Automated synthetic cell-based screening for designed proteins with emergent functions

Designing minimal biological systems with emergent functions such as spatiotemporal self-organization is a central goal of bottom-up synthetic biology. While computational optimization and design show promise in accelerating functional protein engineering through Design-Build-Test-Learn cycles, screening libraries for complex functions remains a major challenge. Conventional screens typically lack the spatiotemporal resolution and cell-like confinement required in bottom-up synthetic biology. Here, we present PUREdrop, an automated microfluidic platform that encapsulates and expresses protein libraries in thousands of picoliter-sized synthetic cells per construct. PUREdrop distributes these across predefined wells of a 96-well plate for time-lapse imaging, enabling parallel quantification of expression kinetics and emergent functions. To demonstrate the platform's potential, we first screen computationally re-designed variants of the bacterial cell division protein FtsZ, and identify variants with altered bundling phenotypes and distinct kinetics. We then extend our screening procedure to general protein modulators of FtsZ and identify a combination that anchors filaments to the interface, producing a ring-like phenotype. PUREdrop bridges computational protein engineering and synthetic cell research, elevating the rational engineering of complex biological function to the next level.