation circuits in silico. This modeling pipeline provides a pre-screening metric for binder affinity and receptor performance, guiding experimental validation and reducing the need for iterative testing.
Validated binders and receptor designs were experimentally confirmed in mammalian cells, closing the design–build–test–learn loop and demonstrating the predictive accuracy of our computational models. These data are incorporated into SPARC’s mathematical model of receptor dimerization and intracellular phosphorylation, which predicts circuit behavior and ligand sensitivity across different part combinations. The integration paves the way for streamlining the development of complex phosphorylation circuits and ensuring that each addition to the library is both computationally optimized and biologically verified.