Topology-Driven Discovery of Transmembrane Protein -Palmitoylation.

Protein -palmitoylation is a reversible lipophilic posttranslational modification regulating a diverse number of signaling pathways. Within transmembrane proteins (TMPs), -palmitoylation is implicated in conditions from inflammatory disorders to respiratory viral infections. Many small-scale experiments have observed -palmitoylation at juxtamembrane Cys residues. However, most large-scale -palmitoyl discovery efforts rely on trypsin-based proteomics within which hydrophobic juxtamembrane regions are likely underrepresented. Machine learning- by virtue of its freedom from experimental constraints - is particularly well suited to address this discovery gap surrounding TMP -palmitoylation. Utilizing a UniProt-derived feature set, a gradient boosted machine learning tool (TopoPalmTree) was constructed and applied to a holdout dataset of viral -palmitoylated proteins. Upon application to the mouse TMP proteome, 1591 putative -palmitoyl sites (i.e. not listed in SwissPalm or UniProt) were identified. Two lung-expressed -palmitoyl candidates (synaptobrevin Vamp5 and water channel Aquaporin-5) were experimentally assessed. Finally, TopoPalmTree was used for rational design of an -palmitoyl site on KDEL-Receptor 2. This readily interpretable model aligns the innumerable small-scale experiments observing juxtamembrane -palmitoylation into a proteomic tool for TMP -palmitoyl discovery and design, thus facilitating future investigations of this important modification.