Basic Charge Clusters and Predictions of Membrane Protein Topology

The topology predictor SPLIT 4.0 (http://pref.etfos.hr) predicts the sequence location of transmembrane helices by performing an automatic selection of optimal amino acid attribute and corresponding preference functions. The best topological model is selected by choosing the highest absolute bias pa...

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Bibliographic Details
Published in:Journal of Chemical Information and Computer Sciences 2002-05, Vol.42 (3), p.620-632
Main Authors: Juretić, Davor, Zoranić, Larisa, Zucić, Damir
Format: Article
Language:English
Subjects:
Amino Acid Motifs
Membrane Proteins - chemistry
Protein Conformation
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Summary:The topology predictor SPLIT 4.0 (http://pref.etfos.hr) predicts the sequence location of transmembrane helices by performing an automatic selection of optimal amino acid attribute and corresponding preference functions. The best topological model is selected by choosing the highest absolute bias parameter that combines the bias in basic charge motifs and the bias in positive residues (the “positive inside rule”) with the charge difference across the first transmembrane segment. Basic charge motifs, such as the BBB, BXXBB, and BBXXB motifs in α-helical integral membrane proteins, are significantly more frequent near cytoplasmic membrane surface than expected from the Arg/Lys (B) frequency. The predictor's accuracy is 99% for predicting 178 transmembrane helices in all membrane proteins or subunits of known 3D structure.
ISSN:0095-2338
1549-960X
1520-5142
DOI:10.1021/ci010263s