Computational design of polypeptide-based compartments for synthetic cells

Abstract

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 are limited by their fragility under mechanical forces or osmotic pressure. Elastin-like polypeptides (ELPs) composed of repetitive (VPGXG) sequences present alternative building blocks with which to construct the delimiting membrane of synthetic cells possessing high 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.