Discovering molecular features of intrinsically disordered regions by using evolution for contrastive learning

• Published in: PLoS computational biology Vol. 18; no. 6; p. e1010238
• Main Authors: Lu, Alex X, Lu, Amy X, Pritišanac, Iva, Zarin, Taraneh, Forman-Kay, Julie D, Moses, Alan M
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 01-06-2022; Public Library of Science (PLoS)
• Subjects: Amino Acid Sequence; Biology and Life Sciences; Computer and Information Sciences; Evolution, Molecular; Intrinsically Disordered Proteins - chemistry; Protein Conformation; Proteome - metabolism; Research and Analysis Methods; Social Sciences
• ISSN: 1553-7358; 1553-734X; 1553-7358
• DOI: 10.1371/journal.pcbi.1010238

A major challenge to the characterization of intrinsically disordered regions (IDRs), which are widespread in the proteome, but relatively poorly understood, is the identification of molecular features that mediate functions of these regions, such as short motifs, amino acid repeats and physicochemical properties. Here, we introduce a proteome-scale feature discovery approach for IDRs. Our approach, which we call "reverse homology", exploits the principle that important functional features are conserved over evolution. We use this as a contrastive learning signal for deep learning: given a set of homologous IDRs, the neural network has to correctly choose a held-out homolog from another set of IDRs sampled randomly from the proteome. We pair reverse homology with a simple architecture and standard interpretation techniques, and show that the network learns conserved features of IDRs that can be interpreted as motifs, repeats, or bulk features like charge or amino acid propensities. We also show that our model can be used to produce visualizations of what residues and regions are most important to IDR function, generating hypotheses for uncharacterized IDRs. Our results suggest that feature discovery using unsupervised neural networks is a promising avenue to gain systematic insight into poorly understood protein sequences.