Masami Ikeda

Discrimination of Golgi Type II Membrane Proteins Based on Their Hydropathy Profiles and the Amino Acid Propensities of Their Transmembrane Regions

Membrane proteins in the Golgi apparatus play important roles in biological functions, predominantly as catalysts related to post-translational modification of protein oligosaccharides. We succeeded in extracting the characteristics of Golgi type II membrane proteins computationally by comparison with those of Golgi no retention proteins, which are mainly localized in the plasma membrane. Golgi type II membrane proteins were detected by combining hydropathy alignment and a position-specific score matrix of the amino acid propensities around the transmembrane region. We achieved 96.2% sensitivity, 93.5% specificity, and a 0.949 success rate in a self-consistency test. In a 5-fold cross-validation test, 88.0% sensitivity, 85.5% specificity, and a 0.867 success rate were achieved.

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.

A discrimination method for Golgi type II membrane proteins based on the hydropathy alignment and the position-specific score matrix around their transmembrane regions

Golgi membrane proteins contribute protein glycosylation, which is one of post-translational modification. It plays an important role in the cellular processes such as cell-cell adhesion, signal transfer, and subcellular localization. In this regard, the development of a computational method to discrimination of Golgi membrane proteins from the mammal genomes is desired. In this study, we succeeded in the feature extraction of the characteristics of Golgi type II membrane proteins (GLs) by comparison with post-Golgi type II membrane proteins (PGs) except the Golgi retention type mainly localized in the plasma membrane. The nonredundant datasets of GLs (344 sequences) and PGs (356 sequences) were obtained from Swiss-Prot release 57.0. GLs were detected by combining hydropathy alignment and position-specific score matrix (PSSM) around the transmembrane region. Each sequences were aligned by superpositioning the highest average hydrophobicity position. The PSSM was estimated based on position-specific amino acid propensities of the alignment position in the region of −14 to +18. Our method can discriminated GLs from PGs with 96.2% sensitivity and 93.5% specificity in a self-consistency test. Furthermore, 89.8% sensitivity and 87.0% specificity were achieved in 5-fold cross-validation test.