Identification of mammalian GPI-anchored proteins based on amino acid propensities in their GPI attachment signal sequences

Attachment of glycosylphosphatidylinositol (GPI) is one of the most important posttranslational modifications, playing an important role in vital eukaryote activities. GPI-anchored proteins (GPI-APs) are characterized by a pro-peptide of hydrophobic residues and small amino acid residues near the GPI-anchoring site. Here, we describe a new method for identifying GPI-APs based on hydropathy profiles and a position-specific scoring matrix (PSSM). First, the sequences of mammalian GPI-APs from the UniProt Knowledgebase/Swiss-Prot protein sequence database release 54.0 were scanned for their average hydropathy with several different window sizes. Hydrophobic regions were observed not only in the signal-peptide but also in the pro-peptide at the C-terminus. Non-GPI-anchored proteins (non-GPI-APs) with similar hydropathy profiles to those of the GPI-APs were used as the negative control. The sequences were aligned according to the residue sizes in the C-terminal region, and the position-specific amino acid propensities were analyzed according to their alignment positions in both the GPI-APs and the negative controls. The PSSM was devised using each amino acid propensity and a matching score was estimated for each dataset. The accuracy achieved in discriminating between GPI-APs and the negative controls was evaluated, and the GPI-APs were detected with 96.5% sensitivity and 97.3% specificity on a self-consistency test and with 85.0% sensitivity and 92.7% specificity on a 4-fold cross-validation test.