Basic Charge Clusters and Predictions of Membrane Protein Topology

Abstract

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 alpha-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.