Computational differentiation of N-terminal signal peptides and transmembrane helices

Yuan, Z., Davis, M. J., Zhang, F. S. and Teasdale, R. D. (2003) Computational differentiation of N-terminal signal peptides and transmembrane helices. Biochemical And Biophysical Research Communications, 312 4: 1278-1283. doi:10.1016/j.bbrc.2003.11.069


Author Yuan, Z.
Davis, M. J.
Zhang, F. S.
Teasdale, R. D.
Title Computational differentiation of N-terminal signal peptides and transmembrane helices
Journal name Biochemical And Biophysical Research Communications   Check publisher's open access policy
ISSN 0006-291X
Publication date 2003-01-01
Sub-type Article (original research)
DOI 10.1016/j.bbrc.2003.11.069
Volume 312
Issue 4
Start page 1278
End page 1283
Total pages 6
Editor Baumeister
W
Place of publication San Diego, USA
Publisher Academic Press
Language eng
Subject C1
270100 Biochemistry and Cell Biology
780105 Biological sciences
Abstract Signal peptides and transmembrane helices both contain a stretch of hydrophobic amino acids. This common feature makes it difficult for signal peptide and transmembrane helix predictors to correctly assign identity to stretches of hydrophobic residues near the N-terminal methionine of a protein sequence. The inability to reliably distinguish between N-terminal transmembrane helix and signal peptide is an error with serious consequences for the prediction of protein secretory status or transmembrane topology. In this study, we report a new method for differentiating protein N-terminal signal peptides and transmembrane helices. Based on the sequence features extracted from hydrophobic regions (amino acid frequency, hydrophobicity, and the start position), we set up discriminant functions and examined them on non-redundant datasets with jackknife tests. This method can incorporate other signal peptide prediction methods and achieve higher prediction accuracy. For Gram-negative bacterial proteins, 95.7% of N-terminal signal peptides and transmembrane helices can be correctly predicted (coefficient 0.90). Given a sensitivity of 90%, transmembrane helices can be identified from signal peptides with a precision of 99% (coefficient 0.92). For eukaryotic proteins, 94.2% of N-terminal signal peptides and transmembrane helices can be correctly predicted with coefficient 0.83. Given a sensitivity of 90%, transmembrane helices can be identified from signal peptides with a precision of 87% (coefficient 0.85). The method can be used to complement current transmembrane protein prediction and signal peptide prediction methods to improve their prediction accuracies. (C) 2003 Elsevier Inc. All rights reserved.
Keyword Biochemistry & Molecular Biology
Biophysics
Signal Peptide Prediction
Transmembrane Helix Prediction
Hydrophobic Region
Feature Vector
Linear Discriminant Function
Proteome Analysis
Integral Membrane-proteins
Prediction
Topology
Q-Index Code C1

 
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Created: Wed, 15 Aug 2007, 05:34:06 EST