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Prediction of Potential GPI-modification Sites in Proprotein Sequences

Prediction of Potential GPI-modification Sites in Proprotein Sequences,10.1006/jmbi.1999.3069,Journal of Molecular Biology,Birgit Eisenhaber,Peer Bork

Prediction of Potential GPI-modification Sites in Proprotein Sequences   (Citations: 145)
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Glycosylphosphatidylinositol (GPI) lipid anchoring is a common posttranslational modification known mainly from extracellular eukaryotic proteins. Attachment of the GPI moiety to the carboxyl terminus (ω-site) of the polypeptide follows after proteolytic cleavage of a C-terminal propeptide. For the first time, a new prediction technique locating potential GPI-modification sites in precursor sequences has been applied for large-scale protein sequence database searches. The composite prediction function (with separate parametrisation for metazoan and protozoan proteins) consists of terms evaluating both amino acid type preferences at sequence positions near a supposed ω-site as well as the concordance with general physical properties encoded in multi-residue correlation within the motif sequence. The latter terms are especially successful in rejecting non-appropriate sequences from consideration. The algorithm has been validated with a self-consistency and two jack-knife tests for the learning set of fully annotated sequences from the SWISS-PROT database as well as with a newly created database “big-Π“ (more than 300 GPI-motif mutations extracted from original literature sources). The accuracy of predicting the effect of mutations in the GPI sequence motif was above 83%. Lists of potential precursor proteins which are non-annotated in SWISS-PROT and SPTrEMBL are presented on the WWW-page http://www.embl-heidelberg.de/beisenha/gpi/gpi_prediction.html The algorithm has been implemented in the prototype software “big-Π predictor” which may find application as a genome annotation and target selection tool.
Journal: Journal of Molecular Biology - J MOL BIOL , vol. 292, no. 3, pp. 741-758, 1999
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