HyperMPNN ‒ A general strategy to design thermostable proteins learned from hyperthermophiles

Stability is a key factor to enable the use of recombinant proteins in therapeutic or biotechnological applications. Deep learning protein design approaches like ProteinMPNN have shown strong performance both in creating novel proteins or stabilizing existing ones. However, it is unlikely that the stability of the designs will significantly exceed that of the natural proteins in the training set, which are biophysically only marginally stable. Therefore, we collected predicted protein structures from hyperthermophiles, which differ substantially in their amino acid composition from mesophiles. Notably, ProteinMPNN fails to recover their unique amino acid composition. Here we show that a retrained network on predicted proteins from hyperthermophiles, termed HyperMPNN, not only recovers this unique amino acid composition but can also be applied to proteins from non-hyperthermophiles. Using this novel approach on a protein nanoparticle with a melting temperature of 65°C resulted in designs remaining stable at 95°C. In conclusion, we created a new way to design highly thermostable proteins through self-supervised learning on data from hyperthermophiles.