Mukai Yuri, Yoshizawa Masao, Sasaki Takanori, Ikeda Masami, Tomii Kentaro, Hirokawa Takatsugu, Suwa Makiko
Department of Electronics and Bioinformatics, School of Science and Technology, Meiji University, 1-1-1 Higashimita, Tama-ku, Kawasaki 214-8571, Japan.
Biosci Biotechnol Biochem. 2011;75(1):82-8. doi: 10.1271/bbb.100571. Epub 2011 Jan 7.
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.
高尔基体中的膜蛋白在生物学功能中发挥着重要作用，主要作为与蛋白质寡糖翻译后修饰相关的催化剂。通过与主要定位于质膜的高尔基体无保留蛋白进行比较，我们成功地通过计算提取了高尔基体II型膜蛋白的特征。通过结合亲水性比对和跨膜区域周围氨基酸倾向的位置特异性评分矩阵来检测高尔基体II型膜蛋白。在自一致性测试中，我们获得了96.2%的灵敏度、93.5%的特异性和0.949的成功率。在5折交叉验证测试中，灵敏度为88.0%，特异性为85.5%，成功率为0.867。
