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

Yuri Mukai, Masao Yoshizawa, Hirotaka Tanaka, Takanori Sasaki, Masami Ikeda

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

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.

Original languageEnglish
Title of host publicationProceedings of the 2nd International Conference on Trendz in Information Sciences and Computing, TISC-2010
Pages82-87
Number of pages6
DOIs
Publication statusPublished - 1 Dec 2010
Event2nd International Conference on Trendz in Information Sciences and Computing, TISC-2010 - Chennai, India
Duration: 17 Dec 201019 Dec 2010

Publication series

NameProceedings of the 2nd International Conference on Trendz in Information Sciences and Computing, TISC-2010

Conference

Conference2nd International Conference on Trendz in Information Sciences and Computing, TISC-2010
CountryIndia
CityChennai
Period17/12/1019/12/10

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Keywords

  • Discrimination
  • Golgi
  • Hydropathy alignment
  • Position-specific amino acid propensity
  • Transmembrane region

Cite this

Mukai, Y., Yoshizawa, M., Tanaka, H., Sasaki, T., & Ikeda, M. (2010). A discrimination method for Golgi type II membrane proteins based on the hydropathy alignment and the position-specific score matrix around their transmembrane regions. In Proceedings of the 2nd International Conference on Trendz in Information Sciences and Computing, TISC-2010 (pp. 82-87). [5714613] (Proceedings of the 2nd International Conference on Trendz in Information Sciences and Computing, TISC-2010). https://doi.org/10.1109/TISC.2010.5714613