Cross-species identification of hydroxylation sites for ARD and FIH interaction

Ankyrin repeat domain (ARD) proteins contain various numbers of internal repeat units. They are considered as one important factor to influence hypoxia response through hydroxylation interaction with Factor Inhibiting HIF (FIH) enzymes which can repress HIF under normoxia environment. In this study, we adopted sequence based method and applied conserved hydroxylation motif patterns for identifying ASN/ASP/HIS hydroxylation sites on ARDs. First, a set of known ARD proteins was collected, and all corresponding repeat units were manually constructed and verified by removing redundant units. All extracted segments served as fundamental seed units to retrieve all ARDs proteins from 5 different species. Those ARD candidates were automatically segmented and a conserved hydroxylation motif pattern was applied for identifying all hydroxylation sites. As a result, the retrieval performance for ARDs achieved a sensitivity of 82% and a specificity of 98% for human species based on a testing dataset of 1,244 protein sequences. For hydroxylation site prediction, a sensitivity of 72.2% and a positive prediction value of 62% were achieved based on a set of 18 experimentally verified hydroxylation residues.