Scientists Design Ultra-Stable Synthetic Proteins That Could Change Drug Discovery

By Dr. Chinta SidharthanReviewed by Lily Ramsey, LLMFeb 3 2025

What if we could design proteins that mimic nature’s signaling mechanisms but with enhanced precision and stability? A recent study published in Nature Chemistry ventured into the groundbreaking realm of synthetic protein design, focusing on G protein-coupled receptors (GPCRs), which are vital for cell signaling and drug discovery.

The researchers employed computational tools to re-engineer the adenosine A2A receptor and craft stable, signaling-active proteins by redesigning their hydration and molecular interactions.

These designs pave the way for innovative protein-based solutions in medicine, synthetic biology, and biotechnology, offering insights into creating novel, highly stable proteins for applications ranging from drug discovery to biosensors.

​​​​​​​Study: Computational design of highly signalling-active membrane receptors through solvent-mediated allosteric networks. Image Credit: Volha_R/Shutterstock.com

G Protein-Coupled Receptors

Proteins are nature’s functional building blocks and perform diverse tasks such as signaling, binding, and catalysis. G protein-coupled receptors (GPCRs) are a particularly versatile class of proteins that are responsible for translating extracellular signals into intracellular responses.

Despite their importance in drug development and cellular communication, designing synthetic proteins that replicate the intricate functions of natural GPCRs has proven challenging.

Advances in computational modeling have enabled researchers to design proteins with high stability and precise structural features. Yet, striking a balance between stability and functionality, especially for proteins in dynamic systems like cell signaling, remains elusive.

GPCRs serve as a model system due to their complex interaction networks involving ligands, ions, and hydration, which facilitate structural and functional transitions. Understanding and replicating these transitions is critical for advancing protein engineering and for applications in pharmaceuticals and synthetic biology.

The Current Study

The present study addressed these knowledge gaps by exploring new design approaches for engineered GPCRs. Here, the researchers utilized computational tools to design novel GPCR variants with enhanced signaling activity and stability, focusing on the adenosine A2A receptor (A2AR).

They employed the St. Petersburg genome assembler or SPaDES computational framework to analyze and redesign the interactions between transmembrane helices and solvent molecules within the receptor’s core.

The analysis targeted 22 specific sites within the A2AR structure, emphasizing solvent-mediated hydrogen bonding, conformational stability, and protein-ion interactions.

To develop these designs, SPaDES integrated solvent molecules directly into the modeling process, optimizing hydration networks crucial for structural transitions. Computational sequences were restricted to specific amino acid categories to ensure compatibility with the protein’s highly packed transmembrane regions.

Furthermore, nine single-point mutants and five combinations of designs were selected for further validation and to ensure a balance in criteria such as structural stability in active versus inactive states and hydration connectivity.

The resulting GPCR models were analyzed using advanced molecular dynamics simulations and experimental techniques. Additionally, crystallization trials for the most promising variant, Hyd_high7, were also conducted using lipidic cubic phase methods to produce high-resolution structural data.

Furthermore, fluorescent thermal stability assays provided additional insights into the proteins’ robustness. By focusing on water-mediated hydrogen bonding and ion binding in the critical structural motifs, the study demonstrated a novel approach to designing proteins that retain their natural complexity while achieving synthetic stability and function.

Results

The researchers found that it is possible to design GPCRs with enhanced signaling activity and stability through computationally optimized solvent-mediated interactions. The engineered Hyd_high7 variant demonstrated significant signaling activity, maintaining an active-like conformation even without a bound G protein, which is typically required for full receptor activation.

Further analysis of Hyd_high7 revealed a novel hydration network between the major transmembrane helices that facilitated structural stability and efficient signal transduction.

These designs also incorporated strong water-mediated hydrogen bonding networks at critical sites that enabled smooth transitions between active and inactive states.

The researchers noted that specific mutations improved the receptor’s thermostability while preserving its dynamic response to agonists, though some designs exhibited reduced ligand-induced activation compared to the native receptor.

One of the major observations was that Asp2.50 — a conserved residue in the receptor core —played a critical role in maintaining hydration and stabilization across functional states. By altering polar and hydrophobic interactions at this site, the researchers successfully modulated receptor activation.

Another significant finding was the ability to design active-state GPCR structures with unprecedented stability and reduced conformational shifts, offering new opportunities for drug design and synthetic biology applications.

Conclusions

Overall, the study demonstrated a pioneering approach to engineering proteins with tailored stability and activity by reprogramming solvent-mediated interactions.

By successfully designing GPCRs with enhanced structural and functional properties, the researchers offered new tools for advancing drug discovery, synthetic biology, and biotechnology.