Biology subjects

BARTH, P.

Publications and source records attributed to BARTH, P..

3 recordsLinked to original sources

bioRxiv2025

De novo design of light-regulated dynamic proteins using deep learning

Recent advances in deep learning have enabled accurate design of static protein structures, but the de novo design of protein functions controlled by programmable, intramolecular conformational changes remains an unsolved challenge. Here, we present a general deep learning-guided framework for designing dynamic, multi-domain proteins allosterically regulated by light. By integrating photoresponsive domains into de novo scaffolds, we engineered conformational switches that exhibit precise, reversible structural transitions upon illumination. Structural, spectroscopic, and functional analyses validated our designs and demonstrated precise spatio-temporal optogenetic control of diverse cellular processes, including subcellular localization, intercellular signaling, and population-level behaviors. This work establishes a broadly applicable strategy for encoding long-range allosteric control through designed intramolecular motions, and opens new avenues for programming dynamic protein functions from first principles, with implications for basic research, synthetic biology, and therapeutic development.

biophysics↗

bioRxiv2025

Designed allosteric biosensors for engineered T cell therapy of cancer

Adoptive cell therapy with chimeric antigen receptor (CAR) T cells has transformed standard-of-care for selected hematologic malignancies, but relapses are frequent and efficacy against solid tumors remains limited1,2. The tumor microenvironment (TME) plays a key role in tumor progression3, and both soluble and cellular TME components can limit CAR-T cell function and persistence4. Targeting soluble TME factors to enhance anti-tumor responses of engineered T cells through chimeric receptors is not yet broadly explored due to the unpredictable signaling characteristics of synthetic protein receptors. Here we developed a protein design platform for the de novo bottom-up assembly of allosteric receptors with programmable input-output behaviors that respond to soluble TME factors with co-stimulation and cytokine signals in T cells, called T-SenSER (TME-sensing switch receptor for enhanced response to tumors). We developed two sets of T-SenSERs targeting vascular endothelial growth factor (VEGF) or colony stimulating factor 1 (CSF1), that are both selectively enriched in a variety of tumors. Combination of CAR and T-SenSER in human T cells enhanced anti-tumor responses in models of lung cancer and multiple myeloma, in a VEGF or CSF1-dependent manner. Our study sets the stage for the accelerated development of synthetic biosensors with custom-built sensing and responses for basic and translational cell engineering applications.

bioengineering↗

bioRxiv2023

Uncovering and engineering the mechanical properties of the adhesion GPCR ADGRG1 GAIN domain

Key cellular functions depend on the transduction of extracellular mechanical signals by specialized membrane receptors including adhesion G-protein coupled receptors (aGPCRs). While recently solved structures support aGPCR activation through shedding of the extracellular GAIN domain, the molecular mechanisms underpinning receptor mechanosensing remain poorly understood. When probed using single-molecule atomic force spectroscopy and molecular simulations, ADGRG1 GAIN dissociated from its tethered agonist at forces significantly higher than other reported signaling mechanoreceptors. Strong mechanical resistance was achieved through specific structural deformations and force propagation pathways under mechanical load. ADGRG1 GAIN variants computationally designed to lock the alpha and beta subdomains and rewire mechanically-induced structural deformations were found to modulate the GPS-Stachel rupture forces. Our study provides unprecedented insights into the molecular underpinnings of GAIN mechanical stability and paves the way for engineering mechanosensors, better understanding aGPCR function, and informing drug-discovery efforts targeting this important receptor class.

biophysics↗