Computational Design of Polypeptide-Based Compartments for Synthetic Cells

Synthetic cells are prevalent models for understanding and recapitulating complicated functions of natural cells such as DNA replication and protein expression. Lipid-based vesicles are widely employed but limited in real-world applications due to its fragility under mechanic forces or osmotic pressures. Elastin-like polypeptides (ELPs), composed of repetitive (VPGXG) sequences present alternative building block for synthetic cells with structural stability and tolerance of harsh environmental stress. In this work, we present a high-throughput virtual screening pipeline combining coarse-grained simulations, alchemical free energy calculations, Gaussian process regression, and Bayesian optimization to traverse a library of amphiphilic diblock ELPs for mutant sequences predicted to form thermodynamically stable bilayer vesicles. From our screening campaign, we have identified a range of novel ELP candidates with enhanced predicted stability. Analysis of our screening data exposes new rational design principles that suggest incorporating particular guest residues in hydrophilic blocks -- including histidine, tyrosine, and threonine -- and in hydrophobic blocks -- including alanine, phenylalanine, cysteine, and isoleucine -- to enhance the thermodynamic stability of ELP bilayer vesicles. The computational pipeline greatly accelerates the discovery of ELP building blocks for synthetic cells, exposes new design principles for these molecules, and furnishes a transferable framework for designing peptides with desirable structural or functional properties.