HaloMPNN: retraining ProteinMPNN on halophilic proteomes for salt-tolerant enzyme design

Abstract

Machine learning-guided protein sequence redesign is now routinely used to optimize multiple properties relevant for protein engineering, most prominently thermostability and recombinant expression levels. Salt tolerance is a valuable property for "blue-biotechnology"- enabled biomanufacturing, yet no generative computational method exists to redesign proteins for increased salt tolerance. We hypothesized that a training dataset heavily biased toward salt-adapted proteomes would yield a model capable of designing proteins with halophilic properties. To test this, we retrained the sequence redesign model ProteinMPNN on proteins from "salt-in" extreme halophiles such as Haloarcula marismortui, a Dead Sea archaeon that grows optimally near 3-4 M NaCl, roughly six times the salinity of seawater, and accumulates molar concentrations of salts in its cytoplasm. Our model, HaloMPNN, redesigns non-halophilic proteins so that their properties shift towards those of natural halophilic proteins: lower predicted isoelectric point, greater surface acidity, and reduced surface and core hydrophobicity. Redesigning a broad range of non-halophilic proteins with SolubleMPNN, ProteinMPNN, and HyperMPNN shows that this shift is specific to HaloMPNN rather than a generic consequence of sequence redesign. HaloMPNN therefore offers both a route to designing candidate salt-tolerant enzymes and a means of identifying the characteristics that underlie halophilic adaptation.