title: Discrimination of Golgi type II membrane proteins based on their hydropathy profiles and the amino acid propensities of their transmembrane regions.
abstract: 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.
authors.affiliation: Department of Electronics and Bioinformatics, School of Science and Technology, Meiji University, 1-1-1 Higashimita, Tama-ku, Kawasaki 214-8571, Japan. yuri@isc.meiji.ac.jp
authors.forename: Yuri
authors.initials: Y
authors.lastname: Mukai
authors.forename: Masao
authors.initials: M
authors.lastname: Yoshizawa
authors.forename: Takanori
authors.initials: T
authors.lastname: Sasaki
authors.forename: Masami
authors.initials: M
authors.lastname: Ikeda
authors.forename: Kentaro
authors.initials: K
authors.lastname: Tomii
authors.forename: Takatsugu
authors.initials: T
authors.lastname: Hirokawa
authors.forename: Makiko
authors.initials: M
authors.lastname: Suwa
mesh_terms: D000818:Animals; D002462:Cell Membrane / Q000737:chemistry* / Q000378:metabolism; D019295:Computational Biology / Q000379:methods*; D006056:Golgi Apparatus / Q000737:chemistry* / Q000378:metabolism; D006801:Humans; D057927:Hydrophobic and Hydrophilic Interactions; D008565:Membrane Proteins / Q000737:chemistry* / Q000378:metabolism; D051379:Mice; D021381:Protein Transport; D016415:Sequence Alignment
chemical_list: D008565:Membrane Proteins