Nucleic Acids Research, 2003, Vol. 31, No. 13 3631-3634
© 2003 Oxford University Press
Prediction of lipid posttranslational modifications and localization signals from protein sequences: big-
, NMT and PTS1
Research Institute of Molecular Pathology, Dr. Bohr-Gasse 7, A-1030 Vienna, Republic of Austria
*To whom correspondence should be addressed. Tel: +43 179730557; Fax: +43 17987153; Email: frank.eisenhaber{at}imp.univie.ac.at
Many posttranslational modifications (N-myristoylation or glycosylphosphatidylinositol (GPI) lipid anchoring) and localization signals (the peroxisomal targeting signal PTS1) are encoded in short, partly compositionally biased regions at the N- or C-terminus of the protein sequence. These sequence signals are not well defined in terms of amino acid type preferences but they have significant interpositional correlations. Although the number of verified protein examples is small, the quantification of several physical conditions necessary for productive protein binding with the enzyme complexes executing the respective transformations can lead to predictors that recognize the signals from the amino acid sequence of queries alone. Taxon-specific prediction functions are required due to the divergent evolution of the active complexes. The big-
tool for the prediction of the C-terminal signal for GPI lipid anchor attachment is available for metazoan, protozoan and plant sequences. The myristoyl transferase (NMT) predictor recognizes glycine N-myristoylation sites (at the N-terminus and for fragments after processing) of higher eukaryotes (including their viruses) and fungi. The PTS1 signal predictor finds proteins with a C-terminus appropriate for peroxisomal import (for metazoa and fungi). Guidelines for application of the three WWW-based predictors (http://mendel.imp.univie.ac.at/) and for the interpretation of their output are described.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  J. Ren, L. Wen, X. Gao, C. Jin, Y. Xue, and X. Yao CSS-Palm 2.0: an updated software for palmitoylation sites prediction Protein Eng. Des. Sel., November 1, 2008; 21(11): 639 - 644. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 I. B. Kuznetsov ProBias: a web-server for the identification of user-specified types of compositionally biased segments in protein sequences Bioinformatics, July 1, 2008; 24(13): 1534 - 1535. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. D. O. Martin, G. L. Vilas, J. A. Prescher, G. Rajaiah, J. R. Falck, C. R. Bertozzi, and L. G. Berthiaume Rapid detection, discovery, and identification of post-translationally myristoylated proteins during apoptosis using a bio-orthogonal azidomyristate analog FASEB J, March 1, 2008; 22(3): 797 - 806. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. Orlean and A. K. Menon Thematic review series: Lipid Posttranslational Modifications. GPI anchoring of protein in yeast and mammalian cells, or: how we learned to stop worrying and love glycophospholipids J. Lipid Res., May 1, 2007; 48(5): 993 - 1011. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Reumers, S. Maurer-Stroh, J. Schymkowitz, and F. Rousseau SNPeffect v2.0: a new step in investigating the molecular phenotypic effects of human non-synonymous SNPs Bioinformatics, September 1, 2006; 22(17): 2183 - 2185. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. H. Lin, L. Y. Han, H. L. Zhang, C. J. Zheng, B. Xie, and Y. Z. Chen Prediction of the functional class of lipid binding proteins from sequence-derived properties irrespective of sequence similarity J. Lipid Res., April 1, 2006; 47(4): 824 - 831. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Fankhauser and P. Maser Identification of GPI anchor attachment signals by a Kohonen self-organizing map Bioinformatics, May 1, 2005; 21(9): 1846 - 1852. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. R. MacPherson, S. M. Lohmann, and S.-A. Davies Analysis of Drosophila cGMP-dependent Protein Kinases and Assessment of Their in Vivo Roles by Targeted Expression in a Renal Transporting Epithelium J. Biol. Chem., September 17, 2004; 279(38): 40026 - 40034. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. Cabrero, V. P. Pollock, S. A. Davies, and J. A. T. Dow A conserved domain of alkaline phosphatase expression in the Malpighian tubules of dipteran insects J. Exp. Biol., September 1, 2004; 207(19): 3299 - 3305. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 F. Elortza, T. S. Nuhse, L. J. Foster, A. Stensballe, S. C. Peck, and O. N. Jensen Proteomic Analysis of Glycosylphosphatidylinositol-anchored Membrane Proteins Mol. Cell. Proteomics, December 1, 2003; 2(12): 1261 - 1270. [Abstract] [Full Text] [PDF]
|
|