Deep learning enables the design of functional de novo antimicrobial proteins

Abstract

Protein sequences are highly dimensional and present one of the main problems for the optimization and study of sequence-structure relations. The intrinsic degeneration of protein sequences is hard to follow, but the continued discovery of new protein structures has shown that there is convergence in terms of the possible folds that proteins can adopt, such that proteins with sequence identities lower than 30% may still fold into similar structures. Given that proteins share a set of conserved structural motifs, machine-learning algorithms can play an essential role in the study of sequence-structure relations. Deep-learning neural networks are becoming an important tool in the development of new techniques, such as protein modeling and design, and they continue to gain power as new algorithms are developed and as increasing amounts of data are released every day. Here, we trained a deep-learning model based on previous recurrent neural networks to design analog protein structures using representations learning based on the evolutionary and structural information of proteins. We test the capabilities of this model by creating de novo variants of an antifungal peptide, with sequence identities of 50% or lower relative to the wild-type (WT) peptide. We show by in silico approximations, such as molecular dynamics, that the new variants and the WT peptide can successfully bind to a chitin surface with comparable relative binding energies. These results are supported by in vitro assays, where the de novo designed peptides showed antifungal activity that equaled or exceeded the WT peptide.