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Estimating the length of transmembrane helices using Z-coordinate predictions

¹ Stockholm Bioinformatics Center, Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
² Department of Biological Applications and Technology, University of Ioannina, GR 451 10, Greece

(RECEIVED May 29, 2007; FINAL REVISION October 24, 2007; ACCEPTED October 31, 2007)

Zpred2 is an improved version of ZPRED, a predictor for the Z-coordinates of -helical membrane proteins, that is, the distance of the residues from the center of the membrane. Using principal component analysis and a set of neural networks, Zpred2 analyzes data extracted from the amino acid sequence, the predicted topology, and evolutionary profiles. Zpred2 achieves an average accuracy error of 2.18 Å (2.17 Å when an independent test set is used), an improvement by 15% compared to the previous version. We show that this accuracy is sufficient to enable the predictions of helix lengths with a correlation coefficient of 0.41. As a comparison, two state-of-the-art HMM-based topology prediction methods manage to predict the helix lengths with a correlation coefficient of less than 0.1. In addition, we applied Zpred2 to two other problems, the re-entrant region identification and model validation. Re-entrants were able to be detected with a certain consistency, but not better than with previous approaches, while incorrect models as well as mispredicted helices of transmembrane proteins could be distinguished based on the Z-coordinate predictions.

Keywords: membrane proteins; computational analysis of protein structure; protein structure prediction

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