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

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  • MUKAI Yuri
    Department of Electronics and Bioinformatics, School of Science and Technology, Meiji University
  • YOSHIZAWA Masao
    Department of Electronics and Bioinformatics, School of Science and Technology, Meiji University
  • SASAKI Takanori
    Department of Electronics and Bioinformatics, School of Science and Technology, Meiji University
  • IKEDA Masami
    Consolidated Research Institute for Advanced Science and Medical Care, Waseda University
  • TOMII Kentaro
    Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST)
  • HIROKAWA Takatsugu
    Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST)
  • SUWA Makiko
    Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST)

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  • Discrimination of Golgi type 2 membrane proteins based on their hydropathy profiles and the amino acid propensities of their transmembrane regions

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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.

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